Gene Literature Dashboard

In recent years, there has been an increase in the incidence of urinary stones, including infection urinary stones, especially in highly developed countries. One of the areas where the cause of the increased morbidity in these countries can be found is food products and their ingredients, which are not as common in other countries. Very often, attention is drawn to the greater consumption of highly processed food, the production of which uses flavour enhancers and various preservatives. One of the substances used in the food industry as an acidity regulator or antioxidant is phosphoric acid. It is used in the production of many products from food, sweets, beers to soft drinks, e. g. Coca-Cola. In this paper, we present the results of research on the effect of phosphoric acid (H₃PO₄) on the mineralization and growth of carbonate apatite Ca₁₀(PO₄)₆CO₃ (CA) and hydroxyapatite Ca₁₀(PO₄)₆(OH)₂ (HAP), which are one of the main components of infection urinary stones, next to struvite. The research was conducted in an artificial urine environment in two ways: in the presence of Proteus mirabilis bacteria and without them. In the latter case, bacterial urease activity was simulated by adding an aqueous ammonia solution. The results obtained, both in the presence of bacteria and without them, indicate that phosphoric acid present in artificial urine causes a shift in the mineralization of CA and HAP towards a lower pH, which means that these components mineralize earlier in artificial urine compared to the control sample. On the other hand, the amount of solid phases formed is smaller, the higher the concentration of phosphoric acid. The effect of phosphoric acid on the mineralization of CA and HAP was explained on the basis of theoretical speciation analysis of chemical complexes formed in urine in the presence of the tested acid. This analysis indicates that the experimentally observed shift in the formation of solid phases towards a lower pH with increasing phosphoric acid concentration is related to the earlier appearance of C₁₀(PO₄)₆(OH)₂ complexes, forming HAP, and not to C₁₀(PO₄)₆CO₃ complexes, forming CA. It should be remembered that the described effect of this acid on the formation of CA and HAP is possible only when the urinary tract is infected with urease-positive bacteria. In the absence of infection, phosphoric acid will not cause the formation of solid phases characteristic of infection urinary stones.

Myeloid malignancies exhibit considerable heterogeneity with overlapping clinical and genetic features among subtypes. We present a data-driven approach that integrates mutational features and clinical covariates at diagnosis within networks of their probabilistic relationships, enabling the discovery of patient subgroups. A key strength is its ability to include presumed causal directions in the edges linking clinical and mutational features, and account for them aptly in the clustering. In a cohort of 1323 patients, we identify subgroups that outperform established risk classifications in prognostic accuracy. Our approach generalises well to unseen cohorts with classification based on our subgroups similarly offering advantages in predicting prognosis. Our findings suggest that mutational patterns are often shared across myeloid malignancies, with distinct subtypes potentially representing evolutionary stages en route to leukemia. With pancancer TCGA data, we observe that our modelling framework extends naturally to other cancer types while still offering improvements in subgroup discovery.

Synovial joints develop from mesenchymal structures called interzones, with progenitor cells differentiating into specialized cartilaginous and fibrous tissues of the joint. Platelet-derived growth factor receptor-α (PDGFRα) is a tyrosine kinase expressed by cells of the limb bud, but its role in limb development is unknown. To investigate PDGFRα function, we generated mice expressing mutant PDGFRα with a point mutation (D842V) that increases receptor signaling. Mutant hindlimbs are immobile with knee joints fused by cartilage and lacking ligaments and menisci. The interzone marker Gdf5 is initially expressed at E12.5 but is downregulated thereafter, suggesting a defect in interzone maintenance. Omics analysis of the joint tissues identifies ectopic cartilage matrix expressing genes for cartilage and fibrotic tissue. Thus, elevated PDGFRα signaling corrupts joint development by downregulating Gdf5 and redirecting interzone progenitors into a fibrocartilage fate. This suggests that tight regulation of tyrosine kinase activity is necessary for the development of the mouse knee joint.

The spread of antimicrobial-resistant bacteria, especially in developing countries, is a critical healthcare issue. Among these, extended-spectrum beta-lactamase (ESBL)-producing bacteria are particularly concerning due to their resistance to third- and fourth-generation cephalosporins. Traditional methods for assessing bacterial resistance involve culturing bacteria on selective media from fecal samples, which may lead to selection bias. Alternatively, real-time PCR allows for detecting resistance genes directly from fecal DNA, providing a broader view of resistant bacteria. In this study, we evaluated the utility of a real-time PCR assay targeting ESBL-producing genes as a comprehensive detection method for ESBL-producing resistant bacteria in fecal samples. Additionally, we conducted a multinational comparative analysis of the colonization status of residents using this approach. The study analyzed ESBL genes in fecal samples from 161 residents in four countries: Ecuador, Ghana, Vietnam, and Japan. Samples from Ecuador, Ghana, and Vietnam, where ESBL carriage was notably high, revealed gene variations by country, with <i>bla</i>TEM genes being most common except in Ghana, where <i>bla</i>SHV genes predominated. These variations suggest that different bacterial hosts carry ESBL genes across countries. Quantitative PCR results further highlight that <i>bla</i>TEM is the most abundant ESBL gene. Although gene presence does not confirm antibiotic resistance, these findings underline significant ESBL carriage in low- and middle-income countries. The study emphasizes that gene detection in fecal samples is valuable for understanding resistant bacteria spread in communities.IMPORTANCEThe rise of antimicrobial-resistant bacteria, particularly extended-spectrum beta-lactamase (ESBL)-producing strains, poses a serious threat to healthcare in developing countries. This study utilized real-time PCR to detect ESBL genes directly from fecal DNA of 161 participants across four countries, offering a comprehensive analysis without the biases of traditional culture-based methods. High ESBL gene carriage rates were found in Ecuador, Ghana, and Vietnam, with regional differences in gene prevalence: <i>bla</i>TEM dominated in most countries, while <i>bla</i>SHV was most frequent in Ghana. These results highlight the widespread community-level dissemination of ESBL genes in low- and middle-income countries, underscoring the importance of using gene detection as a tool for assessing the spread of resistant bacteria.

<h4>Purpose</h4>Measuring hepatic flux rates of transportable substrates has the potential for assessing liver function. PET imaging of a PET-enabled substrate may provide a more straightforward measurement of time-dependent substrate concentration through the liver than MRI using an MRI contrast agent. Here we synthesized and evaluated the hepatobiliary transport of a new hepatospecific PET agent designed for stable Cu²⁺ chelation and transport by hepatic OATPs, [⁶⁴Cu]Cu-EOB-NOTA.<h4>Procedures</h4>EOB-NOTA was synthesized, its two enantiomers separated by chiral HPLC, and individually radiolabeled with [⁶⁴Cu]Cu²⁺. Cocktails of each enantiomer of [⁶⁴Cu]Cu-EOB-NOTA and Gd-EOB-DTPA were formulated for simultaneous PET/MRI imaging of hepatic flux by PET and MRI. Two mouse models were evaluated: wild-type mice and mice expressing only human hepatic OATPs.<h4>Results</h4>In wild-type mice, [⁶⁴Cu]Cu-EOB-NOTA hepatic influx and efflux was high, but slower compared to Gd-EOB-DTPA. Neither enantiomer of [⁶⁴Cu]Cu-EOB-NOTA exhibited detectable transport into the liver in mice expressing human OATPs. This was validated by waste clearance studies and in vitro uptake assays in cells engineered to express rodent and human OATPs.<h4>Conclusion</h4>[⁶⁴Cu]Cu-EOB-NOTA exhibited no detectable hepatic uptake by transgenic mice expressing human hepatic transporters. This finding was surprising given the efficient transport of the structurally similar metal chelate Gd-EOB-DTPA, and underscores challenges in the design of imaging molecular probes, including poor predictability for hepatic transport, and the value of validating new agents in mice expressing human hepatic transporters.

<h4>Purpose</h4>To validate the feasibility of using late iodine enhancement (LIE)-derived ECV on iodine density images using spectral detector computed tomography (SDCT; CT-ECV) and to assess the potential of CT-ECV for risk stratification among patients with non-ischemic heart failure (NIHF).<h4>Materials and methods</h4>Forty-five subjects who underwent cardiac SDCT and CMR were included in the validation group to calculate and compare CT-ECV with CMR-ECV to validate CT-ECV feasibility. Another 117 subjects (82 patients with NIHF, 35 controls) who underwent SDCT were included in the experimental group to explore the potential of CT-ECV for risk stratification. ECV was measured via iodine density images and CMR T1 mapping in accordance with American Heart Association 16-segment models.<h4>Results</h4>In the validation group, there was no significant difference between CT-ECV and CMR-ECV (P = 0.293), with an insignificant bias. In the experimental group, CT-ECV in patients with NIHF was significantly higher than in controls (P < 0.05). In 82 patients with NIHF, CT-ECV in HFrEF ( HF with reduced ejection fraction: LVEF ≤ 40%) patients was statistically higher than that of HFmEF (HF with mildly reduced ejection fraction: LVEF 41-49%) and HFpEF (HF with preserved ejection fraction: LVEF ≥ 50%) patients (P < 0.05) and a significant difference among patients with NIHF with varied New York Heart Association classes (all P < 0.05); In addition, Kaplan-Meier survival curves and Log-rank test demonstrated that NIHF patients with CT-ECV ≥ 31.29% had higher probability of MACE than NIHF patients with CT-ECV < 31.29% (P < 0.001).<h4>Conclusion</h4>LIE-derived CT-ECV on iodine density images using SDCT is a promising practical alternative to CMR-ECV, with the potential to assist with risk stratification among patients with NIHF.

Protein misfolding is linked to many neurodegenerative disorders, such as Huntington's disease. The increase of glutamine-encoding CAG repeats in the first exon of huntingtin (<i>HTT</i>) causes Huntington's disease. Protein fragments of Htt exon 1 with polyQ expansion (mutant HTT, mHtt) are prone to aggregation, resulting in oligomers, amyloid fibrils, or large inclusion bodies. Previous studies demonstrate mHtt SUMOylation, a process of covalent attachment of small ubiquitin-like modifiers (SUMO) to target proteins. Protein polySUMOylation further triggers its ubiquitination and segregation by the polySUMO axis. Here, we examined how SUMOylation regulates aggregation and degradation of Htt103QP-GFP, a model mHtt, in budding yeast. We first confirmed Htt103QP-GFP SUMOylation in budding yeast. We also found that recruitment of the SUMO E2-conjugating enzyme to Htt103QP-GFP accelerates its aggregation, but recruitment of a SUMO protease to Htt103QP-GFP delays this process. Disruption of the polySUMO axis led to increased Htt103QP-GFP aggregation. Interestingly, the results from fluorescence recovery after photobleaching assay and treatment with a biomolecular condensate-disrupting chemical indicate that SUMOylation accelerates biomolecular condensate formation of Htt103QP-GFP. Importantly, impaired SUMOylation delays Htt103QP-GFP proteasomal degradation and accelerates formation of SDS-insoluble Htt103QP-GFP aggregates. Together, these results indicate that SUMOylation facilitates proteasomal degradation of misfolded proteins by retaining their solubility.

Enzymes have been recognized as highly efficient biocatalysts, whereas characteristics such as poor stability and single reaction type greatly significantly limit their wide application. Hence, the exploitation of suitable carriers for immobilized enzymes enables the provision of a protective layer for the enzyme, with the capability of chemical and biological cascade catalysis. Among the various immobilization carriers, metal-organic frameworks (MOFs), covalent organic frameworks (COFs) and hydrogen-bonded organic frameworks (HOFs) have been emerging as a promising strategy to surpass the inherent instability and other limitations of free enzymes. Specifically, the integration of such artificial porous materials as carriers improves the stability and reusability of enzymes, while simultaneously affording a platform for multifunctional applications. Herein, this review systematically discusses the various preparation strategies and advantages of artificial porous materials, while elucidating the effects of different immobilization methods on enzyme activity. Furthermore, the innovative applications of artificial porous materials as multifunctional carriers in the field of enzyme immobilization fields such as enzyme carriers, photocatalysts, chemical catalysts and sensing are also comprehensively summarized here, thus demonstrating their multifunctional characteristics and promising applications in addressing complex biotransformation challenges.

<h4>Introduction</h4>The prevalence of dementia is increasing, both worldwide and in China. This disease is associated with numerous restrictions for those affected but also for caregivers and society. Due to the limited effectiveness of pharmacological interventions, more research on non-pharmacological interventions is needed. For the non-pharmacological multimodal MAKS (M: motor training, A: activities of daily living training, K: cognitive training, S: social-communicative setting) intervention, positive effects on cognition, activities of daily living, and the occurrence of behavioural and psychological symptoms of dementia were identified in two randomised controlled trials in different settings in Germany. Thus, the German MAKS intervention was culturally adapted for China and will now be tested for its efficacy in Chinese nursing homes in a randomised controlled trial.<h4>Methods and analysis</h4>Participants will be residents of Chinese nursing homes in Shenyang, Nanjing and Dalian, fulfilling the ICD-10 criteria for Alzheimer's dementia, the psychometric criteria for mild to moderate dementia (MMSE 10-23) and none of the exclusion criteria. With n=200, effects with an effect size of Cohen's d=0.45 and a power of 1-β = 0.80 can be detected. Screening and data collection at baseline, t6 and t12 will be conducted via face-to-face contact by proxy raters in the nursing homes (i.e., trained nursing staff not involved in the intervention) and master students as external testers for the performance tests on cognition and activities of daily living. Participants will be randomly allocated to the intervention or control group. SinoMAKS (i.e., the Chinese version of the MAKS intervention) will be conducted at least three times a week for six months by trained MAKS therapists. The control group will receive care as usual for 12 months after baseline. Thus, the treatment phase is six months with follow-ups after six and 12 months after baseline. In the open phase, from t6 to t12, the nursing homes are free to offer SinoMAKS to the intervention group residents. In line with international guidelines, the primary population for analysis is the intention-to-treat sample. Global cognition (measured with the Addenbrooke's Cognitive Examination-III) is the primary outcome. The hypotheses will be analysed using multiple linear regression with the outcome variables as dependent variables.<h4>Ethics and dissemination</h4>All procedures were approved by the Ethics Committee of the Medical Faculty of the Friedrich-Alexander-Universität Erlangen-Nürnberg (Ref. 24-162-B) and the Ethics Committee of the China Medical University (Ref. [2024]181). Written informed consent will be obtained from all participants or-if applicable-their legal representatives. Results will be published in peer-reviewed scientific journals and conference presentations.<h4>Trial registration number</h4>ISRCTN10262531.

m⁶A RNA methylation is essential for many aspects of mammalian development but its roles in chondrogenesis remain largely unknown. Here, we show that m⁶A is necessary for chondrogenesis and limb morphogenesis using limb progenitor-specific knockout mice of Mettl14, an essential subunit in the m⁶A methyltransferase complex. The knockout disrupts cartilage anlagen formation in limb buds with 11 downregulated proteins known to dysregulate chondrogenesis and shorten limb skeletons upon mutation in mice and humans. Further studies show a gene regulatory hierarchy among the 11 proteins. m⁶A stabilizes the transcript and increases the protein level of GDF5, a BMP family member. This activates the chondrogenic transcription factor genes Runx2 and Runx3, whose mRNAs are also stabilized by m⁶A. They promote the transcription of six collagen genes and two other chondrogenic genes, Ddrgk1 and Pbxip1. Thus, this study uncovers an m⁶A-based cascade essential for chondrogenesis during limb skeletal development.

The polygenic contribution to heart development and function along the health-disease continuum remains unresolved. To gain insight into the genetic basis of quantitative cardiac phenotypes, we utilize highly inbred Japanese rice fish models, Oryzias latipes, and Oryzias sakaizumii. Employing automated quantification of embryonic heart rates as core metric, we profiled phenotype variability across five inbred strains. We observed maximal phenotypic contrast between individuals of the HO5 and the HdrR strain. HO5 showed elevated heart rates associated with embryonic ventricular hypoplasia and impaired adult cardiac function. This contrast served as the basis for genome-wide mapping. In an F2 segregation population of 1192 HO5 x HdrR embryos, we mapped 59 loci (173 genes) associated with heart rate. Experimental validation of the top 12 candidate genes by gene editing revealed their causal and distinct impact on heart rate, development, ventricle size, and arrhythmia. Our study uncovers new diagnostic and therapeutic targets for developmental and electrophysiological cardiac diseases and provides a novel scalable approach to investigate the intricate genetic architecture of the vertebrate heart.

Glioblastoma (GBM) is the most common and deadly malignant tumor of the nervous system. RIMS1, a member of the RAS gene superfamily, plays a critical role in signaling pathways regulating cell growth and differentiation. However, the prognostic value of RIMS1, particularly its relationship with immune cell infiltration in gliomas, has not been fully explored. RIMS1 expression in glioblastoma cells and tissues was assessed using bioinformatics platforms. The association between RIMS1 expression levels and overall survival was analyzed using Kaplan-Meier analysis and Cox regression model. To evaluate the proliferative and migratory capacity of GBM cells, we conducted CCK-8, colony formation, transwell, and scratch assays. With data from The Cancer Genome Atlas (TCGA), we investigated the correlation between RIMS1 expression and immune cell infiltration levels and assessed the prognostic impact of RIMS1 on GBM patient survival, focusing on its potential involvement in immune pathways. Lower RIMS1 expression was associated with poorer overall survival and was linked to patient age, gender, and tumor grade. Importantly, RIMS1 expression showed a significant correlation with immune cell infiltration levels, suggesting that RIMS1 influences glioblastoma survival, at least in part, through immune-related mechanisms. In glioblastoma patients, elevated RIMS1 expression may serve as an independent prognostic biomarker, potentially through its impact on immune cell infiltration.

Much remains unknown regarding T follicular helper 17 (T_FH17) cells commonly found in autoimmune patients. We previously showed that (and here ask why) egress of gut segmented filamentous bacteria (SFB)-induced T_FH cells from Peyer's patches (PP) to systemic sites promotes arthritis. We found splenic T_FH17 cells are gut derived. Functional analyses using fate-mapping mice revealed a c-Maf-dependent and SFB-induced T_H17-to-T_FH cell reprogramming that dominantly occurs in PPs. Unlike conventional T_FH cells, T_H17-derived T_FH cells are highly migratory and atypically concentrated in the dark zone of germinal centers (GCs). Compared to conventional T_FH cells, T_H17-derived T_FH cells express higher levels of T_FH-associated functional molecules and more robustly conjugate with B cells. Gain- and loss-of-function studies demonstrated their dominance in promoting GC B cells and arthritis. Notably, murine gut T_H17-derived T_FH signatures exist in rheumatoid arthritis patients. Thus, gut T cell plasticity generates atypical, potent T_FH cells promoting systemic autoimmunity.

Disruption of the circadian clock is associated with the development of inflammatory bowel disease (IBD), but the underlying mechanisms remain unclear. Here, we observe that mice in the early active phase (Zeitgeber time 12, ZT12) of the circadian clock are more tolerant to dextran sodium sulfate (DSS)-induced colitis, compared to those in the early resting phase (ZT0). The expression of the circadian gene Bmal1 peaks in the early resting phase and declines in the early active phase. Bmal1 knockout in the intestinal epithelium reduces DSS-induced inflammatory symptoms. Mechanistically, BMAL1 promotes apoptosis by binding to apoptosis-related genes, including Bax, p53, and Bak1, and promotes their expression. Intriguingly, we observe circadian apoptotic rhythms in the homeostatic intestinal epithelium, while Bmal1 deletion reduces cell apoptosis. Consistently, reducing Bmal1 expression by the REV-ERBα agonist SR9009 has the best therapeutic efficacy against DSS-induced colitis at ZT0. Collectively, our data demonstrate that the Bmal1-centered circadian clock is involved in intestinal injury repair.

<h4>Aim</h4>Diffuse large B-cell lymphoma (DLBCL) is an aggressive lymphoma and DLBCL cells are highly sensitive to ferroptosis. The purpose of this research was to evaluate the role and molecular mechanism of peroxiredoxin 1 (PRDX1) on ferroptosis in DLBCL.<h4>Methods</h4>The expression of PRDX1 in DLBCL tissues and cells was detected using bioinformatics analysis and reverse transcription quantitative PCR. The impacts of PRDX1 on DLBCL cell proliferation, apoptosis, migration, invasion, and ferroptosis were assessed through a series of in vitro experiments. A xenograft tumor model was constructed to verify the roles of PRDX1 in vivo. Transcriptome sequencing was conducted to identify PRDX1-mediated signaling pathways. Anisomycin, an agonist of mitogen-activated protein kinase (MAPK), was used to explore the modulation of PRDX1 on the MAPK pathway.<h4>Results</h4>PRDX1 expression was upregulated in DLBCL. PRDX1 knockdown inhibited DLBCL cell proliferation, migration, and invasion, promoted apoptosis, and suppressed xenograft tumor growth. PRDX1 knockdown boosted erastin-induced ferroptosis by increasing the levels of iron and MDA, while decreasing the levels of GSH. It also promoted COX2 protein expression and inhibited GPX4 and SLC7A11 protein levels. PRDX1 knockdown reduced the phosphorylation levels of MEK and ERK both under conditions with or without erastin induction. The MAPK/ERK pathway agonist anisomycin, significantly reversed the inhibitory effects of PRDX1 knockdown on the malignant behaviors of DLBCL cells and the promotion of ferroptosis.<h4>Conclusion</h4>PRDX1 knockdown facilitates erastin-induced ferroptosis and obstacles DLBCL progression by inhibiting the MAPK/ERK pathway, offering a potential treatment strategy for DLBCL treatment.

The differentiation of human pluripotent stem cells (hPSCs) provides access to a wide range of cell types and tissues. However, hPSC-derived lineages typically represent a fetal stage of development, and methods to expedite the transition to an aged identity to improve modeling of late-onset disease are limited. In this study, we introduce RNAge, a transcriptome-based computational platform designed to enable the evaluation of an induced aging or a rejuvenated state. We validated this approach across independent datasets spanning different tissues and species, and show that it can be used to evaluate the effectiveness of existing age-retaining or age-modulating interventions. We also used RNAge to perform an in silico compound screen using the LINCS L1000 dataset. This approach led to the identification and experimental confirmation of several novel compounds capable of inducing aging or rejuvenation in primary fibroblasts or hPSC-derived neurons. Additionally, we observed that applying this novel induced aging strategy to an hPSC model of Alzheimer's disease (AD) accelerated neurodegeneration in a genotype-specific manner. Our study offers a robust method for quantifying age-related manipulations and unveils compounds that significantly broaden the toolkit for age-modifying strategies in hPSC-derived lineages.

<h4>Background</h4>Tailoring surveillance and treatment strategies for stage II colon cancer (CC) after curative surgery remains challenging, and personalized approaches are lacking. We aimed to identify a gene methylation panel capable of stratifying high-risk stage II CC patients for recurrence beyond traditional clinical variables.<h4>Methods</h4>Genome-wide tumor tissue DNA methylation data were analyzed from 562 stage II CC patients who underwent surgery in Germany (DACHS study). The cohort was divided into a training set (N = 395) and an internal validation set (N = 131), with external validation performed on 97 stage II CC patients from Spain. DNA methylation markers were primarily selected using the Elastic Net Cox model. The resulting prognostic index (PI), a combination of clinical factors and selected methylation markers, was compared to baseline models using clinical variables or microsatellite instability (MSI), with discrimination and prediction accuracy assessed through time-dependent receiver operating characteristic curves (AUC) and Brier scores.<h4>Results</h4>The final PI incorporated age, sex, tumor stage, location, and 27 DNA methylation markers. The PI consistently outperformed the baseline model including age, sex, and tumor stage in time-dependent AUC across validation cohorts (e.g., 1-year AUC and 95 % confidence interval: internal validation set, PI: 0.66, baseline model: 0.52; external validation set, PI: 0.72, baseline model: 0.64). In internal validation, the PI also showed a consistently improved time-dependent AUC compared with a combination of MSI and tumor stage only. Nevertheless, the PI did not improve the prediction accuracy of CC recurrence compared to the baseline model.<h4>Conclusions</h4>This study identified 27 tumor tissue DNA methylation biomarkers that improved the discriminative power in classifying recurrence risk among stage II colon cancer patients. While this methylation panel alone lacks sufficient prediction accuracy for clinical application, its discriminative improvement suggests potential value as part of a multimodal risk-stratification tool.

<h4>Background</h4>Schizophrenia (SCZ) is a complex and heterogeneous disorder with unclear underlying mechanisms. Identifying key gene diseases and constructing biological regulatory networks were beneficial in expanding our understanding of the pathogenesis of SCZ.<h4>Methods</h4>We conducted whole transcriptome sequencing of induced pluripotent stem cells (iPSCs) derived from 5 SCZ patients and 5 healthy controls to analyze differences in mRNA and non-coding RNA expression profiles. Differentially expressed mRNAs (DE mRNAs) were explored for their functions and pathways, and lncRNA-miRNA-mRNA regulatory networks were constructed to understand post-transcriptional regulation mechanisms. Additionally, correlation analyses between competitive endogenous RNAs (ceRNAs), hub genes, and clinical phenotypes of SCZ patients (positive/negative and cognitive symptoms) were performed.<h4>Results</h4>We identified 139 DE mRNAs, 154 lncRNAs, and 19 miRNAs. Significant enrichment of pathways related to apoptosis, inflammatory response, hypoxia, KRAS signaling, and IL6_JAK_STAT3 signaling were observed. Ten hub genes, CCK, CCNA1, CDH5, GATA2, GRPR, NPY, PRKG2, TLE6, ZEB1and ZEB2, were identified, of which ZEB1 and GATA2 were positively correlated with positive symptoms of SCZ, while CDH5 and GRPR were associated with memory. The ceRNA regulatory network (TPM1-AS/ADPGK-AS1/MIRLET7BHG-hsa-mir-3180/3180-3p-LRRC15/TUBA8 and MIRLET7BHG- hsa-mir-3187-3p- CCDC92/ TDRD6/ TMEM26/ ATP1A2) was established, which was also significantly associated with positive, negative and cognitive symptoms of SCZ.<h4>Conclusions</h4>This study identified potential hub genes, pathways, and lncRNA-miRNA-mRNA regulatory networks in iPSCs that provide new insights into the molecular mechanisms of SCZ. The identified hub genes and ceRNA showed significant correlations with various clinical phenotypes of SCZ, offering potential biomarkers and therapeutic targets.

Intestinal stem cell (ISC) signaling maintains the balance of self-renewal and differentiation. Herein, the role of phosphatidylinositol 3-kinase (PI3K) signaling in ISC responses to radiation was interrogated using Villin-Cre pik3r1^lox/lox (p85^ΔIEC) mice and p85α-deficient human enteroids (shp85α). Lethal whole-body irradiation in mice was performed to monitor PI3K-mediated survival responses. Rectal biopsies from patients with radiation proctitis were examined by immunohistochemistry for the PI3K/Akt- and Wnt-target survivin. The intestinal epithelial cells (IECs) from p85^ΔIEC mice showed increased protein levels of phosphorylated phosphatase and tensin homolog, phosphorylated Akt^Ser473, survivin, cyclin D1, and ρ-β-catenin^Ser552, as well as increased mRNA for ISC/progenitor cell. In situ hybridization showed that enhanced PI3K signaling reduced leucine-rich repeat-containing G-protein coupled receptor 5 (Lgr5⁺) cells but enhanced AXIS inhibition protein 2 (Axin2⁺) cells. The shp85α enteroids showed increased mRNA expression of Wnt targets and transcription factor ASCL2, needed for dedifferentiation-mediated restoration of ablated ISCs. The p85α-deficient enteroids showed reduced HES1 mRNA and increases in secretory (ATOH1/MATH1) signaling determinants GFI1 and SPDEF, indicative of reduced NOTCH signaling. Seahorse analyses and phosphorylated p38 staining in IEC^Δp85 mice indicated that enhanced PI3K signaling led to increased IEC mitochondrial respiration and reactive oxygen species generation. Expression of survivin correlated with the radiation injury in patients. The current data indicate that PI3K signaling increased mitochondrial reactive oxygen species generation and ISC activation that improved IEC recovery from radiation-induced injury. The results suggest that increasing PI3K signaling and induced mitochondrial respiration may improve mucosal healing in patients with radiation injury.

JOURNAL/nrgr/04.03/01300535-202602000-00046/figure1/v/2025-05-05T160104Z/r/image-tiff Unlike mammals, zebrafish possess a remarkable ability to regenerate their spinal cord after injury, making them an ideal vertebrate model for studying regeneration. While previous research has identified key cell types involved in this process, the underlying molecular and cellular mechanisms remain largely unexplored. In this study, we used single-cell RNA sequencing to profile distinct cell populations at different stages of spinal cord injury in zebrafish. Our analysis revealed that multiple subpopulations of neurons showed persistent activation of genes associated with axonal regeneration post injury, while molecular signals promoting growth cone collapse were inhibited. Radial glial cells exhibited significant proliferation and differentiation potential post injury, indicating their intrinsic roles in promoting neurogenesis and axonal regeneration, respectively. Additionally, we found that inflammatory factors rapidly decreased in the early stages following spinal cord injury, creating a microenvironment permissive for tissue repair and regeneration. Furthermore, oligodendrocytes lost maturity markers while exhibiting increased proliferation following injury. These findings demonstrated that the rapid and orderly regulation of inflammation, as well as the efficient proliferation and redifferentiation of new neurons and glial cells, enabled zebrafish to reconstruct the spinal cord. This research provides new insights into the cellular transitions and molecular programs that drive spinal cord regeneration, offering promising avenues for future research and therapeutic strategies.

