Gene Literature Dashboard

Mendelian susceptibility to mycobacterial disease (MSMD) is a rare clinical syndrome that is characterized by selective vulnerability to intracellular pathogens. Deficiency in IL12RB1 is the most common type of MSMD but the heterogeneity of its clinical Manifestation Makes precise diagnosis difficult. Here, we report a previously healthy 29 year-old woman who had suffered from disseminated infection with Mycobacterium tilburgii, which is a rare, unculturable environmental mycobacteria, for over 2 years. We used whole exome sequencing to detect a novel compound heterozygous variant in the IL12RB1 gene. Immunological analysis of the patient's peripheral lymphocytes showed a barely detectable level of IL-12Rβ1, a reduced population of follicular helper T (Tfh) cells and impaired production of IFN-γ in response to IL-12/IL-23 stimulation. Metagenomic next-generation sequencing was used to identify the causative pathogen and to analyze drug susceptibility. The infection was contained by a combination of anti-mycobacterial drugs and IFN-γ supplementary treatment. An RNA-seq analysis, using follow-up blood samples, revealed the limited success of these treatments over 6 months. Our findings support the screening for inherited immunological problems in patients with difficult-to-treat mycobacterial infections. The suboptimal response to prolonged anti-mycobacterial drugs and IFN-γ supplementation warrants the development of novel therapeutic strategies for MSMD patients.

The Comcáac (also known as Seri) are an indigenous community from the central coast of the Sonoran Desert in Mexico. Genetic studies conducted on this population since the late 1990s have revealed marked genetic differentiation resulting from pronounced genetic drift caused by a historical bottleneck, which is consistent with anthropological and linguistic records. Research has examined allele frequencies and genetic variants associated with cirrhosis risk, pathogen adaptation, forensic markers, vitamin and sugar metabolism, body mass index, immune responses, cytochrome genes, genetic distances with other groups, and migration patterns. While early investigations relied on classical genetic approaches, more recent studies have employed omics technologies, including whole-genome sequencing. Analyses of the Comcáac genome provide valuable insights into the phenotypic traits and medical predispositions of this community.

<h4>Background</h4>Bladder cancer is a prevalent malignant tumor in the urinary system, ranking tenth among malignant tumors globally. Currently, the primary treatment methods include surgery, chemotherapy, immunotherapy, and emerging neoadjuvant therapies. These treatments have effectively reduced the mortality rate associated with bladder tumors. However, the prognosis for bladder cancer patients remains poor due to the high rates of recurrence, metastasis, and drug resistance. Therefore, identifying the pathological features and tumor immune environment of each patient to develop optimal treatment strategies is an urgent health issue.<h4>Methods</h4>We analyzed a single-cell dataset of bladder cancer to identify key signaling pathways and chromosomal mutations among different subgroups of bladder tumors. Additionally, we sought to identify ligand-receptor pairs between malignant bladder tumor epithelial cells and other cell subgroups. Using the TCGA-BLCA database and COX regression analysis, we screened key ligand-receptor pairs closely related to patient prognosis. We then used LASSO regression analysis to construct a bladder cancer risk prediction model based on these key ligand-receptor pairs (LR.Riskscore). To evaluate the impact of different LR.Riskscores on prognosis and clinical benefits for bladder cancer patients, we used Kaplan-Meier survival curves, risk forest plots, nomograms, and decision curve analysis. We also conducted cellular experiments, including clone formation, CCK8 assays, Transwell migration assays, and scratch assays, to elucidate the important cellular role of the key receptor CXCR4 in bladder tumor cells. Finally, we utilized the IMvigor210 bladder cancer immunotherapy dataset to reveal the correlation between the LR.Riskscore risk equation and bladder cancer immunotherapy.<h4>Results</h4>We constructed a bladder cancer risk prediction model based on key ligand-receptor pairs, including CXCL12_CXCR4, VEGFA_FLT1, PDGFRA_PDGFC, WNT2_SFRP4, and HLA-E_KLRC1. This model effectively predicted the prognosis and immunotherapy responsiveness of bladder cancer patients, significantly enhancing clinical benefits compared to conventional clinical features. Additionally, our cellular experiments confirmed the oncogenic role of the key receptor CXCR4 in bladder cancer.<h4>Conclusion</h4>Our risk prediction model significantly improves the evaluation of prognosis and the prediction of immunotherapy responsiveness in bladder cancer patients. This advancement promotes the development of precise, individualized treatment strategies for bladder cancer.

Tregs are critical for maintaining immune homeostasis, and their adoptive transfer can treat murine inflammatory disorders. In patients, Treg therapies have been variably efficacious. Therefore, new strategies to enhance Treg therapeutic efficacy are needed. Tregs predominantly depend on oxidative phosphorylation (OXPHOS) for energy and suppressive function. Fatty acid oxidation (FAO) contributes to Treg OXPHOS and can be important for Treg "effector" differentiation, but FAO activity is inhibited by coordinated activity of the isoenzymes acetyl-CoA carboxylase-1 and -2 (ACC1 and ACC2). Here, we show that small-molecule inhibition or Treg-specific genetic deletion of ACC1 significantly increases Treg suppressive function in vitro and in mice with established chronic graft-versus-host disease. ACC1 inhibition skewed Tregs toward an "effector" phenotype and enhanced FAO-mediated OXPHOS, mitochondrial function, and mitochondrial fusion. Inhibiting mitochondrial fusion diminished the effect of ACC1 inhibition. Reciprocally, promoting mitochondrial fusion, even in the absence of ACC1 modulation, resulted in a Treg functional and metabolic phenotype similar to that seen with ACC1 inhibition, indicating a key role for mitochondrial fusion in Treg-suppressive potency. Ex vivo-expanded, ACC1 inhibitor-treated human Tregs similarly augmented suppressor function, as observed with murine Tregs. Together, these data suggest that ACC1 manipulation may be exploited to modulate Treg function in patients.

Membrane transporters are essential for human health, mediating the movement of nutrients, electrolytes, metabolites and other molecules across cellular and organellar membranes. Genes encoding these proteins account for approximately 5.2% of the human protein coding genome. Nearly half of these belong to the solute carriers (SLC) supergroup, the largest class of membrane transport proteins, collectively termed the "SLC-ome." The current SLC-ome comprises 464 SLCs organized into 76 SLC families, of which 24% (111 SLCs) remain orphan transporters with unknown or incompletely characterized function. An additional 52 SLC-like proteins bring the total to 516 membrane transport proteins. SLCs function as molecular gatekeepers, and their dysfunction contributes to a wide spectrum of human diseases, including cancer, diabetes, and immunological, cardiovascular and neurodegenerative disorders. Pathological consequences of SLC defects include hypertension, hyperglycemia, hypercholesterolemia, nutritional deficiencies, metal ion imbalance, oxidative stress, and dysfunction of mitochondria, lysosomes, endoplasmic reticulum and Golgi apparatus. In addition, genetic defects in SLCs are the cause of many rare diseases. Several SLCs require additional subunits to form functional heteromeric complexes, while others exhibit additional or alternative roles, such as acting as transceptors. In this review, we provide updated physiological, structural, mechanistic, and pharmacological insights for each of the 516 human SLC and SLC-like proteins. We also summarize their classification, structural architecture, transport mechanisms and pharmaceutical relevance, and present the most recent SLC gene nomenclature assignments approved by the HUGO Gene Nomenclature Committee (HGNC).

Down syndrome (DS, or Trisomy 21) is one of the most common genetic causes of intellectual disability. DS results in both abnormal neurodevelopment and accelerated neurodegeneration, but the molecular mechanisms underlying abnormal corticogenesis are incompletely understood. To gain molecular insight into the prenatal neurobiology of DS, we performed single-nucleus sequencing, spatial transcriptomics, and proteomics on mid-gestational prenatal human cortex. We captured altered expression dynamics of lineage commitment genes and de-repression of transposable elements in DS neural progenitor cells, which suggest changes to the fate and functionality of neuronal and glial cells. Given the importance of linking human and model system pathobiology, we also performed highly multiplexed RNA in situ spatial transcriptomics on a well-established trisomic mouse model (Ts65Dn) to study the cellular landscape of the trisomic brain during early development and maturation. We profiled the spatial transcriptome of > 240,000 cells in the mouse brain and identified trisomy-associated gene expression patterns in the molecular control of neurogenesis and gliogenesis. Together, our study provides an extensive resource for understanding of the complex multicellular processes underlying DS neurodevelopment.

<h4>Background</h4>The molecular characterisation of pediatric acute lymphoblastic leukemia (pALL) is essential for accurate diagnosis and risk stratification. However, standard-of-care (SoC) methods have limited sensitivity and resolution.<h4>Methods</h4>This study evaluates the clinical utility of emerging genomic technologies-including optical genome mapping (OGM), digital multiplex ligation-dependent probe amplification (dMLPA), RNA sequencing (RNA-seq), and targeted next-generation sequencing (t-NGS)-in the largest cohort of pALL patients analysed to date, with 60 cases using OGM.<h4>Results</h4>Considering clinically relevant alterations identified with at least two different methods, OGM as a standalone test demonstrated superior resolution, detecting chromosomal gains and losses (51.7% vs. 35%, p = 0.0973) and gene fusions (56.7% vs. 30%, p = 0.0057), while resolving 15% of non-informative cases. Combining dMLPA and RNA-seq was the most effective approach, achieving precise classification of complex subtypes and uniquely identifying IGH rearrangements undetected by other techniques. OGM identified clinically relevant alterations in 90% of cases, and the dMLPA-RNAseq combination reached 95%, compared to 46.7% with SoC techniques.<h4>Conclusions</h4>Integrating these technologies into diagnostic workflows overcomes SoC limitations. OGM and the dMLPA-RNAseq combination emerge as front-line strategies, addressing pALL heterogeneity, streamlining molecular testing, and informing treatment decisions to improve outcomes.

Meat quality and carcass traits are the most economically important traits affecting the value and the quality characteristics of the animal at slaughter. In this study, we analyzed the genomes of 295 domestic cattle from 20 global breeds using next-generation sequencing to identify signatures of positive selection associated with meat production and quality traits. The results of population genetic analysis revealed genetic differentiation among worldwide cattle groups. We observed clustering of samples in agreement with their geographic origins and production characteristics. We further observed noticeable genetic variety between cattle groups from different geographical regions. Generally, the lowest genetic diversity was determined for commercial cattle breeds, while the highest genetic diversity was found in African local cattle breeds. Our search for putative selective genomic regions in beef cattle populations revealed several candidate genes such as BMP2, EGR1, MAGEL2, U6, TMEM201, ELK3 and 5S_rRNA that were previously explored to be associated with carcass traits and meat quality in beef cattle. The enriched pathways and candidate genes discovered in this study could supply a basis for future improvement through the use of whole-genome technologies and selective breeding.

<h4>Background</h4>Migraine is a highly prevalent neurological disorder with complex pathophysiology and limited treatment efficacy. Emerging evidence suggests immune cell involvement in migraine, but the specific regulatory mechanisms remain unclear. This study aimed to identify immune cell-type-specific genetic drivers of migraine and prioritize potential therapeutic targets.<h4>Methods</h4>We conducted a Mendelian randomization (MR) analysis integrating single-cell expression quantitative trait loci (sc-eQTL) data from 14 immune cell types with large-scale genome-wide association studies (GWAS) of migraine. Colocalization analysis, protein-protein interaction (PPI) networks, linkage disequilibrium score regression (LDSC), phenome-wide association studies (PheWAS), and drug repurposing databases were utilized to validate findings and assess therapeutic potential and safety.<h4>Results</h4>We identified 25 immune cell-specific eGenes causally associated with migraine, including CDC42, NELFCD, HOXB3, HAX1, and FHL3. Several genes, such as CDC42 and HAX1, were implicated across multiple immune cell types. Subtype-specific analyses revealed differential gene effects in migraine with aura (MA) and without aura (MO). Genetic correlation and pleiotropy analyses linked eGenes to comorbid traits such as depression, gastrointestinal disorders, and blood pressure. PheWAS suggested minimal adverse associations for prioritized genes like GINM1 and TMA7. Drug repurposing identified FDA-approved agents, including hydroxychloroquine sulfate (NELFCD) and bazedoxifene (CDC42), as potential migraine therapies.<h4>Conclusion</h4>This study reveals immune cell-specific genetic contributors to migraine and highlights druggable targets for therapeutic development. Integrating sc-eQTL with multi-omics and pharmacological data provides a novel framework for precision medicine in migraine.

Acetylcholine (ACh) is an essential neurotransmitter that has recently gained attention for its multifunctional role in tumor immune regulation. By binding neuronal loss to nicotinic and muscarinic receptors, ACh directly promotes tumor cell proliferation and migration while modulating immune cell functions, thereby influencing the tumor microenvironment. Additionally, ACh plays a crucial role in tumor angiogenesis and stromal remodeling. Recent studies suggest that combining ACh modulators with immune checkpoint inhibitors and other therapies may improve treatment efficacy and overcome resistance. This review highlights current research developments regarding ACh in tumor immune regulation, explores its underlying mechanisms and clinical potential, and provides a theoretical basis for developing personalized therapeutic strategies.

BACKGROUND: Bladder carcinoma (BC) is a malignant tumor that originates from the epithelial cells of the urinary system. Currently, the main diagnostic methods suffer from disadvantages including being invasive, having high costs, and low sensitivity and specificity. Therefore, there is an urgent need to develop a non-invasive, high-performance method for diagnosing BC. MATERIALS AND METHODS: We developed a urine DNA detection panel utilizing two methylation biomarkers for the diagnosis of BC. A total of 467 urine samples were collected from the First Affiliated Hospital of Anhui Medical University for DNA methylation analysis. The methylation levels of Vimentin and POU class 4 homeobox 2 gene (POU4F2) were analyzed in a training set of 306 urine samples (92 cases and 214 controls), and in an independent validation set of 161 urine samples (59 cases and 102 controls) using Real-Time PCR (RT-PCR). RESULTS: The Vimentin/POU4F2 combined methylation panel achieved an AUC of 0.935 (95% CI: 0.889–0.981), with sensitivity, specificity, and accuracy of 86.44% (95% CI: 0.772–0.957), 96.08% (95% CI: 0.923–0.998), and 92.55% (95% CI: 0.886–0.965) for diagnosing BC. Notably, for patients with stage I and low-grade BC, the sensitivity was 90.00% for both. Additionally, it demonstrated specificities of 96.30% and 95.83% for patients with other urinary diseases and malignancies in other systems. CONCLUSIONS: Our study provides evidence that the two-gene methylation panel based on urine DNA detection demonstrates strong performance in diagnosing BC with high sensitivity and accuracy, offering a promising strategy for early screening and adjunctive diagnosis of BC.

<h4>Background</h4>Phosphate solubilizing bacteria (PSB) can break down insoluble forms of phosphorus such as Ca₃(PO₄)₂. In several soil grown crops, PSB inoculation improved phosphorus nutrition. However, positive results are inconsistent and there is comparably little information about PSB efficacy in soilless culture systems. This study aimed to identify phosphate solubilizing bacteria (PSB) from a greenhouse rhizobacteria collection that could be used to improve floriculture crop growth and health under phosphorus limiting conditions.<h4>Results</h4>A bromophenol blue (pH indicator) based colorimetric assay was used to identify bacterial isolates that acidified the culture media. From the collection of 1044 bacteria, 35 isolates that reduced media pH were identified, and their phosphate solubilization capacity was quantified. The top 14 PSB were selected for whole-genome sequencing. The isolates belonged to genera Enterobacter (8), Pantoea (5), and Raoultella (1). In planta effects of strains C2B11 and C8D10 were evaluated in French marigolds (Tagetes patula) grown in a peat-based substrate (pH = 7). Phosphorus was supplemented weekly as insoluble Ca₃(PO₄)₂. C2B11 and C8D10 inoculated marigolds were greener than non-inoculated controls. Only C2B11 increased shoot digital biomass and bloom area.<h4>Conclusions</h4>Bromophenol blue proved useful to identify bacteria that reduced culture media pH, but not all identified isolates showed high phosphate solubilization. Pantoea formicae C8D10 and Pantoea trifolii C2B11 strains improved growth or health of marigolds grown in soilless substrate under phosphate limiting conditions. We showed the applicability of bromophenol blue for high-throughput PSB identification. C8D10 and C2B11 are phosphate solubilizing bacteria native to soilless substrate systems, and both strains have potential for use as biostimulants to support phosphorus management in ornamental greenhouse production.

Despite some clinical success, ovarian cancer (OC) patients rarely achieve durable benefit from current immunotherapies, suggesting a need for strategies that improve OC immune recognition. We previously reported that engineered T cells secreting folate receptor alpha (FRα)-targeted bispecific T cell engagers (FR-B T cells) elicit robust antitumor responses in OC, in part by engaging endogenous T cells. Here, we use clinical OC specimens and preclinical OC to evaluate FR-B T cells combined with PD-1 blockade. Assessing the tumor microenvironment during acute and prolonged FR-B T cell + anti-PD-1 responses revealed broad immune cell engagement/reorganization. Early CD8+ T cell-driven responses and myeloid cell influx were followed by accumulation of CXCL13-producing macrophages, activated B cells, and effector memory CD4+ T cells with durable response, hallmarks that were diminished with progressive disease. Resistant OC (characterized by FRα loss and metabolic reprogramming) emerged at disease relapse, suggesting a need to target additional vulnerabilities to extend responses. As FR-B T cells promoted epitope spreading beyond FRα, we employed a booster vaccine to enhance antitumor immunity, improving OC control. Our findings point to rationally combining FR-B T cells with PD-1 blockade in OC and an opportunity to apply personalized cancer vaccines to limit OC relapse.

Histone post-translational modifications (PTMs) play a crucial role in regulating gene expression and maintaining DNA integrity, and their aberrations are linked to various diseases, including cancer. While lysine acetylation and methylation have been extensively studied, recent research has uncovered additional PTMs that significantly contribute to chromatin structure and function. Mass spectrometry is the most effective analytical method for studying histone PTMs; however, computational limitations often restrict the analysis to common modifications. Unrestrictive search strategies have the potential to enable a more comprehensive characterization of the histone modification landscape. In this work, we systematically assess the application of unrestrictive search approaches to histone data. After evaluating the limitations of these methods, we develop a novel bioinformatics workflow, named HiP-Frag (histone PTM analysis with FragPipe), which enables the identification of 96 sites decorated with uncommon PTMs on core histones-60 of which were previously unreported-as well as 55 histone marks on linker histones, including 13 novel ones, purified from human cell lines and primary samples. The expanded histone PTM analysis enabled by this strategy is among the first to extract previously unexplored epigenetic information from mass spectrometry raw data. This approach paves the way for a facilitated and more streamlined identification of uncommon and yet unannotated histone modifications, supporting a deeper dissection of the histone code and the understanding of the potential biological role of the novel epigenetic marks.

Excessive intracellular copper accumulation triggers cuproptosis, a novel regulated cell death process with therapeutic potential. Analyzing 566 The Cancer Genome Atlas samples alongside lung adenocarcinoma (LUAD)-specific microarray and single-cell sequencing data, we identified 109 cuproptosis-associated genes, of which <i>C1QBP</i> and <i>PFKP</i> emerged as key prognostic markers. Four-gene risk model stratified patients into high- and low-risk groups with distinct survival outcomes, where high-risk scores correlated with advanced TNM stages. Clinical validation confirmed that elevated <i>C1QBP</i>/<i>PFKP</i> expression in LUAD tissues predicted shorter progression-free survival. Functional assays demonstrated that silencing <i>C1QBP</i> or <i>PFKP</i> increased intracellular copper concentration, suppressed proliferation, and inhibited invasion, mechanistically linking these genes to cuproptosis dysregulation. Our findings nominate <i>C1QBP</i>/<i>PFKP</i> as actionable targets for LUAD therapy, offering both prognostic biomarkers and copper-metabolism-directed treatment strategies.

Analysis of selection signatures in the genomes of farm animals enables the detection of genomic regions affected by selection and contributes to the identification of genes underlying adaptive and productive traits. This research aimed to identify loci under selection pressure and to detect candidate genes in Dzhalgin Merino sheep by performing a comparative genomic analysis with the related Australian Merino and Rambouillet breeds. A total of 293 animals were included in the analysis, comprising Dzhalgin Merino (n = 53), Australian Merino (n = 50), Australian Industry Merino (n = 88), and Rambouillet (n = 102). Whole-genome SNP genotyping data for Dzhalgin Merino were generated within this study, while data for Australian Merino, Australian Industry Merino, and Rambouillet were obtained from the SheepHapMap project. For the purposes of analysis, Australian Merino and Australian Industry Merino were combined into a single group (n = 138). To enhance the reliability of the results, three independent methods were employed to detect selection signatures: the fixation index (FST), analysis of linkage disequilibrium variation (varLD), and the cross-population number of segregating sites by length (xp-nSL). The study showed that Dzhalgin Merino have unique genetic signatures potentially associated with adaptation and productivity, which opens up new opportunities for their selection. The identified genes can become the basis for developing new breeding programs aimed at improving both the productive qualities and the adaptive abilities of the breed. Further research should be aimed at a detailed investigation of gene structure within loci under selection pressure and at clarifying the mechanisms by which these genes influence animal phenotypes. A total of 185 genes were identified within genomic regions exhibiting selection signatures. Among these, particular attention was given to <i>EPHA6</i>, <i>MLLT3</i>, <i>ROBO1</i>, <i>KIAA0753</i>, <i>MED31</i>, <i>SLC13A5</i>, and <i>ELAVL4</i>, which are involved in biological processes such as growth, development, and reproduction. The identified genes represent potential targets for breeding programs aimed at increasing productivity and adaptive capacity of the breed.

Tuberculosis (TB) is one of the leading infectious causes of mortality worldwide. Although a significant proportion of the population (up to 36%, depending on the region) is infected with the latent form of TB, only about one in ten of these people will develop an active form of the disease in their lifetime. This is due to a complex interaction between the host's genetic predisposition and environment. However, the genetic determinants of TB are not well established and have been insufficiently explored in previous genome-wide association studies (GWAS) with sparse and incongruent results. We reviewed recent evidence on host genetic susceptibility to TB, highlighting population-specific characteristics, host-pathogen coevolution, and the limitations of conventional GWAS approaches in terms of clinical and genetic heterogeneity. While rare variants with high penetrance, such as <i>TYK2</i> P1104A, lead to monogenic susceptibility, most heritable risk results from the cumulative effect of numerous common variants. This cumulative effect may be summarized using polygenic risk scores (PRSs). Although their use has been proven for non-communicable diseases, PRSs are not applied to infectious disease susceptibility. To date, no PRS model for susceptibility to tuberculosis has been consistently validated. The development of PRSs for TB susceptibility is limited by phenotypic heterogeneity, population structure, and co-adaptation between host and pathogen. Another major challenge is to take into account the considerable influence of environmental factors. This difficulty in modeling environmental influences probably explains the current lack of a clinically applicable PRS for TB susceptibility. However, taking these caveats into account, polygenic models could improve risk stratification at the individual level compared to single-variant association and allow for earlier targeted treatment and prophylaxis.

Major depressive disorder (MDD) is one of the most common diseases, affecting millions of people worldwide. Existing antidepressants do not allow sustainable remission to be achieved in many cases, probably due to insufficient understanding of the etiopathogenesis of MDD. The aim of this study was to identify the key genes, pathways, and master regulators associated with MDD based on a combination of genomic and transcriptomic data analyses. We performed a transcriptome-wide association study (TWAS) to identify the increase and decrease in transcription of particular genes that can be associated with MDD risk, the results of which were used to perform a pathway enrichment analysis that elucidated the pathways and processes associated with MDD. Besides changes in the metabolism of neurotransmitters, the association of some other processes with MDD was revealed, including changes in phospholipid and glycan metabolism, chromatin remodeling, RNA processing and splicing, and cell-extracellular matrix interaction. The transcriptomic analysis performed for brain regions mostly confirmed genome-level findings. The gene expression changes in the brain related to MDD were mostly sex-specific, and the transcription of many genes was changed in the opposite direction in males and females. Finally, master regulators were found, which are the proteins responsible for the transcriptional regulation of the revealed genes and represent the most important proteins contributing to MDD development.

<i>Bacteroides fragilis</i>, a prominent commensal of the human gut microbiota, plays a vital role in immune system regulation through its capsular polysaccharide A (PSA), which requires a glycolipid anchor structurally reminiscent of lipid A. While canonical <i>Escherichia coli</i> lipid A acts as a potent TLR4 agonist contributing to septic shock and inflammatory disorders, certain <i>B. fragilis</i>-derived glycolipids demonstrate antagonistic effects, offering potential as anti-inflammatory agents. In this study, we report the synthesis and preliminary computational evaluation of a library of glycolipids inspired by <i>B. fragilis</i> lipid A. Three lipid As, including a tetra-acylated 1-phosphoryl lipid A analog (Tetra C-1), were synthesized and assessed using molecular docking simulations targeting the human TLR4/MD-2 complex. Docking results reveal that Tetra C-1 exhibits more favorable antagonist binding characteristics compared to the well-studied TLR4 antagonist Eritoran. This work highlights a microbiota-informed strategy for the development of novel TLR4 antagonists, potentially enabling targeted modulation of innate immunity for therapeutic applications in inflammatory diseases and as vaccine adjuvants.

Despite major advances in oncology, cancer therapy continues to face persistent challenges due to intratumoral heterogeneity, drug resistance, and the poor clinical translation of experimental therapeutics. Conventional preclinical models such as 2D cultures and animal systems often fail to accurately recapitulate the tumor microenvironment immune contexture, and patient-specific variability limiting their predictive power. While nanomedicine and advanced drug delivery platforms offer promising solutions, their translational success is hindered by insufficient integration with physiologically relevant tumor models. In this review, we critically examine how patient-derived organoids derived from patient tumors serve as next-generation platforms for modeling cancer heterogeneity, therapeutic response, and biomarker discovery. We further explore how the integration of PDOs with functional biomaterials, extracellular matrix mimetics, and organ-on-chip systems enables dynamic co-culture environments that capture tumor-stroma-immune interactions with high fidelity. By linking the biological underpinnings of resistance, such as genetic mutations, altered signaling, metabolic rewiring, and immune evasion, with smart biomaterial design and drug screening workflows, we propose a unified roadmap for precision oncology. Additionally, we highlight the emergence of PDO biobanks, co-culture innovations, and high-throughput phenotypic screening as essential tools for improving clinical translation. This interdisciplinary synthesis underscores the transformative potential of PDO-based platforms in accelerating personalized cancer therapy.

<h4>Background</h4>Newborns undergo rapid metabolic and organ adaptations after birth, which are compromised in premature newborns, leading to adverse health outcomes. Molecular mechanisms underlying these transitions remain poorly understood due to limited tissue availability. To address this gap, we characterized tissue transcriptomes using autopsy samples from a unique newborn cohort.<h4>Methods</h4>We analyzed liver (LI), heart (HM), and skeletal muscle (SM) transcriptomes using RNA sequencing in 41 predominantly premature newborns who died shortly after birth. Nearly 14,000 protein-coding gene transcripts per tissue were detected.<h4>Results</h4>Tissues exhibited distinct expression profiles, with LI showed the highest number of tissue-specific genes. SM gene expression correlated strongly with gestational age at birth (i.e., the prenatal development), while LI was influenced by the duration of postnatal survival (i.e., the postnatal development). HM displayed minimal changes, suggesting stable myocardial metabolism during the perinatal transition. Weighted Gene Co-expression Network Analysis (WGCNA) identified tissue-specific gene co-expression modules linked to clinical traits such as gestational age, birth weight, survival duration, nutrition, and exposure to catecholamine treatment. The key functional annotations, validated by differential expression analysis, revealed that LI and SM modules were enriched for mitochondrial metabolism and oxidative phosphorylation genes, with more pronounced prenatal development in SM, and a postnatal increase in both tissues. Data suggests that energy metabolism in SM matures first, followed by the development of muscle functions. Hepatic modules were associated with a postnatal increase in the steroid hormone/xenobiotic metabolism, and a decline in hematopoietic activity. Robust annotations to ribosome activity suggested tissue-specific changes in protein synthesis, which declined prenatally in SM, postnatally in HM. Notably, the supply of exogenous glucose and nutrition type were strongly associated with hepatic gene expression, highlighting the central role of the liver in postnatal metabolic adaptation.<h4>Conclusion</h4>Overall, our study highlights tissue-specific perinatal gene regulation, with mitochondrial maturation emerging as a crucial driver of postnatal adaptation, explaining vulnerabilities in preterm infants. We provide a unique resource for characterizing developmental changes in tissue transcriptomes during the fetal-to-neonatal transition in human newborns.

<h4>Objective</h4>This study explores the prognostic value of the <i>CLEC4E</i> gene in systemic lupus erythematosus (SLE) through bioinformatics analysis and evaluates its role in disease diagnosis and progression.<h4>Methods</h4>Gene expression datasets related to SLE (GSE17755, GSE50772, and GSE61635) were obtained from the GEO (Gene Expression Omnibus) database. Intersection analysis was performed using the Jvenn tool with a screening threshold of |log2FC| > 1 and P< 0.05 to identify differentially expressed genes (DEGs). The resulting DEGs were then cross-referenced with immune-related genes in the GeneCards database (relevance score > 8) to further prioritize candidates with immunological relevance. Peripheral blood from 360 SLE patients and 360 healthy controls was collected for <i>CLEC4E</i> expression analysis via RT-qPCR. Disease activity was evaluated using the SLEDAI score, and patients were grouped accordingly. Pearson and Spearman correlation analysis to investigate the relationship between <i>CLEC4E</i> and immune indicators. Logistic regression and <i>ROC</i> analyses were conducted to assess diagnostic and prognostic value. Kaplan-Meier analysis evaluated survival outcomes.<h4>Results</h4>Bioinformatics analysis identified six SLE-related DEGs, namely <i>ISG15</i>, <i>HERC5</i>, <i>TNFAIP6</i>, <i>IFIT3</i>, <i>OASL</i>, and <i>CLEC4E.</i> Further intersection with immune-related genes from the GeneCards database (relevance score > 8) ultimately highlighted <i>CLEC4E</i> as the key gene for clinical validation. The expression level of <i>CLEC4E</i> was significantly higher in SLE patients compared with healthy controls. <i>ROC</i> analysis showed good diagnostic performance (AUC = 0.7744). <i>CLEC4E</i> expression was higher in active SLE, and multivariate analysis identified <i>CLEC4E</i>, C3, C4, ANA, and anti-dsDNA as independent predictors of disease activity. <i>CLEC4E</i> demonstrated moderate diagnostic value for distinguishing active from inactive disease (AUC = 0.6360). Higher <i>CLEC4E</i> expression was associated with worse prognosis (<i>P</i> = 0.0002). The combined diagnostic performance with other biomarkers (C3, C4, ANA, anti-dsDNA) showed a remarkable AUC of 0.9407.<h4>Conclusion</h4><i>CLEC4E</i> is a potential biomarker for SLE diagnosis, disease activity assessment, and prognosis evaluation.

Lipopolysaccharides (LPS) from Gram-negative bacteria represent a significant challenge across various industries due to their prevalence and pathogenicity and the limitations of existing detection methods. Traditional approaches, such as the rabbit pyrogen test (RPT) and the Limulus Amebocyte Lysate (LAL) assay, have served as gold standards for endotoxin detection. However, these methods are constrained by high costs, lengthy processing times, environmental concerns, and the need for significant reagent volumes, which limit their scalability and application in resource-limited settings. In this study, we introduce an innovative microfluidic platform that integrates the LAL assay within microdroplets, addressing the critical limitations of traditional techniques. By leveraging the precise fluid control and reaction isolation offered by microdroplet technology, the system reduces reagent consumption, enhances sensitivity, and enables high-throughput analysis. Calibration tests were performed to validate the platform's ability to detect LPS, using colorimetric measurements. Results demonstrated comparable or improved performance relative to traditional systems, achieving lower detection limits and greater accuracy. This work demonstrates a proof-of-concept miniaturisation of the pharmacopoeial LAL assay. The method yielded low intra-assay variability (σ ≈ 0.002 OD; CV ≈ 0.9% over n = 50 droplets per point) and a LOD estimated from calibration statistics after path-length normalisation. Broader adoption will require additional comparative validation and standardisation. This scalable, cost-effective, and environmentally sustainable approach offers a practical solution for endotoxin detection in clinical diagnostics, biopharmaceutical production, and environmental monitoring. The proposed technology paves the way for advanced LPS detection methods that meet stringent safety standards while improving efficiency, affordability, and adaptability for diverse applications.

<h4>Background/objectives</h4>Lactate (LA) is a key metabolite in exercise metabolism, transported across cell membranes by monocarboxylate transporters (MCTs). Although genetic variation in <i>MCT</i> genes has been linked to LA kinetics, evidence in athletic populations remains limited. This study investigated nine MCT1 polymorphisms (rs4301628, rs12028967, rs10857983, rs3789592, rs10776763, rs1049434, rs6537765, rs7556664, rs7169) in relation to LA metabolism.<h4>Methods</h4>337 Polish and Czech males (elite athletes, sub-elite competitors, physically active controls) performed two maximal Wingate tests. Buccal swabs were collected for DNA extraction and single nucleotide polymorphism (SNP) genotyping. LA was assessed before and after the tests.<h4>Results</h4>Five variants (rs3789592, rs7556664, rs7169, rs1049434, rs6537765) remained significantly associated with LA measured 30 min after the second Wingate (LA30') and delta clearance capacity (DCC) in elites (codominant and recessive models: <i>p</i> = 0.01-0.03; false discovery rate (FDR)-adjusted <i>p</i> = 0.02-0.04). Rs10776763 showed the broadest associations, surviving FDR for LA30' in all models (<i>p</i> = 0.003-0.03; FDR-adjusted <i>p</i> = 0.01-0.03) and for LA accumulation capacity (ACC) in the recessive model (<i>p</i> = 0.01; FDR-adjusted <i>p</i> = 0.03). Rs12028967 also supported a clearance role, with LA30' significant in elites (<i>p</i> = 0.004; FDR-adjusted <i>p</i> = 0.01) and DCC in the overall cohort (<i>p</i> = 0.02; FDR-adjusted <i>p</i> = 0.03). In contrast, rs4301628 and rs10857983 demonstrated isolated LA30' effects in elites (<i>p</i> = 0.004-0.01; FDR-adjusted <i>p</i> = 0.01), and no production-phase endpoint other than rs10776763 survived FDR; ACC remained significant in the recessive model (<i>p</i> = 0.01; FDR-adjusted <i>p</i> = 0.03).<h4>Conclusions</h4>The results suggest that <i>MCT1</i> polymorphisms contribute to differences in LA metabolism and warrant replication in larger, more diverse cohorts.

Measurement of the oxygen consumption rate, or respirometry, is a powerful and comprehensive method for assessing mitochondrial function both <i>in vitro</i> and <i>in vivo</i>. Respirometry at the whole-organism level has been repeatedly performed in the model organism <i>Caenorhabditis elegans</i>, typically using high-throughput microplate-based systems over traditional Clark-type respirometers. However, these systems are highly specialized, costly to purchase and operate, and inaccessible to many researchers. Here, we develop a respirometry assay using low-cost commercially available optical oxygen sensors (PreSens OxoPlates^®) and fluorescence plate readers (the BMG FLUOstar), as an alternative to more costly standard respirometry systems. This assay uses standard BMG FLUOstar protocols and a set of custom scripts to perform repeated measurements of the <i>C. elegans</i> oxygen consumption rate, with the optional use of respiratory inhibitors or other interventions. We validate this assay by demonstrating the linearity of basal oxygen consumption rates in samples with variable numbers of animals, and by examining the impact of respiratory inhibitors with previously demonstrated efficacy in <i>C. elegans</i>: carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (a mitochondrial uncoupler) and sodium azide (a Complex IV inhibitor). Using this assay, we demonstrate that the sequential use of FCCP and sodium azide leads to an increase in the sodium azide-treated (non-mitochondrial) oxygen consumption rate, indicating that the sequential use of respiratory inhibitors, as standard in intact cell respirometry, may produce erroneous estimates of non-mitochondrial respiration in <i>C. elegans</i> and thus should be avoided.

The association of serum bile acid levels with liver cirrhosis severity is of interest. Hence, 100 patients were admitted, among them 50 patients had variable severity of liver cirrhosis and 50 patients were controls. Serum bile acid levels were measured and their association was also analyzed with clinical parameters like Child-Pugh score, MELD score and liver function tests. The results indicate that serum bile acid concentrations are strongly associated with the severity of liver cirrhosis and potentially as a disease progression biomarker. Thus, the clinical value of bile acids as a marker for the severity of liver cirrhosis is shown.

Long non-coding RNAs have emerged as pivotal regulators of diverse biological processes, particularly in the modulation of regulated neuronal cell death pathways. This review highlights the roles of long non-coding RNAs in programmed neuronal cell death, focusing on apoptosis, necroptosis, ferroptosis, and pyroptosis. Dysregulation of these processes contributes to neurodegenerative disorders and neurological injuries, emphasizing the importance of understanding how long non-coding RNAs influence these pathways. Apoptosis, essential for neuronal development, can lead to pathology when misregulated. Necroptosis, a caspase-independent inflammatory process, involves the modulation of necrosome components. Pyroptosis, mediated by inflammasomes, affects inflammasome assembly and cytokine release. Ferroptosis, driven by iron accumulation and lipid peroxidation, is influenced by changes in antioxidant defenses. By detailing the roles of long non-coding RNAs in these mechanisms, this review underscores their therapeutic potential for mitigating neuronal loss.

The mitochondrial genomic homeostasis is essential for the function of the oxidative phosphorylation system and cellular homeostasis. Mitochondrial DNA is particularly susceptible to aging-related oxidative stress due to the lack of a histone coat. Disturbances in mitochondrial DNA may contribute to functional decline during the aging process and in neurodegenerative diseases, leading to further impairment of mitochondrial DNA and initiating a vicious cycle. To date, it remains unclear how disturbed mitochondrial DNA is involved in the etiology of pathological aging and neurodegenerative diseases. The purpose of this review is to clarify the crucial roles of mitochondrial DNA homeostasis in the pathogenesis of neurodegenerative diseases. Mitochondrial DNA is distributed within nucleoids and is then transcribed into polycistronic mitochondrial DNA molecules within the mitochondrial granule region. Within the ultrastructure of the mitochondrial nucleoid and granule, a group of essential mitochondrial proteins involved in DNA replication, DNA transcription, RNA translation, RNA surveillance, and RNA degradation plays a crucial role in maintaining mitochondrial structure, genome integrity, and mitochondrial DNA processing. The uniparentally inherited mitochondrial DNA undergoes heritable polyploid variations, which include homoplasmy and heteroplasmy. Accumulating mitochondrial DNA alterations, such as deletions, point mutations, and methylations, occur during the pathogenic processes of neurodegenerative diseases. The increased mitochondrial DNA alterations can be propagated by the rise of deleterious heteroplasmy in neurodegenerative diseases, ultimately resulting in impairment to the oxidative phosphorylation system, biogenesis defects, and cellular metabolic dysfunction. Therefore, developing appropriate gene editing tools to rectify aberrant alterations in mitochondrial DNA and targeting the key proteins involved in maintaining mitochondrial DNA homeostasis can be considered promising therapeutic strategies for neurodegenerative diseases. Although therapeutic strategies targeting mitochondrial DNA in diseases show great potential, challenges related to efficacy and safety require a better understanding of the mechanisms underlying mitochondrial DNA alterations in aging and neurodegenerative diseases.

