Gene Literature Dashboard

<h4>Background</h4>Variants in STX1B/syntaxin-1B are linked to a spectrum of fever-associated epilepsy syndromes. While studies in murine models have provided mechanistic insights, their relevance to human disease in a heterozygous context may be limited.<h4>Methods</h4>We investigated two pathogenic STX1B variants using isolated single neurons and neuronal network cultures derived from patient-specific induced pluripotent stem cells. These carried either a de novo p.G226R variant, associated with severe developmental epilepsy, or an InDel variant (p.K45delinsRCMIE/p.L46M) linked to a transient familial seizure syndrome. Synaptic function and network excitability were assessed using patch-clamp and multi-electrode array recordings, alongside morphological and transcriptomic profiling.<h4>Findings</h4>G226R exhibited both gain- and loss-of-function characteristics, with increased miniature excitatory postsynaptic current frequency in networks but not in autapses, and synaptic failure during sustained high-frequency stimulation. For the InDel variant, the predicted loss-of-function phenotype based on reduced syntaxin-1B levels was not detectable at the single-cell level, likely masked by compensatory synaptic upregulation. At the network level, however, both variants were associated with neuronal hyperexcitability, characterised by more frequent and prolonged bursting activity, with a much stronger phenotype in G226R-containing networks. Transcriptomic profiling revealed a differential dysregulation of synaptic and other neuronal genes.<h4>Interpretation</h4>The divergence between morphological, electrophysiological and transcriptomic findings suggests that compensatory mechanisms may contribute to network hyperexcitability. Initially engaged to maintain homoeostasis, they may ultimately contribute to a pathological network state. The graded severity of network alterations across STX1B variants correlates with the clinical phenotypes.<h4>Funding</h4>BMBF (Treat ION-01GM2210A, SNAREopathies-01EW1809A), 2023 FEBS Summer Fellowship, Fortüne programme (2610-0-0), EKFS college precise.net, Open Access Publishing Fund of University of Tübingen.

<h4>Background</h4>Single-cell and single-nucleus RNA sequencing have transformed our understanding of human skeletal muscle biology, yet reproducibility and cross-study comparison remain limited by the lack of a unified reference framework and consistent cell-type annotation.<h4>Methods</h4>We systematically searched for scRNA-seq and snRNA-seq datasets from adult human skeletal muscle. Seven eligible studies were retrieved and harmonised. We benchmarked multiple integration strategies to construct a joint reference atlas and derived modality-aware marker panels. Selected findings were validated by immunofluorescence in muscle biopsies.<h4>Findings</h4>We generated a harmonised atlas comprising 122,000 cells and 630,000 nuclei from 88 healthy individuals and resolved 17 major skeletal muscle cell populations, spanning mononuclear compartments and multinucleated myofibers. Cross-modality analysis identified tissue- and modality-aware marker panels and nominated both established and previously unrecognised markers. NOVA1 emerged as a selective marker of fibro-adipogenic progenitors and was validated at the transcript and protein levels. Focusing on myonuclei, pseudotime modelling reconstructed differentiation trajectories from quiescent muscle stem cells to mature type I and type II myofibers and revealed lineage-specific programs, including transient activation of protocadherin-γ genes during type I myofiber differentiation. We further provide an interactive web application for marker-based cell-type prediction using the reference atlas.<h4>Interpretation</h4>This integrated reference atlas and accompanying annotation tool establish a standardised framework for human muscle transcriptomics, promoting consistent cell-type assignment and providing a baseline for future studies of muscle development, ageing, and disease.<h4>Funding</h4>Else Kröner-Fresenius-Stiftung and the German Research Foundation.

Neutrophils exhibit substantial functional heterogeneity shaped by both developmental stage and cellular maturation, but their mechanisms remain incompletely defined. CD11c (ITGAX) is traditionally considered as a cell surface marker of dendritic cells. We recently reported that it is highly expressed intracellularly in neutrophils and contributes to their maturation; however, its role at the cell surface is unclear. Here, we showed that surface CD11c expression level was heterogeneous across neutrophils, enabling classification into CD11c^hi and CD11c^-/lo populations. CD11c^hi neutrophils display enhanced phagocytic capacity and features of neutrophil aging, including increased CXCR4 and reduced CD62L expression. Bulk RNA sequencing across the three pediatric age groups revealed that differentially expressed genes (DEGs) between CD11c^hi and CD11c^-/lo neutrophils were observed most in infants followed by preschool age children. Infant neutrophils exhibited reduced phagocytic capacity and distinct gene expression patterns compared to older children. Functional interrogation of candidate genes (ANXA2, COL6A3, DCN) demonstrated their role in regulating phagocytosis without affecting reactive oxygen species production. Machine learning analysis further identified age-dependent ontology of the DEGs associated with cell surface CD11c expression, including pathways related to adhesion, extracellular matrix interactions, stress responses, and metabolic regulation. Integrative network analysis positioned CD11c linked to cytoskeletal remodeling and phagocytosis. Collectively, these findings support a model in which developmental age establishes the baseline transcriptional landscape of neutrophils, while CD11c serves as a marker of neutrophil aging rather than acting as a primary driver of transcriptional reprogramming.

<i>Citrus nippokoreana</i>, a traditional Korean citrus species, is rich in flavonoids and polyphenols with antioxidant properties; however, its neuroprotective potential remains unclear. Neurodegeneration is closely associated with oxidative stress, neuronal apoptosis, and impaired synaptic signaling. In this study, we investigated the effects of <i>C. nippokoreana</i> peel extract (CNE, 30% ethanol) using <i>in vitro</i> and <i>in vivo</i> models. CNE significantly protected HT22 hippocampal neurons against glutamate-induced oxidative stress by reducing intracellular reactive oxygen species (ROS) and apoptosis, while regulating AKT/Nrf2-associated antioxidant pathways and enhancing BDNF/CREB signaling. In a scopolamine-induced mouse model, oral administration of CNE (50 or 100 mg/kg/day) improved cognitive performance in behavioral tests. CNE also restored the expression of BDNF, CREB, and HO-1, and reduced acetylcholinesterase activity in the hippocampus. Histological analysis confirmed reduced neuronal damage. Furthermore, serum metabolomics revealed modulation of tryptophan metabolism, phosphatidylcholine species, and redox-related pathways. To explore constituents potentially contributing to the neuroprotective effects of CNE, major compounds identified by phytochemical profiling were screened in glutamate-induced HT22 cells. Several phytochemicals exhibited protective effects, suggesting that the biological activity of CNE may result from the combined actions of multiple constituents rather than a single compound. These findings suggest that CNE attenuates oxidative stress-induced neuronal damage and improves cognitive function through coordinated regulation of antioxidant defense, neurotrophic signaling, and cholinergic function.

<b>Background:</b> Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality, with resistance to immunotherapy posing a major clinical challenge. Natural killer (NK) cells exhibit impaired infiltration and cytotoxicity in HCC; however, the mechanisms underlying NK cell-mediated immune evasion are still poorly understood. This study investigated how NOP2/Sun RNA methyltransferase 2 (NSUN2), a 5-methylcytosine (m⁵C) RNA methyltransferase, induces metabolic reprogramming and immunosuppression to drive HCC progression. <b>Methods:</b> We conducted a genome-wide CRISPR screen in HCC cells cocultured with NK cells. To delineate the downstream mechanisms, we integrated profiling of the m5C epitranscriptome, transcriptome, and chromatin landscape with metabolic characterization. The impact of <i>NSUN2</i> on histone lactylation and programmed cell death 1 ligand 1 (PD-L1) transcription was further investigated. Functional assays in vitro and in vivo using syngeneic murine models and pharmacological inhibition validated these findings. Clinical relevance was assessed using patient tissues, The Cancer Genome Atlas dataset, and immunotherapy cohorts. <b>Results:</b> Genome-wide CRISPR screening in HCC cell-NK cell coculture models identified <i>NSUN2</i> as a key suppressor of NK cell-mediated cytotoxicity. Mechanistically, NSUN2-mediated RNA m⁵C modification enhanced the messenger RNA stability and expression of glycolytic enzymes, including enolase 1 (<i>ENO1</i>), pyruvate kinase M1/2 (<i>PKM</i>), and lactate dehydrogenase A (<i>LDHA</i>), thereby increasing lactate production. Accumulated lactate promoted histone H3 lysine 18 lactylation (H3K18la), which enhanced chromatin accessibility at the <i>CD274</i> (encoding PD-L1) promoter and recruited signal transducer and activator of transcription 3 (STAT3) to drive PD-L1 expression, ultimately inhibiting NK cell-mediated cytotoxicity. Clinically, high NSUN2 expression was associated with elevated PD-L1 levels, poor prognosis, and immunotherapy resistance in patients with HCC. In vivo, <i>NSUN2</i> knockout increased NK cell infiltration and suppressed tumor growth, while the STAT3 inhibitor TTI-101 combined with anti-PD-L1 therapy enhanced NK cell cytotoxicity and inhibited HCC progression. <b>Conclusions:</b> Our data demonstrated that NSUN2 drove immune evasion in HCC by coupling m⁵C-dependent glycolytic reprogramming with H3K18la-mediated epigenetic activation of PD-L1. These findings suggest that NSUN2 could represent a critical nexus between m⁵C RNA methylation and immunosuppression, providing a therapeutic rationale for combination immunotherapy in HCC.

Congenital dyserythropoietic anemia is a group of hereditary disorders characterized by erythroid hyperplasia and ineffective erythropoiesis, resulting in anemia of varying severity. Congenital dyserythropoietic anemia Type 1 (CDA-1) is classically associated with biallelic mutations in the CDAN1 gene. Here, we report the first case of compound heterozygous CDAN1 mutations p.(D1043V) and p.(S1036F) in clinical practice, presenting in a 24-year-old woman with mild, asymptomatic macrocytic anemia and hyperferritinemia. These variants are currently classified as variants of uncertain significance; however, this report represents the first clinical case of this compound heterozygous CDAN1 variant combination in a patient with a phenotype consistent with CDA-1. As the phenotypic boundaries of CDA-1 continue to expand, clinicians should consider CDA-1 in the differential diagnosis of unexplained macrocytic anemia, even in the absence of severe anemia.

<h4>Purpose</h4>Low back pain (LBP) is a heterogeneous pain condition with a measurable genetic contribution, but the genes, brain cell types, and spatial tissue contexts through which inherited risk is expressed remain unclear. We aimed to define cell-type-specific and spatially contextualized genetic mechanisms underlying LBP.<h4>Methods</h4>FinnGen R12 LBP GWAS summary statistics (42,521 cases and 353,224 controls) were integrated with brain single-nuclei eQTL data across eight major brain cell classes. We evaluated genome-wide polygenic signal using LDSC, prioritized genes using MAGMA and PoPS, and performed brain cell-type-specific eQTL-anchored Mendelian randomization, primarily based on single-instrument Wald ratio estimates, followed by Bayesian colocalization. Spatial genetic mapping was conducted using gsMap in an E16.5 murine embryonic atlas and two adult human lumbar spinal cord Visium sections. Selected candidates were assessed by RT-qPCR in neuronal-like and astroglial-like inflammatory cell models.<h4>Results</h4>LDSC supported interpretable polygenic signal for LBP. MAGMA and PoPS showed partial gene-level convergence, with TCF4 and TMEFF2 supported by both approaches. Across 1641 tested gene-cell type exposures, significant eQTL-anchored MR associations were concentrated in excitatory neurons, oligodendrocytes, inhibitory neurons, and astrocytes. Integrated eQTL-anchored MR, colocalization, and gene-prioritization evidence highlighted CLEC18A, QPRT, and GMPPB as higher-priority non-MHC candidates with moderate, but not strong, colocalization support. gsMap localized LBP-associated enrichment to neuroaxis-related embryonic regions, including brain, spinal cord, sympathetic nerve, and dorsal root ganglion, and to neuronal-like niches in adult lumbar spinal cord. RT-qPCR showed model-dependent expression changes, with QPRT and LGI4 preferentially responsive in neuronal-like SH-SY5Y cells and GMPPB and DPYSL5 responsive in astroglial-like U251 cells.<h4>Conclusion</h4>These findings support neuronal and glial regulatory programs as plausible contributors to LBP genetic susceptibility and highlight CLEC18A, QPRT, and GMPPB as higher-priority non-MHC candidates with moderate colocalization support. The results provide a spatially contextualized framework for candidate prioritization in LBP, while emphasizing the need for larger cell-type-specific eQTL resources and functional validation before therapeutic or mechanistic conclusions can be drawn.

High-grade serous ovarian carcinoma (HGSC) responds poorly to immune checkpoint blockade, partly due to a macrophage-dominated immunosuppressive microenvironment. We integrated single-cell spatial proteomics and spatial transcriptomics across 50 HGSC tumors and applied SPACEstat to resolve higher-order immune communities and their transcriptional programs. We identified six immune community types, with macrophage-dominated Myelonets representing the predominant spatial pattern of immune organisation. In chemotherapy-exposed tumors, Myelonets showed coordinated lipid metabolism–immunosuppression and inflammation–MHC-II macrophage transcriptional programs, with SPP1, C1Q, VEGF, MMPs, and CCL18 linked to immunosuppressive states and fibroblasts emerging as key mediators of macrophage communication. Chemotherapy contracted large Myelonets while increasing CD8+ T-cell organization into Lymphonets. Persistent macrophage dominance within Myelonets was associated with adverse outcomes among patients who achieved a complete response to treatment. Together, we identify Myelonets as clinically relevant, multicellular immunoregulatory niches sustained by spatiotemporally coordinated macrophage programs and stromal crosstalk.

Disseminated cancer cells (DCC) in non-metastatic carcinoma patient bone marrow (BM) are predictive of metastasis. Those detected by epithelial cytokeratin or EpCAM expression have poorly-characterized transcription profiles due to their extreme rarity: 1∼2 cells per 2x 10 6 BM cells in every third non-metastatic patient. We here characterize the transcriptomes of DCCs. Single-cell RNA-sequencing (scRNA-seq) of 864 EpCAM-positive cells (from 1,151 cancer patients) in BM or lymph nodes (LN) revealed plasma, immune, myeloid, erythroid progenitor cells and two candidate DCC populations, termed M0-DCC and M1-DCC. M0-DCC, mostly from non-metastatic M0-stage patients, displayed the highest known adult stemness scores, and were transcriptomically reminiscent of human cleavage-stage, preimplantation embryos. M1-DCC represented cancer cells undergoing the epithelial-mesenchymal transition (EMT), corresponding to later, implanting and gastrulating embryos. Detection of early-embryo-like DCC categorised patients at highest risk for metastatic progression. Furthermore, high M0-DCC scores predicted the metastatic potential of human cell lines from the Cancer Cell Line Encyclopedia. M0-DCC gene expression profiles can be reversibly induced from M1-DCC-like cells in vitro . The close correspondence between gene expression profiles in immediate early embryonic development and metastatic founder cell candidates provides strong evidence that the onset of cancer and metastasis recruits mechanisms employed in fertilization.

Fission increases the number of crypts in the intestine during neonatal growth and also restores crypt density after injury by bifurcation of a pre-existing parent crypt into daughter crypts. While fission is typically symmetric in healthy crypts, it is more asymmetric in diseases, and the relationship between parent crypt shape and daughter crypt (a)symmetry is difficult to study as crypt budding and fission are stochastic in organoid models and difficult to control in vivo. Here, a photoresponsive hydrogel is introduced to spatiotemporally control daughter crypt emergence from mature parent crypts in intestinal organoids, enabling longitudinal tracking of crypt bifurcation in vitro. Variation of the photopatterned dimensions tunes parent crypt shape and reveals that both fission efficiency and crypt symmetry depend on parent crypt geometry. Epithelial boundary analysis identified parent crypt curvature as a key factor influencing daughter crypt symmetry. High-curvature or narrow crypts yielded symmetric daughter crypts, whereas wider parent crypts with lower epithelial curvature generated progressively more asymmetric crypts. Mechanistically, non-muscle myosin IIA acts as one key regulator of crypt symmetry. Overall, this work introduces a reproducible and spatiotemporally controllable in vitro model of crypt fission, allowing identification of mechanical determinants of fission that influence intestinal regeneration and development.

Huntington's disease (HD) is a neurological condition with limited treatment. Its hallmarks are progressive loss of neurons, chorea, cognitive, motor, and metabolic impairments. The current study uses 3-nitropropionic acid (3-NP) to cause HD-like indications in rats. L-theanine (L-TH), an active component of Camellia sinensis, has already been shown to possess anti-inflammatory and anti-oxidant effects. The impact of the isolated phytoconstituent, L-TH, on 3-NP-induced changes in three distinct brain regions was assessed in the current study. The animals received a 7-day pretreatment consisting of normal saline, extract of C. sinensis (100 and 200 mg/kg b.w., i.p.), L-TH (10 mg/kg b.w., i.p.), and standard Tetrabenazine (TBZ, 25 mg/kg, b.w., i.p.). The administration of 3-NP (10 mg/kg b.w., i.p.) to the treatment groups began on the 8th day of the protocol and continued until the 21st day. The brain homogenates underwent biochemical and neurochemical assessments. In conclusion, L-TH improved behavioral outcomes and attenuated 3-NP-induced neurochemical alterations in brain homogenates. Histopathological analysis revealed lower levels of tissue damage in the L-TH-treated group compared to the 3-NP group. Molecular docking studies further indicated favorable interactions of L-TH with the HTT protein. These findings suggest that L-TH may attenuate 3-NP-induced Huntington's disease-like alterations in rats. However, additional studies using genetic HD models and molecular mechanisms are required to confirm its therapeutic efficacy and underlying mode of action.

Spinocerebellar ataxia type 2 (SCA2) is a neurodegenerative disorder that shows cerebellar glucose hypometabolism, systemic hypermetabolism and weight loss. This study aimed to explore novel molecular mechanisms of disease for SCA2, based on the assessment of blood glucose homeostasis. A case-control and correlational study was conducted in 79 normoglycemic Cuban patients with SCA2 and 83 sex- and age-matched control subjects during a fasting state. A subset of 20 patients with SCA2 and 19 control individuals underwent an oral glucose tolerance test (OGTT). Several indices for assessing blood glucose homeostasis, derived from the fasting state or the OGTT, were included in the study. Fasting glucose levels showed a small increase, whereas the QUICKI index for insulin sensitivity was slightly decreased among patients. Markers of glucose homeostasis derived from the OGTT were no different between patients and controls. Fasting insulin levels, QUICKI, McAuley´s, HOMA2-%S, HOMA2-IR, and HOMA2-%β indices showed weak to moderate correlations with markers of body composition. McAuley´s, TyG, HOMA2-IR, and HOMA2-%β indices correlated with the age at onset, progression rate, or INAS count. Patients with SCA2 with mild-to-moderate ataxia do not have any major alteration in blood glucose homeostasis. Markers of glucose homeostasis associate with body composition and have nominal modifying effects on disease severity and progression rate in patients with SCA2, with McAuley's index showing effects more consistently. Further studies are needed to describe the changes in blood glucose homeostasis in the different stages of disease, and to delve into its pathophysiological relevance.

Excipients are widely used to suppress the self-association of therapeutic proteins, yet their mechanisms of action are not well understood and often assumed to be nonspecific. Here we show that excipient-mediated solubilization of therapeutic antibodies is markedly molecularly specific. Using a high-throughput combinatorial droplet microfluidic platform, we systematically quantify the effects of common pharmaceutical excipients across a diverse panel of monoclonal antibodies (mAbs). Although all studied excipients enhance solubility, their effects can vary significantly between antibodies, spanning dynamic ranges from approximately 7-fold to over 200-fold. Integrating experimental solubilization measurements with sequence- and structure-derived molecular descriptors, we identify interpretable physicochemical determinants underlying excipient responses; for example, the histidine effect is strongly dependent on mAb dipole moment. Our findings reveal trends that highlight the molecular specificity and complexity of antibody-excipient interactions, as well as the limitations of purely generic formulation rules. Overall, this study provides a quantitative framework for analyzing excipient effects across diverse antibodies and supports the development of predictive approaches for rational formulation design. The integration of high-throughput experimentation with molecular feature analysis offers a foundation for improving our understanding and prediction of antibody-specific formulation behavior.

<h4>Background</h4>HLA-B27 is strongly associated with a spectrum of immune-mediated diseases, including axial spondyloarthritis (axSpA), psoriatic arthritis (PsA), inflammatory bowel disease (IBD), and acute anterior uveitis (AAU). However, the shared molecular mechanisms and cross-disease diagnostic biomarkers remain poorly defined. This study aimed to identify common gene signatures and potential diagnostic biomarkers across HLA-B27-related diseases using bioinformatics analysis and experimental validation.<h4>Methods</h4>Gene expression datasets for axSpA, PsA, ulcerative colitis (UC), Crohn's disease (CD), and AAU were retrieved from the Gene Expression Omnibus (GEO) database. Disease-specific diagnostic genes were identified via differential expression analysis, least absolute shrinkage and selection operator (LASSO) regression, and receiver operating characteristic (ROC) curve analysis (AUC > 0.9). Shared biomarkers were determined by intersecting differentially expressed genes (DEGs) across all five diseases. Protein-protein interaction (PPI) networks, functional enrichment analyses, and single-sample gene set enrichment analysis (ssGSEA) were performed to explore biological pathways and immune infiltration patterns. Competing endogenous RNA (ceRNA)-transcription factor (TF) regulatory networks were constructed, and potential therapeutic agents were predicted using the Drug-Gene Interaction Database (DGIdb). Finally, the expression of candidate genes was validated by RT-qPCR and Western blot in peripheral blood mononuclear cells (PBMCs) from patients with ankylosing spondylitis (AS) and UC.<h4>Results</h4>A total of 2485, 380, 2682, 2232, and 481 DEGs were identified for axSpA, PsA, UC, CD, and AAU, respectively, with ABCD2 being the only shared biomarker across all five diseases. Disease-specific diagnostic gene panels were established (3 genes for axSpA, 6 for PsA, 15 for UC, 9 for CD, and 4 for AAU). Two major gene clusters were uncovered: an arthritis-related cluster (LAG3, IL15, PRF1, TBX21, IL2RB) and an extra-articular disease-related cluster (IL6, FN1, F2R, HIF1A, ANGPT2). Immune infiltration profiles varied significantly across diseases. Regulatory network analysis revealed complex ceRNA-TF interactions and identified several candidate drugs. In PBMCs, ABCD2 was upregulated in AS and UC, PRF1 in AS, and FN1, IL-6, and F2R in UC.<h4>Conclusion</h4>This study identifies ABCD2 as a potential cross-disease biomarker and two context-dependent key gene clusters for HLA-B27-associated immune-mediated diseases, providing exploratory candidates for future research.

Autophagy plays a critical role in maintaining cellular homeostasis and regulating stem cell fate. Although microRNAs (miRNAs) are being increasingly recognized for their ability to modulate autophagy and pluripotency in human pluripotent stem cells (hPSCs), the underlying molecular mechanisms remain incompletely understood. This study defines a role for miR-150 deficiency in biasing ectoderm-mesoderm lineage specification in hPSCs and identifies SOX2 as a key downstream node regulated primarily through altered mRNA stability, with additional involvement of an autophagy-associated pathway. miR-150-deficient hPSCs were generated by CRISPR/Cas9-mediated deletion of the miR-150 locus. A range of molecular and cellular techniques were used to investigate how miR-150 regulates SOX2 and KLHL20 expression, modulates the KLHL20-ULK1 interaction, and influences autophagy-mediated SOX2 degradation. Directed differentiation protocols were used to determine the role of miR-150 in germ layer lineage specification. The loss of miR-150 led to increased SOX2 expression by stabilizing its mRNA, resulting in elevated SOX2 protein levels in hPSCs. Concurrently, miR-150 deficiency increased KLHL20 mRNA stability, disrupted ULK1-mediated autophagy, and inhibited SOX2 degradation. Functional assays demonstrated that miR-150 fine-tunes SOX2 expression through dual regulation of mRNA stability and autophagy via the KLHL20-ULK1 axis, maintaining a balanced commitment to the mesodermal and ectodermal lineages. These findings establish miR-150 as a regulator of SOX2 activity and autophagy in hPSCs. By targeting both SOX2 and the KLHL20-ULK1 axis, miR-150 coordinates SOX2 turnover through complementary mechanisms, ensuring precise mesodermal and ectodermal lineage commitment. This multiregulatory strategy provides new insights into how miRNAs integrate intracellular signaling pathways to direct stem cell fate decisions.

Phycocyanobilin, a bioactive compound derived from Arthrospira platensis C1, was investigated for its potential role in systemic lupus erythematosus (SLE) based on its structural similarity to bilirubin, with a Tanimoto score of 93%. Molecular docking revealed favorable binding affinities between phycocyanobilin and several protein targets, including EGFR, FYN, HLA-B, LCK, LYN, and TP53. Target prediction further identified LYN kinase as a key candidate. Molecular dynamics simulations demonstrated stable binding of the phycocyanobilin-LYN complex, with interaction profiles comparable to those of the native ligand, staurosporine. Binding free energy and residue-level analyses supported strong and stable interactions, highlighting key contributions to complex stability. Overall, these findings provide mechanistic insight into the interaction between phycocyanobilin and LYN, suggesting that this compound may modulate LYN-associated signaling pathways and warrants further investigation in the context of SLE.

Neurons actively shape immune responses that maintain central nervous system integrity. We identify SPP1 (secreted phosphoprotein 1) as a neuron-derived signal that reprograms microglia into a neuroprotective, homeostatic state after injury and during neurodegeneration. In mouse models of glaucoma and optic nerve damage, neuronal SPP1 enhances microglial autophagy, debris clearance, and anti-inflammatory activity, preserving neuronal survival and visual function. SPP1 is elevated in neurons of human and primate glaucomatous retinas, where SPP1⁺ cells show increased resilience. In Alzheimer's disease brain, neuronal SPP1 correlates with neuronal survival, while microglia around Aβ plaques display defective autophagy. In human iPSC co-cultures, SPP1 enhances microglial Aβ clearance and prevents neurodegeneration. Thus, SPP1 defines a protective neuron-microglia axis in glaucoma and possibly other neurodegenerative diseases.

Endothelial dysfunction is recognized to contribute to chronic tissue remodeling in the lung, yet endothelial-derived mechanisms driving these processes remain largely undefined. Here, we show that endothelial inactivation of the LATS1 and LATS2 kinases, key suppressors of the transcriptional regulators YAP and TAZ, elicits distinct responses depending on endothelial identity within different pulmonary vascular beds. Our data indicate that LATS1/2 inactivation in general capillary endothelial cells induces a reactive capillary injury-like state, whereas a separate endothelial population located within veins adopts a distinct profibrotic state. We show that expansion of this reactive venous endothelial cell population, which is marked by EBF1 and ACKR1 expression, is associated with fibroblast activation, macrophage accumulation, and epithelial remodeling, collectively generating a microenvironment characteristic of fibrotic lung disease. We further demonstrate that pharmacologic inhibition of YAP/TAZ-TEAD signaling prevents stromal and immune remodeling and fibrotic lesion formation following endothelial LATS1/2 inactivation. These findings identify LATS1/2-mediated restraint of YAP/TAZ as essential for lung endothelial homeostasis and highlight a distinct venous cell response as a direct contributor to fibrotic lung remodeling.

Metastatic relapse can arise years after apparently successful treatment because disseminated cancer cells (DCCs) persist in reversible states of cellular, angiogenic, or immune-mediated dormancy. The strongest direct evidence that acute viral inflammation can disturb this equilibrium currently comes from experimental breast-cancer lung-dormancy models in which influenza A virus or SARS-CoV-2 promoted DCC cell-cycle re-entry and metastatic expansion, with interleukin-6 (IL-6) required for the initial awakening phenotype. Human findings reported in the same study are observational and do not establish that respiratory viral infection causes metastatic relapse. This hypothesis-generating Perspective therefore separates direct viral-dormancy evidence from direct inflammation-dormancy evidence, established metastatic-niche biology, mechanistic extrapolation, and unvalidated clinical hypotheses. We critically evaluate IL-6/JAK/STAT3 signaling, the time-dependent balance between antiviral and antitumor immunity, neutrophil extracellular trap-mediated matrix remodeling, epithelial RNA sensing, endothelial and perivascular responses, and selected extracellular-vesicle mechanisms. The evidence does not establish a universal infection-to-niche-to-relapse pathway across cancers or organs. Instead, it supports a context-dependent model in which respiratory infection may transiently perturb the DCC-niche equilibrium in susceptible settings. Priority studies should independently replicate the pulmonary phenotype, define causal timing, distinguish local lung injury from systemic effects, test cross-cancer and cross-organ generalizability, and prospectively evaluate human associations. No post-viral biomarker panel, intensified imaging strategy, or pathway-directed intervention is currently validated for routine clinical use.

Members of the Wiskott-Aldrich syndrome protein (WASP) family orchestrate cytoskeletal reorganization that modulates B-cell receptor (BCR) signaling and B-cell fate decisions. WHAMM, a WASP-family nucleation-promoting factor member that associates with actin, membranes and microtubules, has not been functionally characterized in B cells. To investigate the role of WHAMM in B-cell development and function, we analyzed a conditional mouse model in which Whamm was deleted in the B-cell lineage. WHAMM-deficient mice exhibited altered splenic B-cell composition, characterized by an accumulation of splenic transitional B cells and a reduction of follicular B cells. Meanwhile, WHAMM deficiency altered the spatial organization and kinetics of proximal BCR signaling, and modified the dynamics of BCR-induced actin remodeling. However, WHAMM-deficient B cells showed largely preserved BCR internalization, antigen presentation, PI3K-AKT-mTOR signaling, ROS production, and mitochondrial membrane potential. Together, this work indicates that WHAMM helps shape splenic B-cell populations and regulates proximal BCR signaling and actin dynamics, while several downstream functional responses remain largely preserved in this study.

Respiratory syncytial virus (RSV) causes acute lower respiratory tract infection in young children, the elderly, and immunocompromised hosts, and no RSV vaccine or therapy exists for infants, beyond prophylaxis. PIWI-interacting RNAs (piRNAs), small non-coding RNAs acting through P element-induced wimpy testis (Piwi) proteins, remain largely unexplored. We characterized PIWIL4 expressions and function during RSV infection or poly(I:C) stimulation, a proxy of viral infection. PIWIL4 was expressed in primary and immortalized small airway epithelial cells following RSV infection. While PIWIL4 knockdown did not affect RSV replication, it decreased cytokine and growth factor secretion, altered gene and piRNA expression, and modulated pathways involved in cytokine production, metabolism, and airway remodeling. Limited overlap between piRNA targets and transcriptomic changes suggests PIWIL4 regulates airway epithelial cell responses partly independently of piRNAs. Our study positions PIWIL4 as a key regulator of airway epithelial cell responses to viral infections.

<h4>Background</h4>METTL5, an N6-methyladenosine (m6A) RNA methyltransferase, has been implicated in tumor progression, but its prognostic value and non-invasive prediction in lung adenocarcinoma (LUAD) remain unclear. This study aimed to develop a pathomics-based machine learning model to predict METTL5 expression from histopathological images and evaluate its prognostic significance in LUAD.<h4>Methods</h4>A total of 327 LUAD patients from The Cancer Genome Atlas (TCGA) with matched hematoxylin and eosin (H&E) slides, transcriptomic, and clinical data were included and randomly divided into training and validation sets (7:3). Quantitative histopathological features were extracted using PyRadiomics. Feature selection was performed via maximum relevance minimum redundancy (mRMR) and recursive feature elimination (RFE), followed by construction of a Gradient Boosting Machine (GBM) model. A pathomics score (PS) was generated to assess prognostic relevance. Survival analyses, gene set variation analysis (GSVA), tumor mutational burden (TMB), immune infiltration analysis, and in vitro functional assays were conducted.<h4>Results</h4>METTL5 overexpression was independently associated with poor overall survival [hazard ratio (HR) =1.637, P=0.007]. The model achieved good predictive performance [area under the curve (AUC) =0.847 in the training set and 0.752 in the validation set]. High PS was significantly associated with worse survival and remained an independent prognostic factor (HR =1.563, P=0.03). Elevated PS correlated with altered metabolic pathways, increased TMB, and immune microenvironment changes. METTL5 knockdown reduced proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) in A549 cells.<h4>Conclusions</h4>The pathomics-based model accurately predicts METTL5 expression and provides prognostic stratification in LUAD, supporting its potential as a practical imaging-derived biomarker.

<title>Abstract</title> <p>Schizophrenia (SCZ) is a highly polygenic disorder and is associated with several comorbidities, including depression, cardiovascular disease, and diabetes; yet the biological pathways underlying this clustering remain poorly understood. This study examined associations between a polygenic risk score for SCZ (PRS-SCZ) and circulating protein levels in 44,661 participants of the UK Biobank. We assessed 1,459 proteins (with ≤ 10% missingness) spanning neurological, inflammatory, cardiometabolic, and oncology panels. After adjustment for technical (population structure, genotyping chip), individual (age, sex, lifestyle), and clinical (comorbidities and medication) variables and multiple testing correction, the standardised PRS-SCZ was significantly negatively associated with C2, RNASET2, BTN2A1, CDSN, HLAE, LTA, MICA-MICB, CNTN3, FCER2, INHBC and CPVL concentrations, and positively with ICAM3, BTN3A2, IL5RA, SLAM7 concentrations. These protein biomarkers may provide insights into the biological pathways underlying schizophrenia and/or its comorbidities.</p>

<title>Abstract</title> <p> <bold>Introduction:</bold> Gestational adaptations require central autonomic recalibration via the hypothalamic paraventricular nucleus (PVN), yet how chronic hypertension alters its transcriptomic response during pregnancy remains unknown. We investigated PVN transcriptomic and cardiovascular autonomic profiles in pregnant normotensive (Wistar) and spontaneously hypertensive rats (SHRs) to uncover mechanisms underlying gestational hypothalamic adaptations to hypertension. <bold>Methods</bold> : Radiotelemetry-equipped Wistar rats and SHRs were evaluated for blood pressure, short-term variability, and baroreflex sensitivity alongside PVN bulk RNA-sequencing across virgin and late-pregnant states. <bold>Results</bold> : Both strains exhibited physiological gestational blood pressure drops. However, pregnant SHRs displayed blunted chronotropic reactivity, elevated cardiac sympathetic drive (increased LF HR and LF/HF ratio), and a doubling of spontaneous baroreflex sensitivity. Transcriptomically, pregnant Wistars showed a minimal homeostatic response (33 DEGs: e.g. <italic>Cish, Igfbp3, Irf7</italic> ). In stark contrast, pregnant SHRs underwent massive transcriptomic reprogramming (951 DEGs), marked by loss of astrocytic potassium buffering ( <italic>Kcnj10</italic> , <italic>Kcnb1</italic> ), chaperone depletion ( <italic>Hspa1a</italic> , <italic>Hspa1b</italic> ), excitatory neuropeptide elevation ( <italic>Hcrt</italic> , <italic>Trh</italic> ), and neuroimmune activation ( <italic>Zap70</italic> , <italic>Fcrl2, Itgam, Cmklr1</italic> ). Crucially, intersecting baseline hypertensive DEGs with gestational shifts in SHRs unmasked a significant inverse correlation, where 95.9% of hypertension-altered genes (140/146) underwent active directional reversal during pregnancy ( <italic>Hspa1a, Hspa1b, Ptgds, Per1</italic> ), enriching for translational, ribosomal, and bioenergetic pathways. <bold>Conclusion:</bold> Pre-existing chronic hypertension converts gestational PVN adaptation from a subtle homeostatic adjustment into an extensive genomic requirement (951 vs 33 DEGs). This massive transcriptomic remodeling represents an active counter-regulatory program in SHRs to sustain pregnancy to term, mitigating autonomic risk via heightened baroreflex sensitivity </p>

Osteoclastogenesis is driven by tightly coordinated transcriptional programs downstream of receptor activator of nuclear factor-κB ligand (RANKL) signaling, in which reactive oxygen species (ROS) function as essential secondary messengers. Although extracellular peroxiredoxin 1 (PRDX1) has been implicated in the suppression of osteoclast differentiation, the role of intracellular PRDX1 in regulating osteoclastogenic signaling remains poorly understood. Here, we identify intracellular PRDX1 as a redox-sensitive negative regulator of osteoclastogenesis and bone resorption. PRDX1 deficiency markedly enhanced osteoclast differentiation, bone resorption activity, and osteoporotic phenotypes in vivo. Transcriptomic and mechanistic analyses revealed that PRDX1 attenuates osteoclastogenic gene transcription by blocking the nuclear factor kappa B (NF-κB)/p65 signaling axis. Loss of PRDX1 increased intracellular ROS accumulation, promoted p65 nuclear translocation and promoter occupancy, thereby amplifying osteoclastogenic transcriptional programs. Mechanistically, PRDX1 underwent TNF receptor associated factor 6 (TRAF6)-mediated Lys67-dependent ubiquitylation and lysosomal degradation in response to RANKL signaling. In addition, RANKL-induced Src activation promoted phosphorylation of PRDX1 at Tyr194, which enhanced TRAF6-mediated ubiquitylation without substantially altering overall TRAF6 binding. Together, these findings reveal a PRDX1-ROS feedback loop that modulates NF-κB activity during osteoclastogenesis and identify regulated PRDX1 degradation as a mechanism by which RANKL signaling amplifies osteoclastogenic responses. These findings establish intracellular PRDX1 as an important modulator of skeletal homeostasis, suggesting its potential relevance as a pharmacological target in diseases characterized by excessive bone resorption.

Intervertebral disc (IVD) degeneration, a leading cause of chronic lower back pain, is associated with loss of vacuolated notochordal cells (NCs) and fibrotic remodeling of the nucleus pulposus. Emerging therapies increasingly focus on NCs, which are rare but therapeutically relevant cells for regenerating degenerated IVDs. In this study, we used CRISPR-based transactivation (CRISPRa) to direct the differentiation of human induced pluripotent stem cells (iPSCs) into the NC lineage. We tested CRISPRa-mediated activation of NOTO, TBXT, FOXA2, SOX5, SOX6, and SOX9, coupled with single-cell sequencing of Aggrecan-2A-mScarlet reporter iPSCs. This approach identified the SOX5/6/9 combination (SOX-trio) as critical for promoting NC lineage commitment. The SOX-trio yielded the largest cell population expressing a range of genes previously associated with NC identity, including SHH, FOXA1, FOXA2, FOXJ1, FN1, ALCAM, KRT8, and KRT18. Our study demonstrates the integration of CRISPRa with single-cell technologies as a powerful platform for investigating and enriching iPSC-derived NCs, supporting future regenerative strategies across various fields.

<h4>Objective</h4>This study aimed to establish and verify reference intervals (RIs) for coagulation factor XII (FXII) and antithrombin III (ATIII) in an adult population from the Jiangsu region of China and to evaluate the influence of analytical platform on RI interpretation.<h4>Methods</h4>We retrospectively analyzed data from 301 apparently healthy adults attending the Health Examination Center of Nanjing Drum Tower Hospital. Plasma FXII and ATIII activities were measured in parallel using two automated coagulation analyzers, the Sysmex CS-5100 and CS-6500. Statistical analysis followed CLSI EP28-A3 guidelines. Distribution normality was assessed to determine the appropriate method for RI establishment: the non-parametric percentile method for non-normally distributed data and the parametric method for normally distributed data. Analyzer-related agreement was further assessed using Bland-Altman analysis. The derived RIs were verified using an independent sample set of 20 apparently healthy adults.<h4>Results</h4>FXII showed a non-Gaussian distribution, whereas ATIII showed an approximately Gaussian distribution. For the CS-5100 analyzer, the RI was 32.2%-109.1% for FXII and 84.1%-104.7% for ATIII. For the CS-6500 analyzer, the corresponding RIs were 37.1%-111.1% for FXII and 86.1%-106.7% for ATIII. The newly established RIs differed from the manufacturer-provided ranges currently used in routine practice. No clinically meaningful sex-based partitioning was identified. Although analyzer-related differences were statistically significant, Bland-Altman analysis showed modest mean biases between the CS-6500 and CS-5100 platforms, with mean differences of +5.09% for FXII and + 1.17% for ATIII. All verification samples fell within the proposed RIs.<h4>Conclusion</h4>This study established and verified regional RIs for FXII and ATIII in healthy adults from Jiangsu, China. Although analyzer-related differences between the CS-5100 and CS-6500 platforms were modest, the findings highlight the importance of local RI verification when applying manufacturer-derived intervals or changing analytical platforms. These locally derived RIs may improve the interpretation of FXII and ATIII results and reduce unnecessary follow-up testing caused by inappropriate generic intervals.

We describe a 1-year-2-month-old boy with <i>KMT2A</i>-rearranged leukemia presenting with concurrent acute myeloid leukemia in bone marrow and B-lymphoblastic leukemia/lymphoma in a right calf mass. Both lesions harbored an identical <i>KMT2A::MLLT10</i> fusion, confirming common clonal origin. This represents the first documented case of spontaneous "spatial lineage divergence" at diagnosis, distinct from therapy-induced lineage switch. The finding highlights the potential need for multi-site biopsy and molecular profiling in extramedullary disease.

<h4>Background</h4>Dysregulation of multivesicular bodies (MVBs) in Alzheimer's disease (AD) contributes to aberrant tau secretion via extracellular vesicles (EVs). This may potentially explain our previous paradoxical observation of elevated free-form p-tau217 alongside reduced p-tau217⁺ EVs in plasma. This study aimed to investigate the mechanisms underlying the reduction of p-tau217⁺ EVs to uncover AD therapeutic targets.<h4>Methods</h4>By integrating hippocampal spatial transcriptomics of human brain with EV proteomics of cerebrospinal fluid, we identified key regulators of p-tau217⁺ EV release. Subsequently, we investigated the mechanisms underlying the synthesis and secretion of p-tau217⁺ EVs. The regulatory roles of these candidate proteins were systematically evaluated through shRNA knockdown and interference with a synthetic peptide in both Aβ₄₂-treated cells and AD model mice.<h4>Results</h4>Heat shock protein family A member 8 (HSPA8) was identified as a crucial regulator of EV biogenesis and release, mediating the Aβ-SNAP29 interaction to disrupt SNARE complex assembly and impair p-tau217⁺ EV secretion. In AD models, HSPA8 inhibition with shRNA rescued p-tau217⁺ EVs and improved cognitive function. Additionally, blocking the Aβ-SNAP29 interaction with a selective peptide inhibitor for HSPA8 reversed the decline in p-tau217⁺ EV and cognitive deficits.<h4>Conclusions</h4>These findings reveal a role of HSPA8 in regulating the MVB-mediated EV release and tau propagation, and highlight HSPA8 as a promising therapeutic target for modifying AD progression.

Heart and kidney diseases frequently coexist, but the genetic basis of this relationship remains unclear. We analyzed genetic data from large-scale studies to investigate how kidney function (estimated glomerular filtration rate, eGFR) and six common cardiovascular diseases share genetic risk factors. Using MiXeR method, and conjunctional false discovery rate (conjFDR) to identify overlapping genetic regions, we found 478 shared genomic loci between eGFR and cardiovascular diseases. These shared genes are involved in tissue development and structure. We also identified 29 genes that could be targeted by existing medications approved by the US Food and Drug Administration, such as PRKAG2, PDE1A, and IGF1R. Among these, genetically predicted higher level of IGF1R expression is associated with a higher eGFR, which reflects good kidney function and is protective against cardiorenal diseases, such as atrial fibrillation, and myocardial infarction. These findings reveal genetic overlap between kidney function and cardiovascular diseases, highlighting potential targets for understanding and treating cardiorenal syndrome.

<h4>Background</h4>Breast cancer remains a leading cause of female mortality worldwide, with therapeutic benefit limited by tumor heterogeneity and drug resistance. Identification of novel therapeutic targets through integration of genetic causality inference and functional validation is urgently needed.<h4>Methods</h4>Plasma protein quantitative trait loci (pQTL) from the Fenland cohort (~10,700 individuals) and the FinnGen R10 SomaScan subset (n = 828) were integrated with breast cancer genome-wide association study data from the Breast Cancer Association Consortium (122,977 cases and 105,974 controls). Causal protein-disease relationships were inferred using summary-data-based Mendelian randomization (SMR), with colocalization and HEIDI tests. Multi-level validation was performed using TCGA-BRCA transcriptomic data. Functional validation included CCK-8, EdU, wound healing, Transwell invasion, and flow cytometry apoptosis analysis evaluated <i>CPNE1</i> knocdown and/or overexpression of <i>the MST1 gene</i> which encodes macrophage-simulating protein (MSP).<h4>Results</h4>SMR identified 23 proteins in Fenland and 10 in FinnGen at FDR < 0.05. MST1/MSP and CPNE1 were supported in both datasets with PP.H4 ≥ 0.80 and non-significant HEIDI tests. Genetically predicted circulating MSP was positively associated with breast cancer risk, whereas circulating CPNE1 showed an inverse association. TCGA-BRCA showed higher <i>CPNE1</i> mRNA in tumors (P = 2.57×10⁻²⁵) and lower <i>MST1</i> mRNA (P = 3.04×10⁻²³). <i>CPNE1</i> expression was highest in triple-negative breast cancer and correlated positively with clinical stage (ρ = 0.211), whereas <i>MST1</i> expression was lowest in triple-negative breast cancer and correlated inversely with stage (ρ = -0.164). In T47D and MDA-MB-231 cells, <i>CPNE1</i> knockdown and <i>MST1</i> overexpression each reduced proliferation, migration, and invasion and increased apoptosis; the combined group showed greater changes than either single intervention.<h4>Conclusion</h4>This study prioritizes <i>the MST1 gene</i>, which encodes MSP, and <i>CPNE1</i> as candidate proteins for further investigation in breast cancer. However, the circulating-protein associations, tumor-mRNA patterns, and cell-autonomous perturbations represent distinct and directionally discordant biological contexts. The findings therefore support context-dependent candidate roles and justify mechanistic, in vivo, and formal interaction studies, but do not yet establish therapeutic efficacy or synergy.