Hunan Province, located in Central-South China, has a hot and humid climate, which has shaped the unique characteristics of its cattle. In this study, we analyzed the genomic diversity of 110 indigenous Hunan cattle using whole-genome sequencing and found that they have a mixed ancestry of indicine and taurine. By grouping the cattle based on their collection regions (western, central, southeastern, and southern Hunan), we used an unsupervised three-component Gaussian model to classify the runs of homozygosity (ROH) and calculated the genomic inbreeding coefficient based on runs of homozygosity (FROH) to assess inbreeding levels. The results showed that western Hunan cattle had the highest level of hybridization, while southern Hunan cattle had the lowest. Through selective sweep analysis, we identified candidate genes and pathways related to environmental adaptation and homeostasis. Notably, the <i>SLC5A2</i> gene showed strong selection signals across all four regions and exhibited a distinct haplotype compared to other referenced cattle breeds. Additionally, we detected introgression from wild species into Hunan domestic cattle and analyzed their Y-chromosome haplotypes.

The brain-derived neurotrophic factor (BDNF) has become one of the cornerstones of neuropathology, influencing synaptic plasticity, cognitive resilience, and neuronal survival. Apart from its molecular biology, BDNF is a powerful target for transformative benefit in precision medicine, leading to innovative therapeutic approaches for neurodegenerative and psychiatric diseases like Alzheimer's disease (AD), Parkinson's disease (PD), major depressive disorder (MDD), and post-traumatic stress disorder (PTSD). Nevertheless, clinical applicability is obstructed by hurdles in delivery, patient-specific diversity, and pleiotropic signaling. Here, we summarize findings in BDNF research, including its regulatory pathways and diagnostic/prognostic biomarkers and integrative therapeutic approaches. We describe innovative delivery systems, such as lipid nanoparticle-based mRNA therapies and CRISPR-dCas9-based epigenetic editing that bypass obstacles such as BBB (blood-brain barrier) and enzymatic degradation. The recent implementation of multiplex panels combining BDNF biodynamic indicators with tau and amyloid-β signaling markers showcases novel levels of specificity for both early detection and potential therapeutic monitoring. Humanized preclinical models like iPSC-derived neurons and organoids point to the key role of BDNF in neurodeveloping and neurodegenerative processes, paralleling advances in bridging preclinical observation and clinical environments. Moreover, novel therapeutic tools delivering TrkB activators or the implementation of AI-based dynamic care platforms enable tailored and scalable treatments. This review also aims to extend a framework used in the understanding of BDNF's relevance to traditional neurodegenerative models by situating more recent work detailing BDNF's actions in ischemic tissues and the gut-brain axis in the context of systemic health. Finally, we outline a roadmap for the incorporation of BDNF-centered therapies into worldwide healthcare, highlighting ethical issues, equity, and interdisciplinary decomposition. The therapeutic potential of BDNF heralds a new era in neuroscience and medicine, revolutionizing brain health and paving the way for the advancement of precision medicine.

γδ T cells, a type of specialized T cell, differ from alpha-beta T cells due to the presence of γ and δ chain surface T cell receptors. These receptors allow them to directly recognize and bind antigenic molecules without the requirement of attachment to MHC or APC antigen presentation. Given their intrinsic properties and functional versatility, γδ T cells are under intensive investigation as carriers for chimeric antigen receptor (CAR) in the context of cancer therapy. In this regard, γδ CAR-T cells have demonstrated great potential to overcome the limitations of antigen recognition with the help of dual antigen identification mechanisms. However, there are still technological challenges that need to be addressed. This discussion focuses on the research status and future development prospects of γδ T cells and γδ CAR-T cells, aiming to provide valuable insights for the follow-up research and practical application of γδ CAR-T cells.

Human milk oligosaccharides (HMOs) are a diverse group of complex carbohydrates that play crucial roles in infant health, promoting a beneficial gut microbiota, modulating immune responses, and protecting against pathogens. Central to the synthesis of HMOs are glycosyltransferases, a specialized class of enzymes that catalyse the transfer of sugar moieties to form the complex glycan structures characteristic of HMOs. This review provides an in-depth analysis of glycosyltransferases, beginning with their classification based on structural and functional characteristics. The catalytic activity of these enzymes is explored, highlighting the mechanisms by which they facilitate the precise addition of monosaccharides in HMO biosynthesis. Structural insights into glycosyltransferases are also discussed, shedding light on how their conformational features enable specific glycosidic bond formations. This review maps out the key biosynthetic pathways involved in HMO production, including the synthesis of lactose, and subsequent fucosylation and sialylation processes, all of which are intricately regulated by glycosyltransferases. Industrial methods for HMO synthesis, including chemical, enzymatic, and microbial approaches, are examined, emphasizing the role of glycosyltransferases in these processes. Finally, the review discusses future directions in glycosyltransferase research, particularly in enhancing the efficiency of HMO synthesis and developing advanced analytical techniques to better understand the structural complexity and biological functions of HMOs.

<h4>Background</h4>Identifying genomic regions associated with traits of interest and their biological processes provides valuable insights into the phenotypic variability of these traits. This study aimed to identify candidate genes and genomic regions associated with 16 traits currently evaluated by the Brazilian Association of Zebu Breeders (ABCZ). These traits include reproductive traits such as age at first calving (AFC), stayability (STAY), and scrotal circumference at 365 (SC365) and 450 days (SC450). Growth traits include birthweight (BW), expected progeny difference for weight at 120days of age (EPD120), as well as weight at 120 (W120), 210 (W210), 365 (W365), and 450 days of age (W450). Carcass traits include body conformation (BC), finishing score (FS), marbling (MARB), muscularity (MUSC), finishing precocity (FP), and ribeye area (REA).<h4>Methods</h4>A dataset containing 304,782 Nellore cattle genotyped with 437,650 SNPs (after quality control) was used for this study. The Algorithm for Proven and Young (APY), implemented in the PREGSF90 software, was used to compute the GAPY-1 matrix using 36,000 core animals (which explained 98% of the variance in the genomic matrix). Subsequently, the SNP solutions were estimated by back-solving the Genomic Estimated Breeding Values (GEBVs) predicted by ABCZ using the single-step GBLUP method. Genomic regions were identified using sliding windows of 175 consecutive SNPs, and the top 1% genomic windows, ranked based on their proportion of the additive genetic variance, were used to annotate positional candidate genes and genomic regions associated with each of the 16 traits.<h4>Results</h4>The top 1% windows for all traits explained between 2.779% (STAY) to 3.158% (FP) of the additive genetic variance, highlighting the polygenic nature of these traits. Functional analysis of the candidate genes and genomic regions provided valuable insights into the genetic architecture underlying these traits in Nellore cattle. For instance, our results revealed genes with important functions for each trait, such as <i>SERPINA14</i> (plays a key role for the endometrial epithelium) identified for AFC, <i>HSPG2</i> (associated with morphological development and tissue differentiation) identified for BW, among others.<h4>Conclusion</h4>We identified genomic regions and candidate genes, some of which have been previously reported in the literature, while others are novel discoveries that warrant further investigation. These findings contribute to gene prioritization efforts, facilitating the identification of functional candidate genes that can enhance genomic selection strategies for economically important traits in Nellore cattle.

Long-read sequencing (LRS) was introduced as the third generation of next-generation sequencing technologies with a high accuracy rate in genomic variant identification for some of its platforms. Due to the structural complexity of many pharmacogenes, the presence of rare variants, and the limitations of genotyping and short-read sequencing approaches in detecting pharmacovariants, LRS methods are likely to become increasingly utilized in the near future. In this review, we aim to provide a comprehensive discussion of current and future applications of long-read genotyping methods by introducing the opportunities and advantages as well as the challenges and disadvantages of state-of-the-art LRS platforms for the implementation of pharmacogenomic tests in clinical and research settings. New approaches to data processing, as well as the challenges and pitfalls of performing such tests in daily practice, will be explored in detail. We provide references to resources for those who are interested or intend to employ LRS in pharmacogenomics screening, both in clinical and research settings.

Oncocytomas are clinically benign tumors composed of cells with abundant granular eosinophilic cytoplasm due to a high mitochondrial content. While typically non-metastatic, rare cases of metastatic oncocytomas have been documented. This report describes a unique case involving transcriptome analysis to identify genes associated with the oncocytoma signature. A 57-year-old woman presented to the emergency department with COVID-19 pneumonia. Incidentally, a CT chest scan revealed a large mass in the left upper quadrant. Further imaging of the abdomen and pelvis identified a 14 cm left renal mass and multiple low-density hepatic lesions. A liver biopsy confirmed a PAX-8 and CD10 positive carcinoma, consistent with metastatic renal cell carcinoma. Following neoadjuvant therapy, the patient underwent a left radical nephrectomy, partial hepatectomy, and cholecystectomy. This case emphasizes the rarity of metastatic oncocytoma and the importance of genomic testing in elucidating its molecular underpinnings. By identifying specific genetic alterations linked to the oncocytoma signature, genomic analysis offers critical insights into potential mechanisms of metastasis. These findings could enhance diagnostic accuracy and guide the development of targeted therapeutic strategies in rare metastatic cases of oncocytoma.

Adenosine diphosphate-ribosylation (ADPRylation) is a reversible posttranslational modification that plays a crucial role in cellular homeostasis and disease development. ADPRylation is produced via nicotinamide adenine dinucleotide hydrolysis and modifies proteins via corresponding transferases, mainly poly(ADP-ribose) polymerases (PARPs), the inhibitors of which have been used in the clinical treatment of cancer. ADPRylation is involved in various physiological processes, including pathogen infection, inflammation, DNA repair, and neurological disorders. In neurodegenerative diseases (NDs), dysregulated ADPRylation contributes to protein aggregation, neuroinflammation, and metabolic disturbances, while targeted modulation shows therapeutic potential. ADPRylation differentially regulates neurodegenerative processes, and PARP inhibitors can reduce neuroinflammation, oxidative stress, and metabolic dysfunction. However, challenges such as poor blood-brain barrier penetration and cell type-specific responses limit clinical translation. This review summarizes recent findings on the role of ADPRylation and PARPs in NDs, highlighting their involvement in protein aggregation and cellular signaling. It emphasizes the importance of ADPRylation in neuronal cells and supports the development of precision therapies targeting this pathway to address current treatment challenges in NDs.

Mitochondrial ribosomal proteins (MRPs) are essential components of mitochondrial ribosomes, responsible for translating proteins encoded by mitochondrial DNA and maintaining mitochondrial energy metabolism and function. Emerging evidence suggests that MRPs exhibit significant expression changes in multiple cancer types, profoundly affecting tumor biology through modulating oxidative stress levels, inducing metabolic reprogramming, disrupting cell cycle regulation, inhibiting apoptosis, promoting mitophagy, and remodeling the tumor microenvironment. Specifically, MRPs have been implicated in tumor cell proliferation, migration, invasion, and apoptosis, highlighting their potential as therapeutic targets. This review summarizes the multifaceted roles of MRPs in cancer, focusing on their impact on the tumor microenvironment and their potential as prognostic biomarkers and therapeutic targets. We also explore the implications of MRPs in precision oncology, particularly in patient stratification and the design of metabolic targeted therapies, offering new insights and research directions for the precise prevention and treatment of cancer.

Exosomes, as vital mediators of intercellular communication, play a critical role in the progression of cardiovascular disease (CVD). Recently, macrophage-derived exosomes (Mφ-Exos) have garnered increasing attention because of their significant potential in early diagnosis, pathological processes, and therapeutic applications for CVD. Exosomes contain diverse nucleic acids (e.g., miRNAs, mRNAs, and long noncoding RNAs (lncRNAs)) and proteins, which serve as specific biomarkers that regulate various stages of CVD. For example, miRNAs encapsulated within exosomes (e.g., miR-21, miR-133a, and miR-155) are closely associated with atherosclerosis, myocardial infarction, coronary artery disease, and stroke, and changes in their abundance can serve as diagnostic and prognostic indicators. Additionally, the composition of Mφ-Exos, including miRNAs, lipids, and proteins, plays a significant role in the initiation, progression, and inflammation of CVD. Research on Mφ-Exos provides new directions for early diagnosis, mechanistic exploration, and novel therapeutic targets in CVD. However, challenges remain regarding exosome isolation and identification technologies. Future studies need to further explore the biological properties of exosomes and develop more efficient, economical, and straightforward isolation methods. This review summarizes the multifaceted regulatory roles of Mφ-Exos in CVD, encompassing key processes such as inflammation, angiogenesis, metabolism, and cell death. Research has shown that M1-Exos promote the progression and exacerbation of CVD through pro-inflammatory and pro-fibrotic mechanisms, while M2-Exos demonstrate significant therapeutic potential via anti-inflammatory, pro-angiogenic, and metabolic reprogramming pathways. These findings not only reveal the complex mechanisms of Mφ-Exos in CVD but also provide new perspectives and potential targets for early diagnosis and precision treatment of the disease.

Stimuli-responsive cellulose hydrogels have garnered significant attention in the biomedical field owing to their extensive applications in tissue engineering and controlled drug delivery systems. Derived from cellulose and its derivatives, they are synthesized through physical or chemical cross-linking techniques, offering notable advantages such as cost-effectiveness and excellent biocompatibility. These hydrogels can respond to environmental stimuli, including pH variations, temperature fluctuations, and light exposure, enabling targeted drug release and promoting tissue regeneration. In tissue engineering, Stimuli-responsive cellulose hydrogels are used for the repair and regeneration of skin, bone, and other critical tissues. In drug delivery, they are optimized for oral, nasal, and ocular administration, as well as advanced cancer therapies. In addition, Stimuli-responsive cellulose hydrogels exhibit significant potential in disease diagnostics, particularly their conductive variants, which show promise in biosensing and diagnostic applications. However, despite their potential, challenges such as immune compatibility, long-term stability, and scalability in production remain barriers to clinical translation. Future research efforts should focus on multifunctional integration, advanced intelligent design, and enhanced stimulus responsiveness to fully unlock their potential in biomedical applications and facilitate their transition from laboratory research to practical use.

<b>Background/Objectives</b>: In this paper, we report the development of the first chrome-doped hydroxyapatite in a poly (vinyl alcohol) (PVA) matrix enriched with amoxicillin for biomedical applications. The development of chromium-doped hydroxyapatite coatings in a PVA matrix enriched with amoxicillin aims to provide new biomaterials with improved physico-chemical and biological properties, making them promising candidates for biomedical applications. <b>Methods:</b> Through ultrasound studies, we obtained valuable information on the stability of the samples. X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), Fourier-transform infrared (FTIR) spectroscopy, metallographic microscopy (MM), and atomic force microscopy (AFM) were employed for the characterization of the samples. The biocompatibility of the CrHApAPV and CrHApAPV-Ax coatings was assessed using the MG63 human osteoblast-like cell line. To evaluate the cytotoxic potential of these coatings, the cell viability was quantified using the MTT assay after 24 h of incubation. The antibacterial activity of the coatings was evaluated with the aid of the reference strain <i>Pseudomonas aeruginosa</i> ATCC 27853 (<i>P. aeruginosa</i>). <b>Results</b>: The XRD patterns of CrHApAPV and CrHApAPV-Ax samples were examined to evaluate the effects of PVA and amoxicillin on the lattice parameters, unit cell volume, and average crystallite sizes. The results of the in vitro antibacterial assay demonstrated that both the CrHApAPV and CrHApAPV-Ax coatings exhibited very good antibacterial properties for all the tested time intervals. <b>Conclusions:</b> Our results underline the stability of the analyzed samples. Moreover, our physico-chemical and biological studies highlight that CrHApAPV and CrHApAPV-Ax coatings could be considered promising materials for biomedical uses.

Interest in the subject of umbilical cord clamping is long-standing. New evidence reveals that placental transfusion, facilitated by delayed cord clamping (DCC), reduces death and need for blood transfusions for preterm infants without evidence of harm. Even a brief delay in clamping the cord shows improved survival and well-being, but waiting at least two minutes is even better. We propose that three major benefits from DCC contribute to reduced mortality of preterm infants: (1) benefits from the components of blood; (2) assistance from the continued circulation of blood; and (3) the essential mechanical interactions that result from the enhanced volume of blood. The enhanced blood volume generates mechanical forces within the microcirculation that support the newborn's metabolic and cardiovascular stability and secure short- and long-term organ health. Several unique processes prime preterm and term newborns to receive the full placental transfusion, not to be misinterpreted as extra blood or over-transfusion. Disrupting cord circulation before the newborn's lung capillary bed has been fully recruited and the lungs can replace the placenta as a respiratory, gas-exchanging organ may be harmful. Early cord clamping also denies the newborn a full quota of iron-rich red blood cells as well as valuable stem cells for regeneration, repair, and seeding of a strong immune system. We propose that delayed cord clamping and intact-cord stabilization have the potential to save lives by protecting many neonates from hypovolemia, inflammation, and ischemia.

<h4>Background</h4>Chicken eggshells and bone waste are waste materials rich in calcium (Ca) and phosphorus (P), and they are often discarded despite their potential value. These materials are promising precursors for hydroxyapatite (HA), a biocompatible material structurally similar to natural bone that is widely used in biomedical applications.<h4>Aim</h4>To evaluate the Ca and P contents of broiler chicken eggshells and bone waste and to synthesize HA from these waste materials. The results highlight the potential of broiler chicken bones as a sustainable source of HA, particularly for veterinary bone graft applications.<h4>Methods</h4>Eggshell and chicken bone waste samples were collected from restaurants. The samples were washed, cleaned, dried, and heated at 800°C to produce calcite. The resulting calcite suspension was synthesized by heating it at 70°C and gradually mixing it with an ammonium phosphate ((NH₄)₂HPO₄) suspension over 30 minutes. During the mixing process, the solution pH was maintained above 9. The HA synthesized from eggshells was then analyzed using titration to determine Ca content and spectrophotometry to measure P content.<h4>Results</h4>The analysis revealed that eggshells contained 15.986 ± 0.188% Ca and 13.794 ± 0.176% P, whereas chicken bones had higher Ca and P levels, with 18.9 ± 0.386% Ca and 13.906 ± 0.320% P. The average Ca:P ratio was 1:1.158 for eggshells and 1:1.359 for chicken bones.<h4>Conclusion</h4>This study demonstrates the feasibility of converting poultry industry waste into valuable biomaterials to promote sustainable practices. The higher Ca and P levels observed in chicken bones than in eggshells may offer superior potential for treating pet fractures.

A network neuroscience perspective can significantly advance the understanding of neurodegenerative disorders, particularly frontotemporal dementia (FTD). This study employed an innovative multiplex connectomics approach, integrating cortical thickness (CTH) and fluorodeoxyglucose-positron emission tomography (FDG-PET) in a dual-layer model to investigate network alterations in FTD subtypes across two geographically distinct sites. The cohort included groups of behavioral variant FTD (bvFTD), primary progressive aphasia (PPA), mild cognitive impairment (MCI), and cognitively normal (CN) individuals who were analyzed from two separate sites. Site 1 included 28 bvFTD, 20 PPA, and 27 MCI participants, whereas Site 2 included 26 bvFTD, 43 PPA, and 43 CN individuals, respectively. Utilizing CTH and FDG-PET data after standard preprocessing, a multiplex network pipeline in BRAPH2 toolbox was used to derive multiplex participation coefficient (MPC) between the groups. The analysis revealed an increase in global MPC as an indicator of disease in PPA at both sites. Additionally, nodal MPC alterations in the anterior cingulate, frontal, and temporal lobes in PPA were compared with bvFTD. Comparisons with the CN showed that nodal MPC alterations were more extensive in PPA when compared with bvFTD. These findings underscore the potential utility of multiplex connectomes for identifying network disruptions in neurodegenerative disorders, offering promising implications for future research and clinical applications.

Functional connectivity (FC) reflects brain-wide communication essential for cognition, yet the role of underlying biophysical factors in shaping FC remains unclear. We quantify the influence of physical factors-structural connectivity (SC) and Euclidean distance (DC), which capture anatomical wiring and regional distance-and molecular factors-gene expression similarity (GC), and neuroreceptor congruence (RC), representing neurobiological similarity-on resting-state FC. We assess how these factors impact graph-theoretic and gradient features, capturing pairwise and higher-order interactions. By generating <i>remnant functional networks</i> after selectively removing connections tied to specific factors, we show that molecular factors, particularly RC, dominate graph-theoretic features, while gradient features are shaped by a mix of molecular and physical factors, especially GC and DC. SC has a surprisingly minor role. We also link FC alterations to biophysical factors in schizophrenia, bipolar disorder, and attention deficit/hyperactivity disorder (ADHD), with physical factors differentiating these groups. These insights are key for understanding FC across various applications, including task performance, development, and clinical conditions.

<h4>Background</h4>Fatty liver disease and metabolic dysfunction-associated steatotic liver disease (MASLD) have recently been recognized as a major global health issue, and there is much evidence linking MASLD with a range of extrahepatic comorbidities. The current study evaluated extrahepatic comorbidities in patients with MASLD and highlighted the necessity of a multidisciplinary approach to its management.<h4>Methods</h4>A cross-sectional study was conducted at a tertiary center in Tehran. Fatty liver was diagnosed via ultrasonography findings. Exclusion criteria included those with other liver diseases, such as chronic viral hepatitis. Participants underwent liver stiffness measurement using Fibroscan, and clinical data and liver function tests were collected, and questionnaires for DASS-21 and the Pittsburg Sleep Quality Index (PSQI) were completed. We conducted a chi-square test and ANOVA test to evaluate and explore the extrahepatic comorbidities and manifestations associated with fatty liver disease.<h4>Results</h4>Of the 385 study participants, 50.6% had severe steatosis, and 29.1% had severe fibrosis. Several comorbidities, such as hypertension (fibrosis: <i>P</i>=0.033, steatosis: <i>P</i>=0.011), diabetes (fibrosis: <i>P</i>=0.006, steatosis: <i>P</i>=0.002), and poor sleep quality (fibrosis: <i>P</i>=0.015), were significantly associated with the severity of non-alcoholic fatty liver disease (NAFLD). There were statistically significant differences in mean scores of depression and anxiety across different levels of fibrosis and steatosis (<i>P</i><0.05).<h4>Conclusion</h4>MASLD is a multisystem disorder with widespread extrahepatic manifestations impacting many organs and systems. Patients with MASLD should be screened for comorbidities such as diabetes, cardiovascular disease, and mental health conditions to improve overall health outcomes and prevent disease advancement.

<h4>Introduction</h4> HFE genetic variants, especially C282Y homozygosity (C282Y+/+), can increase systemic iron and cause hemochromatosis, though expression varies. Excess iron can lead to liver disease/cancer, yet factors influencing liver iron beyond HFE genotype remain unclear. We investigated genetic/environmental factors influencing liver iron, including HFE genotype and hemochromatosis diagnosis. <h4>Methods</h4> We analysed 37,287 European ancestry UK Biobank participants (mean age 64.1, SD 7.6) with HFE genotypes and MRI-estimated liver iron concentrations (MRLIC). Linear regression assessed MRLIC associations with genetic and environmental factors, adjusting for age, sex, and genetic covariates. <h4>Results</h4> Mean MRLIC was highest in undiagnosed C282Y+/+ males and females (2.56 and 2.31mg/g) vs. diagnosed (1.23 & 1.51mg/g, p=0.0001 & 0.0004). Other HFE genotypes had nominal increases vs. those without HFE genetic variants. Higher MRLIC was associated with higher alcohol intake (β=0.11, 95%CI: 0.09–0.11, p=6.0×10 −128 ; >30 vs. 1–14 units/week), frequent red/processed meat consumption (β=0.08, 95%CI: 0.07–0.09, p=3.7×10 −54 ; ≥3 times/week vs. none), high waist-height ratio (β=0.01, 95%CI: 0.006–0.02, p=6.4×10 −5 ) and genetically predicted transferrin saturation (β=0.22, 95%CI: 0.19– 0.26, p=3.8×10 −46 ). Lower MRLIC was associated with underweight BMI (β=−0.06, 95%CI: −0.09 – −0.03, p=1.1×10 −4 ), proton pump inhibitor use (β=−0.03, 95%CI: −0.04 – −0.03, p=3.5×10 −17 ), and ≥4 cups/day of tea (β=−0.01, 95%CI: −0.02 – −0.003, p=0.005 vs. non-drinkers). Among C282Y+/+ individuals (n=91), tea ≥4 cups/day was associated with lower MRLIC (β=−0.99, 95%CI: −1.89 – −0.08, p=0.03). <h4>Conclusion</h4> Undiagnosed C282Y+/+ individuals had excess liver iron vs. diagnosed, likely due to treatment. Genetic and environmental factors influence liver iron beyond C282Y+/+. Tailored lifestyle advice could benefit those at risk of hemochromatosis.

Acute myeloid leukaemia (AML) is a prevalent haematologic malignancy characterized by significant heterogeneity. Despite the application of aggressive therapeutic approaches, AML remains associated with poor prognosis. Circular RNAs (circRNAs) constitute a unique class of single-stranded RNAs featuring covalently closed loop structures that are ubiquitous across species. These molecules perform crucial regulatory functions in the pathogenesis of various diseases through diverse mechanisms, including acting as miRNA sponges, interacting with DNA or proteins, and encoding functional proteins/polypeptides. Recently, numerous circRNAs have been confirmed to have aberrant expression patterns in AML patients. In particular, certain circRNAs are closely associated with specific clinicopathological characteristics and thus have great potential as diagnostic/prognostic biomarkers and therapeutic targets in AML. Herein, we systematically summarize the biogenesis, degradation, and functional mechanisms of circRNAs while highlighting their clinical relevance. We also outline a series of online databases and analytical tools available to facilitate circRNA research. Finally, we discuss the current challenges and future research priorities in this evolving field.

Surgical resection, radiotherapy and chemotherapy are the primary strategies of treating cancers globally. However, the current treatment methods bring new disease burdens to patients due to postoperative complications and multiple side effects, especially in surface tumours such as oral squamous cell carcinoma (OSCC). In this study, we developed a microwave cold atmospheric plasma (CAP) device in conjunction with tumour microenvironment-responsive nanohydroxyapatite (nHA) for the first time. The synergistic effects of CAP and nHA combined application on OSCC were evaluated in both in vitro and in vivo experiments. The synergistic effects of CAP and pH-responsive NH₂-nHA on the apoptosis, intracellular reactive oxygen species (ROS) and calcium ion concentration of OSCC cells were investigated in vitro. The synergistic induction of CAP with NH₂-nHA exhibited optimal tumour-specific inhibitory effects on OSCC. The results revealed that the combined application of CAP with NH₂-nHA induced apoptosis of tumour cells in vitro and killed 84.0% of tumours in vivo. Mechanistically, CAP enhances extracellular ROS production, while NH₂-nHA amplifies intracellular calcium ion (Ca²⁺) concentrations, synergistically increasing intracellular ROS levels to provoke oxidative stress in OSCC cells, ultimately triggering the mitochondrial apoptosis pathway. In conclusion, the combined utilisation of CAP and NH₂-nHA presents a promising avenue as a novel, selective, and non-invasive strategy in the management of OSCC.

<i>Klebsiella pneumoniae</i> is a clinically important pathogenic bacteria that poses a serious threat to human health. In particular, the emergence of hypervirulent and multidrug-resistant <i>K. pneumoniae</i> has posed great challenges in clinical anti-infective therapy. In the <i>K. pneumoniae</i> genome, mobile genetic elements (MGEs), such as plasmids, prophages, transposons, and insertion sequences, enhance bacterial viability and adaptation by mediating the horizontal transfer of virulence genes, antibiotic resistance genes, and other adaptive genes. This paper reviews the types and characteristics of the main MGEs in <i>K. pneumoniae</i>, focusing on their effects on bacterial virulence and antibiotic resistance, with the aim of providing clues for developing infection control measures and new antibacterial drugs.

Free-standing tissue structures tethered between pillars are powerful mechanobiology tools for studying cell contraction. To model interfaces ubiquitous in natural tissues and upgrade existing single-region suspended constructs, we developed Suspended Tissue Open Microfluidic Patterning (STOMP), a method to create multi-regional suspended tissues. STOMP uses open microfluidics and capillary pinning to pattern subregions within free-standing tissues, facilitating the study of complex tissue interfaces, such as diseased-healthy boundaries (e.g., fibrotic-healthy) and tissue-type interfaces (e.g., bone-ligament). We observed altered contractile dynamics in fibrotic-healthy engineered heart tissues compared to single-region tissues and differing contractility in bone-ligament enthesis constructs compared to single-tissue periodontal ligament models. STOMP is a versatile platform - surface tension-driven patterning removes material requirements common with other patterning methods (e.g., shear-thinning, photopolymerizable) allowing tissue generation in multiple geometries with native extracellular matrices and advanced four-dimensional (4D) materials. STOMP combines the contractile functionality of suspended tissues with precise patterning, enabling dynamic and spatially controlled studies.

Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is a multifactorial, immune-mediated condition marked by chronic gastrointestinal inflammation. This condition significantly impairs patients' quality of life and represents a major public health challenge globally. Pathogenesis of IBD arises from complex interplay among genetic predisposition, environmental factors, immune dysregulation, and microbial dysbiosis. Although significant strides have been made in unraveling these mechanisms, existing therapeutic options remain inadequate in addressing the full spectrum of clinical needs, underscoring the urgent demand for innovative strategies. Regenerative medicine has emerged as a promising frontier, offering novel tools for therapeutic development. We briefly consolidated current knowledge on IBD pathogenesis and treatments, emphasized the pivotal potential of human intestinal organoids (including adult stem cell-derived organoids and pluripotent stem cell- derived organoids) as a robust platform for mechanistic studies and treatment exploration. Leveraging this technology, we aim to advance personalized and next-generation therapies for IBD.