No abstract available.

No abstract available.

The brain-gut axis is a bidirectional signal transduction system between the gastrointestinal tract and the central nervous system that integrates neural, endocrine, and immune functions. In recent years, the role of the intestinal flora in regulating neural function and affecting the progression of different neurological diseases has received increasing attention. Akkermansia muciniphila is a mucin-degrading bacterium of the intestinal flora present in the intestinal mucus layer that can regulate host immunity, the intestinal barrier and neuroimmune homeostasis. In recent years, a growing body of literature has suggested that Akkermansia muciniphila may play beneficial roles in nerve injury and regeneration by regulating brain-gut axis signalling. This review comprehensively summarizes the latest research results on the role of Akkermansia muciniphila in neurological diseases such as spinal cord injury, multiple sclerosis, Parkinson's disease, and Alzheimer's disease. The mechanisms by which Akkermansia muciniphila regulates inflammatory cytokines, neurotransmitters, and short-chain fatty acids are also highlighted. Various Akkermansia muciniphila -based interventions, such as those involving outer membrane proteins, extracellular vesicles, and pasteurized Akkermansia muciniphila , are discussed, and their therapeutic potential in restoring intestinal homeostasis, alleviating neuroinflammation, and supporting neuronal repair is explored. Although promising results from animal models have been reported, significant challenges remain in translating these findings into clinical practice and therapeutic applications. The differences in Akkermansia muciniphila colonization efficiency, host responses, and intervention strategies in different disease states limit the results of these studies. In addition, Akkermansia muciniphila may exhibit different mechanisms of action in acute and chronic neurodegenerative diseases, and thus more targeted mechanistic studies are needed. Despite these limitations, Akkermansia muciniphila represents a novel and potent pathway for the modulation of the brain-gut axis to support neural repair and functional recovery. By enhancing intestinal barrier integrity and regulating neuroimmunity, Akkermansia muciniphila has broad prospects as a microbial candidate for the treatment of central nervous system diseases. Future research should focus on optimizing the administration method and clinical trials to verify its efficacy, ultimately providing new treatment options in the field of neural regeneration and microbial therapy.

<h4>Objective</h4>This study aimed to explore potential associations between polyunsaturated fatty acid (PUFA) metabolism and laryngeal cancer (LC) using a combination of Mendelian randomization (MR) and integrative bioinformatics, while investigating its potential immunogenic implications.<h4>Methods</h4>Transcriptomic data from the GEO database were integrated to identify differentially expressed genes (DEGs) in LC. Gene Set Enrichment Analysis (GSEA) was performed in addition to Gene Ontology and KEGG enrichment analyses to characterize biological functions. MR analysis was employed to assess the potential causal link between PUFA metabolism and LC risk. PUFA-associated genes were screened for druggability using the DGIdb database. Furthermore, an lncRNA-miRNA-mRNA (ceRNA) regulatory network was constructed, and immune cell infiltration in LC was profiled using CIBERSORT with LM22 signature matrix to uncover immunoregulatory associations with PUFA pathway genes.<h4>Results</h4>A total of 730 DEGs were identified from a combined cohort of 30 LC and 31 normal samples. GSEA and enrichment analysis revealed significant involvement in fatty acid metabolism and immune-related pathways. MR analysis demonstrated a statistically significant but modest association between PUFA metabolism and LC risk (OR = 0.9996, 95% CI = 0.9992-0.9999, p = 0.020). A network of key PUFA pathway genes (e.g., ADH1B, ADH1A, ALDH7A1, CYP2J2, PTGIS) was linked with multiple drug targets. A focused sub-network of regulatory interactions among lncRNAs, miRNAs, and mRNAs was elucidated. Immune infiltration analysis revealed distinct correlations between pathway gene expression and immune cell populations, particularly showing PTGIS positively correlated with activated mast cells and negatively with naive B cells.<h4>Conclusions</h4>Our findings suggest a potential mechanistic link between PUFA metabolism and LC susceptibility, generating hypotheses that PUFA-associated pathways may modulate immune microenvironment characteristics. This computational study provides preliminary insights into potential immunometabolic therapeutic strategies in laryngeal cancer that warrant experimental validation.

<h4>Introduction</h4>This study aimed to elucidate the spectrum of clinical manifestations, cytomorphology, immunophenotype, and the molecular genetic features of lymphoblastic lymphoma/acute lymphoblastic leukemia (LBL/ALL) in the context of serous effusions (SE).<h4>Methods</h4>A retrospective analysis evaluated the cytomorphological features, immunophenotype, and the cyto-histological correlations of twenty-one LBL/ALL associated with SE. Concurrently, bone marrow (BM) aspiration samples were analyzed using an integrated approach, including flow cytometry, reverse transcription PCR (RT-PCR), next-generation sequencing (NGS), or whole transcriptome sequencing (WTS).<h4>Results</h4>Of the 21 cases of SE LBL/ALL, 16 cases were T-LBL/ALL and 5 cases were B-LBL/ALL. The cases included 17 pleural, 2 peritoneal, and 2 pericardial fluid samples. Both T-LBL/ALL and B-LBL/ALL in SE exhibit a blast-like morphology, characterized by small to medium size, irregular nuclear membranes, and inconspicuous nucleoli, alongside frequent nuclear fragmentation and apoptotic bodies. LBL/ALL express immaturity markers such as terminal deoxynucleotidyl transferase (7/17, 41.2%), CD10 (6/12, 50%), CD43 (8/8, 100%), and CD99 (6/6, 100%). T-LBL/ALL and B-LBL/ALL specifically express T-cell markers (CD2 [3/6, 50%], CD3 [10/12, 83.3%], CD5 [2/11, 18.2%], CD7 [10/10, 100%]) or B-cell markers (CD20 [3/5, 60%], CD79a [4/4, 100%], PAX5 [5/5, 100%]), respectively. A high proportion of primitive and immature lymphocytes exceeding 25% in BM was observed in T-LBL/ALL (5/7) and in one case of B-LBL/ALL. No BCR/ABL gene rearrangements were detected in any cases. Furthermore, fusion gene MLL::ENL and PLCALM::MLLT10, as well as mutations in genes including WT1, NOTCH1, PAX5, IKZF, ARID1A, BCOR, SETD2, ARID2, TET2, JAK3, NF1, and CEBPA, were identified in LBL/ALL through RT-PCR, NGS, or WTS analyses.<h4>Conclusion</h4>The integration of clinical manifestations, cytological evaluation, and gene expression profiles is instrumental in achieving accurate diagnosis, subclassification, and prognosis of LBL/ALL within the context of SE.

Hydroxyapatite (HA) functionalized nanoparticles are particularly important in bone and tooth regeneration. This study continues previous work aimed at understanding the interaction of cycline antibiotics with different HA surfaces, now incorporating the effect of hydration on adsorption energies as calculated using density functional theory. The strength of these interactions was analyzed through the quantum theory of atoms in molecules (QTAIM). The adsorption isotherm of nearly stoichiometric HA followed Langmuir-Freundlich kinetics. Minocycline exhibited higher adsorption energy than doxycycline and tetracycline. The nonhydrated adsorption behavior of minocycline is compared to earlier results for doxycycline and tetracycline, while this study also evaluates adsorption on hydrated HA surfaces for all three molecules. Minocycline displays more stable adsorption than the others, in agreement with experimental findings. Our results reveal that the influence of water cannot be neglected: although it does not prevent cycline-HA interactions, it can stabilize previously unstable configurations through hydrogen bonding between cyclines and water molecules. QTAIM analysis indicates that a combination of electrostatic interactions and medium-to-strong covalent character governs the adsorption mechanism.

Recurrent/metastatic head and neck squamous cell carcinoma (HNSCC) is an aggressive malignancy with a significant unmet need for enhancing immunotherapy response given current modest efficacy. Here, we perform an in vivo CRISPR screen in an HNSCC mouse model to identify immune evasion genes. We identify several regulators of immune checkpoint blockade (ICB) response, including the ubiquitin C-terminal hydrolase 5 (UCHL5). Loss of Uchl5 in tumors increases CD8⁺ T cell infiltration and improved ICB responses. Uchl5 deficiency attenuates extracellular matrix (ECM) production and epithelial-mesenchymal-transition (EMT) transcriptional programs, which contribute to stromal desmoplasia, a histologic finding we describe as associated with reduced anti-PD1 response in human HNSCCs. COL17A1, a collagen highly and specifically expressed in HNSCC, mediates in part Uchl5-mediated immune evasion. Our findings suggest an unappreciated role for UCHL5 in promoting EMT in HNSCC and highlight ECM modulation as a strategy to improve immunotherapy responses.

Common genetic variation detected by genome-wide association studies (GWAS) partially explains variability in the spectrum of cardiac phenotypes. In this work, we explore genetic correlations among 58 cardiac-related traits/diseases, detecting novel ones. We subsequently employ multi-trait analysis of GWAS (MTAG), which meta-analyzes genetically correlated traits, to improve genomic loci discovery and prediction in atrial fibrillation (AF), coronary artery disease (CAD), and heart failure (HF). We identify 19 novel loci specific for AF, 131 for CAD, and 141 for HF. Polygenic scores (PGS) in 15,177 Canadian individuals show similar results when PGS are derived from conventional GWAS versus MTAG summary statistics, although MTAG-PGS improve prediction and discrimination of CAD in females [∆R² 1.735% (95% Confidence Interval (CI): 0.609-2.856); Net reclassification index 0.208 (95%CI: 0.139-0.277)]. This work describes new relevant genetic correlations among cardiac-related traits/diseases and supports MTAG to improve loci discovery in common cardiovascular diseases and potentially improve the prediction of CAD in females.

Biomolecular condensates enable the coordination of cellular activities with high spatiotemporal selectivity. Many techniques have been developed to characterize protein condensate. However, direct visualization of protein structure in phase-separated condensate remains underexplored. Here we develop in situ quantitative imaging of secondary structure in protein condensates by stimulated Raman scattering (SRS) microscopy. Characteristic spectra of four secondary structures are obtained from protein amide I vibration analysis. Hyperspectral SRS imaging reveals significant enrichments and disordered to ordered structural changes during phase separation of ALS-related proteins. Time-lapse imaging of protein aging process directly visualizes heterogeneous β-sheet formation on the condensate surface. And secondary structures of mutant proteins are imaged to correlate amino acid sequence to phase separation property. Live-cell label-free imaging of protein structure is further demonstrated to exhibit pronounced heterogeneity in subcellular aggregates. Therefore, our technique provides crucial molecular-level information to investigate protein phase separation and its transition in pathological aggregation.

<h4>Background</h4>Cholecystectomy, a common surgery, may cause metabolic changes linked to bile acid metabolism. Early studies suggest a possible link between cholecystectomy and Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD) and metabolic syndrome, but findings are inconclusive. This 6-month study aimed to assess how elective cholecystectomy affects metabolic syndrome development and MASLD progression in a Middle Eastern population.<h4>Methods</h4>Participants included 51 patients undergoing elective cholecystectomy and 49 matched controls. MASLD grade and metabolic syndrome status were assessed at baseline and six months post-intervention using ultrasonography and standard clinical criteria.<h4>Results</h4>A total of 100 patients were included in the present study, with 51 assigned to the cholecystectomy group and 49 to the control group. Over a six-month follow-up period, individuals in the cholecystectomy group experienced a significant decrease in body mass index (BMI) (p < 0.05) and fasting blood sugar (FBS) levels (p < 0.05). However, this group also exhibited a significant increase in systolic blood pressure (SBP) and diastolic blood pressure (DBP) (p < 0.05). In contrast, the control group showed significant improvements in FBS (p < 0.05) and HDL cholesterol levels (p < 0.05). Logistic regression analysis revealed that undergoing cholecystectomy was linked to a higher likelihood of developing metabolic syndrome (OR = 9.63, p < 0.05).<h4>Conclusions</h4>Our findings highlight the potential metabolic implications of cholecystectomy. Cholecystectomy was associated with reduced BMI and improved fasting glucose but significantly increased blood pressure over 6 months. Highlighting the need for careful metabolic monitoring post-surgery.

<h4>Background</h4>Epigenome-wide association studies (EWAS) are a highly promising approach that can inform precision environmental health. However, current EWAS are underpowered and increasing sample sizes will require substantial resources. Therefore, alternative approaches for identifying candidate biomarkers through EWAS are critical. Here, we provide proof of principle that maximizing exposure variance in EWAS enables effective candidate biomarker detection, even in small sample sizes.<h4>Methods</h4>We profiled genome-wide DNA methylation in whole blood from individuals from Madre de Dios, Peru, with either high methylmercury (MeHg) exposure (> 10 µg/g total hair mercury; N = 16) or low MeHg exposure (< 1 µg/g total hair mercury; N = 16).<h4>Results</h4>We identified nine differentially methylated CpG sites (FDR < 0.05), which is comparable to the number identified by much larger EWAS. The most significantly different CpG site was in an intronic enhancer of the SLC5A7 gene, which encodes the L-type amino acid transporter 1 (LAT1) that facilitates MeHg transport. Our Gene Ontology and transcription factor motif enrichment analyses identified genes involved in outcomes linked to MeHg toxicity, including immune response, neurotoxicity, and type 2 diabetes (T2D).<h4>Conclusions</h4>Similar EWAS in global populations with known high exposure variance can be leveraged to develop targeted, custom sequencing panels and microarrays limited to replicated, validated biomarkers of a given exposure.

<h4>Background</h4>Streptococcus suis poses a significant threat to both humans and pigs, causing severe disease such as meningitis, septicaemia, and sudden death. The type VII secretion system (T7SS) plays a crucial role in exporting effectors that mediate bacterial competition and colonization in polymicrobial environments. Although Leu-x-Gly (LXG) polymorphic toxins are among the main effectors secreted by the T7SS, the mechanism underlying their secretion remains to be fully elucidated.<h4>Results</h4>Here, we identified a complex repertoire of LXG effectors in S. suis, comprising at least five distinct LXG-domain groups and 14 C-terminal toxin types. We focused on one LXG effector, LXG1-CT3, from the virulent strain WUSS351, demonstrating its pore-forming activity and essential role in S. suis competition and virulence. Additionally, we discovered that a small protein family, DUF4176, partners with each cognate C-terminal toxin, stabilizing the corresponding LXG effector prior to secretion, thereby enhancing bacterial competitiveness.<h4>Conclusions</h4>These findings deepen our understanding of S. suis competition and pathogenesis, while offering new insights into the T7SS-mediated secretion of LXG effectors.

<h4>Background</h4>Related studies have shown that propionate metabolism-related genes (PMRGs) were associated with the progress of cancers. However, the roles of PMRGs in ovarian cancer (OC) were unclear.<h4>Methods</h4>In this study, OC-related transcriptome data and clinical information were extracted from The Cancer Genome Atlas (TCGA),Genotype-Tissue Expression (GTEx) and Gene Expression Omnibus (GEO) databases. Firstly, the differentially expressed genes (DEGs) between OC and healthy control (HC) samples were screened by differential expression analysis. Then, the differentially expressed PMRGs (DE-PMRGs) were obtained by intersecting the DEGs with PMRGs. Next, the enrichment analyses of DEGs and DE-PMRGs were conducted to investigate the functions. Moreover, the biomarkers of OC were screened and the risk score was calculated. Then, the nomogram predicting the survival of OC was constructed. Furthermore, the tumor microenvironment analyses and drug sensitivity analysis were proceeded. In addition, the transcription factor (TF)-mRNA regulatory network was constructed to reveal the potential molecular-level regulation of biomarkers. Additionally, the expression levels of biomarkers in IOSE-80, OVCA429, hey and OVCAR-8 were detected through the Quantitative Real-time Polymerase Chain Reaction (qRT-PCR). Immunohistochemistry (IHC) was performed to validate the protein expression of key biomarkers (CETP, ALDH5A1, and PTH) in ovarian cancer tissue microarrays.<h4>Results</h4>Totals of 280 DE-PMRGs were obtained by intersecting the 9,466 DEGs and 531 PMRGs, and these genes were associated with steroid and fatty acid metabolic process. Five biomarkers (ALDH5A1, CETP, GRIA1, PTH, and TPMT) were identified, and the nomogram was constructed with risk score, age and TMB. Among them, GRIA1 was a negative factor, while age and risk score were negatively associated with patients' survival. Noticeable, the tumor purity was low and the level of immune escape was high in OC groups. Besides, AKT.inhibitor.VIII,A.443654,LFM.A13,BMS.509744 and BMS.536924 were positively associated with the risk score. Furthermore, the TF-mRNA regulatory network of OC was constructed, among them, EGR1 was the key TF which could regulate ALDH5A1 and TPMT simultaneously. The qRT-PCR proved the up-regulated expression levels of ALDH5A1, CETP, PTH and TPMT in OVCA429, hey and OVCAR-8. IHC results confirmed significantly higher protein expression of CETP, ALDH5A1, and PTH in ovarian cancer tissues compared to normal controls (p < 0.05), further validating their roles as potential prognostic biomarkers.<h4>Conclusion</h4>This study identified 5 biomarkers associated with the prognosis of OC, which might be helpful in understanding the roles of PMRGs in the development of OC in depth. The IHC validation provided additional evidence at the protein level, reinforcing the clinical relevance of these findings.

<h4>Background</h4>Clinical exome and genome sequencing has transformed the diagnostic workup of patients with genetic disorders. The extensive body of evidence supporting the application of this clinical genomics approach in pediatric patients stands in stark contrast to the relative paucity of evidence for its use in the adult population. Here, we describe the largest cohort to date of adult patients who underwent clinical exome and genome sequencing for suspected genetic diagnoses.<h4>Methods</h4>A total of 2763 adult patients (2529 families) from all regions of Saudi Arabia are included in this cohort (2202 exomes, and 561 genomes).<h4>Results</h4>The diagnostic rate is 38.9% spanning 535 Mendelian genes and revealing clinical diagnostic errors in 38% of patients with positive reports. Structured feedback using C-GUIDE demonstrates clinical utility in 90% of positive cases. Consistent with the highly consanguineous nature of the local population, the majority (61%) of diagnosed phenotypes are recessive (94.6% homozygous) and founder variants account for 85% (414/487) of these variants. The same population characteristic has also led to the encounter of extremely rare, even novel recessive disorders including a highly penetrant novel RNF43-related hemochromatosis, NFXL1-related syndrome of hyperlaxity, short stature, and kidney disease, as well as autosomal recessive forms of typically dominant disorders. Multilocus phenotypes are observed in 5% of cases although only 26.7% of these are caused by two recessive variants. That 70% of molecular diagnoses encountered in our cohort are typically described in pediatric patients allowed us to observe highly unusual clinical presentations in the adult population. This delayed diagnosis also represents a missed opportunity for effective treatment in many instances and we note the availability of treatment for 26% of diagnosed conditions. Of particular interest are patients with monogenic disorders that could be overlooked as common multifactorial adult diseases (e.g., diabetes, dyslipidemia, stroke, chronic kidney disease, and dementia). Finally, we note the opportunities of deploying adult clinical genomics in an underrepresented population where 45.5% (373/819) of encountered variants are completely absent in gnomAD.<h4>Conclusions</h4>Our results illustrate numerous benefits of a clinical genomics approach in adult medicine and argue for a broader implementation than currently practiced.

Neuroinflammation plays a critical role in the pathogenesis of aging-related neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Multiple Sclerosis. It involves the activation of glial cells and the release of pro-inflammatory mediators and reactive oxygen and nitrogen species, which, when chronically sustained, contribute to neuronal damage and cognitive decline. Recent evidence suggests that regular physical exercise exerts neuroprotective effects by modulating neuroinflammatory pathways and enhancing brain health. Exercise has been shown to regulate the activity of microglia and astrocytes, strengthen the blood-brain barrier, and reduce systemic and gut-derived inflammation-all of which are implicated in the progression of neurodegeneration. Additionally, exercise influences inflammasome signaling, a key component in the innate immune response, further mitigating inflammation-induced neuronal injury. This review summarizes current findings on the impact of physical activity on inflammation and inflammasome pathways in aging-related neurodegenerative diseases, highlighting the therapeutic potential of exercise as a non-pharmacological intervention. Further research is warranted to optimize exercise protocols for maximal neuroprotective benefits.

All cells in the central nervous system (CNS) are considered mechanosensitive, but how they collectively respond to a concussive head impact and contribute to the transition from the primary to secondary injury remains unknown. Using a mouse model for mild traumatic brain injury (mTBI) or concussion, we report that blocking the activity of TRPV4 transient receptor potential channels inhibits mTBI-induced sequential changes of neurons and glial cells, as well as behavioral disturbances. A concussive head impact immediately induces axonal varicosities, preceding NMDA-receptor-mediated microglial activation and cortical demyelination. Afterward, these changes differentially and partially recover. Blocking TRPV4 channels before or after head impact markedly suppresses axon-glial and behavioral changes or enhances their recovery, respectively. Using knockout mice and AAV-Cre-mediated acute and cell-type-specific deletion, we further show that neuronal TRPV4 channels, as an mTBI target, regulate the homeostasis of axon mechanosensation and their hyperactivation causes axonal varicosity formation followed by axon-to-glia mechanotransduction.

<h4>Aim</h4>To study the neurodegenerative diseases that cause progressive intellectual and neurological deterioration (PIND) in children in the UK.<h4>Method</h4>This active prospective epidemiological study asked UK paediatricians to notify all childhood cases of PIND via the British Paediatric Surveillance Unit. Clinical data were obtained using a questionnaire or via a site visit. An independent PIND study Expert Group classified the cases.<h4>Results</h4>Between May 1997 and April 2024 (27 years), 2373 children with PIND were identified who had an underlying diagnosis to explain their deterioration. There were six cases of variant Creutzfeldt-Jakob disease plus 2367 children (1265 males, 1102 females) with other diseases. The lifetime risk of having a diagnosed disease causing PIND was 0.1 in 1000 live births. Asian British children made up 28.6% of the 2183 cases with known ethnicity. Excluding variant Creutzfeldt-Jakob disease, diagnosed children had 259 diseases, identified before death in 99% of children (only 39 were known to have had postmortems). Increasingly, diagnosis was made using genetic studies. Sixty-one per cent (157 of 259) of the diseases were inborn errors of metabolism, affecting 78% of diagnosed children. There were 43 lysosomal diseases.<h4>Interpretation</h4>This unique epidemiological study of many rare childhood neurodegenerative diseases provides valuable practical information about the presentation, clinical features, and inheritance of these complex disorders.

<h4>Background</h4>Colorectal cancer metastasis, especially liver metastasis, is characterized by significant intricate diversity and remains a major contributor to patient mortality. Despite its clinical importance, the precise molecular mechanisms driving metastasis remain poorly understood.<h4>Methods</h4>To investigate the molecular drivers of metastasis heterogeneity, we performed a comprehensive proteomic analysis of non-metastatic (NM) colorectal cancer tissues, as well as metachronous (MM) and synchronous (SM) metastatic tissues.<h4>Results</h4>Our analysis revealed distinct biological features associated with colorectal cancer liver metastasis. Notably, we identified P53-mediated hyperproliferation as a common initiating factor in the occurrence of CRC. Additionally, metabolic dysregulation emerged as a key hallmark of CRC liver metastasis. Importantly, MM tumors exhibited suppressed ferroptosis and activation of the TGF-β signaling pathway, while SM tumors displayed inhibited anoikis and activation of the WNT signaling pathway, accompanied by activated angiogenesis. Most strikingly, CEACAM6 was identified as the only protein exhibiting a stepwise decrease in expression from NM to MM and further to SM, underscoring its unique role in metastatic progression.<h4>Conclusions</h4>These findings provide new insights into the molecular complexities underpinning colorectal cancer liver metastasis. Our identification of CEACAM6 as a differential marker highlights its potential as a diagnosis marker and therapeutic target, offering new avenues for the treatment of metastatic CRC.

Liposomes made from phosphorothioate lipids are shown to penetrate cells better and differently than conventional phosphodiester liposomes. DSP_SC phosphorothioate liposomes are synthesized, characterized and labeled with either internal doxorubicin or membrane-bound flippers. Inhibition experiments reveal that their penetration of HK cells is independent of endocytosis and occurs by thiol-mediated uptake (TMU). Dynamic covalent exchange with phosphorothioate sulfurs as pseudo-thiolates is confirmed and explored to modify liposomes and activate TMU. Mechanosensitive flipper probes and colocalization experiments reveal that phosphorothioate liposomes cross the plasma membrane in intact form with negligible endocytosis and little fusion. In the cytosol, fast-emitting flipper probes and non-released doxorubicin in punctate objects that partially co-localize with lipid droplets but not lysosomes suggest that the liposomes apparently stay at least partially intact and incorporate disorganizing lipid components from lipid droplets. In clear contrast, conventional DSPC liposomes bind to the cell surface in intact form and neither fuse nor cross the plasma membrane. These results support and translate recent insights from cell-penetrating oligonucleotides to phosphorothioate lipids, highlight the importance of understanding the dynamic covalent chemistry of phosphorothioates, and identify flipper dendrons as promising tools to elucidate liposomal delivery.

Neutrophils respond rapidly to inflammation and infection via defense mechanisms, including degranulation, reactive oxygen species production, and neutrophil extracellular trap formation (known as "NETosis"). As the most abundant neutrophil components, granule proteins constitute the major mediators of neutrophil effector functions and likely orchestrate their functional diversity. However, a systematic profile of these proteins, particularly their temporal release dynamics during inflammatory responses, remains uncharacterized. Here, we performed a "multistate" proteomic study to explore circulating neutrophils' dynamic responses to diverse infectious and inflammatory signals over time. Circulating neutrophils exhibited both conserved and stimulus-specific protein expression programs. Through integrated characterization of the cellular and secretory proteome landscapes, we delineated the release patterns of canonical granule proteins and identified inflammatory mediators, including soluble membrane receptors. Notably, granule membrane receptors were translocated to the cell surface and shed via proteolytic cleavage, highlighting their dynamic regulation and diversity. These findings revealed the complexity of the neutrophil degranulation program, demonstrating its stimulus-dependent and temporally layered nature. Our study provides a functional atlas of neutrophil degranulation upon inflammation, which would strengthen our understanding of neutrophil activation in inflammation and facilitate the exploration of inflammation management therapies.

<h4>Background</h4>The ileum integrates nutrient absorption with mucosal immunity, yet its cell-type-specific functions remain poorly defined. Disruption of epithelial or immune pathways contributes to nutrient deficiency, Crohn's disease, and impaired barrier integrity. Single-cell RNA sequencing (scRNA-seq) provides the resolution needed to uncover epithelial differentiation and immune crosstalk that bulk approaches cannot resolve.<h4>Objectives</h4>This study aimed to map ileal cellular heterogeneity and define epithelial differentiation, nutrient metabolism programs, and epithelial-immune interactions relevant to health and disease.<h4>Methods</h4>scRNA-seq was performed on ileal cells from 8-wk-old male C57BL/6J mice. Gene expression and clustering were analyzed using Seurat, with pseudotime trajectory, cell-cell communication, and pathway enrichment analyses applied to characterize intestinal dynamics.<h4>Results</h4>A total of 32,076 ileal cells were identified, including 6 epithelial types and multiple immune populations. Enterocyte subclusters showed distinct nutrient-related functions: Ent_C1, C4, C7, and C8 were enriched for vitamin A absorption; Ent_C0, C1, C2 and C7 for carotenoid metabolism; and Ent_C1, C4, C7, C8, and C9 for vitamin B12 absorption. Coexpression of β-carotene oxygenase 2 (Bco2) and IL 18 (Il18) occurred across enterocytes, stem cells, and goblet cells, whereas noncanonical goblet cells exhibited high Bco2-Il18 expression together with signatures of fatty acid metabolism and stress responses. Plasmacytoid dendritic cells were identified as central regulators of immune-epithelial interactions.<h4>Conclusions</h4>This study provides the first integrated single-cell atlas of the mouse ileum, profiling both epithelial and immune cells and revealing nutrient metabolism programs and epithelial-immune crosstalk relevant to intestinal health and disease.

The recent resolution of the koi carp (Cyprinus carpio) genome framework through high-throughput sequencing has enabled novel insights into sex determination mechanisms. Whole-genome resequencing (WGS) was performed on koi carp, yielding 1,341,975 high-quality SNPs. Integrated analyses, including gene annotation, GO functional classification, and KEGG pathway enrichment, identified four core genes (sox6, wnt7ba, gnrhr4, and mrps30) significantly associated with vertebrate sex-determination pathways. Validation through PCR-RFLP and Sanger sequencing confirmed that SNP3, a sexually dimorphic locus within the exon region of gnrhr4, demonstrated a sex identification accuracy of 100 % (n = 20).This study not only provides a practical molecular marker for sex-controlled breeding but also advances the theoretical understanding of epigenetic regulatory networks underlying sex determination in teleost fishes.

<h4>Objective</h4>This study analyzes the characteristics and clonal dynamics of <i>Vibrio vulnificus</i> isolated from a Chinese hospital between 2021 and 2024.<h4>Methods</h4>We performed whole genome sequencing (WGS) on the six collected <i>Vibrio vulnificus</i> isolates. Antibiotic susceptibility testing was conducted using the bioMérieux automated antimicrobial susceptibility testing system. The clonal dynamics were studied through phylogenetic analysis, and the clinical diagnostic value indicators for bloodstream infections (BSI) were evaluated using the receiver operating characteristic (ROC) curve.<h4>Results</h4>The six <i>Vibrio vulnificus</i> strains collected in this study were phylogenetically closely related, including two of sequence type ST678 and one each of ST696, ST675, ST607, and ST367. All strains tested positive for the <i>vcgC</i> gene; five were positive for 16S rRNA type A, and one showed type AB. Virulence gene profiling revealed that the strains universally carried exotoxins (VvhA, RTX), adhesion factors (TadZ/CpaE, IlpA, VWA), and motility-associated genes (cheW/R, motA, flgC). Notably, one strain harbored a broader array of virulence factors, including effector protein secretion systems (ompA, vipA/tssB, sciN/tssJ), biofilm formation-related genes (mrkA/B/C), and siderophores (fepA/B, entE/F, iucA/B), which may significantly enhance its pathogenicity. According to CLSI guidelines for <i>Vibrio</i> spp. all isolates were resistant to ampicillin but susceptible to third-generation cephalosporins, carbapenems, tetracyclines, quinolones, and folate pathway inhibitors. ROC curve analysis showed that high-sensitivity C-reactive protein (HS-CRP), lactate (Lac), procalcitonin (PCT), and other indicators were of good clinical value for the early diagnosis of bloodstream infection caused by <i>Vibrio vulnificus</i>.<h4>Conclusion</h4>This study represents the inaugural whole-genome sequencing research conducted on <i>Vibrio vulnificus</i> isolates from eastern China. It comprehensively examines the current species, antibiotic resistance, virulence genes, and clinical characteristics of infected individuals, elucidating the pathogenic mechanisms and epidemiological features of <i>Vibrio vulnificus</i>. The findings offer essential references for clinical diagnosis and treatment.

<h4>Background</h4>Epidemiological studies have revealed a close association between psoriasis and non-alcoholic fatty liver disease (NAFLD), but the causal relationship and underlying mechanisms remain unclear.<h4>Materials and methods</h4>In this study, we used genome-wide association study (GWAS) data from the MRC Integrative Epidemiology Unit (MRC-IEU) to investigate the causal relationship between psoriasis and NAFLD, as well as potential mediators. Two-sample and two-step MR analyses were conducted, followed by bulk and single-cell transcriptomic analyses to validate our MR findings. In vivo validation was performed using Enzyme-Linked Immunosorbent Assay (Sample of patients (n=10)), immunohistochemistry, and liver bulk transcriptomic analysis.<h4>Results</h4>The two-sample MR analysis revealed that genetically predicted psoriasis significantly increased the risk of NAFLD (OR = 1.07, 95% CI = 1.03-1.12, <i>p</i> = 0.001). Mediation analysis suggested that psoriasis was associated with elevated plasma Interleukin-1 receptor antagonist protein (IL-1RA) levels (OR = 1.02, 95% CI = 1.00-1.05, <i>p</i> = 0.031), which in turn raised the risk of NAFLD (OR = 1.15, 95% CI = 1.04-1.27, <i>p</i> = 0.006). In vivo experiments demonstrated elevated IL-1RA levels in the skin and plasma of psoriasis patients. Similarly, imiquimod (IMQ)-induced psoriasis mouse models exhibited increased IL-1RA levels in plasma and liver, accompanied by liver inflammation. MR and colocalization analysis indicated a positive correlation between IL-1RA, apolipoprotein B, and cholesterol.<h4>Conclusion</h4>Our study demonstrates that genetically predicted psoriasis increases the risk of NAFLD, and plasma IL-1RA may serve as a potential mediator between psoriasis and NAFLD.

<h4>Objective</h4>Ferroptosis is an iron-dependent, non-apoptotic form of metabolic cell death driven by lipid peroxidation. While Glutathione Peroxidase 4 (GPX4) is the canonical ferroptosis suppressor, recent evidence highlights additional selenoproteins, including Thioredoxin Reductase 1 (TXNRD1) and Peroxiredoxin 6 (PRDX6), as critical modulators of ferroptotic sensitivity. We compared three mechanistically distinct ferroptosis inducers, RSL3 (a covalent GPX4 inhibitor), auranofin (a TXNRD1 inhibitor), and artesunate (ART; a pro-oxidant derivative of artemisinin), in MDA-MB231, A549 and HepG2 cell lines.<h4>Method</h4>Cell viability (MTT) and wound-healing assays quantified cytotoxic and anti-migratory effects. Our inhibitor study using Ferrostatin-1(Ferro) and Liproxstatin-1(Lipo), in combination with ferroptosis inducers, confirmed the specificity of ferroptosis. Beyond GPX4, TXNRD1 and PRDX6 constitute a complementary selenium-dependent axis safeguarding cancer cells from ferroptosis. Dual targeting of GPX4 and TXNRD1, or disruption of PRDX6-mediated selenium trafficking, potentiates ferroptosis death and impedes metastatic traits.<h4>Results</h4>Using in silico methods, we confirmed the interaction between drug and protein molecules. Among the tested compounds, RSL3 and auranofin exhibited strong binding affinity towards all the targeted proteins, including GPX4, TXNRD1, and PRDX6, suggesting their potential as effective ferroptosis pathway inhibitors.<h4>Conclusions</h4>These findings nominate multi-selenoproteins inhibition as a promising strategy to overcome ferroptosis resistance.

Glycosphingolipids (GSLs) constitute the most structurally diverse subgroup of the sphingolipid family and play crucial roles in a wide variety of cellular functions. The expression of GSLs is tightly controlled during development, with each GSL series exhibiting distinct functional roles in adhesion or signaling, depending on cell type. Genetic defects in lysosomal GSL-degrading enzymes result in GSL storage disorders. However, aberrant and increased expression of GSLs has also been observed in various cancer cells, promoting tumor survival and impairing anti-tumor immunity. Additionally, viruses, pathogens, and bacterial toxins have been found to bind to host GSLs. Therefore, inhibiting GSL synthesis could be a potential therapeutic strategy for such infections or cancers. Here, we discuss the synthesis and classification of GSLs and review their role in disease and treatment.

The primary challenge in developing oral nanocarriers lies in achieving a balance between mucus penetration and cellular endocytosis. Overcoming this dilemma tends to require multiple surface properties on design of nanocarriers, but it is not favorable to clinical translation due to the complex preparation procedure and availability of commercial material. Herein, we innovatively constructed a hydrophilic-lipophilic balanced micelles only composed of poly (lactic acid)-b-poly (ethylene glycol) (PLA-PEG) or poly (lactic acid)-b-poly (carboxybetaine) (PLA-PCB) for oral delivery. The hydrophobic core of micelles was reasonably exposed by adjusting the size and the molar mass ratio of hydrophilic to hydrophobic segment of polymer, and significantly enhanced cellular internalization were observed in both micelles. In addition, the hydrophobic force driven by the core of micelles was multiply confirmed as the primary factor in enhancing cellular uptake, while time-dependent endocytosis of micelles was also verified. Although the hydrophilic segment of micelles exhibited limited functionality during the adsorption-endocytosis process of micelles, their construction could significantly mediate the intracellular trafficking process. Both <i>in vivo</i> and <i>ex vivo</i> imaging suggest that micelles exhibited good retention abilities in small intestine as well as colon after gavage administration. Remarkably, the oral bioavailability of paclitaxel (PTX) in both PTX-loaded micelles exceeded 29 % and exhibited significant oral antitumor efficacy, indicating excellent potential for oral delivery via micelles. Furthermore, poly (butyric ester)-based micelles were much capable of relieving symptoms in colitis mice induced with dextran sulfate sodium salt (DSS). These results reveal that the micelles with hydrophilic-lipophilic balance possess a broad-spectrum oral therapeutic potential and are available in potential clinical practice.