CFTR modulators like elexacaftor-tezacaftor-ivacaftor (ETI) improve morbidity in cystic fibrosis (CF), but their systemic effects on young children are not yet clear. We hypothesize that ETI has anti-inflammatory effects and reverse disease-associated molecular signatures in children with CF. This exploratory pilot study evaluates the cellular mechanisms of ETI on peripheral immune cells in children (<12 years) with CF using a multi-omics approach. Seventeen children with CF (median age 8.7 years, 26% female) and 12 controls (median age 9.6 years, 42% female) were included for blood RNA-sequencing, proteomics and phosphoproteomics. Baseline pathway enrichment analysis revealed systemic inflammation, transmembrane transporter deficiencies, reduced protein kinase, and GTPase activity. Three months post-ETI, anti-inflammatory effects, epigenetic modulation, and increased protein kinase activity were observed, indicating partial reversal of cellular abnormalities. ETI modified systemic inflammatory, epigenetic, and phosphorylation pathways in young children with CF, offering insights into CF pathology and potential biomarkers for treatment monitoring.

Identification of gene expression changes in postmortem brain tissue of Alzheimer's disease donors compared to controls has implicated numerous biological pathways for Alzheimer's disease pathophysiology. Nonetheless, there is still limited understanding of how gene expression dysregulation underpins specific proteinopathies core to Alzheimer's disease. Here, we investigate brain transcriptomic changes in a well-characterized cohort of Alzheimer's disease donors to identify genes and networks that associate with Alzheimer's disease endophenotypes, including neuropathology measures (Braak stage, Thal phase and cerebral amyloid angiopathy score) and Alzheimer's disease-related brain protein levels (Apolipoprotein E, Amyloid-β 40, Amyloid-β 42, tau and phospho-Tau). Bulk transcriptome measures were collected from the temporal cortex tissue of 477 Alzheimer's disease donors. Following quality control, transcriptome-wide association studies were performed for each endophenotype. We used weighted gene co-expression network analysis to build co-expression networks and integrated transcriptome with epigenetic and genetic data from the same donors. We detected a total of 5740 Bonferroni-significant temporal cortex gene associations with Alzheimer's disease endophenotypes, most of which were with brain tau levels. We discovered tau-associated co-expression modules enriched in known and novel Alzheimer's disease pathways. We found that a <i>beneficial (or neutral)</i> brain biochemical state of higher total tau and lower phospho-Tau is associated with increased levels of synaptic, DNA damage/repair, nucleic acid metabolism and myelin processes. In contrast, in a detrimental state with lower total and higher phospho-Tau, there is upregulation of vascular and immune, and downregulation of mitochondrial and myelin pathways. There are brain gene expression perturbations that are associated with Alzheimer's disease endophenotypes. While some of these associations are common across multiple endophenotypes, many are distinct for different Alzheimer's disease-related proteins. Based on these findings, we propose a hypothetical model of <i>dynamic brain gene expression changes</i> that track with progressive Alzheimer's disease proteostasis. These expression changes hold potential to serve as dynamic, precision biomarkers of brain Alzheimer's disease progression. This study demonstrates the potential of integrative multi-omics and deep Alzheimer's disease endophenotypes in well-characterized brain tissues to precisely uncover the complex biology of Alzheimer's disease.

<h4>Objective</h4>Depression is a heterogeneous psychiatric disorder and a growing public health concern, characterized by its high prevalence, recurrence rate, and association with suicide. There is evidence suggesting that both genetic susceptibility and environmental factors can regulate gene expression through DNA methylation, thereby influencing the occurrence and development of depression. The olfactory sensory neuropeptide 1 (<i>OLFM1</i>) protein is a risk factor for mental disorders. However, there are no reports yet regarding the correlation between the <i>OLFM1</i> gene and depression, nor have there been any studies on the association between <i>OLFM1</i> gene DNA methylation and depression.<h4>Methods</h4>Genomic DNA was extracted from peripheral blood samples of patients with depression (<i>n</i> = 100) and healthy controls (<i>n</i> = 100) using the QIAamp DNA Blood Mini Kit. Subsequently, the extracted genomic DNA was subjected to bisulfite treatment using the EZ DNA Methylation-Gold™ kit. DNA methylation levels of 107 CpG sites in six fragments of <i>OLFM1</i> exon 1 and its downstream were detected by the Illumina HiSeq platform using MethylTarget™ technology.<h4>Results</h4>Methylation levels across the overall <i>OLFM1</i> CpG island and its six fragments (<i>OLFM1</i>-1 to <i>OLFM1</i>-6) were significantly reduced in the depression group relative to controls. Analysis of the <i>OLFM1</i> gene fragments revealed that 84 of 107 CpG sites were significantly hypomethylated in depressed individuals. When patients were divided by sex, male patients displayed hypomethylation at 65 CpG sites, substantially more than the 37 sites found in females.<h4>Conclusion</h4><i>OLFM1</i> hypomethylation is associated with depression and may serve as a potential epigenetic biomarker.

<h4>Objective</h4>To identify plasma protein biomarkers associated with incident non-fatal major adverse cardiovascular events (MACE) in diabetic kidney disease (DKD) patients.<h4>Research design and methods</h4>We analyzed 317 DKD patients from the UK Biobank. Plasma proteomics and clinical data (demographics, metabolism, renal function) were integrated. In an exploratory discovery phase, three sequential Cox regression models (crude, socio-demographic-adjusted, socio-demographic-metabolic adjusted) screened non-fatal MACE-associated proteins. To prevent information leakage, the cohort was then randomly split into training (70%) and testing (30%) sets; machine-learning feature selection, hyperparameter optimization, and final model development were performed exclusively within the training set. The associated proteins were input into the four-step machine-learning pipeline (LASSO-Cox, random survival forest, Boruta, XGBoost-Cox). Predictive performance was validated using Kaplan-Meier survival analyses, longitudinal trajectory modeling, and ROC benchmarking. An interactive web application was deployed for clinical implementation.<h4>Results</h4>Of 1,463 plasma proteins, 561 were associated with non-fatal MACE across Cox models, with 14 overlapping proteins. Nine core proteins (ANG, IL1R1, CXCL14, ESAM, PTGDS, HAVCR1, FGFR2, IGSF8, CCL3) were validated: ANG showed the strongest non-fatal MACE association (HR = 3.88, 95%CI 2.33-6.48, p<0.001), and all high-expression groups had elevated non-fatal MACE risk. GO/KEGG enrichment highlighted inflammatory-immune pathways like positive regulation of MAPK cascade, Cytokine-cytokine receptor interaction and PI3K-Akt signaling pathway as key mechanisms. The model integrating proteins, demographic factors, and clinical variables achieved the highest predictive performance across non-fatal MACE (AUC = 0.768), myocardial infarction (MI) (0.808), and stroke (0.816) outcomes, with superior stability in cross-validation. CoxBoost + Elastic Net framework was selected as the optimal framework via benchmarking of 101 algorithms. The model demonstrated favorable calibration in high-risk patients and yielded positive net clinical benefit across decision thresholds of 5% to 45%. The web tool (https://jiangli2941.github.io/MACE-prediction-v2/) enables input of 28 variables, outputs non-fatal MACE risk status, risk probability, and highlights abnormal indicators.<h4>Conclusion</h4>Plasma proteomics combined with machine learning identifies robust non-fatal MACE predictors in DKD.

<h4>Background</h4>Lung cancer remains a leading cause of cancer incidence and mortality globally. Metabolic reprogramming promotes tumor progression and shapes an immunosuppressive tumor microenvironment. Galactose metabolism is involved in multiple malignancies, but its prognostic value in lung adenocarcinoma (LUAD) remains unclear. This study aimed to develop and internally validate a galactose metabolism-related multigene prognostic model for LUAD.<h4>Methods</h4>A retrospective prognostic model development and internal validation study was performed using RNA sequencing (RNA-seq) and clinical data from 585 LUAD patients in The Cancer Genome Atlas (TCGA). Differential expression, functional enrichment, univariate and multivariate Cox regression were applied to construct a prognostic gene signature. Internal validation was performed using bootstrap resampling. Model performance was evaluated by time-dependent receiver operating characteristic (ROC), C-index, calibration, and Kaplan-Meier analysis. Associations between the model and immune infiltration, immunotherapy responsiveness, and tumor stemness were also analyzed.<h4>Results</h4>A six-gene prognostic model (<i>GALT, GANC, PGM1, GALM, B4GALT1, PGM2</i>) was developed. The model showed good discrimination with 1-, 3-, and 5-year area under the curve (AUC) values of 0.719, 0.693, and 0.684, respectively. The low-risk group exhibited significantly longer survival, increased antitumor immune infiltration (CD8+ T cells, M1 macrophages, activated CD4+ memory T cells), higher expression of T cell proliferation-related genes, lower immune checkpoint expression, better predicted immunotherapy response, and lower tumor stemness compared with the high-risk group.<h4>Conclusions</h4>We developed and internally validated a six-gene prognostic model for LUAD based on galactose metabolism. The model shows moderate prognostic performance and is associated with antitumor immunity and tumor stemness. It may be used for prognostic risk stratification and to guide personalized immunotherapy in LUAD.

Glutathione peroxidase 4 (GPX4) is a selenocysteine (Sec)-containing antioxidant enzyme and the only known mammalian enzyme capable of directly reducing membrane-embedded phospholipid and cholesterol hydroperoxides. It is recognized as a central regulator of ferroptosis, modulating cellular redox balance and influencing cell fate under oxidative stress. Despite a decade of research, critical gaps remain. Existing reviews largely focus on isolated diseases or single targeting strategies, and few provide an integrated framework that spans molecular regulation, physiological function, and clinical translation. The regulatory networks that control GPX4, from transcription to post-translational modifications and protein interactions, remain incompletely defined, and its ferroptosis-independent functions are underexplored. Moreover, the context-dependent and bidirectional roles of GPX4 across different diseases have not been systematically analyzed to guide appropriate therapeutic strategies. To address these gaps, this review delineates the structural basis and isoform-specific functions of GPX4, maps its multilayered regulatory network, and defines its roles across key physiological and pathological processes, including cancer, neurodegeneration, ischemia-reperfusion (I/R) injury, and autoimmune diseases. We also evaluate GPX4-targeted chemical strategies and analyze four core translational barriers: target specificity, systemic toxicity, acquired resistance, and tissue delivery, with evidence-based solutions for each. We conclude by identifying unresolved mechanistic questions and outlining priorities to accelerate clinical translation.

Understanding the molecular mechanisms driving selective neuronal vulnerability to different neurodegenerative disorders remains a crucial, unsolved question. Here, we explored the case of Huntington's disease (HD), where the striatum and, specifically, dopamine receptor 1 (D1R) and dopamine receptor 2 (D2R) medium-sized spiny neurons (MSNs) exhibit differential susceptibility to the HTT CAG-repeat expansion mutation, with D2R-neurons being impacted earlier and more significantly. To unravel differences between D2R and D1R MSNs, we employed a multidimensional approach, integrating genomic, transcriptional, pattern distribution, and somatic instability analyses. Specifically, we used Htt CAG knock-in mouse models harboring 18 (Htt^Q20: "control") or ~190 (Htt^Q175: "HD") consecutive CAG repeats, expressing tdTomato and EGFP under the control of Drd1 and Drd2 promoters, respectively. First, comprehensive genomic and transcriptomic analyses following fluorescence-activated cell sorting (FACS) of dissociated striatal neurons revealed distinct gene expression profiles with a significant upregulation of oxidative phosphorylation and translation pathways in D1R-positive neurons already at the pre-symptomatic stage. These transcriptional changes were not accompanied by major copy number variations, as shown by parallel genomic analysis. Secondly, histological analyses revealed a greater proportion of D1R-positive neurons compared to D2R-positive neurons in HD mice, particularly in the ventral-medial neostriatum, with D2R-positive neurons presenting an increased nuclear accumulation of mutant huntingtin aggregates. In summary, our integrative study suggests that the distinct vulnerability of MSNs in HD might result from a combination of an early transcriptional compensatory response of D1R neurons together with specific susceptibility of D2R neurons.

Associations between various genetic variants and the risk of hepatocellular carcinoma (HCC) have been extensively explored but produced contradictory results. The aim of the present systematic meta-analysis was to determine and validate genetic variants that are associated with HCC risk. Two-step literature searches of PubMed, Embase, Web of Science, and Google Scholar databases and various meta-analyses were performed, and a comprehensive field synopsis and epidemiological evidence were provided. A total of 20,081 publications were identified, of which 830 were deemed eligible for inclusion. Eventually, 36 variants in 27 genes were identified to be associated with HCC risk. Moreover, cumulative epidemiological evidence of an association was graded as moderate for nine variants in eight genes (<i>ESR1</i> rs2234693, <i>GRP78</i> rs430397, <i>HLA-DP</i> rs3077, <i>HLA-DQ</i> rs2856718, <i>MnSOD</i> rs4880, <i>TNFα</i> rs361525, <i>HFE</i> rs1800562 and rs1799945, and <i>UGT1A7</i> High/Low) and strong for three variants in three genes (<i>IL-1B</i> rs1143627, <i>COL18A1</i> rs7499, and <i>NQO1</i> rs1800566); <i>HFE</i> rs1800562 was deemed to have a false-positive association. Thus, 11 variants in 11 genes were identified to be associated with HCC risk. This synopsis helps elucidate the mechanisms of carcinogenesis of HCC and provides insights into the early diagnosis and novel treatments of HCC by targeting those potential genes.

<h4>Background</h4>Glioblastoma (GBM) is characterized by high invasiveness and metabolic heterogeneity. Protein Tyrosine Phosphatase Receptor Type Z1 (PTPRZ1) has been implicated in glioma stemness and tumor grade progression, while the molecular mechanism remains unknown.<h4>Methods</h4>Integrated bioinformatics analysis of TCGA dataset and TMA IHC profiling were used to explore clinical relevance of PTPRZ1, and potential molecular mechanisms of PTPRZ1 involved glioma progression. Ivy Glioblastoma datasets analysis and multiregional GBM IHC were performed to spatially characterize the expression patterns of PTPRZ1 in GBM tissues. Zebrafish xenograft model was established to elucidate the role of PTPRZ1 in driving glioblastoma cell migration. Western blotting, mitochondrial functional assays, Transwell migration assays, and human GBM tissue multiplexing were employed to investigate the mechanism of PTPRZ1 mediated glioma cell mobility via maintaining mitochondrial functions.<h4>Results</h4>Spatial profiling revealed that PTPRZ1 is significantly enriched in the infiltrating areas and peritumoral margins of GBM, and acts as a poor prognosis factor in lower grade astrocytoma, proneural and mesenchymal GBM. Mechanistically, PTPRZ1 expression was found to be strongly correlated with cell adhesion molecules (CAMs) and mitochondrial metabolism across multiple glioma subtypes. Knockdown of PTPRZ1 triggered a shift from elongated to fragmented mitochondrial morphology by specifically downregulating the mitochondrial fusion protein OPA1. This mitochondrial dysfunction led to a metabolic shift toward glycolysis and a marked accumulation of ROS, which suppressed N-cadherin expression, thereby impairing glioma cell migration. These findings were corroborated in vivo, where PTPRZ1 depletion significantly reduced disseminated tumor foci in a zebrafish model.<h4>Conclusion</h4>Our study demonstrates that PTPRZ1 drives glioblastoma migration by sustaining an OPA1-dependent mitochondrial fusion program, which suppresses mitochondrial ROS levels and subsequently stabilizes a pro-migratory phenotype via N-cadherin expression. Targeting the PTPRZ1/OPA1/ROS axis represents a promising therapeutic strategy to inhibit the invasive expansion of GBM cells.

<h4>Background</h4>Alzheimer's disease (AD) is a progressive neurodegenerative disorder of late life that causes cognitive and functional decline and substantial mortality. Machine learning (ML) is increasingly used to discover patterns in clinical and biomarker data that support earlier and more accurate AD detection.<h4>Objectives</h4>This scoping review addresses three core research questions. First, we investigate recent trends in using machine-learning techniques to detect Alzheimer's disease using blood biomarkers. Second, we identify the blood biomarkers involved in Alzheimer's detection and evaluate how machine learning has been applied to improve the diagnostic capabilities of these biomarkers. Third, we highlight significant challenges associated with using machine learning for blood biomarker data in Alzheimer's detection and examine proposed advancements or solutions to handle these problems.<h4>Methods</h4>In June 2025, we searched six academic databases to identify relevant papers on blood biomarkers and ML methods for Alzheimer's Disease. Search queries were developed based on our predefined research questions. Papers were then screened using defined inclusion and exclusion criteria, where titles, abstracts, and full texts of articles were systematically reviewed.<h4>Results</h4>Following the screening approach, we selected 36 papers that fulfilled our inclusion and exclusion criteria. Through careful examination, we classified blood biomarkers into four types: transcriptomics, proteomics, multi-omic biomarkers, and general elemental blood biomarkers. Across these studies, proteomic blood biomarkers consistently emerged as significant indicators for Alzheimer's disease, including Alpha-2-Macroglobulin (A2M), Apolipoprotein E (ApoE), Eotaxin-3 (EOT3), plasma phosphorylated tau (p-tau 181), and neurofilament light chain (NfL). Furthermore, we explored challenges such as small sample sizes, lack of standardization, heterogeneity, and data imbalance.<h4>Conclusions</h4>This review provides insights into how combining blood biomarkers with ML can enhance AD prediction. The review summarizes key challenges and identifies critical gaps for future research.

Stroke is a major cause of long-term disability with variable recovery. While clinical factors such as initial severity play a role, genetic factors are increasingly recognized as important contributors to stroke recovery. Genotype studies are generally focused on a single post-stroke behavioural domain, but some genes might relate to broad mechanisms of plasticity. This study therefore aimed to identify cross-phenotypic genetic variants associated across two or more stroke recovery domains. DNA from Stroke, Stress, Rehabilitation, and Genetics study participants was genotyped, resulting in 9 814 610 variants. In order to examine cross-phenotypic results, we first conducted genome-wide association studies on the six recovery domains: motor (grip force), cognition (Telephone Montreal Cognitive Assessment), depression (Patient Health Questionnaire-8), stress (Primary Care Post-Traumatic Stress Disorder Screen), functional status (Stroke Impact Scale-Activities of Daily Living), and disability (modified Rankin Scale 0-2 versus 3-6), some of which were tested longitudinally, yielding nine phenotypes. Models were adjusted for age, sex, initial severity (NIH Stroke Scale score), and ancestry. Cross-phenotype associations were identified by evaluating single nucleotide polymorphisms (SNPs) associated (<i>P</i> < 5e-5) with multiple phenotypes. To determine how these genetic variants may relate to biological mechanisms of recovery, we conducted gene enrichment analyses. Participants (<i>n</i> = 565, 59% male) had mild-moderate initial stroke severity (median acute NIH Stroke Scale score = 4). After accounting for the correlation structure among the nine phenotypes, we observed 319 cross-phenotypic SNPs, 3.45 times the expected number. Five of the cross-phenotypic SNPs were linked to genes relevant to neural development, function and plasticity, e.g. <i>ERICH1</i> (rs11778883-C), <i>FOX3</i> (rs55726768-G), <i>LIFR-AS1</i> (rs76401391-T), <i>RPS6KA2</i> (rs113518460-C) and <i>TUBGCP2</i> (rs147150392-C), as were enrichments in <i>RAB5-EEA1</i>, <i>CTNNA1-CTNNB1</i>, <i>CIN85-SH3GL2</i> and <i>ELMO1-DOCK2</i> complexes. Multiple gene enrichments were found, e.g. Stroke Impact Scale-Activities of Daily Living and Patient Health Questionnaire 8 at 3 months were enriched for <i>CREB</i> phosphorylation, which is important for long-term potentiation. We identified cross-phenotypic SNPs associated with multiple behavioural domains of stroke recovery. Some of these genes encode, or regulate, druggable proteins. These genetic factors are not well captured by clinical or neuroimaging assessments and so provide a unique window into stroke recovery. These findings, if validated, suggest that some genes may be broadly important to stroke recovery.

<b>Background</b> Coagulation factor VIII (FVIII) is a critical component of the intrinsic coagulation pathway. While elevated FVIII levels are an established risk factor for venous thromboembolism (VTE), genetic variants in the <i>F8</i> gene directly causing such elevations remain scarce. Here, we report a novel complete <i>F8</i> tandem duplication identified in a female patient with splanchnic venous thrombosis (SVT). <b>Methods</b> We performed genetic testing using a thrombophilia panel targeting 35 genes involved in thrombosis and haemostasis to detect both point variants and copy number variations (CNVs). Family co-segregation analysis and phenotypic assays for FVIII and von Willebrand factor (VWF) were conducted. The structural basis of the identified <i>F8</i> copy number gain was elucidated using optical genome mapping (OGM). Full-length <i>F8</i> mRNA amplification, quantitative PCR, plasma FVIII Western blotting, and X-chromosome inactivation analysis were performed to assess the functional consequences of the duplication. Thrombin generation test (TGT) was employed to assess the hypercoagulable state. <b>Results</b> Genetic testing identified three copies of all 26 exons of the <i>F8</i> gene in the proband, which was also detected in her mother (CNVs = 3) and son (CNVs = 2). One-stage clotting and chromogenic assays confirmed persistently elevated FVIII activity in the proband and her mother, accompanied by increased FVIII antigen levels. The OGM analysis confirmed a 229 kb tandem duplication including the <i>F8</i> gene on one of the proband's X chromosomes. The junction regions exhibited high sequence homology and were rich in repetitive sequences, which precluded precise breakpoint mapping. Full-length <i>F8</i> mRNA amplification revealed no aberrant transcripts, whereas quantitative PCR showed increased <i>F8</i> mRNA expression in all carriers. Plasma FVIII Western blotting indicated FVIII heavy and light chains of expected molecular weights with increased band intensity in carriers. X-chromosome inactivation analysis in female carriers showed no significant skewing. TGT in two available carriers showed increased thrombin generation compared with a normal control at both low (1 pM) and high (5 pM) tissue factor concentrations. <b>Conclusion</b> We identified a novel complete <i>F8</i> tandem duplication associated with increased FVIII expression and a hypercoagulable phenotype in a female patient with SVT. These findings support <i>F8</i> gene dosage gain as a rare gain-of-function mechanism contributing to elevated FVIII levels and thrombophilia, while variation in VWF levels and acquired risk factors may modify thrombotic penetrance.

A substantial number of genetic variants have been associated with high-altitude adaptation (HAA), yet most of them are located in non-coding genomic regions, leaving their specific functions and underlying mechanisms largely unknown. In this study, we analyze whole-genome and transcriptome sequencing data from a self-established cohort comprising 61 native highlanders (NHs) and 164 acclimatized newcomers (ANs), identifying 6,586 cis- and 34,203 trans-expression quantitative trait loci (eQTLs), along with 130 cell type-specific eQTLs. By further combining these data with a large East Asia (~30% Tibetan) genome-wide association study (GWAS) cohort, we employ colocalization and causal inference analyses to prioritize 85 cis-eQTLs associated with HAA and identify several novel candidate causal genes, including EXOC8, which is experimentally confirmed to regulate erythroid differentiation. Additionally, network analysis of these causal genes uncovers multiple regulatory pathways, mainly involving energy metabolism, autophagy, ubiquitination and inflammation. Our study offers a comprehensive eQTL map and reveals causal chains of "variant-gene-phenotype" for HAA-related traits, which provides new insights into potential regulatory mechanisms and targets for prevention and treatment of altitude sickness.

<h4>Introduction</h4>Critically low blood donation rates and recurrent shortages in the blood supply have become pressing challenges in transfusion medicine. Xenotransfusion using porcine red blood cells (pRBCs) represents a promising alternative; however, risks of immune rejection and infection necessitate the development of genetically engineered porcine models - a process that is time-consuming, costly, and technically complex. In this study, we established an immortalized porcine erythroid progenitor cell line as a platform for genetic manipulation and the evaluation of xenotransfusion potential.<h4>Methods</h4>Porcine hematopoietic progenitor cells (CD117⁺) were isolated from bone marrow mononuclear cells and immortalized via lentiviral transduction with E6/E7 oncogenes from Human papillomavirus type 16 (HPV16) and Sus scrofa papillomavirus (SPV2).<h4>Results</h4>The resulting cells were optimized for long-term culture and exhibited stable proliferation. The immortalized porcine erythroid progenitor cells retained the capacity to differentiate into red blood cells.<h4>Discussion</h4>Our findings demonstrate that E6/E7-mediated immortalization facilitates the generation of porcine erythroid progenitor cells capable of differentiating into red blood cells, offering a valuable tool for genetic engineering and a promising avenue toward safe, sustainable heterologous blood transfusion strategies.

<h4>Background</h4>Gastric intestinal metaplasia (GIM) is a typical precancerous lesion of gastric cancer (PLGC). Previous studies have demonstrated that Xinkai Kujiang formula can effectively alleviate GIM, but its underlying mechanism remains largely unclear.<h4>Methods</h4>The GIM rat model was established using 2% sodium salicylate and 20 mmol/L sodium deoxycholate, and then the rats were treated with Banxia Xiexin Decoction (BXD) and Xinkai Kujiang Decoction (XKD) for 4 weeks. Multi-omics analyses including 16 S ribosomal RNA gene sequencing, transcriptomics, single-cell RNA sequencing, network pharmacology, and component identification were performed to explore the therapeutic mechanisms of Xinkai Kujiang formula on GIM.<h4>Results</h4>In the model rats, severe gastric mucosal atrophy was observed, characterized by disordered glands and goblet cells. Following intervention with BXD and XKD, gastric mucosal thickness was restored, glandular structures became regularly arranged, and the number of metaplastic goblet cells markedly decreased. Microbiota profiling of gastric mucosa revealed significant enrichment of <i>Lactobacillus</i> and <i>Enterococcus</i> in the model group. These abundances were reduced in the BXD group, and short-chain fatty acid-producing bacteria such as <i>Alistipes</i> and <i>Lachnospira</i> were enriched. In the intestine, opportunistic pathogens like <i>Streptococcus</i> and <i>Enterococcus</i> were enriched in the model group, whereas <i>Corynebacterium</i> and <i>Bifidobacterium</i> were enriched in the XKD group. Transcriptomic analysis presented that BXD upregulated innate immune-related genes in the gastric mucosa, and single-cell RNA sequencing (scRNA-Seq) showed that XKD alleviated GIM by inhibiting the VEGF and HIF-1α pathways, reducing angiogenesis, suppressing inflammatory infiltration, and regulating energy metabolism.<h4>Conclusion</h4>BXD and XKD improve gastrointestinal microbiota disorders and metabolic disorders, enhance gastric mucosal immunity, and inhibit the VEGF and HIF-1α pathway. Collectively, these multi-omics data provide novel insights into the therapeutic mechanisms of Xinkai Kujiang formula for GIM.

<h4>Background</h4>Chronically activated T-effector (Teff) cells can play a pivotal role in T-cell-mediated diseases including systemic lupus erythematosus subsets, lupus nephritis and graft-vs-host disease (GvHD). Since T cells require diverse costimulation signals to fully activate, proliferate, and differentiate into Teffs, we hypothesized that modulating two costimulatory pathways (CD28 and OX40) with a single bifunctional molecule would provide better control of pathogenic Teffs in autoimmune diseases than currently available T-cell costimulation modulators. We assessed the effects of dual-pathway blockade by M5542, a novel CD80, CD86, and OX40L antagonist and bifunctional fusion molecule. We determined the advantages of M5542 blocking both CD28 and OX40 pathways over single-pathway blockade in <i>in vitro</i> potency and <i>in vivo</i> studies, to more effectively curb T-cell-mediated inflammation in autoimmune diseases.<h4>Methods</h4>M5542, single-agent comparators CTLA-4Ig (abatacept), anti-OX40L, and both single agents in combination were tested for their ability to inhibit proinflammatory cytokine production in a mixed lymphocyte reaction of activated monocyte-derived dendritic cells and T cells from healthy donors or peripheral blood mononuclear cells from individuals with SLE. The target occupancy of CD80 and OX40L on dendritic cells was assessed by flow cytometry. The effects of M5542 and comparators on T-cell-mediated inflammation were assessed using a keyhole limpet hemocyanin (KLH) peptide-induced delayed-type hypersensitivity (DTH) humanized hOX40/hOX40L mouse model. All molecules were also tested for their efficacy to reduce disease in a humanized xenogenic GvHD (xGvHD) mouse model.<h4>Results</h4>M5542 potently reduced proinflammatory cytokine production and dampened T-cell proliferation compared with CTLA-4Ig or anti-OX40L <i>in vitro</i>. M5542 also neutralized OX40L-mediated T-regulatory cell (Treg) dysfunction <i>in vitro</i> and suppressed Teff proliferation in conjunction with Tregs <i>in vitro</i>. Moreover, M5542 dose-dependently reduced T-cell-mediated ear swelling and anti-KLH antibody production in the KLH-DTH mouse model. In the xGvHD model, M5542 demonstrated improved efficacy over CTLA-4Ig or anti-OX40L alone in suppressing human IFNγ and preventing disease.<h4>Conclusion</h4>In this preclinical study, the bifunctional M5542 blocked CD28 and OX40-mediated T-cell inflammation with greater immunomodulatory activity than monofunctional agents and in some assays comparable to or better than the combination of the monofunctional agents. These findings support further evaluation of M5542 in T-cell-driven autoimmune disease settings.

This paper explores the fabrication of hydroxyapatite-capsaicin nanocomposite coatings on Mg-Ag alloy by the electrophoretic deposition (EPD) method at different deposition times and voltages. The microstructure, surface chemistry, hardness, corrosion behavior, and cell proliferation of the deposited layers at different deposition times and voltages were examined. Based on microstructural observations, the deposited layers became denser at higher deposition time and voltage. In addition, the hydroxyapatite-capsaicin nanocomposite became thicker at higher EPD voltage. FTIR and XPS analyses confirmed the successful incorporation of capsaicin into the HAP coating with partial retention of CAP-derived surface functionalities after annealing. Also, the hardness of the coated layer increased with voltage and time. However, EPD voltage was more effective in increasing the hardness. The maximum hardness of 141 HV was obtained at a deposition voltage of 160 V. The hardness profile of the deposited composite showed greater fluctuations with increasing deposition voltage. Electrochemical polarization tests demonstrated that corrosion resistance improved with increasing deposition voltage and time. Furthermore, cell growth was improved at higher EPD time and voltage. MTT assay results confirmed the enhanced cytocompatibility of the HAP-CAP coatings. Also, the Mg²⁺ ion release rate and pH variation decreased as the deposited layer became thicker and denser. The minimum Mg²⁺ ion release rate of 5.2 ppm h^-1 was obtained at a deposition voltage of 160 V. Compared with conventional HAP coatings, incorporation of capsaicin enhanced the biological performance while preserving the structural stability of hydroxyapatite, which thus provides a promising strategy for the development of multifunctional biodegradable implant coatings.

Neural progenitor cell differentiation is a complex process requiring the proper integration of instructive and permissive factors. Instructive cues including signaling molecules and transcription factor networks have been well studied in this context, but permissive factors such as cell homeostasis have not. Cell homeostasis is critical to support the health and stability of a cell and enable the cell to act on instructive differentiation cues. Our study investigates a homeostasis protein, FAF2, and its function in neural progenitor cells. FAF2 is an adaptor protein involved in endoplasmic reticulum (ER) associated degradation to remove misfolded proteins and restore ER homeostasis. Here we show that knocking out <i>Faf2</i> in neural progenitor cells results in increased ER stress signature at the protein and transcription level, indicating a conserved functional role in neural progenitor cells. Induced neural differentiation of FAF2 deletion cells shows a failure of neurite development but RNA-seq indicates genes that support neural differentiation are induced. Reducing ER stress in FAF2 knockout cells with a small molecule inhibitor can rescue neural differentiation, providing evidence that excess ER stress contributes to the inhibited differentiation. Taken together, these results reveal that FAF2 is a critical protein in neural progenitor cells for the maintenance of ER homeostasis and execution of neural differentiation.

Keloid, as a unique form of pathological scar, involves complex interactions across multiple dimensions in its pathogenesis, including genetic susceptibility, epigenetic regulation, immune microenvironment disorders, metabolic reprogramming, abnormal mechanical force transduction, and fine-tuning by non-coding RNAs. At the genetic level, alleles such as HLA-DRB1*15, HOX gene family, and high-frequency mutation genes including MUC4 constitute the foundation of congenital susceptibility; at the epigenetic level, reduced DNA methylation and imbalanced m6A modification promote fibrosis by regulating target genes such as COL1A1. In core signaling pathways, TGF-β/Smad, MAPK/ERK, PI3K/AKT/mTOR, and Wnt/β-catenin pathways form a cross-talk network, driving persistent activation of fibroblasts and excessive extracellular matrix deposition. Characteristics of the immune microenvironment include M2-like macrophage polarization, Th17/IL-17 axis activation, and chronic low-grade inflammation maintained by inflammatory factor networks such as CXCL12. Regarding metabolic reprogramming, keloid cells exhibit "Warburg effect" features, prioritizing aerobic glycolysis while suppressing oxidative phosphorylation, alongside ferroptosis resistance and abnormal sphingolipid metabolism. Mechanical forces trigger the opening of mechanosensitive PIEZO1 ion channels, inducing abnormal calcium influx and subsequent YAP/TAZ nuclear translocation, which creates a self-amplifying vicious cycle alongside elevated matrix stiffness. Furthermore, lncRNAs, circRNAs, and miRNAs finely regulate the fibrotic process through competing endogenous RNA (ceRNA) networks and m6A modification-dependent mechanisms. The integration of these multidimensional mechanisms provides a theoretical basis for developing multi-target combination therapeutic strategies. Future research should promote the application of precision medicine in keloid management through multi-omics integration and artificial intelligence algorithms. Microenvironment; Metabolic reprogramming; Mechanical force transduction.

Arrestins were originally defined as terminators of G protein-coupled receptor (GPCR) signaling, yet structural and mechanistic advances now reveal them as programmable, spatiotemporal integrators of cellular signaling. Recent cryo-electron microscopy studies have revealed a diverse spectrum of GPCR-arrestin engagement modes, including core-, tail-, loop-, side-engaged, and membrane-anchored conformations, across GPCR classes and arrestin isoforms. These structures reveal that arrestin recruitment operates as a conditional, allosterically regulated process rather than a binary on-off switch. The selection of the arrestin microstate is governed by layered regulatory inputs, including GPCR kinase-dependent phosphorylation barcodes, membrane and lipid cofactors, and isoform-specific mechanics, which together define the signaling geometry, duration, and subcellular localization. This structural logic provides a mechanistic foundation for biased signaling, noncanonical endosomal signaling, and GPCR-independent arrestin functions. Importantly, emerging therapeutic strategies, including intracellular allosteric modulators and molecular glues, demonstrate that arrestin signaling can be reprogrammed by directly sculpting transducer assemblies rather than ligand efficacy alone. Here, we synthesize recent structural, biochemical, and physiological insights to outline how arrestins decode regulatory inputs into signaling outcomes and how this knowledge enables the development of next-generation, structure-guided GPCR therapeutics.

African swine fever remains a major constraint on global pig production because effective treatment is unavailable, and disease control relies primarily on biosecurity and outbreak management. Field observations from endemic regions increasingly suggest that some domestic pigs can survive exposure to ASFV. Therefore, the aim of this study was to characterize genomic differences between Mozambican Landim pigs that survived or died after natural ASFV infection and to identify variants potentially associated with differential disease survival. Whole-genome sequencing was performed on 32 naturally exposed Landim pigs, including 16 survivors and 16 non-survivors, and the resulting reads were aligned to the Sscrofa11.1 reference genome. Variant frequencies were compared between groups, and functional annotation was performed. Genetic structure was assessed using PCA, genetic distance-based clustering, and admixture. The data revealed marked genomic differentiation between survivors and non-survivors. Comparative analysis identified 4,804 polymorphisms that significantly differentiated, of which 45.0% were intergenic. Missense variants were identified in the TTC12 and WWC1 genes, and functional annotation of genes harboring significantly differentiating variants indicated processes related to immune regulation, T-cell activation, intracellular signaling, cytoskeletal organization, vesicular transport, ubiquitin-dependent proteostasis, and lipid metabolism. Given the marked genetic stratification between survivor and non-survivor groups, the observed differences between them cannot be unambiguously separated from underlying population structure. Therefore, although some of the identified variants may contribute to differential survival following ASFV exposure, the findings should be considered exploratory and require validation in larger, independent, genetically comparable populations.

Ferroptosis is a distinct modality of programmed cell death driven by iron-dependent lipid peroxidation, exerting a pivotal regulatory influence on the infection dynamics and immune responses associated with zoonoses. This article systematically elucidates the mechanistic interplay between significant zoonotic pathogens and the core regulatory networks of host ferroptosis, encompassing iron metabolism, the antioxidant defense systems typified by GPX4, and lipid peroxidation. Furthermore, it synthesizes current advancements and challenges regarding small molecules, natural products, and bioactive components of traditional Chinese medicine that target key ferroptotic checkpoints for anti-infective therapy. This review aims to establish a theoretical foundation for the development of novel, precision prevention and control strategies for zoonoses, grounded in ferroptosis modulation within the "One Health" perspective.

Splenomegaly is a defining feature of myelofibrosis, yet the contribution of splenic mesenchymal stroma to disease progression remains unclear. We combined spatial and single-nucleus transcriptomics of patient spleens with spatial and single-cell transcriptomics, as well as imaging analyses, of murine spleens to map extramedullary hematopoiesis niches. Activated red pulp reticular cells localize near hematopoietic stem and progenitor cells, and early disease is characterized by marginal zone disruption with lymphoid depletion preceding stromal remodeling. Trajectory analyses reveal a shift in reticular cells from hematopoiesis-supportive to inflammatory and pro-fibrotic states, driven by macrophage- and megakaryocyte-derived signals that activate complement and induce tumor necrosis factor α (TNF-α), transforming growth factor β (TGF-β), extracellular matrix, and Thbs1 programs. Non-hematopoietic complement component C3 deficiency or pharmacological C3 inhibition suppresses these pathways, restores splenic architecture, and reduces splenomegaly and bone marrow fibrosis. These findings identify complement-dependent stromal reprogramming as a mechanism governing hematopoietic niches and as a targetable axis in myelofibrosis.

<h4>Background</h4>Mendelian susceptibility to mycobacterial disease (MSMD) is a subset of inborn errors of immunity (IEIs) predisposing to clinical infections from less virulent mycobacterial species. Variants in 22 genes, particularly in IL-12Rβ1, have been identified that impair interferon-gamma (IFN-γ)-mediated immunity. We report a new rare MSMD patient with a homozygous <i>IL12RB1</i> variant who presented with severe and persistent ascites.<h4>Case report</h4>We investigated a 30-month-old girl who developed an abscess and lymphadenopathy (LAP) in the left axilla after receiving a BCG vaccine. She was diagnosed and treated for BCG-osis. She presented with ascites, which gradually worsened, along with symptoms of liver dysfunction. Her portal hypertension (PHT) was considered the most likely cause of ascites after exclusion of other common causes. The whole exome sequencing (WES) revealed a homozygous rare variant (c.635G>A; p.Arg212Gln) in the <i>IL12RB1</i> gene. Sanger sequencing analysis confirmed that both parents were heterozygous carriers of the variant. She made a good recovery after receiving the appropriate antimycobacterial and ascites treatments, with significant resolution of her symptoms. Because disseminated <i>M. bovis</i> BCG infection occurred in the setting of IL-12Rβ1 deficiency, prolonged susceptibility-guided antimycobacterial therapy with adjunctive IFN-γ1b and close follow-up by infectious disease and immunology, was planned.<h4>Conclusion</h4>This case highlights severe persistent ascites as an unusual manifestation of PHT in IL-12Rβ1 deficiency associated with MSMD. Evaluation for PHT should be considered in MSMD patients with abdominal distension, gastrointestinal symptoms, hepatosplenomegaly, abnormal liver function tests, growth failure, or unexplained free abdominal fluid.

Diabetic nephropathy (DN) is a major microvascular complication of diabetes. Hypoxia-inducible factor 1-alpha (HIF1A) and ferroptosis contribute to the progression of DN, but the circulating biomarkers associated with these pathways are still unknown. In this study, the whole-blood transcriptomic datasets in the Gene Expression Omnibus were combined with ferroptosis-related genes from the FerrDb database and published literature. The differentially expressed genes of HIF1A and of DN were intersected, and then the feature selection with Boruta and SVM-RFE was performed, followed by external validation, immune infiltration analysis, prediction of regulatory network, drug-target prediction, and RT-qPCR validation. We identified 773 HIF1A-related genes, 1445 DN-related genes, and 22 overlapping candidate genes. Using machine-learning analysis, nine core genes were identified, including SLC7A5 and SLC2A14, which consistently upregulated in both training and validation datasets and corroborated by RT-qPCR. Both genes were positively associated with activated natural killer cells and negatively associated with monocytes in estimated circulating immune-cell composition analysis. Regulatory-network and DrugBank analyses generated hypotheses regarding upstream miRNAs and potential compound interaction. These findings identify SLC7A5 and SLC2A14 as candidate circulating biomarkers related to HIF1A expression and ferroptosis-related gene signatures in DN. Further large-cohort and functional studies are required to confirm their diagnostic and mechanistic relevance.

Upconversion nanoparticles (UCNPs) convert tissue-penetrating near-infrared photons into sharp visible emissions, offering background-free optical readouts for deep-tissue imaging. Here we report multilayer NaLuF₄:Yb,Tm@NaLuF₄ UCNPs that simultaneously act as fluorescent probes and radioisotope precursors. Under 980 nm excitation, the particles generate bright blue and red upconversion signals for real-time tracking. At the same time, their lutetium-rich core can be neutron-activated in a single step to yield β^-- and γ-emitting ¹⁷⁷Lu. The β-particles confine cytotoxic dose within a 2 mm range, whereas the co-emitted γ photons enable quantitative single-photon emission computed tomography (SPECT). To enhance the tumor selectivity of the nanoplatform, we grafted a c-Met DNA aptamer onto the PEGylated shell, guiding the nanoconstructs to target head and neck squamous cell carcinoma (HNSCC) with amplified c-Met receptor levels. The aptamer markedly enhances cellular uptake, improves therapeutic indices, and limits off-target irradiation. Moreover, the optical modality remains non-radioactive, allowing pre-treatment imaging without patient exposure, and supplements the relatively low (∼10%) γ yield of ¹⁷⁷Lu for accurate intra-procedural localization. Collectively, this single nanosystem unites targeted radiotherapy, radionuclide therapy, SPECT, and NIR-mediated optical imaging, delivering a coherent "see-and-treat" strategy for HNSCC. The modular design also provides a versatile platform that can be transferred to other solid tumors bearing actionable biomarkers across diverse clinical oncology imaging and therapy settings.

<h4>Aim</h4>Episodic Migraine (EM) is a highly prevalent and disabling neurological disorder. Recent therapeutic advances have targeted the calcitonin gene-related peptide (CGRP), a neuropeptide implicated in the pathophysiology of migraine. Promising outcomes have been obtained with monoclonal antibodies and, more recently, with a new class of drugs consisting of small-molecule CGRP receptor antagonists, known as gepants. Atogepant, an oral agent of the gepant class, has demonstrated efficacy in migraine prevention, yet its effects on central brain activity and neurotransmitter circuits remain largely unclear. This exploratory study investigates changes in brain functional connectivity and changes related to key neurotransmitter systems, following 12 weeks of treatment with atogepant in a group of EM patients.<h4>Methods</h4>This is an exploratory single-arm longitudinal study assessing clinical and neuroimaging changes before and after 12 weeks of atogepant treatment. We enrolled patients diagnosed with EM according to ICHD-3 criteria, without prior exposure to anti-CGRP therapies. Participants underwent clinical assessments (monthly migraine days MMD, acute drugs intake MAM) and resting-state functional MRI (rs-fMRI) before and after 12 weeks of treatment with atogepant 60 mg once daily. Longitudinal functional connectivity analyses were performed at the whole-brain level with a region-of-interest analysis. Additionally, longitudinal neurotransmitter-related functional connectivity was investigated within the serotoninergic and the dopaminergic systems.<h4>Results</h4>A total of 15 patients completed the evaluation. A significant group-level reduction in MMD (T = -7.09, <i>p</i> < 0.001) and MAM (T = -6.35, <i>p</i> < 0.001) following 12 weeks of atogepant treatment was observed, accompanied by a reduction of allodynia symptoms, albeit not statistically significant. Patients exhibited significant longitudinally increased functional connectivity, involving the right superior frontal gyrus, bilateral putamen, left pallidum, left anterior and bilateral posterior cingulate cortex. The greater the longitudinal increase in anterior-posterior cingulate cortices connectivity, the larger the improvement in MMD, MAM, and allodynia symptoms after treatment. Additionally, longitudinal connectivity changes were observed within the orbitofrontal cortex in the mesocorticolimbic dopaminergic system.<h4>Discussion</h4>In this exploratory cohort, significant clinical improvement after atogepant treatment was accompanied by longitudinal functional connectivity changes in EM patients. These preliminary findings may reflect either direct or indirect central modulation linked to atogepant treatment. A deeper understanding of the observed central changes may help to clarify the mechanisms underlying anti-CGRP therapies for migraine.