<h4>Introduction</h4>Childhood obesity is defined as a medical condition characterised by abnormally high amounts of body fat relative to lean body mass, which increases the risk of adverse health outcomes among children and adolescents from birth to 18 years. The prevalence of childhood obesity, which has serious healthcare implications, is surging, together with its healthcare burden. In this review we explore the intricate interplay of hereditary, environmental, behavioural, cultural and metabolic factors contributing to the global increase in childhood obesity rates. We examine the influence of prenatal factors, genetic predispositions and epigenetic mechanisms on obesity susceptibility and treatment strategies, emphasising the importance of a multilevel life course framework to understand the multifactorial causes of obesity.<h4>Methods</h4>This narrative review examines the epidemiology, burden, aetiology and impact of childhood obesity by focusing on published literature and the efficacy of multilevel interventions. Comprehensive algorithms are provided to illustrate the causes of childhood obesity through the lens of a multilevel life course framework, taking into consideration individual, family, community and societal factors.<h4>Results</h4>Genetic predispositions, including inherited tendencies towards emotional eating, metabolic variations and body fat distribution, significantly influence a child's obesity risk. Environmental factors, such as limited access to nutritious food, sedentary behaviour, insufficient opportunities for physical activity and obesogenic environments, contribute to the increasing prevalence of childhood obesity. Prenatal influences, including maternal hyperglycaemia and nutritional exposures, lead to epigenetic alterations that predispose children to obesity and metabolic disorders. The social environment, including parental influences, cultural norms and peer dynamics, shapes children's dietary habits and physical activity levels. Additionally, the review highlights the importance of early detection of metabolic alterations associated with paediatric obesity and insulin resistance and the potential for epigenetic mechanisms as therapeutic targets. Recommendations are made for tailored medical nutrition therapy, screening for syndromic obesity and multilevel interventions targeting individual and societal factors.<h4>Conclusions</h4>This review underscores the necessity of a comprehensive, multilevel approach that integrates genetic, environmental, behavioural and cultural factors along with lifestyle modifications and public health initiatives to address the complex and multifaceted issue of childhood obesity effectively. Targeted interventions across the life course, policy reforms, community engagement and technological innovations are recommended to mitigate obesity risks and promote long-term health. An infographic is available for this article. INFOGRAPHIC.

Synovial sarcoma is an aggressive soft-tissue cancer driven by the chimeric SS18::SSX fusion oncoprotein, which disrupts chromatin remodeling by combining two antagonistic transcriptional regulators. SS18 participates in BAF complexes that open chromatin, while the SSX genes are cancer-testis antigens that interface with chromatin decorated with monoubiquitinated histone H2A placed by polycomb repressive complex activity. Because KDM2B brings polycomb repressive complex to unmethylated CpG islands, it is plausible that methylation directly determines the distribution of SS18::SSX to target loci. Given that synovial sarcoma is also characterized by a peculiarly low DNA hypomethylation profile, we hypothesized that further disturbance of DNA methylation would have a negative impact on synovial sarcoma growth. DNMT1 disruption by CRISPR/Cas9 targeting or pharmacological inhibition with cytidine analogs 5-aza-2'-deoxycytidine (decitabine) and 5-azacytidine led to decreased genome-wide methylation, redistribution of SS18::SSX, and altered gene expression profiles, most prominently including upregulation of tumor suppressor genes, immune-related genes, and mesenchymal differentiation-related genes. These drugs suppressed growth of synovial sarcoma cell lines and drove cytoreduction in mouse genetic models. DNMT1 inhibitors, already approved for treating myelodysplastic syndromes, warrant further clinical investigation for synovial sarcoma as repurposed, targeted treatments exploiting a vulnerability in the intrinsic biology of this cancer.

The direct reprogramming of cells has tremendous potential in in vitro neurological studies. Previous attempts to convert blood cells into induced neurons have presented several challenges, necessitating a less invasive, efficient, rapid, and convenient approach. The current study introduces an optimized method for converting somatic cells into neurons using a nonsurgical approach that employs peripheral blood cells as an alternative source to fibroblasts. We have demonstrated the efficacy of a unique combination of transcription factors, including NEUROD1, and four Yamanaka reprogramming factors (OCT3/4, SOX2, KLF4, and c-MYC), in generating glutamatergic neurons within 3 wk. This approach, which requires only five pivotal factors (NEUROD1, OCT3/4, SOX2, KLF4, and c-MYC), has the potential to create functional neurons and circumvents the need for induced pluripotent stem cell (iPSC) intermediates, as evidenced by single-cell RNA sequencing and whole-genome bisulfite sequencing, along with lineage-tracing experiments using Cre-LoxP system. While fibroblasts have been widely used for neuronal reprogramming, our findings suggest that peripheral blood cells offer a potential alternative, particularly in contexts where minimally invasive sampling and procedures convenient for patients are emphasized. This method provides a rapid strategy for modeling neuronal diseases and contributes to advancements in drug discovery and personalized medicine.

Rafeesome, a newly identified multivesicular body (MVB)-like organelle, forms through the fusion of RAB22A-mediated ER-derived noncanonical autophagosomes with RAB22A-positive early endosomes. However, the mechanism underlying the formation of RAB22A-mediated noncanonical autophagosomes remains unclear. Herein, we report a secretory ER-phagy pathway in which the assembly of RAB22A/TMEM33/RTN4 induces the clustering of high-molecular-weight RTN4 oligomers, leading to ER membrane remodeling. This remodeling drives the biogenesis of ER-derived RTN4-positive noncanonical autophagosomes, which are ultimately secreted as TMEM33-marked RAB22A-induced extracellular vesicles (R-EVs) via Rafeesome. Specifically, RAB22A interacts with the tubular ER membrane protein TMEM33, which binds to the TM2 domain of the ER-shaping protein RTN4, promoting RTN4 homo-oligomerization and thereby generating RTN4-enriched microdomains. Consequently, the RTN4 microdomains may induce high curvature of the ER, facilitating the bud scission of RTN4-positive vesicles. These vesicles are transported by ATG9A and develop into isolation membranes (IMs), which are then anchored by LC3-II, a process catalyzed by the ATG12-ATG5-ATG16L1 complex, allowing them to grow into sealed RTN4 noncanonical autophagosome. While being packaged into these ER-derived intermediate compartments, ER cargoes bypass lysosomal degradation and are directed to secretory autophagy via the Rafeesome-R-EV route. Our findings reveal a secretory ER-phagy pathway initiated by the assembly of RAB22A/TMEM33/RTN4, providing new insights into the connection between ER-phagy and extracellular vesicles.

Neuroendocrine prostate cancer (NEPC) presents a formidable clinical challenge owing to its aggressive progression and resistance to conventional therapies. A key driver of NEPC is the overexpression of MYCN, a well-established oncogene associated with neuroendocrine tumors. However, efforts to directly inhibit the N-Myc protein encoded by this gene have resulted in limited success, thereby hindering therapeutic advancements. To overcome this obstacle, we conducted unbiased genome-wide screening using isogenic prostate cancer cell lines to identify the synthetic vulnerabilities of MYCN. Among the identified candidates, NEUROG2 emerged as a significant candidate. Neurog2 is a proneural transcription factor (PTF) known for its role in developmental processes and trans-differentiation of adult cells. Our findings demonstrate that Neurog2 depletion does not affect non-malignant cells but significantly suppresses the growth of MYCN-overexpressing cells and tumors in orthotopic NEPC models. Furthermore, our observations indicate that Neurog2-driven modulation of PTFs potentially contribute to NEPC development. Thus, targeting Neurog2 holds promise as an effective therapeutic strategy for MYCN-overexpressing NEPC.

Current multiple sclerosis (MS) treatments reduce relapse activity but have limited impact on disease progression. Clinical trials targeting progression often fail because of insufficient understanding of its underlying mechanisms. This study analyzed a clinically well-characterized MS autopsy cohort from the Netherland Brain Bank (186 individuals) from which we selected donors exhibiting opposite disease trajectories of slow versus rapid progression. We performed extensive unbiased histology and spatial transcriptomics, which unveiled a distinct MS lesion type marked by an extensive myeloid cell rim with cellular and transcriptional signatures of innate immune activation, inflammatory cytokine production, unfolded protein response and apoptosis. Presence of this particular lesion type was linked to rapid disease progression. An independent translocator protein 18-kDa positron emission tomography study (114 individuals) validates the association between lesions with a broad myeloid cell rim and disease progression in individuals with MS. Our findings offer crucial insights into the mechanisms behind MS progression, identifying broad rim lesions as a biomarker for rapid disease progression and potentially guiding patient selection for future therapeutic trials targeting central nervous system intrinsic inflammation.

Prostate cancer remains the most common male cancer; however, treatment regimens remain unclear in some cases due to a lack of agreement in current testing methods. Therefore, there is an increasing need to identify novel biomarkers to better counsel patients about their treatment options. Microcalcifications offer one such avenue of exploration. Microfocus spectroscopy at the i18 beamline at Diamond Light Source was utilised to measure X-ray diffraction and fluorescence maps of calcifications in 10 µm thick formalin fixed paraffin embedded prostate sections. Calcifications predominantly consisted of hydroxyapatite (HAP) and whitlockite (WH). Kendall's Tau statistics showed weak correlations of 'a' and 'c' lattice parameters in HAP with GG (r_τ = - 0.323, p = 3.43 × 10^-4 and r_τ = 0.227, p = 0.011 respectively), and a negative correlation of relative zinc levels in soft tissue (r_τ = - 0.240, p = 0.022) with GG. Negative correlations of the HAP 'a' axis (r_τ = - 0.284, p = 2.17 × 10^-3) and WH 'c' axis (r_τ = - 0.543, p = 2.83 × 10^-4) with pathological stage were also demonstrated. Prostate calcification chemistry has been revealed for the first time to correlate with clinical markers, highlighting the potential of calcifications as biomarkers of prostate cancer.

<h4>Introduction</h4>The treatment and prevention of diabetic retinopathy (DR) remain significant challenges. Mendelian randomization (MR) has been widely used to explore novel therapeutic targets. In this study, we conducted a systematic druggable genome-wide MR analysis to explore potential therapeutic targets for DR.<h4>Methods</h4>We obtained data on druggable genes and screened for genes within blood expression quantitative trait loci (eQTL), which were then subjected to MR analysis and colocalization analysis with DR genome-wide association studies data to identify genes strongly associated with DR. Additionally, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, protein-protein interaction (PPI) network construction, drug candidate prediction, and molecular docking were performed to provide valuable insights for the development of more effective and targeted therapeutic drugs.<h4>Results</h4>MR analysis of blood eQTLs revealed 30 significant DR-associated druggable genes, with PRKAB1 (OR = 0.935, 95% CI: 0.892 to 0.980) and CNR1 (OR = 0.814, 95% CI: 0.696 to 0.951) being protective genes, whereas CACNA1E (OR = 1.282, 95% CI: 1.050 to 1.565), NME1 (OR = 1.198, 95% CI: 1.028 to 1.397), and CHRNA2 (OR = 1.192, 95% CI: 1.025 to 1.386) were associated with increased risk. KEGG analysis highlighted significant pathways, including adrenergic signaling in cardiomyocytes (hsa04261), the oxytocin signaling pathway (hsa04921), and arrhythmogenic right ventricular cardiomyopathy (hsa05412). PPI network analysis identified two key modules: one comprising BIN1, CDH2, ACTN1, EPAS1, CEBPA, and CTSD nodes, and the other consisting of CACNG6, CACNA1E, CACNA2D3, and RASGRP3 nodes. Drug candidate prediction suggested ethanol and isoflupredone as potential therapeutic interventions, and molecular docking revealed C5's strong protein binding affinity.<h4>Conclusions</h4>This study utilized MR and colocalization analysis to identify potential drug targets for DR. The findings provide promising leads for the treatments of DR, potentially reducing drug development costs.

Epigenetics is the coordination of gene expression without alterations in the DNA sequence. Epigenetic gene expression is regulated by an intricate system that revolves around the interaction of histone proteins and DNA within the chromatin structure. Histones remain at the core of the epigenetic gene transcription regulation where histone proteins, along with the histone modification enzymes, and the subunits of chromatin remodelers and epigenetic readers play essential roles in regulating gene expression. Histone-related disorders encompass the syndromes induced by pathogenic variants in genes encoding histones, genes encoding histone modification enzymes, and genes encoding subunits of chromatin remodeler and epigenetic reader complexes. Defects in genes encoding histones lead to the expression of abnormal histone proteins. Abnormalities in genes encoding histone modification enzymes result in aberrant histone modifications. Defects in genes encoding subunits of the chromatin remodeler complexes result in defective chromatin remodeling. Defects in genes that code for the epigenetic readers (bromodomain proteins) will hinder their ability to regulate gene transcription. These disorders typically present manifestations that impact the nervous system which is particularly sensitive due to its need for specific patterns of gene expression for neural cell function and differentiation. To date, 72 histone-related disorders have been described including 7 syndromes due to defects in histone genes, 35 syndromes due to histone modifications defects, 26 syndromes due to defects in chromatin remodeling, and 4 due to defects in epigenetic readers. In this review article, the molecular basis of histone structure and function is first explained, followed by a summary of the histone-related syndromes.

<h4>Background</h4>Post-traumatic stress disorder (PTSD) is a common and disabling psychiatric disorder. PTSD involves multiple brain regions and is often comorbid with other psychiatric disorders, such as major depressive disorder (MDD). Recent genome-wide association studies (GWASs) have identified many PTSD risk loci and transcriptomics studies of postmortem brain have found differentially expressed genes associated with PTSD cases. In this study, we integrated genome-wide measures across modalities to identify convergent molecular effects in the PTSD brain.<h4>Methods</h4>We performed tandem mass spectrometry (MS/MS) on a large cohort of donors (N = 66) in two prefrontal cortical areas, dorsolateral prefrontal cortex (DLPFC), and subgenual prefrontal cortex (sgPFC). We also coupled the proteomics data with transcriptomics and microRNA (miRNA) profiling from RNA-seq and small-RNA sequencing, respectively for the same cohort. Additionally, we utilized published GWAS results of multiple psychiatric disorders for integrative analysis.<h4>Results</h4>We found differentially expressed proteins and co-expression protein modules disrupted by PTSD. Integrative analysis with transcriptomics and miRNA data from the same cohort pointed to hsa-mir-589 as a regulatory miRNA responsible for dysregulation of neuronal protein networks for PTSD, including the gamma-aminobutyric acid (GABA) vesicular transporter, SLC32A1. In addition, we identified significant enrichment of risk genes for other psychiatric disorders, such as autism spectrum disorder (ASD) and major depressive disorder (MDD) within PTSD protein co-expression modules, suggesting shared molecular pathology.<h4>Conclusions</h4>We integrated genome-wide measures of mRNA and miRNA expression and proteomics profiling from PTSD, MDD, and control (CON) brains to identify convergent and divergent molecular processes across genomic modalities. We substantially expand the number of differentially expressed genes and proteins in PTSD and identify downregulation of GABAergic processes in the PTSD proteome. This provides a novel framework for future studies integrating proteomic profiling with transcriptomics and non-coding RNAs in the human brain studies.

It is extensively documented that tumor hypoxia contributes to the failure of chemotherapy and radiotherapy. Recent evidence suggests that hypoxia is also closely involved in the resistance to immunotherapy. In this review, we highlight how immune cells that are essential for the maximized immunotherapy efficacy, including cytotoxic T cells, dendritic cells, and natural killer cells, can adapt to tumor hypoxia. We then outline previous attempts targeting tumor hypoxia (for example, modulators of tumor cell oxygen consumption, perfusion modulators, hypoxia-activated prodrugs, hypoxia-inducible factor inhibitors, and hypoxia-responsive chimeric antigen receptor T cells) discussing how these approaches have resulted in an improvement of the antitumor response to immunotherapy in preclinical or clinical settings. Lastly, we review various non-invasive techniques to detect the tumor hypoxia and immune responses. We believe that an integration of the biological knowledge of immune cell adaptation to tumor hypoxia with the cutting edge non-invasive imaging technologies may ultimately allow us not only to select for patients who would benefit the most from the immunotherapy but also to monitor their responses in a real-time manner so that we can offer them an optimal personalized medicine in the clinic.

<h4>Background</h4>Hepatitis C virus (HCV) infection is associated with reduced bone mineral density (BMD) and increased fracture risk. The structural underpinnings for skeletal fragility with HCV and contributions of inflammatory cytokines remain unknown. We used high-resolution peripheral quantitative computed tomography (HR-pQCT) to compare skeletal parameters by chronic HCV.<h4>Methods</h4>We conducted a cross-sectional study among 58 participants with chronic HCV and 58 participants without HCV. Volumetric BMD and cortical dimensions of the radius and tibia were determined by HR-pQCT; visceral fat area and appendicular lean mass were assessed by whole body dual-energy x-ray absorptiometry; serum levels of tumor necrosis factor α (TNF-α), interleukin 6, and interleukin 18 were measured. Multivariable linear regression was used to estimate group differences in bone measurements and cytokines.<h4>Results</h4>Participants with chronic HCV had lower radius trabecular volumetric BMD (-24.2 mg hydroxyapatite [HA]/cm³) and lower tibia trabecular volumetric BMD (-20.5 mg HA/cm³), cortical area (-20.9 mm²), and cortical thickness (-0.47 mm) than participants without HCV (all <i>P</i> < .05), independent of age, sex, visceral fat area, appendicular lean mass, and smoking. Mean log TNF-α was higher with chronic HCV (+0.1-log pg/mL; <i>P</i> < .001), but no differences in mean log interleukin 6 or interleukin 18 were observed. Higher log TNF-α was associated with lower radius trabecular volumetric BMD (-99.7 mg HA/cm³), lower tibia cortical volumetric BMD (-91.6 mg HA/cm³), and higher tibia cortical porosity (+1.39%) by HR-pQCT (all <i>P</i> < .05).<h4>Conclusions</h4>Patients with chronic HCV had decreased trabecular volumetric BMD and cortical dimensions and higher TNF-α than individuals without infection, suggesting that HCV-associated inflammation might contribute to bone deficits.

<h4>Background</h4>Osteosarcoma is the most common primary malignant bone tumor in children and adolescents. The aim of this study was to explore the possibility of OS hypoxia subtype for anti-OS mRNA vaccine development and select suitable patients for precision therapy.<h4>Methods</h4>We comprehensively explored hypoxia-related genes (HRGs) as potential sources of tumor neoantigens in OS patients. Gene set enrichment analysis algorithm and consensus clustering analysis were used to determine immune subtypes and evaluate tumor microenvironment. Estimation of stromal and immune cells in malignant tumour tissues using expression data algorithm was used to assess tumour immune activity. The OS hypoxia landscape was visualized using dimensionality reduction analysis based on the DDRTree algorithm. Assessment of clinical samples and molecular experiments were performed to verify the determined tumor antigens.<h4>Results</h4>Four overexpressed and mutated tumor antigens associated with prognosis and infiltration of antigen-presenting cells were identified and verified by clinical samples and molecular experiments. Furthermore, OS patients were stratified into two OS hypoxia subtypes. Interestingly, patients with the OS hypoxia subtype 1 tumor had a superior survival than those with the OS hypoxia subtype 2 tumor. Distinct expressions of immune checkpoint proteins (ICPs) and immunogenic cell death (ICD) modulators were observed in different immune subtype tumors. Finally, the immune landscape of OS showed a high degree of heterogeneity between individual patients.<h4>Conclusion</h4>This study identified potential antigens for the anti-OS mRNA vaccine as well as different OS hypoxia subtypes, guiding more effective immunotherapeutic strategies and selecting appropriate patients for tumor vaccine therapy.

Cell identity genes that exhibit complex regulation are marked by super-enhancer (SE) architecture. Assessment of SEs in natural killer (NK) cells identified Ugcg, encoding the enzyme responsible for glycosphingolipid (GSL) synthesis. Conditional deletion of Ugcg in early hematopoiesis abrogated NK cell generation while sparing other lineages. Pharmacological inhibition of UGCG disrupted cytotoxic granules and cytotoxicity, reduced expansion after viral infection, and promoted apoptosis. B4galt5 transcribes an enzyme downstream of UGCG and possesses SE structure. Addition of its product, lactosylceramide (LacCer), reversed apoptosis due to UGCG inhibition. By contrast, complex GSLs, such as asialo-GM1, were not required for NK cell viability and granule integrity. Ugcg and B4galt5 were upregulated in CD8⁺ T cells during viral infection, correlating with the acquisition of cytotoxic machinery. Antigen-specific CD8⁺ T cells lacking Ugcg failed to expand during infection. Our study reveals a selective and essential role of GSL metabolism in NK and CD8⁺ T cell biology.

The cure rate for chronic neurodegenerative diseases remains low, creating an urgent need for improved intervention methods. Recent studies have shown that enhancing mitochondrial function can mitigate the effects of these diseases. This paper comprehensively reviews the relationship between mitochondrial dysfunction and chronic neurodegenerative diseases, aiming to uncover the potential use of targeted mitochondrial interventions as viable therapeutic options. We detail five targeted mitochondrial intervention strategies for chronic neurodegenerative diseases that act by promoting mitophagy, inhibiting mitochondrial fission, enhancing mitochondrial biogenesis, applying mitochondria-targeting antioxidants, and transplanting mitochondria. Each method has unique advantages and potential limitations, making them suitable for various therapeutic situations. Therapies that promote mitophagy or inhibit mitochondrial fission could be particularly effective in slowing disease progression, especially in the early stages. In contrast, those that enhance mitochondrial biogenesis and apply mitochondria-targeting antioxidants may offer great benefits during the middle stages of the disease by improving cellular antioxidant capacity and energy metabolism. Mitochondrial transplantation, while still experimental, holds great promise for restoring the function of damaged cells. Future research should focus on exploring the mechanisms and effects of these intervention strategies, particularly regarding their safety and efficacy in clinical settings. Additionally, the development of innovative mitochondria-targeting approaches, such as gene editing and nanotechnology, may provide new solutions for treating chronic neurodegenerative diseases. Implementing combined therapeutic strategies that integrate multiple intervention methods could also enhance treatment outcomes.

Neurodegenerative diseases are prevalent conditions that greatly impact human health. These diseases are primarily characterized by the progressive loss and eventual death of neuronal function, although the precise mechanisms underlying these processes remain incompletely understood. Iron is an essential trace element in the human body, playing a crucial role in various biological processes. The maintenance of iron homeostasis relies on the body's intricate and nuanced regulatory mechanisms. In recent years, considerable attention has been directed toward the relationship between dysregulated iron homeostasis and neurodegenerative diseases. The regulation of iron homeostasis within cells is crucial for maintaining proper nervous system function. Research has already revealed that disruptions in iron homeostasis may lead to ferroptosis and oxidative stress, which, in turn, can impact neuronal health and contribute to the development of neurodegenerative diseases. This article primarily explores the intimate relationship between iron homeostasis and neurodegenerative diseases, aiming to provide novel insights and strategies for treating these debilitating conditions.

<h4>Background</h4>Spinal fusion surgeries remain a successful treatment for degenerative disc disease. While autograft is considered the gold standard bone graft, synthetic bone void fillers are increasingly used to limit donor site morbidity while giving sufficient graft volume.<h4>Methods</h4>This retrospective clinical study evaluates MagnetOs Easypack Putty^TM as a standalone graft without autograft in interbody fusion. An independent radiologist blinded to the clinical status provided evaluation of computed tomography (CT) images obtained at 12 months and graded each treated level based on the Brantigan-Steffee-Fraser (BSF) Classification. Twenty subjects were enrolled in the study. A total of 36 spinal levels were treated with an average of 1.8 levels per subject (L2-L3 to L5-S1).<h4>Results</h4>The primary endpoint of CT-based fusion was 94.4% (34/36 levels) based on the presence of bridging bone or locked pseudoarthrosis at 12 months. The high fusion rate was accompanied by consistent improvement in pain scores. Visual analogue scale (VAS) pain scores decreased an average of 25% from 5.3/10 pre-operatively to 2.8/10 at 12 months post-operative, and all subjects who reported pre-operative back or leg pain reported improved pain post-operatively. Although the patient population included risk factors and comorbidities, the fusion rate remained high, and no device-related adverse events (AEs) were observed.<h4>Conclusions</h4>The high fusion rate and favorable safety profile support the performance of MagnetOs Easypack Putty for standalone use without autograft in interbody fusion procedures.

<h4>Background</h4>Despite previous research establishing a connection between OSA and an increased risk of Bradyarrhythmias, the specific causal link between obstructive sleep apnea (OSA) and sick sinus syndrome (SSS) remains unexplored. This study aims to investigate the potential causal relationship between OSA and the development of SSS.<h4>Methods</h4>To evaluate the association between OSA and SSS, we utilized a bidirectional two-sample Mendelian randomization (MR) method. Genetic variant OSA association data were sourced from FinnGens genome-wide association studies, comprising 410,385 individuals, while SSS association data were obtained from deCODE genetics, involving a dataset of 1, 000,187 individuals. Effect estimates were computed through the utilization of inverse-variance weighting (IVW), MR-Egger, weighted median, maximum likelihood techniques, and sensitivity analyses were conducted using the Mendelian Randomization Pleiotropy Residual Sum and Outlier (MR-PRESSO) approaches.<h4>Results</h4>Our MR analyses utilizing IVW (fixed effects) revealed a heightened susceptibility to SSS among individuals with genetically predisposed OSA (OR= 1.493; 95% CI, 1.120-1.990; <i>P</i>= 0.006), utilizing a set of 7 single nucleotide polymorphisms as the instrumental variables. MR-Egger analysis indicated an absence of evidence for genetic pleiotropy, as reflected by the intercept value of -0.002 (SE 0.030, <i>P</i>= 0.930; global <i>P</i>= 0.719), but genetically predicted SSS did not causally contribute to OSA (OR= 0.997, 95% CI: 0.926-1.072, P= 0.930).<h4>Conclusions</h4>This MR analysis suggests a causal link between genetically predicted OSA and increased SSS risk. While finding no evidence for a causal relationship where SSS influences OSA.

Huntington disease's (HD) is a neurodegenerative disorder caused by the expansion of a polyglutamine region (PolyQ) within the huntingtin protein (HTT). Mutated huntingtin (mHTT) is cytotoxic, particularly for striatal medium spiny neurons (MSNs), whose degeneration is the hallmark of HD. Autophagy inducers currently available promote the clearance of toxic proteins. However, due to their low selectivity and the possibility that prolonged autophagy hampers essential processes in unaffected cells, researchers have questioned their benefits in neurodegenerative diseases. Since MSNs express dopamine receptors D2 (DRD2) and D3 (DRD3) and DRD2/DRD3 agonists may activate autophagy, here, we explored how healthy and mHTT-challenged cells respond to prolonged DRD2/DRD3 agonist treatment. Autophagy activation and its effects on mHTT/polyQ clearance were studied in R6/1 mice (a genetic model of HD), their wild-type littermates, and <i>DRD2</i>- and <i>DRD3</i>-HEK cells expressing a pathogenic (Q74) and a non-pathogenic (Q23) polyQ fragment of mHTT treated with the DRD2/DRD3 agonist pramipexole. Two forms of DRD3-mediated autophagy were found: a transient mTORC1-dependent in WT mice and <i>Q23-DRD3</i>-HEK cells and a persistent AMPK-ULK1-activated in R6/1 mice and <i>Q74-DRD3</i>-HEK cells. This also promoted a robust clearance of soluble mHTT/polyQ and neuroprotection in striatal neurons and <i>DRD3</i>-HEK cells. The findings indicate that DRD3-induced autophagy may be a safe, disease-modifying intervention in HD patients.

The myogenic differentiation of muscle satellite cells (MuSCs) is an important biological process that plays a key role in the regeneration and repair of skeletal muscles. However, the mechanisms regulating myoblast myogenesis require further investigation. In this study, we found that STEAP3 is involved in myogenic differentiation based on the Yunan black pig MuSCs model in vitro using cell transfection and other methods. Furthermore, the expression of myogenic differentiation marker genes <i>MyoG</i> and <i>MyoD</i> and the number of myotubes formed by the differentiation of cells from the si-STEAP3 treated group were significantly decreased but increased in the STEAP3 overexpression group compared to that in the control group. STEAP3 played a role in iron ion metabolism, affecting myogenic differentiation via the uptake of iron ions and enhancing IRP-IRE homeostasis. STEAP3 also activated the PI3K/AKT pathway, thus promoting myoblast differentiation of Yunan black pig MuSCs. The results of this study showed that STEAP3 overexpression increased intracellular iron ion content and activated the homeostatic IRP-IRE system to regulate intracellular iron ion metabolism.

Hormone-dependent phosphorylation of steroid receptors is a mechanism for modulating glucocorticoid receptor (GR) transcriptional responses. Evidence indicates that GR phosphorylation can influence receptor transcriptional activation in a gene-specific manner, which could have positive or negative impacts, where the relative level of phosphorylation is an important determinant of overall GR function. This review provides insights into the regulatory mechanism of GR phosphorylation in the brain, cellular and molecular specificity affecting neurovascular function, and the impact of GR phosphorylation in neurological disorders. Furthermore, the role of various endogenous and exogenous factors and sex-dependent associations with GR functional changes due to phosphorylation and other interlinking mechanisms are considered. Finally, we highlight the potential therapeutic approaches which have been evaluated, while challenging GR phosphorylation and the overall influence on the activity of GR in brain disorders.