In recent years, apatite-based materials have garnered significant interest, particularly for applications in tissue engineering. Apatite is most commonly employed as a coating for metallic implants, as a component in composite materials, and as scaffolds for bone and dental tissue regeneration. Among its various forms, hydroxyapatite (HAP) is the most widely used, owing to its natural occurrence in human and animal hard tissues. An emerging area of research involves the use of fluoride-substituted apatite, particularly fluorapatite (FAP), which can serve as a direct fluoride source at the implant site, potentially offering several biological and therapeutic advantages. However, substituting HAP with FAP may lead to unforeseen changes in material behavior due to the differing physicochemical properties of these two calcium phosphate phases. This study investigates the effects of replacing hydroxyapatite with fluorapatite in ceramic-polymer composite materials incorporating β-1,3-glucan as a bioactive polymeric binder. The β-1,3-glucan polysaccharide was selected for its proven biocompatibility, biodegradability, and ability to form stable hydrogels that promote cellular interactions. Nitrogen adsorption analysis revealed that FAP/glucan composites had a significantly lower specific surface area (0.5 m²/g) and total pore volume (0.002 cm³/g) compared to HAP/glucan composites (14.15 m²/g and 0.03 cm³/g, respectively), indicating enhanced ceramic-polymer interactions in fluoride-containing systems. Optical profilometry measurements showed statistically significant differences in profile parameters (e.g., Rp: 134 μm for HAP/glucan vs. 352 μm for FAP/glucan), although average roughness (Ra) remained similar (34.1 vs. 27.6 μm, respectively). Microscopic evaluation showed that FAP/glucan composites had smaller particle sizes (1 μm) than their HAP counterparts (2 μm), despite larger primary crystal sizes in FAP, as confirmed by TEM. XRD analysis indicated structural differences between the apatites, with FAP exhibiting a reduced unit cell volume (524.6 ų) compared to HAP (528.2 ų), due to substitution of hydroxyl groups with fluoride ions. Spectroscopic analyses (FTIR, Raman, ³¹P NMR) confirmed chemical shifts associated with fluorine incorporation and revealed distinct ceramic-polymer interfacial behaviors, including an upfield shift of PO₄^3- bands (964 cm^-1 in FAP vs. 961 cm^-1 in HAP) and OH vibration shifts (3537 cm^-1 in FAP vs. 3573 cm^-1 in HAP). The glucan polymer showed different hydrogen bonding patterns when combined with FAP versus HAP, as evidenced by shifts in polymer-specific bands at 888 cm^-1 and 1157 cm^-1, demonstrating that fluoride substitution significantly influences ceramic-polymer interactions in these bioactive composite systems.

Chromium-doped hydroxyapatite (7CrHAp) and chromium-doped hydroxyapatite in chitosan matrix (7CrHAp-CH) coatings were synthesized in order to address the need for biomaterials with improved physico-chemical and biological properties for biomedical applications. Both chromium-doped hydroxyapatite (7CrHAp) and chromium-doped hydroxyapatite in chitosan matrix (7CrHAp-CH) coatings could represent promising materials for biomedical applications due to their superior properties. This study aims to evaluate the physico-chemical and in vitro biological properties of 7CrHAp and 7CrHAp-CH coatings to determine the impact of chitosan incorporation on the physico-chemical and biological features. The results reported in this study indicate that addition of chitosan improves surface uniformity and biological properties, highlighting their potential for uses in biomedical applications. In this study, coatings of chromium-doped hydroxyapatite (7CrHAp, with x_Cr = 0.07) and its composite variant embedded in a chitosan matrix (7CrHAp-CH) were systematically analyzed using a suite of characterization techniques: X-ray diffraction (XRD), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), Fourier-transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and metallographic microscopy (MM). The results of the XRD analysis revealed that the average crystal size was 19.63 nm for 7CrHAp and 16.29 nm for 7CrHAp-CH, indicating a decrease in crystallite size upon CH incorporation. The films were synthesized via the dip coating method using stable suspensions, whose stability was assessed through ultrasonic measurements (double-distilled water serving as the reference medium). The values obtained for the stability parameter were 2.59·10^-6 s^-1 for 7CrHAp, 8.64·10^-7 s^-1 for 7CrHAp-CH, and 3.14·10^-7 s^-1 for chitosan (CH). These data underline that all samples are stable: CH is extremely stable, followed by 7CrHAp-CH (very stable) and 7CrHAp (stable). The in vitro biocompatibility of the 7CrHAp and 7CrHAp-CH coatings was evaluated with the aid of the MG63 cell line. The cytotoxic potential of these coatings towards MG63 cells was quantified using the MTT assay after 24 and 48 h of incubation. Our results highlight that both 7CrHAp and 7CrHAp-CH coatings exhibit high biocompatibility with MG63 cells, maintaining cell viability above 90% at both incubation times, thus supporting osteoblast-like cell proliferation. Furthermore, the antimicrobial efficacy of both 7CrHAp and 7CrHAp-CH samples was evaluated in vitro against the <i>Pseudomonas aeruginosa</i> 27853 ATCC (<i>P. aeruginosa</i>) reference strain. The in vitro antibacterial activity of the 7CrHAp and 7CrHAp-CH coatings was further evaluated against <i>Pseudomonas aeruginosa</i> 27853 ATCC (<i>P. aeruginosa</i>), <i>Escherichia coli</i> ATCC 25922 (<i>E. coli</i>) and <i>Staphylococcus aureus</i> ATCC 25923 (<i>S. aureus</i>) reference strains. In addition, atomic force microscopy (AFM) analysis was also used to investigate the ability of <i>P. aeruginosa</i>, <i>E. coli</i> and <i>S. aureus</i> cells to adhere and to develop colonies on the surfaces of the 7CrHAp and 7CrHAp-CH coatings. The results from the biological assays indicate that both coatings exhibit promising antibacterial properties, highlighting their potential for being used in biomedical applications, particularly in the development of novel antimicrobial devices.

Fibroblast growth factor 21 (FGF21), a pleiotropic hormone, is a significant modulator of energy homeostasis. We evaluated serum FGF21 levels in patients with a deficiency of mitochondrial aminoacyl-tRNA synthetase (mt-aARSs). Six patients with mitochondrial aminoacyl tRNA synthetase deficiency and twelve healthy volunteers were included in this study. Whole-exome sequencing was used for molecular diagnosis. Serum FGF21 levels in the case group and healthy volunteers were analyzed using the enzyme-linked immunosorbent assay. Exome sequencing test revealed nine different pathogenic variants in the <i>AARS2</i>, <i>EARS2</i>, <i>DARS2</i>, <i>SARS2</i>, and <i>WARS2</i> genes. A statistically significant difference was found between the serum FGF21 levels of the case and control groups: case group (n = 6), 882.49 ± 923.60 pg/mL; control group (n = 12), 20.89 ± 2.63 pg/mL (<i>p</i> < 0.001). The area under the ROC curve for FGF21 in the differential diagnosis of mitochondrial aminoacyl-tRNA synthetase deficiency was 1.000 (0.813-1.000). Sensitivity and specificity were 100%, and positive and negative predictive values were also 100% for an FGF21 cut-off value > 27.4 pg/mL. Assessment of FGF 21 levels as an indicator of mitochondrial damage in mt-aARSs deficiency may provide insight into the level of damage. Investigation of the biochemical mechanisms underlying the different levels of damage caused by different aminoacyl tRNA synthetases will be important in terms of elucidating clinical heterogeneity.

Reperfusion therapy uses thrombolysis and clot removal to restore blood flow in the brain after stroke; however, three months after reperfusion therapy, roughly 46% of stroke patients become independent again. MiRNAs (micro RNA) regulate cerebral ischemia/reperfusion injury, and their transfer between cells via exosomes may differentially affect recipient cells. We examined serum exosomal miRNA levels, stroke treatments, and functional outcomes in stroke patients, and we explored the potential role of estimated differentially expressed miRNA (DEmiRNA) target genes in the brain's reaction to reperfusion after ischemia. The patients in the study received aspirin or reperfusion therapy with either intravenous thrombolysis (rt-PA), mechanical thrombectomy (MT), or a combination of both (rt-PA/MT). Serum samples were collected from stroke patients on days 1 and 10 post-stroke. Serum exosomes' miRNA was analyzed using qRT-PCR. We identified DEmiRNAs, estimated their targets, and performed enrichment analysis. Functional outcomes were assessed using the modified Rankin Scale (mRS) on days 10 and 90 post-stroke. Among studied treatments, only rt-PA/MT lowered DEmiRNA by day 10 vs. other groups. Specifically, patients with unfavorable mRS score exhibited decreased levels of miR-17, miR-20, miR-186 and miR-222 after combined stroke therapy. Functional analysis identified target genes and pathways associated with cytoskeleton remodeling, cell death, autophagy, inflammation, and dementia. In conclusion, unfavorable stroke outcomes following poor rt-PA/MT response could result from lower miRNA expression levels, thus activating cell death and neurodegenerative processes in brain.

Serine/arginine protein kinase 1 (SRPK1) plays a pivotal role in the phosphorylation of SR/RS domain-containing proteins, which are involved in various cellular processes. Its overexpression has been associated with the progression of various malignancies, positioning SRPK1 as a promising target for cancer treatment. In this study, we report the design, synthesis, and preliminary biological evaluation of two hybrid molecules, geo15 and geo140, which combine known SRPK1 inhibitors with the antimetabolites gemcitabine and 5-fluorouracil (5-FU), respectively. These conjugates were synthesized to assess whether hybridization enhances potency compared to the parent compounds, and to investigate potential novel mechanisms of action. <i>In vitro</i> assays were performed to evaluate SRPK1 inhibition and antiproliferative activity in selected cancer cell lines. Among the tested compounds, the JH-VII-139-1-based hybrid geo140 exhibited notable SRPK1 inhibitory potency and cytotoxic effects, demonstrating a favorable profile for further optimization. Interestingly, treatment with geo140 did not appear to alter the overall SRPK1 distribution in interphase cells but resulted in a notable increase of mitotic cells that displayed a substantial accumulation of SRPK1, thus suggesting that the hybrid compound may have an impact on cell cycle progression. This work supports the potential of molecular hybridization as a strategy for the development of novel SRPK1-targeting anticancer agents.

Emerging evidence implicates serine/threonine kinase 32C (STK32C) overexpressed in bladder cancer and brain tissues acts as a molecular target for doxorubicin resistance, yet its role in colorectal cancer (CRC) remains unclear. Thus. this study investigates the oncogenic mechanism of STK32C in CRC and its interplay with HSP90 and the PI3K/AKT/mTOR signaling axis. STK32C was markedly upregulated in CRC cell lines (HCT116, HT29, SW480, SW620) compared to normal fibroblasts (CCD-18Co) with poor prognosis. STK32C depletion suppressed proliferation, migration, and invasion, while promoting apoptosis-as evidenced by increased Bax, Annexin V, TUNEL-positive, and sub-G1 populations, alongside reduced Bcl-2, pro-Caspase-3, and pro-PARP. Mechanistically, STK32C directly bound the N-terminal domain of HSP90, as shown by immunoprecipitation, immunofluorescence, and GST pulldown assays. Consistently, STK32C depletion or HSP90 N-terminal inhibitor Ganetespib reduced STK32C and p-AKT1, while the HSP90 C-terminal inhibitor, epigallocatechin gallate (EGCG) or AKT inhibitor LY294002 did not affect STK32C, implying that STK32C acts as an upstream of AKT. Furthermore, STK32C depletion enhanced 5-fluorouracil (5-FU) efficacy, with synergistic effects confirmed by CompuSyn and SynergyFinder analysis. <i>In vivo</i>, STK32C depletion reduced the growth of HCT116 cells in BALB/c mice with decreased expression of STK32C, HSP90, PCNA, and AKT and activated caspase 3. Overall, these findings suggest STK32C as a novel oncogenic driver in CRC that modulates HSP90 and PI3K/AKT/mTOR signaling and highlights its potential as a therapeutic target alone or in combination with 5-FU.

<h4>Background</h4>The Hispanic population is the fastest-growing ethnic group in the USA and is projected to comprise 30% of the US population by 2050. Despite socioeconomic disadvantages and often presenting with more severe disease phenotypes, previous studies in chronic diseases have shown that Hispanics experience lower overall inpatient mortality compared with other ethnic groups - a phenomenon known as the "<i>Hispanic Paradox</i>". In alcoholic liver cirrhosis (ALC), this paradox is particularly evident: Hispanics frequently develop more advanced forms of alcoholic liver cirrhosis, yet survival outcomes are often similar or even superior to those of non-Hispanic populations. This study aims to assess the risk and burden of alcoholic liver cirrhosis in the Hispanic population and to compare the clinical phenotype of ALC with that observed in non-Hispanic populations.<h4>Methods</h4>This retrospective analysis used the Nationwide Inpatient Sample (NIS) database (2016 - 2019) to examine adults hospitalized with ALC. Patients with other causes of cirrhosis were excluded. Patients were stratified into Hispanic and non-Hispanic groups. Diagnoses, complications, and comorbidities were captured using the International Classification of Disease, 10th Revision (ICD-10) codes. The primary outcome was inpatient mortality; secondary outcomes included length of stay (LOS) and total hospitalization charges (TOTCHG). Statistical analyses were performed using Chi-square, <i>t</i>-tests, and Mann-Whitney U tests.<h4>Results</h4>Among patients hospitalized with alcoholic cirrhosis (n = 1,002,115), 17% were Hispanic. Hispanic patients were younger (mean age 54 vs. 57 years, P < 0.001), more often male (81% vs. 67%, P < 0.001), and had similar Charlson Comorbidity Index (CCI) scores. Despite slightly lower inpatient mortality (5.9% vs. 6.8%, P < 0.001), Hispanics experienced higher rates of complications, including esophageal varices (28% vs. 23%), variceal bleeding (10% vs. 7%), acute liver failure (27% vs. 25%), and hepatocellular carcinoma (4% vs. 2%) (P < 0.001 for all). Median TOTCHG was significantly higher ($46,494 vs. $38,881, P < 0.001) in Hispanic patients.<h4>Conclusions</h4>Hispanic patients with alcoholic cirrhosis (ALC) experience a higher burden of cirrhosis-related complications and increased healthcare utilization compared to other ethnic groups yet exhibit lower observed inpatient mortality. These disparities highlight the need for earlier detection, culturally tailored public health interventions, and improved access to preventive and specialty liver care to improve outcomes in this vulnerable population.

Advances in genomic technologies, including whole exome and genome sequencing, have transformed diagnosis of monogenic disorders such as inborn errors of immunity (IEIs). In high-consanguinity populations like the United Arab Emirates (UAE), where autosomal recessive disorders are prevalent, early genomic screening shifts care from reactive diagnosis to personalized care. UAE national programs remain limited to premarital or neonatal panels, missing disorders with variable onset or incomplete penetrance. We advocate universal genomic screening to integrate disease-causing alleles into clinical care. As proof of concept, we highlight Mendelian susceptibility to mycobacterial disease (MSMD), an IEI defined by impaired interferon-gamma signaling and severe complications following <i>Bacillus Calmette-Guérin</i> (BCG) vaccination and <i>Mycobacterium tuberculosis</i> disease. We propose a tiered approach using MSMD-related genes within exome or genome platforms, enabling scalable, cost-effective implementation and periodic reanalysis as evidence evolves. In the UAE, high consanguinity, genomic infrastructure, and regulatory frameworks position MSMD as an entry point for population genomic screening, advancing precision medicine and prevention.

Aging represents a major risk for human neurodegenerative disorders, such as dementia and Alzheimer's disease, and is associated with a functional decline in neurons and impaired synaptic plasticity, leading to a gradual decline in memory. Previous research has identified molecular and functional changes associated with aging through transcriptomic studies and neuronal excitability measurements, while the role of chromatin-level regulation in vulnerability to aging-related diseases is not well understood. Moreover, the causal relationship between molecular alterations and aging-associated decline in functions of different cell types remains poorly understood. Here, we systematically characterized gene regulatory networks in a cell type-specific manner in the aging mouse hippocampus, a central brain region involved in learning and memory formation, by simultaneously profiling gene expression and chromatin accessibility at a single-nucleus level. The analysis of multiome (RNA and ATAC) sequencing recapitulated the diversity of glial and neuronal cell types in the hippocampus and revealed transcriptomic and chromatin accessibility level changes in different cell types, among which oligodendrocytes and dentate gyrus (DG) neurons exhibited the most drastic changes. We found pronounced aging-dependent chromatin-level changes among neurons, especially for genes related to synaptic plasticity. Our data suggest that BACH2, a candidate transcription factor implicated in aging-mediated functional decline of DG neurons, potentially regulates genes associated with synaptic plasticity, cell death, and inflammation during aging. Taken together, our single-nucleus multiome analysis reveals potential cell type-specific regulators involved in the aging of neurons and glial cells.

Inhibitors of the menin-KMT2A interaction are promising agents for the treatment of KMT2A-rearranged leukemias. We evaluated menin inhibition in patient-derived xenografts of KMT2A-rearranged leukemias with high-risk features. Three acute myeloid leukemias with high-risk fusion partners (mixed-lineage leukemia-10 [MLLT10] and mixed-lineage leukemia-4 [MLLT4]) and two infant acute lymphocytic leukemia (ALL) samples were sensitive to menin inhibition. We also evaluated serial samples from two patients with multiply relapsed ALL. We found that highly pretreated KMT2A::AFF1 ALL samples were much less sensitive compared with cells obtained earlier in the same patients' disease course. Because none of the patients had been treated with a menin inhibitor, resistance in these highly pretreated samples was acquired in the absence of menin-inhibitor exposure. Transcriptomic analysis documented sustained on-target efficacy toward the canonical targets of the menin inhibitor in resistant cells. Targeted genomic analysis documented the emergence of multiple comutations, including RAS pathway and TP53 mutations, although neither was sufficient to induce menin-inhibitor resistance in vitro. Downregulation of KMT3D may account for resistance in one patient; inactivation of KMT2C/D has been reported to result in menin-inhibitor resistance, and KMT2C-edited cells from this patient were selected for in menin-inhibitor-containing growth conditions. Future studies will need to clarify more broadly which genomic/epigenomic alterations drive upfront resistance. Regardless of mechanism, our data support using menin inhibitors upfront or in early lines of therapy before substantial genomic or epigenomic evolution has occurred.

Huntington's Disease (HD) is an inherited neurodegenerative condition caused by an expansion of CAG repeats in the Huntingtin (HTT) gene, leading to a toxic form of the HTT protein. Despite advances in understanding the disease and developing symptomatic treatments, effective therapies for modifying its progression remain limited. Among emerging and novel treatments for central nervous system (CNS) disorders, gene therapy (GT), particularly using adeno-associated virus (AAV)-mediated gene delivery, holds great promise. Numerous preclinical and clinical trials are exploring the benefits of AAVs for treating neurodegenerative and genetic diseases. However, while widely used and investigated in rare and genetic disease treatment, AAVs' potential for HD treatment remains underexplored. The absence of a comprehensive collection of previous reports, advancements, and methodologies regarding exclusively AAV-mediated GT for HD is notable and prompted us to address this gap. The current review compiles the available and emerging information regarding the application of AAVs in HD therapy, outlines the promise of this approach, and highlights the necessity of conducting further studies to achieve efficient HD treatment. The authors hope that the current review will guide further research to unlock the full potential of AAVs in treating HD.

The <i>Krüppel</i>-like factors (KLFs) are a family of transcriptional regulators that play crucial roles in regulating diverse cellular processes including development, proliferation, differentiation, metabolism, and carcinogenesis across various tissues. KLFs play pivotal roles in gastrointestinal pathologies, and exhibit tissue- and cell-type-specific expression patterns throughout the gastrointestinal tract. During gastrointestinal (GI) development, KLFs orchestrate the transition from embryonic to adult gene programming, with specific family members being essential for proper organogenesis and tissue formation. KLFs also function as context-dependent modulators of GI homeostasis, inflammation, and carcinogenesis in adult tissues and interact with major signaling pathways such as PI3K/AKT, NF-κB, Wnt, Notch, MAPK, and TGF-β. This review comprehensively examines the roles of KLFs in GI health and disease, focusing on their expression patterns, regulatory mechanisms, function in normal homeostasis, and therapeutic implications for gastrointestinal disorders.

γ-aminobutyric acid (GABA), the primary inhibitory neurotransmitter in the central nervous system (CNS), regulates neuronal excitability, synaptic plasticity, and oscillatory activity essential for cognition, emotion, and behavior. Disruptions in GABAergic signaling are increasingly recognized as key contributors to a range of neurodevelopmental disorders (NDDs), including schizophrenia (SZ), autism spectrum disorder (ASD), major depressive disorder (MDD), bipolar disorder (BD), and intellectual disability (ID). In this review, we analyze the data available from the literature concerning the components of the GABA pathway. We describe the main steps of GABA metabolism, including GABA synthesis and release, GABA receptors neurotransmission, GABA reuptake and catabolism, and evaluate their involvement in the pathogenesis of neurodevelopmental disorders. We suggest the possibility of existence of so far undescribed mechanisms which maintain the concentrations of GABA at a relatively physiological level when the function of glutamic acid decarboxylases is compromised by mutations. Searching for these mechanisms could be important for better understanding neurodevelopment and could give a clue for future searches for new therapeutic approaches for treating or alleviating the symptoms of BD and SZ. We also argue that the metabolic stage of the GABA pathway has only a minor direct effect on GABA signaling and rather causes clinical effects due to accumulation of neurotoxic byproducts.

The rising global prevalence of inflammatory bowel diseases, including Crohn's disease and ulcerative colitis, is paralleled by an increased risk of colitis-associated colorectal cancer. Persistent intestinal inflammation promotes genetic instability and epigenetic reprogramming within epithelial and immune cells, driving the multistep transition from inflammation to neoplasia. This review integrates human and preclinical model evidence with literature mining and bioinformatic analyses of genetic, epigenetic, and ncRNA data to dissect molecular mechanisms driving colitis-associated colorectal cancer from chronic inflammation. We highlight how pro-inflammatory cytokines (e.g., TNF-α, IL-6), oxidative stress, and microbial dysbiosis converge on key transcriptional regulators such as NF-κB and STAT3, inducing DNA methylation and histone modifications (e.g., H3K27me3); altering chromatin dynamics, gene expression, and non-coding RNA networks (e.g., <i>miR-21</i>, <i>MALAT1</i>, <i>CRNDE</i>); ultimately reshaping pathways involved in proliferation, apoptosis, and immune evasion. This review updates new potential associations of entities with these diseases, in their networks of interaction, summarizing major aspects of genetic and chromatin-level regulatory mechanisms in inflammatory bowel disease and colorectal cancer, and emphasizing how these interactions drive the inflammatory-to-neoplastic transition. By underscoring the reversibility of epigenetic changes, we explore their translational potential in early detection, surveillance, and precision epigenetic therapy. Understanding the interplay between genetic mutations and chromatin remodeling provides a roadmap for improving diagnostics and personalized treatments in inflammatory bowel disease-associated colorectal carcinogenesis.

This review summarizes and compares literature data on the main strategies for the synthesis of saturated and/or partially saturated analogs of six-membered polyazoaromatic heterocycles. With a few exceptions, this data was published within the last 15-20 years. These strategies include, first of all, hydrogenation, which can be carried out in a classical manner (i.e., in the presence of a catalyst and molecular hydrogen) or via hydrogen transfer techniques. Other approaches comprise saturation of aromatic frameworks, which can be achieved using compounds other than hydrogen, such as hydroboration and dearomatic binding, or the creation of saturated or partially saturated polyazo heterocycles through the coupling of two or more molecules. Each of the above strategies has certain advantages and serious shortcomings and limitations. Despite the apparent methodological difficulties, it is demonstrated that the described approaches can sometimes give impressive results, including the production of optically pure products under relatively mild conditions.

Extensive portosystemic shunting in portal hypertension creates a paradox: effective decompression protects against variceal bleeding but complicates liver transplantation through portal steal. We report a 31-year-old man with cryptogenic acute-on-chronic liver failure grade 3 (Model for End-Stage Liver Disease-Sodium (MELD-Na) 31, United Kingdom Model for End-Stage Liver Disease (UKELD) 63). Despite severe portal hypertension on Doppler ultrasound, endoscopy revealed complete absence of oesophageal and gastric varices. CT explained this paradox, demonstrating a large tortuous splenorenal shunt providing highly effective decompression. At transplantation, this protective adaptation caused portal steal, with immediate right posterior sector graft demarcation. Restoration of perfusion required emergent left renal vein ligation. This case highlights how extensive splenorenal shunting can fully mask varices yet create critical intraoperative challenges. The absence of varices in established portal hypertension should prompt investigation for alternative drainage pathways. Even in young patients, comprehensive vascular assessment is essential, as protective anatomical adaptations can precipitate life-threatening operative emergencies requiring specialized surgical intervention.

Temporomandibular disorder (TMD) refers to musculoskeletal conditions that affect the temporomandibular joint (TMJ) and surrounding tissues, often leading to pain, impaired function, and a diminished quality of life. Despite its clinical relevance, diagnosing and managing TMD remains complex due to its multifactorial etiology. Biomarkers, which are quantifiable indicators of biological processes, have gained attention as valuable tools for enhancing TMD diagnosis, prognosis, and treatment monitoring. Various categories of biomarkers, such as molecular, genetic, sensory, and neuroimaging markers, have been investigated in TMD studies. Biomarker assessment typically employs non-invasive methods, including analysis of saliva, serum, or synovial fluid, and advanced imaging techniques. The incorporation of these biomarkers into clinical practice offers the potential for earlier diagnosis, more accurate prediction of treatment responses, and the development of individualized therapeutic strategies.

Drug-induced liver injury (DILI) is a diagnosis of exclusion, but one that requires high clinical suspicion because prompt withdrawal of the offending agent is imperative to improve prognosis. Piperacillin/tazobactam (TZP) is a rare cause of clinically apparent liver injury. This case is an example of DILI caused by TZP that was identified when a hospitalized patient's liver enzymes greatly increased, and hepatic steatosis was subsequently seen on a computed tomography scan. The Roussel Uclaf Causality Assessment Method (RUCAM) score is a tool used to indicate the likelihood of DILI. In this case, the RUCAM score was 7, indicating that the causality assessment of the TZP as the cause of liver injury was probable. This case underscores the importance of maintaining a high index of suspicion for DILI, particularly in patients receiving extended courses of antibiotics, and highlights the need for routine liver function monitoring during therapy with agents known to carry hepatotoxic potential.

<h4>Introduction</h4>The interplay between coronary disease and neurocognitive dysfunction remains unclear with several underlying factors likely contributing to this complex relationship. This study develops a predictive model using a machine learning approach to determine a predictive model of neurocognitive functioning in patients with acute coronary syndrome (ACS).<h4>Methods</h4>Sixty-three patients, enrolled in the phase III cardiac rehabilitation program, underwent a neurocognitive assessment. To predict neurocognitive functioning a cross validated random forest model was used (RF_cv) due to its robustness to non-linear relationships and overfitting, and its successful application in prior disease prediction studies.<h4>Results</h4>The RF_cv model showed an r-squared of 0.978, an RMSE of 0.6309 and a MAE value of 0.479. The top-ten predictors in the model were: HDL, Depression, Glucose, Glycated Hemoglobin, B-Type Natriuretic Peptide, BMI (Kg/m2), Waist-to-Hip Ratio, Cholesterol, Anxiety and Age.<h4>Conclusion</h4>The variance in neurocognitive functioning is explained by a combination of biochemical indicators and body composition, reflecting classical cardiovascular risk factors and depression. The obtained RF-cv predictive model supports early identification of patients for tailored interventions.

<h4>Background</h4> High throughput proteomics has enabled hypothesis free biomarker discovery. However, differences in sample sizes, biological fluid, and quantification technologies have limited replication and validation of the results, and studies on the cross-platform variability are lacking. Here, we present the first orthogonal validation across three platforms in Parkinson’s disease (PD) to understand the technical and biological challenges of proteomic studies. <h4>Methods</h4> We have leveraged publicly available proteomic data from cerebrospinal fluid (CSF), plasma, and urine within the Parkinson’s Progression Markers Initiative (PPMI) cohort, generated using SomaScan5K (CSF), mass spectrometry (MS; CSF, plasma, and urine), and Olink Explore (CSF and plasma). Across platforms, we compared 375 proteins that were consistently quantified. We performed differential abundance analysis comparing PD versus healthy controls followed by sensitivity analyses (mutation carriers, at-risk participants, longitudinal analyses) to further understand the findings. <h4>Results</h4> In CSF, we found significant correlations between effect sizes from the 375 proteins quantified by SomaScan5K and MS (ρ=0.42, p=2.60×10 □ □), as well as SomaScan5K and Olink Explore (ρ=0.15, p=3.15×10□ 3 ) while MS and Olink Explore showed no significant correlations in CSF or plasma. Orthogonal validation identified two proteins (DLK1, GSTA3) replicated between SomaScan5K and Olink Explore and seven proteins (ALCAM, CHL1, CNDP1, NCAM2, PEBP1, PTPRS, SCG2) replicated between MS and SomaScan5K. No proteins replicated between MS and Olink Explore in CSF or plasma. DDC showed consistent dysregulation across analyses. In CSF (Olink Explore), it was dysregulated in PD participants (beta=0.79, p=8.49×10 −16 ), and in at-risk individuals (beta=0.64, p=1.41×10 −7 ) including those with hyposmia (beta=0.70, p=2.13×10 −5 ) and REM Sleep Behavior Disorder (beta=0.52, p=1.00×10 −3 ). In urine, DDC was higher in at-risk individuals (beta=0.43, p=7.28×10 −5 ), driven by LRRK2 + at-risk participants (beta=0.59, p=1.74×10 −6 ), as well as in symptomatic mutation carriers, LRRK2 + (beta=0.68, p=9.08×10 −8 ), and GBA + (beta=0.28, p=0.04). <h4>Conclusions</h4> Biologically, these findings add further evidence that DDC has strong potential as a biomarker. Methodologically, our findings emphasize that platform selection can introduce more variance than that originating from disease status, which limits the reproducibility across technologies. This highlights the challenges and importance of cross-platform validation in proteomic biomarker research, and the translation of those discoveries to the clinic.

Sarcopenia and frailty are complex geriatric syndromes influenced by a combination of genetic and environmental factors. Recent studies suggest that specific genetic variants, DNA methylation patterns and shortened telomeres are associated with age-related diseases and might contribute to the development of both sarcopenia and frailty. In this study, we investigated the contribution of multi-omics data to sarcopenia, frailty, lean mass index (LMI) and handgrip strength in an elderly Lithuanian population. A total of 204 participants (age 82.2 ± 7.6 years) were included, comprising 122 individuals diagnosed with sarcopenia and/or frailty and 82 healthy, community-dwelling older adults. The results showed that LMI was associated with various health and lifestyle factors. Two genetic variants, CLIC5 rs75652203 and GHITM rs17102732, were found to be significantly associated with handgrip strength at the genome-wide level. Additionally, 12 polymorphisms previously linked to sarcopenia were replicated in relationship to LMI: BOK rs76993203, VAMP5 rs1374370, TMEM18 rs12714414, SFMBT1 rs36033494, BANK1 rs13136118, TET2 rs2647239, FOXO3 rs9384679, L3MBTL3 rs13209574, ZFAT rs13267329, CEP57 rs35793328, PCGF2 rs1985352 and MC4R rs66922415. Furthermore, several genes, many of which are involved in immune system processes, were significantly enriched with differentially methylated sites associated with LMI. Shorter telomeres were also associated with both sarcopenia and frailty. Notably, a significant relationship was observed between telomere length and methylation levels in genes related to lifestyle traits and the risk of developing these conditions. These findings provide new insights into the biological mechanisms underlying sarcopenia and frailty, underscoring the important roles of genetic and epigenetic factors in their pathogenesis among older adults.

Major depressive disorder (MDD) is a prevalent and debilitating psychiatric condition with significant societal and economic impacts. Many patients are resistant to current antidepressant therapies, underscoring the need for novel treatments targeting underlying mechanisms. We previously discovered that glutaminase (GLS1), an enzyme converting glutamine to glutamate, is upregulated specifically in activated microglia in mice exposed to Chronic Social Defeat Stress (CSDS). Importantly, GLS1 mRNA was also upregulated in microglia within postmortem brain tissue of MDD patients, highlighting a potential role for microglial GLS1 in MDD pathophysiology. However, existing GLS1 inhibitors lack brain penetrance and/or cause gastrointestinal toxicities, limiting their translational potential. To address this, we utilized a hydroxyl-terminated poly(amidoamine) dendrimer nanoparticle system to selectively target microglial GLS1. Using structurally distinct GLS1 inhibitors, we synthesized two hydroxyl-dendrimer-GLS1 inhibitor conjugates: dendrimer-TTM020 (D-TTM020) and dendrimer-JHU29 (D-JHU29). In the murine CSDS model, we evaluated their microglial target engagement, safety, and efficacy using immunofluorescence, GLS1 activity assays, gastrointestinal histopathology, and a battery of behavioral tests. Using a Cy5 fluorescently labeled hydroxyl-dendrimer (D-Cy5), we confirmed that systemically administered D-Cy5 crossed the blood-brain barrier and was selectively engulfed by activated microglia in mice after CSDS. D-TTM020 and D-JHU29 attenuated CSDS-induced microglial GLS1 activity elevation without affecting non-microglial cells. Furthermore, D-TTM020 and D-JHU29 both alleviated CSDS-induced social avoidance, and D-TTM020 additionally reduced anxiety-like behavior and improved recognition memory. Both conjugates were well tolerated, with no overt or gastrointestinal toxicities. Collectively, these findings suggest that microglia-targeted GLS1 inhibition is a promising therapeutic approach for chronic stress-associated depression.

The era of targeted therapies has significantly advanced our understanding of cancer growth and metastasis. Intrinsic or acquired drug resistance remains a major challenge, rendering clinically overt metastatic disease incurable in most patients. This review first examines key clinical trials and their primary outcomes involving targeted therapies in the most common advanced solid tumors, along with the main mechanisms underlying drug resistance. Recently, micrometastatic disease has emerged as a novel focus of investigation aimed at definitively curing advanced solid tumors. Accordingly, this review explores the biology of micrometastases, current challenges in their detection and monitoring, and the main strategies proposed to prevent their progression. The potential roles of nanotechnology and artificial intelligence-driven predictive models are also discussed. Furthermore, we highlight specific characteristics of micrometastatic disease that favor immune modulation, and we evaluate the effectiveness of an immunotherapy regimen that inhibits immune suppression. The lead time provided by serum tumor markers, used experimentally to better track the progression of otherwise undetectable micrometastatic disease, also forms the mechanistic basis for a novel protocol we propose to prevent relapse in high-risk cancer patients. This innovative protocol holds scientific relevance being supported by an appropriate mathematical model and ready for immediate application in clinical practice.

<h4>Background</h4>The treatment of dermatological diseases has evolved significantly with the advent of advanced therapeutic strategies involving platelet-rich products. These products are rich in morphogens, growth factors, and proteins that play a crucial role in tissue regeneration and wound healing. Their combination with different biomaterials has been engineered to enhance the biomaterials' safety and performance in the context of tissue healing.<h4>Objective</h4>This narrative review aims to explore the current evidence on the biological mechanisms, efficacy, and clinical applications of these combined therapies. Furthermore, we examine the potential advantages of synergistic effects and the challenges associated with optimizing treatment protocols.<h4>Methods</h4>Relevant literature was retrieved through a structured search strategy implemented across PubMed, Scopus, and Google Scholar databases. Studies included investigated co-administration of platelet-rich products with other agents in topical, injectable, or composite formulations for dermatological conditions with no restriction regarding publication date.<h4>Results</h4>The review summarizes in vitro and in vivo biological effects of various biopolymers and active substances combined with platelet-rich products, highlighting diverse application strategies and their effectiveness across dermatological contexts.<h4>Conclusion</h4>Adding platelet-rich products has shown promising results in enhancing therapeutic outcomes for various dermatological conditions, including chronic wounds, burns, scars, and skin aging. Although promising results have been reported, the need for critical thinking regarding the selection of the biomaterial and the platelet-rich products, standardized methodologies, large-scale randomized controlled trials, and long-term follow-up studies is emphasized to fully establish the clinical benefits of these combined treatments in dermatology.

Malignant brain tumors remain highly challenging to treat due to intrinsic and acquired therapy resistance and limited therapeutic options, consequently contributing to poor prognosis. Advancing the understanding of resistance mechanisms alongside novel treatment strategies is essential to improve clinical outcomes. Altered gene expression is common in tumors, and a specific class of non-coding RNAs, particularly long non-coding RNAs (lncRNAs), is frequently deregulated. LncRNAs play critical roles in processes such as cell proliferation, cell cycle arrest, and metastasis in brain cancer, functioning either as tumor promoters or suppressors. They exert their effects through transcriptional and post-transcriptional regulatory mechanisms. Understanding the functional roles of lncRNAs in malignant brain tumors has become a priority, as they are differentially expressed in tumors compared to healthy tissue. These molecules are studied for their potential as therapeutic targets and biomarkers in oncology. This review provides an overview of current research on brain cancer and lncRNAs, emphasizing the need for further investigation into their specific roles in therapy resistance and their involvement in various pathways. A better understanding of lncRNAs and their role in brain cancer could offer valuable insights into their prognostic and therapeutic potential, with the promise of improving early diagnosis and treatment outcomes.

Bone defects, characterized by a loss of skeletal structure integrity, represent a prevalent clinical challenge affecting millions of patients. While bone autografts and allografts offer potential solutions, limitations, including donor scarcity, immune rejection, anatomical constraints, and complications arising from host comorbidities such as diabetes, often lead to unsatisfactory outcomes. This necessitates the need for alternative treatments. Researchers have identified that reactive oxygen species (ROS) play a crucial role in bone regeneration. Although physiological ROS levels are essential for normal healing, excessive ROS accumulation disrupts the balance between bone formation and resorption, hindering regeneration. Antioxidants can mitigate oxidative stress by scavenging ROS or inhibiting their formation, thereby restoring the equilibrium between bone formation and resorption. Advances in nanotechnology have enabled the development of various ROS-scavenging nanomaterials with enhanced therapeutic efficacy. These nanomaterials either function as delivery platforms for conventional antioxidants or as direct ROS-neutralizing agents through intrinsic redox or enzyme-mimicking properties. This review comprehensively summarizes ROS-scavenging nanomaterials for bone tissue regeneration, focusing on their design strategies, underlying mechanisms, applications, and potential for clinical translation.

The putamen plays a key role in motor control, learning, and cognition, with abnormal putamen volumes associated with neuropsychiatric disorders. Using data from the ABCD study, we performed a genome wide association study (GWAS) of putamen volumes, followed by replication and pathway enrichment analyses. We next evaluated the shared genetic architecture of putamen volume and neuropsychiatric disorders—including depression, schizophrenia, Parkinson’s, ADHD, bipolar, and OCD— using SNP associations from this and prior GWASs. We identified 199 genome-wide significant SNP associations in White participants. Most identified SNPs were in gene regulatory regions and in the neuronal growth-linked genes, DCC and DSCAM . Sixteen of the most significant associations observed in Whites were replicated in non-White participants. Twenty-one SNPs from prior GWASs of putamen volumes were also replicated in our ABCD GWAS analysis, including five of the top eight SNPs. There was considerable genetic heterogeneity between White and non-White participants in putamen-linked SNPs with significant differences between the minor allele frequencies across the two groups (Wilcoxon rank-sum test Exact prob < 0.0001). We identified a key pathway ( REACTOME_DSCAM_INTERACTIONS) associated with putamen volume that involves DSCAM gene, netrin-1 protein and/or DCC gene. In addition, 28 unique SNPs from prior GWASs of neuropsychiatric disorders were strongly associated with putamen volume at Bonferroni-corrected significance, while 40 SNPs shared by at least three disorders were associated with putamen volume at a 0.05 threshold. Our findings provide deeper insights into the shared genetic architecture and cross-population differences in genetic associations of putamen volume.