Autoimmune gastritis (AIG) arises from a T-cell-mediated immune attack on the gastric parietal cell and carries a dual neoplastic risk: gastric adenocarcinoma through spasmolytic polypeptide-expressing metaplasia (SPEM) and intestinal metaplasia, and type-1 gastric neuroendocrine tumour (NET) through hypergastrinaemia-driven enterochromaffin-like (ECL) cell hyperplasia. This "one origin, two fates" framework is conceptually established but has never been given a molecular trajectory from an AIG origin, and molecular data for the neuroendocrine endpoint are essentially absent. We integrated public single-cell transcriptomes of the human AIG corpus (GSE271866; three samples, 14,323 cells) and of a histologically staged premalignant cascade (GSE134520; 44,012 cells) with a cross-sectional cohort of approximately 203 AIG patients, treating the two axes asymmetrically: the adenocarcinoma axis was reconstructed at the molecular level, whereas the neuroendocrine axis was clinically and literature anchored. The AIG corpus showed near-absent parietal cells (0.45%) with extensive SPEM (18.6%) and intestinal metaplasia (16.3%). Cascade pseudotime increased monotonically with histological stage (Spearman's <i>ρ</i> = 0.496; unchanged on the unbridged graph) and defined a gastric-to-intestinal progression signature that, transferred to the AIG corpus, tracked the AIG-intrinsic pseudotime (<i>ρ</i> = 0.673). Most AIG metaplastic cells were projected to the strong-metaplasia stage (90.9%; bootstrap 95% CI 84-98%; <i>n</i> = 55), a suggestive rather than definitive placement that is nonetheless consistent with AIG occupying the atrophy-to-metaplasia segment of the adenocarcinoma axis. In the cohort, hypergastrinaemia scaled with corpus atrophy (gastrin-17 versus pepsinogen I/II ratio <i>ρ</i> = -0.413, <i>p</i> = 9.9 × 10^-8), and single-cell analysis confirmed a gastrin-responsive ECL population (<i>HDC</i> ⁺ 93%, <i>CCKBR</i> ⁺ 76%) whose neuroendocrine programme was orthogonal to the intestinal programme of the adenocarcinoma arm. Because AIG is a prototypic autoimmune disease, we frame how the autoimmune infiltrate steers each fate as the central open immunological question. AIG thus enters the metaplasia-to-cancer axis from a corpus, parietal-cell-loss origin and diverges, through a serum-gastrin-ECL bridge, towards the neuroendocrine fate; we provide an interpretable progression signature and a severity-anchored, hypothesis-generating framework-not an outcome predictor, since the cohort is cross-sectional with essentially no neoplastic endpoints-and report the molecular data gap for the neuroendocrine endpoint as a field-level priority.

The alpaca (<i>Vicugna pacos</i>) is a domesticated South American camelid of increasing global relevance, valued for its high-quality fiber, cultural significance, and unique biological traits including heavy-chain-only antibodies. Its reproductive physiology differs fundamentally from that of conventional livestock, encompassing an induced rather than spontaneous ovulatory mechanism in females and an unusually viscous ejaculate in males, differences that constrain the direct application of protocols developed for cattle, sheep, and swine and that have historically limited the pace of genetic improvement in the species. This review provides an integrated account of alpaca reproductive anatomy, follicular and neuroendocrine physiology, seminal plasma biochemistry, and semen cryopreservation, together with the current state of artificial insemination, multiple ovulation and embryo transfer, laparoscopic ovum pick-up, <i>in vitro</i> embryo production, and intracytoplasmic sperm injection. By examining female and male reproductive biology within a single mechanistic framework rather than treating each in isolation, this review draws out the regulatory pathways that connect the two systems and identifies the knowledge gaps that a fragmented, single-sex treatment of the subject would otherwise leave unaddressed. Particular attention is given to the biological determinants that most directly limit ART efficiency and to the translational steps required to move current protocols from experimental proof of concept toward standardized, field-applicable practice. Building on prior reviews that have illuminated individual ART modalities and single-sex reproductive biology, this work is intended to support researchers and practitioners advancing reproductive technology in camelids and the broader effort to conserve and genetically improve alpaca populations worldwide.

Despite advances in delineating the molecular diversity and projection patterns of midbrain dopamine (DA) neurons, subtype-specific contributions to motor learning and movement execution remain poorly defined. Here, we applied intersectional ablation and inhibitory chemogenetics to dissect the roles of calbindin-expressing (CALB1⁺) and nonexpressing (CALB1^-) DA neurons in locomotion. Using newly engineered intersectional autocleavable Caspase3 constructs, we ablated CALB1⁺ or CALB1^- DA neurons in the mouse midbrain. CALB1^- DA neuron ablation caused severe weight loss, whereas CALB1⁺ DA neuron ablation produced no overt health impairments. Nonetheless, loss of either subtype led to a bradykinetic-like phenotype on the initiation and vigor of voluntary movements. Only ablation of CALB1^- DA neurons impaired performance on the accelerated rotarod. To test if these phenotypes are the result of DA subtype activity, we silenced either population using the inhibitory DREADD hM4Di. Consistent with ablation, silencing CALB1^- DA neurons impacted the initial performance on the rotarod, whereas inhibition of CALB1⁺ DA neurons did not impact performance on the first day, but prevented across-day improvement. Silencing both populations impaired the initiation and vigor of voluntary movements. We next investigated whether this locomotor phenotype stemmed from reduced DA release in the dorsolateral striatum (DLS). While CALB1^- silencing abrogated DA transients in the DLS, CALB1⁺ silencing unexpectedly resulted in increased transients in DLS. Thus, our results demonstrate that DA transients in the DLS are not invariably coupled with movement execution. Altogether, these findings uncover both distinct and shared roles of molecularly defined DA subtypes in shaping different aspects of locomotion.

NADPH oxidases (NOXs) have emerged as central hubs that link environmental, metabolic, and immune cues through spatially organized redox signaling. However, their roles across tissues and disease states have not been comprehensively evaluated in an integrated manner. This review integrates recent advances in structural biology, immunometabolism, toxicology, and systems biology to provide an updated, comprehensive, and accessible view of NOX biology. Recent advances in high‑resolution cryo-EM, AlphaFold‑based modeling and molecular dynamics studies have provided new insights into NOX architecture, catalytic sites, post‑translational modifications and regulatory mechanisms, and docking interfaces for RAC1 and p47^phox. Emerging evidence further indicates that cellular NOX-derived ROS can reprogram macrophage and T-cell metabolism, stabilize HIF-1α, and tune the balance between effector and regulatory states, thereby linking NOX activity to checkpoint control and tumor immune escape. A second focus is on how real‑world pollutants converge on NOX isoforms as proximal mediators of redox signaling across lung, vascular, hepatic, renal, and neural tissues. NOX activation during cellular injury may contribute to oxidative stress, mitochondrial dysfunction, inflammasome activation, and fibrotic signaling, through extracellular vesicles, lipid rafts, and noncoding RNAs. Finally, the review evaluates emerging therapeutic strategies, including isoform-selective/pan-NOX/peptide inhibitors, and nanozymes. It also discusses emerging approaches such as exosome-based biomarkers, network pharmacology, and machine learning for patient stratification and pharmacodynamic monitoring. By highlighting key mechanistic gaps and translational opportunities, this review establishes NOXs as actionable nodal regulators at the intersection of immunity, metabolism, environmental exposure, and human disease.

<h4>Background</h4>Type 1 diabetes mellitus (T1DM) is a chronic disease that significantly impacts patients' quality of life. Its prevalence is rising globally each year. This study aims to identify potential biomarkers associated with T1DM through comprehensive bioinformatics analysis, further enhancing T1DM early diagnosis and treatment.<h4>Methods</h4>Transcriptome datasets from T1DM patients and the control group were from the Gene Expression Omnibus (GEO) database. Differentially Expressed Genes (DEGs) were identified and subsequently analyzed using Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction (PPI) network analysis. Hub genes were identified using Enzyme-Linked Immunosorbent Assay (ELISA) on clinical samples comprising 17 T1DM patients and 19 controls. Immune cell infiltration was estimated using the Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) algorithm, while the diagnostic performance of the hub genes was evaluated <i>via</i> receiver operating characteristic (ROC) curve analysis.<h4>Results</h4>A total of 20 up-regulated and eight down-regulated DEGs were identified in the GEO database. Functional enrichment analysis showed that immune activation played an important role in T1DM. The expression levels of the hub genes, <i>CTSG</i> and <i>LTF</i>, were further validated in clinical samples. ROC analysis showed moderate diagnostic performance, with AUC values of 0.75 (training set) and 0.67 (validation set).<h4>Conclusions</h4>The results indicate that <i>CTSG</i> and <i>LTF</i> may serve as promising diagnostic biomarkers for T1DM. Our study is positioned as exploratory with moderate diagnostic relevance rather than definitive biomarker discovery. The findings are preliminary and require further validation before any clinical application.

<h4>Introduction and importance</h4>Primary gastric melanoma (PGM) is an exceedingly rare malignancy, especially in Asian populations, that presents major diagnostic and therapeutic dilemmas.<h4>Presentation of the case</h4>We report the case of a 53-year-old Vietnamese man who presented with only vague epigastric discomfort. During a routine esophagogastroduodenoscopy, a small pigmented lesion was incidentally discovered in the stomach. An initial biopsy confirmed the presence of malignant melanoma, supported by immunohistochemical positivity for SOX10. A subsequent comprehensive workup - including dermatological and ophthalmological evaluations and comprehensive systemic imaging - found no other primary melanocytic sites, thereby fulfilling three of Blecker's criteria. A total laparoscopic gastrectomy with D2 lymphadenectomy was performed. Postoperative histopathology showed no residual tumor in the gastric specimen or in any of the lymph nodes examined.<h4>Clinical discussion</h4>The absence of established treatment standards for PGM necessitated a complex multidisciplinary discussion. Key questions centered on balancing oncologic radicality (total gastrectomy, D2 lymphadenectomy) with patient quality of life, especially given the likelihood of complete excision at the time of the initial biopsy. The finding of no residual disease post-resection complicated the indication for adjuvant systemic therapy. The diagnosis was supported by SOX10 staining and the fulfillment of Blecker's criteria (pending completion of the 6-month surveillance period). The upfront radical approach, though potentially excessive, preempted the need for a second operation to confirm pathological clearance.<h4>Conclusion</h4>This report contributes to the limited literature on PGM, highlighting the importance of early detection, multidisciplinary discussion, and long-term follow-up in such rare presentations.

<h4>Background</h4>Huntington's disease is prevalent globally, with approximately 4.88 cases per 100,000 people, based on a systematic review and meta-analysis of 33 studies published between 2010 and 2022. Despite its significant prevalence, no proper treatment is available that directly addresses Huntington's disease. The existing treatments focus on symptom management, such as controlling chorea and psychiatric symptoms. The drugs used for this purpose may also cause side effects, including depression and Parkinson's disease.<h4>Methods</h4>An integrated experimental and computational approach was employed, involving cold maceration extraction of <i>Sesamum indicum</i>, LC-MS/MS based phytochemical profiling, ADMET screening, molecular docking, molecular dynamics simulations, and MMBPSA binding free energy analysis to identify potential inhibitors of Huntington's diseases associated targets.<h4>Results</h4>Among the LC-MS/MS identified compounds, eight compounds satisfied the ADMET criteria. Valdiate (PubChem CID: 129715809) demonstrated favourable multi-target binding with docking score of -7.3 kcal/mol against HDAC4 and -8.9 kcal/mol against HDAC7. Molecular dynamics simulations confirmed stable protein-ligand interactions, while MMPBSA analysis yielded binding free energies of -23.22 ± 2.45 kcal/mol (HDAC4) and -28.27 ± 2.28 kcal/mol (HDAC7), identifying Valdiate as the most promising potential inhibitor.<h4>Conclusion</h4>Valdiate may serve as a potential inhibitor of mutant huntingtin-associated pathological pathways, pending further <i>in-vitro</i> and <i>in-vivo</i> validation.

The oral cavity represents a highly complex biochemical ecosystem in which host tissues, saliva, microbial communities, and environmental factors interact dynamically to maintain health or promote disease. This narrative review examines a comprehensive overview of the biochemical processes occurring within the oral cavity and examines their implications for oral health and disease. Key aspects discussed include the biochemical composition and functions of saliva, the metabolic activity of the oral microbiota, biofilm formation, and the molecular mechanisms underlying major oral diseases such as dental caries, periodontal disease, and oral mucosal disorders. Particular emphasis is placed on the role of biochemical homeostasis, microbial dysbiosis, inflammation, and oxidative stress in disease pathogenesis. Although substantial progress has been made in characterizing these mechanisms, current evidence remains largely derived from <i>in vitro</i> or reductionist models that do not fully replicate the complexity of the oral environment. In addition, inter-individual variability and host-microbial interactions are still incompletely understood, limiting full translational application. This review also discusses the emerging role of salivary biomarkers as non-invasive diagnostic and prognostic tools, as well as potential therapeutic strategies targeting biochemical pathways. By critically integrating current evidence, this work highlights both advances and remaining gaps in oral biochemistry, emphasizing its relevance for the development of more precise preventive, diagnostic, and personalized approaches in oral healthcare.

<h4>Background</h4>Sceletium tortuosum is an endemic plant in Southern Africa, traditionally used as kanna by the indigenous people and also exploited commercially due to its mood-elevating properties. Mesembrine, a major alkaloid from this plant, acts as a selective serotonin reuptake inhibitor (SSRI), a group of drugs commonly used in antidepressant therapy but with the undesirable side effect of impairing bone mineral formation. The aim of this study was to investigate the potential effects and mechanisms of extracts from this plant on mineralization.<h4>Methods</h4>Both aqueous and ethanolic extracts were prepared from S. tortuosum. Their effects on mineralization were studied using bone-forming SaOS-2 cells. In addition to the effects on cell viability and alkaline phosphatase (ALP) activity, the radical scavenging activity of the extracts was determined using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2',7'-dichlorodihydrofluorescein diacetate (H₂DCF-DA) assays. The alkaloid composition was analyzed by liquid chromatography-mass spectrometry (LC-MS).<h4>Results</h4>It is shown that the S. tortuosum extracts, in contrast to SSRIs, have a significant mineralization-promoting activity in vitro. This result was obtained despite the fact that, as is characteristic for SSRIs, the transient attenuation of the serotonin-induced suppression of cell viability that occurs with increasing serotonin concentrations was inhibited in SaOS-2. The activity of ALP, a marker of differentiated osteoblasts, remained unchanged. It was found that the plant extracts exhibit a pronounced radical scavenging activity not only in the DPPH assay, but also intracellularly using the cell-permeant probe H₂DCF-DA. The alkaloid fraction of the aqueous extract of S. tortuosum consists primarily of the two bioactive alkaloids mesembrine and mesembrenone. Mesembrine proved to be only a weak inducer of mineralization.<h4>Conclusions</h4>The results suggest that the observed osteogenic effects of S. tortuosum are due to a tuned interaction with signaling pathways involving serotonin receptors, serotonin transporters and reactive oxygen species. Due to its mineralization-promoting properties, we conclude that S. tortuosum is of potential interest for the long-term treatment of depressive disorders as an adjunct to antidepressant drugs that increase the risk of osteoporosis.

<h4>Introduction</h4>Recent evidence suggests that individuals with behavioural variant frontotemporal dementia (bvFTD) may experience language changes in a similar, but less severe manner, than what is observed in semantic dementia (SD). Few studies, however, have specifically compared these patient groups or considered the cognitive underpinnings. To explore this in more depth, this study aimed to profile patterns of language performance within both "probable" and "possible" categories of bvFTD and to compare them to SD, while also considering the relationships between language and executive function measures.<h4>Methods</h4>Participants included 106 probable bvFTD, 43 possible bvFTD, 42 SD, and 112 healthy controls from the FRONTIER clinic. Data analysed included the Addenbrooke's Cognitive Examination (ACE-III), single word processing (SYDBAT) and executive function measures (word generativity, mental flexibility, response inhibition and working memory).<h4>Results</h4>Naming and semantic association impairments frequently occurred in probable bvFTD (51% and 49% respectively). Approximately one quarter of possible bvFTD patients also showed language impairments. The SD pattern of pronounced naming impairment as compared to other single word tasks, was not found in the bvFTD groups. Semantic measures from the ACE-III predicted language performance in bvFTD groups; response initiation and suppression also emerged as a significant predictor.<h4>Conclusion</h4>Naming and semantic association deficits commonly arise in probable bvFTD, but may also be observed in some patients with possible bvFTD. The pattern of impairments in bvFTD were not wholly consistent with those seen in SD. Both semantic and executive function measures may be associated with language performance deficits observed in bvFTD.

<h4>Introduction</h4>HD is a hereditary neurodegenerative disease caused by the amplification of the CAG trinucleotide repeat in the HTT gene, leading to a Mutant Huntingtin (mHTT) protein that dysregulates transcription, promotes protein aggregation, induces neuroinflammation, and impairs mitochondrial function. Motor dysfunction, cognitive decline, and mental disorders are manifestations of these biochemical abnormalities. Effective disease-modifying treatments are still limited, even with recent improvements. This review investigates the increasing relevance of Klotho, an anti-aging protein with neuroprotective, antioxidant, and anti-inflammatory characteristics, as a possible therapeutic target in Huntington disease.<h4>Methods</h4>We did a comprehensive literature search across PubMed, Scopus, and Web of Science databases. Klotho's molecular functions in neural protection, energy metabolism, oxidative stress reduction, and anti-inflammatory signalling were investigated in the context of HD pathogenesis.<h4>Results</h4>Klotho appears to influence critical neurodegenerative processes involved in HD. It inhibits NF-κB and NLRP3 inflammasome activity, stimulates antioxidant enzyme expression (SOD, catalase), promotes GluN2B-NMDA receptor-mediated synaptic plasticity, and increases astrocytic aerobic glycolysis via FGFR1-ERK signaling. These functions may mitigate mHTT- induced neuronal damage. Pharmacologic treatments (e.g., PPAR-γ agonists), vitamin D, and lifestyle interventions can all modulate klotho expression.<h4>Discussion</h4>Klotho exhibits neuroprotective effects in Huntington's disease by reducing NF-κB/NLRP3- mediated inflammation, strengthening antioxidant defenses, promoting GluN2B-NMDA- dependent synaptic plasticity, and improving astrocytic metabolic support via FGFR1-ERK signaling. One intriguing treatment approach for mutant huntingtin-induced neurotoxicity is the modification of klotho expression.<h4>Conclusion</h4>Klotho is a promising neurochemical modulator with disease-modifying properties in HD. Its multifunctional protective activities are consistent with important pathological markers of HD, necessitating more preclinical and clinical studies to confirm its translational value.

Semah mahseer (<i>Tor douronensis</i>) is a high-value freshwater cyprinid native to Southeast Asia. This study characterized acute transcriptomic responses in liver and white skeletal muscle following 6 h exposure to hyperthermia (35 °C), hypoxia (dissolved oxygen 2 mg/L), or their combination. Thirty-two RNA-seq libraries yielded approximately 48,504 annotated unigenes. Relative to the control, hyperthermia produced 7776 differentially expressed genes (DEGs) in liver and 1121 in muscle, hypoxia produced 2451 and 318 DEGs, and combined exposure produced 4952 and 717 DEGs, respectively. The response involved heat-shock proteins, endoplasmic-reticulum protein processing, glycolytic and oxygen-sensing pathways, mitochondrial and contractile programs, and apoptosis-associated signaling. Expression directions for 20 selected transcripts were compared by qRT-PCR; the reported cross-platform correlation was <i>r</i> = 0.91, although interpretation remains conditional on validation of reference-gene stability. Qualitative scanning electron microscopy showed region-dependent disruption of skeletal-muscle organization under the stress treatments. Because the study used one acute endpoint, two replicate tanks per condition, a de novo transcriptome, and no direct postmortem flesh-quality measurements, the findings should be interpreted as mechanistic hypotheses requiring independent validation.

The conversion of native prion protein (PrP) into its misfolded isoform, scrapie (PrP^Sc) and its intracellular accumulation represent central events in the pathogenesis of prion diseases. Reduction of native PrP in the central nervous system (CNS) has emerged as a promising strategy for treatment and prevention of prion diseases in humans. To facilitate translation into clinical practice, it is essential to identify at-risk individuals through biomarker development and to elucidate PrP behaviour across prion disease subtypes and biological fluids. Measurements of PrP in accessible biofluids, such as plasma and cerebrospinal fluid (CSF), may provide a pharmacodynamic readout and enable monitoring for PrP-targeted therapies. This study systematically quantifies PrP in plasma and CSF of individuals with sporadic and genetic prion diseases, healthy controls (HC), patients with non-neurodegenerative neurological conditions (ND) and Alzheimer's disease (AD). We analysed 136 plasma and 84 CSF samples, including HC, AD, sporadic Creutzfeldt-Jakob disease (sCJD), as well as symptomatic patients and asymptomatic carriers of the mutations D178N, E200K and P102L. Quantification of PrP was performed using a BetaPrion Human ELISA. Statistical analyses assessed differences between diagnostic groups, associations with demographic factors and <i>PRNP</i> codon 129 polymorphism, and diagnostic accuracy via ROC curves. Plasma PrP was significantly reduced in patients with sCJD (<i>P</i> = 0.043), in symptomatic patients with the E200K (<i>P</i> = 0.0078) and in both symptomatic and asymptomatic D178N carriers (<i>P</i> = 0.0002) compared to HC. Furthermore, symptomatic and asymptomatic D178N carriers had significantly lower plasma PrP levels than patients with AD (<i>P</i> = 0.0025 and <i>P</i> = 0.0041, respectively). In CSF, PrP concentrations were notably lower in D178N symptomatic patients (<i>P</i> = 0.0026) versus non-neurodegenerative (ND) controls. Plasma PrP levels showed no association with age, sex or disease onset and were lower in genetic prion disease patients with the methionine/valine (MV) genotype at <i>PRNP</i> codon 129. The diagnostic accuracy for PrP quantification in plasma as a biomarker discriminated D178N asymptomatic carriers [area under the curve (AUC) = 0.96] and D178N symptomatic patients (AUC = 0.90) from HC with excellent accuracy. In CSF, PrP quantification discriminated D178N symptomatic patients from ND with good accuracy (AUC = 0.64). Taken together, this study defines a characteristic profile of persistently low plasma and CSF PrP in D178N symptomatic and asymptomatic mutation carriers. Low plasma levels in sCJD and E200K, in contrast to P102L, are puzzling. Mutation-specific patterns of PrP need to be considered for monitoring purposes in clinical trials.

<h4>Purpose</h4> Haemochromatosis due to HFE -C282Y homozygosity can lead to excess iron absorption and is typically associated with liver malignancy, plus widespread arthritis. Recent evidence suggests that limb fractures are more common, but little is known about vertebral effects. This study investigated the association of vertebral compression fractures, assessed with intelligent dual-energy X-ray absorptiometry (iDXA), and HFE genotype in a large community cohort. <h4>Methods</h4> UK Biobank data from 227 European genetic ancestry C282Y homozygotes (mean 64.6 years) and 234 age, sex, and BMI-matched controls without common HFE haemochromatosis variants were included. Lateral vertebral assessment scans (iDXA, GE-Lunar) were acquired at imaging reassessment (2014-2020) and reviewed, blind to genotype, for radiological evidence of vertebral fracture. Matched logistic regression models assessed associations between C282Y homozygosity and vertebral fractures. <h4>Results</h4> 78 vertebral fractures (16.9%) were identified within 461 participants. Male C282Y homozygotes had increased odds of vertebral fracture (n=22/89, 24.7%) compared to participants without HFE alleles (n=9/90, 10.0%); Odds Ratio [OR]: 2.95, 95%CI: 1.28–6.85, p=0.01. The association persisted after excluding individuals with a diagnosis of haemochromatosis (OR: 3.37, 95% CI: 1.41–8.10, p=0.007). No excess fracture risk was observed in female C282Y homozygotes (n=23/138, 16.7%) vs those without HFE alleles (n=24/144, 16.7%); OR: 0.99, 95%CI: 0.53-1.87, p=1.00. <h4>Conclusion</h4> In this community-based imaging study, male HFE C282Y homozygotes had a markedly higher likelihood of vertebral fractures than those without HFE variants. These findings support further evaluation of vertebral fracture assessment in C282Y homozygous men to ensure prompt treatment to prevent future fracture if appropriate.

Type 2 diabetes (T2D) is a complex metabolic disorder characterized by hyperglycemia and insulin resistance. Although genome-wide association studies (GWAS) have identified >600 T2D risk loci, the causal genes and the relevant tissues mediating these associations remain largely unresolved. To address this challenge, we performed tissue-specific, ancestry-aware transcriptome-wide association studies (TWAS) across six T2D-relevant tissues: subcutaneous adipose, visceral adipose, brain hypothalamus, liver, skeletal muscle, and pancreas. We conducted ancestry-specific multi-tissue TWAS in European ancestry (EUR) data using summary statistics from the largest EUR GWAS (242,283 cases and 1,569,734 controls) and pre-trained gene expression prediction models derived from 689 EUR individuals from the Genotype-Tissue Expression (GTEx) Project. Conditional analyses were performed to identify independent TWAS signals. We identified 684-750 significant gene-T2D associations per tissue (P < 1.919 × 10 −6 ), implicating both established and novel candidate genes. Among these, JAZF1 and IDE showed consistent association signals across all six tissues, whereas TCF7L2 and WSF1 exhibited heterogeneous effects restricted to a subset of T2D-relevant tissues. Conditional analyses further refined these signals to 289–322 independent TWAS signals per tissue. Together, these finding highlight substantial regulatory heterogeneity in the genetic architecture of T2D and underscore the importance of tissue context in interpreting disease-associated loci. Cross-ancestry replication of EUR-derived TWAS signals was evaluated in African American (AFA) individuals. We conducted an AFA-TWAS using summary statistics from the largest AFA GWAS (50,251 cases and 103,909 controls) in combination with gene expression prediction models trained in 111 AFA individuals from GTEx. We observed significant enrichment of EUR-derived T2D TWAS signals in the AFA TWAS across subcutaneous adipose, visceral adipose, skeletal muscle, and pancreas, whilst enrichment was weaker in liver, likely reflecting limited sample size. Overall, our findings demonstrate that integrating tissue-specific and ancestry-aware TWAS refines the identification of causal genes for T2D, with cross-ancestry replication supporting the robustness of these signals and cross-tissue analyses revealing context-specific effects. However, they also highlight the limited availability of non-EUR datasets and the need for larger, more diverse ancestry-specific transcriptomic resources.

Starvation induces robust food-seeking behavior in animals as a fundamental survival response. In Drosophila, biogenic amine octopamine (OA) plays a critical role in starvation-induced locomotor hyperactivity and awakeness, while the underlying signaling cascade remains not fully understood. Here, we demonstrated that the conserved transcription factor cAMP-Responsible Element Binding Protein (CREB), activated during starvation through the SIK2-CRTC pathway, contributes to starvation-induced sleep reduction. Mechanistically, we found that tyramine β-hydroxylase, the rate-limiting enzyme for OA synthesis, is upregulated by starvation in a CREB-dependent manner. Selective silencing of CREB in OA-producing neurons ameliorated OA-induced sleep suppression, and CREB loss-of-function mutations can partially rescue sleep fragmentation in a Drosophila model of Huntington's disease. Collectively, these findings reveal a novel regulatory role for CREB in sleep homeostasis through the transcriptional control of OA biosynthesis.

RNA splicing expands the functional output of eukaryotic genomes by enabling individual precursor messenger RNA (pre-mRNA) to generate multiple mature transcripts with protein‑coding and regulatory properties. Its fidelity and plasticity depend on coordinated interactions among the spliceosome, trans-acting splicing factors, cis-regulatory elements, and chromatin- and RNA-associated regulatory mechanisms. However, how these components collectively generate cell- and tissue-specific splicing programs, and how their disruption drives disease, remain incompletely understood. In this review, we integrate the molecular regulation of RNA splicing with its physiological, pathological and therapeutic consequences. We describe how spliceosome assembly, splicing regulatory elements, splicing factors, epigenetic modifications, and post-transcriptional processes determine splice-site selection. We then examine how regulated isoform programs support development, tissue specialization, homeostasis, circadian timing, and stress adaptation, and how their failure contributes to cancer and diverse non-neoplastic diseases. In cancer, we highlight the bidirectional interplay between splicing dysregulation and the tumor microenvironment, through which metabolic reprogramming and immune suppression reinforce aberrant splicing. Finally, we assess strategies that modulate the spliceosome, splicing-factor activity, or disease-associated transcripts, and present a perspective on how multi-omics, artificial intelligence, targeted delivery, and combination with immunotherapy could collectively advance the discovery and precision of splicing-directed therapies. We suggest that safe clinical translation will require greater selectivity, reduced off-target toxicity, and preservation of essential physiological splicing.

Shikonin (SHK) possesses potent antitumor activity; however, its severe non‑selective toxicity greatly limits the feasibility of conventional systemic administration for cancer therapy. Likewise, mild photothermal therapy (PTT) has intrinsic limitations, including inadequate induction of immunogenic cell death (ICD) and compensatory activation of immunosuppressive pathways, such as increased IDO1 activity and PD‑L1 expression. In the present study, low‑dose SHK and gold nanorods were co‑encapsulated within a supramolecular hydrogel (mPECT) and administered by intratumoral injection to achieve localized combination therapy with mild PTT. Mild PTT rapidly triggered antitumor immune activation within the immunosuppressive tumor microenvironment, whereas SHK sustained this response by suppressing PTT‑induced IDO1 activation and PD‑L1 upregulation and by markedly enhancing ICD. The mPECT hydrogel enabled prolonged local retention and controlled release of SHK, minimizing rapid systemic exposure while preserving therapeutic efficacy at the tumor site. This localized combination of SHK and mild PTT elicited a robust adaptive antitumor immune response that not only inhibited primary tumor growth but also suppressed the progression of untreated distant tumors and generated durable antitumor immune memory. These findings indicate that a single intratumoral administration of low‑dose SHK‑loaded hydrogel combined with mild PTT can induce potent systemic antitumor immunity, supporting the further development of localized SHK‑based therapeutic strategies for the treatment of immune‑cold tumors.

The basal ganglia (BG) contain multiple parallel neural circuits, each of which may control different behaviors. However, how the distinct parallel BG circuits are molecularly organized is not known. Here, we show that two δ2-protocadherins (PCDHs), PCDH17 and PCDH10, which are homophilic cell adhesion molecules, establish and define two distinct indirect BG circuits that regulate different behaviors. PCDH17 and PCDH10 are expressed in a complementary expression pattern in the BG, anatomically defining two parallel indirect BG connections. Indirect pathway-specific <i>Pcdh17</i> and <i>Pcdh10</i> conditional knockout (cKO) mice show impaired establishment of the indirect BG circuits in a region-preferential manner. Last, the <i>Pcdh17</i> cKO mice show defects in task learning, while the <i>Pcdh10</i> cKO mice show defects in motor/sensory habituation. These results identify PCDH17 and PCDH10 as the molecular organizers for two distinct indirect BG circuits regulating different behaviors and reveal the molecular mechanisms for organizing parallel BG circuits.

Wilson disease (WD) is a rare disorder that may be missed because of atypical presentations. We present a 47-year-old asymptomatic man who was incidentally discovered to have hepatic steatosis and cirrhosis without features of the metabolic syndrome and with normal physical examination and liver function tests. Very low ceruloplasmin and high urine copper prompted evaluation for WD. He had no Kayser-Fleischer rings. Genetic testing revealed a novel homozygous splice-site <i>ATP7B</i> variant (NM_000053.2:c.1707+2dupT p.(?)), the first reported case of homozygosity for this mutation. This case highlights the importance of considering WD in patients with unexplained hepatic steatosis and cryptogenic cirrhosis.

Glutathione is an abundant intracellular low-molecular-weight thiol that contributes importantly to cellular redox homeostasis. Besides its well-established role in the antioxidant defense of the cell, glutathione regulates mitochondrial function, metabolism of toxicants, protein thiol oxidation/reduction, redox signaling, and immunity. Disturbances in glutathione metabolism have been shown to play a role in various diseases; however, it has become clear that changes in glutathione metabolism are a part of a complex, multifactorial process. In this review, we summarize current knowledge of the molecular mechanisms governing glutathione synthesis, recycling, compartmentalization, and biological functions, with particular emphasis on redox signaling, the nuclear factor erythroid 2-related factor 2/Kelch-like ECH-associated protein 1 (Nrf2/Keap1) pathway, and reversible protein S-glutathionylation. We further examine how disturbances in glutathione homeostasis interact with mitochondrial dysfunction, chronic inflammation, metabolic stress, and impaired cellular signaling in Parkinson's disease, Alzheimer's disease, Huntington's disease, multiple sclerosis, Wilson's disease, type 2 diabetes, and nonalcoholic fatty liver disease. We also evaluate current translational interventions targeting restoration of glutathione balance through glutathione supplementation, precursor supplementation, pharmacological modulation of endogenous antioxidant mechanisms, dietary interventions, and changes in lifestyle. Despite the fact that many interventions have been promising at the mechanistic and experimental level, there are still insufficient clinical data because of the problems associated with glutathione availability, tissue specificity, disease variability, and a lack of sufficiently powered clinical trials. The conclusion of this review is that glutathione should not be viewed as a universal therapeutic target; instead, glutathione should be perceived as an important factor contributing to cellular resilience and able to help other disease-specific interventions. Future progress in glutathione-based interventions will likely depend on integrating redox biomarkers, patient stratification, and precision medicine strategies to identify individuals most likely to benefit from targeted modulation of glutathione homeostasis.

<b>Background/Objectives:</b> Cyclin-dependent kinase 2 (CDK2) is a key regulator of cell-cycle progression and a potential anticancer target. This study aimed to identify alkaloid-derived CDK2 ligands using an integrated computational workflow and to obtain preliminary evidence of their effects on cancer-cell viability. <b>Methods:</b> Molecular docking with mVina and fast pulling of ligand (FPL) simulations were benchmarked using 20 experimentally characterized CDK2 inhibitors. A library of 2692 PubChem-derived alkaloids was screened, followed by ADMET evaluation, 100 ns molecular dynamics simulations, and FPL-based relative-affinity re-ranking. The three prioritized compounds were evaluated in HepG2 and HGC-27 cells using an MTT assay after 48 h of exposure. <b>Results:</b> Docking and FPL showed correlations with experimental affinity data of R_Dock = 0.549 ± 0.180 and R_W = -0.676 ± 0.119, respectively. <b>CID 636885</b>, <b>CID 46184320</b>, <b>and CID 101691758</b> were prioritized for detailed evaluation. All three compounds reduced cell viability, with lower IC₅₀ values observed in HepG2 cells than in HGC-27 cells. <b>CID 101691758</b> exhibited the highest growth-inhibitory activity among the tested compounds, with IC₅₀ values of 15.37 ± 0.46 µg mL^-1 in HepG2 cells and 52.64 ± 1.33 µg mL^-1 in HGC-27 cells. <b>Conclusions:</b> The workflow identified three preliminary alkaloid hits, with <b>CID 101691758</b> showing the most favorable combined computational and cell-viability profile. However, the MTT assay does not establish direct CDK2 inhibition or kinase selectivity. Biochemical CDK2 inhibition, target-engagement, and kinase-panel studies are therefore required.

Previous studies indicate that lactylation, a post-translational modification, may play an important role in the progression of cervical cancer (CC). However, the comprehensive roles of lactylation in influencing the tumor microenvironment, immune landscape, and prognosis of CC have yet to be fully elucidated. The bulk RNA-seq and single-cell RNA-seq datasets of CC patients were downloaded from the Cancer Genome Atlas and Gene Expression Omnibus databases, respectively. A total of 630 genes associated with lactylation activity were identified using AUCell algorithm, differential expression, and correlation analyses. Subsequently, a prognostic risk model comprising 17 genes was constructed through univariate Cox and LASSO analyses, which accurately predicted the prognosis of CC patients and was validated in an independent dataset. The nomogram, including risk scores and N staging, outperformed other clinical parameters. The high-risk group was positively related to the glycolysis pathway. Furthermore, bioinformatics analyses further indicated that the high-risk group was associated with a poorer prognosis, pro-tumorigenic pathways, and immunosuppression, and was sensitive to ulixertinib, dasatinib, nutlin-3a, and trametinib. Mendelian randomization analysis suggested that ITGA5 may be causally associated with an increased risk of CC, with caution in causal inference. Additionally, the expressions of several risk genes were validated using real-time qPCR on tissue samples from six CC patients. In conclusion, the lactylation-related gene risk model could accurately and independently predict the prognosis of CC patients, providing insights into therapeutic strategies for CC patients. These bioinformatics-based findings are exploratory and warrant further validation in preclinical and clinical settings.

Vaccinia-related kinase 1 (VRK1) is an oncogenic serine/threonine kinase implicated in tumor progression, yet it remains an intractable target for catalytic degradation. Herein, we report the structure-guided design of a first aptamer-PROTAC chimera for potent and selective degradation of VRK1. Through structure-guided computational truncation and optimization of a parent DNA aptamer, we engineered a high-affinity variant (T4) with a 2.4-fold improved binding affinity (<i>K</i> _D = 0.61 nM) and enhanced selectivity over the homologous kinase VRK2. Conjugating T4 to a CRBN E3 ligase ligand <i>via</i> a flexible linker produced PROTAC-e, which induced rapid, sustained, and dose-dependent VRK1 degradation in HeLa cells, with a DC₅₀ of 105.8 nM and <i>D</i> _max of 91%. Degradation was mechanistically confirmed to depend on the ubiquitin-proteasome system. Functionally, PROTAC-e elicited potent anti-proliferative activity (IC₅₀ = 193.8 nM) and S-phase arrest, directly linking VRK1 depletion to antitumor efficacy. This work not only provides a first aptamer-PROTAC targeting VRK1, a previously intractable kinase, but also establishes a generalizable strategy for the rational design of aptamer-PROTACs, opening a route to target kinases beyond conventional small-molecule scaffolds.

<h4>Introduction</h4>R-loops, RNA-DNA hybrid structures with a displaced single-stranded DNA loop, are key regulators of transcriptional control, chromatin architecture, and genome stability and have emerging roles in inflammatory signaling. However, the relationship between R-loop abundance and strongly modulated inflammatory effector genes in metabolic inflammation and influenza virus infection remains underexplored.<h4>Methods</h4>We performed a locus-centric integrative analysis combining robust differentially expressed genes (DEGs) from multiple inflammatory and infection-related murine and human transcriptomic disease models with experimentally validated multi-cell R-loop annotations from the reference atlas RLoopBase. Our correlation framework evaluated the directional relationship between R-loop abundance and inflammatory gene expression rather than assuming disease-sample-matched R-loop measurements. We further analyzed R-loop regulatory proteins, NRF2-associated R-loop regulators, and overlaps between R-loop regulators and CRISPRi-identified mitochondrial and cellular reactive oxygen species (ROS) regulators.<h4>Results</h4>In angiotensin II-infused apolipoprotein E-deficient (ApoE-/-) mice, a model of abdominal aortic aneurysm (AAA), genomic regions encoding the top significantly upregulated genes exhibited significantly fewer R-loops than those encoding downregulated genes at days 14 and 28. Similarly, in atherosclerotic ApoE-/- mice fed a high-fat diet for 32 and 78 weeks, upregulated genes were associated with fewer R-loops than downregulated genes. Reduced R-loop abundance was also observed in genomic regions encoding the top significantly upregulated genes in liver tissues from patients with non-alcoholic steatohepatitis (NASH), as well as in monosodium urate (MSU)-stimulated lymphatic endothelial cells (LECs) and influenza virus-infected human umbilical vein endothelial cells (HUVECs). R-loop regulatory proteins upregulated during metabolic inflammation were enriched in immune and inflammatory pathways. NRF2 was identified as a regulator of 27 R-loop regulatory proteins, including 10 positively and 17 negatively regulated proteins. Furthermore, 54 R-loop regulatory proteins overlapped with CRISPRi-identified mitochondrial and cellular ROS regulators, suggesting potential reciprocal regulation between R-loop homeostasis and ROS signaling. Disease-associated changes in pro-ROS and anti-ROS R-loop regulatory proteins further linked R-loop regulation to inflammatory and oxidative stress pathways.<h4>Discussion</h4>These findings identify reduced R-loop abundance at genomic regions encoding strongly upregulated inflammatory genes as a shared feature across multiple models of metabolic inflammation and influenza virus infection. The results further suggest that immune-associated R-loop regulatory proteins and the NRF2-ROS axis may contribute to R-loop remodeling during inflammatory disease. This integrative framework provides new insight into the potential role of R-loops and ROS-sensitive R-loop regulators in inflammatory and metabolic diseases and identifies candidate pathways for future mechanistic investigation and therapeutic targeting.

<h4>Clinical characteristics</h4>Leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation (LBSL) is characterized by slowly progressive cerebellar ataxia and spasticity with dorsal column dysfunction (decreased position and vibration sense) in most individuals. The neurologic dysfunction typically involves the legs more than the arms. Deep tendon reflexes are retained. Deterioration of motor skills usually starts in childhood or adolescence but may not start until adulthood. Dysarthria develops over time. Other less common features include epilepsy; learning problems; cognitive decline; and reduced consciousness, neurologic deterioration, and fever following minor head trauma. Individuals with neonatal or early-infantile onset have a severe disease course often associated with early death. Those with childhood onset have slow progression with wheelchair dependence in the teens or twenties. Adult onset is associated with slow progression and mild impairment.<h4>Diagnosis/testing</h4>The clinical diagnosis of LBSL can be established in a proband with characteristic abnormalities observed on brain and spinal cord MRI. The molecular diagnosis can be established in a proband with suggestive findings and biallelic pathogenic variants in DARS2 identified by molecular genetic testing. If molecular results are inconclusive, a functional assay to identify reduced MtAspRS enzyme activity in lymphoblasts can confirm the diagnosis.<h4>Management</h4>Treatment of manifestations: Supportive therapy includes: physical therapy and rehabilitation to improve motor function and prevent contractures and scoliosis; and anti-seizure medication, speech therapy, special education, and social work support as needed. Surveillance: Assess for new neurologic manifestations at each visit; monitor those with seizures as needed; consider brain MRI every few years to monitor progression; monitor developmental progress and educational needs at each visit throughout childhood; assess for family support needs at each visit.<h4>Genetic counseling</h4>LBSL is inherited in an autosomal recessive manner. If both parents are known to be heterozygous for a DARS2 pathogenic variant, each sib of an affected individual has at conception a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being unaffected and not a carrier. Once the DARS2 pathogenic variants have been identified in an affected family member, prenatal testing for a pregnancy at increased risk and preimplantation genetic testing are possible.

Triple-negative breast cancer (TNBC) is an aggressive and immunogenic subtype lacking targeted therapies. While tumor-derived exosomes are known to modulate immune function, their direct impact on human T cell plasticity and antigen specificity remains poorly defined. Here, we conducted a comprehensive single-cell multiomic analysis of primary human T cells exposed to exosomes derived from 17 genomically diverse TNBC cell lines and 35 patient samples. Integrating single-cell RNA-seq, V(D)J sequencing, non-coding RNA profiling, bulk and single-cell cytokine analyses, we uncovered conserved and subtype-specific immunomodulatory programs induced by TNBC exosomes. Exosome-treated T cells displayed skewing toward regulatory and dysfunctional phenotypes, including Th17-like, Treg, and PD-1⁺/PD-L1⁺ Tfh cells. Functional profiling revealed suppression of early activation markers and cytokine responses, alongside selective preservation of cytotoxic features in γδ T and NKT subsets. Transcriptomic and miRNA network analyses demonstrated widespread downregulation of immune effector genes (e.g., HBEGF and TNFSF9) mediated by exosome-delivered regulatory miRNAs (has-miR-98-5p). Notably, exosome-stimulated T cells displayed distinct clonotypic expansions, characterized by the emergence of five tumor-specific γδ TCR clonotypes and 30 unique αβ TCR CDR3 sequences that were absent in mock-treated controls, underscoring the role of exosomes in shaping TCR repertoire dynamics.

<h4>Background</h4>G protein-coupled receptors (GPCRs) are the largest class of membrane-bound receptors and are emerging as targets for the effective treatment of cancer. The role of orphan GPCR GPR52 in cancer has not been characterized. Low mRNA expression of GPR52 in breast tumours correlates with reduced overall survival, leading to the hypothesis that loss of GPR52 supports breast cancer progression.<h4>Methods</h4>CRISPR-Cas9 was used to knock out GPR52 in the human triple-negative breast cancer cell lines MDA-MB-468 and MDA-MB-231. 2D and 3D in vitro studies, electron microscopy, and a zebrafish xenograft model were used to assess the morphology and behaviour of GPR52 KO cells.<h4>Results</h4>Loss of GPR52 was associated with elevated levels of cAMP, increased cell-cell interaction in 2D cultures, more spindle-like morphology on collagen, altered 3D spheroid morphology, and increased propensity to organize and invade collectively. Zebrafish injected with GPR52 KO cells developed a greater total cancer area than control. RNA sequencing and proteomic analyses of GPR52-null cells revealed an increased cAMP signalling signature. Re-expression of GPR52 and inhibition of cAMP production rescued some GPR52 KO phenotypes.<h4>Conclusions</h4>GPR52 loss is a potential mechanism by which breast cancer progression may occur and supports the investigation of GPR52 agonism as a therapeutic option for breast cancer.<h4>Statement of significance</h4>Loss of the orphan GPCR GPR52 in human breast cell lines leads to increased cell clustering, hybrid/partial EMT, and increased tumour burden in zebrafish, further expanding our understanding of mechanisms driving cancer progression and opening the door to novel therapeutic approaches.

Tumor progression depends on an adequate blood supply to sustain oxygen and nutrients delivery. While tumor angiogenesis involves the formation of new blood vessels from pre-existing ones, vessel co-option represents a non-angiogenic vascularization strategy whereby tumor cells utilize pre-existing host vessels. Co-opted vessels have been considered refractory to anti-angiogenic therapies, and pharmacological modulation of co-opted vessels remains limited. In this study, we investigate the effects of low-dose cilengitide on tumor vascular remodeling in vessel co-option and angiogenic metastatic models. Our results reveal that cilengitide exerts distinct vascular effects depending on the mode of tumor vascularization. In vessel co-option-driven tumors, cilengitide treatment is associated with the remodeling of the co-opted vasculature into a more organized normalized vascular network, characterized by an increased number of functional blood vessels and enhanced vascular barrier integrity. In contrast, in angiogenic-driven tumors, cilengitide treatment promotes an expansion of the vascular network consistent with augmented, but structurally immature angiogenesis. Importantly, vascular remodeling in vessel co-option metastases is accompanied by enhanced blood vessel perfusion and reduced hypoxia, which correlates with enhanced responsiveness to chemotherapy. Conversely, in angiogenic metastases, the vascular network induced by low-dose cilengitide fails to support immunocompetent microenvironmental features and is associated with increased chemotherapy resistance. This study provides the first evidence that co-opted vasculature can be therapeutically targeted via integrin inhibition, suggesting vascular normalization remodeling as a potential strategy to overcome resistance in tumors undergoing vessel co-option.