There is an escalating need to comprehend the long-term impacts of nuclear radiation exposure since the permeation of ionizing radiation has been frequent in our current societal framework. A system evaluation of the microbes that reside inside a host's colon could meet this knowledge gap since the microbes play major roles in a host's response to stress. Indeed, our past study suggested that these microbes might break their symbiotic association with moribund hosts to form a pro-survival condition exclusive to themselves. In this study, we undertook metagenomics and metabolomics assays regarding the descending colon content (DCC) of adult mice. DCCs were collected 1 month and 6 months after 7 Gy or 7.5 Gy total body irradiation (TBI). The assessment of the metagenomic diversity profile in DCC found a significant sex bias caused by TBI. Six months after 7.5 Gy TBI, decreased <i>Bacteroidetes</i> were replaced by increased <i>Firmicutes</i> in males, and these alterations were reflected in the functional analysis. For instance, a larger number of networks linked to small chain fatty acid (SCFA) synthesis and metabolism were inhibited in males than in females. Additionally, bioenergy networks showed regression dynamics in females at 6 months post-TBI. Increased accumulation of glucose and pyruvate, which are typical precursors of beneficial SCFAs coupled with the activated networks linked to the production of reactive oxygen species, suggest a cross-sex energy-deprived state. Overall, there was a major chronic adverse implication in male mice that supported the previous literature in suggesting females are more radioresistant than males. The sex-biased chronic effects of TBI should be taken into consideration in designing the pertinent therapeutics.

Bone defects caused by various traumas and diseases such as osteoporosis, which affects bone density, and osteosarcoma, which affects the integrity of bone structure, are now well known. Given this situation, several innovative research projects have been reported to improve orthopedic methods and technologies that positively contribute to the regeneration of affected bone tissue, representing a significant advance in regenerative medicine. This review article comprehensively analyzes the transition from existing methods and technologies for implants and bone tissue regeneration to innovative biomaterials. These biomaterials have been of great interest in the last decade due to their physicochemical characteristics, which allow them to overcome the most common limitations of traditional grafting methods, such as the availability of biomaterials and the risk of rejection after their application in regenerative medicine. This could be achieved through an exhaustive study of the applications and properties of various materials with potential applications in regenerative medicine, such as using magnetic nanoparticles and hydrogels sensitive to external stimuli, including pH and temperature. In this regard, this review article describes the most relevant compounds used in bone tissue regeneration, promoting the integration of these biomaterials with the affected area's bone structure, thereby allowing for regeneration and preventing amputation. Additionally, the types of interactions between biomaterials and mesenchymal stem cells and their effects on bone tissue are discussed, which is critical for developing biomaterials with optimal regenerative properties. Furthermore, the mechanisms of action of the various biomaterials that enhance osteoconduction and osteoinduction, ensuring the success of orthopedic therapies, are analyzed. This enables the treatment of bone defects tailored to each patient's condition, thereby avoiding limb amputation. Consequently, a promising future for regenerative medicine is emerging, with various therapies that could revolutionize the management of bone defects, offering more efficient and safer solutions.

Bile acids and their corresponding intestinal epithelial receptors, the farnesoid X receptor (FXR), the G protein-coupled bile acid receptor (TGR5), play crucial roles in the physiological and pathological processes of intestinal epithelial cells. These acids and receptors are involved in the regulation of intestinal absorption, signal transduction, cellular proliferation and repair, cellular senescence, energy metabolism, and the modulation of gut microbiota. A comprehensive literature search was conducted using PubMed, employing keywords such as bile acid, bile acid receptor, FXR (nr1h4), TGR5 (gpbar1), intestinal epithelial cells, proliferation, differentiation, senescence, energy metabolism, gut microbiota, inflammatory bowel disease (IBD), colorectal cancer (CRC), and irritable bowel syndrome (IBS), with a focus on publications available in English. This review examines the diverse effects of bile acid signaling and bile receptor pathways on the proliferation, differentiation, senescence, and energy metabolism of intestinal epithelial cells. Additionally, it explores the interactions between bile acids, their receptors, and the microbiota, as well as the implications of these interactions for host health, particularly in relation to prevalent intestinal diseases. Finally, the review highlights the importance of developing highly specific ligands for FXR and TGR5 receptors in the context of metabolic and intestinal disorders.

<h4>Objective</h4>Chikungunya virus (CHIKV) is a re-emerging mosquito-borne human pathogen, which poses critical threats to the public health. However, an effective diagnostic method for early CHIKV infection remains scarce. Circular RNAs (CircRNAs) are a novel class of RNAs with important biological functions. They have been shown to be promising biomarkers for many human diseases. In this study, we sought to identify circRNA biomarkers in human peripheral whole blood for the early diagnosis of CHIKV infection.<h4>Design</h4>Candidate circRNA biomarkers were identified by group comparison using a case-control study, which was further validated using an independent cohort. The performance of this signature and its correlation with clinical factors were estimated in both cohorts.<h4>Results</h4>Using two public RNA-seq datasets of CHIKV infection, we developed and validated a 13-circRNA based blood signature that can discriminate CHIKV infectious patients from healthy controls. Furthermore, this blood circRNA signature was correlated with viral load in patients with CHIKV infection. Functional analysis implicated that these biomarker circRNAs were involved in the activation and regulation of immune processes against CHIKV infection.<h4>Conclusion</h4>Collectively, our findings indicated that peripheral blood circRNAs were potential biomarkers for the early diagnosis of CHIKV infection.

Ferroptosis, since its conceptualization in 2012, has witnessed an exponential growth in research interest over recent years. It is regulated by various cellular metabolic pathways during chronic cerebral ischemia and hypoxia, including reactive oxygen species (ROS) generation, iron accumulation, abnormalities in glutathione metabolism, and disruptions in lipid and glucose metabolism. With the deepening and widespread research, ferroptosis has emerged as a critical pathway in the pathogenesis of vascular cognitive impairment and dementia (VCID). This unique cell death pathway caused by iron-dependent phospholipid peroxidation is strongly related to VICD. We examine the impact of phospholipid composition on neuronal susceptibility to ferroptosis, with a particular focus on the critical role of polyunsaturated fatty acids (PUFAs) in this process. Intriguingly, peroxisomes, as key regulators of lipid metabolism and oxidative stress, influence the susceptibility of neuronal cells to ferroptosis through the synthesis of plasmalogens and other lipid species. In this Review, we provide a critical analysis of the current molecular mechanisms and regulatory networks of acupuncture for ferroptosis, the potential functions of acupuncture in peroxisomal functions and phospholipid metabolism, and its neuroprotective effects in VCID, together with a potential for therapeutic targeting. As such, this highlights the theoretical basis for the application of acupuncture in VCID through multi-target regulation of ferroptosis. This review underscores the potential of acupuncture as a non-pharmacological therapeutic approach in VCID, offering new insights into its role in modulating ferroptosis and associated metabolic pathways for neuroprotection.

Depressive disorder (a subclass of mental disorders) is characterized by persistent affective symptoms. Without timely therapeutic intervention, it leads to clinical deterioration manifested as reduced quality of life and may increase suicide risk in severe cases. Given its complex etiology, intertwined with intrinsic factors such as genetics and environment, and impacted by various issues such as first-pass effect and blood-brain barrier, the therapeutic efficacy of many antidepressant medications is limited for patients. Therefore, by delving into the exploration of novel antidepressant drugs and biomaterials, this review aims to offer fresh perspectives that may facilitate the discovery of innovative antidepressant medications and enhance their therapeutic outcomes. Notably, the review highlights polymers' crucial role in enhancing antidepressants' pharmacological efficacy and pharmacokinetic properties by optimizing their parameters, and they will undoubtedly become powerful tools in improving antidepressive outcomes in future research.

<b>Background/Objectives</b>: Hypermobile Ehlers-Danlos syndrome (hEDS) is the most common subtype of Ehlers-Danlos syndromes (EDS), a heterogeneous group of hereditary connective tissue disorders. The hallmark features of hEDS include generalized joint hypermobility (GJH), soft or velvety skin, and persistent joint pain. The molecular etiology of hEDS remains unknown, and diagnosis is primarily clinical. The updated diagnostic criteria for hEDS requires the fulfillment of three criteria: (1) GJH, (2) a combination of musculoskeletal and systemic manifestations consistent with a connective tissue disorder, and (3) the exclusion of alternative diagnoses. However, the exclusion process and the role of genetic testing have not yet been fully refined. <b>Methods</b>: This retrospective review utilized data from the Hereditary Connective Tissue Disorders (HCTD) patient registry at the University of Miami, which includes individuals evaluated at the HCTD Clinic using a standardized internal clinical and genetic protocol. We analyzed data from 907 patients referred for hEDS evaluation between June 2019 and December 2022. <b>Results</b>: Among these patients, 178 met the 2017 diagnostic criteria for hEDS. Genetic testing identified an alternative or additional diagnosis in 47 of these individuals (26.4%), with clinical implications requiring distinct management strategies. <b>Conclusions</b>: These findings underscore the importance of criterion three-exclusion of alternative diagnoses-and highlight the critical yet underutilized role of genetic testing in the assessment of joint hypermobility. Furthermore, the results suggest that hypermobility may present a shared phenotype across a spectrum of disorders, including inflammatory diseases, monogenic syndromes, and chromosomal abnormalities.

<b>Background:</b> Understanding the role of repetitive elements (REs) in cancer development is crucial for identifying novel biomarkers and therapeutic targets. <b>Methods:</b> This study investigated the locus-specific dysregulation of REs, including the differential expression and methylation of REs, across 12 TCGA cancer types stratified by their genomic context (i.e., genic and intergenic REs). <b>Results:</b> We found uniquely dysregulated genic REs co-regulated with their corresponding transcripts and associated with distinct biological functions in different cancer types. Uniquely dysregulated intergenic REs were identified in each cancer type and used to cluster different sample types. Recurrently dysregulated REs were identified in several cancer types, with genes associated with up-regulated genic REs involved in cell cycle processes and those associated with down-regulated REs involved in the extracellular matrix. Interestingly, four out of five REs consistently down-regulated in all 12 cancer types were located in the intronic region of the <i>TMEM252</i>, a recently discovered tumor suppressor gene. <i>TMEM252</i> expression was also down-regulated in 10 of 12 cancer types, suggesting its potential importance across a wide range of cancer types. With the corresponding DNA methylation array data, we found a higher prevalence of hypo-methylated REs in most cancer types (10 out of 12). Despite the slight overlaps between differentially expressed REs and differentially methylated REs, we showed that the methylation of locus-specific REs negatively correlates with their expression in some of these 12 cancer types. <b>Conclusions:</b> Our findings highlight the cancer-specific and recurrent deregulation of REs, their functional associations, and the potential role of <i>TMEM252</i> as a pan-cancer tumor suppressor, providing new insights into biomarker discovery and therapeutic development.

<b>Background</b>: Non-alcoholic steatohepatitis (NASH) is characterized by increased production of proinflammatory cytokines, fibrosis, and hepatocyte apoptosis. This study aimed to assess the efficacy of N-acetyl cysteine (NAC), rosuvastatin (RSV), and vitamin E (VE) in patients with NASH. <b>Methods</b>: A double-blinded, parallel, randomized, controlled study was conducted and registered on clinicaltrials.gov (Identifier: NCT06105060), involving 135 NASH participants, who were divided into three groups: the control group (group 1), consisting of patients receiving standard therapy VE at a dosage of 400 IU twice daily. In the treated group (group 2), patients were administered NAC at a dosage of 1200 mg twice daily, while treatment (group 3) received RSV at a dosage of 20 mg once daily. FibroScan^® examination of liver tissue and fibrosis scores, along with tests for liver aminotransferases, lipid profile, glycemic parameters, and renal and hepatic functions, were assessed before and after six months of treatment. <b>Results</b>: The analyzed groups demonstrated a significant reduction in steatosis and lipid peroxidation (<i>p</i> < 0.05). The NAC group demonstrated greater anti-inflammatory and anti-apoptotic effects compared to the RSV group, although this difference was not significant in the control group. NAC is conceded as the only significant antifibrotic agent in liver stiffness measurement (LSM), biological marker findings, and non-invasive liver fibrosis scores (<i>p</i> < 0.05), in addition to its improvement of several metabolic parameters and health-related quality of life. <b>Conclusions</b>: Patients receiving NAC demonstrated safety and efficacy in enhancing steatosis, fibrosis, and metabolic parameters, representing a novel strategy in the management of NASH.

Avian reovirus (ARV) infections significantly impact the global poultry industry, but host responses across infection models remain poorly characterized. Using specific-pathogen-free chicken embryos, this study examined tissue-specific transcriptomic changes following in ovo inoculation with two doses of ARV S1133 at embryonic day 18. Quantitative PCR confirmed dose- and time-dependent viral replication, with the liver exhibiting the highest viral load at 24 h post-inoculation (hpi), whereas the kidneys, intestines, and bursa were only positive at 48 hpi with the higher viral dose. Transcriptomic profiling revealed the intestines mounted an extensive gene expression response, implicating early immune activation. Liver samples demonstrated strong upregulation of antiviral pathways, including interferon signaling and viral replication inhibition, while kidneys and intestines were enriched for coagulation and wound healing pathways. The bursae exhibited minimal immunity-related responses, suggesting insufficient maturation. Functional analyses confirmed tissue-specific immune and metabolic adaptations to infection. These findings indicate that ARV replication efficiency and host molecular responses are dose-, tissue-, and time-dependent. Notably, intestinal responses suggest preemptive immune engagement, while hepatic antiviral mechanisms may play a critical role in restricting viral spread. This study establishes foundational knowledge of host molecular responses to ARV in late-stage embryos, with implications for in ovo vaccination and early immunity.

Flaviviruses are usually transmitted to humans via mosquito or tick bites, whose infections may lead to severe diseases and fatality. During intracellular infection, they remodel the endoplasmic reticulum (ER) membrane to generate compartments scaffolding the replication complex (RC) where replication of the viral genome takes place. In this study, we purified the ER membrane fraction of virus infected cells to identify the proteins that were enriched during flavivirus infection. We found that tripartite motif-containing proteins (TRIMs) including TRIM38, TRIM21, and TRIM14 were significantly enriched during infection with mosquito-borne (West Nile virus strain Kunjin and Zika virus (ZIKV)) and tick-borne (Langat virus (LGTV)) flaviviruses. Further characterizations showed that TRIM21 and TRIM14 act as restriction factors against ZIKV and LGTV, while TRIM38 hinders ZIKV infection. These TRIMs worked as interferon-stimulated genes to mediate IFN-I response against LGTV and ZIKV infections. Restriction of ZIKV by TRIM14 and TRIM38 coincides with their colocalization with ZIKV NS3. TRIM14-mediated LGTV restriction coincides with its colocalization with LGTV NS3 and NS5 proteins. However, TRIM21 did not colocalize with ZIKV and LGTV NS3 or NS5 protein suggesting its antiviral activity is not dependent on direct targeting the viral enzyme. Finally, we demonstrated that overexpression of TRIM21 and TRIM14 restricted LGTV replication.

Cardiac tissue engineering faces challenges due to inadequate vascularization, poor engraftment, and ineffective strategies to control inflammation. This study explores the benefits of geometrically controlled cardiac microtissues over-dispersed cells. Microtissues derived from human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and affixed between two polydimethylsiloxane (PDMS) pillars exhibited cellular alignment and contractile function and were necessary to serve as suitable building blocks for assembling larger tissues. Following implantation into the omentum in nude rats, these tissues exhibited robust engraftment, contractility, and vascularization, with significantly reduced inflammation. Compared to dispersed cells, microtissues demonstrated enhanced vessel network formation, reduced cell death (lower lactate dehydrogenase [LDH]), decreased cytotoxicity (lower cell-free mitochondrial DNA [mtDNA]), and decreased Yes-associated protein (YAP) activation in cardiomyocytes and associated non-cardiomyocyte populations. Cytokine analysis revealed elevated pro-angiogenic factors (placenta growth factor [PIGF], endocan, and angiopoietin-2) and reduced inflammatory markers (interleukin-31 receptor A [IL-31 RA], interleukin [IL]-2 R beta, and OX40 ligand) in microtissues compared with dispersed cells, offering a promising approach for cardiac repair and regeneration.

Phenolic acid esters of cellulose show antioxidative and antimicrobial properties, which are very interesting for a variety of applications, including packaging and medicine. In contrast to simple mixing or encapsulation of phenolic compounds in polymeric materials, covalent linkage to the polymer backbone enables long-term activity and reduces toxicity because leaching of phenolic moieties is avoided. For the synthesis of such polymers, chemical modification of cellulose by polymer analogous reactions must be performed. Cellulose esters of ferulic-, 4-hydroxybenzoic-, vanillic-, protocatechuic-, and gallic acids are synthesized by two different approaches. On the one hand, transesterification of cellulose with corresponding methyl esters in DMSO/DBU/CO₂ is appropriate to synthesize derivatives possessing only one phenolic hydroxyl group, e.g. hydroxybenzoates and vanillates. On the other, conversion with TBS-protected imidazolides is carried out, which allows the synthesis of cellulose esters possessing multiple phenolic hydroxyl groups such as protocatechuates and gallates.

When cells divide, the newly replicated sister chromatids must be segregated evenly to the daughter cells. During mitosis, mechanical force is applied by spindle microtubules in 2 ways: first by pushing on chromosome arms to promote chromosome congression to the cell equator in metaphase, and then by pulling on kinetochores to promote sister chromatid disjunction during anaphase. For segregation to proceed faithfully, the pliable interphase chromatin must be transformed into stiff mitotic chromosomes able to withstand these forces. However, it is unclear how the cell establishes chromosome stiffness and what the consequences are for dividing cells if this stiffness is disrupted. Many of the structural changes imposed on chromosomes in mitosis are driven by Condensin complexes, in conjunction with Topoisomerase IIα. Here, we have combined rapid protein depletion and live cell imaging with in-depth mechanical characterization of purified mitotic chromosomes to probe the roles of Condensins I and II in the establishment and maintenance of the mechanical strength of mitotic chromosomes. We show that Condensin I, but not Condensin II, is required to establish chromosome stiffness and chromatin elasticity, and yet ceases to be required for the maintenance of these properties once chromosome formation has been completed. Nevertheless, depletion of Condensin I from already formed chromosomes still impacts centromeric chromatin and leads to a loss of sister centromere cohesion. We propose that the extensive chromatin loop network established by Condensin I is locked in place by Topoisomerase IIα mediated DNA catenation.

<h4>Background</h4>The skin maintains the body's integrity and serves as the first line of defence against pathogens, stressors and mechanical injuries. Despite the global significance of salmon in aquaculture, how the transcriptomic profile of cells varies during wound healing remains unexplored. Teleost's skin contains adult pluripotent cells that differentiate into various tissues, including bone, cartilage, tendon, ligament, adipose, dermis, muscle and connective tissue within the skin. These cells are pivotal for preserving the integrity of skin tissue throughout an organism's lifespan and actively participate in the wound healing processes. In this study, we characterize the transcriptomic profiles of putative mesenchymal stromal cells (fibroblast-like adult stem cells) in healthy Atlantic salmon tissue and during the wound healing process.<h4>Results</h4>Single-nucleus sequencing and spatial transcriptomics were used to detect transcriptomic changes occurring during wound healing that are commonly associated with mesenchymal stromal cells. We followed the transcriptomic activity of these cells during an in vivo wound healing time course study showing that these cells become more transcriptionally active during the remodelling stage of wound healing. The changes detected give insights into the potential differentiation pathways leading to osteogenic and fibroblast lineages in the skin of Atlantic salmon.<h4>Conclusions</h4>We chart the transcriptomic activity of subclusters of putative differentiating stromal cells during the process of wound healing for the first time, revealing different spatial niches of the various putative MSC subclusters, and setting the stage for further investigation of the manipulation of transitioning cell types to improve fish health.

Polyglutamine (polyQ) tract length expansion (≥ 36 residues) within the N-terminal exon-1 of Huntingtin (Httex1) leads to Huntington's disease, a neurodegenerative condition marked by the presence of intranuclear Htt inclusions. Notably, the polyQ tract in Httex1 is flanked by an N-terminal coiled-coil domain -N17 (17 amino acids), which promotes the formation of soluble oligomers and brings the aggregation-prone polyQ tracts in close proximity. However, the molecular mechanisms underlying the conversion of soluble oligomers into insoluble β-rich aggregates with increasing polyQ length, remain unclear. In this study, extensive atomistic molecular dynamics (MD) simulations (aggregate time ≈0.7 milliseconds) are performed to uncover the interplay between structural transformation and domain "cross-talk" on the conformational ensemble and oligomerization of Httex1 due to polyQ expansion. Notably, MD-derived ensembles of N17-Q_n-P₅ monomers validated against NMR indicated that in addition to elevated α-helicity, polyQ expansion also favored transient, interdomain (N17/polyQ) interactions which resulted in the emergence of β-sheet conformations. Further, interdomain interactions modulated the stability of N17-mediated polyQ dimers and promoted a heterogeneous dimerization landscape. Finally, it is observed that the intact C-terminal proline-rich domain (PRD) promoted condensation of Httex1 through self-interactions involving its P₁₀/P₁₁ tracts while also interacting with N17 to suppress its α-helicity.

<h4>Objective</h4>Mild malformations of cortical development with oligodendroglial hyperplasia in epilepsy (MOGHE) are brain lesions associated with focal epilepsy and characterized by increased oligodendroglial density, heterotopic neurons, and hypomyelination in the white matter. Although previous studies have implicated somatic mutations in the SLC35A2 gene, the cellular and molecular mechanisms underlying MOGHE pathogenesis remain elusive. To address this gap, this study aimed to systematically characterize the cell type composition and molecular alterations of MOGHE lesions at cellular resolution using single-nucleus multiomic profiling.<h4>Methods</h4>We performed single-nucleus multiomic sequencing to obtain paired gene expression and chromatin accessibility profiles of >31 000 nuclei from gray matter and white matter regions of MOGHE lesions and compared the results with publicly available neurotypical control datasets.<h4>Results</h4>The analysis of gray and white matter regions from two MOGHE patients revealed significant cellular composition alterations, including the presence of heterotopic neurons and disease-specific oligodendrocyte populations within the subcortical white matter. MOGHE-specific oligodendrocytes were characterized by the upregulation of synaptic functions and enhanced neuron communication, denoting a possible role in synaptic support and the mediation of glia-neuron interactions in the disease. On the other hand, MOGHE heterotopic neurons were characterized by the upregulation of genes associated with neuronal migration and the Wnt signaling pathway, suggesting a mechanism underlying their atypical localization.<h4>Significance</h4>This high-resolution cell type mapping of MOGHE lesions in clinical samples unveils neuronal and glial populations affected by the disease and provides novel insights into the pathophysiological mechanisms of MOGHE.

<h4>Background</h4>In the development of several cancers, the Forkhead Box M1 (FOXM1) is crucial. The relationship between the immune system and FOXM1 in renal cell carcinoma (ccRCC), which has been verified by bulk RNA sequencing and scRNA sequencing, is the primary subject of this research.<h4>Method</h4>Publicly available data related to FOXM1 and ccRCC were extracted from The Cancer Genome Atlas (TCGA) database. The impact of FOXM1 on the prognosis of ccRCC was examined using Cox regression analysis. Results were verified by immunohistochemistry and quantitative real-time PCR (qRT-PCR). Additionally, single-cell sequencing data were analyzed.<h4>Results</h4>When compared to para-carcinoma tissues, the expression of FOXM1 was considerably higher in ccRCC tissues. Patients with elevated FOXM1 expression had lower survival rates. FOXM1 may be a standalone prognostic factor for ccRCC, according to results of univariate and multivariate Cox regression studies. Reduced FOXM1 expression was linked to higher immunotherapy sensitivity, according to immunocorrelation analysis. This suggests FOXM1 may mediate immunotherapy resistance in ccRCC. Additionally, FOXM1 showed strong associations with tumor mutation load, microsatellite instability, and antitumor immunity. These results imply FOXM1 may regulate antitumor immunity in the ccRCC microenvironment. Consistent results from immunohistochemistry, PCR, and single-cell RNA sequencing confirmed upregulated FOXM1 expression in ccRCC.<h4>Conclusions</h4>According to the findings, FOXM1 might be used as a stand-alone prognostic biomarker for ccRCC. Moreover, FOXM1 has exhibited robust correlations with microsatellite instability, tumor mutation burden, immune response, and immunotherapy efficacy. FOXM1 may promote ccRCC pathogenesis partly by suppressing antitumor immunity and mediating immunotherapy resistance.

Living cells orchestrate a myriad of biological reactions within a highly complex and crowded environment. A major factor responsible for such seamless assembly is the preferential interactions between the constituent macromolecules, that can drive demixing to produce coexisting phases and thus provide dynamic intracellular compartmentalization. However, the way multiple-phase separation phenomena, occurring simultaneously within the cytoplasmic space, influence each other is still largely unknown. Here, we show that the interplay between segregative and associative phase separation within cell-mimicking confinements can lead to rich dynamics between multiple phases and the lipid boundary. Using on-chip microfluidic systems, we encapsulate the associative and segregative components and externally trigger their phase separation within cell-sized vesicles. We find that segregative phases create microdomains and tend to dictate the fate of associative components by acting as molecular recruiters, membrane-targeting agents, and initiators of condensation. The obtained multiphase architecture provides an isolated microenvironment for condensates, restricting their molecular communication as well as diffusive motion, and can further lead to global shape transformation of the confinement itself in the form of wetted, hierarchical domains at the lipid membrane. In conclusion, we propose segregative phase separation as a universal condensation regulation strategy by managing their molecular distribution, process initiation, and spatial localization, including membrane interaction. The presented interplay between the two phase separation systems suggests a distinct design principle in constructing complex synthetic cells and controlling the behavior of artificial membraneless organelles within.

<h4>Purpose</h4>Hematopoietic stem cell transplantation (HSCT) is used as consolidation for pediatric patients with high-risk AML in first complete remission (CR1). The definition of high-risk AML has evolved considerably over the past two decades with the successive identification of new unfavorable risk factors. We conducted a cross-study analysis to determine whether HSCT improves the outcomes of patients with contemporarily defined high-risk AML.<h4>Methods</h4>We combined data from AAML0531 and AAML1031, the last two phase III clinical trials completed by the Children's Oncology Group (COG). These two trials established the prognostic importance of measurable residual disease (MRD) and several high-risk cryptic cytogenetic/molecular (CM) alterations, which were applied to reclassify patients in the current COG phase III clinical trial, AAML1831. We compared the outcomes after HSCT in CR1 with those after chemotherapy alone in CR1 in the redefined high-risk group.<h4>Results</h4>Our study cohort comprised 463 patients with high-risk CM alterations and 72 patients with standard-risk (SR) CM results with positive MRD at end of induction I. In all, 33.9% and 45.8% of these groups underwent HSCT in CR1, respectively. HSCT was associated with decreased relapse and improved disease-free survival (DFS) in both groups. In the high-risk CM group, 5-year DFS was 26.0% (95% CI, 20.6 to 31.6) and 49.8% (95% CI, 41.7 to 57.4; <i>P</i> < .001) in patients receiving chemotherapy alone and HSCT, respectively. In the SR CM and MRD+ groups, DFS was 16.9% (95% CI, 4.3 to 36.7) compared with 50.9% (95% CI, 32.7 to 66.5; <i>P</i> = .032). HSCT was also associated with improvement in outcomes based on multivariable analysis and across subgroups defined by clinical trial and by high-risk CM subtype, with the exception of chromosome 7 or 5 loss.<h4>Conclusion</h4>HSCT was associated with improved outcomes in pediatric patients with contemporarily defined high-risk AML.

<h4>Background</h4>Chronic obstructive pulmonary disease (COPD) and lung cancer are pathologically intertwined, with chronic inflammation fostering carcinogenic transformation through dynamic interactions in the tumor microenvironment.<h4>Methods</h4>This investigation utilized a comprehensive two-sample Mendelian randomization (MR) approach on public genetic datasets to mitigate confounding and determine causality between COPD and lung cancer. We integrated 1400 plasma metabolite characteristics (N = 8299), 731 immune cell attributes (N = 3757), and 4907 plasma protein characteristics (N = 35,559), employing two-sample MR to deduce causal correlations with lung cancer. Sensitivity assessments were executed to fortify the robustness of MR outcomes. Finally, Mendelian mediation analysis was administered to delineate the pathways mediated by plasma immune cells, metabolites, and proteins in the COPD-to-lung cancer continuum. Additionally, we validated our findings using external datasets from the NHANES and TCGA databases to further confirm the reliability of the results.<h4>Results</h4>MR analysis confirmed COPD as a causal risk factor for lung cancer (IVW P-value = 1.38 × 10^-5, OR = 1.63(1.31-2.02). We recognized 96 plasma metabolites (comprising 77 distinct metabolites and 19 ratios), 30 immune cell categories, and 58 plasma proteins as having putative causal associations with lung cancer. Mediation analysis revealed 9 mediator interactions, implicating 3 immune cell types, 1 metabolite, and 5 proteins, Sensitivity analyses verified homogeneity and negated pleiotropic effects.<h4>Conclusion</h4>Our genetic inquiry endorses a causal link from COPD to lung cancer, mediated through plasma-based immunological, metabolic, and proteomic mechanisms. These biomarkers afford groundbreaking insights into the etiology of lung cancer, facilitating its prophylaxis, diagnosis, and therapeutic interventions.

Major Depressive Disorder (MDD) is a common, complex disorder that is a leading cause of disability worldwide and a significant risk factor for suicide. In this study, we have performed the largest molecular analysis of MDD in postmortem human brains (846 samples across 458 individuals) in the subgenual Anterior Cingulate Cortex (sACC) and the Amygdala, two regions central to mood regulation and the pathophysiology of MDD. We found extensive expression differences, particularly at the level of specific transcripts, with prominent enrichment for genes associated with the vesicular functioning, the postsynaptic density, GTPase signaling, and gene splicing. We find associated transcriptional features in 107 of 243 genome-wide significant loci for MDD and, through integrative analyses, highlight convergence of genetic risk, gene expression, and network-based analyses on dysregulated glutamatergic signaling and synaptic vesicular functioning. Together, these results provide an initial mechanistic understanding of MDD and highlight potential targets for novel drug discovery.