Cytoplasmic shortening of mRNA poly(A) tails represses eukaryotic gene expression by inhibiting efficient translation and committing an mRNA to decay. The CCR4–NOT deadenylase machinery interacts with sequence-specific RNA-binding proteins (RBPs), termed RNA adaptors, to target specific transcripts for deadenylation. In contrast, the PAN2–PAN3 deadenylation complex is thought to be predominantly recruited to mRNAs via interaction with the poly(A) binding protein, raising the question of whether it acts in a transcript-specific manner. Here, using biochemical reconstitution, we show that PAN2–PAN3 can also be recruited to specific RNAs via RNA adaptors, including MEX3, YTHDF and ZFP36 proteins. In cells, we find that a diverse range of RNA adaptors interact with both major deadenylation complexes. Thus, our data suggest that, in addition to CCR4-NOT, PAN2-PAN3 also contributes to the specificity of mRNA degradation and the robustness of post-transcriptional regulation of gene expression.

Gastrointestinal injury (GI) is a significant concern in various medical contexts, particularly in patients undergoing antiplatelet therapy, experiencing trauma, or dealing with the effects of medications. The present study investigated the effect of atractylodin, a bioactive compound derived from <i>Atractylodes lancea</i> (Thunb.) DC., traditionally used in medicinal applications. A sepsis animal model was established through cecal ligation and perforation. Mice were treated with atractylodin, with or without silencing of NAD‑dependent protein deacetylase sirtuin‑3 (SIRT3), via transfection with adeno‑associated virus (AAV) vectors. Atractylodin markedly improved mitochondrial function <i>in vivo</i>, as evidenced by increased mitochondrial‑related proteins via western blot analysis (TOM20) and increased mitochondrial membrane potential, as observed via JC‑1 staining. In addition, atractylodin treatment inhibited apoptosis. Together, these changes regulated mitochondrial dysfunction. Moreover, atractylodin improved the prognosis of sepsis‑induced ferroptosis in the stomach and colon tissues. Atractylodin markedly activated SIRT3 while suppressing the expression of ac‑peroxiredoxin‑3 (PRDX3). Notably, the knockdown of SIRT3 diminishes the inhibitory effect of atractylodin on ferroptosis, when AAV‑short hairpinSIRT3 was injected into the stomach and colon tissues of C57 BL/6 mice. Further, atractylodin may have attenuated GI development by preventing mitochondrial dysfunction through the SIRT3/PRDX3 pathway. Hence, protection against mitochondrial dysfunction using atractylodin may be a promising therapeutic strategy against sepsis‑induced acute GI.

The ubiquitin‑proteasome system (UPS) acts as a central regulator for a range of protein components, including ubiquitin, ubiquitin‑activating enzyme (E1), ubiquitin‑conjugating enzyme (E2), ubiquitin ligase (E3), the 26S proteasome and deubiquitinating enzyme. These components function in a coordinated manner to facilitate the repair and degradation of proteins. Among the ubiquitinating enzymes, in conjunction with E1‑activating enzymes and E2‑binding enzymes, it attaches to substrates and promotes the transfer of ubiquitin molecules to target proteins. The S‑phase kinase‑associated protein 1 (SKP1)‑Cullin‑F‑box (SCF) complex is one of the E3 ligases involved in cancer progression, and consists of four primary components: i) SKP1; ii) Cullin 1/coiled‑coil domain containing 53; iii) ring box protein 1/RING‑box 1/RING‑box protein HRT1; and iv) F‑box protein (FBP). Each FBP can recognize and bind to a different set of substrates, which determines the specificity of the targets of the SCF complex. In addition to being components of the SCF complex, FBPs participate in processes such as DNA replication, transcription, cell differentiation and cell death. F‑box protein 2 (FBXO2), a member of the human FBP family, functions as a subunit of FBP ubiquitin ligases and is highly expressed in the cytoplasm of eukaryotic cells. FBXO2 is highly expressed in various malignant tumors, and is closely associated with tumor cell proliferation, migration and invasion. The present review presents the composition of the UPS and FBP families and their roles in malignant tumors, with a focus on advancements in research into the relationships between FBXO2 and various malignant tumors, aiming to acquire a more profound understanding of their potential mechanisms in the development of malignant tumors and to offer novel ideas for tumor therapy.

<h4>Background</h4>Huntington's disease (HD) is characterized by early, selective, progressive vulnerability of striatal medium spiny neurons (MSNs). Proenkephalin (PENK), a precursor of opioid peptides abundantly expressed in MSNs, is a promising biomarker of striatal integrity, but region-specific associations and its potential for early-stage discrimination have not been characterized.<h4>Objectives</h4>We investigated cross-sectional and longitudinal associations between baseline cerebrospinal fluid (CSF) PENK concentration and regional brain atrophy, compared identified patterns with CSF neurofilament light (NfL), and evaluated PENK and NfL for discriminating between HD Integrated Staging System (HD-ISS) stage 0 versus 1 in a far-from-onset HD gene-expanded (HDGE) cohort.<h4>Methods</h4>Whole-brain voxel-based morphometry was performed in 149 participants (72 HDGE, 77 controls) cross-sectionally and 88 participants (54 HDGE, 34 controls) longitudinally over a mean interval of 4.8 years. Voxel-wise linear regression tested associations between baseline biofluid biomarkers and gray/white matter volume, adjusting for age, sex and CAG-Age Product score, with false discovery rate correction. Logistic regression and receiver operating characteristic analyses assessed stage discrimination.<h4>Results</h4>Lower baseline CSF PENK predicted longitudinal gray and white matter loss, predominantly in the striatum bilaterally. Higher baseline CSF NfL predicted widespread longitudinal white matter loss. For stage discrimination, PENK (area under curve [AUC], 0.706; P = 0.0002) outperformed NfL (AUC, 0.661; P = 0.1596) with minimal gain from combining both (AUC, 0.714; joint P = 0.0007).<h4>Conclusions</h4>Lower baseline CSF PENK concentration predicted longitudinal striatal atrophy and CSF PENK outperformed CSF NfL in distinguishing HD-ISS stages 0 and 1, supporting its role as a striatum-specific biomarker with potential to enrich early-stage HD trial cohorts. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Many studies have proposed various comparative genomic methods to probe the molecular basis for adaptive functional convergence between species, conventionally by detecting the convergence of amino acid states between orthologous protein sequences of these species or lineages. However, different amino acids with similar physicochemical properties at a site may contribute to the functional similarity of the protein. Hence, could the convergence of amino acid physicochemical properties, in addition to state convergence, also contribute to adaptive convergence of organismal functions? Here we grouped amino acids into physicochemically similar classes, and developed computational pipelines to detect the Convergence of Amino Acid Properties (CAAP, https://github.com/shanschen33/CAAP) by modifying previous state convergence detection methods. Investigating three organismal convergence cases including echolocating mammals, marine mammals and woody mangroves, we found genes with CAAP that likely contribute to the respective functional adaptation, supported by orthogonal evidence such as functional enrichment and positive selection analyses. Our findings in multiple cases corroborate the hypothesis that CAAP may underlie adaptive convergent evolution of organismal functions, emphasising the importance of considering sequence features more complex than amino acid states when studying adaptive sequence convergence.

In the search for novel therapeutic strategies against cancer, natural compounds such as α-Pinene, a bioactive monoterpene predominantly found in coniferous trees, have emerged as potential modulators of oncogenic processes. The primary objective of this study was to investigate whether α-Pinene can regulate the expression of MATN3 (Matrilin-3), a gene previously associated with poor prognosis in various cancers. Our central hypothesis is that α-Pinene exerts its anticancer effects, at least in part, by downregulating MATN3, thereby impacting oncogenic signaling. The rationale for selecting MATN3 as a target lies in its demonstrated overexpression in multiple cancer types and its established role as both a prognostic marker and a contributor to tumor progression. Extending our research through a comprehensive pan-cancer analysis, we confirmed the association between high MATN3 expression and poor prognosis across multiple cancer types. Further exploration revealed a strong correlation between MATN3 expression and immune infiltration, as well as significant associations with key immunomodulatory genes, suggesting an intricate role of MATN3 in the tumor immune environment. Enrichment analysis pointed to the involvement of MATN3 in the PI3K-AKT signaling pathway. Additionally, we identified connections between MATN3 and extracellular matrix (ECM)-related mechanisms.The downregulation of MATN3 by α-Pinene in HepG2 cells suggests a novel mechanism by which α-Pinene may exert anticancer effects, potentially through the disruption of key oncogenic and immune-related pathways. This study not only underscores the anticancer potential of α-Pinene but also establishes MATN3 as a critical target and biomarker across a spectrum of cancers. Our findings advocate for further clinical investigations into α-Pinene's therapeutic potential, particularly focusing on its impact on MATN3 and related pathways in diverse cancer contexts.

The lysosome integrates anabolic signaling and nutrient sensing to regulate intracellular growth pathways. The leucine-rich repeat-containing 8 (LRRC8) channel complex forms a lysosomal anion channel and regulates PI3K-AKT-mTOR signaling, skeletal muscle differentiation, growth, and systemic glucose metabolism. Here, we define the endogenous LRRC8 subunits localized to a subset of lysosomes in differentiated myotubes. We show that LRRC8A affects leucine-stimulated mTOR; lysosome size; number; pH; expression of lysosomal proteins LAMP2, P62, and LC3B; and lysosomal function. Mutating an LRRC8A lysosomal targeting dileucine motif sequence (LRRC8A-L706A;L707A) in myotubes recapitulates the abnormal AKT signaling and altered lysosomal morphology and pH observed in LRRC8A knockout cells. In vivo, LRRC8A-L706A;L707A knock-in mice exhibit increased adiposity, impaired glucose tolerance and insulin resistance associated with reduced skeletal muscle PI3K-AKT-mTOR signaling, glucose uptake, and impaired incorporation of glucose into glycogen. These data reveal a lysosomal LRRC8-mediated metabolic signaling function regulating lysosomal function, systemic glucose homeostasis, and insulin sensitivity.

Genetic variants can have sex-specific, sex-biased, or sexually antagonistic fitness effects, yet their roles in fitness-related traits remain unclear. Using pooled phenotype sorting and sequencing of male <i>Drosophila melanogaster</i> from natural populations, we identified starvation resistance-associated variants, many in regulatory regions or altering protein sequences. RNA interference experiments showed that 85.7% (66 of 77) of the candidate genes with nonlethal knockdown effects influenced starvation resistance. Of these, 49 had sex-dependent effects, including 12 with sexually antagonistic effects-all increasing resistance in females but decreasing it in males. These patterns were not explained by sex-biased expression or knockdown efficiency. Analysis of the <i>Lnk</i> gene revealed that both nonsynonymous mutations and expression changes had sex-dependent effects. Our findings indicate that polygenic architecture, sex-dependent effects, and pleiotropy jointly shape evolutionary outcomes and that some variants maintained by these forces may enable rapid responses to environmental change.

Prevalence of seizures is 1 to 5/1,000 neonates. The most common causes of neonatal seizures are hypoxic-ischemic encephalopathy (HIE), vascular events (hemorrhages, stroke), and infections. We assessed prevalence and etiology of seizures defined according to the recent Brighton and International League of Epilepsy (ILAE) criteria in a neonatology monocenter cohort.In a retrospective cross-sectional cohort study of all 12,154 neonates born in our three maternities from January 1, 2022 to December 31, 2023 seizures were categorized by frequency, etiology, risk profile, semiology, and EEG. A total of 19 neonates (male: <i>n</i> = 11 [57.9%]; full-term: <i>n</i> = 11 [57.9%]; preterm very low birth weight [VLBW]: <i>n</i> = 6 [31.6%]; preterm >1,500 g birth weight: <i>n</i> = 2 [10.5%]) were identified.In 19/12,154 neonates, seizures were confirmed by application of the ILAE criteria. Preterm VLBW was found in 174 neonates with birth weight <1,500 g. Seizure incidence was 1.6/1,000 in all neonates and 3.4% in VLBW infants. HIE was the most frequent etiology in term infants (30.8%), followed by vascular events in preterm >1,500 g and term infants (30.8%). Vascular events were the most common cause in preterm VLBW infants (83.3%). Whole exome sequencing (WES) was performed in four cases (21.1% of neonates with seizures).Incidence of neonatal seizures in our center is in the lower range and leading seizure etiologies are comparable to the literature. Early recognition of neonatal seizures including the detection of electrographic-only seizures and early WES to identify rare genetic defects possibly offering tailored treatment options have the potential to further raise the standard of neonatal care and improve neurodevelopmental outcome.

In vitro-transcribed and circularized RNAs (ivcRNAs) represent a robust platform for sustained protein translation, offering promising potential for localized therapeutic delivery in joint diseases. Osteoarthritis (OA), the most prevalent degenerative joint disorder, remains a major clinical challenge due to its progressive nature and the lack of disease-modifying treatments. In this study, we identify Musashi2 (Msi2) deficiency in articular chondrocytes as a key contributor to OA pathogenesis. To evaluate the efficacy of ivcRNA-mediated protein replacement therapy, we developed a localized delivery strategy that enables high-yield and prolonged protein expression in chondrocytes. Using a destabilization of the medial meniscus (DMM) mouse model, we demonstrate that intra-articular delivery of ivcRNA encoding MSI2 effectively mitigates OA progression in male mice. Furthermore, therapeutic supplementation of SOX5, a downstream effector of MSI2, via ivcRNA delivery further validates this approach. Our findings establish ivcRNA-based protein replacement as a potential RNA therapeutic strategy for osteoarthritis.

Imaging-based spatial transcriptomics (ST) is evolving as a pivotal technology in studying tumor biology and associated microenvironments. However, the strengths of the commercially available ST platforms in studying spatial biology have not been systematically evaluated using rigorously controlled experiments. We use serial 5 μm sections of formalin-fixed, paraffin-embedded surgically resected lung adenocarcinoma and pleural mesothelioma samples in tissue microarrays to compare the performance of the ST platforms (CosMx, MERFISH, and Xenium (uni/multi-modal)) in reference to bulk RNA sequencing, multiplex immunofluorescence, GeoMx, and hematoxylin and eosin staining data. In addition to an objective assessment of automatic cell segmentation and phenotyping, we perform a manual phenotyping evaluation to assess pathologically meaningful comparisons between ST platforms. Here, we show the intricate differences between the ST platforms, reveal the importance of parameters such as probe design in determining the data quality, and suggest reliable workflows for accurate spatial profiling and molecular discovery.

Metabolic dysfunction-associated fatty liver disease (MAFLD) is a problem worldwide. Oxidative stress is important factor in beginning and progress of MAFLD. This study is the first clinical trial with the aim of determining the effect of Pistacia atlantica Sub. Kurdica gum on oxidative status in patients with metabolic dysfunction-associated fatty liver disease. In this double-blind randomized clinical trial 50 patients with metabolic dysfunction-associated fatty liver disease were randomized into two groups: those given syrup containing Pistacia atlantica sub. Kurdica gum (Group A), those on placebo (Group B). Over a two-month period, Group A given syrup containing 500 mg of P. atlantica sub. Kurdica gum per each tablespoon and Group B given syrup without P. atlantica sub. Kurdica gum. Anthropometric measures, serum oxidative markers and physical activity were evaluated at the beginning and end of the intervention. We observed a significant decrease in fatty liver grade in group A (P = 0.03). In the end of intervention had not been show significant change in serum total antioxidant capacity (TOS) in group A (P = 0.91) and group B (0.70). Serum total oxidant status (TAC) had been show increase in group A and decrease in group B but this changes not significant as within group (P = 0.36, P = 0.53, respectively) and between group (P = 0.66). The mean of Malondialdehid (MDA) had significant decrease from baseline in group A (P = 0.002) and had non-significant increase in group B (P = 0.65). The between-group comparison of changes of MDA had been show a significant difference (P = 0.025). As well as, after adjusting for baseline characteristics (Age, Gender, Physical activity, BMI), there were not significant differences between A and B groups in the changes comparison of TOS and TAC except for MDA (p < 0.032). Weight had significant decrease in group A (P = 0 < 001). Pistacia atlantica sub. Kurdica gum can improve some oxidative status indices, particularly lipid peroxidation and subsequently MAFLD in patient with metabolic dysfunction-associated fatty liver disease, but further studies with larger samples, longer duration and dose-response assessment will be needed.Trial registration: IRCT20231219060466N1, 2024-01-05 (https//irct.behdasht.gov.ir/).

The secretion of α-synuclein from presynaptic terminals is controlled by neuronal activity through a calcium-dependent mechanism. To address the role of voltage gated calcium channels in this process, we used reverse brain microdialysis to monitor α-synuclein release in vivo in the presence of selective channel inhibitors. Our results revealed that the ω-conotoxin GVIA-sensitive N-type calcium channels are the major mediators of stimulated α-synuclein secretion in mouse striatum.

This study aims to explore and analyse the potential antioxidant and anticancer potential of various citrus-mediated nanoformulations (CMNs), focusing on their effectiveness in scavenging free radicals and inducing cytotoxicity in cancer cells. This research employs a meta-analysis approach to assess data from multiple studies on CMNs. This study is the first meta-analysis to evaluate the antioxidant and anticancer properties of CMNs concurrently. This study offers a novel perspective by examining citrus species, plant parts utilised, nanoparticle types, particle sizes, and coating materials. The analysis employs the Population, Intervention, Comparison, and Outcome (PICO) framework and complies with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The analysis utilizes Hedges' effect size and includes validation through fail-safe N. The IC₅₀ evaluation (µg/mL) revealed a significant effect of CMNs on antioxidant activity (d₊₊ = 3.49; P < 0.05). The IC50 value of 3.49 in the CMN indicates that a lower concentration is sufficient to inhibit 50% of the free radical activity, reflecting a stronger antioxidant potential than that of the control group. However, the overall antioxidant assay results (d₊₊ = 0.2; P = 0.309) and radical inhibition (%) for CMNs (d₊₊ = 0.1; P = 0.602) did not significantly differ. Subgroup analysis provided further insights, showing that both citrus peel and polyvinyl alcohol significantly reduced IC₅₀ values (d₊₊ >1; P < 0.05). In addition, radical inhibition significantly increased in CMNs derived from Citrus paradisi (d₊₊ = 3.05; P = 0.015), followed by those derived from Citrus limon (d₊₊ = 2.25; P < 0.01) and Citrus reticulata (d₊₊ = 1.03; P = 0.025). Various types of nanoformulations, such as Ag chitosan-NP (silver nanoparticle with chitosan), Ag-NP (silver nanoparticles), cerium dioxide nanoparticle (CeO₂-NPs), hydrogel-based nanocomposite (Hydrogel-NPCs), pectin-based nanoemulsion (Pectin-NPEs), titanium dioxide nanoparticle (TiO₂-NP), and whey-based nanoemulsion (Whey-NPEs), also significantly enhanced free radical scavenging activity (d₊₊ >1; P < 0.01). In terms of anticancer activity, CMN has a strong effect size (|d₊₊| >1; P < 0.05), with species such as Citrus macroptera and plant parts such as juice showing highly positive effects (d₊₊ = 2.25; P < 0.001). Additionally, nanoparticles with sizes between 101 and 500 nm exhibited significant effectiveness (d₊₊ = 2.26; P < 0.001). These findings indicate that citrus-derived compounds have potential as anticancer agents by actively enhancing the antioxidant capacity of healthy cells. The significant antiproliferative activity observed across multiple cancer cell lines, supported by robust statistical analyses, demonstrates the potential of CMNs as a natural therapeutic approach for cancer prevention and treatment.

Immunity during pregnancy must be precisely balanced, because the mother's body needs to effectively fight pathogens while maintaining tolerance of the semi-allogeneic fetus. Factors that participate in achieving the proper immune balance during pregnancy include glycoproteins that expose sugar residues recognized by specific lectin receptors. Several types of lectins and their ligands have been detected at the maternal-fetal interface, and changes in their expression levels have been correlated with pregnancy complications. Although the presence of potential sugar ligands for human macrophage galactose-type lectin (MGL), including LacdiNAc and (sialo)Tn antigen, has been detected in amniotic fluid, placenta and fetal tissues, the interaction between them and its possible role have not been elucidated so far. The aims of the present study were to evaluate reactivity of MGL with amniotic fluid proteins and to identify and characterize the amniotic ligands of MGL. The analysis proved the ability of MGL to interact with amniotic glycoproteins and revealed the potential protein carriers of glycans recognized by MGL, including mucins, mucin-like proteins, and uromodulin. Bioinformatics analysis assigned the identified glycoproteins as being involved in immune processes such as regulation of signaling pathways activated in the response to Toll-like receptor (TLR) agonist stimulation or modulation of antimicrobial responses. Our research suggests that MGL-mediated interactions may be involved in maintaining the delicate immune balance during pregnancy. Our results may be helpful in future implementation of modern therapies based on the glycan ligands of MGL in the context of avoiding miscarriages and preterm birth.

Liver cirrhosis is the primary contributor to global mortality associated with chronic liver diseases (CLD). Certain liver infections, including viral hepatitis B (VHB) and C (VHC), alcohol-related liver disease (ALD), and metabolic dysfunction-associated steatotic liver disease (MASLD) are significant contributors to the development of liver cirrhosis. This study aimed to evaluate the prevalence of liver steatosis and fibrosis in individuals with vulnerable conditions. Subjects residing in a rural Romanian county or having lower educational attainment were selected for this study. Following the acquisition of informed consent, a demographic, clinical, and physiological characterization was conducted for each participant. The AUDIT-C questionnaire was obtained from every participant. Transient Elastography (TE) measured liver fibrosis, while blood tests screened for the presence of hepatitis viruses B and C. Among the 571 screened vulnerable subjects, 52.7% were males, and 17.3% were identified as heavy drinkers. Metabolic syndrome was identified in 37.3% of patients and 70% of subjects exhibited a body mass index of ≥ 25 kg/m². Furthermore, 8.5% of participants tested positive for HBs antigen, while 6.1% had HCV antibodies. Additionally, 35.7% of the participants in our study had MASLD, and 7.1% had metabolic dysfunction and alcohol-related liver disease (MetALD) according to the AUDIT-C questionnaire. On TE exams, we found that 9.9% of the participants had advanced fibrosis, 16.1% had cirrhosis, and 24.5% had severe steatosis. Hence, the prevalence of advanced fibrosis and cirrhosis is elevated in asymptomatic healthy individuals from vulnerable conditions in Northeastern Romania, particularly among those with various risk factors. Most of the subjects were identified with MetALD and ALD demonstrating the efficacy of the new nomenclature in identifying the etiology of liver fibrosis.

Nephrolithiasis has a high recurrence rate and imposes a heavy burden on patients and society. Therefore, there is an urgent need to explore new effective targets for nephrolithiasis prevention and treatment. Protein quantitative trait loci (pQTL) data of plasma proteins and plasma protein-protein ratios were used as plasma protein related targets (PPRTs), and genome-wide association studies (GWASs) of nephrolithiasis were used as outcomes. Bidirectional Mendelian randomization analyses were then conducted. The mediating factors between PPRTs and nephrolithiasis were identified. After colocalization analyses, the safety of targeted PPRTs for nephrolithiasis were evaluated. Subsequently, multi-omics data were used to further validate the effects of candidate PPRTs on nephrolithiasis. Finally, molecular docking operations were performed. Six PPRTs were confirmed to be causally associated with nephrolithiasis. The glomerular filtration rate (GFR) was identified as a mediating factor between five PPRTs and nephrolithiasis. There were strong evidences of colocalization of three PPRTs. After safety assessments and multi-omics analyses, BTN3A2 was considered as a potential therapeutic target. Molecular docking analyses indicated that digitoxigenin had the strongest binding ability with BTN3A2. These comprehensive analyses suggested causal relationships between PPRTs and nephrolithiasis, and BTN3A2 might be an advantageous drug target for nephrolithiasis.

Bladder cancer (BLCA) is the most prevalent malignant tumor of the urinary system. Mitophagy is a selective form of autophagy that occurs within the mitochondria. The goal of this study was to determine mitophagy-related biomarkers associated with BLCA and to explore their underlying molecular mechanisms. CTSK, MTERF3, SRC, and CSNK2B were identified as biomarkers. A risk model classified BLCA patients into high-risk group (HRG) and low-risk group (LRG), with HRG patients exhibiting lower survival probabilities. The "chemical carcinogenesis-DNA adducts" and "cytokine-cytokine receptor interaction" signaling pathway were closely associated with HRG and LRG. TP53 had the highest mutation frequencies in the HRG and LRG, respectively. The two groups exhibited significant differences in 14 immune cells, including M2 macrophages. CTSK exhibited the strongest correlation with the naive B cells. A total of 135 drugs differed in sensitivity between HRG and LRG, including KU.55933. The identified regulatory network included ADAMTSL4-AS1-hsa-miR-149-5p-SRC. Expression analysis showed that CTSK was significantly downregulated in the BLCA group, while MTERF3, SRC, and CSNK2B were significantly upregulated. In conclusion, CTSK, MTERF3, SRC, and CSNK2B laid the foundation for targeted therapy in the treatment of BLCA.

Frontotemporal dementia (FTD) is the second most common cause of dementia in patients under 65 years, characterized by diverse clinical symptoms, neuropathologies, and genetic background. Synaptic dysfunction is suggested to play a major role in FTD pathogenesis. Disturbances in the synaptic function can also be associated with the C9orf72 repeat expansion (C9-HRE), the most common genetic mutation causing FTD. C9-HRE leads to distinct pathological hallmarks, such as C9orf72 haploinsufficiency and development of toxic RNA foci and dipeptide repeat proteins (DPRs). FTD patient brains, including those carrying the C9-HRE, are also characterized by neuropathologies involving accumulation of TDP-43 and p62/SQSTM1 proteins. This study utilized induced pluripotent stem cell (iPSC)-derived cortical neurons from C9-HRE-carrying or sporadic FTD patients and healthy control individuals. We report that the iPSC neurons derived from C9-HRE carriers developed typical C9-HRE-associated hallmarks, including RNA foci and DPR accumulation. All FTD neurons demonstrated increased cytosolic accumulation of TDP-43 and p62/SQSTM1 and changes in nuclear size and morphology. In addition, the FTD neurons displayed reduced number and altered morphologies of dendritic spines and significantly altered synaptic function indicated by a decreased response to stimulation with GABA. These structural and functional synaptic disturbances were accompanied by upregulated gene expression in the FTD neurons related to synaptic function, including synaptic signaling, glutamatergic transmission, and pre- and postsynaptic membrane, as compared to control neurons. Pathways involved in DNA repair were significantly downregulated in FTD neurons. Only one gene, NUPR2, potentially involved in DNA damage response, was differentially expressed between the sporadic and C9-HRE-carrying FTD neurons. Our results show that the iPSC neurons from FTD patients recapitulate pathological changes of the FTD brain and strongly support the hypothesis of synaptic dysfunction as a crucial contributor to disease pathogenesis in FTD.

Cardiac myxoma, the most common primary heart tumor, remains poorly understood at the molecular level. Here, we combined single-nucleus RNA sequencing, third-generation transcriptomics, and untargeted metabolomics to dissect its origin and pathology. Single-cell analyses demonstrate an endothelial origin driven by aberrant endothelial-to-mesenchymal transition (EndMT), with pseudotime and RNA-velocity tracing a continuum from endothelial-like to mesenchymal-like and metabolically active states. We identify two distinct myxoma subtypes: Subtype 1, marked by MAPK/WNT/EGFR pathway activation, and Subtype 2, characterized by ribosomal and oxidative phosphorylation signatures alongside immune-evasive programs. Third-generation data highlight extracellular matrix remodeling and endothelial signaling, while metabolomics reveal dysregulated purine, nicotinic acid, and nicotinamide metabolism. Notably, MET-PTK2 signaling emerges as a potential driver of tumor initiation and progression. These integrated findings define the cellular architecture and metabolic adaptations of cardiac myxoma and lay the foundation for future interventions.

<h4>Background</h4>Small RNAs regulate gene expression in species across the tree of life. miRNAs, which impact a variety of cellular and physiological processes ranging from development and stress adaptation to host defense, are one of the best characterized classes of small RNA. Many miRNAs are produced from longer non-coding transcripts generated from host genes via a series of RNA cleavage reactions. The location of a small RNA within a host gene can shape the processing of the mature small RNA. For example, a type of miRNAs derived from host gene intronic sequence, referred to as miRtrons, are Drosha-independent and reliant on splicing for biogenesis. Relatedly, processing of a small RNA from an exon of a protein-coding mRNA, in principle, may destabilize it and compromise translation of the host gene. Prior to extensive transcriptome analysis, informatics analyses identified six human miRNAs embedded in exons of protein-coding genes and experimental studies have characterized additional anecdotal examples. Still, whether protein-coding mRNAs encoding small RNAs represent an appreciable class of host genes given the now recognized complexity of the transcriptome is unclear.<h4>Results</h4>Our analysis finds 201 small RNAs (118 human and 83 mouse) encoded by expressed exons of protein-coding genes (5'-UTR, CDS, 3'-UTR). Forty-six of these cases (29 human and 17 mouse) are also present in MirGeneDB which includes the most up-to-date miRNA classifications. Many of these small RNAs are poorly characterized with 96% of the protein-coding host gene relationships identified here not previously known. Furthermore, the identification of nearly fifty human and mouse small RNAs embedded within coding exons of canonical ORFs suggests that overlapping hybrid genes might be more common than previously appreciated in higher organisms. Expression analysis for a subset of these small RNAs indicates that many display differential expression across human tissues with the pattern correlating significantly with the expression of the candidate protein-coding host gene.<h4>Significance</h4>Overall, our analysis suggests that the number of protein-coding transcripts serving as host genes is greater than previously recognized. Our small RNA host gene classifications may serve as a resource to shed new light on small RNA biology, specific host genes, and gene regulation.

<h4>Background</h4>The degree to which alternative RNA splicing influences the function and structure of voltage gated calcium channel (VGCC) splice variants is poorly understood. Here we used long-read RNA-sequencing to catalog rat Cacna1e (Cav2.3) splice variants, and computationally prioritize which are likely to impact channel function.<h4>Result</h4>We sequenced Cacna1e transcripts from rat thalamus using Oxford Nanopore sequencing yielding the structure of 2,110 Cacna1e splice variants. Of these, up to 154 had the potential encode for a functional channel based on predicted amino acid sequences. Our analysis revealed a total of 31 cassette splicing events (in various combinations) potentially affecting channel function, with three cassette exons appreciably expressed and conserved.<h4>Conclusion</h4>Our work both provides the first long-read sequencing of Cacna1e and the first computational evaluation of Cacna1e splice variants for future follow-up. This overall strategy to provide the field with prioritized transcripts will improve our understanding of Cacna1e function, its role in disease pathophysiology, and serve as a general approach to evaluate splice variant function across multiple ion channel types.

BACKGROUND: Prenatal nicotine exposure (PNE) has been shown to significantly impact fetal development, leading to various pathologies in adulthood. OBJECTIVES: In this study, we analyzed the epigenetic effects of PNE on the proximal colon. RESULTS: We show here that PNE decreases the length of the colon crypts and induces a higher Ki-67 index. The genes related to metabolic pathways, tight junctions, and neurodegenerative processes were downregulated in PNE colons, and genes related to inflammation and oxygen transporter activity were upregulated. We observed a decrease in acetylated H4Ac and H3K9Ac marks. Genome-wide DNA methylation analysis demonstrated reduced DNA methylation of genes related to cell adhesion and metabolic pathways and increased methylation levels at thermogenesis, GABAergic synapsing, and non-alcoholic fatty liver disease-related genes. The Notch signaling pathway was deregulated in PNE rats. CONCLUSION: PNE leads to perturbation of proximal colon functioning, plausibly through nicotine-induced epigenetic alterations.

BACKGROUND: Sexual maturation is a key developmental process important for reproductive success. Understanding the molecular mechanisms behind variation in sexual maturation can provide insights into reproductive biology and how life history variation is encoded in the genome. Atlantic salmon (Salmo salar) has become an excellent sexual maturation research model due to its diversity of life history strategies and its ecological and economic importance. A major challenge has been the lack of a comprehensive transcriptional investigation of reproductive tissues that captures the dynamic transcriptional changes across individuals, tissues, and developmental stages. Long non-coding RNAs (lncRNAs) also play crucial roles in maturation, yet their functions in salmon maturation remain underexplored. RESULTS: In this study, we sequenced 98 transcriptomes and found substantial transcriptomic complexity in the gonad and pituitary tissues of Atlantic salmon. We identified transcripts corresponding to 2,364 putative newly characterized protein-coding genes and 4,421 putative long intergenic non-coding RNAs (lincRNAs), many with tissue-specific expression. Gene co-expression network analysis (WGCNA) revealed tissue-specific gene network modules, linked to GO terms including Wnt signaling in immature testis, lipid metabolism, and cilia assembly in mature testis, ribosome biogenesis and DNA repair in the ovary, and hormone activity in pituitary. We identified new copies of known genes, such as gh1, pou3f2, and ier5 associated with the regulation of gonadal and pituitary functions. Some lncRNAs and their nearest genes showed correlated expression within modules, suggesting potential regulatory roles. Candidate lincRNAs indicated cis-acting regulatory potential on genes like tnfrsf11b and fgl1, which are implicated in immune privilege during gonadal development and sperm quality control. CONCLUSIONS: Our study provides a comprehensive transcriptomic analysis of Atlantic salmon gonad and pituitary tissues, significantly improving the functional annotation of the Atlantic salmon genome. These findings reveal key regulatory pathways and novel molecular players involved in sexual maturation, particularly in the testis. Importantly, our study highlights the regulatory potential of lncRNAs in reproductive biology and maturation age variation, advancing our understanding of the molecular mechanisms governing sexual maturation. They further unlock future gene expression analyses and regulatory network reconstruction for dissecting the roles of lncRNAs in Atlantic salmon life history variation.

<h4>Background</h4>Some individuals exposed to traumatic stressors develop psychiatric disorders while others remain resilient. The Brief Resilience Scale (BRS) assesses the ability to "bounce back" from stress and is a widely used measure of trait resilience. We performed the first genome-wide association study of BRS in the UK Biobank (UKB).<h4>Methods</h4>Beginning 2022, a subset of UKB participants completed an on-line mental-health questionnaire that included the six-item BRS. BRS data and genome-wide typing and imputation were available for 124,774 participants of European ancestry. Genome-wide linear tests of BRS were performed, followed by SNP-based heritability and cross-trait genetic correlation analyses. Nominally significant loci (P < 5 × 10^-6) were followed up for candidate gene mapping.<h4>Results</h4>SNP-based heritability of BRS was 7.3% and strong genetic correlations (r_g) were observed with neuroticism (r_g, - 0.70 to - 0.44), depression (r_g, - 0.63 to - 0.37) and anxiety (r_g, - 0.81 to - 0.46). Three loci met genome-wide significance (P < 5 × 10^-8, near VRK2, TNKS/MSRA and RAB36) and 29 loci met nominal significance (P < 5 × 10^-6). None of these were replicated in prior GWAS using different measures of resilience. The strongest candidate genes prioritized on the basis of both functional and biological evidence include VRK2 (2p16.1) (previously associated with neuropsychiatric disorders) and MSRA (8p23.1) (reduces methionine sulfoxide to methionine). Others at nominally significant loci include SLC6A9 (1p34.1) (encodes a glycine transporter), NPY (7p15.2) (involved in stress response), CADPS2 (7q31.32) (involved in synaptic vesicle exocytosis), and PCDH9 (13q21.32) (involved in neural tissue cell adhesion).  CONCLUSIONS: Our findings provide further support for a genetic basis to trait resilience and one shared with psychiatric disorders and personality traits including depression, anxiety, and neuroticism. Our promising loci warrant replication but offer new biological insight to resilience.

<h4>Background</h4>Super-enhancers (SEs) are implicated in the regulation of the onset and progression of Crohn's disease (CD). However, the precise mechanisms remain unclear. This study aims to investigate the diagnostic potential and molecular mechanisms of SE-related genes (SERGs) as biomarkers for CD from a transcriptomics perspective.<h4>Methods</h4>Data on CD and SERGs were retrieved from public databases. Differential expression analysis, the Maximal Clique Centrality algorithm, and two machine learning methods were applied, complemented by receiver operating characteristic analysis and expression level assessment to identify biomarkers and construct a nomogram for evaluating their diagnostic value. Enrichment and immune infiltration analyses were performed subsequently. Unsupervised clustering categorized CD samples into distinct subtypes based on the biomarkers, and functional and immune microenvironmental differences among these subtypes were examined. Immunohistochemical experiments confirmed the elevated protein expression of hub genes in colonic tissues from patients with CD relative to healthy controls (P < 0.05).<h4>Results</h4>PAQR5, IFITM3, PSMB8, and IRF1, were identified as biomarkers for CD, demonstrating robust diagnostic performance, with area under curve (AUC) values of 0.988, 0.973, 0.959, and 0.940, respectively. When integrated into a nomogram, the AUC reached 0.991. Except for PAQR5, the other three genes showed significantly higher expression in CD samples, a trend confirmed clinically by immunohistochemical experiments. These biomarkers were involved in areas such as immune regulation, cell biology, and sensory perception. Immunoassays further elucidated the specific infiltration patterns of different immune cells in CD and highlighted the importance of these biomarkers in regulating immune cell functions. Additionally, we classified the CD samples into two subtypes, with the biomarkers exhibiting significant expression differences between the subtypes. These two subtypes possessed distinct immune microenvironments, with the biomarkers showing moderate correlation with the differential immune cells between the subtypes.<h4>Conclusion</h4>PAQR5, IFITM3, PSMB8, and IRF1 serve as biomarkers for CD, offering substantial diagnostic and immune regulatory value. These biomarkers differentiate CD into two subtypes, providing insights for personalized therapeutic strategies.