<h4>Background</h4>Diarrhea is a leading cause of morbidity and mortality among children in developing countries. Rotavirus is a significant cause of acute watery diarrhea in children under 5 years of age, which can be fatal. This study is aimed at investigating the prevalence of rotavirus gastroenteritis (RVGE) in children and characterizing the prevalent circulating genotypes.<h4>Material and methods</h4>A cross-sectional study was conducted, enrolling 173 children under the age of 5 years who presented with acute diarrhea lasting less than 2 weeks at the University of Maiduguri Teaching Hospital between 2017 and 2018. Stool samples were collected and screened for rotavirus antigen using the lateral flow immunochromatographic method. Stool samples that screened positive were further investigated for VP7 (i.e., G type) and VP4 (i.e., P type) rotavirus genotypes using reverse transcription-polymerase chain reaction (RT-PCR).<h4>Results</h4>The prevalence was determined to be 28% by the immunochromatographic method and 14.5% by RT-PCR (<i>N</i> = 173). The identified G types included G1, G2, G1G2, G9, G12, and G NT (G nontypeable), whereas the P types identified were P4, P6, and P8. The most frequently observed rotavirus genotype combination was G9P[6] 7 (28%), while mixed genotype infection with unusual strain G1G2P[4, 6, 8] 1 (4%) was also detected.<h4>Conclusion</h4>This study reported a high prevalence of RVGE in the northeast region of Nigeria. As the current ROTAVAC in use in routine immunization in Nigeria comes to its third year, it is necessary to evaluate the vaccine efficacy so as to reduce the deaths associated with RVGE in Nigeria.

<h4>Background/objectives</h4>Mitochondrial Complex V (Complex V [CX-V], or ATP synthase) is the terminal enzyme of oxidative phosphorylation and is responsible for the majority of cellular ATP production. An increasing body of evidence suggests that CX-V dysfunction may contribute to mitochondrial impairment observed in neurodegenerative disease. This review evaluated current research on the structure, regulation, and function of CX-V, examined the consequences of CX-V dysfunction, and assessed its proposed role in neurodegenerative disorders.<h4>Methods</h4>A comprehensive review of the published literature was carried out, with emphasis on primary research investigating CX-V structure and function, inherited CX-V disorders, and experimental evidence linking CX-V dysfunction to neurodegenerative disease. The reviewed studies used a range of experimental approaches, including structural biology, biochemical studies, patient-derived cellular models, animal models and post-mortem human tissue.<h4>Results</h4>Current evidence demonstrates that disruption of CX-V impairs ATP production, alters mitochondrial membrane potential, and oxidative phosphorylation, and that pathogenic variants cause primary mitochondrial disease. Across Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis/frontotemporal dementia, glaucoma and inherited optic neuropathies, alterations in CX-V activity, regulation and structural integrity are consistently associated with mitochondrial dysfunction. Direct evidence supporting CX-V as a primary driver of neurodegeneration remains very limited, with many observations originating from broader studies of general mitochondrial dysfunction.<h4>Conclusions</h4>CX-V dysfunction represents a recurring feature of mitochondrial impairment across a variety of neurodegenerative disorders and may exacerbate neuronal vulnerability by disrupting cellular bioenergetics. Current evidence indicates that CX-V may serve as a common downstream target of multiple pathological pathways rather than acting as a primary pathological factor. Future studies require direct assessment of CX-V activity in clinically relevant human models and patient tissues to determine its contribution to disease progression and examine its potential as a therapeutic target.

Growth and body conformation traits are key determinants of meat production efficiency and economic performance in sheep. However, the genetic architecture underlying these complex traits remains incompletely understood, particularly across multi-breed populations. In this study, we performed a genome-wide association study (GWAS) for seven growth and developmental traits in a combined population of 401 sheep, including Qira Black, Kyrgyz, Dorset × Hu crossbred, and Suffolk × Karakul crossbred sheep. After genotype harmonization and quality control, 47,674 autosomal SNPs were retained for analysis. Population structure was assessed using principal component analysis, and association testing was conducted using a mixed linear model incorporating breed, principal components, and a kinship matrix. A total of 44 independent loci were detected at a nominal significance threshold, encompassing 112 candidate genes. The strongest association was identified for cannon bone circumference near <i>RPS6KA5</i> (Chr7; <i>p</i> = 1.40 × 10^-7). Several biologically relevant genes involved in osteogenesis, cartilage development, and metabolic regulation were detected, including <i>STEAP3</i>, <i>SLC26A2</i>, <i>PPARGC1B</i>, <i>COL11A1</i>, <i>CALN1</i>, and <i>CITED2</i>. Two genomic regions exhibited pleiotropic effects, which were identified as being associated with multiple traits, suggesting shared genetic regulation of correlated skeletal characteristics. These findings are consistent with a polygenic architecture underlying growth trait in sheep and highlight candidate genomic regions potentially involved in skeletal development and body conformation. Although further validation is required, the identified loci provide preliminary evidence for regions that may influence growth-related phenotypes and offer a reference for future molecular breeding efforts in indigenous and crossbred sheep populations.

<b>Background/Objectives</b>: Colorectal cancer (CRC) remains a leading cause of cancer-associated mortality worldwide. The current therapeutic interventions are heavily constrained by the development of resistance and severe systemic toxicity. To address these challenges, this study integrated a multi-disciplinary framework involving high-throughput in silico screening followed by in vitro experimental validation to identify novel genetic targets of CRC and evaluate the efficacy of FDA-approved drugs. The primary objective was to identify safe and selective therapeutic agents capable of modulating their effect. <b>Methods</b>: The methodology employed a systematic screening of recent large-scale Genome-Wide Association Studies (GWASs) to pinpoint novel targets, followed by in silico pathogenicity prediction, homology modelling and high-throughput virtual screening of over 1615 FDA-approved drugs. The prioritized candidates were validated in vitro using MTT cytotoxicity assays and differential gene expression analysis across CRC cell lines (HCT116 and HT29) and a non-tumorigenic control, Human embryonic kidney cell line HEK293. <b>Results</b>: In silico analysis identified <i>CLUH</i>, <i>CLSTN3</i> and <i>SLC11A2</i> as novel potential targets. Based on in silico predicted deleterious mutations and subsequent molecular docking-based virtual screening, Telmisartan, Dutasteride and Venetoclax were prioritized. This prioritization was supported by their high binding affinity and dose-dependent cytotoxicity in MTT assays; thus, suggesting their repurposing potential for CRC treatment. Telmisartan exhibited a superior therapeutic profile not only in terms of the statistically significant cytotoxicity (<i>p</i> < 0.01), but also its selective effect on HCT116 and HT29 when compared to high safety profile in HEK293. This was further validated when Telmisartan selectively downregulated <i>CLUH</i> and <i>SLC11A2</i> in CRC cell lines, HCT116 and HT29 while maintaining expression levels in the non-cancerous HEK293 cell line remained significantly unaffected. Furthermore, a 100 ns molecular dynamics simulation confirmed the stable binding conformation and structural reliability of the SLC11A2 (Trp179Ser)-Telmisartan complex. <b>Conclucions</b>: Our findings conclude that Telmisartan is a promising candidate for drug repurposing for CRC treatment and capable of modulating selected novel biomarkers <i>CLUH</i> and <i>SLC11A2</i>. However, further multi-omics-based confirmatory studies and pre-clinical validation studies are needed in the future to confirm the long-term efficacy of this repositioning strategy.

Skeletal muscles can undergo remodeling in response to physical, nutritional, and environmental conditions. To understand skeletal muscle remodeling associated with mammalian hibernation, we investigated the remodeling of skeletal muscles throughout hibernation in Syrian hamsters. We found that hibernating hamsters under winter-like hibernation-induction conditions exhibited lower skeletal muscle mass and thinner muscle fibers, particularly fast-twitch fibers of Type IIb and IIx, than euthermic hamsters kept under summer-like conditions. However, hamsters that were unresponsive to hibernation induction under winter-like conditions (UnHIB) were less susceptible to decreases in muscle mass and fiber size. The expression levels of Mstn and Sln, which were predominantly detected in fast-twitch or slow-twitch muscle fibers, respectively, were significantly altered in hibernating but not in UnHIB hamsters. Thus, we identified skeletal muscle remodeling associated with hibernation.

The development of Alzheimer disease (AD) involves a cluster of pathogenic processes, including amyloid-beta (Aβ) deposition, tau-mediated neurodegeneration, chronic neuroinflammation, oxidative stress (OS), metabolic dysregulation, and disruption of circadian rhythms. Nuclear hormone receptor, Retinoic Acid-Related Orphan Receptor Alpha (RORα) was shown to regulate multiple neuroprotective pathways such as inflammatory signaling (NF-κB suppression), mitochondrial integrity and mitophagy, redox homeostasis [upregulation of glutathione peroxidase 1 (GPX1), and mitochondrial superoxide dismutase 2, (SOD2)], calcium-dependent synaptic architecture [inositol 1,4,5-trisphosphate receptor type 1 (ITPR1), Purkinje cell protein 4 (PCP4)], and circadian rhythm stability [period 2 (PER2), brain and muscle ARNT-like 1 (BMAL1)]. Multi-omics network analyses place RORα within regulatory networks that are co-associated with key AD-related genes and supports an associational, network-based relationship for <i>RORA</i>. Preclinical gene-augmentation studies using adeno-associated viral vectors report that RORα overexpression reduces APP levels, remodels the complement regulator CD59 glycoprotein (CD59), inhibits OS, and enhances neuronal survival, although these effects were established largely in retinal and other non-AD systems. These findings support the potential of <i>RORA</i> as a therapeutic target through genetic intervention, but direct demonstration of AD-modifying efficacy <i>in-vivo</i> is still lacking. Investigational <i>RORA</i>-focused gene therapy in retinal degenerative diseases provides proof-of-concept for, but does not yet establish, applicability within the central nervous system. Taken together, this evidence nominates <i>RORA</i> as a candidate system-level regulator that may help restore disrupted homeostatic transcriptional networks in AD, a hypothesis that remains to be tested. We propose that RORα functions as a transcriptional hub coupling three homeostatic axes that fail in AD; the circadian, mitochondrial-metabolic, and immune-inflammatory axes, and that its regional expression changes in AD (hippocampal up-regulation vs. suprachiasmatic down-regulation) represent a compensatory response that ultimately fails. Cell-type-specific expression profiling is required to determine in which regions augmentation may be therapeutically appropriate. Restoring RORα is therefore could be network-stabilizing rather than single-pathway intervention.

<h4>Background</h4>Resistance to anti-TNFα therapy (e.g., infliximab) in ulcerative colitis (UC) remains a significant clinical challenge, with the underlying cellular and spatial mechanisms poorly understood.<h4>Methods</h4>We integrated bulk transcriptomics, single-cell RNA sequencing (scRNA-seq), and spatial transcriptomics (ST) from clinical cohorts to systematically map the cellular landscape and identify key determinants of treatment response, followed by validation in independent clinical cohorts and <i>in vitro</i> functional experiments.<h4>Results</h4>Multi-omics cross-analysis pinpointed insulin-like growth factor-binding protein 5 (IGFBP5) as a fibroblast-specific, spatially enriched gene strongly associated with infliximab non-response. Functional analyses linked IGFBP5 to inflammatory pathways and a distinct immune-activated microenvironment. Cell-cell communication analysis revealed that IGFBP5-high fibroblasts exhibit enhanced crosstalk with monocytes, endothelial cells, and T cells via VEGF, MIF, and WNT signaling. Validation in clinical samples and functional experiments confirmed elevated expression of IGFBP5 and its downstream effectors EGR1 and VEGFR2 in non-responders, Mechanistically, IGFBP5 promoted activation of the VEGFR2/EGR1 signaling axis and enhanced the secretion of inflammatory mediators, including IL-6, CXCL12, and CCL2, thereby contributing to a pro-inflammatory fibroblast phenotype.<h4>Conclusions</h4>This study establishes fibroblast-derived IGFBP5 as a central mediator of anti-TNFα resistance in UC. The IGFBP5-EGR1-VEGFR2 axis may represent a candidate predictive biomarker and a promising target for overcoming treatment resistance.

<h4>Objective</h4>Adrenocorticotropic hormone (ACTH) is an effective treatment for infantile epileptic spasms syndrome (IESS); however, its mechanism of action remains incompletely understood. This study aimed to evaluate ACTH treatment response at the level of protein-protein interactions (PPIs) in patients with confirmed and presumed monogenic developmental and epileptic encephalopathies (DEEs).<h4>Methods</h4>Medical records of patients with DEEs followed at our center between 2017 and 2025 were retrospectively reviewed. Patients receiving ACTH therapy who harbored pathogenic, likely pathogenic, or variants of uncertain significance (VUS) were included in the study, whereas those with chromosomal abnormalities and insufficient clinical or follow-up data were excluded. Clinical and electroencephalographic (EEG) responses to ACTH therapy were evaluated at the 2-week (day 14) and 3-month follow-up visits. Maintenance of a ≥50% reduction in seizure frequency at 3-month follow-up defined responders. Gene Ontology and PPI network analyses were performed to investigate relationships between genotype and treatment response.<h4>Results</h4>Among the 245 patients with DEEs, 69 had a confirmed genetic etiology, of whom 10 met the inclusion criteria. At 2-week follow-up, 5 of 10 patients (SCN2A, ELOVL4, CACNA1E, TRRAP) achieved seizure freedom, while 3 (PIGT, SCN1A, ZNF526) showed ≥50% reduction. At month 3, 66.6% (6/9) of patients were classified as responders. At 1 year, patients with SCN2A and PIGT variants showed sustained ≥50% seizure reduction, normalization of background EEG activity, and resolution of epileptiform discharges. PPI analysis revealed network interactions between CALM-SCN2A/CACNA1E and PRKAC-SCN1A, whereas the TRRAP-ATF2 interaction showed low confidence, and no reliable interaction was identified for PIGT.<h4>Significance</h4>These findings suggest that ACTH may be associated with sustained electroclinical improvement in selected genetically defined DEEs. The identified network-level interactions between ion channel-related genes and intracellular signaling pathways provide a potential molecular framework for understanding variability in treatment response.

Hyperexcitability of lateral (La) and basolateral (BL) amygdalar nuclei (BLA) is a hallmark of anxiety-related disorders in humans. Excitation of BLA projection neurons (PN) is fine-tuned by inhibitory interneurons (INs), and monoaminergic afferents to the BLA modulate PN and IN activity. In the present study, BLA-neurons immunoreactive(ir) for parvalbumin (PV) or neuropeptide Y (NPY) and their interrelations with serotonergic and catecholaminergic afferents were analyzed in wildtype (WT) and in serotonin (5-HT) transporter knockout (5-HTT KO) mice, a mouse model for anxiety- and stress-related disorders. In both genotypes, PV- and NPY-ir neurons possess perisomatic appositions by serotonergic and tyrosine hydroxylase-ir afferents. Dual immunolabeling shows no colocalization of PV and NPY. Qualitative analysis of NPY/somatostatin(SOM) dual labeling in WT and 5-HTT KO mice documents colocalization of the peptides in neurons with predominantly fusiform somata, and single labeling for NPY in neurons with predominantly round somata. Quantification of PV- and NPY-ir neurons documents a reduction in numbers and densities of NPY-ir neurons of the BLA in 5-HTT KO mice while PV-ir neuron numbers and densities remain unchanged. Quantitative PCR shows increased expression of Npy receptor 2, Som receptor 4, and corticotropin releasing factor receptor 1 in the BLA of 5-HTT KO mice. mRNA for the peptides is unchanged, indicating that it may be NPY propeptide translation which is reduced in 5-HTT KO mice. Taken together, the results document an effect of life-long serotonin imbalance on the BLA NPY-system, which may contribute to increased anxiety-like behavior in 5-HTT KO mice.

Pediatric acute myeloid leukemia (AML) is a highly heterogeneous malignancy, with cytogenetic and molecular abnormalities playing a critical role in determining prognosis and guiding treatment decisions. Despite therapeutic advances, patients with high-risk genetic mutations and translocations continue to experience suboptimal outcomes. As new targeted therapies emerge, the treatment of pediatric AML could undergo a paradigm shift, where "one-size-fits-all" chemotherapy is no longer the only frontline approach. Identifying genetic markers inform risk stratification and have greater impact on shaping the therapeutic approach, including the integration of targeted therapies such as FLT3 and menin inhibitors into frontline therapy. Furthermore, pediatric AML treatment options are being driven by recent discoveries in adult AML, broadening their clinical trials to include pediatric patients, in part due to the RACE for Children Act that went into effect in August 2020. This review identifies the most prevalent high-risk cytogenetic lesions in pediatric AML, emphasizing their incidence, prognostic significance, and implications for clinical management. By synthesizing current research on these key genetic abnormalities and their associated therapies, we aim to provide an updated perspective on the evolving landscape of high-risk pediatric AML management that can then lead to the establishment of an agile framework to rapidly evaluate, approve, and deploy novel agents.

<h4>Background/objectives</h4>Depression and anxiety disorders exhibit significant clinical heterogeneity, which complicates diagnosis and treatment. This study investigated whether tripartite interactions between biological sex, the serotonin transporter gene promoter region (5-HTTLPR), and brain-derived neurotrophic factor (BDNF) G196A polymorphisms explain specific symptom-level variations.<h4>Methods</h4>A community sample of 271 Australian adults was genotyped for common 5-HTTLPR (short/long) and BDNF (G/A) variants. Participants completed self-reported measures of anxiety (SAS), depression subtypes (SDS; clinical content scales), and psychological resilience (CDRISC). Morning salivary cortisol, BMI, and substance use were assessed as potential confounds. Statistical analyses utilised a three-way factorial ANCOVA to test for interactions on raw scores, controlling for age. Significant omnibus interactions were decomposed via planned stratified ANCOVAs within each 5-HTTLPR stratum.<h4>Results</h4>The BDNF GA genotype exerted opposite effects on anxiety and anhedonia depending on sex and 5-HTTLPR background. In females, GA was associated with increased symptoms on an ss background, whereas in males, GA was associated with increased symptoms on an ll background. These effects were highly specific to anxiety and anhedonic depression, while depressed mood, cognitive, and somatic subtypes remained unaffected. Findings were independent of cortisol, BMI, smoking, alcohol use, and psychological resilience.<h4>Conclusions</h4>The findings reveal a complex, sex-dependent genetic interaction that selectively influences anhedonia and anxiety. They should be interpreted in the context of modest subgroup sizes following genotype stratification and require replication in larger independent cohorts. Nonetheless, this study highlights the value of considering sex-stratified genetic backgrounds and symptom specificity to advance personalised precision medicine in psychiatry.

Regenerative medicine and tissue engineering approaches based on decellularized extracellular matrix (dECM) present the advantage of a relatively biomolecule-rich matrix that directs cell function in a tissue-specific manner. To evaluate compositional changes during standard ink processing, six porcine tissues (artery, breast, dermis, epidermis, muscle, and nerve) were independently decellularized and formulated into biocompatible inks, tracking matrisome complexity via comparative liquid chromatography-tandem mass spectrometry (LC-MS/MS). Results revealed a core matrisome found overlapping in all decellularized tissues, alongside tissue-specific components correlating with predicted functional definitions. Although the proportion of collagens (mostly the α1 chains of collagen type I and III) increased in the final inks, a median of 55 matrisomal proteins was detected. This complexity is far superior to non-dECM-based inks in terms of mimicking native tissues. Our results support the use of dECM-based inks and biomaterials in mimicking native tissue ECM complexity, demonstrating tissue-specific composition, which can improve future therapeutic approximations.

Clinically used opioids, such as morphine, primarily act through the <i>μ</i>-opioid receptor (MOR), encoded by the <i>OPRM1</i> gene, which undergoes extensive alternative splicing. More than 20 <i>OPRM1</i> isoforms have been identified, yet functional characterization has largely focused on the canonical MOR-1 variant. With the emergence of three-dimensional human cerebral organoids (hCOs) derived from induced pluripotent stem cells (iPSCs), it is now possible to model human-specific neuronal responses to opioids more accurately. In this study, we established hCOs as a functional platform to investigate the impact of morphine on <i>OPRM1</i> pre-mRNA splicing and opioid signaling. We generated iPSC-derived hCOs and neurons, after which they were treated with or without morphine and screened using cellular and molecular/biochemical assays. Our results revealed that morphine exposure selectively induced the MOR-1X isoform in hCOs and iPSC-derived neurons in a dose-dependent manner as revealed by RT-PCR and RT-qPCR. We utilized CRE/CREB overexpression plasmid and lentiviral constructs to measure effects of morphine on cyclic AMP (cAMP) signaling. Upon morphine withdrawal, cells expressing MOR-1X exhibited markedly enhanced cAMP superactivation, a molecular hallmark of opioid dependence, compared with MOR-1. Furthermore, isoform-specific knockdown of MOR-1X by a short hairpin RNA (shRNA) effectively abolished this cAMP overshoot in iPSC-derived neurons. Collectively, these findings identify MOR-1X as a morphine-inducible isoform with a potential key role in the molecular mechanisms underlying opioid signaling, adaptation, and dependence in the brain.

Hashimoto's thyroiditis (HT) and diabetes mellitus are highly prevalent chronic immune-mediated disorders that frequently co-occur and share genetic susceptibility, T-helper (Th) 1/Th17 skewing, and regulatory T-cell (Treg) dysfunction. Among individuals with type 1 diabetes mellitus (T1DM), autoimmune thyroiditis is the most common comorbid autoimmune disease. Extracellular vesicles (EVs) have emerged as important mediators linking autoimmune and metabolic inflammation. This review compares how EVs remodel the immune microenvironment in HT, type 2 diabetes mellitus (T2DM), and related disease contexts, with attention to donor cells, cargo, recipient pathways, biomarkers, and therapeutic implications. In HT and T1DM, EVs can deliver organ-specific autoantigens, whereas in classical T2DM current evidence more strongly supports EVs as carriers of stress signals, chemokines, and immunoregulatory miRNAs that shape islet inflammation and insulin resistance rather than autoantigen presentation; latent autoimmune diabetes in adults is considered separately. Across these diseases, recurrent EV-miRNA programs and DAMP/NLRP3 signaling converge on Treg/Th17 imbalance and M1/M2 macrophage polarization. We also emphasize the marked asymmetry of evidence maturity, with substantially stronger <i>in-vivo</i> and clinical support on the T2DM side than on the HT side. This asymmetry is treated as an explicit interpretive boundary throughout the review. We assess circulating and urinary EV cargoes as liquid-biopsy candidates and discuss EV-based drug delivery, engineered immunomodulatory EVs, and modulation of EV biogenesis. Translational claims remain limited by heterogeneity, manufacturing, and safety challenges, particularly in organ-specific autoimmune disease. In this review, the term "immune-metabolic crossroads" refers to shared mechanisms, shared biomarker opportunities, and partially overlapping therapeutic entry points.

α2-3-sialylated glycosphingolipids (α2-3-GSLs) are major constituents of neuronal membranes and lipid rafts, where they shape receptor compartmentalization, signal-complex assembly, and cell-cell communication. Their biological effects, however, vary by molecular subtype, cell type, disease stage, concentration, and local microenvironment. This review synthesizes evidence on spatiotemporal alterations in α2-3-GSL profiles and their relationships to neuroinflammation, immune responses, proteostasis, and programmed cell death across Parkinson's disease, Alzheimer's disease, Huntington's disease, multiple sclerosis, and Guillain-Barré syndrome. Particular attention is given to GM1, GD1a, and GD3 and to mechanisms involving TLR4/NF-κB, PI3K/AKT, autophagy-lysosomal function, complement, damage-associated molecular patterns (DAMPs) recognition, and death-receptor signaling. Evidence is stratified into relatively well-supported, model-specific or incomplete, and conceptually inferred mechanisms. On this basis, we propose a lipid-inflammation-immunity-cell death framework that organizes potentially shared downstream processes while explicitly retaining disease-specific differences. This framework is not a validated universal causal pathway; rather, it provides an analytical structure for identifying evidence gaps and testable hypotheses. Disease-specific and parallel cross-disease studies, coupled with spatial lipidomics, <i>in vivo</i> tracing, and subtype-selective interventions, will be required to determine when α2-3-GSL manipulation is protective, neutral, or harmful and to support rational clinical translation.

Endometriosis is frequently managed with hormonal suppression that can induce hypoestrogenism during a period when many patients are still accruing peak bone mass. This narrative review summarizes current clinical and mechanistic evidence on bone health in endometriosis and its treatments and discusses a preliminary conceptual framework for risk stratification and monitoring. This review discusses two hypothetical converging pathways: (1) an intrinsic pathway in which chronic systemic inflammation may shift bone remodeling toward resorption (via cytokine-mediated effects on osteoclastogenic and Wnt signaling pathways and oxidative stress), and (2) an iatrogenic pathway in which ovarian suppression, most notably with gonadotropin-releasing hormone agonists/antagonists and some progestin-based regimens, reduces estrogen exposure and can lead to measurable short-term bone mineral density loss. Available observational data generally do not show clinically meaningful bone mineral density deficits or excess fracture incidence in untreated endometriosis, but treatment-associated bone mineral density loss is well documented; long-term fracture outcomes and bone-quality measures remain insufficiently studied. We compare the skeletal safety signals across commonly used therapies, discuss the role and limitations of add-back therapy, and highlight when baseline evaluation and follow-up assessment (including consideration of trabecular bone score) may be warranted in higher-risk patients.

<h4>Background</h4>Neurodegenerative diseases (NDDs) pose a major health challenge due to their high prevalence and the lack of effective treatments; ginseng, as medicine and food homology, has potential neuroprotective effects.<h4>Methods</h4>This article provides a systematic review of research conducted over the past five years on the use of ginseng to treat NDDs, summarizing and analyzing the findings in four key areas: active components, mechanisms of action, clinical applications, and novel delivery strategies.<h4>Results</h4>Ginsenosides are the core active ingredients in ginseng, while polysaccharides, essential oils, and peptides also exert synergistic effects through various pathways; their mechanisms of action include regulating Aβ/tau protein aggregation, inhibiting microglial activation, reducing glutamate excitotoxicity, and restoring mitochondrial function and antioxidant balance. In models of AD, PD, HD, and ALS, ginseng's active components have been shown to improve both behavioral and pathological indicators, while novel delivery strategies (nanoparticles, exosomes, and engineered cellular carriers) can significantly enhance blood-brain barrier permeability and brain-targeting efficiency.<h4>Conclusion</h4>Ginseng exhibits protective effects against NDDs through multiple mechanisms of action. However, current evidence is largely limited to preclinical studies, and future efforts should focus on advancing the clinical translation of safe and effective brain-targeted delivery systems.

<title>Abstract</title> <p>Psychiatric and neurological clinical syndromes show considerable overlap, and these have been largely captured by genetic correlation studies. Detailed, hypothesis-generating investigations into the transcriptomic and interactome patterns of risk-related genes, particularly that of their first-order interactors, are lacking. In this study, we examined brain spatiotemporal expression and interactome patterns of risk genes associated with five syndromes with overlapping symptom clusters: obsessive-compulsive disorder (OCD), Huntington’s disease (HD), Parkinson’s disease (PD), schizophrenia (SZ), and bipolar disorder (BD). The disease gene set, when taken alone, showed no significant interconnectivity in the interactome. However, inclusion of first-order interactors revealed extensive connectivity, exceeding degree-matched random expectations, indicating that the disease genes are embedded within cohesive subnetworks. This enrichment persisted after hub removal, suggesting connectivity is driven by distributed, disease-relevant interactions, rather than global network structure. At the network level, OCD showed a prenatal expression signature with enrichment in foetal structures. Interestingly, the network expression profile of PD, a late-onset syndrome, resembled that of OCD, which presents earlier in life. Further analyses showed that these co-expression signals did not come uniformly from the full syndrome networks, but from groups of highly interconnected proteins that formed specific PD and OCD network modules, and occurred in close proximity in the interactome. They show a prenatal expression signature in the developing prefrontal cortex, and share enrichment for ribosome-related processes. Together, our findings support a network-based model of brain disorders in which genetic risks act through distributed, yet coherent, modules which are organised across brain regions and developmental time periods.</p>

Huntington disease (HD) is a progressive neurodegenerative disease caused by an expanded CAG repeat in the <i>HTT</i> (<i>huntingtin</i>) gene, leading to the accumulation of mutant HTT (mHTT). IL17A (interleukin 17A), a proinflammatory cytokine primarily secreted by Th17 and γδ T cells, has been implicated in immune-mediated neurodegeneration. However, the role of IL17A in the pathogenesis of HD remains poorly understood. Here, we identify IL17A as a critical pathogenic factor in HD that promotes neuroinflammation, mHTT aggregation, and autophagy-lysosomal dysfunction. IL17A disrupts autophagic flux by downregulating CTSB and CTSD, inducing SQSTM1/p62 and MAP1LC3B-II/LC3-II accumulation, and impairing lysosomal reformation. Mechanistically, IL17A suppresses lysosomal biogenesis by inhibiting the nuclear translocation of TFE3. This regulation occurs via a novel GSK3B/GSK-3β-TFE3 signaling pathway. Therapeutic neutralization of IL17A with a monoclonal antibody (IL17A mAb) ameliorates disease phenotypes in R6/2 HD mice, improving motor performance, extending survival, and reducing gliosis. IL17A mAb also attenuates mHTT aggregation and enhances neuroprotective signaling, as evidenced by increased expression of DLG4/PSD-95, phosphorylated CREB1, and BDNF. Moreover, IL17A mAb restores autophagy-lysosomal function by facilitating the clearance of protein aggregates and upregulating lysosomal enzymes and biogenesis markers, including CTSB, CTSD, PIP5K1A, and LAMP2. These findings establish IL17A as a key modulator of HD pathophysiology and highlight IL17A inhibition as a promising therapeutic strategy for targeting autophagy-lysosomal dysfunction in HD.<b>Abbreviations:</b> 3-MA; 3-methyladenine; Aβ, amyloid beta; AIF1/Iba1, allograft inflammatory factor 1; ALP, autophagy-lysosomal pathway; ALR, autophagic lysosomal reformation; ATG7, autophagy related 7; ATG5, autophagy related 5; Baf A1, bafilomycin A1; BBB, blood-brain barrier; BDNF, brain derived neurotrophic factor; CSF, cerebrospinal fluid; CTSB, cathepsin B; CTSD, cathepsin D; DLG4/PSD-95, discs large MAGUK scaffold protein 4; GFAP, glial fibrillary acidic protein; GSK3B/GSK-3β, glycogen synthase kinase 3 beta; HD, Huntington disease; HTT, huntingtin; ICV, intracerebroventricular; IL17A, interleukin 17A; IL17A mAb, IL17A monoclonal antibody; IL17RA, interleukin 17 receptor A; IV, intravenous; LAMP2, lysosomal-associated membrane protein 2; MAP1LC3B/LC3B, microtubule-associated protein 1 light chain 3 beta; mHTT, mutant HTT; RBFOX3/NeuN, RNS binding protein, fox-1 homolog (C. elegans) 3; p-CREB1/CREB, phospho-cAMP responsive element binding protein 1; PIP5K1A, phosphatidylinositol-4-phosphate 5-kinase, type 1 alpha; PPP1R1B/DARPP-32, protein phosphatase 1 regulatory inhibitor subunit 1B; rIL17A, recombinant IL17A; SQS, self-quenched substrate; SQSTM1/p62, sequestosome 1; MAPT/tau, microtubule-associated protein tau; TDG, tideglusib; TFE3, transcript factor E3; TFEB, transcript factor EB; Th17, T helper 17; TX-100, Triton X-100; WT, wild-type.

<h4>Aim</h4>To investigate the transcriptional profiling of ocular surface ectoderm (OSE) derived from human embryonic stem cells (hESC), and identified CACNG6 and AQP3 as the surface markers of OSE.<h4>Methods</h4>hESCs were differentiated into OSE, neuroectoderm (NE), surface ectoderm (SE), and other surface ectoderm (OE) cells <i>in vitro</i>. RNA-seq was performed to analyze transcriptomic profiling of hESC-derived OSE, NE, OE, and SE. The differential expressed genes (DEGs) were identified, and Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and protein-protein interaction (PPI) network analyses were performed to screen the signals and hub genes associated to OSE commitment. Also, the highly expressed transcription factors (TFs) and membrane proteins (MPs) in OSE cells were identified.<h4>Results</h4>Transcriptome analysis revealed that OSE development is dually regulated by signals associated with both SE and NE development. The signaling pathways such as Hippo, encoding extracellular matrix (ECM)-receptor interaction, and transforming growth factor-β (TGF-β) might delineate the surface ectodermal phenotype of OSE, with <i>FN1</i>, <i>COL1A1</i>, and <i>TGFB1</i> identified as hub genes. Additionally, pathways such as axon guidance, might elucidate the influence of NE in OSE commitment, and with <i>PAX6</i>, <i>LHX2</i>, <i>FOXG1</i>, <i>SOX2</i>, <i>MSI1</i>, and <i>DCLK1</i> recognized as the hub genes. Genes implicated in retinoic acid (RA) synthesis (<i>ALDH1A1</i>, <i>ALDH1A3</i>, and <i>RDH10</i>) exhibited high expression in OSE, indicating the significant role of the RA signaling pathway in OSE development. Furthermore, OSE-specific transcription factors and surface markers (<i>CACNG6</i> and <i>AQP3</i>) were identified.<h4>Conclusion</h4>This study reveals the transcriptome profiling of OSE, which could provide insights into the characteristics of OSE and the underlying molecular mechanisms involved in its derivation.

Asymmetric transcription of noncoding RNA LincGET is currently recognized as the earliest event regulating the first cell fate decision in mammalian embryogenesis. However, whether key protein factors modulate this process remains elusive. Here, we identify RBBP7 as the earliest protein factor regulating developmental cell fate in mammals. Loss of RBBP7 drives cells towards ICM lineage. In mouse late 2-cell embryos, unequal translation of Rbbp7 contributes to its asymmetric protein distribution, which subsequently induces inversed asymmetric histone acetylation H3K9ac by interaction with HDAC1, thereby promoting cell differentiation. Interestingly, RBBP7 and LincGET exhibit a consistent asymmetric tendency but direct different cell fates; depletion or overexpression of both Rbbp7 and LincGET restored the cell fate bias, suggesting a coordinated regulatory mechanism during initial lineage specification. In summary, our study reveals RBBP7 as a new protein factor and elucidates its role in the first cell fate decision.

Neurodegeneration with brain iron accumulation (NBIA) comprises a genetically heterogeneous group of rare movement disorders characterized by progressive neurodegeneration and selective basal ganglia iron deposition. Recent discoveries have fundamentally reshaped the understanding of NBIA, indicating that defects in coenzyme A metabolism, mitochondrial bioenergetics, lipid remodeling, autophagy-lysosomal pathways, and ferroptosis precede and promote secondary iron dyshomeostasis rather than resulting from primary abnormalities in iron metabolism. This review integrates recent mechanistic and translational evidence (2020-2026) across both common and underrepresented NBIA subtypes, including pantothenate kinase-associated neurodegeneration, phospholipase A2-associated neurodegeneration, COASY protein-associated neurodegeneration, mitochondrial enoyl-CoA reductase protein-associated neurodegeneration, mitochondrial membrane protein-associated neurodegeneration, β-propeller protein-associated neurodegeneration, fatty acid hydroxylase-associated neurodegeneration, neuroferritinopathy, and mitochondrial DNA-associated forms. Unlike previous reviews, this synthesis consolidates findings from patient-derived induced pluripotent stem cell neuronal and glial models, compartment-specific iron localization, advanced neuroimaging biomarkers, and emerging therapeutic strategies within a unified mechanistic framework. Collectively, the evidence supports a paradigm in which mitochondrial dysfunction and lipid metabolic failure initiate disease progression, whereas iron accumulation amplifies oxidative injury and lipid peroxidation, thereby increasing ferroptotic cell death and neuronal degeneration, providing an updated foundation for biomarker discovery, mechanistically informed therapeutic development, and precision medicine approaches in NBIA.

<h4>Background</h4>Gastric cancer remains a leading cause of cancer-related mortality worldwide, underscoring the critical need for effective prevention through the management of precancerous lesions. Gastric intestinal metaplasia (GIM) is a key precursor, with its incomplete subtype (IIM) conferring a substantially higher risk of malignant progression compared to complete intestinal metaplasia (CIM). However, IIM is not merely a static histological variant but represents a dynamic, transitional epithelial state of mixed gastric and intestinal differentiation, driven by chronic inflammation. Its accurate identification and clinical management pose significant challenges.<h4>Summary</h4>This review synthesizes current evidence on IIM as a high-risk transitional phenotype in gastric carcinogenesis. We detail its cellular origins, primarily from spasmolytic polypeptide-expressing metaplasia (SPEM) via chief cell reprogramming (paligenosis), and its characteristic hybrid molecular signature. Diagnostically, definitive subtyping relies on histochemical staining (e.g., AB-PAS), as conventional endoscopy and histology lack sufficient precision, highlighting a barrier to routine risk stratification. Epidemiologically, IIM is associated with a 4- to 11-fold increased risk of gastric cancer compared to CIM. While Helicobacter pylori eradication may induce partial regression, patients with IIM retain a significant residual cancer risk, necessitating ongoing surveillance. Emerging endoscopic techniques (e.g., narrow-band imaging) and molecular biomarkers (including DMBT1, AQP5, TROP2, and OLFM4) show promise for improving in vivo detection and risk assessment, with combinatorial biomarker strategies potentially better capturing IIM's hybrid phenotype. Current classification systems have limitations, including the frequent coexistence of subtypes and a lack of validated biomarkers for precise risk stratification.<h4>Key messages</h4>1、IIM is a biologically unstable, transitional lesion with a markedly elevated risk of progression to gastric adenocarcinoma, warranting its distinction from CIM in clinical practice. 2、 Reliance on specialized pathology for diagnosis limits widespread risk stratification, creating an urgent need for reliable endoscopic predictors and validated molecular biomarkers. 3、Even after successful H. pylori eradication, patients with IIM require long-term endoscopic surveillance due to persistent cancer risk. Future strategies must integrate IIM subtyping into personalized surveillance protocols to enhance gastric cancer prevention.

In individuals on effective antiretroviral therapy (ART), integrated HIV proviruses persist within CD4 T cells, forming a viral reservoir that rebounds if treatment is stopped. Identifying and targeting these rare, infected cells is critical for advancing therapies, but methods to study reservoir cells are limited, and their unique properties remain largely unknown. We applied DAb-seq, a high-throughput method that combines single-cell DNA and surface protein sequencing, to profile ~527,000 CD4 T cells from the blood of six individuals on ART. Infected cells were distributed across all CD4 T cell subsets but were enriched in central memory subsets and in a CD4 subset with Th17-like signatures expressing high levels of integrin β7. Attempts to identify surface markers distinguishing infected from uninfected cells revealed epitopes that largely reflected the subsets most enriched for infection. However, while central memory T cells harbored the majority of HIV, proviruses with a greater number of genomic regions were enriched relative to their more defective counterparts in the CD4 Naïve, transitional memory (Ttm), and regulatory (Treg) subsets, suggesting that these subsets differentially maintain more complete proviral genomes. In summary, we developed DAb-seq as an open-source platform to link proviral sequences to cellular phenotypes, revealing heterogeneity in surface protein expression and proviral fate across infected subsets.

Pancreatic ductal adenocarcinoma (PDAC) has a very poor prognosis and remains highly refractory to standard chemotherapy owing to its unique tumor microenvironment (TME) and metabolic reprogramming. A defining feature of PDAC is that the near-ubiquitous presence of oncogenic KRAS mutations, together with NRF2 activation, generates abnormally high levels of reactive oxygen species (ROS) and renders the cells strongly dependent on an amplified glutathione (GSH)-based antioxidant program (the SLC7A11-GSH-GPx4 axis) for survival. This single metabolic axis simultaneously neutralizes drug-induced ROS to sustain chemoresistance and, through GPx4-mediated detoxification of lipid peroxides, suppresses ferroptosis-an iron-dependent, apoptosis-independent form of cell death. Because ferroptosis does not rely on the apoptotic or immune machinery that PDAC readily evades, its induction directly exploits this redox-metabolic vulnerability, distinguishing the GSH-GPx4 and iron-metabolism axes from conventional immune- or DNA-damage-based targets. This review analyzes the regulatory mechanisms of GSH homeostasis linked to treatment resistance in PDAC and discusses nanoparticle therapeutics rationally designed around the two central ferroptosis pathways: the GSH-GPx4 axis and the iron-metabolism axis.

Dementia with Lewy bodies (DLB) is increasingly conceptualised not merely as a disorder of neuronal death but as a primary synaptopathy in which the functional collapse of synaptic transmission and plasticity precedes, and predicts, neurodegeneration and clinical decline. Two genetic determinants dominate the heritable risk architecture of DLB: the α-synuclein gene <i>SNCA</i>, in which both copy-number variation and missense mutations exert dose- and conformation-dependent effects, and GBA1, encoding the lysosomal hydrolase glucocerebrosidase (GCase), the single most influential genetic risk factor for the disease. Here we synthesise evidence that these loci converge on a shared pathogenic endpoint-the impairment of activity-dependent synaptic plasticity. We argue that <i>GBA1</i> loss-of-function and the resulting accumulation of glucosylceramide stabilise specific neurotoxic α-synuclein proteoforms, including soluble oligomers and self-templating conformational strains bearing defined post-translational modifications. These proteoforms are trafficked to, and enriched within, presynaptic terminals, where they disrupt SNARE-complex assembly and synaptic-vesicle dynamics, while postsynaptically they perturb NMDA and AMPA receptor trafficking, dysregulate dendritic calcium, and compromise synaptic mitochondrial bioenergetics. The net consequence is a metaplastic shift away from long-term potentiation (LTP) and toward aberrant long-term depression (LTD), a signature of synaptic failure detectable before frank pathology. We map these molecular events onto disease-relevant circuits-particularly the cholinergic basal forebrain and hippocampal-cortical and thalamocortical networks-and relate them to the defining neuropsychiatric features of DLB, including cognitive fluctuations and recurrent visual hallucinations. Finally, we evaluate emerging therapeutic strategies that target the GBA1-α-synuclein axis and that aim to restore synaptic plasticity directly. Positioning DLB within the framework of genetically determined plasticity deficits clarifies its kinship with other neuropsychiatric disorders and identifies the synapse as the most tractable node for early, disease-modifying intervention. We further examine how GBA1 allele severity and zygosity grade the phenotype, which genetic and environmental factors modify penetrance in carriers, and what distinguishes this synaptopathy from those driven by PSEN1/PSEN2, MAPT, or HTT, and we summarise the therapeutic pipeline-including enzyme augmentation and adeno-associated viral GBA1 gene therapy-that targets it.

The BTBR T+ Itpr3tf/J (BTBR) strain is a widely used model of neurodevelopmental disorders, characterized by an altered neuroanatomy, including a full-penetrant agenesis of the corpus callosum. While the adult BTBR brain has been studied thoroughly, less is known about how its brain develops prenatally and about when neurodevelopmental trajectories begin to differ from neurotypical strains. Here, we conducted a comparative histological analysis of fetal brain development across multiple developmental stages in BTBR and C57BL/6J (B6) mice, focusing on neocortical and midline development. BTBR mice showed lower fetal weight but comparable somite counts (assessed at 12.5 days post coitum, dpc) compared to B6 controls, indicating similar developmental timing. Neocortical layering showed a reduced ventricular zone fraction in BTBR fetuses at 15.5 dpc, without a change in overall cortical thickness. Concurrently, midline cell populations immunoreactive for the glutamate aspartate transporter (GLAST) failed to undergo remodeling in subsequent stages, resulting in the failure to form a GLAST+ indusium griseum and the lack of callosal projections crossing the midline at 17.5 dpc, which instead develop normally in B6 fetuses. These findings offer structural correlates for the early neuropathology of the BTBR brain.

Skeletal muscle development and regeneration rely on coordinated transcriptional programs controlled by muscle stem cells and their progeny. Nuclear Factor I X (NFIX) plays essential roles in fetal myogenesis and adult muscle regeneration. However, the mechanisms regulating its transcription and isoform expression remain unclear. Here, integrating multi-omics analyses with in vitro functional assays, we define the transcriptional and epigenetic landscape controlling Nfix expression during skeletal muscle development and regeneration. We show that <i>Nfix</i> promoter usage is dynamically regulated according to myogenic cell state: promoter 2 is associated with quiescent and stem-like states, whereas promoter 1 is activated during myogenic commitment and regeneration. These programs are accompanied by differential enhancer accessibility and DNA methylation changes within the <i>Nfix</i> locus, indicating coordinated epigenetic regulation. We further demonstrate that alternative promoter usage and exon 7/9 splicing generate distinct NFIX isoforms affecting myoblast proliferation and fusion, while transcriptomic profiling identified NFIX-dependent networks involved in muscle structure and metabolism. Overall, our findings uncover multilayered mechanisms controlling Nfix expression and identify promoter- and isoform-specific NFIX programs associated with stem, regenerative, and differentiated myogenic states. These results provide a molecular framework for future therapeutic strategies targeting NFIX in muscle diseases.

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a strong genetic component, and lupus nephritis (LN) represents one of its most common and severe organ-specific manifestations. This review synthesises current evidence on the genetic architecture of SLE and LN, with a particular focus on identifying shared and distinct genetic susceptibility loci and highlighting knowledge and data gaps in highly burdened African populations. Across studies, most risk loci, including <i>HLA-DRB1</i>, <i>TNFSF4</i>, <i>IRF5</i>, <i>STAT4</i>, <i>TNFAIP3</i>, <i>BANK1</i>, <i>BLK</i>, <i>ITGAM</i>, and <i>FcγR2A/FcγR3A</i>, converge on key immune pathways such as antigen presentation, type I IFN signalling, B-cell activation, and immune complex clearance. The findings support a substantial genomic overlap between SLE and LN, with most variants contributing to systemic immune dysregulation rather than kidney-specific susceptibility. A limited number of loci, including <i>PDGFRA</i>, <i>HAS2</i>, and <i>SLC5A11</i>, have been implicated in renal involvement, while <i>APOL1</i> G1/G2 risk variants are associated with renal disease progression and adverse kidney outcomes among individuals of African ancestry. Despite these advances, relatively few loci have been definitively linked to LN independent of SLE, reflecting both biological overlap and limitations in study design. Moreover, the existing literature is heavily skewed toward European, Asian, and admixed populations, with minimal representation of continental African cohorts. Given the high genetic diversity and disproportionate disease burden in African populations, this represents a critical knowledge gap. Improved inclusion of diverse populations, coupled with high-resolution genomic and functional studies, will be essential to refine causal variant identification and enhance understanding of disease mechanisms. Ultimately, insights into population-specific genetic risk may enable earlier identification of high-risk individuals and support the development of precision medicine strategies for SLE, specifically LN.