Different glioblastoma (GBM) subtypes have been identified based on the tumor microenvironment (TME). The discovery of new therapies for these hard-to-treat tumors requires a thorough characterization of preclinical models, including their TME, to apply preclinical results to the most similar GBM subtype. Using single-nucleus RNA sequencing (snRNA-seq), we characterized the tumor and TME in an immunocompetent mouse model with intracranially implanted GBM stem cells at different stages and treatments. Visium spatial transcriptomics confirmed the location of annotated cells. This model exhibits GBM targets related to integration into neural circuits - Grik2, Nlgn3, Gap43 or Kcnn4-, immunoevasion - Nt5e, Cd274 or Irf8- and immunosuppression - Csf1r, Arg1, Mrc1 and Tgfb1. The landscape of cytokines, checkpoint ligands and receptors uncovered Mrc1, PD-L1, TIM-3 or B7-H3, among the immunotherapy targets that can be addressed in this model. The comparison with human GBMs unveiled crucial similarities with TME^Med GBM, the most frequent subtype.

<h4>Introduction</h4>In Uganda, colorectal cancer (CRC) is steadily increasing according to the Kampala Cancer Registry. In the West, microsatellite instability is detected in 90% of hereditary nonpolyposis colon cancers (HNPCC) which account for 1-2% of all CRC, and 15% of sporadic CRC. Germline mutations in MLH1 and MSH2 account for 90% of HNPCC in the West, whilst the remainder of cases are due to mutations in MSH6 and PMS2. The aim of this study was to determine the microsatellite instability (MSI) status and determine the proportions of MLH1, MSH2, and MSH6 pathological mutations in Ugandan CRC patients.<h4>Methodology</h4>This was a cross-sectional study carried out between 1st January 2008 to 15th September 2021. Patients were recruited prospectively from 16th September 2019 to 16th September 2021, from Masaka Regional Referral Hospital, Mulago National Referral Hospital, Uganda Martyrs' Hospital Lubaga and Mengo Hospital. From 1st January 2008 to 15th September 2019, CRC FFPE tissue blocks were obtained from the archives of the Department of Pathology, Makerere University. Data was abstracted from the medical case files for demographics, topography and stage. The histopathological subtype and grade of CRC were obtained by two consultant pathologists from the H&E slides. DNA was extracted from CRC formalin-fixed paraffin-embedded (FFPE) tissue blocks. Library preparation was completed using the Qiagen custom design panel. The custom panel represented 56 genes. The MLH-1, MSH2, MSH6, BRAF and KRAS genes were sequenced using the above library preparation and NGS sequencing. The MSI status was obtained if one of the MSI genes, MLH1, MSH2 or MSH6 was pathologically mutated. If none of the genes was pathologically mutated it was considered MSI negative, microsatellite stable (MSS). Immunohistochemistry was carried out to determine whether MLH1 and PMS2 was MMR proficient or deficient. Categorical data was summarized using frequencies and proportions corresponding to each of the three histopathological subtypes and MSI status subtypes. Continuous and categorical variables were analyzed using the chi-square and Fischer's exact tests. A p -value ≤ 0.05 was considered statistically significant for all the analyses.<h4>Results</h4>Out of 127 CRC patients, the mean(SD) age of MSI cases was 55.6(16.9) years and of MSS cases was 55.4(15.5) years. The majority were MSS, 75(59.06%) followed by MSI, 52(40.9%). There were 14(11.02%) MLH-1 mutations, 30(23.62%) MSH2 mutations, and 26(20.47%) MSH6 mutations. BRAF mutational analysis showed only 5(3.9%) having pathologic missense BRAF V600 mutations. KRAS mutations consisted of only 8(6.3%) having pathologic missense KRAS mutations.<h4>Conclusions</h4>The high rate of MSI in Ugandan colorectal tumours was mainly associated with a lack of BRAF mutations and a high frequency of MSH2 and MSH6 MMR gene mutations. In CRC patients, identification of the causative mutation is recommended, however in a resource-limited setting, MSI testing and immunohistochemistry is more cost effective. In Ugandan CRC patients who meet at least one of the Bethesda criteria, MSI testing and immunohistochemistry may therefore be offered to obtain the MSI status of the tumour.

<h4>Background</h4>Deciphering the functionality and dynamics of brain networks across different regions and age groups in non-human primates (NHPs) is crucial for understanding the evolution of human cognition as well as the processes underlying brain pathogenesis. However, systemic delineation of the cellular composition and molecular connections among multiple brain regions and their alterations induced by aging in NHPs remain largely unresolved.<h4>Methods</h4>In this study, we performed single-nucleus RNA sequencing on 39 samples collected from 10 brain regions of two young and two aged rhesus macaques using the DNBelab C4 system. Validation of protein expression of signatures specific to particular cell types, brain regions, and aging was conducted through a series of immunofluorescence and immunohistochemistry staining experiments. Loss-of-function experiments mediated by short hairpin RNA (shRNA) targeting two age-related genes (i.e., VSNL1 and HPCAL4) were performed in U251 glioma cells to verify their aging effects. Senescence-associated beta-galactosidase (SA-β-gal) staining and quantitative PCR (qPCR) of senescence marker genes were employed to assess cellular senescence in U251 cells.<h4>Results</h4>We have established a large-scale cell atlas encompassing over 330,000 cells for the rhesus macaque brain. Our analysis identified numerous gene expression signatures that were specific to particular cell types, subtypes, brain regions, and aging. These datasets greatly expand our knowledge of primate brain organization and highlight the potential involvement of specific molecular and cellular components in both the regionalization and functional integrity of the brain. Our analysis also disclosed extensive transcriptional alterations and cell-cell connections across brain regions in the aging macaques. Finally, by examining the heritability enrichment of human complex traits and diseases, we determined that neurological traits were significantly enriched in neuronal cells and multiple regions with aging-relevant gene expression signatures, while immune-related traits exhibited pronounced enrichment in microglia.<h4>Conclusions</h4>Taken together, our study presents a valuable resource for investigating the cellular and molecular architecture of the primate nervous system, thereby expanding our understanding of the mechanisms underlying brain function, aging, and disease.

Lignocellulosic biomass offers a vast and renewable resource for biofuel production and carbon management solutions. The effective conversion of lignocellulosic biomass into economically competitive biofuels and bioproducts demands a comprehensive understanding of its complex structure and composition, often requiring a range of analytical tools to achieve meaningful insights. However, for the analysis of rigid solids, many traditional methods necessitate dissolution or chemical/physical modification of the sample, which limit our ability to capture an intact view of its structural components. This highlights the need for non-destructive approaches, such as solid-state nuclear magnetic resonance (ssNMR), which preserves the sample's natural state while providing deep, molecular-level insights. While advanced multi-dimensional ssNMR on ¹³C-enriched materials has recently proven exceptionally valuable for elucidating the complex macrostructure of biomass, isotopic enrichment is expensive, laborious and is clearly infeasible at large scales. In this review, we explore the role of solid-state NMR methods at natural isotopic abundance as essential tools for the non-destructive, in-depth characterization of lignocellulosic biomass and bioenergy materials in their native and unaltered state. After a brief introduction to the basic principles of solid-state NMR, we first describe the acquisition and interpretation of routine 1D ¹³C ssNMR spectra of lignocellulose and other related biopolymers and products. We then delve into more advanced ssNMR approaches, including key spectral editing techniques, probing polymer dynamics, and various 2D methods applicable at natural abundance. Understanding of domain miscibility as observed from proton-based spin diffusion effects is a theme throughout. Our aim is to highlight key examples where ssNMR provides valuable insights into the composition, structure, dynamics, and morphology of rigid biomaterials relevant to the bioenergy economy, revealing both the native structures and fundamental transformations that occur across conversion and decomposition pathways. We hope that this review encourages a broader adoption of ssNMR methods in bioenergy research, where it can serve as a pivotal analytical tool for achieving sustainable biomass utilization and advancing a carbon-efficient bioeconomy.

Decidualization is a multistep and complex physiological process used to aid the development of an implanting embryo. To date, the potential genes regulating decidualization have not been elucidated. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is widely used in gene expression studies, with relative quantification being the predominant method due to its simplicity, cost-effectiveness, and lower sample requirements. This method determines gene expression levels by normalizing to reference genes. However, the selection of stable reference genes for studies on decidualization remains a challenge. Based on the RNA-seq dataset from human endometrial stromal cells (ESCs) and differentiated ESCs (DESCs), ten new candidate reference genes were identified. The expression of these ten candidates, along with the commonly used reference gene β-actin, was measured in ESCs, DESCs, and decidual stromal cells (DSCs) through RTqPCR. Five algorithms were used to systematically identify suitable reference genes. The results indicated that Staufen double-stranded RNA binding protein 1 (STAU1) was most stable for induced decidualization in vitro, showing consistent expression in ESCs and DSCs. Using STAU1 as the reference gene, the expression levels of insulin like growth factor binding protein 1 and prolactin in DESCs were significantly higher than those in ESCs. Stau1 was further validated with both natural pregnancy and artificially induced decidualization mouse models. Based on our bioinformatics analysis, we also propose that kelch like family member 9 and TSC complex subunit 1 may serve as additional reference genes. Our findings offer valuable insights for gene expression studies of endometrial decidualization.

Metabolic dysfunction-associated steatotic liver disease (MASLD) encompasses pathologies from simple steatosis and steatohepatitis (MASH) to cirrhosis. Hepatic inflammation is a common cause of liver pathogenesis, with macrophage activation as a key indicator of both acute and chronic liver dysfunction. While M1 macrophages promote inflammation and M2 macrophages suppress it, their roles in MASLD are dynamic and shift according to disease stage and liver microenvironment. Tripartite motif (TRIM) family proteins, which possess E3 ubiquitin ligase activity, are involved in various cellular processes, including intracellular signaling, development, apoptosis, protein quality control, innate immunity, autophagy, and carcinogenesis. TRIM38 negatively regulates innate immunity and inflammation triggered by viruses, Toll-like receptor 3 and 4, and tumor necrosis factor α/interleukin-1β signaling; however, its role in liver pathogenesis remains unclear. This study investigates the role of macrophage TRIM38 in metabolic liver disease to identify key targets for controlling inflammation. TRIM38 overexpression suppressed lipopolysaccharide-induced macrophage activation and metabolic stress-induced hepatic lipid accumulation. Mechanistically, TRIM38 interacted with heat shock protein family A member 5 (HSPA5) and stabilized it via K63-dependent ubiquitination. This TRIM38-HSPA5 axis promoted the expression of M2 macrophage markers (arginase 1 and retinoic acid-related orphan receptor α), thereby ameliorating liver steatosis. Single-cell RNA sequencing revealed significant downregulation of TRIM38 expression in the liver macrophages of patients with MASLD and negative regulation of liver inflammation via modulation of macrophage polarization. Hence, macrophage TRIM38 suppresses metabolic liver disease progression via HSPA5-mediated M2 macrophage polarization and provides insights into potential therapeutic targets.

Tau accumulation is closely related to cognitive symptoms in Alzheimer's disease (AD). However, the cellular drivers of tau-dependent decline of memory-based cognition remain elusive. Here, we employed in vivo Neuropixels and patch-clamp recordings in mouse models and demonstrate that tau, independent of β-amyloid, selectively debilitates complex-spike burst firing of CA1 hippocampal neurons, a fundamental cellular mechanism underpinning learning and memory. Impaired bursting was associated with altered hippocampal network activities that are coupled to burst firing patterns (i.e., theta rhythms and high-frequency ripples) and was concurrent with reduced neuronal expression of CaV2.3 calcium channels, which are essential for burst firing in vivo. We subsequently identify soluble high molecular weight (HMW) tau, isolated from human AD brain, as the tau species responsible for suppression of burst firing. These data provide a cellular mechanism for tau-dependent cognitive decline in AD and implicate a rare species of intracellular HMW tau as a therapeutic target.

<h4>Objective</h4>This study was conducted to identify lncRNAs associated with fat deposition in Kele pigs and investigate their molecular regulatory mechanisms.<h4>Methods</h4>Six healthy 10-month-old male Kele pigs were selected as the experimental subjects and divided into high backfat thickness (>5%, H) and low backfat thickness group (<5%, L). Subcutaneous adipose tissue of each group was collected for whole-transcriptome RNA sequencing (RNA-seq). Subsequently, the biological functions of identified lncRNAs were investigated to explore their regulatory mechanisms on fat deposition in Kele pigs.<h4>Results</h4>RNA-seq revealed 493 differentially expressed lncRNAs (p<0.05), with TCONS_00185937 and TCONS_00161198 implicated in fat deposition. Correlation analysis showed that the expression of TCONS_00185937 was significantly negatively correlated with backfat thickness, and the expression of TCONS_00161198 was significantly positively correlated with backfat thickness, and negatively correlated with eye muscle area. The pEGFP-TCONS_00185937 was transfected into subcutaneous fat precursor cells, it was found that the expression levels of TCONS_00185937 and its target genes MOGAT2 and ATGL were significantly higher than control group (p<0.05). Similarly, pEGFP-TCONS_00161198 transfected cells found that the expression levels of TCONS_00161198 and its target genes CSF3R and ACC were significantly higher than control group (p<0.05). The induced differentiation of transfected cells found that the OD510 absorption value of pEGFP-TCONS_00161198 group was higher than that of the control group. Triglyceride content was significantly higher than that of control group (p<0.01), while OD510 absorption value and triglyceride content of pEGFP-TCONS_00185937 group were lower than that of control group.<h4>Conclusion</h4>The above results indicate that TCONS_00161198 and TCONS_00185937 may have regulatory effects on their target genes, thereby affecting fat deposition in pig subcutaneous fat precursor cells. This work provides a theoretical basis for the regulation of fat deposition in Kele pigs.

Six enantiomers of three racemic sigma-1 receptor (σ₁R) ligands were resolved, and absolute configuration was determined. Their high σ₁R potency and selectivity were determined through in vitro binding assays, further validated by molecular docking analysis. Central Nervous System Multiparameter Optimization algorithm (CNS MPO) predicts efficient brain penetration for these enantiomers. Six C-11 radiotracers were radiosynthesized successfully, ex vivo biodistribution in rats showed that (-)-[¹¹C]7 had high brain uptake of ∼4.8-fold for 5 min versus 60 min. Mouse brain PET imaging studies showed (-)-[¹¹C]7 and (-)-[¹¹C]16 have in vivo binding specificity for σ₁R. Macaque PET scans showed high brain uptake for all six radiotracers, with (-)-[¹¹C]7 peaked at ∼45 min (SUV 2.5), possessing the best washout kinetics and highest cerebellum-to-white matter ratio (∼3.1), in agreement with in vitro or ex vivo measures of σ₁R expression. Radiometabolite analysis showed that no newly formed radiometabolite was observed post-injection of (-)-[¹¹C]7. Our data suggest that further evaluation is warranted to determine that (-)-[¹¹C]7 is a suitable PET radiotracer for imaging σ₁R in the brain of animal and human.

Prostate cancer is one of the most prevalent malignancies globally. This cancerous condition originates within the prostate gland, an integral part of the male reproductive system. The molecular mechanism underlying cancer is among the key areas of research in the scientific community. Cancer, being a multifactorial disease, is controlled by many factors ranging from environmental to genetic to epigenetic factors. Epigenetic regulation holds a crucial role in tumorigenesis and its progression. Epigenetics refers to alterations in the genome that happen without any changes to the DNA sequence itself; they may be triggered by multiple factors ranging from environmental to dietary factors. It includes methylation of DNA and histone modifications. Histone modifications, including histone methylation, histone acetylation, and histone ubiquitination, play a crucial role in the pathogenesis and progression of prostate cancer. These epigenetic modifications via transcriptional regulation affect key cellular processes and are thus implicated in prostate cancer and other cancers. These epigenetic markers could be used as both diagnostic and prognostic markers and also could be used as novel therapeutic targets against prostate cancer and other malignancies. Here in this review article, we have summarized different histone modifications and their mechanistic and therapeutic implications in prostate cancer.

Mitochondria, as the primary energy factories of cells, play a pivotal role in maintaining nervous system function and regulating inflammatory responses. The balance of mitochondrial quality control is critical for neuronal health, and disruptions in this balance are often implicated in the pathogenesis of various neurological disorders. Mitochondrial dysfunction not only exacerbates energy deficits but also triggers neuroinflammation through the release of damage-associated molecular patterns (DAMPs), such as mitochondrial DNA (mtDNA) and reactive oxygen species (ROS). This review examines the mechanisms and recent advancements in mitochondrial quality control in neurological diseases, focusing on processes such as mitochondrial fusion and fission, mitophagy, biogenesis, and protein expression regulation. It further explores the role of mitochondrial dysfunction and subsequent inflammatory cascades in conditions such as ischemic and hemorrhagic stroke, neurodegenerative diseases and brain tumors. Additionally, emerging research highlights the significance of mitochondrial transfer mechanisms, particularly intercellular transfer between neurons and glial cells, as a potential strategy for mitigating inflammation and promoting cellular repair. This review provides insights into the molecular underpinnings of neuroinflammatory pathologies while underscoring the translational potential of targeting mitochondrial quality control for therapeutic development.

Basal cell carcinoma (BCC) is the most common type of non-melanoma skin cancer (NMSC). However, few biomarkers have been developed for the diagnosis of BCC. This study aimed to uncover novel BCC biomarkers for diagnosis and treatment via transcriptome and pathogenesis investigations. Microarray datasets of BCC tissues were downloaded from the Gene Expression Omnibus (GEO) database and differentially expressed genes (DEGs) were identified. A total of 558 DEGs were identified between BCC and normal samples from the GSE125285 and GSE42109 datasets. 69 DEGs were expressed in a tissue/organ-specific manner, of which three tissue-specific key genes were finally identified. The three genes showed high performance for BCC diagnosis with AUCs of ≥0.8, indicating that they have high diagnostic significance. CIBERSORT analysis revealed an increase in resting NK cells, M1 macrophages and a decrease in dendritic cells in the immune microenvironment of BCC patients. In addition, versican (VCAN) may be involved in the polarization of M1 macrophages in skin cancer. When VCAN was knocked down, the skin cancer cell line A431 was weakened in terms of proliferation, migration and invasion. Meanwhile, the expression of the key oncogenic factors DDX5 was also reduced and apoptosis was promoted through the BAX/BCL-2/c-Caspase3 pathway. The cell-derived xenograft model study in nude mice showed that knockdown of VCAN in tumour cells significantly suppressed tumour size compared to control tumour cells, suggesting that VCAN is one of the important genes for tumourigenesis. Meanwhile, we examined the level of macrophage M1 polarization in tumour samples from a cell-derived xenograft mouse model, and VCAN knockdown significantly reduced macrophage M1 polarization compared to controls. We also detected the expression of VCAN in tumour samples from BCC patients and verified that VCAN expression was significantly higher in BCC than in normal skin tissue. Thus, VCAN could be a potential clinical target for the diagnosis and treatment of BCC.

<b>Background:</b> Breast cancer is a complex and heterogeneous disease characterized by distinct molecular subtypes with varying prognoses and treatment responses. Multiple factors influence breast cancer outcomes including tumor biology, patient characteristics, and treatment modalities. Demographic factors such as age, race/ethnicity, menopausal status, and body mass index have been correlated with variations in incidence, mortality, and survival rates. Over the past decade, comprehensive genomic profiling has been widely used to identify molecular biomarkers and signatures to develop novel therapeutic strategies for patients. For instance, the FLEX registry (NCT03053193) enrolled stage I-III breast cancer patients across 90 institutions in the United States and stratified risk groups based on a 70-gene signature (MammaPrint^®-MP) and molecular subtype based on an 80-gene signature (BluePrint^®-BP). This study aimed to identify the gene expression patterns and biomarkers associated with breast cancer risk and progression by integrating transcriptomic and clinical data. <b>Methods:</b> Targeted 111 unique gene expression and clinical data points from 978 breast cancer samples, representing each BP subtype (26% Luminal A, 26% Luminal B, 25% Basal, 23% HER2), obtained from Agendia Inc. These genes were selected based on their involvement in the mercapturic acid pathway, white and brown adipose tissue markers, inflammation markers, tumor-associated genes, apoptosis, autophagy, and ER stress markers. All statistical analyses, including principal component analysis (PCA), were performed using R version [4.4.0]. Prognostic values and genetic alterations were investigated using various web-based programs as described in the Methods section. <b>Results:</b> PCA of gene expression data revealed distinct clustering patterns associated with risk categories and molecular subtypes, particularly with principal component 4 (PC4). Genes related to oxidative stress, autophagy, apoptosis, and histone modification showed altered expression across risk categories and molecular subtypes. Key differentially expressed genes included <i>SOD2</i>, <i>KLK5</i>, <i>KLK7</i>, <i>IL8</i>, <i>GSTM1/2</i>, <i>GLI1</i>, <i>CBS</i>, and <i>IGF1</i>. Pathway analysis highlighted the enrichment of processes related to autophagy, cellular stress response, apoptosis, glutathione metabolism, deacetylation, and oxidative stress in high-risk and basal-like tumors compared with Ultralow and Luminal A tumors, respectively. <b>Conclusions:</b> This study identified gene expression signatures associated with breast cancer risk and molecular subtypes. These findings provide insights into the biological processes that may drive breast cancer progression and could inform the development of prognostic biomarkers and personalized therapeutic strategies.

The piggyBac+TET-on transposon induction system has a high efficiency in integrating exogenous genes in multiple cell types, can precisely integrate to reduce genomic damage, has a flexible gene expression regulation, and a strong genetic stability. When used in conjunction with somatic cell nuclear transfer experiments, it can precisely and effectively reveal the intrinsic mechanisms of early biological development. This study successfully reprogrammed black-boned sheep fibroblasts (SFs) into induced pluripotent stem cells (iPSCs) using the piggyBac+TET-on transposon system and investigated their impact on early embryonic development. Seven exogenous reprogramming factors (bovine OCT4, SOX2, KLF4, cMyc, porcine NANOG, Lin-28, and SV40 Large T) were delivered into SFs, successfully inducing iPSCs. A growth performance analysis revealed that iPSC clones exhibited a raised or flat morphology with clear edges, positive alkaline phosphatase staining, and normal karyotypes. The transcriptome analysis indicated a significant enrichment of iPSCs in oxidative phosphorylation and cell proliferation pathways, with an up-regulated expression of the ATP5B, SDHB, Bcl-2, CDK1, and Cyclin D1 genes and a down-regulated expression of BAX (<i>p</i> < 0.05). Somatic cell nuclear transfer experiments demonstrated that the cleavage rate (85% ± 2.12) and blastocyst rate (52% ± 2.11) of the iPSCs were significantly higher than those of the SFs (<i>p</i> < 0.05). The detection of trilineage marker genes confirmed that the expression levels of endoderm (DCN, NANOS3, FOXA2, FOXD3, SOX17), mesoderm (KDR, CD34, NFH), and ectoderm (NEUROD) markers in iPSCs were significantly higher than in SFs (<i>p</i> < 0.01). The findings demonstrate that black-boned sheep iPSCs possess pluripotency and the potential to differentiate into all three germ layers, revealing the mechanisms by which reprogrammed iPSCs influence early embryonic development and providing a critical foundation for research on sheep pluripotent stem cells.

Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by social interaction deficits and repetitive behaviors. While precise causes of ASD remain elusive, growing evidence highlights that an imbalance in excitatory and inhibitory (E/I) signaling is a pivotal factor in ASD development and modulation. Balanced E/I neurotransmission is critical for circuit formation, synaptic plasticity, and developmental timing. However, key questions persist, including the critical perturbation window, neurological and neurodevelopmental effects, and clinical implications of E/I imbalance. This study investigated early-life modulation of the GABAergic system's impact on E/I balance and ASD-like behaviors in mice. Mice were treated with bicuculline, a GABAA receptor antagonist, from postnatal days 7-11, and behavioral tests were conducted during adolescence. Results revealed deficits in social interaction in both male and female mice and increased repetitive behaviors in bicuculline-treated male mice. Electrophysiological recordings in the mPFC indicated reduced resting membrane potential, heightened neuronal excitability, and a shift in the E/I ratio. In the hippocampus, recordings displayed enhanced LTP and altered synaptic plasticity. DEG analysis of the PFC in bicuculline-treated mice unveiled aberrant gene profiles related to the regulation of synaptic function. Clinical significance and underlying mechanisms of abnormal brain activity, neurodevelopment, and ASD-related behaviors prompted by neonatal bicuculline treatment require further investigation. Nevertheless, these results suggest that GABAergic signaling disruption during the neonatal period might contribute to ASD-related brain pathophysiological changes.

Heart failure (HF) is a condition characterized by high morbidity, mortality, and a substantial healthcare burden, in which inflammation plays a pivotal role. This review provides a comprehensive overview of inflammation in HF progression, highlighting the dynamic alterations in immune cell populations-such as monocytes/macrophages and neutrophils-and regulatory mechanisms of key signaling pathways, including JAK and NLRP3. Furthermore, the clinical relevance of inflammatory biomarkers in predicting disease prognosis is also discussed. Emerging evidence indicates that exercise intervention can enhance cardiac function by promoting the expression of anti-inflammatory cytokines (e.g., IL-10) and mitigating myocardial fibrosis, oxidative stress, and apoptosis. Future studies should investigate how exercise modulates critical inflammatory pathways-such as TLR/MyD88/NF-κB and the NLRP3 inflammasome-and aim to establish personalized exercise protocols tailored to patients' inflammatory profiles and disease stages. Such insights may pave the way for innovative therapeutic strategies in HF management.

The heat shock factor 1 (HSF1) is a master transcription regulator that orchestrates the expression of heat shock proteins (HSPs) in response to various cellular stresses. Dysfunction of HSF1 contributes to the pathogenesis of a spectrum of acute and chronic diseases, including cancer. Consequently, the modulation of HSF1 activity through the development of small molecules emerges as a promising therapeutic strategy for disease treatment. The activation of HSF1 is a multifaceted process, governed by a complex interplay of regulatory mechanisms, including post-translational modifications, protein-protein interactions, and a balance between its activation and inactivation. Recently, a plethora of compounds, ranging from synthetic to naturally derived, that either inhibit or activate HSF1 was identified, holding considerable potential for the treatment of numerous human diseases. In this comprehensive review, we elucidate the sophisticated mechanisms underlying activation of human HSF1, introduce its role in the etiology of diseases, and provide a comprehensive summary of the inhibitors and activators of HSF1 that have been discovered to date. This review not only offers novel insights for the development of small molecule therapeutics targeting HSF1 but also charts new territories in the design of innovative interventions for the amelioration of disease.

Missense variants in the O-GlcNAc transferase ( OGT) gene have recently been shown to segregate with a syndromic form of intellectual disability (OGT-ID), underscoring the importance of protein O-GlcNAcylation in brain function. However, the underlying pathophysiological mechanisms linking ID to potential OGT malfunction—whether developmental, neurophysiological, or both—remain unclear. Here, we present comprehensive analyses encompassing behaviour and brain architecture of a rodent model carrying the pathogenic C921Y OGT-ID variant. These mice show a range of behavioural deficits, including hyperactivity, impulsivity, and associative learning phenotypes. Structural studies, using micro-computed tomography and magnetic resonance imaging, revealed reduced skull size, microcephaly, reduced cortical thickness and hypoplastic corpus callosum. Detailed histological analyses revealed dysplastic changes in the neocortex, predominantly affecting the superficial layers of cingulate cortex. Mechanistically, quantitative proteomic analyses revealed O-GlcNAc dyshomeostasis associated with distinct perturbed molecular pathways involved in brain development. Taken together, these data reveal neurodevelopmental defects associated with O-GlcNAc dyshomeostasis and provide a platform for dissecting mechanism and treatments of OGT-ID.

<h4>Background</h4> Chronic kidney disease (CKD) affects approximately 14% of the UK population and is associated with significant exercise intolerance, partly due to skeletal muscle dysfunction. While exercise is a potential therapeutic strategy, the molecular response of skeletal muscle to exercise in CKD remains poorly understood. This study aimed to characterise transcriptomic changes in skeletal muscle 24 hours after aerobic (AE) or combined aerobic and resistance exercise (CE) in non-dialysis CKD. <h4>Methods</h4> This study utilised muscle biopsies from participants in the ExTRA CKD trial with stage 3b–4 CKDages 3b-4 (AE: 24 (15-32) ml/min/1.73m 2 ; CE: 25 (19-31) ml/min/1.73m 2 ). Participants (n=4 per group) were randomised to 12 weeks of thrice-weekly AE or CE. Vastus lateralis skeletal muscle biopsies were collected at baseline and 24h after the first bout of exercise. RNA was extracted for Bulk RNA sequencing. Bulk RNA sequencing was performed, and differentially expressed genes (DEGs) were identified between baseline and post-exercise samples, followed by pathway enrichment analysis. <h4>Results</h4> Following AE, 1480 genes were upregulated and 1554 downregulated. CE resulted in 556 upregulated and 115 downregulated genes. The most upregulated gene after AE was CHI3L1 (log₂FC 10.7), followed by SAA2 and PTX3 , all associated with inflammation. After CE, SFN (log₂FC 6.8) and MT1A were among the most highly upregulated. Enrichment analysis showed strong activation of inflammatory and cellular senescence pathways, and downregulation of mitochondrial function-related processes, particularly after AE. <h4>Conclusion</h4> Both AE and CE triggered robust inflammatory gene expression responses in CKD skeletal muscle, indicative of early repair processes. Unexpectedly, mitochondrial-related pathways were downregulated, aligning with previous findings of impaired mitochondrial adaptation in CKD. These results highlight mitochondrial dysfunction as a potential barrier to effective exercise adaptation and a possible therapeutic target in this population.