<h4>Backgrounds</h4>Adolescence is a critical stage in the development of cardiovascular disease. The American Heart Association has introduced a state-of-the-art algorithm called "Life Essential 8" (LE8) designed to quantify cardiovascular health (CVH). Research on the association of trace metal elements with cardiovascular disease in adolescents is inconsistent. This study aims to examine the association between trace metal elements and ideal CVH in adolescents.<h4>Methods</h4>This cross-sectional study included 5724 adolescents who participated in the National Health and Nutrition Examination Survey (NHANES) from 2005 to 2018. CVH was assessed using Life's Essential 8 (LE8) developed by the American Heart Association (AHA). Exposure factors were trace metal elements (iron, iodine, cadmium, lead, mercury, selenium, and manganese).<h4>Results</h4>More than half of the adolescents had non-ideal CVH and only 40.8% achieved ideal CVH scores. Of the CVH measures, high blood glucose (96.1%), body mass index (81.3%), blood pressure (77.4%), and physical activity (65.0%) had high proportions of "ideal" values. However, diet, lipids and nicotine intake had lower rates of achieving the ideal CVH criteria (26.9%, 42.6% and 47.6%, respectively). The results of regression logistic showed that iron and mercury were negatively associated with the occurrence of non-ideal CVH (adjusted ORs of 0.997 [95% CI 0.995,0.999] and 0.913 [95% CI 0.840,0.991], and that urinary iodine, blood cadmium, lead, and selenium were positively associated with the occurrence of non-ideal CVH (adjusted ORs of 1.432 [95% CI 1.054,1.945], 3.845 [95% CI 2.278,6.491], and 1.010 [95% CI 1.003,1.017], respectively). No correlation between manganese and CVH was observed.<h4>Conclusions</h4>There is an urgent need to intervene in the CVH of children and adolescents. It is important to emphasize the need to maintain adequate iron intake while reducing iodine, cadmium, lead, and selenium intake.

<h4>Introduction and aims</h4>Understanding the identity of odontogenic cells is fundamental to advancing research in tooth development and regeneration. We aim to explore the cellular composition, differentiation pathways, and regulatory networks in human embryonic teeth during the transition from the cap stage to the early bell stage.<h4>Methods</h4>The spatial RNA sequencing and single-nucleus RNA sequencing to human embryonic tooth germs were obtained from four healthy aborted specimens and integrated with public database. The spatial and temporal gene expression patterns, cell distributions, and interactions in tooth germ and surrounding periodontal tissues spanning postconception weeks 12 to 18 were examined and validated by immunohistochemistry.<h4>Results</h4>Our analysis identified diverse cell types, including 10 epithelial and nine mesenchymal subpopulations, alongside smooth muscle cells, endothelial cells, macrophages, and Schwann cells. We characterized epithelial and mesenchymal lineages by defining their signature genes, regulatory transcription factors, spatial distributions, and differentiation trajectories, while revealing conserved and distinct features between oral and odontogenic cells. Developmental stage-specific intercellular communications were delineated for epithelial and mesenchymal compartments. Notably, SPP1+ macrophages mediated crosstalk with odontoblasts via SPP1-integrin receptor interactions, whereas Schwann cells contributed to the signalling landscape via SEMA3C/MDK/PDGFC ligands.<h4>Conclusions</h4>This study reveals the cellular heterogeneity present in human embryonic teeth during early development, identifies key genes governing the differentiation of epithelial and mesenchymal cells, and provides valuable transcriptomic resources for investigating human embryonic tooth development.<h4>Clinical relevance</h4>Characterizing cells into more precise subgroups will enhance the potential to select optimal cell types for regenerative applications. The characteristic genes in differentiated cells could serve as potential inducers to guide the directed differentiation of stem cells.

<h4>Objective</h4>To describe the neonatal intensive care unit outcomes of infants born extremely preterm to mothers who test positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during pregnancy.<h4>Study design</h4>Prospective study (March 1, 2020-April 30, 2023) at 16 Eunice Kennedy Shriver National Institute of Child Health and Human Development Neonatal Research Network centers of inborn infants (birth weight 401-1000 g and/or gestational age <29 weeks) born to mothers tested for SARS-CoV-2 during pregnancy. Frequency of maternal SARS-CoV-2 detection, vertical transmission rate, and association of maternal SARS-CoV-2 positivity during pregnancy with infant outcomes were determined.<h4>Results</h4>During the 38-month study, 4548 extremely preterm infants were born to 4072 mothers tested for SARS-CoV-2 during pregnancy. Overall, 7% (297/4072) of mothers had a positive SARS-CoV-2 test; 1% (2/181) of tested infants were positive at age <72 hours. The majority of outcomes (eg, bronchopulmonary dysplasia and retinopathy of prematurity) did not differ between infants of test-positive vs test-negative mothers. Infants of test-positive mothers were more likely to be diagnosed with necrotizing enterocolitis (NEC) than those of test-negative mothers (14% vs 11%; P = .03). In adjusted analyses, infants born to test-positive mothers were more likely to develop NEC (risk ratio [RR] 1.40; 95% CI, 1.03-1.89; P = .03) or the combined outcome of death within 12 hours of age or NEC (RR 1.33; 95% CI, 1.09-1.62; P < .01) but not death within 12 hours of age (RR 1.22, 95% CI, 0.92-1.62; P = .16) or before discharge (RR 0.83, 95% CI, 0.55-1.26; P = .38).<h4>Conclusions</h4>Among infants <29 weeks' gestation, vertical transmission of SARS-CoV-2 was infrequent. Maternal SARS-CoV-2 positivity was associated with NEC but not with other infant outcomes or mortality.<h4>Trial registration</h4>ClinicalTrials.gov ID. Generic Database: NCT00063063. https://clinicaltrials.gov/study/NCT00063063.

Protein kinase A (PKA) is found in all mammalian tissues and plays a critical role in mediating many signaling processes. The structure and phosphorylation mechanism of the catalytic subunit of PKA (PKA-C) have been extensively studied in interaction with linear pseudosubstrate inhibitors, peptide substrates, or protein fragments. To date, however, there have been only a few studies examining how PKA recognizes full-length, folded proteins. Here, we utilized solution NMR spectroscopy in combination with replica-averaged restrained molecular dynamics (RARMD) calculations to investigate the interactions between PKA-C and Raf Kinase Inhibitory Protein (RKIP). RKIP is a member of the phosphatidylethanolamine binding protein (PEBP) family, which regulates important kinase pathways such as the Raf/MAPK pathway and the β-adrenergic receptor/cAMP-dependent PKA signaling cascade. The X-ray structure of RKIP reveals a compact fold, with the phosphorylation consensus sequence well-structured and essentially inaccessible to the kinase. Using Carr-Purcell-Meiboom-Gill (CPMG) and chemical exchange saturation transfer (CEST) experiments, we discovered that RKIP undergoes a conformational equilibrium between a compact fold and a more open conformation, where the C-terminal helix splays away from the RKIP core and exposes its phosphorylation sequence, allowing the kinase to bind and phosphorylate this substrate. The dynamic interplay between the kinase and the substrate may represent a common mechanism for kinases to recognizes well-folded substrates.

<h4>Background</h4>The tumor microenvironment (TME) is a complex network driving endometrioid endometrial cancer (EC) progression. Previous analyses of the EC TME were often limited by a lack of detailed cellular annotations. Integrating single-cell RNA sequencing (scRNA-seq) data offers a comprehensive approach to reconstruct the TME, aiming to uncover novel mechanisms and therapeutic targets.<h4>Methods</h4>We integrated public scRNA-seq data from 15 EC and 5 normal endometrium samples. Through detailed cell annotation, we performed comprehensive bioinformatic analyses, including pseudotime trajectories, copy number variation, and cell communication, to investigate mechanisms of EC development.<h4>Results</h4>We identified nine cell types and characterized subpopulations of epithelial, macrophage, lymphocyte, and stromal fibroblast cells. The SOX9+LGR5- epithelial subtype showed elevated malignancy and NFKB pathway enrichment. The M2_like2 macrophage subtype played a critical role, engaging in robust MIF-(CD74+CD44) mediated communication with SOX9+LGR5- cells. Experimental validation confirmed MIF co-expression with E-cadherin in EC tissues. Furthermore, the transcription factor NFKB2 was found to mediate MIF's effect on the CD44 receptor in malignant epithelial cells. A pericyte-to-fibroblast transition in stromal cells may also support tumor growth, while an increase in CD8 exhausted/Treg cells and a decrease in cytotoxic CD8 cells suggest potential immune evasion.<h4>Conclusion</h4>Our single-cell analysis details the EC TME landscape, revealing robust communication between M2_like2 macrophages and SOX9+LGR5- epithelial cells. We highlight a key mechanism where NFKB2 mediates MIF's pro-tumorigenic effects via the CD44 receptor, offering new insights into EC progression and potential therapeutic targets.

<h4>Background</h4>As a major histopathological subtype of gastric cancer (GC), stomach adenocarcinoma (STAD) is an important malignant tumor in the digestive system. Increasing evidence also indicates that endoplasmic reticulum (ER) stress plays a pivotal role in the pathogenesis and progression of GC. Therefore, this study aims to screen and identify vital ER stress-related genes that could contribute to the malignant development and poor prognosis for STAD.<h4>Methods</h4>A novel ER stress-related risk score signature was developed employing machine learning techniques. Then, a prognostic prediction nomogram was also built based on the clinicopathological characteristics and the risk score signature. The tumor immune microenvironment characteristics and pathway enrichment analysis in different risk groups were also explored. Furthermore, through the single-cell RNA sequencing (scRNA-seq) analysis, the study highlighted Cytochrome P450 Family 19 Subfamily A Member 1 (CYP19A1) as the pivotal research target and detected its effect on cell proliferation by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and the expression of ER stress-related genes by RT-qPCR in STAD.<h4>Results</h4>Based on the evaluation of five screened key ER stress-related genes (<i>AKR1B1</i>, <i>SERPINE1</i>, <i>ADCYAP1</i>, <i>MATN3</i>, <i>CYP19A1</i>), our ER stress-related risk score signature offers a novel approach for assessing STAD prognosis hazards. The novel prognostic prediction nomogram based on the signature also accurately predicted the survival outcomes of patients with STAD. Furthermore, the expression of <i>CYP19A1</i> is significantly higher in STAD tissues than in normal tissues. High expression of <i>CYP19A1</i> was related to a poor survival outcome for patients with STAD. Besides, compared to normal gastric epithelial cells, the expression of <i>CYP19A1</i> was significantly higher in STAD cell lines. Silencing the expression of <i>CYP19A1</i> significantly inhibited the cell proliferation ability and decreased the expression of ER stress-related genes, including <i>ATF4</i>, <i>DDIT3</i> and <i>XBP1</i> in STAD.<h4>Conclusions</h4>In conclusion, our study developed a novel prognosis prediction signature and identified the novel diagnostic and therapeutic target CYP19A1 for patients with STAD.

Tomato bacterial wilt and apple fire blight, caused by <i>Ralstonia solanacearum</i> and <i>Erwinia amylovora</i>, respectively, are highly destructive diseases that threaten global agriculture productivity. Increasing resistance of these pathogens to conventional antibiotics and copper-based pesticides highlights the urgent need for sustainable, eco-friendly biocontrol alternatives. This study aimed to evaluate the biocontrol potential of the azomycin-producing <i>Streptomyces</i> sp. JCK-8368 (hereafter JCK-8368) against tomato bacterial wilt and apple fire blight, and to investigate its possible resistance-inducing mechanism. The culture filtrate (CF) of JCK-8368, containing azomycin, was applied to the plant at 1,000-fold (100 ng/mL), 500-fold (200 ng/mL), and 250-fold (400 ng/mL) dilutions via foliar spraying or soil drenching. Purified azomycin was tested at concentrations from 1 ng/mL to 1000 ng/mL. Disease severity and control efficacy were assessed, and expression of defense-related genes (<i>PR1</i>, <i>PR2</i>, <i>PR3</i>, and <i>PR5</i>) was also analyzed. Foliar spraying and soil drenching with JCK-8368 CF significantly reduced tomato bacterial wilt severity, with control efficacies of 52.22% (1000-fold), 11.11% (500-fold), and 35.55% (250-fold) in foliar application, 90.00%, 77.78%, and 52.22% in soil drenching, respectively. The reversed dose-response pattern in soil drenching indicated higher efficacy at lower concentrations. In apple fire blight control, soil drenching with CF at a 1,000-fold dilution achieved foliar spraying (78.38%) efficacy, exceeding soil drenching (50.88%). In particular, purified azomycin most effectively reduced tomato bacterial wilt at 100 ng/mL (57.14% efficacy) and showed a clear dose-dependent effect from 1 to 100 ng/mL. The plants treated with JCK-8368 CF and azomycin upregulated defense-related genes such as <i>PR1</i>, <i>PR2</i>, <i>PR3</i>, and <i>PR5</i>, suggesting systemically acquired resistance and pathogenesis-related defense pathways. This is the first report demonstrating the application of azomycin against plant bacterial diseases, showing that low concentrations of JCK-8368 and purified azomycin can effectively control tomato bacterial wilt and apple fire blight through induced resistance. Azomycin-producing <i>Streptomyces</i> sp. JCK-8368 offers a promising, sustainable alternative to chemical pesticides, warranting further field validation and formulation development for agricultural use.

<h4>Background</h4>Chronic liver diseases and depression are both major public health concerns worldwide, particularly among aging populations. However, evidence on the prospective association between depressive symptoms and the risk of developing chronic liver diseases remains limited. The aim of this study is to explore the potential association in middle-aged and older Chinese adults.<h4>Methods</h4>Data for this study were obtained from the China Health and Retirement Longitudinal Study (CHARLS), and 11,272 participants without prior liver disease were finally included in this study. Depression was assessed using the CESD-10, with scores analyzed as continuous variables and chronic liver diseases were self-reported based on physician diagnosis. By adjusting for multiple covariates, Cox proportional hazards regression models were used to estimate hazard ratios and restricted cubic spline models were applied to assess the potential non-linear relationships.<h4>Findings</h4>Over a mean follow-up period of 6.85 years, a total of 570 participants were finally diagnosed with chronic liver diseases. Multivariate regression analyses revealed a significant association between CESD scores and the risk of liver diseases among study participants even accounting for all potential covariates (HR: 1.020, 95% CI: 1.006-1.033, <i>p</i> = 0.004).<h4>Conclusion</h4>We identified a significant association between depressive symptoms and subsequent development of chronic liver diseases. Based on observational findings, depressive symptoms may represent a potential early marker of liver disease risk. These findings highlight the importance of integrating mental health assessments into early routine clinical care.

<b>Background/Objectives</b>: Methotrexate (MTX) is associated with hepatotoxicity, but distinguishing MTX-induced liver injury from hepatic dysfunction due to metabolic syndrome (MetS) is challenging. This study investigates the incidence of hepatic outcomes in long-term MTX users with and without MetS and metabolic dysfunction-associated steatotic liver disease (MASLD) using real-world data. <b>Methods</b>: This cohort study used the TriNetX research network to identify U.S. adults (≥18 years) on MTX, excluding those with pre-existing liver injury. Patients were grouped by MetS status (MTX-MetS vs. controls) and further sub-stratified based on MASLD status. Propensity score matching (1:1) was adjusted for demographics, comorbidities, and treatment. The primary outcomes included hepatic-enzyme elevations, hyperbilirubinemia, prolonged INR, and clinically significant drug-induced liver injury (DILI) at 3-, 5-, and 10-year follow-up. <b>Results</b>: Among 324,219 MTX users, 59,733 MTX-MetS patients were propensity matched with 59,733 controls. MTX-MetS patients demonstrated increased 10-year odds of hepatic-enzyme elevations (aOR = 1.41; 95%CI: 1.38-1.46), hyperbilirubinemia (aOR = 1.40; 95%CI: 1.32-1.49), prolonged INR (aOR = 1.58; 95%CI: 1.49-1.67), clinically significant DILI (aOR = 1.49; 95%CI: 1.41-1.57), and liver cirrhosis (aOR = 1.48; 95%CI: 1.35-1.63) compared to the controls. Patients with and without MASLD showed similar hepatic-enzyme, bilirubin, and INR elevations, with higher odds of DILI with MASLD (aOR = 1.56; 95%CI: 1.28-1.89). <b>Conclusions</b>: This study highlights the increased liver injury risk in MTX users with MetS and MASLD. Further studies are needed to distinguish the effects of MTX and metabolic dysfunction on liver outcomes.

The development and function of the heart are governed by a highly coordinated network of regulatory mechanisms, among which miRNAs play a central role. These small, non-coding molecules modulate gene expression predominantly through mRNA degradation. This narrative review aims to summarize current knowledge about biogenesis, its impact on heart development and function, and its clinical implications in pediatric cardiology. We discuss how specific miRNAs contribute to shaping the normal heart and influencing the pathogenesis of congenital malformations. Furthermore, we review disease-specific miRNA signatures identified in the most common congenital heart defects and some acquired diseases, including hypoplastic left heart syndrome (HLHS), tetralogy of Fallot (TOF), bicuspid aortic valve (BAV), septation defects, cardiomyopathies, arrhythmias, and myocarditis. Many studies indicate that circulating and tissue miRNAs can become non-invasive biomarkers for early diagnosis and disease monitoring. Experimental data suggest their potential use in treatment despite many delivery and safety challenges. However, further research is necessary to fully exploit the potential of miRNAs and effectively translate these findings into clinical practice in pediatric cardiology.

Excessive abdominal fat deposition accompanying rapid growth in broiler chickens seriously affects production efficiency. Using divergently selected broiler lines from Northeast Agricultural University, we integrated transcriptome sequencing, whole-genome resequencing, and three-dimensional genomic data to identify key SNPs affecting abdominal fat deposition. From 3,850,758 initial SNPs, 22,721 high-quality SNPs were selected (|ΔAF| ≥ 0.9) and validated to obtain 7341 reliable SNPs. GWAS identified 16 SNPs significantly associated with abdominal fat weight, while LD analysis revealed 22 highly linked SNPs, finally determining 2302 candidate SNPs. Transcriptome analysis identified 825 differentially expressed genes (<i>p</i> ≤ 0.05, |FC| ≥ 1.5). Functional annotation revealed 201 SNPs located in differentially expressed gene regions, including 8 coding SNPs and 193 non-coding SNPs, with an additional 15 SNPs potentially regulating through long-range chromatin interactions. Mechanistic analysis showed that coding SNPs regulate gene expression by altering codon translation rates or mRNA stability, while non-coding SNPs regulate transcription by affecting transcription factor binding. Phenotypic association analysis demonstrated that all 213 SNPs can cause ≥2-fold differences in abdominal fat weight, with 182 SNPs causing ≥3-fold differences. This study successfully identified 213 functional SNPs affecting abdominal fat deposition in broilers and revealed their molecular basis for regulating fat metabolism through multiple mechanisms, providing important genetic markers for low-fat breeding in broilers.

Repairing the central nervous system (CNS) remains one of the most difficult obstacles to overcome in translational neurosciences. This is due to intrinsic growth inhibitors, extracellular matrix issues, the glial scar-form barrier, chronic neuroinflammation, and epigenetic silencing. The purpose of this review is to bring together findings from recent developments in genome editing and computational approaches, which center around the possible convergence of clustered regularly interspaced short palindromic repeats (CRISPR) platforms and artificial intelligence (AI), towards precision neuroregeneration. We wished to outline possible ways in which CRISPR-based systems, including but not limited to Cas9 and Cas12 nucleases, RNA-targeting Cas13, base and prime editors, and transcriptional regulators such as CRISPRa/i, can be applied to potentially reactivate axon-growth programs, alter inhibitory extracellular signaling, reprogram or lineage transform glia to functional neurons, and block oncogenic pathways in glioblastoma. In addition, we wanted to highlight how AI approaches, such as single-cell multi-omics, radiogenomic prediction, development of digital twins, and design of adaptive clinical trials, will increasingly be positioned to act as system-level architects that allow translation of complex datasets into predictive and actionable therapeutic approaches. We examine convergence consumers in spinal cord injury and adaptive neuro-oncology and discuss expanse consumers in ischemic stroke, Alzheimer's disease, Parkinson's disease, and rare neurogenetic syndromes. Finally, we discuss the ethical and regulatory landscape around beyond off-target editing and genomic stability of CRISPR, algorithmic bias, explainability, and equitable access to advanced neurotherapies. Our intent was not to provide a comprehensive inventory of possibilities but rather to provide a conceptual tool where CRISPR acts as a molecular manipulator and AI as a computational integrator, converging to create pathways towards precision neuroregeneration, personalized medicine, and adaptive neurotherapeutics that are ethically sound.

Avian genome editing has historically lagged behind mammalian research. This disparity is primarily due to a unique reproductive biology that precludes standard techniques like pronuclear injection. A pivotal breakthrough, however, came from the development of efficient in vitro culture systems for primordial germ cells (PGCs). This has established the chicken as a tractable and powerful model for genetic engineering. Our review chronicles the technological evolution this has enabled, from early untargeted methods to the precision of modern CRISPR-based systems. We then analyze the broad applications of these tools, which are now used to engineer disease resistance, enhance agricultural traits, and develop novel platforms such as surrogate hosts and oviduct bioreactors. Collectively, these advances have established PGC-based genome editing as a robust and versatile platform. Looking forward, emerging precision editors and the expansion of these techniques to other avian species are poised to drive the next wave of innovation in poultry science and biotechnology.

<h4>Background</h4>Bladder cancer is highly malignant, but specific biomarkers and molecular targets are lacking. The aim of this study was to screen bladder cancer progression-related differential genes based on those associated with tumor-node-metastasis (TNM) staging, and to validate them by <i>in vitro</i> and <i>in vivo</i> experiments.<h4>Methods</h4>Common genes were screened and prognostically analyzed by cross-analyzing differential genes in The Cancer Genome Atlas (TCGA) database for bladder cancer stages T1-2 and T3-4, N1 and N2, and M0 and M1. The functions were further identified by enrichment analysis, and the biological functions of the differential genes in bladder cancer were verified using <i>in vivo</i> and <i>in vitro</i> experiments.<h4>Results</h4>The shared gene polypeptide N-acetylgalactosaminyltransferase 16 (<i>GALNT16</i>) was identified by cross-analysis of differential genes between T1-2 and T3-4 stages, N1 and N2 stages, and M0 and M1 stages. Further analysis showed that <i>GALNT16</i> was involved in a variety of signaling pathways and biological functions, especially related to tumor metastasis, and correlated with immune cell infiltration status. In addition, <i>ex vivo</i> and <i>in vivo</i> functional experiments demonstrated that <i>GALNT16</i> was able to influence the expression of epithelial-mesenchymal transition (EMT) pathway-related proteins, thereby promoting the proliferation, migration and invasive ability of bladder cancer.<h4>Conclusions</h4><i>GALNT16</i> can promote malignant progression of bladder cancer and may be a valuable diagnostic and prognostic marker and potential therapeutic target for bladder cancer.

<b>Background/Objectives:</b><i>FAM72B</i> (Family with sequence similarity 72 member B) is a gene whose function is not yet fully elucidated and which belongs to the <i>FAM72</i> gene family. Recent studies have indicated that it is involved in the regulation of stem cell proliferation and DNA repair and serves as a valuable prognostic biomarker for a few types of cancer. This study aimed to systematically investigate the expression profile of <i>FAM72B</i> in pan-cancer, its role in the tumor immune microenvironment, and its potential as a prognostic and immunotherapeutic biomarker. <b>Methods:</b> Using bioinformatics tools such as SangerBox3.0, GEPIA2.0, Kaplan-Meier Plotter, and cBioPortal, we systematically analyzed the correlation of <i>FAM72B</i> expression levels with various cancer types, clinical pathological parameters, prognostic value, genetic mutations, genomic heterogeneity, immune checkpoint genes, immune cell infiltration levels, and single-cell-level characteristics. <b>Results:</b><i>FAM72B</i> was found to be overexpressed in most cancers and significantly associated with poor prognosis, although it may exert a protective effect in some cancers like thymoma (THYM). Its expression level was positively correlated with tumor mutation burden (TMB), microsatellite instability (MSI), neoantigen (NEO) levels, and expression of immune checkpoint genes in most cancers, suggesting that patients with high <i>FAM72B</i> expression may respond better to immune checkpoint inhibitors. Moreover, <i>FAM72B</i> expression was significantly correlated with the infiltration levels of various immune cells in the tumor immune microenvironment across pan-cancer. Single-cell sequencing results also demonstrated a significant correlation between <i>FAM72B</i> and the biological functional states of multiple cancers. <b>Conclusions:</b><i>FAM72B</i> holds promise as a potential pan-cancer prognostic biomarker and therapeutic target, providing a novel basis for the development of personalized treatment strategies.

Protein kinases are important molecules of Alzheimer's Disease (AD), driving neuronal demise and the emergence of the disease's destructive hallmarks. Cdk5 has recently been highlighted as a key therapeutic target for AD. This study evaluated the expression levels of Cdk5 and Mcl1 (Cdk5's substrate) in blood samples of 61 AD, 55 Mild Cognitive Impairment (MCI), and 57 Geriatric Controls (GC), and explored the in vitro inhibition of Cdk5. The serum levels of Cdk5 and Mcl1 were measured by Surface Plasmon Resonance (SPR) and verified by Western blot and RT-PCR. Molecular modeling and simulation studies were used to identify a potent hit targeting Cdk5 and validated by binding studies using SPR. The peptide rescue effect was analyzed by MTT assay in the AD cellular model. SPR analysis revealed a significant change in Cdk5 and Mcl1 levels in the serum samples of AD and MCI compared to GC. Results were validated by Western blot and RT-PCR. Binary logistic regression analysis revealed that the concentration of both Cdk5 and Mcl1 was independently associated with disease after adjusting for certain parameters. ROC analysis established an optimum diagnostic cutoff value for Cdk5 [24.97 ng/µL (AUC-0.90)] and Mcl1 [23.08 ng/µL (AUC-0.94)] with high sensitivity and specificity. The peptide YCWS strongly binds to Cdk5's ATP binding site, confirmed by molecular modeling and SPR. In the AD cellular model, peptide YCWS rescued neurotoxicity, increased Mcl1 levels, and reduced destructive hallmarks by inhibiting Cdk5. It can be concluded that Cdk5 is a promising molecule as a circulatory biomarker for the diagnosis of the early stages of AD, and its peptide inhibitor YCWS is a potential therapeutic agent.

5-Aminolevulinic acid (5-ALA) is used clinically for photodynamic therapy and fluorescence-guided diagnosis and surgery due to its selective accumulation in malignant cells, where it is converted into photoactive protoporphyrin IX (PpIX) via the heme biosynthesis pathway. The resulting buildup allows for selective visualization or destruction of the tissue under specific light exposure, particularly in pre-malignant and malignant skin lesions, brain tumors, and bladder cancer. More recently, 5-ALA and 5-ALA-induced PpIX have attracted interest for emerging diagnostic and therapeutic approaches. For instance, PpIX is being investigated as a potential marker for liquid biopsy. PpIX-mediated photodynamic therapy also shows promise for targeting specific cancer cell populations, including dormant cancer cells and cancer stem cells. In addition, the benefits of 5-ALA in neurological and mental health are under investigation, as disruptions in heme biosynthesis are increasingly linked to neurodegenerative diseases, chronic fatigue, and mood and sleep disorders. This review highlights these expanding research directions, discusses current challenges, and explores potential opportunities for 5-ALA-based applications.

Chronic hepatitis C (CHC) is linked to iron overload, which significantly correlates with liver fibrosis. This study aimed to assess whether genetic polymorphisms related to iron metabolism are associated with fibrosis severity, predict improvement in fibrosis after HCV clearance with direct-acting antivirals (DAAs) and influence iron-related metabolic markers before treatment. A total of 329 CHC patients were included, 134 of whom received DAAs therapy. Liver fibrosis was assessed using transient elastography (FibroScan), and biochemical parameters were measured using standard methods. Eighteen genetic polymorphisms within five iron metabolism-related genes were analyzed using PCR-RFLP, endpoint genotyping, or next-generation sequencing (NGS). Before DAA treatment, patients with severe fibrosis showed higher levels of serum iron (Fe), total iron-binding capacity (TIBC), and ferritin (Ft). SLC40A1 rs1439816_GG was associated with an increased risk of severe fibrosis compared with GC or CC genotypes. SLC40A1 rs11568351_GC genotype was linked to a higher likelihood of remaining cirrhotic after HCV clearance. Elevated iron parameters were observed in carriers HFE C282Y_CY, TF IVS 11 G>A, and BMP2 570 A>T. Overall, polymorphisms in iron metabolism genes may influence both the severity of liver fibrosis prior to treatment, its regression after DAA therapy and the regulation of iron metabolism in CHC patients.

Despite numerous research efforts and several effective vaccines and therapies developed against coronavirus disease 2019 (COVID-19), drug repurposing remains an attractive alternative approach for treatment of SARS-CoV-2 variants and other viral infections that may emerge in the future. Cellular polyamines support viral propagation and tumor growth. Here we tested the antiviral activity of two polyamine metabolism-targeting drugs, an irreversible inhibitor of polyamine biosynthesis, α-difluoromethylornithine (DFMO), and a non-steroidal anti-inflammatory drug (NSAID), Sulindac, which have been previously evaluated for colon cancer chemoprevention. The drugs were tested as single agents and in combination in the human Calu-3 lung adenocarcinoma and Caco-2 colon adenocarcinoma cell lines and the <i>K18-hACE2</i> transgenic mouse model of severe COVID-19. In the infected human cell lines, the DFMO/Sulindac combination significantly suppressed SARS-CoV-2 N1 Nucleocapsid mRNA by interacting synergistically when cells were pretreated with drugs and additively when treatment was applied to the infected cells. The Sulindac alone and DFMO/Sulindac combination treatments also suppressed the expression of the viral Spike protein and the host angiotensin-converting enzyme 2 (ACE2). In <i>K18-hACE2</i> mice, the antiviral activity of DFMO and Sulindac as single agents and in combination was tested as prophylaxis (drug supplementation started 7 days before infection) or as treatment (drug supplementation started 24 h post-infection) at the doses equivalent to patient chemoprevention trials (835 ppm DFMO and 167 ppm Sulindac). The drugs' antiviral activity in vivo was evaluated by measuring the clinical (survival rates and clinical scores), viral (viral load and virus infectivity), and biochemical (plasma polyamine, Sulindac, and Sulindac metabolite levels) endpoints. Prophylaxis with DFMO and Sulindac as single agents significantly increased survival rates in the young male mice (<i>p</i> = 0.01 and <i>p</i> = 0.027, respectively), and the combination was effective in the aged male mice (<i>p</i> = 0.042). Young female mice benefited the most from the prophylaxis with Sulindac alone (<i>p</i> = 0.001) and the DFMO/Sulindac combination (<i>p</i> = 0.018), while aged female mice did not benefit significantly from any intervention. Treatment of SARS-CoV-2-infected animals with DFMO or/and Sulindac did not significantly improve their survival rates. Overall, our studies demonstrated that DFMO and Sulindac administration as the prophylaxis regimen provided strong protection against the lethal outcome of SARS-CoV-2 infection and that male mice benefited more from the polyamine-targeted antiviral treatment than female mice. Our findings underscore the importance of evaluation of the antiviral activity of the drugs in the context of sex and age.

<h4>Background and objective</h4>Lung adenocarcinoma (LUAD), as the main subtype of non-small cell lung cancer (NSCLC), faces clinical challenges including molecular heterogeneity, late diagnosis, and aggressive growth, leading to a low 5-year survival rate. Biomarkers are critical for early detection, accurate differentiation of benign/malignant lesions, and guiding personalized treatment strategies. Proteomic technologies using liquid biopsy show potential by analyzing protein changes and post-translational modifications (PTMs) to identify novel biomarkers and unravel cancer mechanisms. This review examines proteomic advances in LUAD, compares platform strengths, lists validated protein markers, and discusses challenges like specificity and regulations. It aims to develop a precision medicine framework by integrating multi-omics data for improved diagnosis and treatment.<h4>Methods</h4>This study conducted a literature review by searching the PubMed and Web of Science databases for original articles written in English from 2002 to 2025, using the keywords "lung adenocarcinoma" OR "LUAD" AND "biomarkers" AND "proteomics" OR "SomaScan" OR "spatial proteomics" to identify the latest research findings in the field of proteomics technology and LUAD biomarkers. The included studies mainly focused on the current landscape of biomarkers in the diagnosis, treatment, and prognosis of LUAD.<h4>Key content and findings</h4>This review discusses high-throughput methods for comprehensive protein profiling in accessible biospecimens (tissues, blood, urine) to identify biomarkers for LUAD. We systematically evaluate emerging proteomic strategies, including mass spectrometry (MS), proximity extension assays (PEAs), spatial proteomics techniques, and SomaScan platforms-coupled with innovative computational frameworks have revolutionized biomarkers discovery and their translational potential in developing precision diagnostics and targeted therapies. Additionally, the review addresses challenges in integrating proteomics with genomics, transcriptomics, and metabolomics, offering new methodologies and expanding research in life sciences. As technological advancements continue, it is anticipated that more potential biomarkers will be conducted to validate the broader application in LUAD treatment, addressing early-stage disease complexities and aiding in selecting more effective treatment strategies.<h4>Conclusions</h4>By synthesizing cutting-edge evidence on proteome-driven LUAD biomarkers, this review elucidates actionable strategies to refine early detection protocols and mechanism-informed personalized treatment frameworks, directly advancing precision oncology initiatives for this prevalent malignancy through biomarker-guided clinical decision-making and multi-omics integration.

Red blood cell (RBC) membrane lipid peroxidation during blood bank storage profoundly impacts transfusion efficacy; however, the genetic determinants underlying RBC resilience remain incompletely defined. Here, we identify a critical role for glutathione peroxidase 4 (GPX4) - a pivotal enzyme protecting against iron-dependent lipid peroxidation (ferroptosis) - in regulating RBC storage quality and post-transfusion survival. Conditional erythroid-specific deletion of <i>Gpx4</i> in mice exacerbated lipid hydroperoxide accumulation, oxidation and ubiquitination of membrane proteins, and reduced RBC recovery after transfusion. Multi-omics analyses in 13,091 human blood donors from the REDS RBC Omics cohort identified regulatory intergenic (rs8178962), intronic and missense genetic variants in GPX4 (rs73507255, rs8178967), particularly prevalent among donors of African descent, that were linked to increased lipid peroxidation and compromised post-transfusion hemoglobin increments. Single protein- and metabolome-wide association studies (pQTL/mQTL) highlighted genetic variants associated with enhanced (rs8178962) or impaired GPX4 expression, disrupted glutathione homeostasis, lipid hydroperoxide accumulation, accelerated membrane damage, and activation of ferroptotic signatures during RBC storage. These effects were exacerbated by genetic traits impairing redox homeostasis, including glucose 6-phosphate dehydrogenase (G6PD) deficiency (African variant rs1050828 V68M/N126D). Storage of murine RBCs in presence of the ferroptosis inhibitor ferrostatin-1 prevented storage-induced lipid peroxidation and boosted post-transfusion recovery, a beneficial effect in part phenocopied by supplementation of lipophilic antioxidants vitamin E and Lands cycle fueling via L-carnitine, and in part ablated by GPX4 inhibition via the covalent inhibitor ML210. This study offers mechanistic insights into RBC ferroptosis and positions GPX4 genetic status as a promising biomarker for precision transfusion medicine.

Adolescent depression is a heritable psychiatric condition with rising global prevalence and severe long-term outcomes, yet its biological underpinnings remain poorly understood. We conducted the first genome-wide association study of adolescent-onset depression, comprising 102,428 cases (diagnosis or clinical symptom thresholds) and 286,911 controls, including diverse ancestries. Cross-ancestry meta-analysis identified 52 independent variants across 17 loci; European-only analysis found 61 variants at 29 loci, with a SNP-based heritability of 9.8%. Comparative analyses revealed two genes unique to adolescent-onset versus lifetime depression, enriched in neuronal subtypes, and two genes as potential drug repurposing targets. Polygenic scores were associated with adolescent-onset depression across ancestries, persistent depression trajectories, more severe outcomes, as well as reduced cortical volume, surface area and white matter integrity. Genetic correlation and Mendelian randomisation analyses support shared genetic liability and causal links with early puberty and modifiable health and behavioural risk factors. These findings uncover novel genetic loci and refine biological pathways underlying adolescent-onset depression, revealing age-specific mechanisms and early intervention opportunities.

Small intestinal neuroendocrine tumors (SI-NETs) represent the most frequent neoplasms of the small intestine, with loss of chromosome 18 as the most common genetic aberration. To date, no highly frequently mutated genes have been identified on chromosome 18 or elsewhere. This study aimed to explore the potential role of methyl-CpG binding domain protein 2 (MBD2), located at 18q21.2, as a tumor suppressor gene in SI-NETs. By immunohistochemistry, we found undetectable or very low levels of MBD2 expression in 64% of the analyzed SI-NETs, and overall, very low levels of mRNA and protein expression were observed. Overexpression of MBD2 in the SI-NET cell line, GOT1, reduced cell growth and induced apoptosis, though cell migration remained unaffected. In addition, MBD2 expression decreased cell proliferation and migration capacity of the neuroendocrine cells NCI-H727 but showed no effect on apoptosis. Furthermore, MBD2 expression in both cell lines was found to upregulate E-cadherin but downregulate the levels of N-cadherin and vimentin in GOT1 and NCI-H72, respectively, as determined by western blot analysis. These results suggest that MBD2 plays a role in inhibiting the epithelial-mesenchymal transition process and may function as a potential tumor suppressor gene in SI-NETs. Future studies to elucidate the underlying mechanisms are warranted.

Porcine reproductive and respiratory syndrome virus (PRRSV) is a major swine pathogen that causes significant economic losses worldwide. The nucleocapsid (N) protein, the most abundant viral protein in infected cells, plays roles beyond its structural function, influencing various host cellular processes. Here, we report the identification of 301 cellular protein candidates interacting with PRRSV N using EGFP immunoprecipitation combined with label-free quantitative mass spectrometry. The analysis underscores the versatile nature of the N protein in targeting a wide range of cellular proteins and processes across multiple subcellular compartments. We observed strong enrichment of ribosomal proteins, nucleolar proteins involved in ribosome biogenesis, splicing factors, RNA helicases, and DNA-binding proteins involved in chromatin remodeling and DNA damage response. Additionally, we identified proteins involved in viral RNA sensing and intrinsic antiviral mechanisms that may contribute to the immunosuppressive properties of the viral protein. Several interactions were validated and further characterized for RNA dependence, including MYBBP1A, NCL, IGF2BP1, UPF3B, G3BP1, EIF2S1, RFC4, ABCF1, PPM1G, NSUN2, and NOP2. Notably, RTCB and MYBBP1A were identified as host dependency factors for PRRSV infection. Our findings expand the current understanding of PRRSV-host interactions and reveal novel N-interacting proteins that may contribute to viral pathogenesis and immune evasion.