Human gastric organoids (HGOs) are 3D cultures of primary gastric epithelial cells that serve as in vitro models for gastric epithelial physiology, development, and disease. The extracellular matrix (ECM) material that organoids are maintained in provides crucial signals to the epithelial cells, regulating their function and growth. We here describe the application of human gastric ECM (hgECM) for HGO cultures, to provide a tissue- and species-specific growth matrix. We prepared hgECM from human gastric tissue by decellularization and then compared HGO growth, differentiation, and function in hgECM and in the traditionally used Matrigel. The composition, structure, and rheological properties of the hgECM were determined using tandem mass spectrometry, scanning electron microscopy, and rheometry. Transcriptional profiles of HGOs grown in hgECM and Matrigel were compared using single cell RNA sequencing (scRNAseq). Proteome analysis showed that hgECM was rich in collagens, whereas Matrigel was predominantly composed of glycoproteins such as laminin. The structure of hgECM was fibrous, befitting its collagen composition, while Matrigel was porous. The viscosity and stiffness of hgECM were found to be lower than Matrigel. HgECM supported robust growth of HGOs. ScRNAseq showed that cell type composition of HGOs in each ECM was comparable. However, HGOs in hgECM had reduced expression of genes associated with stem cells, epithelial-mesenchymal transition, stress, and inflammation compared to HGO grown in Matrigel. Conversely, HGO culture in hgECM increased expression of gastric tissue-specific genes and of genes associated with growth and metabolism. HgECM hydrogels were highly compatible with HGO culture, and improved homeostatic functions of HGOs, including growth, differentiation, and reduced inflammation. HgECM may serve as a tissue- and species-specific growth matrix for HGO culture to improve the physiological relevance of organoid models.

Excessive dietary fructose consumption contributes to the rapidly increasing prevalence of obesity, metabolic syndrome, and chronic kidney disease worldwide, and accumulating preclinical evidence has confirmed that excess fructose exposure provokes severe mitochondrial dysfunction, which serves as a critical upstream driver of progressive metabolic disturbance and renal tissue injury. Conventionally, fructose-induced mitochondrial damage is thought to originate from harmful intermediate metabolites produced during intracellular fructose catabolism, while the potential direct pathogenic effect of intact unmetabolized fructose is largely overlooked. It remains unclear whether free fructose can directly target core mitochondrial complexes to initiate functional defects independent of its metabolic breakdown. Here, we report a fructose metabolism-independent mechanism in which fructose structurally remodels the translocase of the outer membrane (TOM) complex, obstructing the import of nuclear-encoded mitochondrial proteins and inhibiting mitochondrial ribosome biogenesis as well as oxidative phosphorylation. In vitro biochemical assays confirm that fructose non-covalently binds to TOM22 and induces subtle but functionally critical conformational changes in the TOM complex, thereby blocking the transmembrane translocation of mitochondrial ribosome subunits. Notably, disrupting the fructose-TOM22 binding efficiently recovers abnormal ribosome trafficking, restores compromised oxidative phosphorylation, and ameliorates mitochondrial dysfunction and glomerular pathological lesions in fructose-treated podocytes and mouse injury models. Our findings establish an innovative mechanistic paradigm that fructose acts as a direct allosteric modulator of mitochondrial membrane complexes, identifying TOM structural remodeling as a previously unrecognized molecular trigger of fructose-associated mitochondrial and metabolic disorders.

<h4>Background and objectives</h4>CSF inflammatory biomarkers in Huntington disease (HD), a neurodegenerative CAG-triplet expansion disorder, usually increase with disease progression. CSF leukocytes as an inflammatory marker have not been explored in HD. We explored high-precision CSF-leukocyte counts across different HD stages in the multicenter prospective biosample HD study HDClarity and their association with CSF neurofilament light chain (NFL) and cytokine and chemokine patterns.<h4>Methods</h4>A cross-sectional case-control study of the first average CSF leukocyte count of HDClarity study control participants (N = 94) and those carrying a repeat-expanded Huntingtin (<i>HTT</i>) allele (N = 335) categorized as having successive stages of presymptomatic and motor manifest HD as predefined by the HDClarity protocol (early presymptomatic [N = 48]: disease burden score [DBS] <250; late presymptomatic [N = 93]: DBS ≥ 250; early manifest HD [N = 171]: total functional capacity [TFC] 7-11; and late motor manifest HD [N = 23]: TFC < 11) was performed. CSF-NFL was available in 165. Results were juxtaposed with an independent single-center data set of 18 CSF cytokines and chemokines (57 CSFs, 19 control, 6 early and 8 late presymptomatic HD CSFs, and 19 manifest HD CSFs).<h4>Results</h4>CSF leukocytes peaked in late premanifest (median, interquartile range: 1.0/µL, 0.33-1.33/µL) when compared with early premanifest (0.0/µL, 0.0-1.0/µL) but also early (0.33/µL, 0.0-1.0/µL) and late manifest HD (0.0/µL, 0.0-0.67/µL). CSF leukocytes in late premanifest HD were higher than in controls (0.0/µL, 0.0-1.0/µL). A CSF-leukocyte peak at a DBS between 256 and 344 closely corresponded to the late premanifest HD peak. Higher CSF leukocytes in late premanifest HD were associated with higher CSF-NFL levels. Exploratory analysis of CSF cytokine and chemokine levels revealed that low interleukin (IL)-7 but high vascular endothelial growth factor (VEGF) and C-C motif chemokine ligand (CCL)22 levels may distinguish HD from control CSF; high VEGF, IL-6, and IL-15 early from late premanifest HD CSF; and low CCL2, CCL17, and IL-8 late premanifest from manifest HD CSF. When consecutively applied, these patterns identified late premanifest HD participants with a 75% sensitivity (95% CI 41%-96%) and 90% specificity (78%-96%).<h4>Discussion</h4>CSF leukocytes peaking in late premanifest HD, their association with increased CSF-NFL, and the corresponding stage-specific chemokine/cytokine changes indicate a temporally dynamic, probably neurotoxic inflammatory signaling network in HD.

Live cells in tissue are plastic, phenotypically dynamic, and modify their function in response to genetic and environmental perturbations. To unleash the power of live-cell imaging to identify phenotype-genotype-function coupling over time, we report the development of a standardized Shape-Appearance-Motion (SAM) "phenome" and SAM-Phenotype-Observation-Tool (SPOT), that act as an image-"transcriptome" and image-"transcriptome analyzer" respectively, and provide an unbiased and comprehensive description of morpho-dynamic phenotypes without prior knowledge. We apply SAM-SPOT to our simulated organoids database with known ground-truth and >1.6 million mouse and human organoid instances with defined genetic and chemical perturbations. SAM-SPOT can effectively and robustly characterize 3D morpho-dynamics from 2D projection videos. Combined with single-cell RNA sequencing, SAM-SPOT reveals that altered WNT signaling, but not mutant RAS or p53, predisposes intestinal organoids to irregular morphogenesis. SAM-SPOT advances biomedical discovery by empowering live-cell imaging to identify phenotype-genotype-function relationships through large-scale and cost-effective label-free live-cell imaging.

<h4>Objective</h4>Fibroblast-like synoviocytes (FLS) in rheumatoid arthritis (RA) synovium acquire a unique aggressive phenotype and produce cytokines that perpetuate inflammation and proteases that contribute to cartilage destruction. Actin-bundling protein Fascin-1 (FSCN1) is involved in FLS migration and invasion, but its role and mechanism in FLS phenotypic activation remain unclear.<h4>Methods</h4>FSCN1 expression was analyzed in the synovium from healthy controls (n = 6), patients with RA (n = 6), and patients with osteoarthritis (n = 6) with written informed consent obtained before sample collection, as well as synovium from control (n = 6) and arthritic mice (n = 6). Transcriptome profiling, RNA immunoprecipitation sequencing, and mass spectrometry analysis were performed to determine the underlying mechanism. FLS-specific FSCN1 knockout, FSCN1 intra-articular overexpression mice, and FSCN1 inhibitors were used to characterize the role and therapeutic potential of FSCN1 in experimental arthritis (n = 5-8).<h4>Results</h4>FSCN1 was significantly increased in RA synovium and predominantly localized to PDPN-positive FLS (P < 0.001). FSCN1 overexpression enhanced F-actin remodeling, FLS migration, invasion, proliferation, and inflammatory activation and exacerbated synovitis and cartilage damage in arthritis mouse models (P < 0.0026). Conversely, FLS-specific FSCN1 ablation reduced knee swelling, pain-related behavior, synovial inflammation, and Osteoarthritis Research Society International scores in arthritis mouse models (P < 0.0196). Mechanistically, FSCN1 promoted F-actin fiber formation, spatially sequestered tripartite motif-containing protein 38 (TRIM38), inhibited TRIM38-mediated IGF2BP1 ubiquitination, and sustained PI3K-AKT/NF-κB signaling. The FSCN1 inhibitors imipramine and NP-G2-044 suppressed FLS activation and alleviated arthritis pathology in mice (P < 0.001).<h4>Conclusion</h4>Pharmacologic inhibition of FSCN1 restrains synovial inflammation and joint destruction by suppressing the aggressive phenotype change of FLS, representing a promising therapeutic strategy against RA.

Neurodegenerative diseases (NDs) are marked by selective neuronal vulnerability and progressive failure of neural circuits. Increasing evidence indicates that neuronal loss is not driven by a single terminal event, but emerges from interacting regulated cell death (RCD) programs. These programs are closely coupled to mitochondrial injury, proteostatic collapse, lysosomal stress, metabolic imbalance, glial state transitions, and chronic neuroinflammation. Yet, how distinct death pathways are organized across cell types, disease stages, and disease-specific microenvironments remains unresolved. This review examines RCD as an integrated pathogenic network in major NDs. Caspase and B-cell lymphoma 2 (BCL2) family signaling, receptor-interacting protein kinase 1 (RIPK1), RIPK3, and mixed lineage kinase domain-like protein activation, NOD-like receptor family pyrin domain containing 3 and gasdermin signaling, GPX4-linked lipid peroxidation control, and autophagy lysosomal failure are discussed as convergent stress response modules rather than isolated pathways. Across Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease, these modules shape neuronal fate through disease-specific interactions with mitochondrial dysfunction, iron dyshomeostasis, inflammasome activation, and microglial metabolic remodeling. We further evaluate emerging therapeutic strategies that target cell death crosstalk, restore autophagy lysosomal competence, or improve delivery to the central nervous system, highlighting the importance of molecular selectivity, cellular context, disease stage, and translational feasibility.

Huntington's disease (HD) is a devastating neurodegenerative disorder characterized by the expansion of cytosine-adenine-guanine (CAG) repeats within the huntingtin (HTT) gene. Given their therapeutic potential, small-molecule strategies have gained significant traction, leading to the design of numerous lead candidates aimed at diverse pathological hallmarks of HD. These developmental efforts target various facets of the disease, including the inhibition and degradation of mutant huntingtin (mHTT) proteins, alleviation of motor dysfunction, and the provision of neuroprotective effects. For instance, gossypol acetate has been identified to induce the autophagic degradation of mHTT. Furthermore, these small molecules modulate critical signaling pathways within HD neurons, such as the store-operated calcium (SOC) channels, dopamine- and cAMP-regulated phosphoprotein 32 (DARPP-32), ataxia-telangiectasia mutated (ATM)/ataxia-telangiectasia and rad3-related (ATR)-p53 pathway, and the kynurenine (KYN) metabolic pathway. While currently explored small-molecule therapies have demonstrated preclinical efficacy, further clinical investigation is imperative to expand the chemical space of viable HD therapeutics. This review critically summarizes the design, synthesis, and structural motifs of small-molecule candidates, clinically used agents, and antioxidant natural products, providing a structural framework to guide the rational design and development of next-generation anti-HD compounds.

<h4>Purpose</h4>There is a bidirectional association between rheumatoid arthritis (RA) and inflammatory bowel disease (IBD). Patients with RA exhibit a higher prevalence of IBD, those with IBD are at a significantly increased risk of developing RA. The shared molecular mechanisms and key bridging molecules underlying remain to be explored.<h4>Methods</h4>Transcriptomic datasets from GEO were analyzed using WGCNA, differential expression, and immune-related genes to identify shared RA-IBD signatures. Least Absolute Shrinkage and Selection Operator (LASSO) and Support Vector Machine-Recursive Feature Elimination (SVM-RFE), were employed to prioritize diagnostic markers. Single-cell RNA sequencing datasets were used to localize the cellular source of the hub gene. Subsequently, two independent large-scale peripheral blood datasets were retrieved to further provide transcriptomic profiles of circulating immune cells, serving as a "bridge" between RA and IBD. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. Findings were validated using collagen-induced arthritis (CIA) and dextran sulfate sodium (DSS) mice models, as well as in vitro TNF-α stimulation of MH7A and Caco-2 cells.<h4>Results</h4>Intersection analysis identified 19 core immune-driven genes shared between RA and IBD, both diseases are characterized by a highly activated immune profile, particularly T cell lineages. Among these, ISG20 emerged as a critical molecular link, exhibiting high diagnostic efficacy for RA and IBD. Single-cell transcriptomic analysis further revealed that ISG20 is predominantly expressed in T cell populations in both RA synovium and IBD colon. In peripheral blood datasets, 29 "bridge genes" were identified and found to be significantly enriched in chemokine signaling. Experimental validation confirmed that ISG20 mRNA levels were significantly upregulated in inflamed synovial tissues of CIA and colon of DSS mice, and in TNF-α-stimulated MH7A and Caco-2 cells.<h4>Conclusion</h4>ISG20 serves as a crosstalk molecular link across the RA and IBD. These findings provide molecular landscape for shared pathogenesis and diagnostic window for patients predisposed to the RA-IBD co-occurrence clinical phenotype.

Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system characterized by inflammatory demyelination, neurodegeneration, and progressive disability. Clinically isolated syndrome (CIS) often represents the first overt presentation of MS. We performed an exploratory cross-sectional transcriptomic investigation of peripheral blood mononuclear cells (PBMCs) from healthy controls (HC, <i>n</i> = 40), CIS patients (<i>n</i> = 49), and Relapsing-Remitting MS (RRMS, <i>n</i> = 53) patients using the ArrayExpress dataset E-MTAB-11415. Differential expression analysis was performed using limma, adjusting for age and sex. Functional enrichment and network analyses were conducted using clusterProfiler, STRING, and Cytoscape. Although Principal Component Analysis (PCA) showed partial overlap among groups, pathway-level analyses revealed coherent alterations in translation, ribosome biology, mitochondrial protein synthesis, and stress-response regulation. In CIS compared with HC, cytoplasmic and mitochondrial ribosomal genes were predominantly downregulated, suggesting reduced translational capacity in PBMCs. This was accompanied by altered expression of translation-initiation and transcriptional regulators, whereas genes involved in stress-adaptive translational control, including <i>GCN1</i>, <i>YARS1</i>, <i>QARS1</i>, and <i>SIL1</i>, were selectively upregulated. Conversely, RRMS compared with CIS showed upregulation of ribosome-related and biosynthetic programs. Overall, these findings suggest that CIS may be characterized by peripheral translational restraint and adaptive stress response activation, whereas RRMS progression is associated with biosynthetic reactivation.

Xishuangbanna (XIS) cucumber (<i>Cucumis sativus</i>) originated from low-altitude southwest China and shows extreme cold sensitivity. Nano-hydroxyapatite (nHAP), known for its high bioavailability and surface reactivity relative to bulk HAP, was applied to enhance the cold tolerance of XIS seedlings. We optimized fertilization timing and fertilizer concentration. By determining physiological parameters alongside gene expression profiling and transcriptomic analysis, we preliminarily dissected the physiological and molecular mechanisms underlying nHAP-enhanced chilling tolerance. nHAP application preserved free and bound water even at 24 h into the cold-stress treatment, as detected by nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI). Exposure to cold stress caused a chilling injury index (CII) of 73.33%, while foliar spraying of nHAP at gradient concentration reduced CII values by 9.09-54.55%. At the same time, electrolyte leakage and malondialdehyde content were decreased by 6.68-61.41% and 12.92-67.16% respectively; chlorophyll content increased by 0.01-73.42%; SOD, POD, and soluble protein content increased by 10.54-161.53%, 16.50-154.33%, and 2.03-63.26%, respectively. Soil application of nHAP showed a similar but weaker effect than foliar spraying on alleviating chilling injury, and the optimal concentration was 1000 mg/L. Quantitative Real-Time PCR (qRT-PCR) revealed that foliar spraying of nHAP upregulated the gene expression of Superoxide dismutase genes (<i>CsCu/ZnSOD</i> and <i>CsMnSOD</i>) and major facility superfamily genes (<i>CsSPX-MFS1</i> and <i>CsSPX-MFS2</i>) in the cold treatment. We then profiled the transcriptome changes in seedling leaves during the cold treatment after foliar spraying of nHAP. Without nHAP application, cold stress resulted in a total of 6795 differentially expressed genes (DEGs), which were functionally enriched in plant-pathogen interaction and plant hormone signal transduction pathways. Under nHAP application, cold stress only caused 776 DEGs, which were functionally enriched in plant hormone signal transduction and galactose metabolism. These findings suggest that nHAP could improve the cold tolerance of cucumber seedlings through boosting antioxidant activity and plant hormone signaling pathways.

The ability of CD8 T cells to mediate protective immunity while limiting immunopathology depends on critical transcription factors such as Smad4 and Eomes that regulate differentiation of activated CTLs. Disruption of transcriptional programs mediated by Eomes and Smad4 in activated CTLs has been implicated in viral infections, chronic inflammation and cancer. Smad4 and Eomes have been shown to be critical for differentiation of memory cells, particularly TRM cells. To understand the gene regulation programs mediated by Smad4 and Eomes, we have done an integrated RNAseq and ChIPseq analysis using CD8 T cells that are isolated from Smad4KO (S4KO), EomesKO, and Smad3/Smad4-DKO (S34-DKO) mice. We identified overlapping and distinct gene expression programs mediated by Smad4 and Eomes that are associated with shaping CD8 T cell identity and functional bias. They act as critical regulators of genes involved in T cell differentiation, metabolic programming and epigenetic control in CD8 T cells. Smad4 and Eomes regulate the genes involved in tissue residency and OXPHOS-linked mitochondrial bioenergetics. Finally, we showed that canonical TGF-beta signaling is active in the absence of Smad4 or Eomes and abrogated only when both Smad3 and Smad4 are deleted. Surprisingly, CD8 T cells lacking both Smad3 and Smad4 are more enriched for TRM signature genes compared to Smad4 or Eomes-deficient CD8 T cells.

<h4>Background</h4>Osteonecrosis of the femoral head (ONFH) is a progressive and disabling orthopedic disorder characterized by impaired bone remodeling and microvascular dysfunction. Emerging evidence identifies post-translational modifications (PTMs) as critical molecular switches linking external pathogenic stimuli, such as glucocorticoids and alcohol, to intracellular signaling dysregulation in ONFH.<h4>Main body</h4>This review comprehensively summarizes the regulatory roles of major PTMs-including phosphorylation, acetylation, methylation, and ubiquitination-in key cell types governing femoral head homeostasis, namely, bone marrow-derived mesenchymal stem cells, osteoblasts, osteocytes, osteoclasts, and vascular endothelial cells. Aberrant PTMs disrupt the osteogenic-adipogenic balance, impair angiogenesis, and trigger multiple forms of programmed cell death, including apoptosis and ferroptosis, collectively driving the pathological progression towards bone necrosis. Particular emphasis is placed on phosphorylation-dependent signaling pathways (e.g., PI3K/Akt, GSK-3β/β -catenin, JAK2/STAT3, and AMPK/mTOR), ubiquitin-mediated mitochondrial quality control, and acetylation-driven epigenetic regulation. Furthermore, we highlight emerging PTM-targeted small-molecule interventions that show promise in restoring osteogenesis, preserving endothelial function, or suppressing cell death.<h4>Conclusion</h4>Future research directions include decoding cell type-specific "PTM codes", integrating multi-omics analyses, and developing patient-derived organoid models. Advancing these areas may collectively enable earlier diagnosis and more precise, mechanism-based therapies for ONFH.

Inflammatory bowel disease (IBD), which includes ulcerative colitis and Crohn's disease, represents a chronic, immune-mediated pathology in which genetic susceptibility, environmental exposures, and microbial perturbations converge to destabilize intestinal homeostasis. Despite a steady global rise in incidence affecting more than 10 million people worldwide, current single-pathway biologic and small-molecule therapies still leave 30-40% of patients without durable remission, with progression to stricturing, fistulizing, or transmural complications. Yet the mechanistic integration of innate and adaptive immune networks, epithelial barrier dysfunction, and microbiota‑driven inflammation remains fragmented. This review summarizes recent advances in understanding the pathophysiological mechanisms driving IBD, focusing on innate and adaptive immune networks. Current therapies, including cytokine or integrin-targeting biologics and small-molecule inhibitors like Janus Kinase (JAK) antagonists, are critically evaluated in light of their restricted pathway coverage. In response to these challenges, emerging strategies are examined targeting nonimmune pathways, including microRNA‑124-mediated gene regulation, fecal microbiota transplantation, and mesenchymal stromal cell therapies that combine immunomodulation with tissue repair. The development of effective IBD therapies is likely to benefit from combining complementary treatment strategies, guided by molecular and cellular profiling. This review underscores a paradigm shift from monotherapies to integrated, multitarget approaches as the new frontier in IBD management.

Currently, the global incidence of head and neck squamous cell carcinoma (HNSCC) continues to increase, with a large proportion of cases being diagnosed at advanced stages. Conventional oncological treatments are often associated with poor quality of life, while the aggressive biological behavior of these tumors results in recurrence in approximately half of treated patients according to current evidence. The need for rapid, targeted diagnosis and personalized treatment has driven research toward the identification of tumor biomarkers with diagnostic, prognostic, and predictive value for treatment response. In this scoping review, we performed a comprehensive literature search to map the available evidence on tumor biomarkers in HNSCC. We identified a wide range of biomarkers, several of which exhibit overlapping roles, and classified them according to their genomic, proteomic, cytokine-related, tumor microenvironment, metabolic, and microbiota-associated characteristics. This scoping review also summarizes the current evidence regarding biomarkers involved in carcinogenesis, treatment response and therapy resistance, while highlighting their current level of clinical applicability. Although only a limited number of biomarkers have currently been implemented in routine clinical practice in head and neck cancers, the studies included in this review identified several promising candidates with the potential to be incorporated into clinical practice following further prospective validation and methodological standardization. Many additional biomarkers are still under investigation, opening new perspectives for future diagnostic and therapeutic targets and supporting the development of personalized multimodal treatment strategies for patients with HNSCC.

<b>Background/Objectives</b>: Host genetic variation contributes to the heterogeneous clinical outcomes of coronavirus disease 2019 (COVID-19), yet evidence from Southeast Asian populations remains limited. <b>Methods</b>: We investigated host genetic factors associated with COVID-19 severity in Vietnamese patients infected with the SARS-CoV-2 Delta variant using whole-exome sequencing. A total of 48 unvaccinated patients were enrolled. During sample-level quality control, one sample was excluded because the genetically inferred sex was discordant with the information recorded in the clinical medical record, leaving 47 samples (23 severe/critical and 24 mild/asymptomatic) for downstream genetic analyses. Gene-based association analysis was performed using MAGMA, followed by functional enrichment and interaction network analyses with Metascape and GeneMANIA. <b>Results</b>: Population structure analysis showed that the study participants clustered closely with the East Asian (EAS) reference population. No individual variant reached the prespecified multiple-testing-adjusted threshold, and no gene-level association survived Benjamini-Hochberg correction. Using a nominal MAGMA gene-based <i>p</i> < 0.01 threshold solely for exploratory prioritization, 44 genes were selected for downstream functional analyses. Functional enrichment highlighted RNA processing and mRNA maturation, together with mitochondrial, metabolic, immune-regulatory, and cellular homeostasis pathways. Network topology analysis further identified several highly connected genes, including CPSF4, MRPS34, ATP5MF, BUD31, SNRPD3, and HDAC1. <b>Conclusions</b>: These hypothesis-generating findings are consistent with a potentially polygenic contribution to severe COVID-19 and provide an exploratory systems-level framework for understanding host genetic susceptibility in the Vietnamese population, while identifying biologically plausible candidate genes and pathways for future validation.

Intrahepatic cholangiocarcinoma (iCCA) is histologically classified into the small duct type (SDT) and large duct type (LDT), although their morphological differential diagnosis can be difficult. We aimed to identify new immunohistochemical markers to classify SDT and LDT with high sensitivity and specificity. We compared the gene expression profiles of SDT and LDT using cases obtained from our institution (n = 8) and The Cancer Genome Atlas database (n = 28). We selected the candidate molecules that were up-regulated in LDT, were minimally or not expressed in SDT, and had specific and available antibodies suitable for immunohistochemistry. We finally selected ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 (ST6GalNAc1), Breast carcinoma amplified sequence-1 (BCAS-1), and Olfactomedin 4 (OLFM4), which were expressed in 100%, 100%, and 98.3% of 58 LDT cases, respectively. ST6GalNAc1 was expressed in 3.8% of 52 SDT cases, whereas BCAS-1 and OLFM4 were expressed in 48.1% and 34.6% of SDT cases, respectively. ST6GalNAc1 was also expressed in intraductal papillary neoplasm of the bile duct (100%, n = 17) and only the adenocarcinoma component corresponding to LDT among the combined hepatocellular-cholangiocarcinoma cases (100%), but not in hepatocellular carcinoma (n = 26). In small biopsy specimens, ST6GalNAc1 was expressed in 100% of LDT (n = 18) and 12.5% of SDT (n = 16) samples. ST6GalNAc1 expression was associated with significantly shorter overall survival (P = 0.012) and remained significant after adjustment for tumor subtype (hazard ratio 2.595; 95% confidence interval, 1.433-4.699; P = 0.002). ST6GalNAc1 is useful for iCCA subtype identification with high sensitivity and specificity, showing promise to become a more powerful tool when combined with other markers.

Lung cancer remains a major cause of cancer-related mortality, and reliable molecular targets with therapeutic relevance are still needed. This study aimed to identify key genes associated with lung cancer progression and explore the potential regulatory effect of resveratrol. The GSE43458 dataset, including 80 lung cancer samples and 30 control samples, was used for differential expression analysis and weighted gene co-expression network analysis (WGCNA). Intersecting genes were subjected to protein-protein interaction network construction, Cytoscape-based hub gene screening, functional enrichment analysis, and immune infiltration analysis. Single-cell RNA sequencing data from GSE131907 were further analyzed to characterize cellular heterogeneity and hub gene distribution. Resveratrol was predicted as a candidate compound, followed by molecular docking with hub proteins. Finally, CCK-8, Western blotting, and qRT-PCR assays were performed in BEAS-2B and A549 cells. A total of 1,655 differentially expressed genes were identified, and WGCNA identified the 252-gene turquoise module as the module most strongly associated with the lung cancer phenotype (r = - 0.86, P = 6.0 × 10⁻³⁵). Intersection analysis yielded 250 candidate genes, representing 15.1% of all differentially expressed genes. Five hub genes, CASP3, DDX54, TP53BP1, CDKN2A, and ABT1, were identified and showed significantly increased expression in lung cancer tissues (P < 0.05). Functional enrichment analysis linked the candidate genes to apoptosis, cell-cycle regulation, DNA damage repair, immune responses, and cancer-related pathways, while immune infiltration and single-cell analyses revealed marked remodeling of immune and stromal components. Molecular docking predicted potential interactions between resveratrol and the five hub proteins, with the most favorable docking scores observed for TP53BP1 (- 7.0 kcal/mol) and DDX54 (- 6.9 kcal/mol). In vitro validation further showed that resveratrol treatment significantly reduced the mRNA and protein expression of the identified hub genes in A549 cells (P < 0.05). This study identified five lung cancer-associated hub genes and provided preliminary evidence that resveratrol may modulate their expression. These findings provide a multi-level molecular framework for further investigation of resveratrol-responsive networks in lung cancer.

Lineage-determining transcription factors (TFs), such as p63 in epithelial tissues, establish normal tissue identity but can also drive carcinogenesis. The epigenetic basis for these divergent effects, however, is unclear. Here, we show that p63 reorganizes three-dimensional (3D) chromatin topology in squamous cell carcinoma (SCC) through cooperation with the tumor-selective partner TF, FOXK1. Multi-omic profiling across normal and malignant states reveals that p63 enhances connectivity between cis-regulatory elements near oncogenes and promotes a secondary enhancer looping architecture, in which p63 and FOXK1-enriched enhancers indirectly contact target promoters via FOXK1-associated intermediate anchors lacking p63 binding. FOXK1 mediates p63-dependent chromatin looping, as FOXK1 loss selectively weakens p63-dependent loops and reduces transcription of associated target genes. The p63-FOXK1 interaction is observed in human tumor samples but not in normal tissues. Together, our findings define an epigenetic mechanism by which a lineage master TF and tumor-restricted partner TF reshape 3D chromatin structure to drive oncogenic transcription, with implications for tumor cell identity and therapy.

Brain perivascular macrophages maintain brain physiology, yet their transcriptional regulators and functions in health and disease remain unclear. Using single-cell multi-omics and functional experiments, we identify cellular musculoaponeurotic fibrosarcoma oncogene (cMAF) as a key transcription factor for brain perivascular macrophages, and conditional deletion of cMAF disrupts their phenotype in vivo. Functionally, cMAF drives insulin-like growth factor-1 (IGF1) expression in perivascular macrophages, enabling communication with endothelial cells. Consistently, cMAF deletion in perivascular macrophages causes transcriptional alterations in cerebral arteries, affecting vascular functions. Notably, cMAF emerges as the main transcription factor for human perivascular macrophages, suggesting conservation of this transcriptional module. During Alzheimer's disease (AD), human perivascular macrophages upregulate cMAF and IGF1 to enhance communication with vascular cells, and this response is abrogated in APOE4 carriers. Lastly, we explore an uncharacterized polymorphism in cMAF, providing evidence that the cMAF program is protective against AD. Targeting cMAF in perivascular macrophages may offer new therapeutic strategies for neurodegenerative and cerebrovascular diseases.

Autophagy plays a central role in cellular degradation and recycling pathways, and the LC3B protein is essential for this process. Dysregulation of LC3B has been implicated in oncogenesis. In this study, we used a computational approach to design a novel peptide nucleic acid (PNA) targeting the RNA-binding domain of LC3B, with the aim of inhibiting its function. The RNA AAUAAA polyadenylation signal was used as a starting point to design new PNAs with high affinity for LC3B. Molecular dynamics simulations and binding free-energy calculations on the RNA-AAUAAA/LC3B complex enabled the identification of promising PNA analogues. The lead candidate, a PNA with the sequence AATAAA, was synthesized, and its biological activity was investigated through biophysical and cellular assays. Cell viability was evaluated in the human prostate cell lines PNT1A and PNT2, as well as in the prostate cancer cell lines PC3 and DU145, while its efficacy in inhibiting autophagy was assessed in PC3 cells. The combined computational, biophysical and cellular results support AATAAA-PNA as an LC3B-binding hit whose cellular effects are consistent with modulation of LC3B-associated autophagy and mRNA-decay pathways. Overall, this study presents an <i>in silico</i> strategy for the design and development of LC3B inhibitors based on the RNA AAUAAA motif. The designed PNA represents a promising hit compound for further optimization in cancer therapy.

Inflammation can either encourage or suppress tumor growth, thus having a two-sided effect on cancer development. This depends on the balance between pro-tumor and anti-tumor immune responses within the tumor microenvironment (TME). Pro-tumor inflammation, driven by specific immune cells, enhances blood flow and nutrient supply to tumors, promoting the activation of dormant cancer cells (DCCs). Conversely, antitumor inflammation hinders blood flow and can force active cancer cells into a state of dormancy. Tumors actively shift this balance towards pro-tumor inflammation to create a favorable environment for growth. Therefore, anti-inflammatory therapy may be an integral part of comprehensive cancer immunotherapy. This review explores how different anti-inflammatory medications, such as glucocorticoids, non-steroidal anti-inflammatory drugs (NSAIDs), antihistamines, anti-leukotrienes, statins, drugs that block pro-inflammatory cytokines, agents that inhibit oxidative phosphorylation, antioxidant vitamins, anti-angiogenic drugs, and low-dose chemotherapy, can be used to combat cancer. Granulocyte counts and erythrocyte sedimentation rate (ESR) can be used to assess inflammation levels and the effectiveness of anti-inflammatory treatments. We advocate for a paradigm shift in cancer treatment, moving away from aggressive tumor destruction, which triggers uncontrolled tumor regeneration, toward long-term immunological control of tumor growth while preserving the patient's overall health.

Since the discovery of truncated mutations of adenomatous polyposis coli proteins in familial adenoma patients in 1991, the mechanism of cytosolic β-catenin regulation has been intensively studied, and now it is very well known that the central role of the canonical Wnt/β-catenin is in colorectal cancer. However, Wnt signaling is very complicated because of the presence of almost 20 Wnt ligand genes, six Frizzled seven-transmembrane receptors, and three LRP co-receptors. In addition, research in the past two decades illuminated the existence of the other Wnt signaling-non-canonical Wnt signaling (Wnt/PCP and Wnt/Ca²⁺ pathways), and an increasing number of studies have shown the potential role of non-canonical Wnt signaling in cancer recently. One of the well-studied Wnt ligands in non-canonical Wnt signaling is Wnt-5a. However, the role of Wnt-5a and non-canonical pathways in cancer is mosaic-i.e., it may involve tumor-promoting or suppressing pathways. In certain cancers, non-canonical Wnt signaling may mainly act as a tumor promoter, yet the results are very controversial in colorectal cancer. Elucidating the role of non-canonical Wnt signaling in colorectal cancer may be very important to further reduce the risk of colorectal cancer, especially in patients who do not carry truncated mutations of adenomatous polyposis coli. In this review, I would like to mainly discuss the apparent controversy surrounding non-canonical Wnt signaling in colorectal cancer, and I would like to point out a few potential reasons contributing to the mysterious roles of Wnt5a-initiated non-canonical signaling in colorectal cancer.

<b>Background/Objectives</b>: Glioblastoma (GBM) is the most lethal primary brain malignancy in adults, with a median overall survival of approximately 15 months. Temozolomide (TMZ) resistance develops in virtually all patients, and no second-line regimen has improved outcomes over the past two decades. The DNA methyltransferase inhibitor decitabine (DAC) has attracted interest as a chemosensitizer, but whether it directly reverses the TMZ-resistance transcriptome or operates through distinct, complementary mechanisms has not been tested at multi-omics resolution. <b>Methods</b>: We performed an integrative six-layer multi-omics analysis across five public GEO datasets (bulk RNA-seq, EPIC 850K methylation, and 21,676 single cells) re-purposed from studies conducted for unrelated aims, formally tested DAC-mediated reversal of the TMZ-resistance transcriptome across 11,707 genes, mapped pharmacogenomic targets with DGIdb v5, and built an exploratory, hypothesis-generating 11-gene prognostic model internally validated in TCGA-GBM (n = 166) and externally tested in the independent CPTAC-GBM cohort (n = 96). <b>Results</b>: DAC reprogrammed transcription across 1114-1882 differentially expressed genes per cohort and reactivated 146 direct epigenetic targets, identifying INPP5D/SHIP1 as the top-ranked direct epigenetic-reactivation target. Genome-wide reversal analysis across 11,707 co-detected genes showed a negligible effect (Spearman ρ = 0.073), but single-cell analysis revealed significant per-cell attenuation of MES-like and stem-like programs (Δ = -0.071 and -0.135, respectively; both <i>p</i> < 0.001). The 11-gene risk model achieved a Harrell's C-index of 0.706 (apparent); after correcting for the two-stage gene selection with a full-pipeline bootstrap, the optimism-corrected C-index was 0.63, and external validation in an independent cohort (CPTAC-GBM, n = 96) showed only near-chance discrimination (C-index 0.55), indicating that the signature does not generalize and is exploratory. Pharmacogenomic mapping yielded 734 unique therapeutic agents (230 FDA-approved) across 69 druggable targets after excluding AR. Most of these agents are not GBM-directed, so this catalog-level mapping is hypothesis-generating rather than a set of therapeutic recommendations. <b>Conclusions</b>: DAC does not broadly reverse the TMZ-resistant transcriptome but acts through three complementary mechanisms: epigenetic reactivation of INPP5D/SHIP1, cancer-testis-antigen and type I interferon induction, and per-cell attenuation of mesenchymal-stem-like transcriptional intensity, supporting hypotheses for rationally designed DAC-based combination therapy in TMZ-resistant GBM.

In the biosynthesis of heme the tetrapyrrole hydroxymethylbilane is converted enzymatically to uroporphyrinogen III whereas conversion to uroporphyrinogen I occurs spontaneously. Both are substrates for uroporphyrinogen decarboxylase (UROD) but only the III isomer is a precursor of heme. These porphyrinogens are easily oxidised to the respective uroporphyrins and trace amounts occur in the urine of healthy humans and animals. Large quantities of uroporphyrins I and III, as well as other oxidation products, occur in the liver and urine of patients with some porphyrias and after poisoning of people and animals by chemicals, such as hexachlorobenzene (HCB) and 2,3,7,8-tetrachorodibenzo-<i>p</i>-dioxin (TCDD). In the acquired disorder sporadic porphyria cutanea tarda (sPCT) and chemical-induced porphyria, hepatic UROD is inhibited, ostensibly by a partially oxidised uroporphyrinogen. The processes leading to oxidation of the uroporphyrinogens are interactions of a variety of external, internal and genetic factors. In some experimental systems, cytochrome P450 1A2 is implicated in the oxidation of uroporphyrinogens and uroporphyria and many patients and in vivo studies demonstrate the influence of iron. The article reviews the present state of knowledge of uroporphyrinogen oxidation, susceptibility and outcomes, and illustrates areas that require further exploration to explain fully the mechanisms of sPCT and the related uroporphyria caused by chemicals of toxic concern.

Alzheimer's disease (AD) and HIV-associated neurocognitive disorder (HAND) share progressive cognitive decline. Their common molecular mechanisms remain poorly understood. Current therapeutic approaches lack effective biomarkers for early diagnosis and intervention. We integrated transcriptomic profiles from multiple independent cohorts across brain tissues and blood. We systematically evaluated diagnostic performance using machine learning algorithms including Random Forest, Support Vector Machine, and XGBoost. Notably, FOXO3 emerged as the top cross-disease biomarker. FOXO3 achieved diagnostic accuracy in AD temporal cortex (area under the curve [AUC] = 0.922, 95% CI: 0.885-0.959). FOXO3 showed diagnostic performance in HAND frontal cortex (AUC = 0.771, 95% CI: 0.724-0.818). FOXO3 expression positively correlated with APP (R = 0.558). FOXO3 expression negatively correlated with MAPT (R = -0.690) and SORL1 (R = -0.856). ACE showed strong positive correlation with FOXO3 (R = 0.685), suggesting vascular involvement. STAT3 and ZNF341 were identified from 21 transcription factor candidates. STAT3 ranked first in HAND integrated cohort (n = 107, AUC = 0.759). STAT3 may function as an inflammatory mediator through JAK-STAT signaling. ZNF341 showed strongest transcriptional association with disease status (β = 5.09 in AD, β = 4.85 in HAND). The two-gene panel (FOXO3-ZNF341) achieved diagnostic accuracy in blood samples (AUC = 0.764, n = 329). This performance approaches clinical utility thresholds. Blood-based detection offers non-invasive diagnostic potential. Saturation analysis identified three molecules as optimal panel size. Marginal AUC gains declined below 0.02 beyond this threshold. FOXO3, STAT3, and ZNF341 showed stable selection frequency (97%, 65%, and 100%, respectively). PI3K-Akt and FoxO signaling pathways were enriched, which are known to regulate apoptosis and cell survival. Taken together, these computational findings indicate FOXO3 transcriptional regulatory activity in neurodegeneration. The three-molecule panel represents candidate blood-based diagnostic biomarkers. These candidate biomarkers warrant further investigation in independent clinical cohorts.

The SKN-1/Nrf transcription factor family is integral to metabolic homeostasis. There are three SKN-1 isoforms in Caenorhabditis elegans, each with different functions. One of these, SKN-1B, is expressed specifically in neurons and controls hermaphrodite behaviour in response to food. In a laboratory environment C. elegans hermaphrodites must allocate energy efficiently between exploratory food-seeking behaviour, reproduction, and survival, whereas males have to balance both food-seeking with mate-seeking exploratory behaviours. Here, we evaluate the role of SKN-1B in male behaviour and show that SKN-1B acts in a sexually dimorphic manner to control exploratory behaviour, mitochondrial morphology, and mitochondrial function. Moreover, we show that SKN-1B is expressed in a sexually dimorphic pattern, and that SKN-1B influences gene expression on a much broader scale in males compared to hermaphrodites. This analysis identified a neuronal signalling pathway, specifically in males between SKN-1B, the TGF-β ligand DAF-7 and the chemosensory regulator ODR-10, and that this pathway contributes to increased exploratory behaviour in skn-1b mutant males. Taken together our findings identify SKN-1B as a sex-specific neuronal switch to control food searching and mating behaviours. Sexual dimorphism is essential for optimizing survival and reproductive success and our findings establish SKN-1B as a regulator of sex-specific behavioural and metabolic traits. This work provides new insights into neuronal regulation of metabolism and behaviour, with implications for sex-specific physiological adaptations in other species.

<h4>Background</h4>Colorectal cancer (CRC) is one of the common malignant tumors of the gastrointestinal tract, encompassing both colon cancer and rectal cancer. This study explores the therapeutic potential of T. wilfordii in CRC through network pharmacology, molecular docking, and in vitro experiments.<h4>Methods</h4>Active components of T. wilfordii were screened using oral bioavailability (OB ≥ 30%) and drug-likeness (DL ≥ 0.18) criteria. Protein-protein interaction network analysis, gene ontology functional enrichment, and kyoto encyclopedia of genes and genomes pathway enrichment were performed to identify candidate targets and signaling pathways. Molecular docking and molecular dynamics simulations were used to predict compound-target binding modes and to assess the dynamic stability of selected docked complexes. In vitro experiments, including CCK-8 assay, EGFR kinase activity assay, EGF rescue assay, and Western blot analysis, were conducted to evaluate the anticancer activity of key components and the involvement of EGFR signaling in CRC cell lines (HT29 and HCT116).<h4>Results</h4>A total of 51 active compounds were identified from T. wilfordii, with 23 core components selected for further analysis. PPI network analysis identified TP53, AKT1, EGFR, STAT3, and mTOR as central candidate targets, and KEGG enrichment analysis highlighted cancer-related pathways including PI3K/Akt, Wnt/β-catenin, and mTOR. Molecular docking, interpreted with target-specific reference-ligand redocking benchmarks, prioritized several core components, including β-Sitosterol (Lei3), Tryptophenolide (Lei4), Tripterifordin (Lei8), Isoxanthohumol (Lei9), and Stigmasterol (Lei16), as compounds with favorable AutoDock Vina docking scores toward EGFR. MD simulations supported the relative stability of the docked EGFR-Lei4 complex under the simulation conditions. In vitro EGFR kinase activity assay showed that Lei4 directly inhibited recombinant EGFR kinase activity in a concentration-dependent manner, with an IC₅₀ value of 1.38 ± 0.12 μM. In cell-based assays, Lei4 inhibited HT29 and HCT116 cell proliferation in a dose-dependent manner, with IC₅₀ values of 27.98 ± 3.56 μM and 28.0 ± 3.6 μM, respectively. EGF partially reversed Lei4-induced proliferation inhibition, and Western blot analysis showed that Lei4 decreased the phosphorylation levels of EGFR, ERK1/2, and JUN without markedly altering total protein expression.<h4>Conclusion</h4>T. wilfordii may exert anti-CRC effects through a multi-component, multi-target, and multi-pathway mechanism. Tryptophenolide (Lei4) showed moderate but reproducible anti-CRC activity and directly inhibited EGFR kinase activity in vitro, supporting EGFR pathway inhibition as one mechanism contributing to its cellular effects. These findings provide a basis for further optimization and mechanistic evaluation of T. wilfordii -derived active compounds in CRC.

Myeloid sarcoma (MS) is a rare extramedullary tumor composed of immature myeloid cells that is most associated with acute myeloid leukemia (AML), whereas isolated bilateral breast involvement without bone marrow disease is exceptionally uncommon. We report the case of a 38-year-old woman who presented with bilateral breast masses, both classified as BI-RADS 5 on imaging. Ultrasound-guided core needle biopsies of both breast lesions established the diagnosis of myeloid sarcoma, with immunohistochemical positivity for MPO, CD34, CD56, and CD117. Peripheral blood and bone marrow examinations showed no evidence of AML, and FDG PET/CT confirmed isolated extramedullary disease, providing accurate staging and monitoring treatment response. The patient received AML-type induction chemotherapy followed by salvage FLAG-IDA chemotherapy for residual disease and consolidative radiotherapy, achieving complete metabolic remission that was maintained at 6-month follow-up. This case highlights the diagnostic challenges of isolated bilateral breast myeloid sarcoma and emphasizes that histopathological confirmation with immunohistochemistry, complemented by FDG PET/CT, is important for accurate diagnosis, staging, treatment assessment, and multidisciplinary management.