Huntington's disease (HD) is a neurological condition caused by an excessive expansion of CAG repeats in the Huntingtin (HTT) gene. Although experiments have shown an altered epigenetic landscape and chromatin architecture upon HD development, the structural consequences on the HTT gene remain elusive. Structural data are only available for model nucleosome systems and yeast systems with human nucleosomes. Here, we use our experimentally validated nucleosome-resolution mesoscale chromatin model to investigate folding changes of the HTT gene associated with HD. We investigate how the histone fold domain of the variant macroH2A1, a biomarker of HD, affects the genome structure by modeling HD-like systems that contain (i) 100% canonical, (ii) 100% macroH2A1, (iii) 50% canonical and 50% macroH2A1, and (iv) 100% hybrid cores (one canonical H2A and one macroH2A1 per nucleosome). Then, we model the mouse HTT gene in healthy and HD conditions by incorporating the CAG expansion and macroH2A1 cores, reducing the linker histone density and tail acetylation levels, and incorporating genomic contacts. Overall, our results show that the histone fold domain of macroH2A1 affects chromatin compaction in a fiber-dependent manner (i.e., nucleosome distribution dependent) and can thus both enhance or repress HTT gene expression. Our modeling of the HTT gene shows that HTT is less compact in the diseased condition, which could accelerate the production of the mutated protein. By suggesting the structural biophysical consequences of the HTT gene under HD conditions, our findings may help in the development of diagnostic and therapeutic treatments for HD.

Episodes of worsening heart failure (HF) are a major cause of unplanned hospitalizations. Their onset is usually preceded by an early increase in intracardiac pressures with subsequent worsening of symptoms due to congestion. Implantable devices allowing daily remote pulmonary artery pressure (PAP) monitoring are useful to identify early haemodynamic changes so that medical therapy can be adjusted at an early stage, before symptom onset, and HF-related hospitalizations be prevented. Second, the use of these devices may help to maintain clinical stability keeping PAP in the target range on a day-to-day basis. The CardioMEMS system allows remote PAP monitoring, and PAP-guided medical therapy has reduced HF-related hospitalizations in prospective, randomized, controlled clinical trials in symptomatic patients with HF, independent of their left ventricular ejection fraction. The safety and feasibility of other devices, like the Cordella implantable PAP sensor, have also been demonstrated and clinical usefulness in larger patient populations is currently being assessed in several trials. Most of the studies testing remote PAP monitoring were reported after the 2021 European Society of Cardiology HF guidelines. An update of the clinical significance and potential implications for clinical practice of these systems seems therefore warranted. The aim of this clinical consensus statement is to summarize current knowledge on remote PAP-guided management of patients with HF, with a special focus on current evidence from clinical trials, potential impact on clinical practice and management aspects.

The experiment was designed to consider effects of different amounts of metabolizable energy and protein on mammary gland development, mRNA abundance of genes related to vascular function and angiogenesis of Sistani goats. A total of 32 pregnant Sistani goats were selected on day 100 of gestation and allocated randomly to four treatments: (1) basal diet that meets metabolizable energy (ME) and protein (MP) requirements of goats during late gestation, as recommended by the National Research Council = NRC (2007) (C). (2) A diet with 10% higher levels of ME than recommendations (E). (3) A diet with 10% higher levels of MP than recommendations (P), and (4) a co-addition diet with 10% higher levels of both ME and MP than recommendations (EP). The four diets were fed from 100 days prepartum to 30 days after parturition. Mammary biopsies were obtained 24 h after parturition. Feed intake (g/day), colostrum (kg/day) and milk (kg/month) productions increased when extra E and P were provided together prepartum and early postpartum (P < 0.05). Relative mRNA abundances of vascular endothelial growth factor (VEGF, 4.68-fold), tyrosine kinase tie2 receptor (RTK, 4.61-fold), vascular endothelial growth factor receptor 1 (VEGFR1, 5.15-fold), angiopoietin I (ANGPT1, 4.86-fold), cyclooxygenase I (COX1, 4.5-fold), prostacyclin synthase (PTGIS, 5.66-fold), thromboxane A2 synthase (TBXAS, 98-fold) increased significantly in the mammary gland with the co-addition of E and P. Histological results documented that alveolar area (epithelium + luminal space, µm2), average number of epithelial cells per alveolus, and relative area occupied by overall epithelial cells (per slide) were increased significantly, when co-addition of E and P were fed in late gestation. In summary, increasing the dietary supply of ME and MP peripartum resulted in greater milk production, stimulated mammary gland alveolar development and affected the mRNA abundance of genes associated with both angiogenesis and milk secretion in Sistani goats.

Individual variations in the freezability properties of sheep semen may be related to the antioxidant levels of sperm. PRDX6 is a key antioxidant protein in sperm, but its relationship with the freezability properties of sheep semen remains unclear. This study, using Hu sheep as the research subject, investigated the levels of PRDX6 in sperm with different freezability properties. A positive correlation was found between the levels of PRDX6 and sperm freezability. Furthermore, when different concentrations of PRDX6 recombinant protein were added to high-freezing-resistant (HF) and low-freezing-resistant (LF) sperm, it was revealed that 20 μg/ml of PRDX6 recombinant protein significantly improved various sperm quality parameters in both HF and LF sperm and reduced the differences in sperm freezability properties. Finally, adding a PRDX6 peroxidase activity inhibitor (Ethacrynic acid) or a calcium - independent phospholipase A2 (iPLA2) activity inhibitor (MJ33) to the diluent significantly reduced the freezability parameters of sperm. This indicates that PRDX6 protects sperm from freezing damage through two pathways. In summary, this study reveals the crucial role of PRDX6 in the freezability properties of sheep semen. It suggests that increasing the levels of PRDX6 in sperm may be an effective strategy to improve the quality of cryopreserved semen. Future research can further explore the molecular mechanisms regulating the levels of PRDX6, providing a scientific basis for the optimization of sheep semen cryopreservation techniques.

Cancer cells are often described as voracious consumers of nutrients, with glucose frequently cited as a key energy source; however, their metabolic plasticity allows them to adapt and utilize various substrates, including lipids and amino acids, to sustain growth and survival. However, the metabolic demands of immune cells within the tumor microenvironment (TME) are less commonly discussed despite their critical role in shaping the immune response. In this review, we explored the intricate interplay between immunometabolism and innate immunity cells in gastrointestinal cancers. We focused on how metabolic pathways, including glycolysis, fatty acid oxidation, and amino acid metabolism, drive the immunosuppressive functions of myeloid-derived suppressor cells (MDSCs) and tumor-associated neutrophils (TANs), tumor-associated macrophages (TAMs) and innate lymphocyte subsets such as NK cells. These cells contribute to a hostile immune landscape, supporting tumor growth and evasion from immune surveillance in a phenomenon of tumor-derived immunosuppression. Additionally, we investigated the influence of dietary interventions on the metabolic reprogramming of these immune cells, highlighting how nutrition can modulate the TME. Finally, we discussed emerging therapeutic strategies that target metabolic vulnerabilities in MDSCs, TANs, NK cells, and monocytes, offering a novel avenue for enhancing antitumor immunity. By dissecting these mechanisms, we aim to provide insights into how metabolic pathways can be harnessed to improve cancer treatment outcomes. This review underscores the importance of understanding immunometabolism not only as a driver of immune suppression but also as a potential therapeutic target in gastrointestinal cancer.

Extrachromosomal circular DNAs (eccDNAs) are heterogeneous circular DNA molecules derived from genomic DNA, and believed to be involved in intercellular communication and in natural biological processes. Extracellular vesicles (EVs) are membrane-bound particles released from all cells, and have been shown to contain various classes of nucleic acids. EVs can play a role in intercellular communication and may be used as biomarkers. This constitutes the first study to demonstrate that EVs derived from healthy human dermal fibroblasts carry eccDNA. eccDNA from EVs and their corresponding donor cells were isolated and sequenced on the Oxford Nanopore MinIon platform, followed by the identification of potential eccDNAs through four different bioinformatic pipelines, namely ecc_Finder, cyrcular-calling, CReSIL, and Flec. Our main findings demonstrate that EVs derived from human dermal fibroblasts carry eccDNA; there is variability in the number of eccDNAs identified in the same sample through different pipelines; and there is variability in the identified eccDNAs across biological replicates. Additionally, eccDNAs characterized in this research had (a) sequences as small as 306 base pairs and as large as 28,958 base pairs across all samples, (b) uneven chromosomal distribution, and (c) an average of 49.7% of the identified eccDNAs harboring gene fragments. Future implications for this novel research include using this framework method to elucidate factors and conditions that may influence the skin aging process and related biogenesis in human dermal cells.

The large yellow croaker (<i>Larimichthys crocea</i>) is a cornerstone species in Chinese marine aquaculture, yet bacterial infections-particularly visceral white nodules disease (VWND) caused by <i>Pseudomonas plecoglossicida</i>-severely compromise its production. This study aimed to elucidate the immunoregulatory mechanisms of tripartite motif-containing protein 38 in the large yellow croaker (<i>Lctrim38</i>) during bacterial infections, with an emphasis on host-pathogen interactions involving <i>P. plecoglossicida</i>, to evaluate its potential for disease-resistant breeding applications. The full-length cDNA of <i>Lctrim38</i> was cloned and characterized, with structural analysis revealing a conserved domain architecture comprising RING, B-box, coiled-coil, and PRY-SPRY motifs. Functional characterization through <i>Lctrim38</i> overexpression in large yellow croaker kidney cells (PCK cells) demonstrated significant modulation of key immune-related pathways, including TGF-β, PI3K-Akt, IL-17, and PPAR. Notably, <i>Lctrim38</i>-mediated inhibition of NF-κB signaling was shown to downregulate pro-inflammatory cytokines (TNF-α, IL-6, IFN-γ), establishing its role as a negative regulator of inflammatory responses. These findings provide insights into the immune mechanisms of Trim38 in large yellow croakers and highlight its potential as a molecular target for disease resistance breeding. Future research should explore its broader functions, including its antiviral potential.

Precision medicine stems from a new approach to the prevention, diagnosis and treatment of patients, due to the shift in focus away from pathology and towards the uniqueness of the individual, personalising the diagnostic-therapeutic pathway. This paradigm shift has been made possible by the emergence of new high-throughput technologies capable of generating large amounts of data on multiple levels of a biological system, identifying pathology-related genes, transcripts, proteins and metabolites. Metabolomics plays a primary role in this context, providing, through non-invasive sampling, a very close image of the phenotype of the organism being studied by detecting metabolites, end products downstream of gene transcription, present in cells, tissues, organs and biological fluids. The enormous amount of data that these modern technologies make available, together with the need to elucidate the complex interplay of the various biological levels by combining data from distinct omics, has led to the need to employ advanced informatics techniques, among which artificial intelligence has recently emerged. These innovations are of great interest in the field of perinatology, representing an attempt to optimise the diagnostic timeline for the most critical newborns. In addition, they may contribute to the improvement of prevention strategies available to date. All these contributions prove to be crucial at very vulnerable life stages, allowing crucial intervention opportunities. In this review, we have analysed studies that have integrated metabolomics with at least one other omics in the perinatal field, attempting to highlight the usefulness of multiomics integration and the different methods employed.

<h4>Background</h4>Bladder cancer (BLCA) is the most common type of malignancy affecting the urinary tract, characterized by high recurrence rates, propensity for progression, metastatic potential, and multidrug resistance, all of which ultimately contribute to an unfavorable prognosis. RNA-binding proteins (RBPs) play a critical role in cancer development and have been associated with the progression and prognosis of the disease. However, comprehensive investigations into the biological functions and molecular mechanisms of RBPs in BLCA remain limited. The study aims to explore the relationship between RBPs and prognosis in BLCA, and to develop and validate an RBPs-based prognostic signature, providing new insights for the diagnosis and treatment of BLCA.<h4>Methods</h4>Clinical data and RBPs expression profiles of BLCA patients were sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). A systematic bioinformatics analysis was conducted to identify differentially expressed RBPs and assess their prognostic significance. The optimal predictive model was selected by integrating multiple machine learning algorithms, enabling the identification of hub genes associated with BLCA prognosis and developing an RBP-related gene signature. To evaluate the prognostic signature's efficacy, survival curves and receiver operating characteristic (ROC) curves were generated. A nomogram was constructed and validated to predict the survival of BLCA patients at 1, 3, and 5 years. Furthermore, analyses of immune infiltration and gene set enrichment analysis (GSEA) were conducted to explore the roles of RBPs in immune cell interactions and elucidate underlying biological pathways.<h4>Results</h4>A prognostic signature was effectively developed using nine RBPs (OAS1, MTG1, DUS4L, IGF2BP3, NOL12, PABPC1L, ZC3HAV1L, TRMT2A and TRMU), represented as risk score, through the integration of 13 combinatorial machine learning algorithms. Kaplan-Meier analysis revealed that the high-risk group exhibited a significantly poorer overall survival (OS) probability compared to the low-risk group. The areas under the ROC curves for the risk score model at 1, 3, and 5 years were 0.661, 0.655, and 0.676, respectively. The nomogram, which integrated clinical characteristics and risk scores, demonstrated robust prognostic accuracy. Furthermore, single-sample gene set enrichment analysis (ssGSEA) demonstrated significant correlations between both the risk score model and hub RBPs with the immune status of BLCA patients. GSEA indicated that major signaling pathways enriched in the high-risk group included extracellular matrix (ECM) components and interaction, as well as cytokine and receptor interaction.<h4>Conclusions</h4>This study successfully identified and developed a prognostic signature based on nine RBPs, accompanied by a nomogram for predicting survival probability in BLCA patients. Our findings demonstrate that these nine RBPs function as significant biomarkers for forecasting the prognosis and immune status in BLCA, suggesting their potential as therapeutic targets for BLCA.

<h4>Background</h4>Non-obstructive azoospermia (NOA) is a severe form of male infertility, affecting 10-20% of azoospermic men. Although some NOA genes have been identified, the genetic causes of spermatogenesis failure in NOA remain unclear. This study aimed to identify and characterize genes and mutations associated with NOA.<h4>Methods</h4>Thirty NOA patients were selected for whole-exome sequencing (WES). Patients with chromosomal abnormalities, chromosome copy number issues, or Y chromosome microdeletions were excluded. Relevant genes and mutations in NOA patients were comprehensively screened using WES, MutationTaster software, and related databases. Sequencing results were analyzed for allele screening, mutation deleteriousness, and mutation site prediction to identify potential NOA-associated genes. The study also predicted altered gene function due to mutations and assessed pathogenicity from DNA sequence alterations.<h4>Results</h4>The study screened 37 genes with 56 variant loci, identifying 27 genes with 34 variant loci related to NOA, including <i>CFAP65</i>, <i>SEPTIN12</i>, <i>ZMYND15</i>, <i>DNAH2</i>, <i>CEP112</i>, <i>SHOC1</i>, <i>DNAH10</i>, <i>ACTL9</i>, <i>CFAP43</i>, <i>DNAH17</i>, <i>DNAH1</i>, <i>ARMC2</i>, <i>AK7</i>, <i>PMFBP1</i>, <i>FSIP2</i>, <i>SPATA16</i>, <i>TSGA10</i>, <i>SPEF2</i>, <i>CFAP69</i>, <i>TTC21A</i>, <i>NDNF</i>, <i>ADCY10</i>, <i>GATA4</i>, <i>CYP17A1</i>, <i>CHD7</i>, <i>CHD7</i>, <i>SEMA3A</i>, and <i>CFTR</i>. Notable findings included the variant c.1223C>A p.S408* in the <i>CFAP65</i> gene and potential associations of genes such as <i>CFAP43</i>, <i>CFAP69</i>, <i>ZMYND15</i>, <i>DNAH17</i>, and <i>DNAH2</i> with spermatogenic disorders.<h4>Conclusions</h4>The study identified genes related to spermatogenic disorders in azoospermia, providing a reference for clinical genetic diagnosis and basic NOA research.

<h4>Background</h4>Chromosomal microdeletions in the 3q26-3q28 region are rare and often associated with fetal growth restriction (FGR), microcephaly, and dysmorphic features. However, the precise genetic mechanisms and phenotypic spectrum remain incompletely understood. This study reports a novel <i>de novo</i> 3q27.1-3q27.2 microdeletion and refines the critical region for this syndrome.<h4>Case description</h4>Here we report a 10-month-old girl with FGR and postnatal growth retardation. Molecular cytogenetic investigation [chromosomal single nucleotide polymorphism (SNP) microarray analysis] identified a <i>de novo</i> interstitial 1.56 Mb microdeletion of 3q27.1-3q27.2. The clinical and molecular findings in this patient were compared with the previous literature on cases with overlapping interstitial 3q-deletions. We identified the smallest region of overlap (SRO) carried on chromosome 3q27.1 as the critical region associated with this microdeletion syndrome, where dishevelled segment polarity protein 3 (<i>DVL3</i>) and adaptor related protein complex 2 subunit Mu 1 (<i>AP2M1</i>) may be associated with FGR.<h4>Conclusions</h4>This study identifies <i>DVL3</i> and <i>AP2M1</i> as likely contributors to FGR in 3q27.1-3q27.2 microdeletion syndrome and expands the phenotypic spectrum to include hepatic involvement. The findings underscore the importance of early genetic testing in FGR cases and provide insights for future research on genotype-phenotype correlations. Functional studies are needed to validate the roles of these genes in growth and development.

<h4>Background</h4>Prediction of prognosis in patients with hepatocellular carcinoma (HCC) by single-omics profiling has been widely studied. However, the prognosis related to biomarkers of multiple omics has not been investigated. We aimed to establish and validate a prediction model for prognosis prediction of resectable HCC combining multi-omics and clinicopathological factors.<h4>Methods</h4>The training cohort involved multi-omics data of 330 patients with resectable HCC (stage I-IIIA) at mutational, copy number variation (CNV), transcriptional, and methylation levels from The Cancer Genome Atlas (TCGA) database, along with clinicopathological information. The validation cohort involved samples from 40 HCC patients of Beijing Youan Hospital. Univariate and multivariate analyses were performed in single-omics with clinicopathological variables regarding patient prognosis, and independent risk factors were combined to establish the multi-omics model. The predictive accuracy was assessed by the receiver operating characteristic (ROC) method.<h4>Results</h4>The mutational, copy number, transcriptional, and methylation alterations in HCC were characterized. <i>TP53</i>, <i>CTNNB1</i>, and <i>TTN</i> were among the genes with the top mutational frequency, and <i>FBN1</i> and <i>MAP1B</i> mutations were independent risk factors for patient overall survival (OS). 1q21.3 and 1q23.3 ranked the highest in copy number amplifications, and 8p12 and 8p23.3 ranked the highest in deletions, and <i>CSMD1</i>, <i>TP53</i>, and <i>RB1</i> were genes with the most frequent CNVs. <i>AFP</i>, <i>GPC3</i>, and <i>TERT</i> were among genes with the most significant aberrant transcription, and the transcription of <i>CCNJL</i>, <i>FRMD1</i>, and <i>GRPEL2</i> were independent risk factors for OS. Both hypermethylation and hypomethylation can be observed. The aberrant methylation of <i>CXorf15</i>, <i>DACT2</i>, <i>GP6</i>, <i>KIAA1522</i>, and <i>PDIA3</i> were independent risk factors. Single-omics models were established with independent risk factors, and were validated by internal and external datasets. A prognostic model for OS with multi-omics independent risk factors and clinicopathlogical information was established. Internal and external validation achieved an optimal maximal area under the curve (AUC) of 0.98 at 1 year and 0.88 at 2 years, respectively.<h4>Conclusions</h4>A multi-omics model combining molecular aberrancies and clinicopathological information was established and proved to be optimal for prognosis prediction of resectable HCC. This model may be helpful for therapeutic strategy selection and survival assessment.

Extracorporeal shock wave lithotripsy (ESWL), although a highly effective method for the treatment of kidney stones, can cause significant kidney damage. Since urinary protein composition directly reflects kidney function, proteomic analysis of this fluid may be useful to identify changes in protein levels induced by patient exposure to ESWL as a sign of kidney damage. To this end, we collected urine samples from 80 patients with nephrolithiasis 2 h before and 24 h after exposure to ESWL, which were concentrated and subsequently processed with a commercially available enrichment method to extract low-abundance urinary proteins. These were then separated by 2D electrophoresis and subsequently analyzed by a proteomic approach. A large number of proteins were identified as being related to inflammatory, fibrotic, and antioxidant processes and changes in the levels of some of them were confirmed by Western blot analysis. Therefore, although further experimental confirmation is needed, our results demonstrate that ESWL significantly influences the low urinary protein profile of patients with nephrolithiasis. Notably, among the identified proteins, matrix metalloproteinase 7, alpha1-antitrypsin, and clusterin, as well as dimethyl arginine dimethyl amino hydrolase 2 and ab-hydrolase, may play an important role as putative biomarkers in the monitoring and management of ESWL-induced renal damage.

<h4>Background</h4>Von Willebrand factor (VWF) and coagulation factor VIII (FVIII) plasma levels are associated with increased risk for venous thromboembolism (VTE).<h4>Objectives</h4>This study aimed to determine the thrombotic risk of rare and common variants of 27 genes linked to VWF or FVIII plasma levels in genome-wide association studies.<h4>Methods</h4>Exon sequences of 27 genes linked to plasma levels of VWF or FVIII in genome-wide association studies were analyzed for common and rare variants in 28,794 subjects without VTE (born during 1923-1950, 60% women), who participated in the Malmö Diet and Cancer study (1991-1996), with a follow-up time until 2018. Hazard ratios (HRs) were determined. <i>P</i> values were Bonferroni-corrected (<i>P</i> value = .05/27 <.0019). Common variants were analyzed individually. Rare qualifying variants (<0.1%) were collapsed.<h4>Results</h4>None of the 27 genes were associated with VTE in the rare variant collapsing analysis. Three common exon variants were significantly associated with VTE: rs8176719 (frameshift) in <i>ABO</i> (HR = 1.30; 95% CI, 1.20-1.42; <i>P</i> = 3.9 × 10^-10), rs1800291 (p.Asp1260Glu) in <i>F8</i> (HR = 1.29; 95% CI, 1.08-1.55; <i>P</i> = .00046 for men; HR = 1.17; 95% CI, 1.06-1.29; <i>P</i> = .00019 for women), and rs1063856 (p.Thr789Ala) in <i>VWF</i> (HR = 1.10; 95% CI, 1.04-1.17; <i>P</i> = .00057). A risk score of these 3 variants was dose-dependently associated with VTE (5 risk alleles): HR = 2.8; 95% CI, 1.7-4.7; and <i>P</i> value = .00008. The area under the curve for VTE in receiver operating characteristics for the risk score was similar to FV Leiden (0.55 vs 0.54).<h4>Conclusion</h4>The risk score of 3 common variants in <i>VWF</i>, <i>F8</i>, and <i>AB0</i> genes is associated with VTE risk similar to FV Leiden.

<h4>Background</h4>Factor V Leiden (FVL) and prothrombin gene mutations (PGMs), as well as recently developed polygenic scores (PGSs), have been consistently associated with venous thromboembolism (VTE) risk in European ancestry populations.<h4>Objectives</h4>This study aimed to develop an optimized risk-assessment tool combining mutations and PGS for diverse ancestry populations.<h4>Methods</h4>The association of VTE risk with FVL/PGM and PGS was tested using multivariable analyses in the UK Biobank. A genetic probability for VTE (GenProb-VTE) combining PGS and FVL/PGM was developed. Its discriminative and reclassification performances over FVL/PGM alone were assessed using observed VTE rate and the continuous net reclassification index, respectively. Results were validated in the Genomic Health Initiative of Endeavor Health, an ancestry-diverse health care system-based biobank.<h4>Results</h4>Among 432,831 participants in the UK Biobank, FVL, PGM, and PGS were significantly and independently associated with VTE risk (<i>P</i> < .001). Compared with FVL/PGM alone, GenProb-VTE identified 1.5 times more high-risk subjects whose observed VTE rates exceeded those of FVL/PGM carriers. GenProb-VTE also significantly reclassified VTE risk from the model with FVL/PGM alone, with continuous net reclassification index of 0.10 (<i>P</i> < .001). VTE risk was reclassified in FVL/PGM heterozygous carriers (51%) and homozygous/compound heterozygous carriers (46%) as well as noncarriers (14%). These results were validated among 16,341 participants in the Genomic Health Initiative, in participants of both European and non-European ancestry.<h4>Conclusion</h4>GenProb-VTE, an optimized tool combining PGS with FVL/PGM, significantly improves VTE risk assessment compared with FVL/PGM alone in diverse ancestry populations. It provides a novel tool for genetic risk assessment of VTE.

Antibodies are critical for the immune response and serve as important tools due to their ability to recognize specific amino acid sequences, or epitopes. Based on the latter, they are utilized as diagnostic tools in biological and biomedical research. Huntington’s disease (HD) is a neurodegenerative condition caused by CAG repeat expansions in the huntingtin (HTT) gene and characterized by amyloid-like protein deposits in patients. Multiple anti-HTT antibodies are used in HD research for their ability to recognize specific HTT inclusions in both post-mortem tissue and in laboratory conditions. Some of the antibodies are seen as detectors of distinct structural motifs. However, most knowledge of their binding mechanism stems from studies of soluble monomers or short fragments of the epitopes, rather than the aggregated, misfolded target protein. Here, we investigate how MW8 antibodies interact with HTT exon 1 (HTTex1) fibrils, using solid-state NMR, electron microscopy, and complementary techniques. Magic angle spinning NMR revealed localized impacts of the antibody on exposed parts of the HTTex1 fibrils: the flanking segments that form its ‘fuzzy coat’. Antibody binding affected the structure and dynamics of the fuzzy coat, but also modulated the propensity for forming supramolecular fibril clusters, which has important implications for (reducing) cytotoxicity.

Atherosclerosis, a leading cause of coronary artery disease (CAD), is heavily influenced by hypercholesterolemia (HC). Proteomics research has shown promise in identifying biological markers for CAD diagnosis and prognosis. This cross-sectional study aimed to identify novel biomarkers for detecting HC and CAD. Through the analysis of proteome data from healthy controls (n = 45) and patients diagnosed with HC (n = 51) or CAD (n = 32), distinct protein patterns associated with each condition were identified. Significant alterations in protein levels were identified with a false discovery rate (FDR)-corrected q-value of <0.05. Subsequent receiver operating characteristic (ROC) analysis, with an area under the curve (AUC) greater than 0.75, was conducted. CAD patients exhibited significantly increased levels of the cholesterol-metabolizing protein proprotein convertase subtilisin/kexin type 9 (PCSK9) and varied levels of the angiogenesis-related protein stromal-cell-derived factor-1 (SDF-1) compared to controls. In pairwise comparisons among the study groups, 65 proteins showed significant differential expression. Notably, 14 of these proteins had significant correlations with blood cholesterol levels. Additionally, 22 of the identified proteins were associated with CAD or HC pathways, with nine proteins being common to both conditions (APO E, APO E3, MMP-3, PCSK9, SDF-1, APO B, PAFAH, 60 kDa heat shock protein, and TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 fusion). Nevertheless, this is an exploratory study, and validation studies are needed to confirm these potential protein biomarkers for CAD in the context of HC.

Obesity is a heterogeneous and multifactorial disease with a strong genetic component. While polygenic obesity accounts for most common cases, rare monogenic variants contribute, particularly in severe, early-onset obesity. Among the lesser-studied candidates are UCP3 and PCSK1, genes involved in key metabolic pathways. RECENT FINDINGS: The UCP3 p.Val192Ile (c.574G > A) and PCSK1 p.Asn221Asp (c.661 A > G) variants have been independently associated with metabolic pathways, including fatty acid oxidation and hormone processing, as well as a modestly increased risk of obesity. Clinical and genetic characterization of two patients with severe early-onset obesity revealed the co-occurrence of these variants, which were associated with metabolic disturbances such as insulin resistance. PURPOSE OF THE REVIEW: This narrative review examined the functional and clinical significance of UCP3 and PCSK1 variants in severe obesity, presenting two case reports to illustrate their potential impact. Our findings support a potential model in which rare variants in distinct metabolic genes may interact synergistically to exacerbate disease severity. Further studies are needed to elucidate their combined functional effects and contributions to obesity pathogenesis.

Colorectal cancer (CRC) progression is driven by complex metabolic alterations, including aberrant N-glycosylation patterns that critically influence tumor development. However, the metabolic and functional roles of N-glycosylation in CRC remain poorly understood. Herein, comprehensive proteomic and N-linked intact glycoproteomics analyses are performed on 45 CRC tumors, and normal adjacent tissues (NATs) are matched, identifying 7125 intact N-glycopeptides from 704 glycoproteins. Through analysis of glycoform expression profiles and structural characteristics, a glycosylation site-protein function association network is constructed to uncover metabolic dysregulation driven by N-glycosylation in CRC. Moreover, an arithmetic model is developed that integrates N-glycan expression patterns, which effectively distinguishes tumors from NATs, reflecting metabolic reprogramming in cancer. These findings identify Chloride Channel Accessory 1 (CLCA1) and Olfactomedin 4 (OLFM4) as potential metabolic biomarkers for CRC diagnosis. Immunohistochemistry and Cox regression analyses validated the prognostic power of these markers. Notably, the critical role of specific N-glycosylation at N196 of Adipocyte plasma membrane-associated protein (APMAP) is highlighted, a key player in tumor metabolism and CRC progression, providing a potential target for therapeutic intervention. These findings offer valuable insights into the metabolic roles of N-glycosylation in CRC, advancing biomarker discovery, enhancing metabolic-based diagnostic precision, and improving personalized treatment strategies targeting cancer metabolism.