<h4>Background</h4>Little is known regarding the shared genetic architecture underlying the phenotypic associations between depression and preterm birth (PTB). We aim to investigate the genetic overlap and causality of depression with PTB.<h4>Methods</h4>Leveraging summary statistics from the largest genome-wide association studies for broad depression (N_total = 807,533), major depression (N_total = 173,005), bipolar disorder (N_total = 414,466), and PTB (N_total = 226,330), we conducted a large-scale genome-wide cross-trait analysis to assess global and local genetic correlations, identify pleiotropic loci, and infer potential causal relationships.<h4>Results</h4>Positive genetic correlations were observed between PTB and broad depression (<i>r_g</i> = 0.242), major depression (<i>r_g</i> = 0.236), and bipolar disorder (<i>r_g</i> = 0.133) using the linkage disequilibrium score regression, which were further verified by the genetic covariance analyzer. Local genetic correlation was identified at chromosome 11q22.3 (harbors <i>NCAM1-TTC12-ANKK1-DRD2</i>) for PTB with depression. Cross-trait meta-analysis identified two loci shared between PTB and broad depression, two loci shared with major depression, and five loci shared with bipolar disorder, among which three were novel (rs7813444, rs3132948 and rs9273363). Mendelian randomization demonstrated a significantly increased risk of PTB for genetic liability to broad depression (odds ratio [OR]=1.30; 95% confidence interval [CI]: 1.11-1.52) and major depression (OR=1.27; 95%CI: 1.08-1.49), and the estimates remained significant across the sensitivity analyses.<h4>Conclusions</h4>Our findings demonstrate an intrinsic link underlying depression and PTB and shed novel light on the biological mechanisms, highlighting an important role of early screening and effective intervention of depression in PTB prevention, and may provide novel treatment strategies for both diseases.

The intestinal environment determines the biochemical activity of individual microbial strains. The functions of microbial strains in their native environments often cannot be accurately predicted based solely on genomic information or the biochemical properties of cultivated isolates. In some cases, even the activity of intracellular enzymes does not correlate with the functional activity of bacteria. To address this challenge, we developed an enzymatic activity visualization platform that uses active intracellular enzymes as molecular baits to capture specific substrate probes. This platform links enzyme-mediated biochemical activity to their <i>in situ</i> localization, isolation, phylogenetic identification, and functional validation. This platform uses substrate-based probes designed to target isozymes, namely enzymes with different sequences but capable of catalyzing the same chemical reactions on a given substrate. Combined with a highly specific alkyne-azide cycloaddition reaction, these probes enable fluorescent visualization of strains harboring isozymes in human gut microbiota under anaerobic conditions. In addition, the platform can be integrated with fluorescence-activated cell sorting and 16S rRNA amplicon sequencing to isolate and taxonomically identify functional guilds containing isozymes physically. By performing metabolic capacity tests, fluorescence imaging, and proteomic analyses on four positive and three negative reference strains, we validated that our probes exhibit selectivity at the bacterial cell level. Using the platform, we successfully identified functional guilds involved in the reduction of sennoside A, a widely used laxative prodrug activated by gut bacteria. Importantly, we found that phylogenetically distinct bacteria perform similar metabolic activities toward sennoside A and discovered a novel sennoside A-reducing enzyme, StNfrA, from these functional guilds. The mechanistic study on StNfrA proved that our platform distinguished sennoside A-reducing bacteria species from microbiota by the enzymatic activity. Overall, these findings demonstrate that this enzymatic activity visualization platform is a powerful tool for the reliable localization, isolation, and identification of functional guilds in complex microbial communities.

This study investigated 17α-estradiol's effects on aged hypothalamic physiological activity via long-term administration. Single-nucleus transcriptomic sequencing (snRNA-seq) was performed on pooled hypothalami from each group: aged male Norway brown rats treated with 17α-estradiol (O.T), aged controls (O), and young controls (Y). Supervised clustering of neurons (based on neuropeptides/receptors) evaluated subtype responses to aging and 17α-estradiol. Aging-induced elevation of neuronal cellular metabolism, stress, and reduced synapse formation-related pathways were significantly attenuated by 17α-estradiol. Neuron population analysis showed that subtypes regulating food intake, reproduction, blood pressure, stress response, and electrolyte balance were sensitive to 17α-estradiol. 17α-estradiol increased serum oxytocin (Oxt) and hypothalamic-pituitary-gonadal (HPG) axis activity (elevated plasma Gnrh, total testosterone; reduced estradiol). Gnrh1 upregulation mediated its effects on energy homeostasis, neural synapse, and stress response. Notably, <i>Crh</i> neurons in O.T showed prominent stress phenotypes, distinct from <i>Agrp/Ghrl</i> neurons. Thus, HPG axis and energy metabolism may be key 17α-estradiol targets in male hypothalamus. Additionally, our results demonstrate that supervised clustering (based on neuropeptides/receptors) effectively assesses the responses of hypothalamic neuron subtypes to aging and 17α-estradiol treatment.

<h4>Introduction</h4>Single-cell transcriptomic analyses in adult mice show that cortical projection neuron subclasses exhibit heterogenous gene expression profiles that reflect their projection targets and laminar and areal positions. Further analyses revealed that projection neurons within the same subclass also exhibit transcriptomic heterogeneity. Recent evidence suggests that differences in maturation state reflect one source of this heterogeneity. The MET receptor tyrosine kinase, a regulator of synapse maturation, is expressed in a subpopulation within cortical projection neuron subclasses, providing an experimental model to address transcriptomic heterogeneity within developing projection neuron subclasses.<h4>Methods</h4>Single-cell RNA sequencing and smFISH were used to identify transcriptomic differences between Met+ and Met- projection neuron populations in the mouse visual and frontal cortices during the early phase of synapse formation and dendritic growth.<h4>Results</h4>Analyses confirmed enrichment of Met in select projection neuron subclasses and further identified astrocytes as the major source of its ligand, Hgf. No genes were expressed uniquely in Met+ or Met- projection neurons within a subclass; rather, there were graded differences in gene expression between the populations. While the identity of differentially expressed genes varied between subclass and cortical area, there was a consistent overrepresentation of genes associated with axon growth, as well as synapse structure, development, and function, with a subset associated with the MET interactome. Further, compared to Met- projection neurons, expression differences in genes associated with maturation indicate less mature excitatory synapses and spines in the Met+ population at this age.<h4>Conclusion</h4>The current findings provide support for the hypothesis that Met+ projection neurons are in a less mature state than Met- projection neurons within the same subclass. Further, the data are consistent with converging lines of biochemical and electrophysiological evidence that MET contributes to asynchronous maturation of developing cortical circuits.

The liver circadian clock and hepatic transcriptome are highly responsive to metabolic signals generated from feeding-fasting rhythm. Previous studies have identified a number of nutrient-sensitive signaling pathways that could interpret metabolic input to regulate rhythmic hepatic biology. Here, we investigated the role of O-GlcNAcylation, a nutrient-sensitive post-translational modification (PTM) in mediating metabolic regulation of rhythmic biology in the liver. We observe daily oscillation of global nuclear protein O-GlcNAcylation in the liver of mice subjected to night-restricted feeding (NRF) using label-free global O-GlcNAc proteomics. Additional site-specific O-GlcNAc analysis by tandem mass tag mass spectrometry further supports temporal differences in O-GlcNAcylation by revealing day-night differences. Proteins involved in gene expression are enriched among rhythmically O-GlcNAcylated proteins, suggesting rhythmic O-GlcNAcylation may directly regulate the hepatic transcriptome. We show that rhythmic O-GlcNAcylation can also indirectly modulate nuclear proteins by interacting with phosphorylation. Several proteins harboring O-GlcNAcylation-phosphorylation interplay motif exhibit rhythmic O-GlcNAcylation and phosphorylation. Specifically, we show that O-GlcNAcylation occurs at a phospho-degron of a key circadian transcriptional activator, circadian locomotor output cycles kaput (CLOCK), thus regulating its stability and transcriptional output. Finally, we report that day-restricted feeding (DRF) in the nocturnal mouse significantly alters O-GlcNAcylation pattern. Whereas global O-GlcNAcylation analysis indicates dampening of global O-GlcNAcylation rhythm in mice fed under DRF, site-specific analysis reveals differential responses of O-GlcNAc sites when timing of food intake is altered. Notably, a substantial number of O-GlcNAcylation sites exhibit inverted day-night profiles when mice are subjected to DRF. This suggests the dysregulation of daily nuclear protein O-GlcNAcylation rhythm may contribute to the disruption in liver transcriptome previously observed in DRF condition. In summary, our results provide new mechanistic insights into metabolic regulation of hepatic transcriptional regulators via interplay between O-GlcNAcylation and phosphorylation and shed light on the deleterious effects of improper mealtimes.

Lupus nephritis (LN) is a type of glomerulonephritis and one of the most serious complications of systemic lupus erythematosus (SLE). LN affects 25-60% of patients with SLE, with incidence and prevalence varying by age, sex, ethnicity and socioeconomic factors. LN predominantly develops within 5 years of an SLE diagnosis and, for many patients, it is the initial manifestation that leads to the recognition of SLE. In some patients, LN may develop late in the disease course, highlighting the importance of persistent awareness of its symptoms and signs. Despite an increasing understanding of disease biology and more effective treatment options, LN remains a substantial cause of morbidity and mortality as it can lead to irreversible kidney failure and associated complications. Risk factors for progression to kidney failure include persistent proteinuria, low glomerular filtration rate, hypertension at diagnosis and frequent disease flares. LN pathogenesis involves complex immune dysregulation, with key pathways including type I interferon signalling, calcineurin activation, and B and T cell dysfunction. Several immunomodulatory drugs are used for the management of LN, and treatment paradigms are increasingly shifting towards multi-agent regimens. Along with appropriate pharmacotherapy, multidisciplinary care tailored to the patient's individual needs, involving rheumatologists, nephrologists, social workers and other health professionals, is crucial for holistically addressing both the immune and non-immune risk factors for progressive kidney function loss and for maximizing kidney lifespan in LN.

The uniform lethality of glioblastoma (GBM) with a survival of less than 2 years despite best available therapy is attributed to treatment resistance due to DNA repair mechanisms that drive disease relapse and tumor heterogeneity. One prognostic factor identified as a reliable biomarker for GBM sensitivity to temozolomide (TMZ) and radiotherapy (RT) is the overexpression of O⁶-methylguanine-methyl-transferase (MGMT) enzyme. Patients with active MGMT were found to receive little benefit from TMZ and RT. They represent a group of great unmet need with no treatment options that significantly improve survival. Recently, several preclinical and clinical studies suggest that the alcohol aversion drug, disulfiram (DSF), inhibited MGMT and improved the efficacy of TMZ in GBM when combined with copper (Cu). However, phase II trial showed that there was no significant survival benefit from oral Cu/DSF. Nevertheless, the major limitation of oral Cu/DSF has been delivery of fragile DSF to the in vivo system. To address this limitation, we developed a novel delivery system using 2-hydroxypropyl beta cyclodextrin (HPβCD) encapsulating the Cu complex of DSF's active metabolite, diethyldithiocarbamic acid (DDC). It was determined that HPβCD stabilized Cu(DDC)₂. In vitro cell culture study revealed that HPβCD-Cu(DDC)₂ inhibited MGMT through the ubiquitin-proteasome pathway. Inhibition of MGMT activity in cell cultures vastly increased the alkylation-induced DNA double-strand breaks, cytotoxicity, and the levels of apoptotic markers like histone family member X (γ-H2AX), JNK-P and cleavage of Poly [ADP-ribose] polymerase 1 (PARP-1). Preliminary intravenous delivery of HPβCD-Cu(DDC)₂ in combination with TMZ in an MGMT-positive patient derived orthotopic xenograft (PDOX) model demonstrated tumor size regression. HPβCD-Cu(DDC)₂ targets MGMT-145-cysteine and its unique cytotoxic mechanism circumvents MGMT-mediated TMZ resistance. This novel delivery system shows promise for overcoming MGMT-mediated resistance in GBM, offering a potential new therapeutic strategy.

Hydroxyapatite (HA) nanoparticles synthesized from bio-waste sources like eggshells offer a sustainable and biocompatible alternative for bone regeneration. This study successfully synthesized nano-hydroxyapatite from chicken eggshell-derived calcium precursors and comprehensively characterized it. X-ray diffraction (XRD) confirmed the formation of a highly crystalline, phase-pure HA structure, while Fourier-transform infrared spectroscopy (FTIR) revealed characteristic phosphate, hydroxyl, and carbonate bands, resembling biological apatite. Scanning electron microscopy (SEM) showed spherical nanoparticles (~ 11.2 nm) with uniform distribution, enhancing bioactivity. Hemocompatibility assays demonstrated concentration-dependent hemolysis, with minimal RBC disruption (< 7%) at 12.5 mg/ml, mitigated further by protein corona formation. In vitro studies revealed excellent osteoblast (MC3T3-E1) adhesion and spreading on HA surfaces, indicating osteoconductivity. Additionally, HA nanoparticles exhibited dose-dependent free radical scavenging activity (up to 84.7% at 200 µg/ml) and significantly suppressed pro-inflammatory cytokines (IL-1β and IL-18) in LPS (Lipopolysaccharide)/ATP (Adenosine triphosphate)-stimulated macrophages, highlighting anti-inflammatory potential. These findings collectively underscore the suitability of eggshell-derived nano-HA for bone tissue engineering, combining eco-friendly synthesis, structural biomimicry, and multifunctional bioactivity to promote osteogenesis and mitigate inflammation.

We investigate the clinical significance of the peroxiredoxin (PRDX) family in multiple myeloma (MM) patients, focusing on its diagnostic and prognostic value, biological role and impact on the immune system. Using bioinformatics tools, such as CCLE, GEO, TCGA-MMRF, Kaplan-Meier plotter, enrichment and CIBERSORT analyses, we systematically characterized the expression levels, impact on survival and biological significance of PRDXs in MM. Bone marrow aspiration and clinical data were subsequently collected from MM patients to validate the findings related to PRDX2 from the databases. Finally, PRDX2 silencing in vitro modulated cell proliferation, immune infiltration and ferroptosis susceptibility. Compared with those in normal plasma cells, the expression levels of PRDX2/4/5/6 were significantly increased in myeloma cells. Furthermore, in relapsed MM cells, PRDX1/2/3/6 expression was significantly upregulated compared with that at baseline. Notably, PRDX2 was found to be highly expressed and associated with poor tumor characteristics, potentially contributing to disease progression and correlating with unfavourable prognosis. PRDX-related genes participate in various biological functions, influence metabolic pathways and may regulate ferroptosis and immune-related pathways in myeloma cells. This study is the first comprehensive analysis of the potential diagnostic and prognostic impact of the PRDXs family in MM, highlighting their significant associations with ferroptosis and the immune microenvironment. These findings provide a strong experimental and theoretical foundation for developing novel therapeutic strategies targeting ferroptosis and immunotherapy in MM.

<h4>Background</h4>Obstructive sleep apnea (OSA), and other sleep disorders, are associated with increased risk of developing diabetes mellitus (DM). We examined whether sleep disorders influence the genetic risk of developing diabetes in Hispanic/Latino individuals.<h4>Methods</h4>We developed Type 2 Diabetes (T2D) polygenic risk score (T2D-PRS) useful in admixed Hispanic/Latino individuals. We estimated the association of the T2D-PRS with cross-sectional (n = 12,342) and incident (n = 6965) DM in the Hispanic Community Health Study/Study of Latinos (ages 18-76, 50.9% female). We conducted a mediation analysis with T2D-PRS as an exposure, incident DM as an outcome, and OSA as a mediator. Additionally, we performed Mendelian randomization (MR) analysis to assess the causal relationship between T2D and OSA.<h4>Results</h4>Here, we show that a 1 standard deviation increase in T2D-PRS has DM adjusted odds ratio (OR) = 2.67, 95% CI [2.40; 2.97] and a higher incident DM rate (incident rate ratio (IRR) = 2.02, 95% CI [1.75; 2.33]). In a stratified analysis based on OSA severity categories the associations are stronger in individuals with mild OSA compared to those with moderate to severe OSA. Mediation analysis suggests that OSA mediates the T2D-PRS association with DM. In two-sample MR analysis, T2D has a causal effect on OSA, OR = 1.03, 95% CI [1.01; 1.05], and OSA has a causal effect on T2D, with OR = 2.34, 95% CI [1.59; 3.44].<h4>Conclusions</h4>These results support a causal association between OSA and DM, with OSA mediating up to 4.7% of the genetic risk for DM. OSA treatment may reduce DM prevalence.

Titanium implants possess bioinert surfaces that limit osseointegration and are prone to bacterial colonization, necessitating functional coatings. This study investigated the electrophoretic deposition (EPD) of composite coatings composed of chitosan (CS), nanohydroxyapatite (nanoHAp), and silver nanoparticles (AgNPs) on grade 2 titanium using an ethanol-acetic acid suspension. The influence of deposition parameters (10-30 V; 3-5 min) on coating microstructure, adhesion, corrosion resistance, wettability, bioactivity, and silver release was systematically examined. The coatings reached a maximum thickness of ~ 7 μm at 30 V/5 min, while the most uniform and adherent coating (class 1, EN ISO 2409) was obtained at 10 V/3 min. Increasing voltage and time produced rougher (Sa up to 1.3 μm) and more porous surfaces, but decreased adhesion. Corrosion resistance improved with coating thickness, with open circuit potentials shifting positively up to + 0.15 V versus the reference electrode. Wettability tests revealed hydrophilic behavior with contact angles of ~ 80°. Bioactivity in simulated body fluid was confirmed by calcium phosphate precipitation on all coated samples, particularly thicker ones. Silver ion release was controlled by deposition parameters, ranging from 0.9 mg/L (10 V/3 min) to 1.8 mg/L (30 V/5 min) after 7 days, indicating a balance between antibacterial functionality and coating integrity. These results demonstrate that ethanol-based EPD can fabricate bioactive, corrosion-resistant CS/nanoHAp/AgNPs coatings with tunable properties. Optimized coatings show potential for biomedical applications, particularly in reducing implant-associated infections while supporting bone integration.

Plasma is a rich source of biomolecules, including proteins, that reflect both health and disease. Due to their key roles in biological processes, proteins hold significant potential as biomarkers, fueling the rise of plasma proteome profiling in recent years. However, comprehensive comparisons of the performance of different plasma proteomics platforms are limited. Our study addresses this gap by conducting a direct comparison of eight platforms, representing both affinity-based and diverse mass spectrometry approaches, and covering over 13,000 proteins. By applying these platforms to the same cohort, we systematically assess their performance, identifying key differences and complementary strengths. Our findings offer valuable insights for researchers, highlighting trade-offs in coverage and their implications for biomarker discovery and clinical applications. This study serves as an essential resource, offering both technical evaluation and biological insights to support the development of novel diagnostics and therapeutics through plasma proteomics.

Existing research indicates that bicalutamide and zoladex show significant potential in treating prostate cancer. However, in the clinical application of treating benign prostatic hyperplasia (BPH), it is limited due to relatively severe side effects, and the specific mechanism of action has not been fully studied. This research aimed to identify and validate key genes linked to the effects of bicalutamide and zoladex in BPH, potentially guiding the development of targeted therapeutic strategies. BPH-related datasets were retrieved from publicly available databases (|log2FC| > 0.5, p value < 0.05). Initially, intersection genes were identified by overlapping results from differential expression analysis (comparing BPH and control groups) with the target genes of bicalutamide and zoladex, which were sourced from database searches. Key genes were then pinpointed using protein-protein interaction (PPI) networks, machine learning algorithms (SVM-RFE and Random Forest), and gene expression analyses (IHC, immunohistochemical). To explore the biological mechanisms underlying these genes, functional enrichment (GO, KEGG and GSEA) molecular docking analyses were performed, construction of lncRNA miRNA mRNA molecular regulatory network, transcription factor (TFs) regulatory network, SNPs analysis, and disease prediction. Validation of gene expression levels was conducted through IHC analysis of clinical samples. The study identified NQO1, CLPP, HMGCR, and SORD as critical genes associated with BPH, all showing significantly reduced expression in BPH samples. These genes were notably co-enriched in the "oxidative phosphorylation" pathway. Moreover, CLPP, HMGCR, and NQO1 exhibited strong binding affinities with bicalutamide and zoladex. Specifically, the NQO1-bicalutamide interaction had a binding energy of -10.8 kcal/mol, while the NQO1-zoladex interaction demonstrated a binding energy of -38.05 kcal/mol. IHC analysis revealed significantly higher expression levels of NQO1, CLPP, HMGCR, and SORD in the treated group compared to the untreated group. This study underscores NQO1, CLPP, HMGCR, and SORD as potential therapeutic targets for BPH, offers mechanistic insights into the efficacy of bicalutamide and zoladex and provides novel insights into potential therapeutic strategies for patients with BPH. However, attention should still be paid to the control of side effects in their clinical application.

<h4>Background</h4>Genetic skeletal disorders are a heterogeneous group of syndromic or non-syndromic diseases characterized by abnormal bone, joint or cartilage development. These disorders generally occur sporadically in ruminants. Although a genetic etiology is often suspected, only a limited number of causal variants have been identified and no comprehensive genetic analyses of a cohort of bovine and ovine skeletal developmental defects have been published. The aims of our study were (1) to propose a nosology of genetic skeletal disorders in cattle and sheep and (2) to contribute to the nosology with a number of novel genomically characterized cases.<h4>Results</h4>Based on a literature review, the proposed nosology of skeletal disorders in cattle and sheep with a confirmed molecular cause was found to comprise 43 different disorders associated with 45 different genes. In addition, horn traits were also included. The disorders were grouped into 21 categories based on the human medical nosology. Thirty novel bovine and nine ovine cases of congenital skeletal disorders were investigated. These represented 19 different disorders, which were grouped into 9 categories. Whole-genome sequencing (WGS) data were generated based on sample availability for either complete trios, affected paternal halfsiblings or isolated single cases. We identified 21 SNVs or small indels for 12 skeletal disorders. Of these, 17 were considered candidate variants affecting 16 different genes, including 11 that were classified as pathogenic and six as likely pathogenic. Additionally, the remaining 4 SNVs were of uncertain significance. Two aneuploidies (trisomy and partial monosomy) were the cause of two different disorders. For eight cases affected by six disorders no variant could be identified. Different modes of inheritance were detected, including spontaneous dominant de novo mutations, autosomal recessive alleles, an X-linked dominant allele, as well as aneuploidies. The overall molecular genetic diagnostic rate was 64%.<h4>Conclusions</h4>Genomic analysis revealed considerable heterogeneity of the described phenotypes in terms of mode of inheritance, affected genes, and variant type. We propose, for the first time in veterinary medicine, a nosology of genetic skeletal disorders in ruminants that may be useful for more precise differential clinicopathological diagnosis. We emphasize the potential of WGS to enhance genetic disease diagnosis and the importance of adopting a nosology for disease categorization.

<h4>Background</h4>The genomic diversity of Chinese Holstein cattle remains insufficiently characterized, and the identification of genes associated with body conformation traits is still limited. In this study, we aimed to explore the genome-wide diversity and population structure, and to identify candidate genes associated with 20 body conformation traits in Chinese Holstein cattle from six farms using the GGP Bovine 50 K single nucleotide polymorphism (SNP) chip.<h4>Results</h4>We analyzed runs of homozygosity and population admixture across farms and observed genetic diversity differences among herds. A genome-wide association study identified 21 significant SNPs linked to five body conformation traits. Notably, a missense mutation in TJP1 (BovineHD2100008355) was associated with foot heel depth. Ten SNPs within intronic regions of genes such as GABRG3, NEGR1, and CDH2 were associated with various udder and leg traits. The remaining ten SNPs were located in intergenic regions and influenced transcription factor binding sites. Among them, BovineHD2100013266, BovineHD0500004109, and BTB-00042676 were shown to regulate transcriptional activity through dual-luciferase reporter assays.<h4>Conclusions</h4>Our findings offer valuable insights for managing genetic inbreeding in cattle farms, enhancing the understanding of the genetic architecture underlying body conformation traits in Holstein cattle, and accelerating the genomic selection process in Chinese Holsteins.

<h4>Background</h4>This study focuses on genetic resistance to infectious pancreatic necrosis (IPN), a highly contagious disease caused by an aquatic birnavirus (IPNV) which especially affects salmonids worldwide. The objectives were to estimate the heritability of IPN resistance and to fine map quantitative trait loci (QTL) using a Bayesian Sparse Linear Mixed Model to identify candidate genes possibly linked to IPN resistance in two successive generations from a French commercial strain of rainbow trout. For each generation, 2000 fish were experimentally exposed by bath to IPNV and mortalities were monitored daily during 5 weeks. All fish were genotyped using a medium-density 57 K single nucleotide polymorphism (SNP) chip and imputed to high-density genotypes (665 K SNPs).<h4>Results</h4>The mean survival rate was 70% after 37 days, with a higher survival rate in the second generation compared to the first one (78% versus 61%). Heritability was moderate (~ 0.20). Approximately 74% of the genetic variance of IPN resistance was explained by several tens of SNPs. In total, 25 QTL were mapped on 10 chromosomes, of which 7 were detected with very strong evidence, on chromosomes 1, 14, 16 and 28. The most interesting QTL were associated to top SNPs with mean survival rate differences over 20% between the beneficial and detrimental homozygous genotypes. Those SNPs were all located within promising functional candidate genes on chromosome 1 (uts2d, rc3h1, ga45b) and chromosome 16 (irf2bp, eif2ak2), which were all associated with regulation of inflammatory pathways. A key factor for the genetic differences in susceptibility to IPNV among fish is the dsRNA-dependent serine/threonine-protein kinase (PKR) encoded by the eif2ak2 gene.<h4>Conclusions</h4>All genes associated with the most significant QTL on chromosomes 1 and 16 are involved in the regulation of inflammatory pathways, strongly suggesting a central role of inflammation in IPN resistance in rainbow trout. These findings offer the possibility of marker-assisted selection for rapid dissemination of genetic improvement for IPN resistance.

This review article explores the possible role of Chinese medicine (CM) in modulating stem cells for regenerative medicine, synthesizing evidence from animal experiments and human trials. The article focuses on how CM modulates the stem cell environment, specifically their roles in delaying cellular senescence and promoting stem cell survival, enhancing proliferation and differentiation, as well as stimulating exosome secretion. It also conducts a critical analysis of methodological rigor and clinical transparency within the included studies to enable a more objective assessment of their reliability and reproducibility. To guarantee the responsible integration of CM and stem cells in future clinical application, it also discussed the safety, efficacy, and heterogeneity of stem cells, as well as delivery methods, alongside the dose-response relationship of CM. The current evidence for CM in stem cell therapy remains constrained by the absence of standardized comparative baselines in animal studies and clinical outcome assessment. This methodological gap not only compromises the evidentiary weight of herbal effects but also introduces confounding variables in studies. The elucidation of CM mechanistic role in stem cell therapeutics necessitates robust interdisciplinary collaboration, this is an imperative and critically urgent thing within peer-reviewed research framework.

<h4>Rationale</h4>Breast cancer (BC) is the most prevalent malignant tumor in women globally. Despite improved cure rates and survival for early- to mid-stage patients, around 30% still progress to metastatic BC due to cancer stem cells (CSCs), which drive tumor recurrence, progression, metastasis, and drug resistance.<h4>Methods</h4>This study used bioinformatics to analyze BC datasets from gene expression omnibus (GEO), cBioportal, and The Cancer Genome Atlas (TCGA), identifying NCAPH as a gene associated with breast cancer stem cells (BCSCs) characteristics. The mRNA stemness index algorithm was used to calculate tumor stemness scores. WGCNA, Lasso regression, and Kaplan-Meier analyses validated the link between NCAPH and BC prognosis. In vitro and in vivo experiments explored NCAPH's effects on BC cells. Transcriptomic sequencing and Gene set enrichment analysis (GSEA) analysis revealed Hippo-YAP1 pathways regulated by NCAPH. Co-immunoprecipitation and immunofluorescence co-localization experiments confirmed the interaction between NCAPH and YAP1, with functional rescue experiments using the YAP1 inhibitor Verteporfin.<h4>Results</h4>Results showed NCAPH was overexpressed in BC, linked to advanced tumor stages and poor prognosis. It enhanced CSCs properties, accelerated cell cycle progression, and promoted proliferation, migration, and invasion in vitro and in vivo. GSEA analysis suggested NCAPH regulates YAP1 in the Hippo signaling pathway. NCAPH promotes LATS1 and YAP1 expression, dephosphorylation, and nuclear translocation, enhancing BCSC traits and malignant phenotypes. Notably, Verteporfin reversed NCAPH-driven BCSC traits and malignant phenotypes.<h4>Conclusion</h4>This study identifies NCAPH as a novel oncogenic factor in BC. NCAPH interacts with YAP1, promoting its nuclear translocation and enhancing BCSC traits and malignancy. Critically, YAP1 inhibition reverses NCAPH-driven effects, validating the NCAPH as a promising therapeutic target.

The molecular mechanisms underlying the pathogenesis of Alzheimer's disease (AD), the most common form of dementia, remain poorly understood. Proteomics offers a crucial approach to elucidating AD pathogenesis, as alterations in protein expression are more directly linked to phenotypic outcomes than changes at the genetic or transcriptomic level. In this study, we develop multiscale proteomic network models for AD by integrating large-scale matched proteomic and genetic data from brain regions vulnerable to the disease. These models reveal detailed protein interaction structures and identify putative key driver proteins (KDPs) involved in AD progression. Notably, the network analysis uncovers an AD-associated subnetwork that captures glia-neuron interactions. AHNAK, a top KDP in this glia-neuron network, is experimentally validated in human induced pluripotent stem cell (iPSC)-based models of AD. This systematic identification of dysregulated protein regulatory networks and KDPs lays down a foundation for developing innovative therapeutic strategies for AD.

Despite their ecological and biotechnological importance, the extent to which microalgae are regulated by epigenetic mechanisms has remained poorly understood. In the model industrial microalga Nannochloropsis oceanica, by comprehensive, multi-dimensional epigenomic analyses, this study uncovers an epigenetic regulatory network responsive to CO₂ levels. This network involves intricate interactions among DNA methylation, histone modifications, dynamic nucleosome positioning, and three-dimensional chromatin organization during adaptation to low-CO₂ conditions. Although DNA methylation is minimal, histone modifications-such as lysine acetylation, crotonylation, and methylation-are associated with active chromatin states and linked to 43.1% of differentially expressed genes. Notably, histone H3K4 di-methylation (H3K4me2) displays a distinct dual-peak profile around the transcription start site and is correlated with chromatin compartment dynamics. Knockout of NO24G02310, a putative H3K4 methyltransferase gene, caused genome-wide shifts in H3K4me2 peaks and decreased H3K4me1 levels, accompanied by direct or indirect downregulation of NoHINT and NoPMA2 expression, slower algal growth, and reduced photosynthetic efficiency (indicated by Fv/Fm), specifically under low-CO₂ conditions. Deletion and overexpression of genes encoding the histidine triad nucleotide-binding protein NoHINT and the plasma membrane H⁺-ATPase NoPMA2 confirmed their roles in growth and photosynthetic efficiency under low CO₂; NoHINT influences growth and NoPMA2 affects photosynthesis. As a previously unrecognized low-CO₂ adaptation mechanism, NO24G02310 likely coordinates the regulation of NoHINT and NoPMA2 through H3K4 modifications. These findings provide a foundation for enhancing microalgal productivity through targeted epigenetic engineering.

Pathogenic variants in the KCNQ2 gene, which encodes a potassium channel subunit, are associated with neonatal seizures, epileptic encephalopathy, intellectual disability, and autism. Although the consequences of disrupted KCNQ2 channel function have been studied in the past, the detailed molecular mechanisms underlying the development of neurological phenotypes remain unclear, and neuronal models of specific patient variants are lacking. We generated patient-specific induced pluripotent stem cells (iPSCs) from fibroblasts from three individuals with distinct KCNQ2 pathogenic variants. We corrected the KCNQ2 variants using CRISPR-Cas9 editing to create isogenic controls and differentiated these iPSCs into glutamatergic neurons to study the effects of each variant on neuronal function. The three KCNQ2 variants were: 1) KCNQ2 c.875_877delTCCinsCCT, L292_L293delinsPF, 2) KCNQ2 c.766G > T, G256W, and 3) KCNQ2 c.821C > T, T274M. Our data revealed longer neurite outgrowth in two patient lines (T274M and G256W). Transcriptional profiling showed that all three KCNQ2 lines co-expressed genes enriched in synaptic transmission/signaling, cell adhesion, and GTPase signal transduction. Functional analyses of neuronal networks revealed increased burst duration in all three KCNQ2 lines compared with their isogenic controls. Furthermore, neurons from the L292_L293delinsPF and T274M lines displayed increased network connectivity associated with increased density of synaptic markers. Finally, we detected hyperexcitable neuronal networks in the G256W line with electrical stimulation of the neural networks on a high-density microelectrode array, and this phenotype was rescued with retigabine. These disease-related phenotypes for each of the KCNQ2 pathogenic variants can be used for drug screening to identify treatment options for the patients.

<h4>Introduction</h4>Psoriasis is a chronic autoimmune skin disorder with a complex genetic basis. However, the codon usage patterns and nucleotide features of psoriasis-related genes remain unexplored, despite their potential to influence gene expression and disease progression.<h4>Methods</h4>We analyzed 79 psoriasis-associated genes to investigate codon usage bias (CUB) and nucleotide composition. Metrics included GC content, effective number of codons (ENC), and relative synonymous codon usage (RSCU). Evolutionary influences were assessed using correspondence analysis, parity rule 2 (PR2) plots, and neutrality plots.<h4>Results</h4>Functional enrichment analysis identified pathway involvement. Comparative genomic analysis evaluated differences in coding sequence and UTR lengths and GC content relative to the genome-wide background. Psoriasis-related genes showed high GC content (mean = 53.3 ± 9.3%) with a strong preference for GC-ending codons, especially at the third codon position (GC3 = 60.6 ± 16.1%). RSCU analysis revealed frequent use of GCC (alanine), CTG (leucine), and GTG (valine). While the mean ENC (46.2 ± 9.9) suggested moderate codon bias, several genes displayed strong bias (ENC < 30). Selection pressure accounted for 71% of codon usage variation, with mutation pressure contributing 29%. Functional enrichment showed significant involvement in IL-17 (FDR = 3.4×10^-3), JAK-STAT (FDR = 3.4×10^-3), and TNF (FDR = 8.0×10^-³) signaling pathways. These genes also tended to have shorter coding sequences and 5'UTRs and higher GC content compared to genome-wide averages.<h4>Conclusion</h4>In conclusion, this study reveals that psoriasis-related genes are under strong selective pressure, enriched in key inflammatory pathways, and exhibit codon and nucleotide features that may optimize expression in inflamed tissues. These insights have translational relevance for designing codon-optimized mRNAs, gene therapies, and diagnostic tools tailored to autoimmune diseases like psoriasis.

Citrullination, a process linked to autoimmune diseases, has been implicated in cancer, but its role in breast cancer (BRCA) remains unclear. This study aimed to identify citrullination-related genes (CRGs) associated with prognosis in BRCA. We utilized datasets from The Cancer Genome Atlas (TCGA-BRCA) and Gene Expression Omnibus (GEO), pinpointing candidate genes by intersecting differentially expressed genes (DEGs) from TCGA-BRCA with known CRGs. Prognostic CRGs were selected using univariate Cox regression and Lasso regression analyses, and a predictive nomogram was created based on independent prognostic factors identified through multivariate Cox regression. Our findings revealed that SEZ6, S100B, SPIB, and TFF1 were key CRGs used to construct a risk model. High-risk BRCA patients exhibited immune-suppressive tumor microenvironments (TMEs) with low CD8⁺ T cell mutation and enrichment in C1/C4 immune subtypes. In contrast, low-risk patients displayed high immune infiltration and enrichment in C2/C3/C6 subtypes. High expression of S100B, SPIB, and TFF1 was associated with increased immune infiltration by NK cells and T cells, while high SEZ6 expression was linked to neutrophil mutations, PD-L1 upregulation, and low CD8⁺ T cell infiltration. Molecular docking studies explored the interactions of these CRGs with entinostat. In conclusion, SEZ6, S100B, SPIB, and TFF1 were identified as significant prognostic genes in BRCA, providing insights into BRCA pathogenesis and potential personalized treatment strategies.

<h4>Background</h4>The mechanisms linking hypercoagulability to disease severity in Crohn's disease (CD) remain poorly understood. Through integrated transcriptomic and single-cell analyses of ileal tissues, we identified a novel CCR6⁺OLFM4⁺ intestinal stem cell subpopulation that bridges coagulation and inflammation in CD.<h4>Methods</h4>A cohort of 78 CD patients was established, utilizing transcriptomic data from three independent ileal samples obtained from the GEO database as discovery and validation datasets. Coagulation-related DEGs (CRGs) were determined via AmiGO 2 and KEGG databases. Based on these CRGs, CD patients were subclustered, coagulation scores were calculated, and gene expression changes were evaluated. Public single-cell RNA sequencing data from CD patient ileal epithelial cells were analyzed to identify key target cells influenced by coagulation. Immune infiltration was evaluated based on coagulation scores across subgroups. Ileal tissues from CD patients with different coagulation statuses were examined using Immunofluorescence Staining.<h4>Results</h4>Single-cell analysis of ileal epithelium revealed a novel CCR6⁺OLFM4⁺ stem cell subpopulation that was significantly expanded in CD patients with hypercoagulability (<i>P</i><0.05). These cells showed marked upregulation of PI3K-Akt signaling and correlated strongly with disease severity. Immunofluorescence validation confirmed a 2.3-fold increase in CCR6⁺OLFM4⁺ cells in the epithelial layer of hypercoagulable CD patients compared to normocoagulable controls. The concurrent activation of coagulation pathways and immune cell infiltration in CD ileum suggests this stem cell subpopulation may serve as a critical link between hypercoagulability and disease progression.<h4>Conclusion</h4>Our findings nominate CCR6⁺OLFM4⁺ stem cells as cellular mediators of coagulation-associated CD progression, suggesting the CCR6-PI3K-Akt axis as a potential therapeutic target requiring validation in larger cohorts.

<h4>Background</h4>Erythropoietic protoporphyria (EPP) is a rare autosomal recessive disorder caused by mutations in the FECH gene, leading to ferrochelatase deficiency and the accumulation of protoporphyrin in various organs. EPP patients with liver damage have atypical histopathological manifestations, which pose challenges for pathological diagnosis.<h4>Content</h4>We report a 29-year-old male with recurrent abdominal pain and scleral jaundice. Initial liver dysfunction suggested autoimmune hepatitis, but liver biopsy revealed dense brownish granular deposits with red birefringence under polarized light, characteristic of EPP. Genetic testing identified a new mutation site (c.804 + 1del), which may be related to the disease. Additionally, the patient also has Gilbert's syndrome.<h4>Conclusion</h4>This case highlights the diagnostic challenges of EPP and the importance of integrating clinical history, histopathology, and genetic testing. Polarized light microscopy is crucial for identifying the characteristic features of EPP. Early genetic testing can guide timely diagnosis and treatment, contributing to the understanding of this rare condition.