Chromatin structure is dynamic and regulated by many factors, including enzymes that chemically modify histones and DNA, chromatin remodeling complexes that physically manipulate nucleosomes and chromatin, and non-enzymatic proteins that bind to DNA or nucleosomes to create specialized regions in chromatin. This multifactorial regulation stems from the need for fine-tuned control, which is key in processes including DNA repair, replication, and gene expression. Linker histones are a family of proteins structurally distinct from the core histones that provide a poorly understood layer of regulation in chromatin. In this review, we introduce the basics of chromatin structure, what is known about how linker histones (H1s) bind to nucleosomes and influence chromatin, and how the individual domains within H1s contribute to these activities. We especially focus on recent studies describing canonical and alternative H1-nucleosome binding and their potential roles in chromatin.

Ultraconserved elements (UCEs) are among the most evolutionarily conserved DNA sequences in vertebrate genomes, yet the biological mechanisms underlying their extraordinary conservation remain poorly understood. Using the recently developed dedUCE database comprising 12,813 human UCEs, we performed a comprehensive genome-wide analysis of their distribution relative to protein-coding genes, transcription factor (TF) genes, and long noncoding RNA (lncRNA) genes. UCEs showed a highly non-random genomic organization, with approximately 40% occurring in clusters within 20 kb genomic intervals. Non-KRAB transcription factor genes exhibited a striking sevenfold enrichment of UCEs compared with random expectation, whereas KRAB zinc-finger genes displayed an approximately tenfold depletion. Beyond TFs, UCE-rich genes were predominantly involved in developmental regulation, chromatin remodeling, RNA processing, and embryonic neurogenesis, whereas similarly large UCE-poor genes primarily encoded membrane proteins, ion channels, and synaptic components required for mature neuronal function. UCEs also demonstrated strong positional bias, with approximately fourfold enrichment near the 3' ends of protein-coding genes but no comparable distribution pattern in lncRNAs. Although lncRNA genes showed only modest overall UCE enrichment, a small subset contained numerous UCEs. These findings demonstrate that UCEs preferentially associate with master developmental regulators rather than downstream neuronal effector genes, providing new insights into the functional organization and evolutionary conservation of the human genome.

<h4>Background</h4>Individuals with attention-deficit/hyperactivity disorder (ADHD) show an elevated incidence of non-small cell lung cancer (NSCLC), usually attributed to smoking. Innate immune activation and chronic inflammation are implicated in both, yet whether shared germline genetics include a component statistically independent of the measured current-smoking phenotype, and whether that liability has an innate immune dimension, remains unclear.<h4>Methods</h4>We applied genomic structural equation modelling to GWAS summary statistics to partition genetic covariance into indirect and conditional direct components with respect to measured current smoking. Among twelve psychiatric and personality traits, only ADHD survived FDR and served as the primary exposure; neuroticism was retained as a secondary exploratory indicator. Component statistics underwent gene-level and tissue-enrichment analyses. We estimated ADHD and NSCLC genetic correlations with inflammatory biomarkers, tested the NSCLC signal for innate-pathway enrichment, and examined <i>CLPTM1L</i> response to non-nicotine stress in lung adenocarcinoma cells.<h4>Results</h4>We found that <i>CLPTM1L</i>, <i>IREB2</i> and the chromosome 15q25 nicotinic-receptor cluster were prioritised within a component statistically independent of the measured current-smoking phenotype, corresponding to approximately 38% of the model-based shared genetic covariance, with lung and brain enrichment. Pathway and biomarker analyses suggested an innate immune and inflammatory dimension, but did not establish a mechanism. ADHD and NSCLC were each positively genetically correlated with C-reactive protein (ADHD rg=0.26, <i>P=</i>8.2×10^-¹³; NSCLC rg=0.13, <i>P</i> = 0.0074); additional inflammatory-trait comparisons were exploratory. The NSCLC signal showed nominal enrichment of innate pattern-recognition-receptor and NF-κB/antiviral pathways. In A549 cells, <i>CLPTM1L</i> protein increased under genotoxic and hypoxic stress, with immunofluorescence 3.4-fold and 2.3-fold above control.<h4>Conclusions</h4>An approximate model-based component of the ADHD-NSCLC genetic covariance was statistically independent of the measured current-smoking phenotype; pathway and biomarker analyses suggested, but did not establish, an innate immune and inflammatory dimension alongside the 15q25 cholinergic axis. <i>CLPTM1L</i> expression was responsive in a non-nicotine pathological cell state, without evidence of mediation or causality. These hypothesis-generating findings nominate innate-immune hypotheses for functional follow-up.

Ferroptosis arises when iron-dependent phospholipid peroxidation overwhelms the system xc--glutathione-GPX4 axis and parallel antioxidant defenses. Within tumors, however, the immune consequence of this death process depends on how iron and oxidized material move between malignant and immune compartments. Tumor-associated macrophages (TAMs) occupy this interface because they recycle iron, engulf dying cells and oxidized membranes, and modify the redox state of neighboring cells. These activities may confine injury to tumor cells, propagate lipid damage into immune cells, or protect malignant cells through vesicle cargo and antioxidant exchange. Ferroptotic death combines loss of viability with iron-dependent phospholipid peroxidation attenuated by an appropriate inhibitor, with genetic corroboration where feasible. Tumor-restricted ferroptosis can support antigen handling while macrophage and dendritic-cell functions remain intact. As oxidized material exceeds local clearance and antioxidant capacity, the same insult can impair CD8+ T cells and phagocytic macrophages and favor immune suppression. Three linked modules organize this process: iron-flux redistribution, lipid-hydroperoxide spectra and receptor sensing, and phagocytic clearance and antioxidant buffering. Iron flux identifies the first injured compartment, lipid species and receptor distribution shape the ensuing immune response, and clearance determines the duration and spread of injury. The framework thereby explains how TAM state, tumor niche, and treatment schedule redirect a common oxidative insult without proposing an additional ferroptosis execution pathway. Clinical translation will require ferroptosis to remain concentrated in the intended compartment while CD8+ T cells and homeostatic phagocytes retain function. Bulk iron, oxidative markers, and transcriptomic signatures provide complementary signals but cannot resolve the injured cell population.

Programmed death-ligand 1 (PD-L1) is a key mediator of tumor immune evasion, but the protein networks governing its post-translational regulation remain incompletely understood. Here, we used PhastID-based proximity labeling to map the PD-L1 proximal proteome and integrated these data with pan-cancer proteomics and immunohistochemical analysis of clinical tumor samples. We found that C-terminal-proximal proteins were enriched in protein degradation, ER-associated quality control, and immune-related pathways, whereas N-terminal-proximal proteins were mainly associated with protein localization and intracellular transport. Integrated analysis identified CAND1, TXN, and FBXO2 as candidate PD-L1 regulators. Knockdown of CAND1, TXN, or FBXO2 reduced PD-L1 protein expression in cancer cells. Mechanistically, CAND1 interacted with PD-L1 and was detected in a complex containing PD-L1 and FBXO22. CAND1 depletion promoted K48-linked ubiquitination and degradation of PD-L1, while deletion of the PD-L1 intracellular domain or mutation of K271 and K281 attenuated PD-L1 ubiquitination. Functionally, CAND1 knockdown enhanced T cell-mediated tumor cell killing, and elevated CAND1 expression was associated with an immunosuppressive tumor microenvironment. Together, our findings define the PD-L1 proximal proteomic landscape and identify CAND1-mediated regulation of PD-L1 stability as a potential mechanism of tumor immune escape.

Cardiovascular diseases (CVDs) are the leading cause of death and disability worldwide, and atherosclerosis (AS) is a major underlying pathology. This review systematically examines the interplay between inflammation and immunity in AS. Disease initiation involves endothelial injury, formation of oxidized low-density lipoprotein (ox-LDL), and innate immune responses, including monocyte and macrophage infiltration and dendritic cell (DC) activation. Macrophages polarize to a proinflammatory M1 phenotype, phagocytose lipids to form foam cells, and release inflammatory mediators such as interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α), thereby exacerbating plaque inflammation. DCs serve as a crucial link between innate and adaptive immunity by presenting antigens to CD4⁺ T cells. T helper 1 (Th1) cells facilitate inflammation through interferon-γ (IFN-γ), whereas regulatory T cells (Tregs) exert protective, anti-inflammatory effects. B cells have dual functions: B1 cells secrete immunoglobulin M (IgM) and provide protection, while B2 cells typically contribute to disease progression. In advanced lesions, immune cells cluster within the arterial wall to form arterial tertiary lymphoid organs (ATLOs), and the identification of neuro-immune-cardiovascular interfaces (NICIs) underscores the involvement of the nervous system. Chronic inflammation results in the thinning of the fibrous cap, thereby heightening the risk of plaque rupture and acute clinical events. Current therapies primarily target inflammatory pathways, including statins, colchicine, and proprotein convertase subtilisin/kexin type 9 inhibitors (PCSK9i), whereas future strategies may focus on directly targeting immune cells.

Zoonoses pose substantial global health risks, highlighting the need to better understand animal-to-human transmission. Reptiles are increasingly recognized as hosts of diverse pathogens, including numerous viruses, yet the diversity and prevalence of reptile pathogens, as well as their potential risk to humans, remain poorly understood. Here, we establish and characterize airway organoids derived from Python regius, providing an in vitro model to study reptile airway infection. Through de novo assembly of a Python regius reference genome, we characterize airway organoids at single-cell resolution, which suggests the presence of diverse cell populations including ionocytes, ciliated, secretory, goblet, endocrine, tuft, and basal cells. The organoids support productive infection with Ball Python Nidovirus (BPNV) and mount a robust epithelial antiviral response through the induction of interferon-stimulated genes, cytokines, and genes involved in chemical defense. As a proof-of-concept, treating organoids with antiviral drugs during infection reduces BPNV levels, highlighting the model's utility for drug testing. By providing a reductionist system of the serpentes airway, these organoids constitute a physiologically relevant in vitro model to study reptile viruses and host-pathogen interactions in their native host.

Heart failure (HF) affects 6.7 million people in the US and includes two major subtypes, HF with reduced ejection fraction (HFrEF) and HF with preserved ejection fraction (HFpEF), with distinct genetic architectures. We meta-analyze genome-wide association studies (GWAS) of 38,781 HFrEF cases, 38,163 HFpEF cases, and 526,135 controls across European, African, Hispanic, and Asian ancestries using the Million Veteran Program and Vanderbilt University DNA Databank (BioVU). We identify 46 genome-wide significant loci for HFrEF (9 novel) and 3 loci for HFpEF (1 novel). Four HFrEF loci are detected in African ancestry participants near CD36, SPI1, TRIM48, and SPNS3, with lead SNPs showing low risk-allele frequencies in European populations. In the all-cause HF meta-analysis (200,070 cases, 2,076,466 controls), we identify 136 loci (12 novel). Gene-based tests, tissue enrichment, transcriptome-wide association, and fine-mapping implicate vascular, metabolic, and TGF-β/Smad signaling pathways and nominate candidate causal genes, clarifying shared and subtype-specific risk across ancestries.

Amyotrophic lateral sclerosis (ALS) is a genetically and biologically heterogeneous neurodegenerative disease in which distinct pathogenic mechanisms operate across patients while overt molecular pathology is confined to only a subset of cells. Such features would act to dilute disease-associated transcriptomic signals and complicate the identification of reproducible molecular signatures across the growing number of ALS single-nucleus RNA sequencing (snRNA-seq) studies. Here, we systematically assessed cross-study reproducibility across four cortical ALS snRNA-seq datasets comprising 140 donors (87 ALS) and tested whether pathology-defined cell states improve detection of conserved molecular signatures. Cell-type annotations were harmonized prior to comparison of cell-type-specific pseudobulk differential expression using gene-level, pathway-level, gene-ranking and alternative polyadenylation analyses. We further examined nuclei exhibiting TDP-43 pathology, identified by expression of the STMN2 cryptic exon. Conventional ALS-versus-control analyses showed limited reproducibility, with minimal overlap of differentially expressed genes or enriched pathways, while fold-change patterns clustered predominantly by study rather than cell type or brain region. Nevertheless, gene-ranking analyses identified reproducible neuronal transcriptional programs, suggesting that biological signal is present but incompletely resolved by current cohort sizes. In contrast, STMN2 cryptic exon-positive nuclei showed substantially greater concordance, revealing robust TDP-43-associated signatures that partially overlapped independent models of TDP-43 dysfunction while also identifying motor cortex-specific changes, including reduced expression of the recently identified ALS risk gene UNC13C . Reproducible ALS-associated alternative polyadenylation changes were not detected, likely reflecting the higher dimensionality and sparsity of polyadenylation site analyses. Together, our findings demonstrate that pathology-defined cell states provide a more reproducible framework for studying ALS transcriptomic alterations than conventional case-control comparisons. We additionally provide an interactive browser to facilitate exploration and comparison of ALS snRNA-seq datasets.

Schizophrenia (SCZ) is a neurodevelopmental disorder characterized by heterogeneous symptoms and multifactorial etiologies. Medial ganglionic eminence (MGE) spheroids generated from first-episode schizophrenia (FES) patients revealed accelerated neurodevelopmental trajectories and enhanced hypoxia responses via single-cell transcriptomics. Notably, FES patient-derived MGE spheroids exhibited defective interneuron migration, disrupted synaptic ultrastructure, and diminished network synchronization. To establish causal links, the gestational hypoxia mouse model recapitulated key pathologies, including reduced progenitor proliferation, abbreviated cell cycles, mismatched interneuron subtypes, and schizophrenia-like behavioral deficits in offspring. Critically, maternal administration of N-acetylcysteine (NAC) restored redox homeostasis and rescued both cellular and behavioral phenotypes. Collectively, these results demonstrate that developmental redox disruption directly impairs GABAergic circuit assembly, while supporting targeted antioxidant pharmacotherapy during gestation as a translatable strategy to mitigate neurodevelopmental risk.

BEST4⁺ cells are a recently identified, functionally specialized intestinal epithelial cell population characterized through single-cell and spatial transcriptomic analyses in humans, pigs, rats, and other vertebrates. These cells characteristically express BEST4, OTOP2, CA7, and GUCY2C, and exhibit particularly high CFTR expression in the small intestine, supporting their roles in luminal pH sensing, fluid-electrolyte homeostasis, and mucus hydration. Emerging evidence from organoid and cross-species studies supports a predominant role for the NOTCH-SPIB signaling axis in driving BEST4⁺ cell differentiation, but their lineage identity and regulatory mechanisms remain incompletely resolved. This review focuses on intestinal epithelial BEST4⁺ cells as a critical cellular hub that connects ion transport physiology with the pathophysiology of secretory diarrhea. We summarize the molecular identity, regional distribution, and cross-species conservation of BEST4⁺ cells. We then evaluate their roles in luminal pH regulation, electrogenic fluid secretion, and mucus barrier integrity. We detail how bacterial enterotoxins activate the GC-C/cGMP/CFTR and cAMP/PKA/CFTR pathways in BEST4⁺ cells to drive pathological fluid hypersecretion, and discuss how viral infections may indirectly engage or amplify BEST4⁺ cell-associated ion-transport pathways. We also outline their relevance to viral diarrhea, inflammatory bowel disease, and cystic fibrosis-associated intestinal dysfunction. Finally, we assess established antidiarrheal approaches and investigational strategies that modulate BEST4⁺ cell-associated pathways, and emphasize the need for cell-type-specific validation in physiologically relevant in vivo models.

mRNA organization into clusters is observed in many cellular contexts, yet the features that govern this process in vivo remain poorly understood. Using super-resolution microscopy, single-mRNA imaging, and genetic perturbations, we investigated how mRNA concentration, the double-stranded RNA-binding protein Staufen, and intermolecular base-pairing driven by an RNA palindrome influence clustering of <i>oskar</i> mRNA in <i>Drosophila</i> embryos. We find that these factors collectively optimize <i>oskar</i> clustering by promoting its dimerization and subsequent oligomerization. Both processes depend on all three factors, although oligomerization is much more sensitive to their perturbation, indicating that the driving force for <i>oskar</i> oligomerization is partially distinct from that governing dimerization. Moreover, <i>oskar</i> palindrome is a potent driver of heterotypic mRNA clustering, further supporting its in vivo role in mediating intermolecular base pairing. Finally, computational analyses identified a subset of candidate mRNAs in the early embryo that are predicted to harbor <i>oskar</i>-like palindromes. Among these, <i>eIF3a</i> mRNA emerged as a potential candidate whose clustering may likewise be driven by intermolecular base pairing. These preliminary observations raise the possibility that mRNA clustering driven by palindrome-mediated intermolecular base pairing may be more widespread than previously appreciated and may represent an important mechanism for controlling mRNA spatial organization during <i>Drosophila</i> development.

Transposable elements (TEs) are a highly diverse group of selfish genomic elements, prevalent across the tree of life, whose uncontrolled propagation poses a threat to genome stability. Recent studies have explored the evolution of <i>Drosophila melanogaster</i> TEs, their coevolution with the host genome, and mechanisms that regulate their activity. However, little is known about their cross-species evolutionary patterns. Long terminal repeat (LTR) retrotransposons are the most active group of TEs in <i>Drosophila</i>. They are broadly separated into retroelements, which are active in the germline, and insect endogenous retroviruses that express in the gonadal soma. Somatic elements are hypothesized to infect the germline through their acquisition of virus-derived proteins such as Envelope and sORF2, thus multiplying through successive generations. In this study, we curated the sequences of LTR retrotransposons in 249 drosophilid genomes, allowing us to study their evolution across these species and highlight their varying degrees of conservation. Furthermore, we reveal multiple instances of Envelope protein loss or inactivation that suggest shifts in the expression pattern of these transposons, likely accompanied by adopting different transcriptional control mechanisms. We contrast this with the evolutionary history of sORF2, which we found to be much more stable. Lastly, we examine variations in transposon LTR regions responsible for transcriptional regulation and use predictive modeling to identify six transcription factors that may regulate their tissue-specific expression. Altogether, we reveal complex, interspecies evolutionary patterns of <i>Gypsy</i>-family LTR retrotransposons and highlight examples of their coevolution with their host genome.

Huntington's disease (HD) is a progressive neurodegenerative disorder with no approved therapies. Despite multiple clinical trials, huntingtin (HTT)-lowering strategies have yet to show meaningful clinical benefit. Both somatic expansion and toxic HTT species are key molecular drivers of HD, yet therapeutic strategies targeting these pathways have never been directly compared or evaluated in combination. Using therapeutic divalent siRNAs, we assessed the long-term impact of silencing MutS homolog 3 (MSH3), a critical regulator of somatic expansion, HTT, or both in Q111 HD mice (>110 CAGs), which develop robust expansion, mutant HTT inclusions, and transcriptional dysregulation by 12 months. Long-term MSH3 silencing blocked somatic expansion, reduced inclusions, and normalized gene expression. HTT silencing alone had a limited effect, whereas combined MSH3/HTT targeting synergistically eliminated inclusions and restored transcriptomic profiles. Parallel treatment in wild-type mice showed no toxicity, supporting the safety of long-term intervention. These findings position somatic expansion as a promising therapeutic target and demonstrate the potential of RNAi-based cosilencing of MSH3 and HTT as a disease-modifying strategy for HD.

The present work aims to determine whether supplementation of cysteine and ascorbic acid in rabbit semen extender can maintain post-thawing sperm physiochemical quality and farm fertility under ambient heat stress conditions, and to clarify the molecular mechanisms involved. Mature bucks (n = 15) were used to collect semen samples, which were pooled and divided into six portions, including the control (C0A0) that extended with Tris-Citric-Glucose (TCG) without any additives. The other extenders were prepared by supplementing TCG with 5 mM cysteine (C5A0); 10 mM cysteine (C10A0); 5 mM cysteine and 5 mM ascorbic (C5A5); 10 mM cysteine and 5 mM ascorbic (C10A5) and 5 mM ascorbic (C0A5). Physiochemical characteristics and transcript abundance of sperm viability and redox status genes were measured in post-thawed semen samples. Results revealed that antioxidant supplementation, especially C5A5 and C10A5, significantly improved post-thaw sperm quality, redox status, and transcript abundance compared to control. This enhanced biochemical profile reduced oxidative stress, subsequently increasing conception rates (ranging from 44.0% to 56.0% in treated groups vs. 40.0% in control) and litter sizes (5.58 - 5.92 in combined treatment groups vs. 4.44 in control). At the molecular regulation level, antioxidant transcripts (SOD1, CAT, PRDX6, TXN, and NRF2) were upregulated while endoplasmic reticulum stress genes (CHOP, XBP1 and ATF6) were downregulated in C5A5 and C10A5 compared with the control. Conclusively, supplementing rabbit semen extenders with cysteine (5 or 10 mM) combined with ascorbic acid (5 mM) synergistically enhance post-thaw sperm quality and in-vivo fertility under ambient heat stress conditions by maintaining sperm DNA and acrosome intactness through modulation of redox enzymes and gene networks regulating cellular death and defense against stress.

Familial erythrocytosis is a rare disorder most often linked to germline alterations affecting erythropoiesis and oxygen-sensing pathways. The <i>EGLN1</i> gene encodes prolyl hydroxylase domain-containing protein 2 (PHD2), a central regulator of the hypoxia-inducible factor (HIF) pathway that modulates erythropoietin (EPO) production. This report describes a mother and son with longstanding erythrocytosis, both harbouring a heterozygous <i>EGLN1</i> variant of uncertain significance (c.806T>C, p.Ile269Thr), in whom secondary causes and <i>JAK2</i>-mutated myeloproliferative neoplasms were excluded. Both individuals required serial phlebotomy for haematocrit control and biochemical as well as molecular testing supported congenital erythrocytosis. The <i>EGLN1</i> variant has been reported rarely and is supported by in-silico and functional data suggesting deleterious effects on PHD2 protein stability and function. Based on the aggregate evidence derived from a European cohort, this variant has previously been proposed to meet the criteria for pathogenic classification under the ACMG guidelines. This case adds clinical and functional evidence supporting ACMG/AMP-based classification of <i>EGLN1</i> c.806T>C (p.Ile269Thr) as likely pathogenic in familial erythrocytosis.

Stromal cell states are altered in active Crohn's disease (CD), but their origin and phenotypic stability are unknown. Using single-cell spatial transcriptomics, RNA sequencing and ATAC sequencing of ~2,500,000 cells, we map 18 distinct stromal cell states within their cellular and cytokine signaling environments in human full-thickness CD bowel. Inflammatory fibroblasts (IFs) reside in immune cell-rich mucosal ulcers and are induced through combinatorial cytokine exposure suppressing submucosal universal fibroblast programs. The IF state is stabilized through transcription factor (TF) activity of GLI3, TWIST1, ETV4, PRDM1 and RELB, and does not spontaneously revert; however, histone deacetylase inhibition destabilizes the IF state, preventing IF secretome-induced epithelial transmigration and activation of neutrophils. The IF open chromatin configuration is distinct from that of fibrotic contractile stroma, which populate adjoining immune-depleted submucosal fibrotic niches. These findings show that microenvironments in pathological tissue niches shape open chromatin configuration of stromal states that are amenable to modulation by epigenetic modifiers.

The hippocampus forms memories of our experiences in populations of coactive pyramidal neurons (PNs)^1-3. Fast-spiking parvalbumin-expressing inhibitory neurons (PV INs) in the dentate gyrus-CA3/CA2 circuit of the hippocampus precisely control PN activity through mossy fibre-dependent feedforward inhibition^4-11. PV INs coordinate experience-dependent changes in their intrinsic excitability, synaptic connectivity, physiology and plasticity properties^9,12-15-referred to here as experience-dependent PV IN plasticity-to regulate PN activity. PV IN impairments in early life, when neural circuitry is highly sensitive to experience, are thought to result in network hyperexcitability, seizures and impaired cognition, which are hallmarks of neurodevelopmental disorders (NDDs)^16-18. Here we designed an input-specific translatome screen to identify regulators of experience-dependent PV IN plasticity genes (XPGs) in the CA3/CA2 subregion of adult hippocampus. We demonstrate that a substantial proportion of upregulated candidate XPGs exhibit haploinsufficiency in autism spectrum disorder, epilepsies, bipolar disorder and schizophrenia, which suggests that there is impaired experience-dependent PV IN plasticity in NDDs. In proof-of-concept experiments, targeted upregulation of a candidate XPG, the homeobox gene Meis2 (ref. ¹⁹), in CA3/CA2 PV INs in an NDD risk mouse model in adulthood is sufficient to restore experience-dependent PV IN plasticity. Moreover, ensemble and sharp-wave ripple properties and cognition were improved, and seizures were suppressed. Thus, experience-dependent PV IN plasticity is a convergent mechanism for NDD risk genes that can be re-instated in adulthood to reverse developmental deficits in circuitry, network excitability and cognition.

<h4>Background</h4>Urine-derived stem cells (USCs) represent an accessible and non-invasive cell source with reported chondrogenic differentiation potential. However, the cellular heterogeneity and transcriptional dynamics underlying USC differentiation remain incompletely understood, limiting their translational interpretation.<h4>Methods</h4>We combined functional differentiation assays with single-cell RNA sequencing to characterize USC differentiation at both phenotypic and transcriptional levels. Chondrogenic and osteogenic differentiation were assessed using histological staining, quantitative PCR, and three-dimensional spheroid cultures. Single-cell transcriptomic analysis was performed on integrated datasets of undifferentiated and differentiated USCs, followed by pseudotime trajectory inference and mapping to a human cartilage reference atlas.<h4>Results</h4>Chondrogenic induction resulted in reproducible acquisition of cartilage-associated features, including glycosaminoglycan-rich extracellular matrix deposition, increased expression of SOX9, and formation of aggrecan-positive spheroids. In this donor, single-cell analysis mapped an inferred differentiation trajectory from proliferative states towards differentiated populations, although the fine-grained pseudotemporal ordering was sensitive to analytical choices and is therefore interpreted qualitatively. Along this inferred trajectory, we identified a candidate transient transcriptional state associated with elevated CDH1 expression and epithelial-like aggregation features. Probabilistic mapping to a human cartilage reference atlas indicated that overall mapping confidence was low (median prediction score 0.34) and that only a minority of cells showed confident transcriptional similarity (prediction score ≥ 0.5) to mature/articular cartilage-associated reference states (7.8% of all cells and 17.6% of chondrogenically induced cells). This confident similarity was concentrated in a few clusters at the differentiated end of the trajectory rather than representing the bulk of the culture, and label-transfer confidence was not equated with chondrocyte identity. Despite this enrichment, differentiated populations exhibited transcriptional heterogeneity, including subsets of cells associated with hypertrophic, fibrocartilage-like, and contractile gene programmes, indicating the presence of multiple differentiation trajectories.<h4>Conclusions</h4>This single-donor proof-of-concept study suggests that USC differentiation may involve a candidate transient, aggregation-associated transcriptional state accompanied by CDH1 expression and gives rise to heterogeneous lineage-associated outcomes, with only a minority of cells acquiring confident transcriptional similarity to mature cartilage. Because these observations derive from one donor, they should be interpreted as hypothesis-generating and require validation across independent donors before donor-independent or translational conclusions for cartilage regeneration can be drawn. These findings nonetheless provide a single-cell resolution framework for future multi-donor validation of USC differentiation and its inherent transcriptional heterogeneity.

Singapore grouper iridovirus (SGIV) is a major viral pathogen threatening grouper aquaculture. The lack of specific antiviral drugs underscores the urgent need to develop safe and effective control strategies. This study demonstrates that tannic acid (TA) exhibits significant anti-SGIV activity in vitro. In grouper spleen (GS) cells, TA inhibited SGIV replication in a concentration-dependent manner. Time-of-addition assays confirmed its antiviral efficacy when applied either before or after SGIV infection. Mechanistically, TA directly interfered with SGIV particle infectivity, viral adsorption, entry and intracellular replication. Network pharmacology analysis suggested TA's targets are associated with host cellular antioxidant pathways, among which Peroxiredoxin 6 (PRDX6) was identified as a potential target of TA. Further experiments confirmed that TA upregulated the Nrf2 antioxidant pathway and suppressed the expression of pro-inflammatory cytokines (IL-1β, IL-8). Notably, TA enhanced the expression of PRDX6, and overexpression of PRDX6 significantly inhibited SGIV replication, indicating that PRDX6 contributes to the antiviral effect of TA. In vivo, TA treatment not only restored PRDX6 expression in infected groupers but also significantly reduced viral load in liver and spleen following SGIV infection. These findings demonstrate that TA inhibits SGIV through direct viral interference and PRDX6-mediated antioxidant modulation, highlighting its potential as a natural therapeutic agent against SGIV.

Left ventricular noncompaction (LVNC) is a cardiomyopathy characterized by excessive trabeculation and deep intertrabecular recesses, yet its molecular mechanisms remain poorly understood. Here, we identify Bcl11b as a novel regulator of cardiomyocyte (CM) growth and ventricular wall maturation. CM-specific deletion of <i>Bcl11b</i> in mice recapitulates key LVNC features, including increased noncompacted-to-compacted ratio, impaired compact layer expansion, reduced CM proliferation and size, and systolic dysfunction. Mechanistically, Bcl11b deficiency leads to marked upregulation of <i>Pou3f2</i>, a transcriptional repressor that further suppresses <i>Titin</i> (<i>TTN</i>) expression. Loss of <i>Bcl11b</i> disrupts sarcomere integrity and reduces TTN protein levels, while forced <i>Pou3f2</i> overexpression similarly represses TTN. Notably, heterozygous loss of <i>Pou3f2</i> rescues the LVNC phenotype in <i>Bcl11b</i>-deficient hearts, restoring CM growth and <i>TTN</i> expression. Our findings identify a critical relationship among Bcl11b, Pou3f2 and TTN that controls CM proliferation and hypertrophic maturation during cardiac development. Dysregulation of this regulatory network impairs ventricular compaction and contributes to the pathogenesis of LVNC, providing new mechanistic insights into disease pathogenesis and highlighting potential therapeutic targets.

Autoimmune encephalitis associated with neuronal autoantibodies is increasingly recognized in veterinary medicine. In cats, previously reported antibodies have primarily targeted components of the voltage-gated potassium channel complex, such as leucine-rich glioma-inactivated 1 (LGI1) and contactin-associated protein-like 2 (CASPR2). Anti-metabotropic glutamate receptor 1 (mGluR1) antibodies are well described in human medicine but have not previously been reported in cats. A 5.5-month-old female domestic shorthair cat was presented for recurrent epileptic seizures and episodic behavioral abnormalities, including pica. Neurological examination revealed mild pelvic limb ataxia. Based on the history of epileptic seizures and behavioral abnormalities, the neuroanatomical localization was consistent with the forebrain. Magnetic Resonance Imaging (MRI) of the brain and cerebrospinal fluid (CSF) analysis were unremarkable. Infectious disease testing from CSF, including polymerase chain reaction (PCR) assays for Feline Coronavirus, <i>Toxoplasma gondii</i>, Feline Herpesvirus, and Rustrela virus, was negative. Neural antibody testing using tissue-based and cell-based assays identified an elevated serum mGluR1 antibody titer (1:80; reference <1:20), whereas cerebrospinal fluid and tissue-based assays were negative. Testing for other neuronal autoantibodies, including LGI1 and CASPR2, was negative. Following optimization of antiseizure therapy, the cat showed clinical improvement, accompanied by a decrease in the serum mGluR1 antibody titer. This report describes the first detection of mGluR1 antibodies in a cat with neurological disease and suggests a potential association between mGluR1 autoimmunity and epileptic seizures and episodic behavioral abnormalities in a cat.

<h4>Background</h4>Extracellular vesicles (EVs) are important mediators of host-microorganism communication at epithelial surfaces. However, their role in shaping corneal epithelial responses to ocular-associated bacteria remains poorly understood. Here, we investigated the species-specific effects of <i>Pseudomonas aeruginosa</i> and <i>Staphylococcus epidermidis</i> on human corneal epithelial cells, focusing on bacterial extracellular vesicles (BEVs), direct microbial contact, and epithelial exosomal remodeling.<h4>Methods</h4>Human corneal epithelial cells were exposed to BEVs or co-cultured with <i>P. aeruginosa</i> or <i>S. epidermidis</i>. Transcriptomic, proteomic, and extracellular vesicle RNA analyses were performed together with functional assays evaluating epithelial metabolic activity, motility, and apoptosis.<h4>Results</h4>BEVs from <i>P. aeruginosa</i> induced a strong pro-inflammatory epithelial response associated with IL-17, TNF, and NF-κB signaling, extracellular matrix remodeling, and increased cell motility. Direct bacterial contact further amplified these effects, triggering extensive transcriptional reprogramming and remodeling of epithelial exosomal cargo, including enrichment of proteasome-associated proteins and apoptosis-related microRNAs. Functional apoptosis assays confirmed that exosomes released following <i>P. aeruginosa</i> exposure acquired a modest but significant pro-apoptotic activity. In contrast, <i>S. epidermidis</i> induced a substantially milder transcriptional response characterized by limited differential gene expression, preferential detection of regulatory non-coding RNAs, and distinct exosomal remodeling associated with cell cycle and signaling pathways. Notably, responses induced by BEVs and direct bacterial contact showed limited overlap, indicating complementary mechanisms of epithelial regulation.<h4>Conclusions</h4>Together, these findings demonstrate that BEVs and direct microbial contact act as complementary and species-specific drivers of corneal epithelial reprogramming. Our results further support a model in which BEVs function as early signaling mediators, whereas epithelial-derived exosomes contribute to the propagation and modulation of these responses across the corneal epithelium.

Following primary spinal cord injury (SCI), mitochondrial dysfunction induces oxidative stress, which in turn exacerbates secondary injury, including neuronal loss and the formation of an inhibitory microenvironment. To intervene in this pathological cascade, we constructed a hierarchically targeted biomimetic nanomedicine (MM@DHM) designed for sequential delivery to the lesion site and subsequently to mitochondria. Macrophage membrane coating mediates first-stage targeting to the injured spinal cord, while triphenylphosphonium (TPP) modification directs second-stage accumulation within mitochondria of lesional cells, enabling precise delivery of the SIRT3 agonist dihydromyricetin (DHM) to its site of action. Mechanistically, MM@DHM activates SIRT3, promotes SOD2 deacetylation, and enhances Pink1-Parkin-mediated mitophagy, consequently alleviating oxidative stress and restoring mitochondrial homeostasis. These integrated cellular effects confer robust neuroprotection, attenuate neuroinflammation, and improve functional recovery in a mouse model of SCI. Collectively, this work demonstrates that mitochondrial targeting represents a promising therapeutic strategy for ameliorating oxidative damage and mitochondrial dysfunction in SCI, and underscores the potential of cascade-targeted nanoplatforms for central nervous system repair.

To elucidate the molecular characteristics of synergistic interactions across the clinical stages of coronary heart disease (CHD)-specifically stable angina pectoris (SAP), unstable angina pectoris (UAP), and acute myocardial infarction (AMI)-through integrated metabolomic and proteomic analyses. Based on a cohort including SAP, UAP, AMI, and healthy controls, metabolomic and proteomic analyses were performed to identify differentially expressed molecules, followed by KEGG pathway enrichment analysis. Pathways co-enriched across both omics platforms were selected to construct metabolite-protein interaction networks. The number of pathways co-enriched in both metabolomic and proteomic analyses increased markedly with disease stage. Only two pathways (histidine metabolism and arginine and proline metabolism) were identified in the SAP stage; this number increased to five in the UAP stage (including ferroptosis and efferocytosis) and expanded to 25 in the AMI stage, encompassing three major functional modules: immune inflammation, metabolic reprogramming, and cell signaling. The core network exhibited a stepwise increase in connectivity, shifting from a sparse structure in the SAP stage to a highly interconnected architecture in the AMI stage, with L-glutamate and KNG1 identified as the central hubs in this cross-sectional network. In addition, CNDP1 exhibited a stage-dependent functional transition, shifting from downregulation in SAP to upregulation in AMI. In this cross-sectional analysis, metabolic dysregulation and immune activation exhibited stepwise increases in interconnectivity across the SAP, UAP, and AMI groups, with the most extensive crosstalk observed in the AMI stage-a network configuration consistent with a tightly coupled "molecular storm". These findings provide novel insights into stage-associated molecular signatures of CHD and identify candidate hub molecules for stage-oriented therapeutic investigation.

The CRISPR-Cas13 system is a programmable gene knockdown tool widely used in basic and clinical research. Meanwhile, RNA-targeting by Cas13 exhibits collateral activity, i.e., cleavage of non-target RNAs, raising serious concerns. Accumulating evidence suggests the collateral activity comes from high expression levels of the Cas13 system. Therefore, controlled expression of the Cas13 system using viral vectors could solve the problem. Adenovirus vectors are efficient gene delivery vehicles and commonly used for clinical therapy. Here, we generated adenovirus vectors carrying a CRISPR-Cas13 system using CasRx (Ad-CasRx). Ad-CasRx efficiently knocked down the on-target reporter with suppressed collateral activity in cell lines, while plasmid transfection-mediated delivery exhibited strong collateral activity. Moreover, Ad-CasRx efficiently knocked down <i>Pcsk9</i> in cultured murine hepatic cells without suppressing abundant endogenous RNAs, suggesting that collateral activity was largely suppressed when targeting endogenous genes with Ad-CasRx. Finally, we targeted hepatic <i>Pcsk9</i> in mice by intravenous administration of Ad-CasRx. <i>Pcsk9</i> mRNA and serum total cholesterol levels were reduced without affecting the expression of major genes related to cholesterol metabolism and hepatic function. Serum ALT levels were not elevated. Overall, controlled delivery of Ad-CasRx enabled <i>in vivo</i> gene knockdown without evident side effects from collateral activity or Cas13 expression itself in liver.

γδ T cells represent a promising avenue for cancer immunotherapy. The Vγ9Vδ2 T-cell receptor (TCR), which is expressed by the predominant subset of γδ T cells, responds to phosphoantigen (pAg)-engaged butyrophilins (BTNs) on various cancer cells. However, the molecular mechanism underlying the pAg-mediated activation of Vγ9Vδ2 TCRs remains a subject of debate. Here, we employed an integrative approach to elucidate the mechanism of pAg reactivity in Vγ9Vδ2 T cells. Our results demonstrate that BTNs form higher-order oligomers in the absence of pAg. Upon pAg binding, these higher-order oligomers dissociate into separate tetramers, enabling Vγ9Vδ2 TCR engagement. This pAg-induced dissociation of higher-order BTN oligomers is critical for pAg-mediated activation of γδ T cells. Our findings reveal a mechanism of BTN higher-order oligomer dissociation-driven pAg sensing, providing valuable insight for future immunotherapeutic strategies.

Zinc (Zn) deficiency affects approximately 1 billion people worldwide with severe consequences for their health, including increased intestinal infections, inflammation, and diarrhea. Accordingly, the intestinal defense barrier is compromised, leading to epithelial destruction and alteration of mucus. However, the processes and the extent to which Zn deficiency affects mucin synthesis in intestinal goblet cells (GCs) remain poorly understood. To this end, we investigated the impact of Zn deficiency on mucin expression and glycosylation in the human GC model HT-29-MTX. Zn deprivation altered the GC transcriptome, affecting genes involved in Zn transport, mucin synthesis and glycosylation. Accordingly, mucus composition was changed in Zn-deficient GCs, significantly increasing MUC2 and MUC17 on the mRNA and protein level. Several Zn transporters, mostly those associated with the early secretory pathway (ESP), were dysregulated, indicating an adaptive response of cellular Zn homeostasis. Additionally, free Zn was markedly reduced in the ESP, a critical location for glycosylation. Zn deficit substantially changed mucin glycosylation, characterized by an increase in sialylation and a strong decrease in complex N-glycans. All these changes involved widespread dysregulation of glycosyltransferase expression, including an increase in COSMC, a Zn-binding chaperone essential for the core 1 O-glycan formation. Collectively, our in vitro findings demonstrate that Zn is a critical regulator of mucin production and glycosylation in GCs. Zn deficiency might weaken the protective and functional qualities of intestinal mucus, increasing the risk of infections and potentially disrupting host-microbiome interactions.

Co-evolution between viruses and autophagy has led to the emergence of viral strategies that manipulate host endoplasmic reticulum (ER) homeostasis, ultimately promoting viral replication. ER turnover is achieved through selective autophagy, also referred to as ER-phagy, which is regulated by the RETREG1/FAM134B (reticulophagy regulator 1) family of reticulon proteins. Nevertheless, how viruses target RETREG1, a receptor for ER-phagy, remains largely unclear. In this study, we demonstrate that infection with Senecavirus A (SVA), an emerging picornavirus, triggers the cleavage of RETREG1, which functions as a negative regulator of viral replication. By screening viral proteins, we identified the SVA 3C protease (3C[pro]) as the executor of this cleavage event. Detailed mapping revealed that residues Q428, E430, and G431 of RETREG1 are involved in its cleavage by the 3C[pro], and the resulting two fragments fail to suppress viral replication. Furthermore, proteolytic cleavage of RETREG1 by 3C[pro] impairs its ability to relieve ER stress and mediate ITPR1 degradation via RETREG1-dependent ER-phagy. This disruption leads to increased ER calcium (Ca²⁺) release and subsequent activation of autophagy through the CAMKK2-PRKAA2-MTOR axis, which ultimately facilitates SVA replication. Taken together, these findings indicate that SVA antagonizes the antiviral function of RETREG1-mediated ER-phagy via its 3C[pro], highlighting RETREG1 as a potential therapeutic target for combating SVA infection.<b>Abbreviations:</b> 2-APB: 2-aminoethyl diphenylborinate; PRKAA2/AMPK: protein kinase AMP-activated catalytic subunit alpha 2; ATL3: atlastin GTPase 3; BHK-21: baby hamster kidney-21; CAMKK2: calcium/calmodulin dependent proteinkinase kinase2; CCPG1: cell cycle progression 1; CKAP4/CLIMP63: cytoskeleton associated protein 4; co-IP: co-immunoprecipitation; CQ: chloroquine; DAPI: 4',6-diamidino-2-phenylindole; DM: double mutant; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; eGFP: enhanced green fluorescent protein; ER: endoplasmic reticulum; GFP: green fluorescent protein; HSPA5/GRP78/BiP: heat shock protein family A (Hsp70) member 5; HA: hemagglutinin; HDAC4: histone deacetylase 4; HEK-293T: human embryonic kidney 293T; hpi: hours post-infection; IFA: indirect immunofluorescence assay; ITPR1/IP3R1: inositol 1,4,5-trisphosphate receptor type 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; LIR: LC3-interacting region; mCherry: monomeric cherry; MTOR: mechanistic target of rapamycin kinase; REEP5: receptor accessory protein 5; RETREG1/FAM134B: reticulophagy regulator 1; RTN3: reticulon 3; SD: standard deviation; SEC61B: SEC61 translocon subunit beta; SEC62: SEC62 preprotein translocation factor; SERP1/RAMP4: stress associated endoplasmic reticulum protein 1; siRNA: small interfering RNA; SQSTM1/p62: sequestosome 1; ST: swine testis; SVA: Senecavirus A; TEM: transmission electron microscopy; TEX264: testis expressed 264, ER-phagy receptor; Tm: tunicamycin; U2OS: human osteosarcoma epithelial cells; UV: ultraviolet; ZVAD-FMK: benzyloxycarbonyl-Val-Ala-Asp(OMe)-fluoromethylketone; μg: microgram; μm: micrometer; μM: micromole.

<h4>Background and aims</h4>Hepatitis E virus (HEV) infection is a significant concern for solid organ transplant (SOT) recipients. However, the extent of this disease among recipients of different organs remains unclear.<h4>Methods</h4>This retrospective cohort study reviewed 63 adult SOT patients with PCR-confirmed HEV infection, including liver, kidney, heart, and lung transplant recipients.<h4>Results</h4>Chronic HEV infection (viral persistence beyond three months) was observed in 64% of infected patients, with a significantly higher occurrence in thoracic organ recipients compared to abdominal organ recipients. Ribavirin therapy, started in 40 patients with chronic infection, resulted in a sustained virological response in 78%. However, thoracic organ recipients exhibited notably lower clearance rates (55%) than abdominal organ recipients (91%). The use of tacrolimus, cyclosporine A, mycophenolate mofetil, azathioprine, or steroids was not linked to the development or eventual clearance of chronic infection. Nonetheless, 4 out of 25 patients (16%) receiving everolimus cleared the infection. spontaneously, compared to 20 of 39 patients (51%) on regimens without everolimus (p = 0.007). Low-dose maintenance ribavirin therapy proved effective in stabilizing liver function and, in some cases, achieving viral clearance. Despite treatment, four patients with chronic HEV infection died from cirrhosis.<h4>Conclusion</h4>This study emphasizes the need for customized treatment Strategies for HEV infection in SOT recipients, highlighting the limitations of serology, the variable response depending on transplant type, and the potential role of long-term ribavirin therapy.

Breast cancer remains a major cause of morbidity and mortality in women, with around 2.3 million new cases and 670,000 deaths worldwide in 2022. Daidzin, a soy isoflavone glycoside from Glycine max, is a candidate bioactive scaffold, but its breast cancer-relevant mechanisms remain poorly defined. This study used an integrated in silico strategy combining network pharmacology and molecular modeling to prioritize daidzin targets and validate key interactions, with sirtinol as a reference compound. Target prediction identified 101 putative daidzin targets, and intersection with breast cancer-associated genes yielded 97 common targets. Protein-protein interaction analysis highlighted hub genes including ALB, TNF, MMP9, CASP3, SRC, ITGB1, MMP2, ESR1, IL2, and HSP90AA1. Enrichment analyses suggested convergence on extracellular/vesicle-related functions, metallopeptidase activity, and pathway modules spanning metabolism, inflammation, endocrine signaling, and cancer circuitry. Docking against ten hub proteins produced binding energies from -6.00 to -11.49 kcal/mol, with the strongest affinity for MMP9 (6ESM; -11.49 kcal/mol), exceeding B9Z (-10.54 kcal/mol) and sirtinol (-10.59 kcal/mol). Molecular dynamics simulations indicated stable complexes, and Molecular Mechanics Generalized Born Surface Area (MMGBSA) supported stronger binding for daidzin-MMP9 (-46.86 ± 3.83 kcal/mol) than sirtinol-MMP9 (-14.12 ± 8.99 kcal/mol). Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) prediction indicated favorable safety-related flags for daidzin, although lower predicted intestinal absorption and Caco2 permeability than sirtinol suggest potential exposure-related limitations. Density Functional Theory (DFT) analysis supported comparatively greater electronic stability. Collectively, the results prioritize a daidzin-MMP9 axis for experimental validation.