Chemoresistance poses a significant clinical challenge in managing glioblastoma (GBM), limiting the long-term success of traditional treatments. Here, a 3D tumoroid model is used to investigate the metabolic sensitivity of temozolomide (TMZ)-resistant GBM cells to iron chelation by deferoxamine (DFO) and deferiprone (DFP). This work shows that TMZ-resistant GBM cells acquire stem-like characteristics, higher intracellular iron levels, higher expression of aconitase, and elevated reliance on oxidative phosphorylation and proteins associated with iron metabolism. Using a microphysiological model of GBM-on-a-chip consisting of extracellular matrix (ECM)-incorporated tumoroids, this work demonstrates that the combination of iron chelators with TMZ induces a synergistic effect on an in vitro tumoroid model of newly diagnosed and recurrent chemo-resistant patient-derived GBM and reduced their size and invasion. Investigating downstream metabolic variations reveal reduced intracellular iron, increased reactive oxygen species (ROS), upregulated hypoxia-inducible factor-1α, reduced viability, increased autophagy, upregulated ribonucleotide reductase (RRM2), arrested proliferation, and induced cell death in normoxic TMZ-resistant cells. Hypoxic cells, while showing similar results, display reduced responses to iron deficiency, less blebbing, and an induced autophagic flux, suggesting an adaptive mechanism associated with hypoxia. These findings show that co-treatment with iron chelators and TMZ induces a synergistic effect, making this combination a promising GBM therapy.

The inhibitory effects of the tumor necrosis factor-α (TNF-α) antibody infliximab (IFX) on colitis are well established. Since IFX dosing is weight-based and associated with various side effects, there is a growing interest in identifying combination therapies that can enhance its efficacy, particularly in overweight inflammatory bowel disease (IBD) patients, to maximize the anti-inflammatory effect while minimizing the required dose. Our research revealed that overweight IBD patients present decreased vitamin D levels in the intestinal epithelium alongside elevated TNF-α levels. In mice fed a high-fat diet (HFD) for four weeks, treatment with the vitamin D analog palicalcitol (PAL) reduced lipid synthesis and TNF-α production in intestinal epithelial cells (IECs). In a 2,4,6-trinitrobenzenesulfonic acid (TNBS)-induced experimental colitis model, PAL treatment mitigated TNF-α-induced damage to the intestinal epithelial barrier and reduced the activation of Th1 and Th17 cells in the lamina propria, thereby reducing colitis development in HFD-fed mice. Notably, the combination of IFX and PAL was more effective than IFX alone in treating colitis in these mice. Overall, our findings suggest that vitamin D inhibits TNF-α production by reducing lipid synthesis in IECs, thereby enhancing IFX therapy in overweight IBD patients.

Aging is closely associated with imbalanced transcription. Regulated transcription in different organs is significantly different during aging, indicating that organ-specific transcriptomics is critical for understanding this process. Here we analyze the transcriptomics of the intestines of 3-, 15-, 30-, 40- and 50-days old female flies, which include young, middle-aged, and old flies. We find that the differential expression of protein-coding genes and lncRNAs is significant in aging, and fly age is characterized by well-separated gene expression trajectories. The highly clustered differentially expressed genes are connected to specific biological processes and signalling pathways. In particular, the Imd and Toll pathways are the top two immune signalling pathways that are highly regulated, and members with increased expression in the Imd pathway span all upstream activating events and include many ubiquitylation-associated factors and regulators of NF-κB factor Relish. Increased expression of Toll pathway members includes sensing mediators for all kinds of microorganisms and multiple proteases in the proteolytic processing cascade. Moreover, the expression of molecular markers of intestinal cells is greatly changed. Enterocyte markers are the most significantly influenced, and enteroendocrine markers AstA and NPF, as well as intestinal stem cell (ISC)/enteroblast (EB) markers Esg and Klu are expressed at low levels in young flies and much higher levels in aged flies. Furthermore, lncRNAs show similar expression trends and clustering patterns to those of protein-coding genes. Lastly, we find that ISC/EB-specific knock-down of 13 out of 19 genes that are highly differentially expressed reduces the lifespan of the fly. Together, the characterized transcriptomics and newly identified functional genes in aging will provide potential targets for preventing intestinal aging and associated disorders.

<h4>Background</h4>Histone deacetylase inhibitors (HDACi) are clinically approved drugs for the treatment of hematological malignancies synergizing with chemotherapy. However, despite the long history of HDACi, the mechanistic underpinnings of this synergism have remained unclear.<h4>Methods</h4>Using transmission electron microscopy, we identified autophagy and ER-stress in HDACi-treated cells. We quantified ER-phagy and ER-stress with reporter systems by using 3D-deconvolution microscopy and flow cytometry. We complemented these data with qPCR and Western blot results. Apoptosis rates were assessed using a caspase assay and flow cytometry, and large public datasets were utilized.<h4>Results</h4>HDAC blockade results in specific upregulation of the selective autophagy receptor FAM134B (RETREG1) and the induction of ER-phagy. Combined with the chemotherapeutic drug Gemcitabine, this results in subsequent elevated ER-stress levels and apoptosis. Inhibiting the distinct ER-stress branches fully rescues this process. Broadening the scope of these findings, certain non-HDAC-inhibitory and clinically approved compounds like Loperamide and Nelfinavir are able to induce FAM134B and could hence constitute novel Gemcitabine-synergizing molecules. Additionally, pancreatic cancer patients with high FAM134B expression have significantly longer survival rates under chemotherapy.<h4>Conclusion</h4>In summary, we provide mechanistic evidence for ER-phagy playing a hitherto unknown central role in the clinical synergy between HDACi and chemotherapy.

To complete its life-cycle in the infected host, Influenza A virus (IAV) hijacks host machineries by expressing multiple viral proteins to bind to specific host proteins. In the era of integrative genomics, there is an opportunity to develop computational techniques to accurately and quickly predict host-pathogen protein-protein interactions (HP-PPI). Our 3-stage computational pipeline shortlisted host proteins (of which stages (i) and (ii) have been previously reported) containing the C3H zinc finger domain as putative interactors of the non-structural protein (NS1) of A/PR8/34 (H1N1), which is a well-characterized laboratory strain. To assess the accuracy of this computational pipeline, the top 7 highest scoring C3H zinc finger proteins were examined in co-immunoprecipitation experiments to determine which pair(s) of interaction is detectable in mammalian cell lines. Interestingly, one of them is CPSF30 which is a known NS1 binder. For the other 6 C3H zinc finger proteins, they have not been reported to be involved in IAV replication and co-immunoprecipitation experiments reveals that 4 of them bind to NS1. As a proof-of-concept, one shortlisted C3H protein was studied using live IAV infection and the knockdown of RC3H1 slightly increased the production of progeny virion, suggesting that it acts as an antiviral host factor.

Vγ9Vδ2 T cells that respond to phosphoantigen (pAg) function as crucial sentinels of the immune system to eradicate pathogen-infected cells and tumor cells. Alpaca (Vicugna pacos) is the first nonprimate species identified to possess the pAg-reactive Vγ9Vδ2 T cell subset. However, the molecular mechanism accounting for the pAg recognition of alpaca Vγ9Vδ2 T cells remains unclear. Here, we report the crystal structures of alpaca butyrophilin 3 (VpBTN3) B30.2 domain in complex with the exogenous pAg analog, HMBPP-08, which is a valuable tool for studying the mechanism of butyrophilin-dependent Vγ9Vδ2 T cell activation, and the endogenous pAg analogue, dimethylallyl (S)-thiolodiphosphate (DMASPP). We elucidated that the function of pAgs is governed by their structural differences. Notably, DMASPP acts as a molecular glue in the interaction between the intracellular B30.2 domains of heterologous butyrophilins in alpaca and human. Interestingly, although HMBPP-08 has stronger affinity than DMASPP to VpBTN3 B30.2 domain, HMBPP-08 did not promote heterologous VpBTNs interaction. These findings establish a novel theoretical framework elucidating the mechanisms of Vγ9Vδ2 T cell activation and demonstrate the conserved evolutionary mechanisms underlying cross-species immune adaptation.

Metabolic alterations in human lipidome significantly impact various chronic diseases including type 2 diabetes (T2D). However, epidemiology and clinical studies have yet to identify clinically meaningful lipid markers for T2D. Fatty acids (FAs) are the backbone of lipid species. However, conflicting results on the essential FAs including omega 3 and omega 6 in the development of metabolic diseases urge deeper evaluations of diverse clinical cohorts including underrepresented populations. This study investigated the lipidomics profiles of 3,000 individuals from a well-characterized cohort of Asian Indians. Untargeted lipidomic profiles were created using blood samples applying reversed-phase liquid chromatography-accurate mass tandem mass spectrometry. Free FAs and lysophosphatidylcholines (LPCs) were upregulated, while sphingomyelin and phosphatidylcholines were decreased in T2D. We observed a significant increase of essential FAs-FA20:4 (AA), FA20:5 (EPA), and FA22:6 (DHA) in T2D after adjusting for age, gender, and body mass index. However, most ω-3 and ω-6 FAs were reduced by 2 to 6-fold in obesity in both genders. We also observed gender differences in age-associated lipid patterns in which cholesterol sulfate and LPC 22:6 were elevated in all age groups in men, but LPC 22:6 rapidly increased after menopause in women, and sphingomyelins increased in men after 40 years. Machine learning analysis identified long-chain FAs, ether-based LPCs, and clinical risk scores among the most informative features associated with T2D. Our study identified lipidomic markers that could be potential mediators of T2D and obesity. Their patterns may underpin gender differences in the pathogenesis of metabolic and cardiovascular diseases.

<h4>Background</h4>Major depressive disorder (MDD) is a polygenic condition with substantial heritability, with genome-wide association studies (GWAS) identifying several risk loci in European populations, including the VRK2 gene. However, the association between VRK2 and MDD in non-European populations, particularly in Han Chinese, remains underexplored.<h4>Methods</h4>We genotyped four VRK2 SNPs (rs2678907, rs11682175, rs1568452, rs1518395) in a cohort of 1878 MDD cases and 1800 controls of Han Chinese descent. Genotyping was performed using SNaPShot, and linkage disequilibrium (LD) was assessed with SHEsis. Associations between the SNPs and MDD were evaluated via logistic regression in PLINK. VRK2 mRNA expression in the amygdala and peripheral blood was quantified by RT-qPCR, with statistical significance determined by ANCOVA and t-tests. A meta-analysis incorporating an independent East Asian GWAS cohort was also conducted.<h4>Results</h4>In our Han Chinese cohort, rs2678907 was significantly associated with MDD (P = 4.17 × 10^-5, OR = 1.217). Meta-analysis with independent East Asian GWAS further confirmed the associations of rs2678907 with MDD. Haplotype analysis of VRK2 SNPs in Han Chinese revealed the haplotypes (T-G for rs11682175-rs2678907 and C-G for rs1568452-rs2678907) associated with an increased MDD risk and elevated VRK2 mRNA expression. Additionally, MDD patients showed significantly higher VRK2 mRNA levels in peripheral blood than controls (P = 1.85 × 10^-7).<h4>Conclusions</h4>These findings provide strong evidence for the role of VRK2 in MDD risk in Han Chinese individuals. Our results underscore the potential of VRK2 as a genetic and expression-based biomarker for MDD, highlighting the importance of accounting for population-specific genetic variations in psychiatric research. Further research is essential to explore the functional implications of VRK2 in MDD pathogenesis.

Anoikis, defined as programmed cell death triggered by the loss of cell-extracellular matrix (ECM) and cell-cell interactions, is crucial for maintaining tissue homeostasis and preventing aberrant cell migration. Cancer cells, however, display anoikis resistance (AR) which in turn enables cancer metastasis. AR results from alterations in apoptotic signaling, metabolic reprogramming, autophagy modulation, and epigenetic changes, allowing cancer cells to survive in detached conditions. In this review we describe the mechanisms underlying both anoikis and AR, focusing on intrinsic and extrinsic pathways, disrupted cell-ECM interactions, and autophagy in cancer. Recent findings (i.e., between 2014 and 2024) on epigenetic regulation of AR and its role in metastasis are discussed. Therapeutic strategies targeting AR, including chemical inhibitors, are highlighted alongside a network analysis of 122 proteins reported to be associated with AR which identifies 53 hub proteins as potential targets. We also evaluate in vitro and in vivo models for studying AR, emphasizing their role in advancing metastasis research. Our overall goal is to guide future studies and therapeutic developments to counter cancer metastasis.

<h4>Background</h4>Social media can significantly impact body image perception among adolescents.<h4>Objective</h4>This study examines how exposure to fitspiration content relates to body esteem, with a focus on gender differences and BMI.<h4>Methods</h4>A cross-sectional online survey was conducted among 211 participants using validated instruments (Body Esteem Scale, A. Sobczak's silhouette scale). Data were analyzed using descriptive statistics and chi-square tests.<h4>Results</h4>Exposure to athletic images decreased self-esteem in 37% of participants, particularly among women (<i>p</i> = 0.004). Gender significantly influenced the tendency to compare oneself with athletic individuals (<i>p</i> = 0.02). BMI was not significantly associated with body image perception (<i>p</i> = 0.05).<h4>Conclusions</h4>Gender-specific patterns in social media-related body image perception highlight the need for targeted interventions to mitigate negative impacts among young adults.

<b>Background/Objectives</b>: Lipid metabolism plays a crucial role in uterine corpus endometrial carcinoma (UCEC); however, its specific mechanisms remain to be fully elucidated. This study aimed to construct a lipid-metabolism-related prognostic model and explore its association with the tumor immune microenvironment. <b>Methods</b>: A total of 552 UCEC and 35 normal tissue samples from The Cancer Genome Atlas (TCGA) database were analyzed to identify differentially expressed lipid-metabolism-related genes (DE-LMRGs). A prognostic risk model was established using univariate Cox analysis, least absolute shrinkage and selection operator (LASSO) regression, and multivariate Cox regression, and its clinical utility was assessed through nomogram construction. Functional enrichment analysis was performed to explore the biological pathways involved. Tumor immune infiltration patterns were evaluated using single-sample Gene Set Enrichment Analysis (ssGSEA), Estimation of Stromal and Immune Cells in Malignant Tumors using Expression Data (ESTIMATE), and Tumor Immune Dysfunction and Exclusion (TIDE) algorithms. Results: Multivariate analysis indicated that the prognostic model had robust predictive value, with AUCs of 0.701, 0.746, and 0.790 for 1-, 3-, and 5-year overall survival predictions. High-risk patients exhibited a suppressed immune microenvironment characterized by reduced immune cell infiltration, lower tumor mutation burden (TMB), and elevated TIDE scores, suggesting potential resistance to immunotherapy. Furthermore, LIPG was identified as a key hub gene through the intersection of nine machine learning algorithms, demonstrating strong associations with both cancer progression and immune infiltration. Functional validation using Cell Counting Kit-8 (CCK-8), wound healing, and transwell migration assays following small interfering RNA (siRNA) transfection demonstrated that LIPG promotes UCEC cell proliferation and migration in vitro. <b>Conclusions</b>: These findings highlight the critical role of lipid metabolism in UCEC progression and immune modulation, with LIPG emerging as a potential prognostic biomarker. The identified lipid-metabolism-related gene signature may provide new insights into tumor microenvironment interactions.

Herein, a detailed account of the efforts leading to the recently published synthesis of the <i>Ganoderma</i> meroterpenoid ganoapplanin, a natural product identified as an inhibitor of T-type voltage-gated calcium channels, is provided. Ganoapplanin, which was isolated as a racemate from the fungus <i>Ganoderma applanatum</i> in 2016, features a complex structure, including a characteristic spiro bisacetal structure, a highly functionalized tetra-<i>ortho</i>-substituted biaryl motif, and a propellane-like dioxatricyclo[4.3.3.0]dodecane scaffold. While the southern terpenoid fragment is available via a diastereoselective titanium-mediated iodolactonization, considerable efforts are required to fuse this fragment with various aromatic fragments. The breakthrough was achieved by a highly efficient two-component coupling strategy that simultaneously fuses the fragments and establishes the crucial biaryl bond. This transformation involves an intramolecular 6-<i>exo</i>-trig radical addition of a quinone monoacetal, followed by an intermolecular aldol addition. Finally, strategic late-stage oxidations enabled the formation of the characteristic spiro bisacetal motif and the completion of the synthesis of ganoapplanin.

Sodium copper chlorophyllin (chlorophyllin, CHL), a semi-synthetic water-soluble derivative of green plant pigment chlorophyll, is associated with potential health benefits; however, systematic preclinical evaluation of its pharmacological and therapeutic potential remains limited. This study investigates safety, toxicology, pharmacokinetics, and efficacy of CHL as an adjunct to breast cancer chemotherapy. Acute and sub-acute oral toxicity of CHL was assessed in mice and rats under Good Laboratory Practice (GLP) conditions following OECD guidelines. Anti-cancer effects and mechanisms were evaluated in 4 T1mouse breast cancer cells using viability assays, colony formation analysis, and proteomics. Cyclophosphamide (CYP)-induced painful bladder syndrome (PBS) was studied in C57BL/6 female mice. In acute toxicity study, up to 5000 mg/kg bw of CHL was well tolerated without any signs of toxicity and death. In the sub-acute toxicity study, no features suggestive of drug-induced toxicity indicated No-Observed Adverse Effect Level (NOAEL) to be beyond 1000 mg/kg bw. CHL showed wide biodistribution, achieving sustained therapeutic concentrations in target tissues. CHL enhanced the anti-proliferative and cytotoxic effects of CYP in 4 T1 breast cancer cells, and proteomics studies revealed disruption in DNA damage repair, microtubule dynamics, and mitochondrial biogenesis, leading to apoptosis. CHL (100 mg/kg bw, oral) showed significant therapeutic benefit for treatment of CYP induced PBS. CHL alleviated PBS symptoms by restoring IL- 22 levels, reducing oxidative stress, and improving bladder functionality. Chlorophyllin appears to be relatively safe even at high doses, demonstrates potentially favorable pharmacology, and may hold promise for mitigating CYP-induced bladder toxicity and enhancing chemotherapy efficacy.

<h4>Objective</h4>This study aims to determine whether rigid autofluorescence imaging can differentiate cholesteatoma from surrounding tissues to reduce residual disease after cholesteatoma surgery.<h4>Study design</h4>Ex vivo proof-of-principle study.<h4>Setting</h4>Erasmus University Medical Center, Rotterdam, the Netherlands.<h4>Methods</h4>Autofluorescence signals of cholesteatoma, mucosa, and bone were measured using confocal microscopy to confirm distinguishable spectral differences. Subsequently, rigid autofluorescence imaging with specific filter settings (λ_e = 405 nm and λ_d > 570 nm) was applied to 14 resected surgical specimens to obtain signal intensity and tissue-specific fluorescence ratios.<h4>Results</h4>Cholesteatoma matrix without keratin exhibited a significantly higher autofluorescence intensity compared to mucosa (P < .03), with a cholesteatoma-to-mucosa ratio of 2.15. Similarly, autofluorescence intensity was elevated in the matrix with keratin (ratio: 2.25, P = .03) and perimatrix with keratin (ratio: 2.29, P = .04) relative to mucosa. Perimatrix without keratin showed a nonsignificant trend (ratio: 1.85, P = .06). Although cholesteatoma and bone showed no significant difference, this is clinically less relevant as bone is easily identifiable during surgery.<h4>Conclusion</h4>Rigid autofluorescence imaging demonstrates significant potential for improving cholesteatoma surgery by reliably differentiating cholesteatoma matrix, both with and without accumulated keratin, from mucosa, showing 2.25- and 2.15-fold higher signal intensities, respectively. This technique could assist otologic surgeons in achieving more complete resections, thereby reducing residual disease rates while preserving surrounding structures. Future research should focus on optimizing the technology for in vivo application, particularly for detecting small cholesteatoma fragments, and further evaluate factors influencing specificity and sensitivity in clinical practice.

Structural maintenance of chromosome protein 4 (SMC4), is a key structural component of mitotic chromosomes. While existing evidence indicates a plausible link between SMC4 and oncogenic manifestations, its precise role in the trajectory of prostate cancer remains ambiguous. The Cancer Genome Atlas (TCGA) database analysis reveals that aberrant expression of SMC4 exhibits a robust prognostic association with metastatic progression. To investigate the function of SMC4, the SMC4 gene is knocked down in RM1-LM cells, a highly metastatic cell clone is developed, using the CRISPR/Cas9 system. The results show that SMC4 knockdown significantly diminished cell proliferation and migration in vitro. Furthermore, in a murine model, RM1-LM cells display higher lung metastasis capabilities than SMC4 knockdown cells. SMC4 knockdown inhibited the activation of mTOR and downregulated the expression of Rheb. KEGG enrichment analyses of the RNA-seq results reveal that cancer signaling pathways and metabolic pathways are enriched. The SMC4 interactome is uncovered through IP-MS and indicates that SMC4 interacts with GLUT1, encoded by Slc2a1. Glycolytic rate assay illustrates that knocking down SMC4 inhibits the cell glycolysis rate and ATP production. Collectively, the data suggests that the interaction between SMC4 and GLUT1, as confirmed by co-IP, promotes prostate cancer cell metastasis through the Rheb/mTOR pathway.

The ubiquitin-editing enzyme A20 is known to regulate inflammation and maintain homeostasis, but its role in self-DNA-mediated inflammation in acute kidney injury (AKI) is not well understood. Here, our study demonstrated that oxidized self-DNA accumulates in the serum of AKI mice and patients. This oxidized self-DNA exacerbates the progression of AKI by activating the cGAS-STING pathway and NLRP3 inflammasome. While inhibition of the STING pathway only slightly attenuates AKI progression, suppression of NLRP3 inflammasome-mediated pyroptosis significantly alleviates AKI progression and improves the survival of AKI mice. Subsequently, we found that Tnfaip3 (encoding A20) is significantly upregulated following oxidized self-DNA treatment. A20 significantly alleviates AKI development by dampening STING signaling pathway and NLRP3-mediated pyroptosis. Moreover, A20-derived peptide (P-II) also significantly alleviates ox-dsDNA-induced pyroptosis and improves the survival and renal injury of AKI mice. Mechanistically, A20 competitively binds with NEK7 and thus inhibiting NLRP3 inflammasome. A20 and P-II interfere with the interaction between NEK7 and NLRP3 through Lys140 of NEK7. Mutation of Lys140 effects on the interaction of NEK7 with A20 and/or NLRP3 complex. Conditional knockout of NEK7 in macrophages or pharmacological inhibition of NEK7 both significantly rescue AKI mouse models. This study reveals a new mechanism by which A20 attenuates oxidized self-DNA-mediated inflammation and provides a new therapeutic strategy for AKI.

Transposable elements (TEs) make up 45% of the human genome, are a source of genetic variability difficult to detect, and involved in processes related to gene regulation and disease. Nanopore sequencing is recognized as one of the best technologies for detecting TEs; however, tools for analyzing of human TE insertions and deletions with nanopore-based data can be improved. RetroInspector is an easy to use, configurable Snakemake pipeline that performs detection, annotation, enrichment, and genotyping of TEs. RetroInspector requires the FASTQ files of the samples and the reference genome to start the identification and analysis of TEs. The user can also set the threshold for the number of supporting reads for the variant filtering. RetroInspector also allows users to compare the results of two samples. Different versions of the reference genome can be used and the presence of retrotransposition features can be annotated. RetroInspector has been run on three nanopore sequencing datasets and validated experimentally using proprietary and public data with over 80% precision.

Immune dysfunction is implicated in the aetiology of psychiatric, neurodevelopmental, and neurodegenerative conditions, but the issue of causality remains unclear impeding attempts to develop new interventions. Using genomic data on protein and gene expression across blood and brain, we assessed evidence of a potential causal role for 736 immune response-related biomarkers on 7 neuropsychiatric conditions by applying Mendelian randomization (MR) and genetic colocalisation analyses. A systematic three-tier approach, grouping biomarkers based on increasingly stringent criteria, was used to appraise evidence of causality (passing MR sensitivity analyses, colocalisation, False Discovery Rate and Bonferroni thresholds). We provide evidence for a potential causal role of 29 biomarkers for 7 conditions. The identified biomarkers suggest a role of both brain specific and systemic immune response in the aetiology of schizophrenia, Alzheimer's disease, depression, and bipolar disorder. Of the identified biomarkers, 20 are therapeutically tractable, including ACE, TNFRSF17, SERPING1, AGER and CD40, with drugs currently approved or in advanced clinical trials. Based on the largest available selection of plasma immune-response related biomarkers, our study provides insight into possible influential biomarkers for the aetiology of neuropsychiatric conditions. These genetically prioritised biomarkers now require examination to further evaluate causality, their role in the aetiological mechanisms underlying the conditions, and therapeutic potential.

<h4>Background</h4>Gastrointestinal (GI) disease/dysfunction persists in people living with HIV (PLWH) receiving suppressive combination anti-retroviral therapy (ART) leading to epithelial barrier breakdown, microbial translocation and systemic inflammation that can drive non-AIDS associated comorbidities. Although epigenetic mechanisms are predicted to drive GI dysfunction, they remain unknown and unaddressed in HIV/SIV infection. The present study investigated genome-wide changes in DNA methylation, and gene expression exclusively in colon epithelial cells (CE) in response to simian immunodeficiency virus infection (SIV) and long-term low-dose delta-9-tetrahydrocannabinol (THC).<h4>Methods</h4>Using reduced-representation bisulfite sequencing, we characterized DNA methylation changes in colonic epithelium (CE) of uninfected controls (n=5) and SIV-infected rhesus macaques (RMs) administered vehicle (VEH/SIV; n=7) or THC (THC/SIV; n=6). Intact jejunum resection segments (~5cm) were collected from sixteen ART treated SIV-infected RMs [(VEH/SIV/ART; n=8) and (THC/SIV/ART; n=8)] to confirm protein expression data identified in the colon of ART-naïve SIV-infected RMs. Transcriptomics data was used to confirm expression of differentially methylated genes. Protein expression of differentially methylated genes and their downstream targets was assessed using Immunofluorescence followed by HALO quantification.<h4>Results</h4>SIV infection in ART-naïve RMs induced marked hypomethylation throughout promoter-associated CpG islands (paCGIs) in genes related to inflammatory response (NLRP6, cGAS), cellular adhesion (PCDH17, CDH7) and proliferation (WIF1, SFRP1, TERT, and HAND2) in CEs. Moreover, low-dose THC reduced NLRP6 protein expression in CE by hypermethylating the NLRP6 paCGI and blocked polyI:C induced NLRP6 upregulation in vitro. In ART suppressed SIV-infected RMs, significant NLRP6 protein upregulation during acute infection was unaffected by long-term ART administration during chronic infection despite successful plasma and tissue viral suppression. In this group, NLRP6 protein upregulation was associated with significantly increased expression of necroptosis-driving proteins; phosphorylated-RIPK3(Ser199), phosphorylated-MLKL(Thr357/Ser358), and HMGB1. Most strikingly, adding ART to THC-treated SIV-infected RMs effectively reduced NLRP6 and necroptosis-driving protein expression to pre-infection levels.<h4>Conclusions</h4>We conclude that DNA hypomethylation-assisted NLRP6 upregulation can lead to its constitutively high expression resulting in the activation of necroptosis signaling via the RIPK3/p-MLKL pathway that can eventually drive intestinal epithelial loss/death. From a clinical standpoint, low-dose phytocannabinoids in combination with ART could safely and successfully reduce/reverse persistent GI inflammatory responses via modulating DNA methylation.

<h4>Introduction</h4>Gastric cancer (GC) is a common malignancy, which is associated with high rates of morbidity and mortality. Despite therapeutic advancements, there is an overall lack of effective treatment options for patients with GC, particularly those with advanced and metastatic disease. The roles of circular (circ)RNAs in tumorigenesis are being increasingly recognized, among which circRNAs are defined as miRNA/protein sponges, scaffolds, or protein coding templates.<h4>Objectives</h4>The aim of the present study is to investigate the functions of circATM in GC and elucidate the underlying molecular mechanism.<h4>Methods</h4>By circRNA sequencing in GC tissues, we identified a novel 526 nt circRNA, circATM, generating from exons 3-6 of the ATM gene. Through circRNA pull-down and RNA immunoprecipitation assays, we identified PARP1 as one of circATM binding proteins. The EdU, colony formation, wound healing, dual-luciferase reporter, cell cycle assays were employed to evaluated circATM functions in vitro. The GC xenograft model was used to determine the role of circATM in vivo.<h4>Results</h4>Knocking down circATM promoted GC cells growth in vivo and in vitro. Meanwhile, the overexpression of circATM increased the levels of p16, p21, and p27, and decreased those of β-catenin and c-Myc. Furthermore, we identified PARP1 as a circATM-interacting partner. Mechanistically, circATM bound to the zinc finger motif of Ⅱ-Ⅲ domains of PARP1 to block its recruitment to sites of DNA damage, triggering cell cycle arrest and sequestering β-catenin from the PARP1/β-catenin/TCF4 complex, leading to the suppression of Wnt/β-catenin signaling. Additionally, circATM facilitated the ubiquitin-proteasome degradation of PARP1, further jeopardizing its ability to mediate DNA damage repair.<h4>Conclusion</h4>Taken together, we defined circATM as a novel gastric tumor suppressor via interacting with PARP1, which indicate that circATM may be a promising biomarker for the diagnosis and therapy of GC.