<b>Background/Objectives</b>: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG nucleotide repeat expansion in the Huntingtin (<i>HTT</i>) gene. Dysregulation of microRNAs (miRNAs), key post-transcriptional regulators of gene expression, has been implicated in HD pathogenesis, although their specific roles remain incompletely understood. <b>Methods</b>: Peripheral blood mononuclear cells from Sicilian HD patients and matched healthy controls were subjected to small RNA sequencing. Differential expression analysis was conducted using DESeq2 (version 1.44.0), with significance defined as |fold change| ≥ 1.5 and adjusted <i>p</i> ≤ 0.05. Ingenuity Pathway Analysis (IPA) was applied to assess functional enrichment, focusing on neurological diseases, inflammatory processes, and miRNA-RNA messenger (mRNA) interaction networks. <b>Results</b>: A total of 790 differentially expressed miRNAs were identified in HD patients (270 upregulated and 520 downregulated). IPA revealed enrichment in pathways related to organismal injury, neurological disease, and inflammatory responses. Four major regulatory networks linked differentially expressed miRNAs to neurodegenerative processes, with target genes involved in neuroinflammation, cellular stress responses, and metabolic dysfunction. Cross-referencing with previous RNA-seq data identified 5721 high-confidence miRNA-mRNA interactions, implicating 721 target genes across 54 key canonical pathways. <b>Conclusions</b>: HD patients exhibit a distinct and reproducible peripheral blood miRNA expression signature. These dysregulated miRNAs may represent accessible biomarkers and provide mechanistic insights into HD pathogenesis, with potential applications for diagnosis, prognosis, and therapeutic development.

<b>Background</b>: The human mitochondrial ClpP is a serine protease located in the mitochondrial matrix responsible for degrading short lived regulatory proteins as well as misfolded or damaged proteins, thereby maintaining cellular homeostasis. Proteastasis dysregulation is linked to tumor progression. <b>Methods</b>: We conducted a literature review (2020-2025) using PubMed and Scopus, focusing on studies addressing ClpP structure, function, activity modulation, and cancer relevance. Keywords included "ClpP", "ClpP activators", "ClpP inhibitors", and "mitochondrial protease". <b>Results</b>: ClpP is upregulated in many tumors compared to normal tissues. Cancer cells depend on ClpP for mitochondrial proteostasis, metabolic adaptation, and survival. ClpP proteolytic activity modulation-via activators or inhibitors-disrupts these processes showing efficacy even in clinical setting. <b>Conclusions</b>: ClpP is emerging as a key player in cancer pathophysiology and holds potential as a therapeutic target. Its selective overexpression in tumors, along with its involvement in mitochondrial homeostasis, makes it a compelling candidate for precision oncology.

PNAs have emerged as a powerful tool in gene editing, particularly for correcting monogenic disorders by enhancing targeted recombination and genomic modifications. This study aimed to establish a gene editing technique using Peptide Nucleic Acid (PNA)/donor DNA-loaded poly lactic-co-glycolic acid (PLGA) nanoparticles at our genomic facilities, with the ultimate goal of correcting disease-causing mutations. Methods involved culturing skin fibroblasts from a healthy Egyptian volunteer without HBB gene mutations in two separate 12-well plates. Oligonucleotides were designed, and nanoparticles were formulated and characterized before being used to treat the cultured fibroblasts. DNA and RNA were extracted from treated cells, followed by molecular analyses to confirm the edits. Results indicated successful encapsulation of nanoparticles and modest, sustained introduction of the desired mutation, accompanied by functional impairment in HBB gene expression. The study successfully established PNA gene editing technology, potentially paving the way for future treatment studies of single-gene disorders.

No abstract available.

Lung epithelial cells, including bronchial and alveolar epithelial cells, serve as the frontline barrier of the respiratory tract and play essential roles in maintaining pulmonary homeostasis and immune defense. Dysfunction of these epithelial cells contributes significantly to the development and progression of various lung diseases. Ferroptosis, an iron-dependent form of regulated cell death characterized by lipid peroxidation and glutathione depletion, has emerged as a key mechanism in pulmonary pathology. It plays distinct roles in benign and malignant lung conditions. In chronic obstructive pulmonary disease and asthma, ferroptosis promotes bronchial epithelial damage, oxidative stress, and persistent inflammation. Pathogens, such as Pseudomonas aeruginosa and SARS-CoV-2, induce ferroptosis to exacerbate epithelial injury. In pulmonary fibrosis, ferroptosis of alveolar epithelial cells contributes to tissue remodeling through oxidative stress and epithelial-mesenchymal transition. In lung cancer, ferroptosis affects carcinogenesis, therapy resistance, and response to radiotherapy. Emerging therapeutic strategies target ferroptosis using inhibitors, such as ferrostatin-1 and deferoxamine, or inducers, such as erastin and sulfasalazine, to modulate cell fate in a disease-specific manner. Natural compounds, such as curcumin, resveratrol, and nanomaterials, further enhance ferroptosis-based treatment potential. Ferroptosis thus offers a novel perspective on lung disease mechanisms and treatment. This article aims to review the role of epithelial cell ferroptosis in benign and malignant lung diseases.

<h4>Background</h4>DOPA decarboxylase (DDC) in cerebrospinal fluid (CSF) is an emerging Parkinson's disease (PD) biomarker, but its association with nonmotor symptoms is unclear.<h4>Objectives</h4>We aimed to determine if baseline DDC was associated with future cognitive decline in PD.<h4>Methods</h4>We correlated baseline CSF DDC, detected using the proximity extension assay, with Montreal Cognitive Assessment (MoCA) score using longitudinal data from 3 cohorts: Biopark, PPMI, and PDBP.<h4>Results</h4>DDC was significantly associated with cognitive decline in both the Biopark cohort (P-value < 0.0001) and the PDBP/PPMI cohorts (P-value < 0.0001). The results were still significant after correcting for levodopa-equivalent daily dose in the Biopark cohort (P-value < 0.0001) and when the analysis was restricted to the de novo subjects, both in Biopark (P-value: 0.0065) and PPMI (P-value<0.0001) cohorts.<h4>Conclusions</h4>CSF DDC is a potential biomarker for the prediction of cognitive decline in PD patients.

Exogenous forces significantly influence mammalian cell behavior, yet current strategies fail to resolve signaling processes between individual cells under conditions that accurately mimic the native microenvironment. This work presents a new cell culture technology capable of applying spatially patterned exogenous forces on individual cells within multicellular clusters encased in three-dimensional (3D) hydrogel matrices. Photothermally powered 3D microgels containing stem cells and integrated force generators are engineered to investigate intercellular communication under anisotropic forces with excellent spatial resolution (≈1 µm). Varying force patterns, such as uniform compression versus spatially heterogeneous tension, are achieved in 3D by relying on the synergistic effect of plasmonic gold nanorods and thermally responsive co-polymers under light actuation. The microgels generate 17-34 nN force locally, which activates mechanically sensitive ion channels in encapsulated cells stimulated with isotropically applied compression and spatially heterogeneous tension in 3D in a selective manner. Spatially patterned exogenous forces trigger F-actin remodeling, nuclear translocation of Yes-associated protein (YAP) and Runt-related transcription factor 2 (RUNX2) in encapsulated cells following cyclic stimulation. Sustained application of exogenous forces over three days is sufficient to regulate stem cell fate toward osteogenesis. This technology allows combinatorial studies of biomolecular and biophysical cues in 3D, making it suitable for applications in mechanobiology and bioengineering.

Repeated application of herbicides like 2,4-dichlorophenoxyacetic acid (2,4-D) in agriculture poses a significant environmental threat and health risk to non-target biota. <i>Cupriavidus</i> sp. strain DSPFs, isolated from Indian agricultural soil, utilizes 2,4-D and various other aromatics as the sole source of carbon and energy. It efficiently degrades high concentrations of 2,4-D (up to 0.3% wt/vol, i.e., 3,000 ppm) within 24 h with a maximum degradation rate of 105 mg L^-1 h^-1. Based on enzyme activity, whole-cell oxygen uptake, high-performance liquid chromatography (HPLC), and liquid chromatography-mass spectroscopy (LC-MS/MS) analyses, the strain was proposed to metabolize 2,4-D via 2,4-dichlorophenol (2,4-DCP) and 3,5-dichlorocatechol <i>ortho</i> ring-cleavage pathway. The key enzyme, 2,4-DCP monooxygenase (24DCPM), was purified to homogeneity and found to be homotetrameric with a native molecular mass of ~255 kDa with ~3.9 mol of FAD per mol of native protein. The enzyme exhibited high catalytic efficiency (<i>K</i>_cat/<i>K</i>_m) of 4.5 and 6.6 µM^-1 s^-1 with NADH and NADPH, respectively. Strain also displayed various plant growth-promoting traits like production of indoleacetic acid, ammonia, siderophores and mineral solubilization. Priming of <i>Vigna radiata</i> (mung bean) seeds with strain enhanced (30-47%) growth of seedlings in non-contaminated soil microcosms, indicating plant growth-promoting potential of the strain. Seed priming with strain significantly reduced 2,4-D toxicity to mung bean seedlings, suggesting the phytoprotective abilities of the strain. Bio-augmentation of 2,4-D-contaminated soil with strain DSPFs could remove >95% of 2,4-D (100 ppm) in 4 days with a degradation rate of 91 mg kg^-1 day^-1. <i>Cupriavidus</i> sp. DSPFs is a promising candidate for the eco-friendly clean-up of agricultural fields and enhancing crop productivity.<h4>Importance</h4>An agricultural soil isolate, <i>Cupriavidus</i> sp. strain DSPFs, is capable of degrading 2,4-dichlorophenoxyacetic acid (2,4-D), a widely used herbicide having deleterious effects on non-target crop plants and other biota. Strain DSPFs efficiently degrade relatively high concentrations of 2,4-D in minimal growth medium as well as in contaminated soil. This efficient degradation by strain can be attributed to the enhanced catalytic efficiency (low <i>K</i>_m and high <i>V</i>_max) of key enzyme 2,4-dichlorophenol-6-monooxygenase (2,4-DCPM). Strain DSPFs mitigate the toxicity caused by 2,4-D to crops and also promote plant growth. This tri-functional (bioremediator-phytoprotecting-plant growth promoting) bacterium has significant potential in the eco-friendly remediation of 2,4-D in agricultural fields to prevent groundwater contamination, reduce phytotoxicity of herbicides, and enhance crop productivity.

The lysosomal damage response is important for the maintenance of cellular homeostasis in human cells. Although the mechanisms underlying the repair and autophagic elimination of damaged lysosomes have been elucidated, the early signal transduction pathways and genes induced in response to lysosomal damage remain elusive. We performed transcriptome and proteome analyses and found that the TAB-TAK1-IKK-NF-κB axis is activated by K63-linked ubiquitin chains that accumulate on damaged lysosomes. This activates the expression of various transcription factors and cytokines that promote anti-apoptosis and intercellular signaling. The findings highlight the crucial role of ubiquitin-regulated signal transduction and gene expression in cell survival and cell-cell communication in response to lysosomal damage. The results suggest that the ubiquitin system is not only involved in the removal of damaged lysosomes by lysophagy, but also functions in the activation of cellular signaling for cell survival.

Glioblastoma (GBM) is the most malignant primary brain tumor in adults, with glioma stem cells (GSCs) as a subpopulation contributing to treatment resistance and recurrence. This study investigates the role of lactate and its regulatory gene, vaccinia-related kinase 1 (VRK1), in the regulation of GSC stemness. Utilizing multiple glioma-related databases and patient-derived GSCs, it is discovered that lactate enhances the stemness and proliferation of GSCs via VRK1. Mechanistically, lactate promotes histone lactylation (H3K18la) at the VRK1 promoter in GSCs, thereby upregulating VRK1 expression. VRK1 enhances Y-box binding protein 1 (YBX1) protein stability by inhibiting its ubiquitination and degradation, and phosphorylates YBX1 to promote its nuclear translocation, thereby regulating GSC stemness and proliferation via the YBX1/SOX2 pathway. Additionally, the VRK1-targeted nanoliposome A/TMZ-siVRK1 effectively suppresses the stemness and proliferation of GSCs, demonstrating its therapeutic potential. In conclusion, lactate regulates the stemness and proliferation of GSCs via the H3K18la/VRK1/YBX1/SOX2 pathway. This study elucidates the role of histone lactylation in stem cell regulation and suggests that VRK1 is a potential therapeutic target for GBM.

The retina is uniquely enriched in polyunsaturated fatty acids (PUFAs), primarily localized in cell membranes, where they govern membrane biophysical properties. During aging, alterations in lipid metabolism lead to reduced content of very long-chain PUFAs (VLC-PUFAs) in the retina, which is associated with normal age-related reductions in contrast sensitivity, diminished photoreceptor function and delayed rod-mediated dark adaptation recovery, and pathological age-related macular degeneration (AMD). <i>ELOVL2</i> (<i>elongation of very long chain fatty acids-like 2</i>) encodes a transmembrane protein that produces precursors to docosahexaenoic acid (DHA) and VLC-PUFAs. The methylation status of the <i>ELOVL2</i> promoter is currently one of the best predictors of chronological age. Here, we show that lower VLC-PUFA abundance in the aged mouse retina is accompanied by a reduction in visual function. Similarly, mice lacking ELOVL2-specific enzymatic activity (<i>Elovl2^C234W</i>) demonstrate reduced contrast sensitivity and slower rod-mediated dark adaptation. Intravitreal supplementation with the direct product of ELOVL2, 24:5n-3, in aged animals improved visual function for up to 4 weeks and reduced accumulation of APOE- and C3d-positive sub-RPE deposits. The gene expression pattern observed in supplemented retinas exhibited a partial rejuvenation profile, including decreased expression of aging-related genes and a transcriptomic signature resembling younger retinas. Last, human genetic data from the IAMDGC and UK Biobank linked two variants in the <i>ELOVL2</i> locus with the onset of intermediate AMD, underlining the translational importance of our findings. Our work highlights VLC-PUFA supplementation as a potential therapeutic opportunity and defines ELOVL2 as a promising target for interventions to prevent age-related vision loss.

This study investigated the effects of diesel particulate matter (DPM) on multiple human organs using 3D spheroids derived from eight human primary cell types. To assess the impact of DPM, we exposed these spheroids to varying concentrations of standardized DPM (Standard Reference Material, SRM 2975) and measured their viability, followed by proteomic analysis using tandem mass tag (TMT) labeling with liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 9,707 proteins were identified, with 128 proteins exhibiting statistically significant changes (P-value < 0.05) in response to DPM exposure, as determined by two-way analysis of variance (ANOVA). Among these, five proteins, including apolipoprotein A-I (APOA1), significantly increased at higher DPM concentrations, while 36 proteins, primarily ribosomal proteins, showed notable decreases even at lower DPM levels. Canonical pathway analysis revealed activation of acute phase response signaling, liver X receptor/retinoid X receptor (LXR/RXR), and farnesoid X receptor (FXR)/RXR pathways across all spheroid types. APOA1 was identified as a potential biomarker for DPM exposure, with increased expression potentially linked to disruption in protein degradation pathways. This study provides valuable insights into the systemic toxicity of DPM, highlighting key proteomic changes across different tissue types and identifying potential biomarkers that could be used to assess exposure levels and health risks related to particulate matter.

Sarcoidosis is characterized by the proliferation of noncaseating granulomas and presents as a complex chronic inflammatory disease. It extensively affects multiple organ systems, with 30-60% of patients experiencing ocular complications, predominantly bilateral granulomatous uveitis. Fatty acid degradation, a fundamental metabolic process, is crucial for cellular energy homeostasis, involving the breakdown of fatty acids to produce acetyl-CoA, NADH, and FADH2, which then enter the citric acid cycle and electron transport chain to generate ATP. Despite its importance, the role of fatty acid degradation genes (FADGs) in the pathophysiology of Ocular sarcoidosis (OS) remains unclear. To identify candidates potentially involved in OS, we intersected differentially expressed genes (DEGs) with a curated list of 177 FADGs. Advanced methodologies, including Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA), were employed to explore biological functions. Further refinement using Lasso regression and Support Vector Machine-Recursive Feature Elimination (SVM-RFE) allowed for the identification of key hub genes and assessment of their diagnostic potential for OS. Our investigation identified two FADGs, ADH1B and ECI1, closely associated with OS. Functional analyses revealed their involvement in processes such as fatty acid metabolic processes, small molecule catabolic processes, and fatty acid oxidation. Importantly, the diagnostic capabilities of these FADGs demonstrated significant efficacy in distinguishing OS from unaffected states. Through rigorous bioinformatics analyses, this study identifies ADH1B and ECI1 as novel biomarker candidates for OS, elucidating their potential roles in the disease's pathogenesis. These findings offer new insights into the molecular mechanisms underlying OS and highlight the diagnostic potential of FADGs in differentiating OS from unaffected conditions.

In this study, bovine cortical bone was investigated under plasma treatment process to investigate the potential for improvements in their structural characteristics. The bone specimens were treatment with low pressure argon cold plasma at different treatment times; 15, 30, and 45 min. Various techniques such as X-ray diffraction, scanning electron microscopy, surface roughness testing and automatic LCR Bridge were utilized to study the plasma-induced modifications on the structural and dielectric properties of the bone. SEM images revealed the elimination of some outer atoms from the bone surface during the 30-minute plasma ablation process, leading to more noticeable grain size of hydroxyapatite. XRD measurements confirmed the obtained results as mentoring the changes in crystallite size and strain parameters. As the treatment time approached 45 min, crystallite size increased, along with surface roughness parameters and relaxation time. These findings contribute to a better understanding of the microstructural and morphological changes occurring on the bone surface during cold argon plasma treatment.

Chimeric antigen receptor (CAR) T cells are highly effective in haematological malignancies¹. However, progressive loss of CAR T cells contributes to relapse in many patients^2-4. Here we performed in vivo loss-of-function CRISPR screens in CAR T cells targeting B cell maturation antigen to investigate genes that influence CAR T cell persistence and function in a human multiple myeloma model. We tracked the expansion and persistence of CRISPR library-edited T cells in vitro and at early and late time points in vivo to track the performance of gene-modified CAR T cells from manufacturing to survival in tumours. The screens revealed context-specific regulators of CAR T cell expansion and persistence. Ablation of RASA2 and SOCS1 enhanced T cell expansion in vitro, whereas loss of PTPN2, ZC3H12A and RC3H1 conferred early growth advantages to CAR T cells in vivo. Notably, we identified cyclin-dependent kinase inhibitor 1B (encoded by CDKN1B), a cell cycle regulator, as the most important factor limiting CAR T cell fitness at late time points in vivo. CDKN1B ablation increased CAR T cell proliferation and effector function, significantly enhancing tumour clearance and overall survival. Our findings reveal differing effects of gene perturbation on CAR T cells over time and in different environments, highlight CDKN1B as a promising target to generate highly effective CAR T cells for multiple myeloma and underscore the potential of in vivo screening for identifying genes to enhance CAR T cell efficacy.

To investigate transcriptomic signatures of Parkinson's disease (PD) and the Parkinsonian subtype of Multiple System Atrophy (MSA-P) in substantia nigra pars compacta (SNpc), we conducted transcriptome analysis using in-situ hybridization on paraffin-embedded SNpc tissues from post-mortem brains. The study included 2 MSA-P patients, 2 PD patients, and 2 healthy controls (HC), with 12 regions of interest (ROIs) selected from the dorsal to ventral and medial to lateral aspects of the SNpc. A total of 72 ROIs from 6 participants were analyzed, and differentially expressed genes (DEGs) were identified by comparing MSA-P, PD and HC groups. The MSA-P group showed 88 upregulated DEGs and 326 downregulated DEGs (adjusted 𝑝<0.05) compared to HC. The downregulated DEGs were significantly enriched in pathways related to ribosomal translation, immune processes, mitochondrial function, and autophagy. Notably, the dorsomedial quadrant was uniquely linked to antigen presentation, while other quadrants showed downregulation of protein synthesis. The PD group exhibited 165 upregulated DEGs and 350 downregulated DEGs (adjusted 𝑝<0.05) compared to HC, with downregulated DEGs associated with ribosomal translation, mitochondrial function, and the ubiquitin-proteasome system. In both MSA-P and PD, the upregulated DEGs were not associated with any pathways or biological process in gene enrichment analysis. In network propagation analysis, amyloid precursor protein was the most significant network hub among DEGs in both MSA-P and PD. Comparing the transcriptomic signatures of SNpc between MSA-P and PD, we found immune/inflammation, mitochondrial function and neural signaling related genes were significantly downregulated in MSA-P compared to PD. Overall, the transcriptomic signature of the SNpc in MSA-P and PD revealed overlapping but distinct features, including alterations in protein synthesis, immune processes, mitochondrial function, and protein degradation systems. Future studies with larger cohorts and functional validation are needed to further elucidate these findings.

<h4>Background</h4>Alzheimer's disease (AD) is characterized by accumulation of amyloid-β (Aβ) plaques, tau neurofibrillary Tangles and synaptic dysfunction. The aim of this study was to map the distributions of synaptic vesicle protein 2A (SV2A) and other synaptic proteins in the brain and the brain-derived extracellular vesicles (BDEVs) of AD patients, analyze their associations with Aβ, tau, and the apolipoprotein E (APOE) ε4 allele, and investigate the biological role of SV2A.<h4>Methods</h4>Mass spectrometry-based proteomics of BDEVs and immunohistochemistry staining were conducted on postmortem brain samples from 57 AD patients and 48 nondemented controls. The levels of SV2A, synaptophysin (SYP), and other synaptic proteins in the brain tissues and the BDEVs, and their associations with Aβ, tau (phospho-tau and Braak stages), other proteins and the APOE ε4 allele, were analyzed.<h4>Results</h4>SV2A levels were significantly lower in AD patients than in nondemented controls, particularly in the hippocampus and entorhinal cortex. APOE ε4 carriers presented further reductions in SV2A levels compared with noncarriers. The SV2A levels in BDEVs and brain tissues were positively correlated with SYP levels and negatively correlated with Aβ and phospho-tau levels. Reductions in SV2A were associated with decreased levels of other synaptic proteins, such as synaptotagmins, GAP43, and SNAP25. SV2A emerged as a central hub with interactions with proteins from subnetworks related to synaptic vesicle formation and fusion.<h4>Conclusion</h4>SV2A levels in brain tissues and BDEVs are reduced in AD patients, particularly in those carrying the APOE ε4 allele, and are correlated with Aβ and tau pathologies. SV2A may serve as a valuable biomarker for monitoring synaptic dysfunction and progression in AD.

Hemolysis and the downstream consequences of cell-free hemoglobin (Hb) and heme contribute to the development of sickle cell disease pulmonary hypertension (SCD-PH). The plasma concentrations of Hb and heme scavenger proteins haptoglobin (Hp) and hemopexin (Hpx) in sickle cell patients are observed to be significantly lower than healthy donors. The unchecked exposure to Hb and heme contribute to vasculopathy and aberrant cardiac function. This is consistent with vascular remodeling co-localized within iron rich macrophages. Based on these observations in patients, we hypothesize that a joint Hb and heme scavenger approach, combining Hp + Hpx as a therapeutic will attenuate hemolysis driven SCD-PH progression in a SCD mouse model. To test the hypothesis, we utilized our validated Berk-SS mouse model of SCD-PH driven by a 10-week moderate hypoxia exposure and weekly subcutaneous administration of Hp + Hpx. At study termination, we analyzed changes in cardiopulmonary iron deposition, right ventricular and pulmonary functional parameters, and multi-omic indices associated with SCD-PH. Our data demonstrates that Hp+Hpx improves pulmonary vascular resistance and right ventricular function including stiffness, afterload, cardiac output, ventricular to vascular coupling ratio, pulmonary vascular resistance and medial hypertrophy. Histological evaluation of lung and right ventricular tissue demonstrates attenuation of cardiopulmonary pathology. Finally, a multi-omic analysis of whole lung and heart tissue demonstrates a rebalancing of proteins related to PH, iron, inflammation, and oxidative stress. This data provides strong pre-clinical evidence for the clinical study of combined Hb and heme scavenger proteins in the treatment of PH-associated SCD.

Condensin-mediated loop extrusion is thought to be one of the primary mechanisms underlying mitotic chromosome assembly. However, how this process is affected by other chromosomal proteins, such as histones, is not well understood. Our previous study showed that in Xenopus egg extracts codepleted of topoisomerase IIα and the histone chaperone Asf1, a highly characteristic chromatin structure called the "sparkler" is assembled. The sparkler is a compact structure assembled on nucleosome-free, entangled DNA in which multiple protrusions radiate from a core. Interestingly, condensin I is concentrated at the tips of the protrusions, whereas the linker histone H1.8 is enriched in the remaining regions of the structure. To understand the biophysical mechanisms underlying sparkler assembly, we construct a model predicting that DNA loops extruded from the entangled DNA undergo phase separation into two domains: loops enriched in condensin I remain as protrusions, whereas those enriched in H1.8 are reeled into the central region. We propose that H1.8 competes with condensin I for DNA binding, thereby reorganizing DNA loops formed by condensin I under this specialized condition.

This study explores the impact of mutations in the exon 2 of the von Hippel-Lindau (VHL) gene, associated with erythrocytosis or von Hippel-Lindau disease. We analyzed 15 missense and synonymous genetic variants to assess their effects on splicing and VHL protein stability. Using in silico predictions and functional assays, we found that some specific mutations impact splicing and reduce protein stability, allowing their clinical classification as pathogenic. This study revealed exonic-splicing regulatory regions. Notably, by performing RNA-protein pull-down, we identified two RNA-binding proteins, hnRNPF and hnRNPAB, as key regulators of VHL splicing. Our findings reveal the limitations of current splicing-prediction tools in recognizing exonic-splicing enhancer (ESE) or silencer (ESS) sequences and suggest that mutations can differentially affect disease phenotypes by influencing both splicing and protein stability. These insights enhance our understanding of the molecular mechanisms underlying VHL-associated disorders and expand the landscape of regulatory elements and protein factors involved in VHL splicing regulation.

Extreme human lifespan, exemplified by supercentenarians, presents a paradox in understanding aging: despite advanced age, they maintain relatively good health. To investigate this duality, we have performed a high-throughput multiomics study of the world's oldest living person, interrogating her genome, transcriptome, metabolome, proteome, microbiome, and epigenome, comparing the results with larger matched cohorts. The emerging picture highlights different pathways attributed to each process: the record-breaking advanced age is manifested by telomere attrition, abnormal B cell population, and clonal hematopoiesis, whereas absence of typical age-associated diseases is associated with rare European-population genetic variants, low inflammation levels, a rejuvenated bacteriome, and a younger epigenome. These findings provide a fresh look at human aging biology, suggesting biomarkers for healthy aging, and potential strategies to increase life expectancy. The extrapolation of our results to the general population will require larger cohorts and longitudinal prospective studies to design potential anti-aging interventions.

Chronic demyelination is a hallmark of multiple sclerosis (MS) and is associated with increased seizure susceptibility. In this study, we used the cuprizone (CPZ) diet induced demyelination model to investigate the progression of hippocampal demyelination and its impact on seizure activity and neurotransmitter dysregulation. Using EEG recordings, immunohistochemistry, Western blotting, ELISA, Golgi staining, and NanoString transcriptomics, we found progressive hippocampal demyelination accompanied by a striking increase in seizure incidence, from 38 % at 6 weeks to 88 % by 12 weeks. Structural degeneration of the CA1 pyramidal layer was marked by reduced dendritic arborization and loss of parvalbumin interneurons. Hippocampal glutamate levels increased as early as 3 weeks and remained elevated, with values (∼2.2 μM) reaching excitotoxic thresholds, along with astrocyte reactivity (glial fibrillary acidic protein) and downregulation of astrocytic glutamate transporter-1, and glutamate aspartate Transporter-1 and modification of aquaporin-4 in CA1. Stratum pyramidal and stratum radiatum region-specific alterations in glutamate transporters and related enzymes (glutamine synthetase, glutamic acid decarboxylase 67, vesicular glutamate transporter 1), further supported neurotransmitter imbalance. Transcriptomic profiling revealed widespread downregulation of myelin, neuronal, astrocytic, glutamatergic, and GABAergic genes at 6 weeks, with partial recovery by 12 weeks. Together, these findings establish a mechanistic link between chronic hippocampal demyelination, glutamate dysregulation, and epileptogenesis offering potential molecular targets for therapeutic intervention in MS-associated epilepsy.

Acute kidney injury (AKI) is common in critically ill children and neonates and imparts an increased risk for morbidity and mortality. Despite a growing recognition of the untoward consequences of AKI, its management continues to rely on supportive care alone, after numerous clinical trials have failed to identify effective disease-modifying therapies. This failure to advance the field is likely due in large part to the heterogeneity of AKI, which demands a precision approach to diagnosis and management. Despite the emergence of several novel AKI biomarkers with the ability to refine the AKI diagnosis beyond what is afforded by changes in serum creatinine and/or urine output alone, widespread translation of these biomarkers to practice has been limited. In this review, we outline a roadmap for AKI risk-stratification, diagnosis, management, and follow-up that is rooted in precision medicine principles and feasible with the tools currently available in pediatric ICUs. This roadmap highlights the importance of dynamic (as opposed to static) assessment of the critically ill child with, at-risk for, and recovering from AKI, and introduces the concept of theragnostic biomarkers that are both the target of and change with treatment, thus helping guide the therapeutic approach. Finally, we highlight the need for re-defining appropriate endpoints in AKI clinical trials testing the interventions proposed here (and others) to ensure we are identifying treatments that will meaningfully improve outcomes for critically ill children with AKI.

Dipolar glass copolymers (DGCs) incorporating 9-anthrylmethyl methacrylate (ANMA) with dipolar monomers 2-(methylsulfonyl)ethyl methacrylate (SO₂MA) and 2-cyanoethyl methacrylate (CNMA) were synthesized <i>via</i> RAFT polymerization to develop high-performance dielectric materials with photo-responsive capabilities. Structural and spectroscopic analyses confirmed successful copolymer formation and anthracene incorporation, enabling ultraviolet (UV)-triggered functionalities. Thermal characterization revealed a significant increase in glass transition temperature (Δ<i>T</i> _g ≈ +28 °C) compared to their homopolymer counterparts, despite a moderate reduction in thermal stability. Dielectric measurements demonstrated high permittivity and low loss factors across a broad temperature range, with distinct γ, β, and α relaxation processes identified. Upon UV irradiation, anthracene photodimerization enabled efficient intramolecular cross-linking under dilute, oxygen-free conditions, leading to the formation of discrete single-chain nanoparticles (SCNPs) as confirmed by combined UV-visible spectroscopy, size-exclusion chromatography, and dynamic light scattering analyses. We explore, for the first time, the use of programmable nanoscale architectures to develop a new generation of single-chain high-dielectric nanomaterials. These materials exhibit high permittivity, relatively low dielectric losses, and suitable thermal properties in terms of glass transition temperature. Our results show that the localized environment and the reduction of long-range entanglements, arising from the collapse of linear DGC precursors into single-chain nanoparticles, do not significantly alter the dielectric response of these entities. As a result, they provide efficient dielectric materials with potential applications in energy storage, flexible electronics, sensors, and smart materials.

Attention deficit hyperactivity disorder (ADHD) is a prevalent neurodevelopmental condition that persists into late adolescence and even adulthood. While a lot of research has addressed the issues of childhood ADHD, manifestation of the condition in adults, particularly females, remains largely obscure. The aim of the present narrative review is to address the sex-specific subtleties of ADHD in adolescent and adult female populations and critically analyze the various intricately complex facets of the associated comorbidities and outcomes, based upon data extracted from scholarly works indexed in online databases (eg, PubMed, Google Scholar, etc). We provide evidences refuting the presumption that ADHD primarily affects men, highlighting the complexity of clinical outcomes and comorbidities, and the consequent misdiagnosis of women as a possible reason. Comprehensive critical assessment of the multiple aspects of psycho-socio-behavioral, cognitive, and other clinical outcomes and comorbidities associated with ADHD in women indicated widespread dysfunctions and atypical characteristics. Furthermore, we also propose the probable utilities of art-based and other unconventional behavioral therapeutic regimens as alternatives and/or additives for the therapy of female ADHD cases to address case- and gender-specific needs and induce an overall improvement in their functioning. While this is not an exhaustive review of the literature, we hope that our points of discussion will generate further interest among scientists, clinicians, and caregivers to address the age and gender specificity of the condition to advance our perspectives of the condition and eventually establish novel therapeutic measures for the same.

<h4>Background</h4>The glymphatic system is a crucial factor in the development of neurodegenerative diseases (NDs) and holds substantial promise for therapeutic strategies. However, despite its growing significance, detailed bibliometric investigations specifically targeting the interplay between the glymphatic system and NDs are still sparse. This study pioneers a comprehensive bibliometric analysis to delineate the intellectual framework and emerging trajectories in glymphatic system research associated with NDs.<h4>Materials and methods</h4>We conducted an exhaustive search of the literature on the glymphatic system and NDs using the Web of Science Core Collection (WoSCC), Scopus, and Pubmed Central (PMC) databases. VOSviewer was applied for bibliometric analysis and visualization to scrutinize geographical distribution, institutional distribution, inter-journal connections, and keyword prevalence. Additionally, CiteSpace was utilized to intuitively explore and analyze journal interactions and citation dynamics. The bibliometrix R package was employed to construct visualized networks of international collaborations, as well as the relationships among authors, keywords, and journals. Data visualization was further enhanced with the aid of the WPS Office.<h4>Results</h4>A total of 865 relevant publications were retrieved, covering 92 countries, 1,471 research institutions, and 367 academic journals. Over the past thirteen years, both the number of publications and citations related to the glymphatic system in NDs have shown a significant upward trend, with neuroscience being the primary research field. Chinese authors over the world published the largest number of articles, while China and United States rank the highest in terms of publication and citation counts, also both demonstrate extensive international collaboration. And the <i>Frontiers series journal</i> publishes the most papers in this field, while <i>Brain</i> is the most frequently cited journal. The University of Rochester is the top-producing institution with an internally well-known Chinese research group. Keyword analysis highlights the glymphatic system, Alzheimer's disease (AD), cerebrospinal fluid, and aquaporin 4 (AQP4) as core topics, with AQP4 polarization identified as a key regulatory factor for metabolic waste clearance. The main NDs under investigation are AD and Parkinson's disease (PD).<h4>Conclusion</h4>This study offers a comprehensive preliminary dissection of the research landscape, identifying current focal points and potential future directions in glymphatic system research related to NDs. By leveraging multiple bibliometric approaches, this study provides valuable insights into this burgeoning field.

The inflammatory bowel diseases (IBD), including Crohn's Disease and Ulcerative Colitis, are chronic, incurable disorders of the gastrointestinal tract. These multifactorial diseases pose an enormous burden on patients, clinicians, and public health systems worldwide. Zinc (Zn) is an essential micronutrient that is required for a wide variety of functions critical to maintaining gastrointestinal health. Zn homeostasis is facilitated by the SLC39/ZIP and SLC30/ZnT families of solute carrier proteins, which collectively distribute Zn with subcellular specificity. Disruptions in Zn homeostasis can have substantial impacts on health, as recent years have seen Zn transporters become increasingly recognized for their importance in health and disease. Although dietary Zn deficiency is rare in the United States, Zn deficiency is common among IBD patients. Disruptions in Zn homeostasis have also been shown to play a role in the progression of IBD. Despite these links, Zn supplementation trials in IBD have shown inconsistent results. This review focuses on the role of Zn and Zn transporters in the development, progression, and treatment of IBD, as well as discussing the challenges and potentially promising future of the study of Zn and Zn transporters in precision health.

Restrictive cardiomyopathy (RCM) is a rare form of heart muscle disease characterized predominantly by diastolic dysfunction and restrictive filling, for which no guideline-supported pharmacological treatment currently exists. We reviewed the clinical trial landscape for RCM to identify emerging therapeutic strategies and trends. Using the TrialTrove database, we identified 63 RCM-related clinical trials (2007-2024) after excluding studies of standard therapies or unrelated conditions. Our analysis shows that research interest in RCM has remained modest but steady, with many trials in early (Phase I) and late (Phase III/IV) stages. Transthyretin stabilizers, particularly tafamidis, accounted for a significant portion of these trials and have demonstrated improved cardiac function and outcomes in transthyretin amyloid cardiomyopathy (ATTR-CM). In addition, novel disease-modifying approaches - including antisense oligonucleotides, RNA interference therapies, and gene-editing strategies - are being explored in clinical trials, reflecting a shift towards targeted treatment of underlying causes. Approximately half of the identified trials have been completed, though a few were terminated early due to insufficient efficacy. These findings highlight a dynamic and evolving therapeutic landscape in RCM. While tafamidis has substantially advanced ATTR-CM management, emerging RNA-silencing and gene therapy techniques hold promise to address the unmet needs in RCM, warranting further large-scale studies to validate their safety and efficacy.

Diabetic cardiomyopathy (DCM) is a specific form of heart disease induced by diabetes, characterized by myocardial fibrosis, oxidative stress, metabolic dysregulation, and cardiomyocyte death. In recent years, circular RNAs (circRNAs), a novel class of non-coding RNAs, have gained increasing attention due to their unique covalently closed structure, high stability, and critical regulatory roles in various diseases. While extensive studies have been conducted on microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the context of DCM, research on circRNAs remains relatively limited and fragmented. Existing reviews often focus on specific aspects without providing a systematic and comprehensive overview. This review aims to summarize the current progress in circRNA research related to DCM, with a particular focus on the molecular mechanisms and regulatory networks through which circRNAs influence metabolic disorders, oxidative stress, myocardial fibrosis, and programmed cell death. In addition, the potential of circRNAs as diagnostic biomarkers and therapeutic targets is evaluated, along with an in-depth discussion of current challenges and future research directions. This work is intended to offer theoretical insights and reference value for both fundamental and translational studies of circRNAs in DCM.

Chronic inflammation, oxidative stress, and insufficient angiogenesis hinder wound healing in patients with diabetes, necessitating long-term management strategies. In this study, we developed pH-responsive hydrogel microneedles (LSI-GCA) based on <i>Lycium barbarum</i> polysaccharide stearate micelles that could achieve real-time pH monitoring and intelligent drug release for effective wound management. LSI-GCA was prepared through hydrophobic modification and isoliquiritigenin (ISO) loading, followed by its combination with a chitosan/anthocyanin backing layer. LSI-GCA exhibited excellent biocompatibility and antibacterial and antioxidant properties by activating the NRF2 pathway and inhibiting pro-inflammatory factors. Animal experiments confirmed that LSI-GCA significantly accelerated wound healing in a diabetic model and promoted angiogenesis, collagen deposition, and M2 macrophage polarization. Genomic and network pharmacological analyses revealed a multi-target synergistic mechanism involving the modulation of EGFR/VEGF signaling to promote proliferation, inhibition of inflammatory pathway (NF-κB), and repair of DNA damage through upregulation of BRCA1/2. This study provides an integrated "monitoring-treatment" strategy for diabetic wounds, offering great potential for clinical transformation and personalized treatment.

Neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease, multiple sclerosis, and amyotrophic lateral sclerosis share converging mechanisms of neuronal dysfunction, including protein aggregation, oxidative stress, and chronic neuroinflammation. Glial cells, once considered passive supporters, are now recognized as central drivers of these processes, offering both pathogenic triggers and therapeutic opportunities. Yet, despite compelling preclinical evidence, the translation of glial-targeted therapies into clinical success has been limited. This review provides a critical synthesis of current knowledge by examining therapeutic strategies through the lens of their translational challenges and failures. This narrative review highlights how interspecies variability of glial phenotypes, shifting neuroprotective versus neurotoxic states, limited biomarker stratification, and delivery barriers have constrained trials, such as anti-triggering receptor expressed on myeloid cells 2 (anti-TREM2) antibodies in AD and glial cell line-derived neurotrophic factor (GDNF) in PD. By analyzing these obstacles across major neurodegenerative disorders, this review argue that the next stage of glial medicine requires precision approaches that integrate stage-specific phenotyping, biomarker-guided patient selection, and innovative delivery platforms. Understanding not only what has been tried but why translation has stalled is essential to chart a roadmap for effective, disease-modifying glial therapies in the aging brain.

Peripheral nerve injuries (PNIs) present significant clinical challenges, often leading to severe motor, sensory, and autonomic dysfunction, with profound impacts on patient quality of life and considerable healthcare costs. This review synthesizes current knowledge on the therapeutic potential of Pulsed Electromagnetic Fields (PEMF) and Low-Intensity Pulsed Ultrasound (LIPUS) as non-invasive modalities for promoting peripheral nerve regeneration. We explore their cellular and molecular mechanisms of action, discuss optimal treatment parameters, and present evidence from preclinical and clinical studies, including their synergistic effects with other therapies and emerging applications beyond neurological repair. Clinical studies have shown that PEMF therapy can significantly reduce neuropathic pain and improve functions, whereas LIPUS demonstrates the ability to enhance nerve conduction.

The secretome of mesenchymal stromal cells (MSCs) can efficiently stimulate regeneration and therefore is a tempting remedy for "cell-free cellular therapy". However, the usage of primary MSC cultures as secretome producers for translation studies has obvious obstacles, including the rapid aging of MSC cultures, the need for a large number of verified donors, and donor-to-donor variability of secretome content. MSCs immortalization makes it possible to overcome those limitations and to obtain secretome-producing cultures with a prolonged lifetime. However, the efficacy and safety of such secretomes are critical issues that limit their usage as therapeutic agents. In this study, we tested in large detail how the immortalization of MSC cultures affects the content, biological activity and safety of their secretome. MSCs immortalization via the overexpression of human <i>TERT</i> gene does not significantly alter the qualitative and quantitative composition of their secretome or its activity according to the results of proteomic analysis, ELISA, qPCR and functional tests in vitro. Moreover, we have demonstrated that the secretome of immortalized MSCs does not contain detectable amounts of telomerase and does not possess any transforming activity. Altogether, our data suggest that immortalized MSC cultures may become a reliable source for obtaining standardized active secretome in large-scale quantities for clinical use.

Considering the increased risk of cognitive deficits and mood disorders programming associated with bisphenol exposure, we used a preclinical model to identify short- and long-term effects of early exposure to Bisphenol A (BPA) and its replacement, Bisphenol S (BPS), on the central cholinergic and serotonergic systems. Wistar female and male rats born to dams exposed to BPA or BPS (both at 10 μg/kg/day or 50 μg/kg/day) during pregnancy and lactation were euthanized at weaning or adulthood. Cholinergic and serotonergic biomarkers were assessed in the frontal cortex and pons + medulla oblongata. BPA and BPS disrupted these systems, with outcomes depending on the specific bisphenol, biomarker, and time point. Effects also varied across brain regions and between sexes. The nicotinic cholinergic receptor showed more pronounced alterations than the presynaptic choline transporter. Both serotonergic receptors-5-HT1AR and 5-HT2R-were affected; however, the serotonergic transporter remained unchanged. Increased binding was the predominant effect for both systems. Maternal exposure to BPA, even at low doses, induces sex-dependent short- and long-term changes in the cholinergic and serotonergic systems of the progeny. BPS affects these same neurotransmitter systems, although leading to compound-specific outcomes. These results pose both BPA and BPS as neurotoxicants that compromise neurodevelopment and program disorders later in life.

Osteosarcoma (OS) is the most common bone-based cancer in both the US and the world in children, teenagers, and young adults. It is an aggressive form of sarcoma which forms mainly in the long bones of the legs and arms, often metastasizing prior to diagnosis. Every year across the globe, there are approximately 28,000 new cases, yet this sarcoma remains difficult to manage with standard treatments, partly due to its solid and immune resistant tumor microenvironment (TME). The quantity of research conducted on OS because of these difficulties has greatly increased over the past decade, meaning a comprehensive review of new findings on the TME may prove beneficial. This article aims to give a broad overview of the components of the TME of osteosarcoma, discuss its resistances and detrimental effects, and illustrate current and future immune therapy treatments which effectively target the microenvironment. Additionally, it will seek to highlight any knowledge gaps in the current literature and propose further studies to improve clinical outcomes. These studies could be beneficial in increasing drug and treatment efficacy for OS.

Background In atopic dermatitis (AD), allergen-specific IgE (sIgE) antibodies is considered to play an important role in the disease's pathogenesis and could be used to identify triggers. However, the association between sIgE and clinical and sub-clinical characteristics of AD varies according to different allergens and different countries. Aim This study aims to assess sIgE antibodies and their association with clinical and sub-clinical characteristics of Vietnamese children with AD. Methods This descriptive cross-sectional study was conducted among 160 children aged 2 to 12 years old, diagnosed with AD based on Hanifin and Rajka's criteria. sIgE antibodies were measured by the EUROLINE Immunoblot test. Results sIgE positivity to at least one allergen was detected in 119 out of 160 (74.4%) children. The top two positive allergens were food allergens (88/160, 55%), and house dust mite allergens (64/160, 40%). sIgE antibodies were more often positive in children with a high tIgE level (p=<0.001), children with a family history of atopic diseases (p=<0.001), and children with moderate and severe AD (p=0.037). sIgE positivity to food allergens was more common in children in the younger age group than children in the middle and oldest age groups (p=<0.001), while sIgE positivity to house dust mite allergens was more common in children in the older age group (p=0.025). Food allergens were more often positive with moderate and severe AD (p=0.01). Limitations The participants did not represent all children with AD attending the National Hospital of Dermatology and Venereology, as we used a convenience sample and excluded those whose parents/guardians declined to participate. In addition, some information, such as medical history, was only obtained from the parent/guardian report. This information may lack reliability. Conclusions Given the high incidence of sIgE antibody positivity and its association with family history of atopic diseases, age, disease severity, and tIgE in Vietnamese children with AD, it would be worthwhile to assess allergen-specific IgE antibodies when there is clinical suspicion of an allergen trigger to advise on allergen avoidance for preventing the exacerbation of AD.

Gastrointestinal stromal tumors (GISTs) are very common mesenchymal neoplasms involving the gastrointestinal tract. Despite having a uniform nuclear morphology, they can show varied histological subtypes. The prognosis is based on tumor size, mitotic rate and location of the tumor. Some cases of GIST can however show marked nuclear pleomorphism. Here we report a case of GIST with marked nuclear pleomorphism without other high-grade features. This case highlights the importance of nuclear pleomorphism and its implications in the perspective of existing prognostic criteria.

Poultry and cattle are the major reservoirs of <i>Campylobacter</i> infection in humans. However, no information is available on <i>Campylobacter</i> spp. in cattle in Mongolia. Thus, this study aimed to assess their prevalence and antimicrobial resistance. Between 2019 and 2023, rectal swabs were collected from cattle on dairy farms around Ulaanbaatar city and in total, 35 <i>Campylobacter</i> spp., including 23 <i>C. jejuni</i>, 7 <i>C. hyointestinalis</i>, 4 <i>C. fetus</i>, and 1 <i>C. lari</i>, were isolated. Multilocus sequence typing of <i>C. jejuni</i> cattle isolates revealed substantial genetic diversity and identified 7 sequence types (STs) including ST61, which is known to be associated with cattle and sheep. Interestingly, the antimicrobial resistance patterns of the <i>C. jejuni</i> cattle isolates completely differed from those of previously reported chicken isolates. Excluding one ciprofloxacin-resistant isolate, all isolates were susceptible to tetracycline and ciprofloxacin. This is the first report on the characterization of <i>Campylobacter</i> spp. in cattle in Mongolia. Although no official statistics of human campylobacteriosis are currently available in Mongolia, data on <i>Campylobacter</i> spp. in food-producing animals represent valuable information for investigating potential sources and infection routes to humans.

Animal slaughtering causes the cessation of oxygen delivery and that of nutrients such as cystine, glucose and others to muscle cells. In muscle cells, the changes in oxygen level and pH cause mitochondria, the endoplasmic reticulum, xanthine oxidase and uncoupled NOS to increase the level of O₂^•-, affecting the generation of H₂O₂ and the release of iron ions from ferritin. The activation of enzymes that remove and dislocate fatty acids from the membrane affects the sensitivity of muscle cells to peroxidation and ferroptosis. Increasing PUFAs in membrane phospholipids, by feeding animals a diet high in w-3 fatty acids, is a driving factor that increases lipid peroxidation and possible muscle ferroptosis. The activation of lipoxygenases by ROS to Fe³⁺-lipoxygenase increases hydroperoxide levels in cells. The labile iron pool generated by a "redox cycle" catalyzes phospholipid hydroperoxides to generate lipid electrophiles, proximate executioners of ferroptosis. Ferroptosis in food muscle cells is protected by high concentrations of vitamin E and selenium. In fresh muscle cells, glutathione peroxidase (GSH-PX) and other endogenous antioxidant enzymes are active and prevent lipid peroxidation; however, muscle heating eliminates enzymatic activities, making cells prone to high non-enzymatic lipid peroxidation. In muscle cells, coupled myoglobin and vitamin E act as a hydroperoxidase, preventing the generation of lipid electrophiles. Free iron ion chelators or effectors such as deferoxamine, EDTA, or ceruloplasmin are strong inhibitors of muscle cell lipid peroxidation, proving that muscle ferroptosis is mostly dependent on and catalyzed by the labile iron redox cycle.

The global rise in high-fat diet (HFD) consumption and obesity has raised concerns about their long-term effects on brain health. This review addresses how HFDs, including ketogenic diets (KDs), influence the central nervous system (CNS) and may contribute to neurodegenerative processes. The findings show that prolonged HFD exposure is associated with altered brain metabolism, increased oxidative stress, neuroinflammation, and impaired synaptic plasticity, particularly in regions like the hippocampus and hypothalamus. These changes may affect cognitive function and accelerate neurodegenerative mechanisms linked to disorders such as Alzheimer's and Parkinson's disease. While certain types of KD appear to exert neuroprotective effects-such as improved motor outcomes in experimental Parkinson's disease models-evidence remains inconsistent, and concerns about their long-term safety persist. This review emphasizes that the impact of high-fat nutrition on the CNS depends on fat type, exposure duration, and individual factors such as age and sex. Overall, further research is needed to distinguish between harmful and potentially therapeutic dietary fat patterns and to better understand their influence on brain health across the lifespan.

<h4>Background</h4>The pathogenesis of lipodystrophy in people living with HIV (PLWHIV) receiving antiretrovirals appears to be multifactorial and may involve genetic factors; however, it is not yet fully understood. We verified the association between single nucleotide polymorphisms in the APOC3-rs2854116, ESR2-rs3020450, HFE-rs1799945 and MMP1-rs1799750 genes and lipodystrophy and its subtypes in PLWHIV receiving antiretroviral.<h4>Methods</h4>Design: cross-sectional study. Lipodystrophy definition was based on self-report. Genotyping of the polymorphisms was performed using real-time polymerase chain reaction.<h4>Results</h4>Lipodystrophy was reported in 204/404 participants (51%), being 89/204 with mixed lipodystrophy, 72/204 with lipohypertrophy, and 43/204 with lipoatrophy. There was no association between APOC3, HFE, and MMP1 polymorphisms and lipodystrophy. The frequency of AA genotype (<i>p</i>=0.004/OR=3.33/CI=1.52-7.29) and of A allele (<i>p</i>=0.031/OR=1.72/CI=1.08-2.75) of the ESR2 polymorphism was higher in individuals with lipoatrophy compared to those without lipodystrophy. In the multivariate analysis, viral load >40copies/mL (<i>p</i>=0.037/OR=2.52/CI=1.03-6.91) and current use of zidovudine (<i>p</i>=0.007/OR=2.97/CI=1.32-6.54) were associated with lipoatrophy.<h4>Conclusion</h4>Participants with lipoatrophy had higher frequency of the AA genotype and the A allele of the ESR2-rs3020450 polymorphism. In addition, viral load >40 copies/mL and current use of zidovudine were associated with lipoatrophy, suggesting a potential involvement of this genetic variant in the pathogenesis of lipoatrophy in PLWHIV receiving antiretroviral.

The innate immune system plays a dual role in both mediating pathogenic processes following tissue damage and acting as a barrier to effective therapeutic delivery. Strategies that evade immune clearance while modulating host immune components offer promising solutions for treating complex chronic diseases, such as fibrosis. Here, an innate immune checkpoint material-based strategy is presented in which mesenchymal stromal cells, coated with a soft conformal microgel and functionalized with the CD47 self-marker agonist, effectively evade clearance by tissue resident macrophages. These engineered cells reverse persistent fibrotic damage in the lungs through a paracrine mechanism. Single-cell RNA sequencing identifies a transitional antigen-presenting macrophage subpopulation that mediates these reparative effects. By combining immune cloaking with the presentation of local signals encoded in the gel coatings, this strategy can be used to design secretory cells for long-term tissue remodeling, enabling a living pharmacy for chronic tissue damage.

<h4>Background</h4>Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a cytosine-adenine-guanine (CAG) repeat expansion in the huntingtin gene. The disease exhibits sex-related differences in symptomatology and disease progression, but the effect on brain structural biomarkers and the interaction between sex and CAG-age product score (CAPS), a widely used index combining the effect of CAG expansion and age, remains underexplored.<h4>Objective</h4>The aim of this study was to investigate the interplay between sex and CAPS on clinical measures and neuroimaging biomarkers in HD.<h4>Methods</h4>We retrospectively analyzed data from Enroll-HD, TRACK-HD/ON, PREDICT-HD, and IMAGE-HD studies, including a combined dataset of 19,738 participants with CAG ≥ 40. Linear mixed models were employed to evaluate the influence of sex and the sex-CAPS interaction on clinical evaluations, including Unified HD Rating Scale (UHDRS) UHDRS and Problem Behaviors Assessment, and neuroimaging biomarkers (striatal volumes and cortical thickness), while controlling for covariates.<h4>Results</h4>Female participants exhibited less pronounced striatal atrophy and cortical thinning with increasing CAPS (caudate: βmale/female = -3.449/-2.931, P = 0.05; putamen: βmale/female = -4.770/-3.902, P < 0.01). Regarding clinical measures, females experience greater motor decline with increasing CAPS (total motor score: βmale/female = 3.008/3.230, P < 0.0001), greater cognitive decline (symbol digit modalities test: βmale/female = -34.52/-38.57, P < 0.0001), and greater functional decline (total functional capacity: βmale/female = -6.413/-6.783, p < 0.05; Independence Scale: βmale/female = -32.26/-34.85, P < 0.001).<h4>Conclusions</h4>The sex-CAPS interaction significantly impacts both clinical and neuroimaging biomarkers of HD, underscoring the importance of incorporating sex-specific considerations into the clinical staging and management of HD. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Colorectal cancer (CRC) remains a significant global health challenge, ranking third in incidence and second in mortality among cancers worldwide. This review addresses the complex landscape of CRC, focusing on incidence, mortality trends, preventive strategies, and the evolving therapeutic approaches, particularly highlighting the role of platinum-based drugs like oxaliplatin (OXP). It also underscores the increasing burden of CRC, with factors such as westernized diets, aging populations, and genetic predispositions contributing to its prevalence. Therapeutically, early detection greatly enhances survival rates, emphasizing the importance of regular colonoscopies and stool tests. For advanced CRC, chemotherapy remains pivotal, with OXP as a cornerstone treatment despite its associated chemotherapy-induced peripheral neurotoxicity (CIPN). The review explores innovative strategies to overcome challenges related to chemotherapy, such as drug resistance and side effects, highlighting recent developments in the field, such as Pt(IV) prodrugs and immunotherapeutic approaches to enhance efficacy while minimizing toxicity. Additionally, this manuscript examines experimental models for drug screening, emphasizing the role of murine models and advanced 3D <i>in vitro</i> systems in CRC research. Overall, the review advocates for a comprehensive approach, integrating prevention, early detection, and personalized treatments to alleviate the global burden of CRC.

Many neurodegenerative diseases, including Alzheimer's (AD), Parkinson's (PD), and Huntington's disease (HD), are associated with proteinaceous deposits in the brain comprising amyloid. The aggregation process leading to these deposits proceeds through a variety of intermediates, i.e., oligomers and fibrils. The heterogeneity of aggregates produced complicates the assignment of specific toxic functions to distinct aggregate species. Here, a simple centrifugation strategy was employed to produce well-characterized and relatively homogeneous populations of huntingtin (htt) aggregates <i>in vitro.</i> After characterization of the resulting aggregate populations, <i>C. elegans</i> were exogenously exposed to these different aggregates species to assess their impact on worm viability. Htt oligomers were identified as the most acutely toxic aggregate form. Nonaggregated htt and fibrils did not significantly reduce <i>C. elegans</i> viability. A variety of methods to manipulate htt oligomers were then tested to demonstrate the ability to modify oligomer toxicity in this model system. Chemically cross-linking htt oligomers reduced their toxicity, suggesting that structural flexibility is important in oligomer toxicity. Stabilizing oligomers with truncated peptides based on the first 17 N-terminal amino acids (Nt17) impacted toxicity when specific acetylation-mimicking point mutations were introduced. Nt17-derived peptides without any mutations did not alter toxicity; however, the addition of acetylation-mimicking mutations toward the C-terminus of the peptide reduces toxicity. Finally, two small molecules that modify htt aggregation, EGCG and riluzole, were tested for their impact on oligomer toxicity. In general, this approach provides a simple method to investigate and manipulate the toxicity of aggregate subpopulation in a quasi-controlled manner.

Palmoplantar pustulosis (PPP) is a chronic inflammatory skin disorder marked by erythematous pustules and desquamation on the palms and soles. While IL-17 pathways are implicated in PPP, IL-17 blockers have shown modest efficacy, underscoring the need for a deeper understanding of IL-17 involvement. To dissect the cellular and spatial architecture of PPP, we performed single-cell RNA-Seq (scRNA-Seq) on lesional, nonlesional, and healthy acral skin to examine cellular composition, transcriptomic profiles, and cell-cell interactions. Unbiased clustering revealed 9 major cell types, including an inflammatory keratinocyte subset enriched in IL-17A/TNF signatures and marked by high IL-36G expression. Within the lymphocyte compartment, we identified a hybrid "regTh17" population coexpressing regulatory markers (FOXP3, CTLA4, TIGIT), IL17F, and IL26. This regTh17 subset was distinguished by elevated IL1R1 and CD39, suggesting an IL-1β-driven differentiation. Spatial analyses demonstrated significant neighborhood enrichment of regTh17 cells with IL-36G+ supraspinous keratinocytes. RegTh17 cells were the predominant source of IL-17F and IL-26 signals, whereas keratinocytes were predicted as their main receivers. We further observed regTh17 coexpressing TNFRSF4 (OX40) and TNFRSF18 (GITR) specifically at sites of IL36G+ keratinocyte interactions, implicating these pathways in amplification of the IL-17/IL-36 inflammatory loop. Together, our integrated single-cell and spatial profiling uncovers Th17 plasticity in PPP, identifies a regTh17-keratinocyte interaction, and highlights IL-17F, IL-26, OX40/OX40L, and GITR/GITRL as candidate targets for precision therapies in this challenging disease.

Mental disorders arise through the interaction of genetic predisposition and environmental influences such as stress. Epigenetic processes, like DNA methylation, could represent a mechanism mediating this interplay in the pathogenesis and maintenance of stress-related mental disorders. Changes in methylation of the serotonin transporter gene (SLC6A4, 5-HTT) are associated with both stress and mental disorders. The present study for the first time longitudinally examines the relationship between the acute stress response and SLC6A4 methylation. For this purpose, 122 healthy adults participated in a standardized acute stress induction paradigm (Maastricht Acute Stress Test; MAST). The stress response was assessed via salivary cortisol collected at seven time points before and after stress induction. SLC6A4 promoter methylation was determined using pyrosequencing of bisulfite-converted DNA from peripheral blood before and 45 min after stress induction. A relative increase in SLC6A4 methylation from before to after the stress test was associated with increased salivary cortisol stress reactivity. Increased SLC6A4 methylation has previously been reported as a potential pathogenetic marker for stress-related mental disorders such as depression and posttraumatic stress disorder (PTSD), and to predict clinical response to both pharmacotherapy and psychotherapy. The present results therefore suggest that acute stress induction may serve as a model paradigm for investigating the potential pathogenetic and treatment mechanisms of stress-related mental disorders.

<h4>Background</h4>Primary mitochondrial diseases comprise a group of inherited disorders that frequently affect the central nervous system. Previous studies have reported brain imaging findings commonly associated with mitochondrial disease. However, longitudinal data on volumetric brain abnormalities, their progression in time, and associations with clinical features of the disease remain limited.<h4>Methods</h4>We conducted a retrospective observational study of 36 patients with genetically confirmed mitochondrial disease at Turku University Hospital (Turku, Finland). A total of 73 brain magnetic resonance scans (1-8 per patient) were analysed using the cNeuro® image quantification tool to assess lobar and regional cortical atrophy. Associations with clinical features, including stroke-like episodes (SLEs), sex, and genetic subtype, were investigated.<h4>Results</h4>Cerebral atrophy was present in all patients and was most pronounced in the temporal and occipital lobes. Patients with a history of SLEs exhibited significantly greater atrophy in both temporal lobes and the right occipital and parietal lobes. Follow-up imaging (available for 15 patients) revealed progressive atrophy, particularly in the occipital lobes, in patients with SLEs. No significant differences in atrophy severity or progression were found between patients with the m.3243A > G variant and those with other genetic causes.<h4>Conclusions</h4>Cerebral atrophy is a common and often progressive feature of mitochondrial disease, even in patients without clinical brain symptoms. Atrophy predominantly affects posterior brain regions, and its progression is particularly evident in patients with SLEs. These findings underline the neurodegenerative nature of mitochondrial disease and highlight the need to develop neuroprotective therapies.

No abstract available.

Jasminum sambac (L.) Aiton, commonly known as Arabian jasmine, is widely used in Thai traditional medicine for mental health ailments. While most studies in humans and animals find that Arabian jasmine reduces stress and anxiety, there are a handful of reports that it can oppose relaxation by increasing autonomic arousal. Using adult zebrafish, we sought to determine whether factors like strain, sex, and personality might contribute to the variable effects of J. sambac on anxiety-related behavior. We extracted the flowers of J. sambac by ultrasonic-assisted extraction with optimal air pressure. Headspace solid-phase microextraction with gas chromatography-mass spectrometry (HS-SPME-GC-MS) identified the main components in the Arabian jasmine flower extract, including linalool (an anxiolytic compound) and benzaldehyde (a potentially anxiogenic compound). We fed three strains of zebrafish (AB, TL, and WIK) a gelatin pellet containing different concentrations of J. sambac (5-20 mg kg-1) and assessed 3-dimensional swim behavior in the novel tank and mirror biting tests. We found that in female AB fish, J. sambac resulted in a decrease in both bottom distance and percent explored during the novel tank test, consistent with an anxiogenic effect; there was no effect in WIK or TL fish. We also found that behavior/personality type influenced the effects of J. sambac where shy AB females increased their percent explored and low activity males increased their bottom distance, consistent with anxiolytic effects. Thus, we find that sex, genetics, and personality interact to influence the anxiety-related effects of Arabian jasmine. This suggests that these factors may contribute to the opposing effects of jasmine previously reported in the literature.

Linker H1 histones are highly susceptible to a variety of post-translational modifications (PTMs) that play a critical role in chromatin dynamics and gene expression. In the present work, trapped ion mobility spectrometry in tandem with ultraviolet photodissociation followed by ultrahigh resolution mass measurements, provided by a Fourier transform ion cyclotron mass spectrometer (TIMS-q-UVPD-FT-ICR MS/MS), enabled direct characterization of the linker H1 histone proteoforms. The proposed method takes advantage of the mobility and mass preseparation of core and linker histones proteoforms prior to UVPD fragmentation and consequent high mass accuracy detection in the FT-ICR MS of the fragment ions for efficient PTM assignment. The application to a bovine histone extraction resulted in the annotation of four H1 variants (H1.2, H1.3, H1.5, and H1.4V), together with their PTM distribution with high sequence coverages (up to 60%); in particular, the H1.4V variant sequence was identified via <i>de novo</i> sequencing. All reported H1 proteoforms and their PTMs (e.g., mono/dimethylation, acetylation, and phosphorylation) were confirmed with complementary top-down liquid chromatography coupled to tandem MS/MS using electron-activated dissociation (LC-q-EAD-ToF MS/MS) and bottom-up analysis. This direct approach shows great promise for global H1 proteoform analysis due minimal sample preparation and large number of proteoform PTM observed.

PBK/TOPK is a mitotic kinase implicated in haematological and non-haematological cancers. Here we show that the key haemopoietic regulators Ikaros and Aiolos require PBK-mediated phosphorylation to dissociate from chromosomes in mitosis. Eviction of Ikaros is rapidly reversed by addition of the PBK-inhibitor OTS514, revealing dynamic regulation by kinase and phosphatase activities. To identify more PBK targets, we analysed loss of mitotic phosphorylation events in Pbk^-/- preB cells and performed proteomic comparisons on isolated mitotic chromosomes. Among a large pool of C2H2-zinc finger targets, PBK is essential for evicting the CCCTC-binding protein CTCF and zinc finger proteins encoded by Ikzf1, Ikzf3, Znf131 and Zbtb11. PBK-deficient cells were able to divide but showed altered chromatin accessibility and nucleosome positioning consistent with CTCF retention. Our studies reveal that PBK controls the dissociation of selected factors from condensing mitotic chromosomes and contributes to their compaction.

<h4>Background</h4>There is a paucity of data on neurodevelopmental outcomes in preterm infants who undergo transcatheter patent ductus arteriosus (PDA) closure (TCPC).<h4>Objective</h4>To evaluate neurodevelopmental impairment (NDI) or death at 2 years among preterm infants treated with TCPC compared to surgical ligation.<h4>Methods</h4>Retrospective cohort study of infants born at <27 weeks' gestation at NICHD NRN sites. Comparisons were made between infants who underwent TCPC and PDA ligation.<h4>Results</h4>TCPC and surgical ligation were performed on 99 and 279 infants, respectively. Death or severe NDI occurred in 49% of infants with TCPC and 40% with surgical ligation. There was no difference in odds of death or severe NDI between the two groups [aOR 1.12 95% CI: 0.55-2.26)].<h4>Conclusion</h4>TCPC had similar odds of death or severe NDI compared to surgical ligation. These findings need to be evaluated in large prospective studies as the management practice around the TCPC evolves.<h4>Clinical trial registration</h4>ClinicalTrials.gov ID: Generic Database: NCT00063063.

Mitotic chromosomes give genome portions the required compaction and mechanical stability for faithful inheritance during cell divisions. They are shaped by the chromosomal condensin complex. Here, we record human chromosome dimensions from their appearance in prophase over successive times in a mitotic arrest. Chromosomes first appear long and uniformly thin. Then, individual chromosome arms become discernible, which continuously shorten and thicken-the longer a chromosome arm, the thicker it becomes. In the search for a molecular explanation of this behavior, given uniform condensin density, the popular loop extrusion model provides no obvious means by which longer chromosome arms become thicker. Instead, we find that simulations of an alternative loop capture model recapitulate key features of our observations, with re-arranging chromatin rosettes underpinning the gradually developing arm length-to-width relationship. Our analyses portray chromosomes as out-of-equilibrium structures in the process of transitioning towards, but on biologically relevant time scales not typically reaching, steady state.

<h4>Background</h4>FET (FUS, EWSR1, and TAF15) fusion oncoproteins are characteristic for several sarcomas and leukemias, including myxoid liposarcoma and Ewing sarcoma. FET oncoproteins interact with the SWI/SNF chromatin remodeling complex subtypes cBAF, PBAF, and GBAF, but their impact on SWI/SNF compositions, interactions, and downstream epigenetic effects remains elusive.<h4>Methods</h4>We employ a comprehensive immunoprecipitation and quantitative mass spectrometry approach to determine the impact of FET oncoproteins on SWI/SNF composition and their interactomes. Validation of complex composition and interaction partners is performed by glycerol gradient sedimentation assays and co-immunofluorescence analysis. Furthermore, we determine the differential chromatin accessibility and gene regulation in FET sarcomas using assay for transposase-accessible chromatin sequencing and RNA sequencing, respectively.<h4>Results</h4>Our data show that FET sarcomas have distinct SWI/SNF complex compositions, with different subunit paralogs and subtype-specific components that utilize distinct sets of interaction partners, including specific transcription factors. We show that FET oncoproteins cause no major disruption of the SWI/SNF complex composition. Instead, FUS::DDIT3-bound SWI/SNF complexes in myxoid liposarcoma cells are enriched in PBAF and GBAF components as well as most interaction partners.<h4>Conclusions</h4>These data suggest that FET oncoproteins act together with fully assembled and functional SWI/SNF complexes and recruited interaction partners. Finally, our data reveal that the SWI/SNF compositions, interactomes, and epigenetic background contribute to the tumor type in FET sarcoma. Trial registration Clinical trial number: not applicable.

<h4>Background</h4>Neuropsychiatric disorders are highly complex conditions and the risk of developing a disorder has been tied to hundreds of genomic variants that alter the expression and/or RNA isoforms made by risk genes. However, how these genes contribute to disease risk and onset through altered expression and RNA splicing is not well understood.<h4>Results</h4>Combining our new bioinformatic pipeline IsoLamp with nanopore long-read amplicon sequencing, we deeply profile the RNA isoform repertoire of 31 high-confidence neuropsychiatric disorder risk genes in Human brain. We show most risk genes are more complex than previously reported, identifying 363 novel isoforms and 28 novel exons, including isoforms which alter protein domains, and genes such as ATG13 and GATAD2A where most expression was from previously undiscovered isoforms. The greatest isoform diversity is detected in the schizophrenia risk gene ITIH4. Mass spectrometry of brain protein isolates confirms translation of a novel exon skipping event in ITIH4, suggesting a new regulatory mechanism for this gene in the brain.<h4>Conclusions</h4>Our results emphasize the widespread presence of previously undetected RNA and protein isoforms in the human brain and provide an effective approach to address this knowledge gap. Uncovering the isoform repertoire of candidate neuropsychiatric risk genes will underpin future analyses of the functional impact these isoforms have on neuropsychiatric disorders, enabling the translation of genomic findings into a pathophysiological understanding of disease.

<h4>Significance</h4>Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) biofilm infections present a critical challenge in orthopedic trauma surgery and are notoriously resistant to systemic antibiotic therapy. Noninvasive, quantitative imaging methods are urgently needed to assess biofilm burden and therapeutic efficacy, especially for emerging photodynamic therapy (PDT) strategies.<h4>Aim</h4>We aim to establish a quantitative framework using a combined bioluminescence and optical coherence tomography (OCT) imaging approach to correlate bioluminescent signal with viable MRSA burden in both planktonic and biofilm states and to determine how biofilm density and structure influence this relationship.<h4>Approach</h4>Bioluminescent MRSA (SAP231-luxCDABE) was cultured in planktonic and biofilm forms using <i>in vitro</i> growth models in 24-well plates and custom macrofluidic devices, respectively. Bacteria bioluminescence intensity (BLI), counted colony-forming units (CFU), and OCT-based biofilm thickness measurements were collected to construct linear regression models to evaluate how well BLI alone, or combined with biofilm density (CFU/volume), predicts bacterial counts across culture conditions.<h4>Results</h4>Bioluminescence strongly correlated with CFU in planktonic cultures ( R2=0.98 ). In biofilms, BLI per CFU decreased with density, indicating metabolic downregulation, and BLI alone was less reliable ( R2=0.59 ). Incorporating biofilm density (CFU/volume) improved prediction ( R2=0.84 ). A joint model for both states showed excellent fit ( R2=0.985 ), but the biofilm versus planktonic group remained a significant factor ( p=0.002 ), revealing systematic differences. This highlights the need for a mixed-model approach that segments subvolumes by morphological features to improve accurate, generalizable CFU estimation across both growth states.<h4>Conclusions</h4>Bioluminescence alone underestimates bacterial burden in dense, metabolically suppressed MRSA biofilms. The combination of BLI with OCT-derived structural metrics enables accurate, nondestructive quantification of viable bacterial load. This approach provides a robust toolset for preclinical evaluation of antimicrobial therapies, particularly for optimizing PDT dosimetry and assessing biofilm response in translational infection models.

Systemic inflammatory state found in obesity increases the risk of developing numerous diseases. While endurance training seems effective to reduce this inflammation, the underlying mechanisms are not fully understood. Among those, extracellular vesicles (EVs) have been proposed to be actors in the anti-inflammatory intercellular crosstalk induced by exercise training. This study aimed to investigate how endurance training modulates the EV proteome in the context of an inflammatory state in adults with obesity. Thirteen lean sedentary adults and 10 sedentary adults with obesity participated in a 12-week endurance training programme. Skeletal muscle, abdominal subcutaneous adipose tissue and venous blood samples were taken prior to and after the training period. The systemic and adipose tissue inflammatory states were assessed, and plasma EVs were isolated by size exclusion chromatography. EV content was analysed by mass spectrometry. EVs isolated from the medium of myotubes stimulated by electrical pulse stimulation in vitro were quantified, and their content was analysed by western blot. After the endurance training, C-reactive protein (CRP) levels decreased in participants with obesity. In abdominal subcutaneous adipose tissue, the phosphorylation state of nuclear factor-kappa B (NF-κB) was not affected by training, but interleukin (IL)-6 and IL-1β protein levels were reduced after the 12 weeks in both groups. Conversely, interferon gamma (IFNγ) level reduction was exclusively found in the obesity group. Despite no changes in EV abundance, EV proteome was modified by training. Among the modified proteins in participants with obesity, the antioxidant enzyme peroxiredoxin (PRDX) 1 abundance was increased after training. Additionally, the PRDX1 content of EVs isolated from stimulated myotubes was increased compared to control conditions. In conclusion, our results suggest that the anti-inflammatory effects of exercise training are not directly mediated by EV anti-inflammatory proteome changes. However, exercise training increases circulating EV antioxidant content, possibly through contractile activity of skeletal muscle during repeated exercise.

SHR02, a derivative of homoisoflavonoid, exhibits potent anti-inflammatory activity in innate immune cells. In this study, we investigated the immunomodulatory effects of SHR02 in dendritic cells (DC2.4) and macrophages (RAW 264.7) under Toll-like receptor (TLR) stimulation. SHR02 significantly suppressed the secretion of pro-inflammatory cytokines (TNF-α and IL-6), reduced nitric oxide (NO) and reactive oxygen species (ROS) production, and downregulated the expression of iNOS and COX-2. Mechanistically, SHR02 inhibited NF-κB phosphorylation in dendritic cells while enhancing Nrf2 nuclear translocation in both cell types. These findings suggest that SHR02 modulates inflammatory and oxidative responses through both NF-κB and Nrf2 signaling pathways and may serve as a promising candidate for the treatment of inflammatory disorders.

Lymphoma remains a significant global health burden, necessitating innovative, targeted therapeutic strategies. Nisin (N), a bacteriocin produced by <i>Lactococcus lactis</i>, has demonstrated antimicrobial and anticancer properties through membrane disruption and apoptotic induction. Urolithin B (UB), a gut microbiota-derived metabolite of ellagitannins, has shown anti-inflammatory and antiproliferative activities in various cancer models. Vincristine (Vinc), a common anti-lymphoma drug, disrupts microtubule formation, leading to cell cycle arrest and apoptosis in cancer cells. This study explored the antiproliferative and pro-apoptotic effects of a triple combination therapy comprising N, UB, and Vinc against human lymphoma cell lines (HKB-11 and Hs 313.T). This study systematically evaluated the synergistic efficacy of both monotherapy and dual and triple combinations and molecular mechanisms using Alamar Blue viability assays, combination index (CI) modelling, reactive oxygen species (ROS) quantification, annexin V/7-AAD flow cytometry, and bottom-up label-free proteomics. The potential cytotoxicity of the combination on normal stromal HS-5 cells was also assessed using the Alamar Blue assay. The N: UB: Vinc combination at 2240: 210: 0.94 µM demonstrated potent synergy (CI values 0.31-0.50 at IC₉₀ - IC₉₅) and induced near-complete growth inhibition (> 99%) in both lymphoma cell lines with reduced toxicity (42.09 ± 1.21% viability) toward normal stromal HS-5 cells. ROS analysis revealed significant oxidative stress, while flow cytometry confirmed enhanced apoptosis (p < 0.0001) in the combination groups. Proteomic profiling of the combination N: UB: Vinc at 2450.94 µM uncovered distinct molecular responses, including upregulation of MAP1LC3B2 (Log₂FC = 1.4), GMNN (Log₂FC = 1.3), and SLC38A2 (Log₂FC = 1.5), promoting apoptosis, cell cycle regulation, and mTOR signaling inhibition. Concurrently, key oncogenic and metabolic proteins were downregulated, including NNMT (Log₂FC = -2.9), PLTP (Log₂FC = -2.5), and CYP4X1 (Log₂FC = -2.0), which implicated the suppression of MAPK-Akt signaling, ferroptosis activation, and lipid metabolism disruption. These results established a mechanistic rationale for combining postbiotics such as N and UB with standard chemotherapy, highlighting a promising avenue for safer and more effective lymphoma management in the future.