Macrophages play critical roles in tumorigenesis and progression; however, their functions in renal cell carcinoma (RCC) remain insufficiently characterized. In this study, we leveraged multiple perspectives, including bulk transcriptomics, single-cell RNA sequencing (scRNA-seq), and spatial transcriptomics, to conduct an integrated analysis of various databases. We identified two macrophage-associated gene signatures, SLC11A1 and IFI30, and established a classifier based on these genes that correlates with different RCC prognoses and molecular patterns. This classifier significantly predicts adverse outcomes for RCC patients and demonstrates marked differences in drug sensitivity analysis and immune infiltration. Furthermore, we conducted an in-depth analysis at the scRNA-seq and spatial transcriptomics levels to characterize the pseudotime trajectory, metabolism, and communication of macrophages expressing SLC11A1 or IFI30. We also validated the expression and functional impact of these two genes in tumor cell lines through clinical samples and in vitro experiments. This study emphasizes the significant association between macrophages and the diverse clinical features and molecular landscapes of RCC. Evaluating the characteristics of macrophages in RCC enhances our understanding of the tumor microenvironment and paves new avenues for targeted therapeutic strategies for RCC.

Although immune checkpoint blockade has improved systemic therapy for hepatocellular carcinoma (HCC), durable benefit is limited by primary resistance, poor tumor penetration of antibodies, and an immunosuppressive tumor microenvironment. We identified integrin β5 (ITGB5) as an oncogenic and immune-associated target in HCC and developed an ITGB5-directed nanobody. Integrative analyses of TCGA/ICGC/TIMER2.0/Human Protein Atlas datasets, tissue microarrays, and functional assays showed that ITGB5 is upregulated in HCC and correlates with poor prognosis, higher tumor grade, increased immunosuppressive macrophage infiltration, reduced CD8+ T-cell abundance, and predicted resistance to sorafenib, oxaliplatin, and axitinib. Gain- and loss-of-function studies demonstrated that ITGB5 promotes proliferation, clonogenicity, migration/invasion, cell-cycle progression, and tumor growth while suppressing apoptosis, with transcriptomic signatures implicating extracellular matrix-receptor interaction, cytokine signaling, TNF/NF-κB, MAPK, and TGF-β pathways. From a yeast-display library we isolated AntiITGB5-Nb#2, a high-affinity nanobody that recognizes human and murine ITGB5, validated by flow cytometry, immunofluorescence, molecular docking, and surface plasmon resonance. AntiITGB5-Nb#2 inhibited growth and motility of ITGB5-high HCC cells and suppressed tumor progression in subcutaneous and orthotopic models, including an immunocompetent murine HCC model, without overt toxicity. Single-cell RNA sequencing revealed tumor microenvironment remodeling characterized by enhanced cytotoxic immune infiltration and reduced immunosuppressive signaling. These results establish ITGB5 as a prognostic, therapeutically actionable target in HCC and support AntiITGB5-Nb#2 as a nanobody-based strategy to complement current therapies.

Attention-Deficit/Hyperactivity Disorder (ADHD) is a highly heritable neurodevelopmental disorder; however, its genetic architecture remains poorly explored in Indigenous populations. This study aimed to analyze and characterize genetic variation in 11 genes (ADGRL3, CDH8, DCC, DUSP6, FOXP1, FOXP2, MEF2C, PCDH7, SEMA6D, SORCS3, and ST3GAL3) previously implicated in ADHD, in an indigenous sample, comparing them with reference populations from the 1000 Genomes Project. Exome data from 64 individuals representing 12 Indigenous groups from the Brazilian Amazon were analyzed. Among the identified, 99 met the inclusion criteria. Four previously unreported variants in the developed reference datasets were identified in ADGRL3, DCC, and FOXP2. Significant differences in allele frequencies were observed for 56 variants compared with continental populations. Multidimensional scaling analysis indicated genetic differentiation of the Indigenous group in relation to other populations. This study highlights the distinct genetic profile of Amazonian Indigenous populations, likely shaped by demographic and evolutionary processes such as genetic drift and founder effects. The identification of exclusive variants and marked allele frequency differences reinforces the importance of including historically underrepresented populations in genomic studies related to ADHD and neurodevelopment, contributing to a broader understanding of human genetic diversity.

Aging is characterized by a decline in function of intestinal stem cells (ISCs), but the extent to which this is shaped by systemic factors is unclear. Here we show that the ISC aging phenotype can be propagated from old to young mice utilizing heterochronic parabiosis, and implicate a role for inflammation in these effects, as anti-inflammatory drugs, including TNF antibodies, restored function. Parabiotic rescue experiments demonstrate that TNFR1 knockout protected young ISCs from the old environment. In young organoids, TNF downregulated crypt budding, while impairing mitochondrial pathways and fatty acid oxidation (FAO). However, aged ISC function was enhanced by boosting mitochondrial fusion, whereas FAO in aged crypts was improved by countering inflammation with salicylate treatment. Thus, these data identify the old environment through the progeronic factor TNF, as a driver of ISC aging phenotypes through intestinal epithelial cell TNF receptor 1 signaling to downregulate FAO, proliferation and regenerative capacity in these cells.

The clinical relevance of mitochondrial RNA modification (MRM) in colorectal cancer (CRC), particularly its value for prognostic stratification, has not been fully defined. We integrated bulk transcriptomic profiles, machine learning-based model screening, single-cell analysis, and experimental validation to identify MRM score-associated prognostic genes and construct a CRC risk model. Seven CRC-related prognostic genes were selected: SPARCL1, MGP, PRELP, PALMD, TNS1, ARHGEF25, and PTGIS. These genes were incorporated into a risk signature with favorable prognostic performance, as supported by nomogram-based assessment. Gene Set Enrichment Analysis indicated that cytokine-related processes may participate in CRC progression. TNS1 showed the strongest positive association with natural killer cells (cor = 0.784, P < 0.05) and the strongest inverse association with type 17 T helper cells (cor = -0.279, P < 0.05). Database-based screening predicted 113 candidate compounds targeting CRC. Single-cell analysis further highlighted smooth muscle cells, epithelial cells, endothelial cells, T cells, and B cells as major cellular populations of interest. SPARCL1, MGP, PRELP, and PALMD increased during both early and late B cell maturation, whereas TNS1 and ARHGEF25 were highly expressed across broader cellular contexts. In conclusion, SPARCL1, MGP, PRELP, PALMD, TNS1, ARHGEF25, and PTGIS may represent MRM score-associated prognostic markers in CRC and require further study.

Type 1 interferon-alpha gene expression signatures have long served as surrogate markers of pathway activity in systemic lupus erythematosus, but recent ultrasensitive assays now allow direct quantification of circulating interferon-alpha. In this cross-sectional study of 252 patients with systemic lupus erythematosus, serum interferon-alpha was measured by single molecule array, and 51 interferon scores were derived from 72 transcripts analyzed by Nanostring. Both serum interferon-alpha and interferon scores showed only modest associations with disease features, but serum interferon-alpha correlated more strongly with disease activity than most interferon scores and better discriminated remission and low disease activity states. These findings indicate that direct measurement of circulating interferon-alpha may provide clinically useful information and could be at least comparable to, and in some respects more informative than, interferon signatures for assessing disease status.

<h4>Introduction</h4>Chronic inflammation has long been associated with cancer initiation, yet the mechanisms linking sustained immune activation to an immune-permissive tumor microenvironment remain incompletely defined. Prevailing explanations such as immune exhaustion (IEX) or free radical mediated tissue damage, fail to account for the active state of immune tolerance, a process driven by potent negative feedback loops that systematically suppress host effector responses.<h4>Methods</h4>To address this gap, we developed an <i>in vitro</i> model of macrophage tolerance driven by sustained Toll-like receptor 4 (TLR4) activation using microbial-associated molecular patterns (MAMPs). This system captures the full kinetic progression of the immune response, tracking macrophages from a resting baseline, through acute activation at 24 hours, to a chronic tolerant endpoint at 7-11 days. Methodologically, cells were maintained under a continuous media exchange (+/- <i>E. coli</i> O111:B4 LPS) featuring high glucose and an elevated volume-to-cell ratio. This setup effectively eliminates autocrine interference and toxic byproducts, successfully isolating the direct consequences of sustained TLR4 signaling across extended durations.<h4>Results</h4>Whole-transcriptome sequencing, validated by RT-PCR and select protein immunoblots, revealed that both "exhaustion" and "tolerance" are mischaracterized. Rather than a passive exhaustion state or a simple trajectory of diminishing returns, the resting-acute-chronic continuum drives a potent, active negative-feedback mechanism across an eight-phase bidirectional trajectory. By days 7-11, macrophages shifted to a TAM-like signature, overexpressing immune checkpoints (PD-L1/MSN, TIM-3, SPP1, CD73, CD44, LILRs) and regulatory suppressive networks (SOCS/JAK/STAT, IL-10, CCL2/7/12, CXCL2), while downregulating classical (H2-D1/K1) and non-classical (H2-Q/T) MHC-I antigen-presenting genes. These alterations coincided with the profound loss of interferon-stimulated genes (ISGs) including the IFIT family, Ly6e, Irf7, Rsad2/Viperin, and the Oas gene family, fundamentally crippling the machinery required for antiviral and antitumor immune surveillance. Moreover, this chronic stage drove the upregulation of degradative proteases (cathepsins, Adam8, S100a8, Klk9, carboxypeptidase D), integrins/adhesion molecules (Itga5, Marcks, Msr1/CD204, Alcam), iron-storage transcripts, lipid translocases (Cd36), and fatty acid-binding proteins. Concurrently, macrophages upregulated Nos2/Cox2 alongside the metabolic collapse of mitochondrial OXPHOS genes and Acod1 (itaconate). Uniquely, this negative feedback loop coincided with a sustained, massive surge in a cluster of poorly characterized small proline-rich proteins (SPRRs), specifically Sprr2b, 2e, 2d, 2f, 2g, 2h, 2i, 2j, and 2k.<h4>Discussion</h4>Overall, these results indicate that chronic inflammatory signaling can ultimately trigger a profound coordinated negative-feedback program consistent with a reduced immune recognition and defense pathway signatures. Ultimately, this study provides a reproducible <i>in vitro</i> macrophage model to investigate immune suppression. It offers deeper insights into how chronic inflammation impairs host defenses against viral and tumor cells.

<h4>Background</h4>Gliomas show intertumoral and intratumoral heterogeneity, and isocitrate dehydrogenase (IDH) status is linked to biological behavior and clinical aggressiveness. Evidence suggests glioma progression depends on reciprocal crosstalk between glioma stem-like tumor cells (GSTCs) and the tumor microenvironment, where immune and vascular remodeling promote plasticity, invasion, and immune evasion. However, GSTC state architecture across IDH backgrounds and its links to vascular-immune cues remain unclear. We aimed to define IDH-associated GSTC states and their functional and regulatory features.<h4>Methods</h4>Single-cell RNA-sequencing data from 33 glioma patients (GSE278456) were analyzed using Seurat integration, clustering, differential expression analysis, and inferCNV-assisted malignant cell identification. Reclustered GSTCs were assessed by Gene Ontology (GO)/Hallmark enrichment, Area Under the Curve-based Cell-wise Gene Set Enrichment Analysis (AUCell), CytoTRACE, Monocle, Slingshot, CellChat, and pySCENIC to characterize states, developmental trajectories, cell-cell communication, and regulatory networks. After CEBPD silencing in U251 and LN229 cells, quantitative real-time PCR (qRT-PCR), Cell Counting Kit-8 (CCK-8), colony formation, Transwell migration, and apoptosis assays were performed.<h4>Results</h4>Six cell populations and five GSTC subgroups were identified. A VIM+ GSTC state (C0), enriched in IDH-wild-type tumors, highly expressed CHI3L1, VIM, LGALS3, VEGFA, and SEC61G. Compared with other states, C0 showed stronger angiogenesis, hypoxia, IL6/JAK/STAT3 signaling, and epithelial-mesenchymal transition-related activities, with enrichment of oxidative phosphorylation, focal adhesion, cell-substrate junction, and actin/cadherin-binding programs. Trajectory analyses placed C0 at an early-to-intermediate node linked to divergent later states, indicating plasticity distinct from a purely proliferative state. CellChat suggested prominent myeloid-to-C0 communication, with OSM as a candidate input and LIFR/IL6ST as the receptor basis. pySCENIC identified a C0-preferential regulon landscape centered on CEBPD, RUNX2, POU2F3, TEAD3, and TEAD4, plus an M2 regulon module associated with stress adaptation and intracellular homeostasis. CEBPD knockdown reduced proliferation, colony formation, and migration while increasing apoptosis.<h4>Conclusion</h4>We identify an IDH-wild-type-enriched VIM+ glioma stem-like state with angiogenic, hypoxic, mesenchymal-like, and inflammatory features, and nominate myeloid-derived OSM signaling and CEBPD as candidate mediators of this vascular-immune-linked malignant phenotype. These findings provide a hypothesis-generating, state-based perspective on glioma progression across IDH backgrounds and highlight candidate biomarkers and mechanistic entry points for validation and therapeutic stratification.

Pancreatic ductal adenocarcinoma (PDAC) ranks among the deadliest malignancies, with only 13% of patients surviving five years after diagnosis. This poor prognosis stems from late detection, treatment resistance, spatial and phenotypic heterogeneity, and a highly immunosuppressive tumor microenvironment. Unlike immunogenic cancers, PDAC is an immunologically 'cold' tumor, marked by minimal immune cell infiltration, defective antigen-presentation machinery, and stromal barriers. While immune checkpoint blockade (ICB) has shown success against various cancers, it has proven largely ineffective when used alone in PDAC. However, emerging research has identified promising new approaches, including neoantigen-targeted vaccines, stromal modulation, and combination therapies such as ICB with chemotherapy, cytokine blockade, and kinase inhibitors. The development of personalized immunotherapy approaches is being refined by predictive biomarkers that assess factors such as T cell infiltration levels, antigen-presenting capacity, and the spatial immune cell landscape. Here, we review the immune landscape of PDAC, current and emerging immunotherapeutic strategies, and highlight the critical role of biomarkers and immune profiling in appropriately categorizing patients. Collectively, these insights provide a foundation for designing rational combination therapies to transform PDAC into a cancer that is more immunologically responsive and amenable to therapy.

Human NHE6 (HsNHE6) is an endosomal Na⁺/H⁺ exchanger essential for maintaining luminal pH and endo-lysosomal trafficking in neurons. HsNHE6 mutations are implicated in devastating neurological syndromes, but mechanistically the transporter remains poorly understood. Here, we present the single-particle cryo-electron microscopy (cryo-EM) structure of HsNHE6 at 3.4 Å, captured in an inward-facing conformation. The structure reveals a homodimeric architecture with 13 transmembrane helices per protomer, with the conserved ion-binding site located at the interface of the core and dimerization domains. Functional assays demonstrate that HsNHE6 reconstituted in liposomes exchanges Na⁺, K⁺, Li⁺, and Rb⁺ for H⁺, with kinetic analysis revealing a preference for K⁺. A structured C-terminal helix interacts with the transmembrane core, jointly forming a hydrophobic cavity containing two non-protein cryo-EM densities consistent with bound lipids that may modulate cation access to the ion-binding site. The remaining distal C-terminus of HsNHE6 is intrinsically disordered, as revealed by NMR and small-angle X-ray scattering, and extends up to 170 Å into the cytosol. Our integrative structural model of full-length HsNHE6 provides a framework for understanding HsNHE6-mediated ion exchange and its disruption in Christianson syndrome.

<h4>Summary</h4> The therapeutic potential of CRISPR–Cas9 genome editing is fundamentally constrained by the requirement for specific short DNA sequences (PAMs) flanking the target site, limiting access to many clinically relevant genomic loci. This stringent PAM requirement is particularly problematic in applications which require precise positioning, such as base editing and allele-specific editing. Although PAM-relaxed variants have expanded the targetable genome, they incur trade-offs in on-target activity, off-target editing, and cleavage kinetics. This highlights an unmet need for variants that are re-targeted to alternative PAMs in order to maintain the specificity and enzymatic performance inherent to stringent dinucleotide PAM recognition. To overcome these limitations, we developed a yeast selection platform to engineering SpCas9 variants with re-specified PAM recognition. Using a clinically relevant Huntington’s disease gene ( HTT ) SNP as a proof-of-concept target, we engineered variants with reciprocal NGC and NGT PAM selectivity, as a step toward allele-specific editing in a large percentage of Huntington’s disease patients. These yeast-selected SpCas9 variants retained their modified activity across multiple endogenous HEK293T loci, demonstrating that this specificity is robust across diverse genomic contexts. The variants surpassed PAM-broadened variants on their respective on-target PAM while displaying broad loss of activity across alternative PAMs, effectively re-specifying PAM recognition toward a single dinucleotide sequence. Retargeted variants recovered on-target cleavage kinetics approaching that of wild-type SpCas9, even under competing substrate conditions, demonstrating that PAM re-specification can simultaneously restore catalytic efficiency and improve specificity. Beyond NGC and NGT, we leveraged our high-throughput platform to engineer Cas9 with re-specified activity across multiple additional non-canonical PAMs in yeast, further demonstrating its utility as a general and programmable framework for expanding the therapeutic reach of precision genome editing.

The human gut microbiome plays a critical role in immune regulation, yet the molecular links between microbiome composition and host gene expression remain incompletely understood. We analyzed associations between host gene expression and microbiome composition in a cohort of 315 healthy individuals, integrating microarray-based gene expression data from three intestinal sites (ileum, transverse colon, and rectum) and six immune cell types with microbiome sequencing data. Using a hierarchical feature aggregation strategy combining principal component analysis, clustering, and covariate correction, we discovered significant associations primarily related to immunity. While microbial profiles were similar across the three intestinal sites, the transverse colon yielded the most "microbiome-host gene expression" associations. Among the immune cell types, CD8+ cells showed the highest number of associations. The first principal component of microbiome composition, reflecting a gradient from commensals (e.g., <i>Ruminococcaceae</i> and <i>Christensenellaceae</i>) to proinflammatory taxa ([<i>Ruminococcus</i>] <i>gnavus</i> and <i>Lachnoclostridium</i>), correlated with the expression of TNF-α-linked genes (<i>HMOX1</i>, <i>CPI17</i>, <i>HSD3B2</i>, and <i>SLC5A1</i>). Among individual genera, <i>Catenibacterium</i> abundance was associated with gene expression in both intestinal and immune cells, including negative associations with MRPS21 (related to mitochondrial function) in the transverse colon and with CD8+ gene programs related to T cell differentiation. These findings align with emerging evidence implicating mitochondrial dysfunction in intestinal inflammation. Our results identify multi-level associations between the gut microbiome and host gene expression, suggesting potential mechanisms by which microbiota shape local and systemic immunity and vice versa. The implicated genes and taxa represent candidates for experimental validation to improve understanding of host-microbiome homeostasis and its disruption in disease.IMPORTANCEThe gut microbiome and immune system are engaged in a complex interplay throughout human life. While most associative studies focus on case-control comparisons-typically examining patients with conditions such as inflammatory bowel disease or metabolic diseases-less is known about the molecular links between the microbiome and immune system in healthy individuals. In this study of a large cohort of healthy individuals, we addressed this gap by applying multiscale modeling to tackle the high dimensionality of host-microbiome data. We identified multi-level associations between microbiome composition and host gene expression in both intestinal tissues and immune cells. These findings offer a valuable reference for understanding baseline host-microbiome communication and highlight molecular candidates-such as TNF-α-related genes and mitochondrial pathways-for future experimental validation.

Lead (Pb) exposure remains a global health concern, particularly because of its adverse effects on neurodevelopment during fetal development and childhood. Early-life exposure to Pb during neuronal differentiation can impair neurodevelopment, although the underlying molecular mechanisms remain unclear. In this study, we investigated the cellular and molecular mechanisms underlying Pb-induced neurotoxicity during neural differentiation using SH-SY5Y cells. Our results demonstrated that Pb exposure caused severe injury to differentiating neural cells, leading to cell death with membrane disruption. This form of cell death was resistant to inhibitors of major regulated cell death pathways but was markedly suppressed by selenium supplementation with selenite or by the addition of selenoprotein P, a selenium transport protein. Transcriptome and protein expression analyses revealed that Pb induced endoplasmic reticulum (ER) stress responses. However, individual knockdown of selected ER-resident selenoproteins, including SELENOK, SELENOS, and SELENOT, did not abolish the protective effect of selenium, indicating that none of these proteins is individually indispensable for protection under the present experimental conditions. Peroxiredoxin 6 (PRDX6) knockout SH-SY5Y cells, which exhibit reduced selenium metabolic activity, remained responsive to the protective effect of selenium against Pb-induced cytotoxicity. Moreover, the glutathione peroxidase (GPx) mimetic ebselen also alleviated Pb toxicity under these conditions. These findings indicate that selenium protects differentiating neural cells against Pb-induced injury through mechanisms involving peroxide-reducing activity as well as additional selenium-dependent pathways. Collectively, our findings provide new insights into the molecular basis of Pb-induced neurotoxicity and support a protective role for selenium-dependent stress resistance against Pb-induced cellular injury.

Acting as the central endocrine hub, the pituitary gland is closely related to the mechanism of adaptation to high-altitude hypoxia. Here, by integratively combining long-read (Oxford Nanopore) and short-read (Illumina) single-cell sequencing approaches, we profiled pituitaries from Diqing Tibetan pigs, inhabiting high-altitude environments (3,200 m) and Diannan small-ear pigs from low-altitude regions (500 m), thereby generating a full-length single-cell atlas, which in turn enabled the identification of molecular mechanisms potentially underlying adaptation to high-altitude hypoxia stress. Systematically delineating pituitary structure and transcriptional dynamics, we profiled 27,339 single cells encompassing 28,932 expressed genes. Leveraging unsupervised clustering coupled with marker-based annotation, we identified ten major cell types. Expression profiling of 20 canonical marker genes revealed pronounced cell-type-specific expression patterns, ten of which were independently validated by immunofluorescence, thus substantiating the accuracy of cell-type annotation. Gene-ontology enrichment analysis further suggested that upregulated genes were predominantly involved in oxidative metabolism and energy production, whereas downregulated genes were significantly associated with protein biosynthesis and translation processes, indicating a functional reprogramming of metabolic pathways. Moreover, comparative analyses between breeds and cell-cell communication analyses highlighted pathway shifts, including broad upregulation of the collagen family and four ligand-receptor pairs that may mediate pituitary intercellular coordination. In parallel, transcription-factor activity analysis nominated several regulators, including EBF3, DBX2, and TCF21, which may collectively contribute to altitude-associated adaptation. Finally, integrating long-read sequencing data revealed widespread transcript isoform diversity, with ~28% novel annotations, indicating considerable isoform complexity in pigs. Our findings delineate cellular heterogeneity, inferred intercellular communication networks, and transcript-isoform diversity in the porcine pituitary, thereby providing a cell-resolved resource for understanding pituitary features associated with high-altitude environments.

An environmentally benign route was employed to synthesize tungsten-silver (W/Ag) co-doped hydroxyapatite (Hap) nanorods using <i>Glycyrrhiza glabra</i> extract as a natural bio-template. Microwave-assisted processing yielded highly crystalline nanorods with hexagonal lattice structure and average dimensions of 50-60 nm in length and 17 nm in diameter. XRD confirmed enhanced crystallinity with crystallite sizes up to 40 nm, while FTIR spectra revealed hydroxyl, phosphate, carbonate, and O-W-O groups, validating successful co-doping. FESEM/TEM analyses demonstrated uniform rod-like morphology, and XPS confirmed effective incorporation of Ca, P, O, Ag, and W with mixed oxidation states. Mechanical testing showed a significant increase in hardness for microwave-synthesized W/Ag Hap (717.8 ± 23.9 HV) compared to Ag-doped (236.7 ± 1.9 HV) and co-precipitated W/Ag HAp (437.2 ± 40.1 HV). Antibacterial assays against <i>Streptococcus mutans</i> and <i>Staphylococcus aureus</i> revealed pronounced inhibition zones and reduced bacterial viability, confirming strong antimicrobial activity. Overall, W/Ag co-doping synergistically enhanced both mechanical strength and antibacterial performance, addressing key limitations of pristine Hap. This green synthesis strategy provides a sustainable pathway to multifunctional bioceramics with promising potential for dental implant and bone regeneration applications.

Fast-spiking parvalbumin-positive (PV⁺) interneurons, a specialized class of inhibitory neurons, possess unique morphological and functional properties that govern spatiotemporal precision in local microcircuits, large-scale network synchronization, and memory-related computations. Since their initial identification in the late 19th century, technological innovations in cellular neuroscience have progressively elucidated the multifaceted roles of these neurons. In this review, we first delineate the embryonic origins and developmental trajectory of PV⁺ interneurons, emphasizing their unique properties for high-frequency firing with remarkable temporal precision. These specialized features enable PV⁺ interneurons to orchestrate network oscillations and critically modulate memory encoding, consolidation, and retrieval, despite their substantial metabolic demands. We subsequently integrate multiple lines of evidence implicating region- and subtype-specific PV⁺ interneuron impairment as a pivotal pathological hallmark in Alzheimer's disease (AD). Furthermore, we dissect molecular and cellular mechanisms driving PV⁺ interneuron dysfunction in AD, including numerical alterations, morphological remodeling, and electrophysiological disruptions. Critically, we propose that the pathological transformation of PV⁺ interneuron physiology emerges as a key driver in AD progression, bridging cellular dysfunction to system-level cognitive failure.

The mantle of bivalves plays a fundamental role in shell formation and maintenance through biomineralization. Experiments performed on mantle-shell preparations using different experimental techniques revealed the presence of phosphorus (P)-containing compounds in the shell as the first mineral phase formed at the growing edge of the periostracum in the freshwater bivalve <i>Limnoperna fortunei</i>. The low P concentration in the shells suggests that phosphate is restricted to the growth regions and occurs at concentrations too low to be detected by techniques such as X-ray diffraction (XRD). Nevertheless, a crystal morphology closely resembling that of hydroxyapatite (HAp) was identified at the shell growth front, and a Ca/P ratio of 1.67, consistent with HAp, was determined in two of these regions. Fourier transform infrared (FTIR) spectroscopy also revealed the principal and most intense absorption band of the phosphate group (PO₄^3-) at 1024 cm^-1. Enzymes such as carbonic anhydrase (CA), or proteins with equivalent functions, are likely involved in phosphate dissolution and the subsequent precipitation of calcium carbonate. In addition, the occurrence of calcium phosphate was confirmed in the shells of the marine bivalve <i>Perna perna</i>. Phosphate dissolution and carbonate precipitation during biomineralization suggest two important evolutionary advantages: first, the release and availability of phosphate, an essential nutrient for energy production and other metabolic functions; and second, the formation of a calcium carbonate shell, a structure indispensable for the protection, mechanical support, and survival of mollusks.

Tandem repeat expansions (TREs) cause over 50 neurological conditions, yet their contribution to neurodegenerative disease risk at a population scale remains incompletely characterized. We performed a TRE association study across 6,539 short tandem repeat loci in 276,411 individuals from the UK Biobank and 44,370 individuals from the All of Us Research Program, using two composite neurodegenerative phenotypes to increase statistical power and capture pleiotropic effects. Meta-analysis across the two cohorts identified associations at eight established pathogenic TRE loci, including C9orf72 , DMPK , HTT , ATXN2 , ATXN3 , CACNA1A , CNBP , and PPP2R2B , recovering known disease-associated expansions from short-read sequencing data at biobank scale. We also identified candidate associations at three additional loci. An intronic AATAA expansion in DAPK1 reached significance (q = 0.0045), with fine-mapping and conditional analysis supporting the repeat as the likely variant underlying the association. An intronic ATTTT expansion in ANK3 (q = 0.034) was observed exclusively in individuals of African and Latino/admixed American ancestry, underscoring the importance of ancestrally diverse cohorts for genetic discovery. An exonic polyalanine expansion in RPL14 was also significant (q = 0.039), where longer alleles were consistently associated with reduced RPL14 expression across independent datasets. Together, these findings identify candidate risk loci for neurodegenerative disease that may expand the contribution of TREs to neurodegenerative disease beyond known repeat expansion disorders.

While it has been reported that antioxidant selenoproteins are crucial for anti-ferroptosis in tumors, it remains unclear whether and how biosynthetic dysregulation of selenoproteins promotes resistance to ferroptosis. By bioinformatics analysis and in vitro confirmatory assays, we screened and identified selenophosphate synthetase 2 (SEPHS2), a key enzyme in a selenoprotein synthesis cascade, as a potential candidate for promoting anti-ferroptosis in tumors. We found that the expression of SEPHS2 was upregulated upon treatment with ferroptosis inducers. Knockdown of SEPHS2 inhibited tumor proliferation, migration and invasion, as well as attenuated selenoprotein biosynthesis to sensitize tumor cells to ferroptosis. Furthermore, our results demonstrated that activating transcription factor 4 (ATF4), a ferroptosis‑related transcription factor, might work as a direct upstream regulator to activate SEPHS2 transcription. Downregulation of ATF4 enhanced sensitivity to ferroptosis, whereas restoration of SEPHS2 expression rescued this effect, suggesting that ferroptosis resistance might be regulated by the ATF4/SEPHS2 axis. Notably, for the in vivo assay, knockdown of either SEPHS2 or ATF4 exhibited the optimal repression of tumor growth when combined with ferroptosis inducers. Thus, our findings highlight that inhibition of ATF4/SEPHS2 signaling might contribute as a novel adjuvant therapeutic strategy to improve the efficacy of ferroptosis-based treatment in tumors.

High temperature stress is a major constraint affecting tomato productivity and fruit quality worldwide. The present study aimed to identify heat-tolerant tomato genotypes using integrated morphological, biochemical, molecular, and GGE (Genotype plus Genotype-by-Environment) biplot analyses under controlled high temperature stress conditions (40 ± 2 °C, day) compared with optimal conditions (26 ± 2 °C, day). Thirty-five tomato genotypes were evaluated for horticultural, reproductive, biochemical, and molecular traits. Heat stress significantly reduced fruit weight, pollen viability, fruit set, total soluble solids, and yield (g/plant). However, substantial genotypic variation was observed among the evaluated lines. Based on Heat Tolerant Index (HTI), ten genotypes namely VRT-06, VRT-67, Superbug, VRT-494, H-88-78-1, VRT-458, VRT-500, ToDVAR-5, VRT-34, and VRT-613 were identified as highly heat-tolerant. Biochemical analysis demonstrated higher proline accumulation, antioxidant enzyme activities like superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), chlorophyll content, and relative water content along with lower malondialdehyde content and electrolyte leakage in tolerant genotypes. GGE biplot and MGIDI (Multi-Trait Genotype-Ideotype Distance Index) analyses identified VRT-06, VRT-67, Superbug, VRT-494, and H-88-78-1 as stable and superior performers across environments. Gene expression analysis revealed significant upregulation of heat-responsive genes (HSP70, HSP90, and HSFA2) and antioxidant defense genes (CAT and SOD1) in tolerant genotypes, particularly VRT-06 and VRT-67, indicating coordinated molecular defense mechanisms under heat stress. Overall, the study identified elite heat-tolerant tomato genotypes and demonstrated the effectiveness of integrating morphological, biochemical, molecular, and multivariate analyses for thermotolerance screening and breeding of climate-resilient tomato cultivars.

<h4>Introduction</h4>Durvalumab administered after definitive chemoradiotherapy has changed the treatment landscape for patients with unresectable stage III non-small cell lung cancer (NSCLC). Evidence describing treatment outcomes in routine clinical settings, particularly in Southeast Asian populations, remains relatively limited.<h4>Methods</h4>We performed a retrospective cohort study at the Vietnam National Cancer Hospital including consecutive patients treated with consolidation durvalumab following concurrent chemoradiotherapy between March 2021 and June 2025. The primary endpoint was progression-free survival (PFS). Secondary endpoints included overall survival (OS), objective response rate (ORR), and safety. Prespecified subgroup analyses evaluated outcomes according to age, molecular alteration status, and timing of durvalumab initiation.<h4>Results</h4>Seventy-nine patients were analyzed, with a median follow-up of 32.9 months (95% CI: 30.9-37.0 months). The mean age was 59.5 ± 9.3 years, and 79.7% were male; 60.7% were current or former smokers with an ECOG 0. Non-squamous histology accounted for 81% of cases, and EGFR or ALK alterations were identified in 27.8%. The ORR was 32.9%. Median PFS was 29.8 months, while median OS was not reached. Older patients showed longer PFS than younger patients (33.0 vs. 15.1 months; p = 0.13). EGFR or ALK alterations were associated with significantly shorter PFS (8.33 vs. 39.65 months; p = 0.009). Morning initiation of durvalumab was associated with numerically longer PFS than afternoon administration (39.65 vs. 16.38 months; p = 0.34). Multivariable analysis identified mutation status as independently associated with PFS, with no significant predictors for OS. Grade 3-5 adverse events occurred in 5.1% of patients, and treatment discontinuation was reported in 8.9%.<h4>Conclusion</h4>In this real-world cohort, consolidation durvalumab showed encouraging clinical outcomes with acceptable safety in patients with unresectable stage III NSCLC.

Major depressive disorder (MDD) is a widespread, recurrent, and severely disabling psychiatric disorder that imposes a heavy global health burden. Although genetic factors contribute to disease risk, growing evidence highlights gene-environment interaction as the core driver of MDD pathogenesis. Epigenetic regulation acts as a precisely molecular interface that translates environmental stressors into stable changes in gene expression and long-term behavioral phenotypes. In this review, we provide a comprehensive and up-to-date overview of epigenetic dysregulation in MDD, covering five major regulatory layers: DNA methylation, histone post-translational modifications, non-coding RNA networks, RNA chemical modifications, and ATP-dependent chromatin remodeling. We emphasize the spatiotemporal specificity, brain regional selectivity, and cell-type. dependency of these epigenetic events, and their roles in disrupting neuroplasticity, hypothalamic-pituitary-adrenal (HPA) axis function, neurotransmitter homeostasis, and neuroinflammation. We further evaluate the translational value of peripheral epigenetic markers for early diagnosis, severity monitoring, and prediction of antidepressant treatment responses. We also discuss emerging epigenetic-targeted therapeutic strategies, including small-molecule inhibitors, RNA-based modulators, and brain-targeted delivery systems. Finally, we address key obstacles to clinical translation, such as tissue heterogeneity, unclear causality, limited reproducibility, and lack of standardized protocols. We propose future directions centered on single-cell multi-omics, longitudinal clinical validation, and sex-and ethnicity-stratified research. This review aims to establish an integrated framework for understanding MDD epigenetics and accelerating the development of precision diagnostic and therapeutic approaches.

<h4>Objective</h4>Asthma is a common chronic lung disease in children, but the role of stress granules (SGs) in its pathogenesis remains unclear. The present study aims to investigate overlapping genes and regulatory mechanisms between childhood asthma (CA) and SGs via integrated bioinformatics and machine learning.<h4>Methods</h4>Machine learning algorithms were applied to screen for potential biomarkers among the candidate genes. Their expression levels were validated, followed by ROC analysis. Multiple bioinformatics analyses, including mRNA-miRNA and transcription factor regulatory networks, were performed to explore their potential functions. Finally, RT-qPCR was used to validate the expression differences between CA and healthy control blood samples.<h4>Results</h4>Through machine learning, 11 candidate genes were initially selected, with 3 potential biomarkers (HNRNPA2B1, RPE, TAF15) determined. These biomarkers showed strong diagnostic performance (AUC > 0.7). GeneMANIA and Gene Set Enrichment Analysis (GSEA) revealed that their functions were enriched in biological processes such as NADPH regeneration. Immunoinfiltration analysis identified four types of differentially infiltrating immune cells: CD56dim natural killer cell, Central memory CD8 T cell, Immature B cell, and Monocyte. Additionally, RT-PCR validation confirmed significantly elevated mRNA expression of HNRNPA2B1, RPE, and TAF15 in CA patients compared to healthy controls, consistent with the bioinformatics predictions.<h4>Conclusion</h4>This study screened out three potential biomarkers related to SGs in CA, offering new insights into disease pathogenesis and potential molecular targets for improved therapy.

Dysregulation of intracellular signaling networks underpins cancer. Yet, resolving signaling networks within distinct or rare cell types in cancer in vivo has been unattainable. Here we develop INSIGHT by integrating cell sorting with mass spectrometry to enable quantitative phosphoproteomics and proteomics of discrete cell types from fixed tissues. Using INSIGHT, we map the signaling network within disseminating glioblastoma cells from patient-derived xenografts implanted in mice. Disseminating tumor cells undergo a proteome-wide shift from proliferative to mesenchymal, neural progenitor-like cell states. In parallel, signaling network and global kinase activity are rewired, transitioning from cell cycle-associated circuitries to those governing synaptic function, neuronal migration, and ion channel activity. Changes begin at the tumor margin and persist in distant brain parenchyma. Hornerin and phosphorylation of Ca²⁺-permeable GluA2 at Y876 were identified as mediators of glioblastoma progression. INSIGHT enables systems-level dissection of cell-type-specific signaling circuitries in vivo across wide range of biological systems.

The precise neuromodulatory mechanisms underlying consciousness and its disorders, despite growing evidence in both animals and humans, remain poorly understood at the subcortical level. The basal ganglia, a key component of the cortico-basal ganglia-thalamo-cortical loop, are known to play a crucial role in mediating consciousness and behavioural responsiveness to the environment. Here, we aimed to present a comprehensive mapping of the distinct contributions of basal ganglia nuclei and their associated neurotransmitter systems in pharmacologically induced and pathological loss of responsiveness. We used functional MRI to provide a systematic investigation of 9 major nuclei (putamen, caudate, nucleus accumbens, globus pallidus external, globus pallidus internal, substantia nigra pars compacta, substantia nigra pars reticulata, ventral pallidus, and subthalamic nucleus) and their functional relationship with 19 major neurotransmitter systems in loss of responsiveness, in both healthy volunteers under propofol anaesthesia (n = 16) and patients with disorders of consciousness (DOC) (i.e. minimally conscious, unresponsive wakefulness syndrome) (n = 22). We found that in pharmacologically-induced loss of responsiveness, the functional connectivity changes of the putamen (Pu) correlated with the norepinephrine transporter (NET), and the globus pallidus external (GPe) with the serotonin transporter (5-HTT) and vesicular acetylcholine transporter (VAChT); additionally, altered connectivity in the ventral pallidum (VeP) was associated with the norepinephrine transporter (NET). In contrast, with pathological-induced loss of responsiveness, we found that connectivity changes of the caudate were associated with the serotonin transporter (5-HTT), dopamine transporter (DAT), and GABAA receptor, and connectivity changes of the substantia nigra pars compacta (SNc) were associated with the cannabinoid (CB1) receptor. Finally, we report that among all basal ganglia nuclei, a key dopamine-rich area of the basal ganglia-the substantia nigra-was found to have the largest DOC subgroup difference in functional connectivity, following stratification based on mental-imagery task responsiveness. Critically, we provide evidence that pharmacological and pathological loss of responsiveness involve distinct neurotransmitter system contributions across individual basal ganglia nuclei, offering a novel framework for targeted therapeutic interventions in patients with disorders of consciousness.

<h4>Introduction</h4>Distant metastasis in distal cholangiocarcinoma (DCC) generally precludes curative treatment. However, chemo-immunotherapy may enable multidisciplinary treatment with curative intent in selected patients. We report a rare case of metastatic DCC with liver metastasis that achieved radiological complete response after gemcitabine, cisplatin, and durvalumab (GCD) therapy, followed by resection of the residual primary lesion.<h4>Case presentation</h4>A 73-year-old woman with a history of total gastrectomy presented with DCC and a solitary liver metastasis. Following endoscopic ultrasound-guided hepaticojejunostomy and eight cycles of gemcitabine, cisplatin, and durvalumab (GCD) therapy, the liver metastasis achieved a radiological complete response. After 16 cycles of durvalumab maintenance therapy, conversion pancreaticoduodenectomy without hepatectomy was performed because disease remained controlled despite residual primary disease. Pathological examination revealed residual viable tumor (ypT2N2M0). Immunohistochemistry suggested differences in the immune microenvironment between the primary tumor and liver metastasis. The patient remained recurrence-free 15 months after surgery.<h4>Conclusions</h4>This rare case highlights the heterogeneous response between the primary tumor and liver metastasis after GCD therapy and demonstrates the potential role of conversion surgery in selected patients with metastatic DCC. It provides important insight into treatment decision-making in this clinical setting.

Adoptive cellular therapies may expand treatment options for pediatric brain tumors by focusing activity on tumor antigens and limiting off-tumor effects. We systematically reviewed preclinical and clinical evidence for CAR T cells, TCR-engineered T cells, and NK or γδ T-cell platforms directed against HER2, B7-H3 (CD276), EGFR806-reactive EGFR, GD2, IL13Rα2, and EphA2 or EphA3, with attention to delivery route, safety, persistence, and combination strategies. Following PRISMA, we searched PubMed, Embase, and Scopus from inception through September 17, 2025, restricted to English. The search yielded 324 records; 103 duplicates were removed; 221 titles and abstracts were screened; 180 full texts were reviewed; and 34 studies were extracted by two independent reviewers. We captured design, tumor and molecular features, product engineering, route and schedule, lymphodepletion, toxicities including cytokine release syndrome, immune effector cell associated neurotoxicity, and tumor inflammation associated neurotoxicity, radiographic or clinical response, survival, and correlatives such as persistence or trafficking in blood, cerebrospinal fluid, or tumor tissue, cytokines, and antigen dynamics. In vivo studies showed reproducible antitumor activity for HER2 in medulloblastoma, GD2 in diffuse midline glioma, and multi-antigen constructs incorporating IL13Rα2 and EphA2 in medulloblastoma and ependymoma, with significant survival advantages compared with controls. γδ T cells targeting the EphA axis selectively killed medulloblastoma with neural sparing; GD2 CAR NK-92 inhibited diffuse intrinsic pontine glioma growth. In early clinical programs, route shaped safety and pharmacodynamics. For GD2, low-dose intravenous induction followed by repeated intraventricular dosing produced objective radiographic regressions and manageable tumor inflammation associated neurotoxicity, while dose-limiting cytokine release syndrome was confined to higher intravenous doses. Intraventricular B7-H3 CAR T cells, given without lymphodepletion, enabled multi-cycle dosing with mainly grade 1 to 2 events and cerebrospinal fluid localized persistence. Weekly intracranial EGFR806 CAR T cells were feasible and well tolerated, with stable disease as the best response in a small cohort. Across trials, persistence and immune activation were most evident in cerebrospinal fluid, supporting cerebrospinal fluid centered pharmacodynamic monitoring. Mechanism-based combinations, including IGF-axis inhibition in diffuse midline glioma and epigenetic priming of GD2 with an integrated safety switch in medulloblastoma, enhanced activity. The evidence supports pediatric-centric antigen selection and a CNS-first, locoregional dosing approach to increase on-tumor exposure and reduce systemic toxicity. Priorities include multi-antigen strategies to prevent escape, incorporation of safety switches, earlier deployment when tumor burden is low, and prospective cerebrospinal fluid pharmacodynamics in multisite phase II studies.

<h4>Purpose</h4>Motivated by the rising incidence of cancers at younger ages, this study compares tumor genomic alterations between adolescents and young adults (AYAs; 18-39 years) and non-AYAs (40 years and older) and explores the relationship with continuous age in patients with relapsed/refractory ovarian, breast, and colorectal cancers accrued to the NCI-MATCH trial.<h4>Methods</h4>Tumor genomic profiles generated by a next-generation sequencing 143-gene panel (NCI-MATCH assay, v2) were analyzed for association with age (AYA/total: 21/455 ovarian, 27/576 breast, 43/759 colorectal cancers). For each gene, AYA and non-AYA DNA alteration proportions were compared (Fisher exact test) and alteration association with continuous age (logistic regression) was evaluated (false discovery rate‑adjusted <i>P</i> value <.1 statistically significant). For colorectal cancer, sex-stratified analysis was also performed.<h4>Results</h4>No significant AYA versus non-AYA differences were observed in the prevalence of gene mutations (single nucleotide variant [SNV]/indel). A significant association of gene amplification with AYAs (odds ratio [OR], 95% CI) was <i>CCND1</i> (0.2, 0.1-0.4), favoring AYAs in breast cancer. Examining age as a continuous variable, significant associations of gene mutations (SNV/indel) with older age, expressed as 5-year OR (OR [95% CI]), were observed: <i>TP53</i> (1.3 [1.1 to 1.4]), ovarian cancer; <i>CDH1</i> (1.4 [1.2 to 1.6]) and <i>PIK3CA</i> (1.1 [1.1 to 1.2]), breast cancer; and <i>BRAF</i> (1.4 [1.2 to 1.7]), female colorectal cancer. Associations with younger age included <i>SMAD4</i> (0.8 [0.7 to 0.9]), male colorectal cancer. Significant associations of gene amplification with age (continuous) were as follows: <i>CCNE1</i> (1.3 [1.1 to 1.6]), older ovarian cancer, and <i>CCND1</i> (0.8 [0.8 to 0.9]), younger breast cancer.<h4>Conclusion</h4>Comparing AYAs with non-AYAs among patients having relapsed/refractory disease, no significant differences in SNV/indel prevalence were observed, but <i>CCND1</i> amplifications were more prevalent in AYA breast cancer. For several genes, DNA alterations were associated with continuous age and may depend on sex in colorectal cancer.

Aspartyl-tRNA synthetase 2 (DARS2), the mitochondrial enzyme responsible for aminoacylation of aspartyl-tRNA, is traditionally known for its effect on protein synthesis. Recently, DARS2 is reported to be implicated in tumorigenesis. However, its specific effect on breast cancer (BC) is poorly understood. The present work employed bioinformatics tools for analyzing DARS2 expression among BC patients and its association with clinicopathological characteristics and patient prognosis. We evaluated DARS2 expression within BC cells and tissues and assessed how DARS2 knockdown or PI3K pathway activation affected cell growth, migration, invasion, apoptosis, as well as cell cycle progression. Mechanistically, we analyzed how DARS2 regulated the PI3K/Akt/GSK-3β/β-catenin pathway. Additionally, a xenograft tumor model was constructed to validate our in vitro findings. According to our observations, DARS2 expression significantly increased in BC cells and tissues. Knockdown of DARS2 markedly suppressed cell growth, invasion, migration, and epithelial-mesenchymal transition (EMT), but enhanced their apoptosis. Mechanistic studies revealed that DARS2 knockdown suppressed the PI3K/Akt/GSK-3β/β-catenin pathway, whereas PI3K pathway activation with 740Y-P reversed the impacts of DARS2 knockdown. In vivo experimental results further verified that DARS2 suppression significantly suppressed tumor growth and metastasis through downregulating the PI3K/Akt/GSK-3β/β-catenin pathway. Collectively, these results indicate that DARS2 promotes the growth, migration, invasion, and EMT of BC cells by regulating the PI3K/Akt/GSK-3β/β-catenin signaling pathway.

Hydroxyapatite (HAp) is a well-known bioceramic material with excellent biocompatibility, bioactivity, and chemical stability. However, its brittleness, low surface reactivity, and limited functionality restrict its use in advanced applications such as drug delivery, catalysis, and sensing. To overcome these limitations, HAp has recently been combined with metal-organic frameworks (MOFs) and MXenes, two emerging classes of functional materials. MOFs provide high surface area and tunable porosity, whereas MXenes offer excellent electrical conductivity and photothermal properties. In turn, HAp enhances the structural stability of these materials by improving the moisture resistance of MOFs and reducing the restacking tendency of MXenes. In both types of composites, HAp primarily acts as a bioactive and ion-rich support, while the MOF or MXene component provides the desired functional properties. This common design strategy forms the basis of the present review, which is the first to comparatively discuss HAp/MOF and HAp/MXene composites within a single framework. The review summarizes their synthesis methods and applications in biomedical engineering, environmental remediation, catalysis, electrochemical sensing, coatings, and agriculture. More importantly, it critically examines whether the reported performance improvements arise from true synergistic interactions or simply from the individual contributions of each component. It also compares the reproducibility of different fabrication strategies, discusses the distinct mechanisms through which HAp improves the stability of MOFs and MXenes, and evaluates the maturity of reported applications based on real-sample testing and <i>in vivo</i> validation. Finally, a comparative summary is provided covering the role of HAp, synthesis strategies, interfacial interactions, advantages, limitations, applications, and current research challenges. This review provides a comprehensive reference for researchers interested in the design and development of HAp-based hybrid composites.

TRPA1 channels function as cold sensors and have been implicated in energy metabolism. We investigated the impact of TRPA1 on thermoregulation. <i>Trpa1</i> ^<i>-/-</i> mice exhibited body weight loss and increased food intake when transitioning from 30°C to mild cold (14 days at 22°C), indicating increased energy metabolism in response to cold. <i>Trpa1</i> ^<i>-/-</i> mice exhibited elevated oxygen consumption, while their core temperature remained unaffected. The BAT proteome in WT mice after 14 days at 22°C showed increased proteins related to glucose utilization and reduced proteins related to lipolysis, whereas <i>Trpa1</i> ^<i>-/-</i> mice revealed increased PRDM16 and proteins associated with peroxisomal/mitochondrial β-oxidation. Transcripts of <i>Cidea, Ucp1, Cpt1a</i>, and <i>Lcad</i> were higher in <i>Trpa1</i> ^<i>-/-</i> mice at 22°C compared to 30°C, relative to WT mice, with <i>Prdm16</i> expression uniquely increased in <i>Trpa1</i> ^<i>-/-</i> mice. Thermographic images revealed higher interscapular surface temperature in <i>Trpa1</i> ^<i>-/-</i> mice exposed to 22°C. These data suggest that the TRPA1 channel reduces metabolic stress and contributes to thermogenic regulation in mice.

<h4>Background</h4>Cardiac contractility is regulated by two myosin heavy chain (MHC) protein isoforms, <i>α</i> and β, encoded by the <i>MYH6</i> and <i>MYH7</i> genes. The intronic regions of these genes encode the microRNAs <i>miR-208a</i> and <i>miR-208b</i>, which are key regulators of cardiac hypertrophy. Functionally relevant long non-coding RNAs (lncRNAs) have also been identified at these loci, such as those transcribed in the antisense direction from the <i>MYH7</i> gene, including the primary <i>miR-208b</i> transcript (<i>MHRT</i>) originating from an internal <i>MYH7</i> promoter. Additionally, <i>MYH7B</i>, another cardiac sarcomeric myosin gene, serves as a precursor for <i>miR-499a-5p</i>.<h4>Aim</h4>This study aimed to comprehensively analyse the expression profiles of <i>MYH6, MYH7,</i> and <i>MYH7B</i> genes, microRNAs (<i>miR-208a-3p, miR-208b-3p, and miR-499a-5p</i>), and the <i>lncRNA MHRT</i> in non-failing and end-stage failing human left ventricles.<h4>Subjects and methods</h4>The relative expression of these transcripts was measured using RT-qPCR in left ventricular samples from 5 non-failing controls and 24 patients with end-stage heart failure, including hypertrophic cardiomyopathy (HCM, <i>n</i> = 4), dilated cardiomyopathy (DCM, <i>n</i> = 10), and coronary artery disease (CAD, <i>n</i> = 10). The findings were validated by comparison with two independent RNA-seq datasets (GSE141910 and GSE116250) for <i>MYH6</i>, <i>MYH7</i>, <i>MYH7B</i>, and <i>MHRT</i>.<h4>Results</h4>Statistical analysis of independent RNA-seq datasets confirmed strong correlations among <i>MYH7, MYH7B,</i> and <i>MHRT</i> transcripts (<i>p</i> ≤ 0.0001), a trend also observed in our RT-qPCR cohort. A profound imbalance in the <i>MYH7B/miR-499-5p</i> ratio was identified, shifting from ∼250:1 in non-failing controls to ∼12-18:1 in failing hearts. The <i>miR-208a-3p/miR-208b-3p</i> expression ratio was heavily skewed toward <i>miR-208b-3p</i> (∼50:1) in all groups, regardless of disease status.<h4>Conclusion</h4>Our results suggest that <i>MYH7, MYH7B</i>, and <i>MHRT</i> transcripts exhibit coordinated expression patterns in human left ventricles, independent of pathological status. We further observed a dissociation between <i>miR-208a-3p</i> and its host gene (<i>MYH6</i>) under physiological conditions and confirmed altered <i>miR-499a-5p/MYH7B</i> relationships, consistent with findings in murine models. Moreover, the expression of two regulatory genes, <i>SOX6</i> and <i>TARBP2</i>, known to modulate <i>MYH7</i> and <i>MYH7B</i> in mice, showed that <i>SOX6</i> is upregulated in the left ventricles of all pathological groups.

<h4>Introduction</h4>To explore the mechanism underlying the effects of combined application of organic fertilizer and compound fertilizer on stem development of foxtail millet, this study used '<i>Jiza Jinmiao 3</i>' as the test material and set up three treatments: sole application of organic manure (Control1), sole application of compound fertilizer (Control2), and combined application of cattle manure-based organic fertilizer and compound fertilizer (Treatment).<h4>Methods</h4>The effects of different fertilizer treatments were analyzed by integrating phenotypic determination, microscopic observation of stem structure, and multi-omics analyses including transcriptomics, metabolomics, and proteomics.<h4>Results</h4>The results showed that compared with the sole application treatments, the combined application treatment significantly promoted phenotypic indicators of foxtail millet such as plant height, stem diameter, and stem fresh weight, and also significantly increased the cross-sectional area of stem vessels, the cell wall thickness of basic tissues, and the stem puncture strength. Multi-omics analyses revealed that differentially expressed genes (DEGs), differentially accumulated metabolites (DAMs), and differentially expressed proteins (DEPs) under the combined application treatment were significantly enriched in pathways related to cell wall development, such as phenylalanine metabolism and phenylpropanoid biosynthesis. Specifically, mapped to the phenylalanine pathway, the expression levels of key genes, metabolites, and proteins including <i>Phenylalanine Ammonia</i>-<i>Lyase</i> (<i>PAL</i>), <i>Phenylalanine</i>/<i>Tyrosine Ammonia</i>-<i>Lyase</i> (<i>PTAL</i>), and <i>Peroxidase</i> gene (<i>PRDX6</i>) were significantly upregulated, and the content of phenylalanine was increased.<h4>Discussion</h4>This study suggests that the combined application of organic fertilizer and compound fertilizer is associated with enhanced stem structural properties (including increased vascular area, cell wall thickness, and stem puncture strength) potentially linked to improved lodging resistance, with the phenylalanine pathway emerging as a candidate pathway, providing a theoretical basis and technical support for optimizing fertilization strategies and improving yield stability in the high-yield cultivation of foxtail millet.

<h4>Introduction</h4>Extracellular vesicles (EVs) are increasingly recognized as active coordinators of metabolic processes rather than mere messengers. By carrying unique subsets of enzymes, metabolites, lipids, and nucleic acids, EVs can directly deliver functional metabolic machinery or dynamically alter intracellular metabolic fluxes in recipient cells. However, their role in regulating specific biochemical pathways remains largely unknown.<h4>Methodology</h4>In the current <i>in silico</i> analysis, we explored the dominant metabolic role of EV cargo using publicly available multi-omics data. For this, the top 500 mRNAs and proteins, along with miRNAs reported at least 10 times in humans across independent studies, as catalogued in the EVpedia database are considered and curated into a comprehensive dataset.<h4>Results</h4>Enrichment analysis of these mRNAs and proteins revealed that carbohydrate metabolic pathways, including glycolysis, the pentose phosphate pathway and the TCA cycle, were over-represented in EVs. Further, to investigate whether EVs carry miRNAs that regulate these pathways, we analyzed the miRNA targets. Enrichment analysis of EV miRNA targets mapped glycolytic regulatory genes, including <i>HK1, HK2, PFKP and PKM</i>. Interestingly, we also found miRNAs targeting genes encoding glucose transporters (SLC2A1, SLC2A3, SLC2A4, and SLC2A14) reported in EVs. Genomic annotation of these miRNAs revealed them to form clusters, including the miR-17-92 cluster, a well-known regulator of glycolysis.<h4>Discussion</h4>While the study has limitations-mainly due to the biological heterogeneity of EVs and the difficulty of standardizing cargo-the results potentially suggest that, by delivering enzymes, their mRNAs, regulatory miRNAs or combinations thereof, EVs could potentially mediate recipient cell glucose metabolism.

<b>Background/Objectives</b>: The physiological adaptations required to sustain elite football performance are influenced by both genetic background and dynamic biochemical responses, although their interaction across a full competitive season remains insufficiently characterized. This study aimed to examine the association between polygenic profiles and longitudinal biochemical adaptations in professional football players. <b>Methods</b>: Forty male professional football players competing in the Spanish league were monitored across two consecutive seasons. Blood samples were collected at six time points representing different phases of the competitive cycle. Biomarkers related to muscle metabolism, iron status, and hepatic function were analyzed. Polygenic profiles were calculated using Total Genotype Scores (TGS) for muscle performance, hepatic resilience, and metabolic efficiency. Associations were initially explored using Pearson correlations and subsequently evaluated using linear mixed-effects models accounting for repeated measurements within subjects. <b>Results</b>: Exploratory correlation analyses identified several associations between polygenic profiles and biochemical markers. Muscle performance TGS was inversely associated with serum iron (r = -0.36, <i>p</i> = 0.017) and positively associated with CK (r = 0.32, <i>p</i> = 0.041), Hb (r = 0.29, <i>p</i> = 0.046), and Hct (r = 0.33, <i>p</i> = 0.024). Hepatic resilience TGS showed inverse associations with ALT (r = -0.39, <i>p</i> = 0.012), urea (r = -0.51, <i>p</i> = 0.011), and BUN (r = -0.51, <i>p</i> = 0.011). Metabolic efficiency TGS was negatively associated with AST (r = -0.43, <i>p</i> = 0.044), ALT (r = -0.33, <i>p</i> = 0.025), and GGT across multiple time points (<i>p</i> = 0.001-0.013). However, although several nominal associations emerged in linear mixed-effects models accounting for repeated measurements, none remained statistically significant after false discovery rate correction. These findings should therefore be interpreted as exploratory and hypothesis-generating. <b>Conclusions</b>: Polygenic profiles may be associated with inter-individual variability in biochemical adaptations throughout a competitive season. These findings suggest the integration of genomic and biochemical data in precision athlete monitoring, while highlighting causal relationships and predictive applications require further investigation.

Ovarian cancer (OC) remains the most lethal gynecological malignancy, mostly due to its frequent diagnosis at advanced stages, early peritoneal dissemination, ascites formation, and limited sensitivity of currently available approaches for early detection. Extracellular vesicles (EVs), particularly exosomes, mediate intercellular communication through the transfer of proteins, lipids, metabolites, and nucleic acids. In OC, EV-associated protein profiles reflect both tumor-cell-intrinsic programs and the complex interactions between malignant cells and the peritoneal microenvironment. This review summarizes current evidence regarding the involvement of exosomal proteins in OC progression, with particular emphasis on epithelial-mesenchymal transition, mesothelial reprogramming, extracellular matrix remodeling, angiogenesis, immune suppression, peritoneal dissemination, and platinum resistance. Mechanistic studies indicate that exosomal proteins, including CD44, the integrin α5β1/asparaginyl endopeptidase complex, annexin A2, low-density lipoprotein receptor-related protein 1, and programmed death-ligand 1, can directly contribute to metastatic niche formation and tumor progression. In parallel, proteomic studies of plasma-, serum-, ascites-, peritoneal-fluid-, and uterine-lavage-derived EVs have identified candidate liquid-biopsy biomarkers, including MUC1, EpCAM, FOLR1, integrins, complement- and coagulation-related proteins, and proteins associated with treatment resistance. To integrate the biological significance of proteins reported in OC-associated exosomes, we additionally performed protein-protein interaction and functional enrichment analyses. These analyses revealed interconnected protein groups associated with cell adhesion, oxidative stress adaptation, secretory remodeling, lipid metabolism, extracellular matrix organization, and inflammatory signaling. Taken together, the available evidence supports exosomal proteome profiling as a promising approach for investigating OC dissemination and developing minimally invasive diagnostic and prognostic tools. However, standardized EV isolation, quantitative proteomics, functional validation, and independent clinical cohorts remain essential for translation into clinical practice.

Canonical signal peptides (SPs) are short N-terminal sequences that direct nascent proteins into the secretory pathway, but their role extends far beyond protein targeting. Advances in sequencing and computational tools have enabled their systematic identification across proteomes, highlighting SPs as critical regulators of protein biogenesis, including endoplasmic reticulum (ER) targeting, translocation, folding, and proteostasis. Clinically, mutations affecting SP function underlie a distinct group of human disorders, while SP-derived fragments are emerging as diagnostic biomarkers and therapeutic targets. In biotechnology, SPs are engineered to enhance recombinant protein production and serve as molecular tags for intracellular delivery. Together, these developments position SPs at the intersection of fundamental cell biology, medicine, and biotechnology. While this review primarily focuses on canonical SPs, it also considers selected non-canonical targeting and topogenic sequences whose dysfunction contributes to protein misfolding, impaired ER translocation, disrupted degradation pathways, and altered intracellular trafficking in neurodegenerative diseases. Aberrations involving both conventional SPs and alternative targeting/topogenic elements contribute to pathological protein aggregation, a hallmark of major neurodegenerative disorders, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington Disease (HD), prion diseases, and amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD); in multiple sclerosis (MS) is primarily an inflammatory demyelinating disease, where abnormal protein exposure, potentially linked to misprocessed SPs, can activate immune responses. By synthesizing current knowledge, the review explores how alterations in targeting determinants influence key proteostasis pathways, acting as upstream modulators of disease-relevant molecular cascades. It further discusses the emerging concept that SP-derived fragments may participate in intercellular communication, adding an additional layer of regulatory complexity.

<title>Abstract</title> <p> We conducted genome-wide meta-analyses (N = 141,505; Estonian Biobank and Norwegian Mother, Father and Child Cohort Study) with polygenic score-based validation (N = 19,857; Dutch Lifelines cohort) of self-reported attention-deficit/hyperactivity disorder (ADHD) symptoms in adults from the general population. We identified eight genetic loci associated with either total symptoms, inattention or hyperactivity-impulsivity domains. Distinct genetic architectures underlying the two symptom domains were demonstrated by their moderate genetic correlation (r _g =0.35, 95% CI 0.26 to 0.43) and by contrasting genetic association patterns across other phenotypes and medical conditions. Hyperactivity-impulsivity showed stronger genetic links with ADHD diagnosis, negative r _g -s (-0.28 to -0.19) with educational traits, and more associations with diagnoses in electronic health records. Whereas inattention was weakly genetically associated with ADHD diagnosis, showed positive r _g -s (0.24 to 0.29) with educational phenotypes, and fewer links with clinical outcomes. This is the first genome-wide study to detect significant signals associated with adult ADHD symptoms and symptom dimensions. </p>

<title>Abstract</title> <p>Pancreatic ductal adenocarcinoma (PDAC) is lethal in ~88% of patients. Immunotherapy has revolutionized cancer therapy for many cancer types; however, PDAC survival rates remain unchanged. Low tumor mutation burden, inefficient antigen presentation, limited response rates to standard-of-care (SoC) therapy, acquired resistance, and a profoundly immunosuppressive microenvironment constrain the efficacy of immunotherapy. Advances in nanotechnology-based vaccines have enabled the precise delivery of mRNA and antigens, thereby potently activating the immune system and opening new avenues for treating PDAC. Here, we report a mannose-grafted nanovaccine (NV) platform that co-packages the gastrointestinal cancer-overexpressed CEACAM5 (CEA5), and immune adjuvants to sensitize antigen-presenting cells (APCs) and enhance their antigen-presenting capacity, promoting efficient lymph node priming and robust CD4⁺ and CD8⁺ T-cell activation. Our NV induced substantial remodeling of the PDAC microenvironment, reflected by increased CD8+ T-cell infiltration and T-cell memory, while decreasing T-cell exhaustion, cancer-associated fibroblast abundance, desmoplasia, pro-tumorigenic metabolic pathways, and angiogenic signaling. NV monotherapy significantly suppressed primary tumor growth and extended survival in a PDAC mouse model. In a tumor resection model, NV-treated mice showed reduced local tumor recurrence and complete prevention of hepatic metastasis. Combination therapy with SoC and a KRAS inhibitor further enhanced tumor control and survival compared with either monotherapy. The translational potential of the NV is supported by patient-derived models, in which NV-pulsed APCs generated functional antigen-specific T cells capable of killing tumor cells. Notably, NV also demonstrated robust antitumor efficacy in a mouse colorectal cancer model, delaying tumor progression and prolonging survival, highlighting the translational potential of this modular platform across gastrointestinal cancers. Collectively, this work establishes a modular and translationally relevant NV platform capable of converting immune-refractory PDAC into a therapeutically responsive disease by amplifying endogenous antitumor immunity.</p>

<h4>Objectives</h4>Hyperferritinemia is common in adults, yet most lack true iron overload. Confusion among metabolic, inflammatory, genetic, and reactive causes drives under-investigation and over-treatment, compounded by SGLT2 inhibitors and, less certainly, GLP-1 receptor agonists. We synthesize the hepcidin-ferroportin axis as the unifying mechanism and a transferrin saturation (TSAT)-guided pathway for workup.<h4>Methods</h4>Narrative review with structured PubMed, Embase, and Cochrane searches through April 2026, written to address the SANRA quality domains.<h4>Results</h4>Ferritin above 10 000 μg/L flags hemophagocytic lymphohistiocytosis (HLH), although the often-cited 90%/96% performance is pediatric; adult HLH-2004 or HScore ≥ 169 reach 82%-95% sensitivity and 60%-94% specificity, lower in ICU populations. The Valenti consensus on metabolic hyperferritinemia is partially validated against clinical outcomes in cohorts applying its grading. A TSAT-guided pathway directs workup toward HFE genotyping, hepatic MRI, or metabolic evaluation; soluble transferrin receptor (sTfR) and the sTfR/log-ferritin index complement ferritin in distinguishing iron deficiency from anemia of inflammation, though sTfR is itself influenced by inflammation.<h4>Conclusions</h4>The hepcidin-ferroportin axis unifies adult hyperferritinemia under TSAT-guided evaluation, though the algorithm does not capture diabetes risk in C282Y homozygosity. SGLT2 inhibitors alter ferritin interpretation; GLP-1 receptor agonists may do so, though dedicated human evidence remains insufficient. Both warrant documentation at review.

SQSTM1/p62 (sequestosome 1) is an important receptor protein involved in many cellular signaling processes, including macroautophagy/autophagy. It is a molecular hub for cellular homeostasis and cellular responses. Within autophagy, SQSTM1 targets ubiquitinated cargo for degradation, maintaining cellular proteostasis. Structurally, SQSTM1 consists of several domains that facilitate its binding to ubiquitinated cargo, the formation of SQSTM1 aggregate inclusions, interactions with MAP1LC3/LC3, and the mediation of clearance via the autophagy pathway. Beyond its structure, post-translational modifications of SQSTM1 dynamically regulate its function within a cell. Post-translational modifications - such as phosphorylation, ubiquitination, acetylation, S-acylation, and S-nitrosylation - are crucial for regulating SQSTM1 function, localization, and interaction with autophagic components, thereby influencing SQSTM1's role in the autophagy pathway. Understanding the role of these protein modifications in modulating autophagy may provide better insight into developing therapeutic strategies for diseases with dysregulated autophagy, such as neurodegenerative diseases. This review will discuss the role of these post-translational modifications in controlling SQSTM1's localization and function in autophagy.<b>Abbreviations</b>: ABHD = α/β-hydrolase domain; AD = Alzheimer Disease; ALS = amyotrophic lateral sclerosis; ATG = autophagy related ; CSNK2/CK2 = casein kinase 2; HD = Huntington Disease; HDAC/KDAC = histone deacetylase/lysine deacetylase; HTT = huntingtin; KAT = lysine acetyltransferase; KEAP1 = kelch like ECH associated protein 1; KIR = KEAP1-interacting region; LIR = LC3-interacting region; LYPLA/APT = lysophospholipase/acyl-protein thioesterase; MAP1LC3/LC3 = microtubule associated protein 1 light chain 3; MEF = mouse embryonic fibroblast; mHTT = mutant huntingtin; MTORC1 = MTOR complex 1; NBR1 = NBR1 autophagy cargo receptor; NEDD4 = NEDD4 E3 ubiquitin protein ligase ; NO = nitric oxide; NFE2L2/Nrf2 = nuclear factor erythroid 2-factor 2; PAT = palmitoyl acyltransferase; PB1 = Phox-BEM1 domain; PE = phosphatidylethanolamine; PLEKHM1 = pleckstrin homology and RUN domain containing M1; PLK2 = polo like kinase 2; PRKA/PKA = protein kinase cAMP-activated; PPT1 = palmitoyl-protein thioesterase 1; RB1CC1 = RB1 inducible coiled-coil 1; SNCA/α-synuclein = synuclein alpha; SNO = S-nitrosothiol; SOD1 = superoxide dismutase 1; SQSTM1 = sequestosome 1; TARDBP/TDP-43 = TAR DNA binding protein ; TBK1 = TANK binding kinase 1; TAX1BP1 = Tax1 binding protein 1; TRIM = tripartite motif containing ; UBA = ubiquitin-associated domain; UBE = ubiquitin-conjugating enzyme; ULK1 = unc-51 like autophagy activating kinase 1; UPS =ubiquitin-proteasome system; USP8 = ubiquitin specific peptidase 8; ZDHHC = zDHHC palmitoyltransferase.

Immune-epithelial interactions are essential for intestinal homeostasis, yet organoid monocultures lack immune components and fail to model how immune cells shape epithelial identity. Here, we establish a macrophage-organoid co-culture integrating bone marrow-derived macrophages (BMDMs) into the intestinal niche to create a controlled, immune-competent system. Under homeostatic conditions, the optimized 5k configuration of BMDMs preserves crypt-like architecture and maintains stem cell localization and secretory lineage organization. TNFα stimulation induces coordinated epithelial remodeling characterized by reduced canonical stem cell marker expression and density-dependent shifts in macrophage phenotype. Transcriptomic profiling confirms enrichment of immune-associated and epithelial stress pathways. Comparative analysis with a DSS-induced murine inflammation model reveals overlapping inflammatory and epithelial remodeling features, supporting physiological relevance. This platform provides a reproducible framework for studying epithelial-immune interactions and inflammatory remodeling under defined conditions, offering a controlled alternative to animal models.

Glioblastoma (GBM) remains lethal despite maximal therapy. The adult subventricular zone (SVZ), a neural stem-cell niche, has been implicated as a potential site of origin, yet the identity and functional properties of putative GBM origin-like cells (GBM-OCs) within the SVZ remain unclear. An SVZ-restricted somatic mutation mouse model (Cre-induced EGFRvIII expression with Trp53 and Pten disruption) was established and mouse SVZ-derived cells were prospectively isolated for functional and molecular profiling. Self-renewal, multipotency, invasive potential and tumour-initiating capacity were assessed relative to control SVZ cells and matched tumour-derived tumourspheres. Whole-genome and RNA sequencing defined genomic and transcriptional alterations during early progression. Mouse GBM-OCs exhibited self-renewal and multilineage differentiation and initiated tumours only after re-implantation into the SVZ (11/29, 38%), whereas direct striatal implantation failed (0/25, 0%), indicating context-dependent tumorigenic potential associated with the SVZ microenvironment. In contrast, tumour-derived tumourspheres retained tumorigenic capacity upon implantation into both the SVZ and the striatum. During progression from mouse GBM-OCs to tumours, whole-chromosome and arm-level aneuploidies accumulated. In patients with GBM, multi-region single-nucleus RNA sequencing of tumour-free SVZ, matched tumours and tumour-free cortex identified rare neural stem cell-like, astrocyte-like and oligodendrocyte precursor-like SVZ populations transcriptionally aligned with GBM programmes. These cells showed single-nucleus RNA-inferred chromosome 7 gain and/or chromosome 10 loss signals, with concordant low-frequency copy-number alterations in the SVZ detected by exome sequencing and enriched in matched tumours. Together, these findings support the presence of SVZ-resident stem or progenitor-like populations with early GBM-associated features, consistent with putative GBM-OCs, and highlight the SVZ niche as a potential target for early detection and niche-informed therapeutic strategies.

<h4>Background</h4>Colon cancer (CC) remains a leading cause of cancer-related mortality worldwide, driven largely by the complex interactions within the tumor microenvironment (TME). Fibroblast activation protein (FAP) is highly expressed in cancer-associated fibroblasts (CAFs) and is associated with poor prognosis, yet its role in coordinating immune evasion and cancer stemness remains to be fully elucidated.<h4>Methods</h4>We integrated multiomics data from TCGA and GEO databases, utilizing bulk RNA-seq and single-cell RNA-seq (scRNA-seq) analyses. Findings were validated via tissue microarray (TMA) immunohistochemistry (IHC). We further employed cell-cell communication analysis, pseudotime trajectory modeling, and the Connectivity Map (CMap) for drug sensitivity prediction and molecular docking.<h4>Results</h4>FAP was significantly upregulated in CC tissues and correlated with advanced clinical stages. scRNA-seq confirmed that FAP is predominantly expressed in CAFs. Functional analysis revealed that FAP-high tumors are enriched in extracellular matrix (ECM) remodeling and immunosuppressive pathways. Cell-cell communication analysis identified that FAP+ CAFs interact with T cells and cancer stem cells (CSCs) primarily through the COL1A1/2-CD44 axis. Specifically, FAP+ CAFs promote the differentiation of naive T cells into regulatory T cells (Tregs) and are positively correlated with various stemness markers, including CD44, ABCG2, and BMI1. Based on these findings, we established a 14-gene prognostic risk model with robust predictive accuracy (area under the curve [AUC] > 0.64) and identified AS604850 and LY364947 as potential therapeutic agents.<h4>Conclusion</h4>Our study demonstrates that FAP+ CAFs orchestrate a dual-functional "immunosuppressive stem cell niche" via the COL1A1/2-CD44 signaling axis. Targeting this FAP-driven niche provides a promising strategy for overcoming immunotherapy resistance and improving clinical outcomes in CC.

Most proteins synthesized in the endoplasmic reticulum (ER) are covalently modified upon addition of pre-assembled oligosaccharides to side chains of asparagine (N) residues. Processing of <i>N</i>-linked oligosaccharides by ER-resident glucosidases, mannosidases and glucosyltransferases determines the fate of the associated polypeptides. Terminally glucose residues are removed from <i>N</i>-glycans to interrupt the engagement of ER-resident glucose-binding chaperones and promote secretion of native polypeptides. Mannose residues are removed to target terminally misfolded proteins for dislocation across the ER membrane and clearance by the cytoplasmic ubiquitin proteasome system (ER-associated degradation, ERAD). Recent evidence highlights the role of persistent <i>N</i>-glycan glucosylation as a signal that promotes ER lectins-driven segregation of misfolded proteins in ER subdomains that are eventually delivered to endolysosomal compartments for ER-to-Lysosome-Associated Degradation (ERLAD). Here we show that the polymerization-prone Portland variant of Neuroserpin (NS_PL) associated with familial encephalopathy with NS inclusion bodies (FENIB) is a client of the ERLAD machinery. Its lysosomal clearance relies on the LC3-dependent delivery branch of ERLAD involving the lectin chaperone Calnexin (CNX), the ERphagy receptor FAM134B and the SNARE protein Syntaxin17 (STX17), which is engaged upon persistent glucosylation of the NS_PL oligosaccharide linked at the asparagine residue at position 321.

The understanding of osteoarthritis (OA) has gradually evolved from the traditional perspective of it being a mere "wear-and-tear" joint disease to a more comprehensive view that characterizes it as a degenerative joint disease marked by chronic low-grade inflammation and immune imbalance. The progression of OA is closely linked to abnormal mechanical loading and the activation of the innate immune system. This narrative review examines the role of mechanosensory-immune signaling networks in OA, with a specific focus on ion channels as receptors for upstream mechanical and chemical stimuli. These channels facilitate signal transduction through ion fluxes, such as Ca²⁺, to key inflammatory pathways, including nuclear factor κB (NF-κB), cyclic guanosine monophosphate-adenylate synthase-interferon gene stimulator (cGAS-STING), adenylate-activated protein kinase (AMPK), and the NLRP3 inflammasome. Furthermore, it integrates signaling axes such as the protein kinase/Yes-related protein (Hippo/YAP) pathway, the Wnt/β-catenin pathway, and the phosphoinositide 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling axes, analyzing their context-dependent bidirectional regulation during cartilage homeostasis maintenance and the degeneration process. The primary contributions of this study include the construction of an integrated mechanobiological-immunological transduction network framework that encompasses "ion channels-signaling pathways-immune responses." This framework highlights the hierarchical crosstalk and positive feedback amplification effects among these pathways, while exploring their dynamic and reversible regulatory characteristics under varying mechanical and inflammatory microenvironments. Ultimately, this framework facilitates a systems-level understanding of the pathological progression of OA and provides a theoretical foundation for the development of multi-target synergistic therapies and stage-specific precision intervention strategies.

Low-temperature stress severely restricts the growth, development, and ornamental value of <i>Osmanthus fragrans</i> Lour. However, the molecular mechanisms by which brassinolide (BR) and melatonin (MT) alleviate low-temperature-induced damage remain unclear. Here, <i>O. fragrans</i> branches were exposed to low-temperature stress (5, 0, -5, -10, -15, and -20 °C for 12 h) and treated with exogenous MT (50, 100, and 200 μM) or BR (0.5, 1, and 2 μM). An integrated approach combining phenotypic observation, physiological measurements, transcriptomics, and metabolomics was employed to elucidate the regulatory mechanisms underlying BR- and MT-mediated cold tolerance. The results showed that low-temperature stress significantly increased electrolyte leakage (EL), malondialdehyde (MDA), and hydrogen peroxide (H₂O₂) accumulation, while reducing superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities. Compared with the control, BR and MT treatments alleviated leaf chlorosis and wilting, reduced oxidative damage, and enhanced antioxidant enzyme activities. Integrated transcriptome-metabolome analyses demonstrated that BR and MT commonly activated phenylpropanoid and flavonoid biosynthesis, thereby promoting antioxidant metabolite accumulation, while suppressing <i>α</i>-linolenic acid and linoleic acid metabolism associated with stress-induced lipid remodeling. Network-based transcriptomic analyses identified transcription factors, including <i>ARF</i>, <i>EIL</i>, <i>bHLH</i>, and <i>GRAS</i>, as potential regulators of cold-responsive pathways. Furthermore, BR primarily regulated hormone-responsive networks, whereas MT mainly maintained redox homeostasis and metabolic reprogramming. These findings reveal the coordinated regulatory mechanisms underlying BR- and MT-mediated cold tolerance, providing potential targets for improving cold resilience in <i>O. fragrans</i>.

<i>Plac1</i> is an X-linked gene essential for placental and embryonic development. A knockout (KO) mouse model was used to define placental gene expression changes associated with Plac1 loss at E16.5 and E18.5 using gene expression microarray. Genes exhibiting at least a 1.5-fold change and FDR < 0.05 were considered significant. At E16.5, 717 genes were downregulated and 796 upregulated in KO placentas relative to wild type (WT), whereas at E18.5, 1121 genes were downregulated and 1151 upregulated. Subsets of highly and uniquely dysregulated genes were examined by gene-level curation alongside systems-level analyses, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Ingenuity Pathway Analysis (IPA), applied to the full differentially expressed gene (DEG) datasets. Downregulated genes were enriched for Rho GTPase-mediated and actin cytoskeleton-based processes, as well as membrane-associated signaling pathways with established roles in placental and embryonic development, vascular function, and branching morphogenesis. Overlap with pathways and molecular features associated with preeclampsia was also observed. In contrast, upregulated genes reflected, in part, immune activation and oxidative stress responses. These findings represent an important exploratory, hypothesis-generating analysis and provide a biologically coherent framework for understanding how Plac1 loss may be associated with placental dysfunction and pregnancy-related disease.

Intermittent fasting (IF) improves metabolic health, in part by remodeling white adipose tissue (WAT), yet the underlying mechanisms remain elusive. Here, we show that IF induces coordinated neurovascular remodeling in visceral WAT, marked by increased angiogenesis and sympathetic innervation. Using tissue clearing and three-dimensional imaging, we find that a 16-week IF regimen increases vascular density and sympathetic nerve fiber branching in perigonadal WAT. Transcriptomic profiling reveals the upregulation of neurotrophic factors, including neuregulin 4 (<i>Nrg4</i>), and browning-associated gene programs. WAT explants from IF-treated mice promote neurite branching in SH-SY5Y neuron-like cells, an effect blunted by ErbB inhibition. <i>In vivo</i> ErbB inhibition further attenuates IF-induced sympathetic remodeling. Human visceral adipose RNA-seq analysis shows a strong positive correlation between NRG4 expression and browning gene signatures. These findings support NRG4-ErbB signaling as a contributor to sympathetic remodeling, linking adipose neurotrophic signaling to metabolic benefits and therapeutic potential in obesity-related disorders.

Gallbladder cancer (GBC) is a highly malignant tumor of the biliary tract system.Although it is less common than other malignant tumors of the digestive system, its incidence and mortality rates have been on a continuous rise. With insidious early symptoms, the majority of patients are diagnosed at an advanced stage when the disease is detected. Surgical resection remains the radical treatment for gallbladder cancer yet many patients lose the opportunity for surgical intervention when seeking medical attention due to the onset of symptoms.In addition, given the high invasiveness and high recurrence rate of gallbladder cancer, systemic therapy beyond surgical treatment is particularly crucial. In recent years, precision medicine centered on immunotherapy and targeted therapy has exhibited certain therapeutic effects and improved the quality of life in patients with advanced cancer. Immunotherapy is a therapeutic modality that prevents immune evasion of tumor cells, primarily by means of immune checkpoint inhibitors such as CTLA-4 and PD- 1/PD-L1 inhibitors, among which PD-1/PD-L1 inhibitors are widely used in the immunotherapy of gallbladder cancer.Following the success of the global Phase III TOPAZ- 1 and KEYNOTE-966 trials, durvalumab in combination with gemcitabine and cisplatin, as well as pembrolizumab combined with gemcitabine and cisplatin, have been approved in multiple countries and recommended by authoritative guidelines as the preferred first-line systemic therapeutic regimens for advanced biliary tract cancers. A number of clinical trials conducted in recent years have initiated subgroup analyses of biliary tract cancer together with detections of biomarkers and the tumor microenvironment, providing guidance for immunotherapy of gallbladder cancer. This article elaborates on the mechanisms of immune checkpoint inhibitors, the unique tumor microenvironment and biomarkers specific to gallbladder cancer, summarizes clinical trials concerning gallbladder cancer and those incorporating gallbladder cancer subgroup analyses, interprets authoritative clinical guidelines and relevant policies, and presents the strategies and procedures adopted by our team for administering immunotherapy to patients with gallbladder cancer in routine clinical practice.

High pathogenicity avian influenza (HPAI) poses a significant threat to poultry. Some chickens show resilience to HPAI, but the mechanisms involved are poorly understood. In this study, we aimed to identify the biological mechanisms associated with resilience to HPAIV infection in chickens. Chickens were inoculated with H7N1 HPAIV and classified as susceptible or resilient based on clinical signs, mortality, histopathological lesions, AIV antigen detection in tissues, and viral shedding. Blood transcriptomic analysis revealed that genes from resilient chickens are involved in the integrin-mediated signaling pathway (ITGA5, ITGA6, ITGB1), as well as in adaptive (BTK, TEC) and innate (TRIM13, LCK, TICAM1) immune pathways. Plasma proteomic profiling revealed that ARF4, EIF4A2, and HNRNPAB (proteins involved in fundamental cellular processes) were less abundant in resilient chickens compared to both controls and susceptible birds. Our results suggest that early modulation of these pathways is associated with resilience to HPAIV and likely reflects early viral control or reduced systemic dissemination rather than the absence of infection.

Glioblastoma remains the most lethal primary malignancy of the central nervous system, and the modest gains achieved with maximal surgery, radiotherapy and temozolomide have not been matched by the immune checkpoint inhibitors and antigen-specific vaccines that reshaped the treatment of many extracranial cancers. The recurrent disappointment of these approaches has been attributed less to a single molecular lesion than to a confluence of obstacles: profound intratumoural heterogeneity, a densely immunosuppressive and myeloid-rich microenvironment, sequestration and exhaustion of conventional T cells, and the practical difficulty of delivering effectors across the blood-brain barrier. Against this background, γδ T cells have attracted interest as an unconventional effector population that recognises transformed cells through stress-associated and metabolic cues rather than peptide-major histocompatibility complex (MHC) complexes, that kills in an MHC-unrestricted manner, and that can be expanded from healthy donors for allogeneic, off-the-shelf use with little expectation of graft-versus-host disease. This narrative review examines, with a deliberately critical lens, the biological rationale and the experimental evidence for γδ T cell-based immunotherapy of glioblastoma. We summarise the developmental biology and functional subsets of human γδ T cells, the natural killer group 2 member D (NKG2D)-, DNAX accessory molecule 1 (DNAM-1)- and T-cell-receptor-dependent mechanisms through which they engage glioblastoma cells and glioma stem-like cells, and the in vitro and animal-model studies that underpin the field, taking care not to overstate efficacy that has so far been demonstrated only in preclinical or early-phase settings. We then weigh the principal opportunities-locoregional and repeated dosing, combination with chemoradiotherapy, checkpoint blockade and antibody-based redirection-against barriers that include limited persistence, uncertain intratumoural trafficking, donor and manufacturing variability, and the unsettled requirements of potency testing and trial design. We give particular weight to what becomes of γδ T cells inside a hostile tumour-the exhaustion-like dysfunction that follows chronic stimulation, the oxygen and glucose dependence of their effector programme, the interleukin-17-polarising signals generated by activated microglia and by genotoxic therapy, and the confounding effect of corticosteroids-together with the engineering and pharmacological strategies proposed to counter them. The first peer-reviewed phase 1 report of intracranially delivered, drug-resistant γδ T cells has now appeared and documents tolerability in a small, single-arm cohort without establishing survival benefit. Throughout, γδ T cells are presented as a biologically plausible but still investigational strategy whose clinical value will be determined by adequately powered trials rather than by mechanistic appeal alone.

<title>Abstract</title> <p>Background The association between placental development and cancer formation was first proposed over a hundred years ago. In our current investigation, we pioneered the application of serological proteome analysis (SERPA) of human placental proteins to detect tumor-associated antigens that trigger autoimmune responses in breast cancer patients. Methods We employed SERPA to examine serum reactivity against first-trimester placental (FTP) proteins in 86 early-stage breast cancer (BrC) patients and 86 non-cancer controls (non-BrC). Following initial screening, we isolated and characterized differentially reactive proteins using LC-MS tandem mass spectrometry. From these, we unambiguously identified 12 placental proteins showing the most pronounced differential expression between patient and control groups. These candidate biomarkers underwent rigorous validation through both ELISA and immunohistochemical (IHC) analyses. Results Our SERPA screening revealed thirty-three placental proteins exhibiting differential immunoreactivity with breast cancer-associated autoantibodies. Subsequent validation of twelve candidates identified six proteins including PDIA3 (p = 0.0059), STIP1 (p = 0.027), CCT2 (p = 0.0025), PARK7 (p = 0.0002), PRDX6 (p = 0.016) and LDHB (p = 0.0083) that showed statistically significant elevated reactivity with BrC patient sera. Gene Ontology analysis demonstrated that these autoantibody-targeted placental proteins primarily participate in immune regulation and cellular stress response pathways. Immunohistochemistry (IHC) staining of placenta using antibodies directed against PARK7 and PRDX6 recombinant proteins (cloned from FTP), localized their expression predominantly to placental cytotrophoblasts. Notably, in IHC staining of breast cancer and normal breast tissues, PARK7 and PRDX6 exhibited distinct subcellular localization patterns, significantly stronger nuclear staining in normal tissues (p < 0.001) versus predominant cytoplasmic localization in malignant specimens (p < 0.0001). Serum immunoreactivity from BrC patients displayed remarkable specificity, targeting nuclear and cytoplasmic compartments of rare cytotrophoblast subpopulations and syncytial nuclear aggregates. Through combinatorial analysis of placental-reactive autoantibodies, we identified a set of promising biomarker panels with specificity and sensitivity ranging from 64–73% and 77–97%, respectively, demonstrating potential for non-invasive breast cancer detection. Conclusion To the best of our knowledge, this study is the first to propose the use of placental proteins for early breast cancer screening. Our findings establish a novel approach for breast cancer detection and identify potential targets for immunotherapy. However, further refinement and clinical adaptation are needed before translation into diagnostic or therapeutic applications.</p>

It is an essential element of mechanobiology to measure the forces of biological cells. In microparticle traction force microscopy, they are inferred from the deformation of elastic microparticles. Two complementary variants have been introduced before: the volume method, which reconstructs surface stresses from the displacements of fiducial markers embedded inside the particles, and the surface method, which infers stresses directly from the deformation of the particle surface. However, a systematic comparison of the two methods has been lacking. Here, we quantitatively compare both approaches using simulated traction fields representing biologically relevant loading scenarios. We find that the surface method consistently reconstructs traction profiles with substantially lower errors than the volume method, which suffers from displacement tracking and stress calculation at the surface. At high noise levels, however, the performance gap becomes smaller. To compare the performance of the two methods in a realistic experimental setting, we developed DNA-based hydrogel microparticles equipped with both fluorescent surface labels and embedded fluorescent nanoparticles, enabling the direct comparison of the two methods within the same system. Compression experiments produced traction profiles consistent with Hertzian contact mechanics and confirmed the trends observed in the simulations. We also show that despite large experimental deformations and strains (both up to 20 percent), linear elasticity theory should still be valid. While our computational workflow establishes a framework to apply both methods, our experimental workflow establishes DNA microparticles as versatile and biocompatible probes for measuring cellular forces.

The downstream effectors that mediate the pro‑viral function of the MAPK pathway during enterovirus 71 (EV71) infection remain poorly defined. Here we show that early growth response 1 (EGR1) is independently regulated by each of the three classical MAPK branches including extracellular signal-regulated kinase (ERK), p38 and c-Jun N-terminal kinase (JNK), and serves as a common downstream target of these pathways to promote EV71 replication and virus-induced cell death. Furthermore, we found that the natural isoflavone calycosin (CA) from <i>Astragalus membranaceus</i> acts as a regulatory probe of the MAPK-EGR1 axis. CA suppresses EV71-induced expression and phosphorylation of ERK, p38, and JNK, as well as the subsequent upregulation of EGR1, thereby inhibiting both viral replication and virus-induced cell death in conventional cell lines and human colonic organoid infection models. This pro-viral axis is conserved among several enteroviruses, including coxsackievirus B3 and enterovirus D68, and CA exhibits broad-spectrum activity against multiple enteroviruses by targeting this axis. Collectively, our findings establish the MAPK‑EGR1 axis as a key host‑dependency node for EV71 and other enteroviruses, and identify CA as a valuable chemical probe for interrogating this axis. This work not only deepens our understanding of the interplay between enteroviruses such as EV71 and their host, but also provides a mechanistic basis for host‑directed antiviral strategies.

Iron overload is a life-threatening disease. Without early diagnosis and treatment, it can cause severe organ damage and even premature death by irreversibly damaging organs such as the heart, pancreas, spleen, or liver. We report here that a gain-of-function mutation in the endolysosomal two-pore channel TPC1 (TPC1^I486T) causes iron overload in mice, whereas mice lacking TPC1 exhibit the opposite phenotype, iron deficiency. Endolysosomal patch-clamp experiments demonstrated a strong gain in both human and mouse TPC1 mutant channel activity compared to wild-type upon activation with the early endosome (EE) associated endogenous ligand phosphatidylinositol 3-phosphate. Mechanistically, it was found that uptake of iron bound to transferrin/transferrin receptor from the plasma membrane as well as the pH in EE, from where Fe²⁺ is being released via DMT1 in a H⁺ dependent manner strongly depend on TPC1 activity.