<h4>Introduction</h4>Colorectal cancer (CRC) poses a significant risk of recurrence and distant metastases. This study investigated the regulatory role of Matrix metalloproteinase-14 (<i>MMP14</i>) in immune function and its impact on CRC prognosis.<h4>Methods</h4>we performed transcriptome sequencing on tumor and adjacent non-cancerous samples from four pairs of patients diagnosed with colorectal cancer. Single-cell transcriptome data were analyzed to explore MMP14 expression and immune microenvironment changes. mRNA expression profiles and clinical data were retrieved from public databases (TCGA and GEO). The association between MMP14 and pathways as well as immune regulators was analyzed. Co-expression genes of MMP14 relevant to prognosis were identified. A prognostic model was then constructed. MMP14 expression was examined using real-time fluorescence quantification PCR (qRT-PCR) and Western blotting (WB). Immunofluorescence was utilized to demonstrate MMP14 expression in colon cancer tissues, while Hematoxylin and eosin (HE) staining was employed to observe the histology of normal tissue and colon cancer tissue.<h4>Results</h4>Machine learning identified MMP14 as a candidate gene. MMP14 was overexpressed in CRC tissues and COLO205 cells. Single-cell transcriptome analysis revealed that MMP14 was highly expressed in fibrocyte cells within the liver metastasis group. Increased MMP14 levels correlated with poor overall survival (OS), progression-free survival (PFS), and advanced TNM stages. Functional assays indicated that silencing MMP14 in COLO205 cells enhanced apoptosis and upregulated the expression of the immune-related cytokine IL-1β. Furthermore, MMP14 exhibited significant correlations with immunomodulators, particularly immunostimulants and immunosuppressants, and was associated with immune cell infiltration within tumor tissues. Additionally, by utilizing co-expressed genes of MMP14 and conducting Cox regression analysis, we developed a risk prediction model comprising three genes (LIMK1, SPOCK3, SLC2A3). The risk scores derived from this model were found to correlate with OS and PFS.<h4>Discussion</h4>MMP14 plays a crucial role in CRC progression. Its overexpression is related to poor prognosis and immune cell infiltration. The prognostic model based on MMP14 co-expression genes may help predict CRC prognosis. However, further studies are needed to validate these findings, such as more <i>in-vitro</i> and <i>in-vivo</i> experiments. In conclusion, MMP14 can serve as a biomarker for evaluating CRC prognosis and immune cell infiltration.

F-box and leucine-rich repeat protein 4 (FBXL4) plays a crucial role in mitochondrial bioenergetics, mitochondrial DNA (mtDNA) maintenance, and mitochondrial dynamics. The variations in the <i>FBXL4</i> gene can give rise to encephalomyopathy mitochondrial DNA depletion syndrome-13 (MTDPS13) characterized by the reduction of mtDNA copy number, leading to deficiencies in mitochondrial functions, which is a serious and rare autosomal recessive genetic disorder. Patients with <i>FBXL4</i> variations are usually diagnosed due to the emergence of symptoms in the early stages of life. Commonly observed are lactic acidemia, developmental retardation, and hypotonia. A portion of patients may be accompanied by comorbidities such as cardiovascular diseases, epilepsy, ophthalmopathy, hearing impairment, and movement disorders. Currently, there have been no reported cases of prenatal diagnosis for <i>FBXL4</i> gene variations. Here, we report for the first time the prenatal diagnosis of a fetus with a compound heterozygous mutation in the <i>FBXL4</i> gene (NM_012160.5: c.1288C>T, p. Arg430* and c.518_523del, p. Glu173_Leu175delinsVal) by trio-WES, the nonsense mutation (c.1288C>T) was reported only once in an unrelated individual and no detailed clinical phenotype; the deletion mutation (c.518_523del) has not been reported yet. Additionally, we monitor prenatal phenotypes of fetus at different stages of pregnancy using ultrasound and magnetic resonance imaging (MRI), present prenatally with nuchal translucency (NT) thickening and progressive brain developmental abnormalities. Our report indicates that the application of trio whole exome sequencing (trio-WES) and imaging monitoring can facilitate prenatal diagnosis of <i>FBXL4</i> gene-related MTDPS13, and this will modify the decision-making process for couples with <i>FBXL4</i> variations.

Diabetic kidney disease (DKD) is one of the major complications of diabetes, and its pathological progression is closely associated with lipid metabolic reprogramming. Under diabetic conditions, renal cells undergo significant lipid metabolic abnormalities, including increased lipid uptake, impaired fatty acid oxidation, disrupted cholesterol efflux, and enhanced lipid catabolism, as adaptive responses to metabolic stress. These changes result in the accumulation of lipids such as free fatty acids, diacylglycerol, and ceramides, leading to lipotoxicity that triggers inflammation and fibrosis. Hypoxia in the DKD microenvironment suppresses fatty acid oxidation and promotes lipid synthesis through the HIF-1α pathway, while chronic inflammation exacerbates lipid metabolic disturbances via inflammatory cytokines, inflammasomes, and macrophage polarization. Targeting lipid metabolism represents a promising therapeutic strategy for alleviating DKD; however, further clinical translational studies are warranted to validate the efficacy and safety of these approaches.

<h4>Background and objective</h4>The primary objective of this study is to evaluate the added value of optical genome mapping (OGM) when integrated into the standard cytogenetic workup (SCGW) for hematological malignancies.<h4>Methods</h4>The study cohort comprised 519 cases with different types of hematological malignancies. OGM and SCGW (including G-banded karyotyping and fluorescence in situ hybridization) were performed on blood and/or bone marrow. The analytical sensitivity of OGM, defined as the detection of all additional cytogenomic aberrations, and its clinical utility, referring to aberrations with diagnostic, prognostic, or therapeutic significance, were assessed.<h4>Results</h4>OGM led to increased analytical sensitivity and clinical utility in 58% and 15% of the cases, respectively. The clinical utility varied across different malignancies, with the highest utility in T-lymphoblast leukemia (52%), followed by mixed phenotype acute leukemia (43%), B-lymphoblastic leukemia (37%), other B-cell lymphomas (22%), mature T-cell leukemia/lymphoma (20%), chronic lymphocytic leukemia (14%), acute myeloid leukemia (13%), multiple myeloma (13%), mantle cell lymphoma (8%), myelodysplastic/myeloproliferative neoplasms (6%), myelodysplastic syndrome (5%), and myeloproliferative neoplasms (0%).<h4>Conclusion</h4>Compared to SCGW, OGM detects additional cytogenomic aberrations in approximately 58% of cases. OGM provides clinical utility at varying rates across different types of hematological malignancies. Given these differences, strategic triaging can help maximize the clinical value of OGM by focusing on diseases where it offers the most significant benefit.

Acute promyelocytic leukemia (APL) is one subtype of acute myeloid leukemia (AML) primarily associated with the typical fusion gene PML::RARA/t(15;17). A small percentage of APL cases are caused by atypical gene transcript variants lacking the PML::RARA. We report one case with two novel NUP98::RARA fusion transcripts in APL lacking the fusion gene PML::RARA/t(15;17). These NUP98::RARA fusion transcripts were identified using next-generation sequencing (NGS), which were confirmed by Sanger sequencing. One of the transcripts differs from the previously reported transcript in terms of break sites and transcript length, which identified as subtype of NUP98::RARA fusion transcript. The other one is the same as previously reported, demonstrating reproducible abnormality of this fusion gene. The patient was treated with all-trans retinoic acid (ATRA), realgar-Indigo naturalis formula (RIF) and chemotherapy. According to the published paper, this is the second report of NUP98::RARA fusion transcript in APL. It is also the first variant APL with der(11)(p15)t(11;17)(p15;q21) and i(17)(q10) chromosome abnormalities. Therefore, we compared and summarized these two cases.

δ-Catenin is a member of the p120-catenin subfamily of armadillo proteins and is known to be upregulated in prostate cancer, promoting tumorigenesis. Unfortunately, the molecular mechanism underlying this effect remains unclear. The carcinogen 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) has been linked to an increased risk of prostate cancer. In this study, we explored the effect of TCDD on δ-catenin in prostate cancer cells. TCDD increased the protein levels of δ-catenin in a dose-dependent manner by enhancing its stability. Moreover, TCDD led to an increase in β-catenin expression but a decrease in E-cadherin levels. Further experiments revealed that TCDD stabilized the expression of δ-catenin by inhibiting its ubiquitination-mediated degradation. Finally, TCDD enhanced the motility and migration ability of prostate cancer cells through δ-catenin. These findings suggest that TCDD plays a role in stabilizing δ-catenin in prostate cancer cells, offering a new perspective on preventing δ-catenin degradation and potentially increasing the predictive value of δ-catenin for prostate cancer.

The constant emergence of drug-resistant mycobacteria, together with the lack of new antibiotics entering the market, has become a global public health problem that threatens the effective treatment of infectious diseases. The development of single molecules targeting different proteins should significantly reduce the emergence of resistant strains, and therefore represent a promising strategy to overcome such an issue. In this challenging context, a new series of 30 lipophilic compounds based on the β-lactone-core has been synthesized by varying the nature of the substituents on the lactone ring. The evaluation of their antibacterial activity against <i>M. tuberculosis</i> and <i>M. abscessus</i>, two major pathogenic mycobacteria, highlighted potential candidates. The VM038, VM040 and VM045 were active only against <i>M. tuberculosis</i>, while VM025, VM026 and VM043 inhibited the growth of both <i>M. tuberculosis</i> and the S and R variants of <i>M. abscessus</i>. Competitive click chemistry activity-based protein profiling revealed several potential <i>M. abscessus</i> target enzymes of VM043, the best extracellular growth inhibitor. Finally, when tested against intracellular bacteria, although VM043 was found inactive, VM025 & VM026 proved to be potent and promising inhibitors of intramacrophagic <i>M. abscessus</i> growth with minimal inhibitory concentrations (MIC_50Raw) comparable to the standard antibiotic imipenem. Overall, these results strengthen the added value of our VM β-lactone derivatives not only in the fight against pathogenic mycobacteria, leading to the arrest of <i>M. abscessus</i> and/or <i>M. tuberculosis</i> growth through multitarget enzyme inhibition, but also as efficient probes to identify novel potential therapeutic targets using chemoproteomics approaches.

Thousands of biomarkers have been discovered to solve the mechanisms of cancer, but dynamic alterations in the parameters that affect cancer progression cause complex disease status. Therefore, it is essential when dealing with cancer to analyze all parameters, including pathway information, to understand the disease mechanism of action. In our study, we applied multi-omics data integration for microbiome, transcriptome, and microbial pathway datasets obtained from colorectal cancer patients. The <i>Cldn7</i> gene and <i>Fusobacteria</i>, which both play roles in the stability of the intestinal barrier, were found to be highly associated with each other (r = 0.71). The Klf3 gene has been identified as a critical regulator in the activation of the WNT1 and WNT/β-catenin signaling pathways. Notably, it exhibited a strong positive correlation with the presence of <i>Fusobacteria</i>, which are also implicated in modulating these pathways. In addition, the glutaryl CoA degradation and p-cymene degradation pathways demonstrated a strong positive association with the expression of the <i>Ahcy</i>, <i>Eis2s2</i>, <i>Hsp90ab1</i>, <i>Psma7</i>, <i>Lbr</i>, <i>Rpl7l1</i>, <i>Cse1l</i>, <i>Cbx3</i>, <i>Ncl</i>, <i>Hspd1</i>, <i>Tpx2</i>, and <i>Top2a</i> genes (r > 0.65), suggesting their potential involvement in the regulation and metabolic integration of these pathways at the transcriptional level.

<b>Introduction:</b> Depression is a pervasive global health issue, affecting millions worldwide and causing significant disability. Despite its prevalence, current diagnostic and treatment approaches often yield suboptimal outcomes. The complexity of depression, characterized by diverse causes and symptoms, highlights the urgent need for advanced diagnostic tools and personalized therapies. Biomarkers, particularly <b>genetic</b> and <b>epigenetic</b> depression biomarkers, offer promise in uncovering the biological mechanisms underlying depression, potentially revolutionizing its management. <b>Aim: Primary aim:</b> To identify biomarkers associated with depressive disorders, with a focus on <b>genetic</b> and <b>epigenetic biomarkers</b>. <b>Secondary aim:</b> To optimize the current classification of biomarkers associated with different types of depressive disorders, with a focus on <b>genetic</b> and <b>epigenetic biomarkers</b>. <b>Methods:</b> We integrated findings with strategic keywords extracted from relevant studies, conducting a thorough literature review across the Google Scholar, PubMed, and Web of Science databases. Lastly, final reference inclusion had stringent criteria: recent, diverse peer-reviewed articles in English, all study designs, ensuring up-to-date coverage of <b>genetic</b> and <b>epigenetic depression biomarker</b> research. <b>Results:</b> The review reveals the classification of <b>genetic</b> and <b>epigenetic biomarkers</b> in regard to the type of biomarker, the system of the human body it derives from, and the sampling entity. All of the findings show promise in diagnosing depression, with the potential of predicting treatment outcomes and guiding personalized therapeutic approaches. We defined the significant correlations between <b>genetic</b> and <b>epigenetic biomarker</b> profiles and clinical parameters such as symptom severity and treatment response, thereby enhancing diagnostic accuracy and guiding treatment strategies tailored to individual patient needs across diverse depressive subtypes and treatment responses. <b>Conclusion:</b> Identifying biomarkers associated with depressive disorders, with a focus on <b>genetic</b> and <b>epigenetic biomarkers</b>, represents a critical step toward improving diagnostic precision and treatment efficacy. By elucidating the complex biological underpinnings of depression, this study contributes to the development of targeted therapies that address the diverse needs of individuals affected by this debilitating group of disorders. Future research should focus on validating these <b>genetic</b> and <b>epigenetic biomarkers</b> in larger cohorts and clinical trials to facilitate their clinical implementation and enhance patient outcomes.

The RNA-binding protein Sex-lethal (Sxl) is classically known as a master regulator of sex determination and mRNA splicing in Drosophila melanogaster . However, this role is not conserved across species, and functions beyond this canonical pathway remain poorly understood. In this study, we uncover a splicing-independent role for Sxl at the chromatin level in the Drosophila brain. Using Targeted DamID (TaDa) profiling in neurons, we identify widespread recruitment of Sxl to promoter regions, independent of sex or RNA binding activity. Notably, Sxl chromatin occupancy exhibits near-complete overlap with Polr3E (RPC37), an RNA Polymerase III subunit, with Sxl binding abolished upon Polr3E knockdown. Depletion of Sxl in mature male neurons induces widespread transcriptional changes, particularly in metabolic genes, and improves negative geotaxis during ageing, phenotypes that closely mirror Polr3E knockdown. Conversely, overexpression of the brain-specific Sxl RAC transcript leads to enhanced tRNA synthesis and upregulated metabolic gene expression. Together, these findings reveal a previously unrecognised role for Sxl in regulating Pol III activity via Polr3E, regulating tRNA synthesis and supporting neuronal metabolism. Given the emerging tie between Pol III regulation and neuronal ageing, our study highlights Sxl as a novel modulator of neuronal homeostasis.

Triple-negative breast cancer (TNBC) accounts for approximately 15% of all Breast Cancer (BC) cases with poorer prognosis and clinical outcomes compared to other BC subtypes due to greater tumor heterogeneity and few therapeutically targetable oncogenic drivers. To reveal actionable pathways for anti-cancer treatment, we use a proteomic approach to quantitatively compare the abundances of 6306 proteins across 55 formalin-fixed and paraffin-embedded (FFPE) TNBC tumors. We identified four major TNBC clusters by unsupervised clustering analysis of protein abundances. Analyses of clinicopathological characteristics revealed associations between the proteomic profiles and clinical phenotypes exhibited by each subtype. We validate the findings by inferring immune and stromal cell type composition from genome-wide DNA methylation profiles. Finally, quantitative proteomics on TNBC cell lines was conducted to identify in vitro models for each subtype. Collectively, our data provide subtype-specific insights into molecular drivers, clinicopathological phenotypes, tumor microenvironment (TME) compositions, and potential pharmacologic vulnerabilities for further investigations.

<h4>Aim</h4>Autism spectrum disorder (ASD) has a strong genetic basis, yet its genetic complexities remain elusive. Current research highlights environmental factors and epigenetic processes, such as DNA methylation, as crucial in ASD development. This exploratory study addresses a gap in understanding epigenetic regulation in the dorsal raphe (DR)-a region regulating multiple neurotransmitters and implicated in ASD-by examining DNA methylation profiles in postmortem ASD and control brains.<h4>Methods</h4>We comprehensively analyzed genome-wide DNA methylation profiles in the DR brain region (seven controls and five ASD) using the Infinium HumanMethylation450 BeadChip (Illumina). Additionally, quantitative polymerase chain reaction was used to measure messenger RNA levels of differentially methylated genes in ASD (11 controls and six ASD).<h4>Results</h4>We identified differentially methylated regions (DMRs) between ASD and controls. These DMRs were located among various genomic regions, including promoters, gene bodies, and intergenic regions. Notably, we found hypermethylation in genes related to olfaction (e.g. OR2C3), which is regulated by serotonin. Additionally, we observed that the hypomethylation of promoter-associated CpG islands in RABGGTB, a gene related to autophagy and synaptic function, corresponded with its increased expression.<h4>Conclusions</h4>Our findings reveal extensive DNA methylation changes in critical genomic regions, shedding light on potential mechanisms underlying ASD. The identification of RABGGTB as a novel candidate gene, not listed in the SFARI database, underscores its significance and warrants further research to explore its role in ASD diagnosis. This study enhances our understanding of the epigenetic landscape in ASD, emphasizing the interplay between genetic and environmental factors in its pathophysiology.

<h4>Background</h4>Lung cancer remains a leading cause of cancer-related mortality worldwide. Its progression is intricately associated with the dynamic regulation of autophagy and RNA-binding proteins (RBPs), which play crucial roles in mRNA stability, alternative splicing, and cellular stress responses.<h4>Objectives</h4>This review aims to systematically analyze the mechanisms through which RBPs and autophagy contribute to lung cancer progression and explore potential therapeutic strategies targeting these pathways.<h4>Methods</h4>We reviewed recent studies on the molecular mechanisms by which RBPs regulate tumor proliferation, metabolic adaptation, and their interaction with autophagy. The review also examines the dual roles of autophagy in lung cancer, highlighting its context-dependent effects on cell survival and death.<h4>Results</h4>The interactions and regulatory networks between RBPs and autophagy involve multiple levels of regulation. RBPs can directly influence autophagy processes and act as microRNA (miRNA) sponges to regulate mRNA stability. The modulation of RBPs affects the expression of autophagy-related genes (ATGs) and autophagosome formation. Additionally, RBPs participate in complex regulatory interactions with non-coding RNAs (ncRNAs), including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and other proteins.<h4>Conclusions</h4>This review proposes innovative therapeutic strategies that combine RBP-targeting approaches (e.g., small molecule inhibitors, CRISPR gene editing) with autophagy modulators (e.g., mTOR inhibitors, chloroquine) to enhance treatment efficacy. Nanoparticle drug delivery systems and epigenetic regulation offer further opportunities for targeted interventions. This review lays a theoretical foundation for advancing lung cancer research and provides novel insights into synergistic therapies that target both RBPs and autophagy to improve treatment outcomes for lung cancer.

Neonatal hypoxic-ischemic encephalopathy (HIE) remains a leading cause of long-term neurologic morbidity. Fifty percent of HIE cases are mild and do not have clearly defined therapeutic interventions. Emergent evidence now demonstrates that up to 25% of children with mild HIE suffer motor and developmental delay by 18 months and 35% have cognitive impairments by age 5 years. Interestingly, the hippocampus, which is responsible for learning and memory, does not show overt injury but does demonstrate volume changes on imaging that correlate with cognitive and behavioral outcomes. Although there is extensive data regarding pathophysiological changes following moderate and severe HIE, there is a paucity of understanding regarding the extent, duration, and compensatory adaptations in the mild neonatal HIE brain. We performed hippocampal proteomic analysis using a swine model of mild neonatal hypoxia-asphyxia. Hippocampi were collected at 24 or 72 hours after injury, and proteomics was performed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Pathway analysis demonstrated that several metabolic pathways are temporally regulated after mild HIE. Specifically, amino acid, carbohydrate, and one-carbon metabolism increased at 24 hours while fat metabolism and oxidative phosphorylation decreased at 24 hours. Downregulation of oxidative phosphorylation was more pronounced at 72 hours. Our data demonstrate that metabolic reprogramming occurs after mild HIE, and these changes persist up to 72 hours after injury. These results provide new evidence that mild HIE disrupts brain metabolism, emphasizing the need for a better understanding of the underlying pathophysiology of mild HIE and development of targeted therapeutic interventions for this population.

Synapses have undergone significant diversification and adaptation, contributing to the complexity of the central nervous system. Understanding their molecular architecture is essential for deciphering the brain's functional evolution. While nicotinic acetylcholine receptors (nAchRs) are widely distributed across metazoan brains, their associated protein networks remain poorly characterized. Using in vivo proximity labeling, we generated proteomic maps of subunit-specific nAchR interactomes in developing and mature <i>Drosophila</i> brains. Our findings reveal a developmental expansion and reconfiguration of the nAchR interactome. Proteome profiling with genetic perturbations showed that removing individual nAchR subunits consistently triggers compensatory shifts in receptor subtypes, highlighting mechanisms of synaptic plasticity. We also identified the Rho-GTPase regulator Still life (Sif) as a key organizer of cholinergic synapses, with loss of Sif disrupting their molecular composition and structural integrity. These results provide molecular insights into the development and plasticity of central cholinergic synapses, advancing our understanding of synaptic identity conservation and divergence.

Early childhood caries (ECC) affects nearly half of preschool children worldwide and characterized by rapid progression across multiple teeth. While Streptococcus mutans (S. mutans) is a keystone species in dental caries, its process for rapid biofilm expansion remains unclear. Using an air-solid interface model simulating the oral environment, we uncovered a novel expansion for S. mutans biofilms. Our findings reveal that S. mutans employs a distinct two-step expansion strategy. Through osmotic pressure, extracellular polymeric substances (EPS) spread and transport bacterial clusters to new sites. Subsequently, the hydroxyapatite surface enables new colony formation. Hydroxyapatite's acid-neutralization properties appear critical for bacterial growth and colonization. Despite successful EPS spreading, environments without hydroxyapatite failed to support new colony formation. These results reveal the unique pattern of rapid ECC progression in sugar-rich environments and establish EPS as a promising therapeutic target, advancing understanding of cariogenic biofilm behavior and preventative strategies for ECC prevention.

C-reactive protein (CRP) serves as a pivotal marker of systemic inflammation, yet its genetic architecture has predominantly been explored within European populations. Our multi-ancestry sequencing-based genome-wide association study (seqGWAS) meta-analysis encompasses 447,369 Europeans, 10,389 Africans, 9685 Asians, and 9200 Hispanics in the discovery set, and 23,521 Europeans, 7160 Africans, 771 Asians, and 5178 Hispanics in the replication set. We identify 113 independent association signals (P_discovery ≤ 5 × 10^-9 and P_replication ≤ 0.05), including 21 loci that passed the conditional analysis, among which 3 are European-specific. Cross ancestry fine-mapping pinpoints 19 of 113 independent signals within the 95% credible set. Functional annotation reveals significant enrichment in blood tissue, H3K27me3 histone marks, and exonic regions. Leveraging the Polygenic Priority Score (PoPS) and gene-based analyses, we implicate 151 genes as potential regulators of CRP levels, 55 of which have not been previously reported. Among these, 17 genes and four proteins show causal evidence or strong colocalization with CRP-related pathologies.

Prenatal ethanol exposure (PE) causes Fetal Alcohol Spectrum Disorders (FASD), characterized by cognitive, behavioral, and emotional deficits, including anxiety and depression. PE-induced alteration in the function of dorsal raphe nucleus (DRN) serotonin (5-HT) neurons is thought to be major contributing factor for increased anxiety. However, the precise neuronal circuits involved are unknown. Using electrophysiology, optogenetics, chemogenetics, and behavioral approaches, we find that PE preferentially potentiates medial prefrontal cortex (mPFC) glutamatergic inputs, but not lateral habenula (LHb), to DRN 5-HT neurons projecting to mPFC. Additionally, PE also increases the strength of LHb but not mPFC excitatory inputs to DRN 5-HT neurons projecting to central amygdala (Ce). This input and target selective effect of PE was mediated by a circuit-specific increase in nitric oxide (NO) signaling. Importantly, chemogenetic inhibition of mPFC-DRN neuronal circuit blunted anxiety-like behaviors in PE rats. As such, our results unraveled the DRN neuronal circuitries affected by PE, which gate FASD-induced anxiety-like behaviors.

<h4>Background</h4>Inflammatory events followed by bacterial infections are related to the progression of the atherosclerosis process. The study investigated the signaling and metabolic pathways of endothelial cells (ECs), macrophages (MQs), vascular smooth muscle cells (VSMCs), and dendritic cells (DCs) after exposure to Gram-negative bacterial infections. Moreover, it aimed at cross-talking and enriching the pathways on the cellular and plaque networks.<h4>Methods and materials</h4>High-throughput expression data series (n = 9) were selected through GEO and MAT data repositories. Upregulated differential expression genes (DEGs) were determined using R software and applied to identify the cellular signaling pathways using Enricher/Reactome tools. Then, the cell networks were visualized using the Cytoscape software and enriched by the pathways of secretory proteins identified using Gene ontology (GO).<h4>Results</h4>The important pathways of the Cytokines (Degree 4, p < 6 × 10^-26), and INF (Degree 4, p < 8.6 × 10^-31) in ECs, Cytokines (Degree 4, p < 9.35 × 10^-8), and GPCR (Degree 3, p < 1.45 × 10^-4) in MQs, NOTCH (Degree 6, p < 0.027) in VSMCs, and Cytokines (Degree 4, p < 1.45 × 10^-17) in DCs were found to be activated and enriched after exposure to Gram-negative bacterial infections on the cell networks. Furthermore, the Netrin- 1 (Degree 6, p < 0.028), and EGFR (Degree 5, p < 0.036) pathways were activated in the intimal thick/xanthoma plaque network while the innate (Degree 9, p < 8.9 × 10^-20) and adaptive (Degree 7, p < 4.1 × 10^-12) immune systems pathways were activated in the fibrous cap atheroma plaque network.<h4>Conclusion</h4>The study revealed the signaling pathways after exposure to Gram-negative bacterial infections on the cell networks in the vessel microenvironment. Furthermore, the cell cross-talks exacerbated these pathways in cells and unstable plaques.<h4>Clinical trial number</h4>Not applicable.

<h4>Background</h4>CMTR1 (cap methyltransferase 1), a key nuclear mRNA cap methyltransferase, catalyzes 2'-O-methylation of the first transcribed nucleotide, a critical step in mRNA cap formation. Previous studies have implicated CMTR1 in embryonic stem cell differentiation and immune responses during viral infection; however, its role in cancer biology remains largely unexplored. This study aims to elucidate CMTR1's function in cancer progression and evaluate its potential as a novel therapeutic target in certain cancer types.<h4>Methods</h4>We conducted a comprehensive multi-omics analysis of CMTR1 across various human cancers using TCGA and CPTAC datasets. Functional studies were performed using CRISPR-mediated knockout and siRNA knockdown in human and mouse basal-like breast cancer models. Transcriptomic and pathway enrichment analyses were carried out in CMTR1 knockout/knockdown models to identify CMTR1-regulated genes. In silico screening and biochemical assays were employed to identify novel CMTR1 inhibitors.<h4>Results</h4>Multi-omics analysis revealed that CMTR1 is significantly upregulated at the mRNA, protein, and phosphoprotein levels across multiple cancer types in the TCGA and CPTAC datasets. Functional studies demonstrated that CMTR1 depletion significantly inhibits tumor growth both in vitro and in vivo. Transcriptomic analysis of CMTR1 knockout cells revealed that CMTR1 primarily regulates ribosomal protein genes and other transcripts containing 5' Terminal Oligopyrimidine (TOP) motifs. Additionally, CMTR1 affects the expression of snoRNA host genes and snoRNAs, suggesting a broader role in RNA metabolism. Mechanistic studies indicated that CMTR1's target specificity is partly determined by mRNA structure, particularly the presence of 5'TOP motifs. Finally, through in silico screening and biochemical assays, we identified several novel CMTR1 inhibitors, including N97911, which demonstrated in vitro growth inhibition activity in breast cancer cells.<h4>Conclusions</h4>Our findings establish CMTR1 as an important player in cancer biology, regulating critical aspects of RNA metabolism and ribosome biogenesis. The study highlights CMTR1's potential as a therapeutic target in certain cancer types and provides a foundation for developing novel cancer treatments targeting mRNA cap methylation.

In spatial transcriptomics data, spatially correlated genes promise to reveal high-interest phenomena like cell-cell interactions and latent variables. But in practice, most spatial correlations arise from the spatial arrangement of cell types, obscuring the more interesting relationships we hope to discover. We introduce InSituCor, a toolkit for discovering modules of spatially correlated genes. InSituCor returns only correlations not explainable by already-known factors like the cell type landscape; this spares precious analyst effort. InSituCor supports both unbiased discovery of whole-dataset correlations and knowledge-driven exploration of genes of interest. As a special case, it evaluates ligand-receptor pairs for spatial co-regulation.

BackgroundSynaptic dysfunction underlies early sensorimotor and cognitive deficits in Huntington's disease (HD) and precedes the degeneration of striatal spiny projection neurons and cortical pyramidal neurons. Movement selection and motor learning, which are impaired early in HD, are regulated by connections between the motor cortex, basal ganglia and thalamus. In particular, plasticity at corticostriatal synapses, including endocannabinoid-mediated long-term depression (LTD), is critical for motor learning. Previously, we found impaired endocannabinoid-mediated LTD, induced by high frequency stimulation (HFS) at corticostriatal synapses in brain slice recordings from pre-manifest HD mouse models, which was corrected by JZL184, an inhibitor of endocannabinoid 2-arachidonoyl glycerol (2-AG) degradation.ObjectiveDetermine the effects of <i>in vivo</i> JZL184 administration on YAC128 HD model and wild-type (WT) littermate mice.MethodsJZL184 was administered to mice orally over a 3-week period and their motor function was assessed using several behavioral tasks. In addition, brain tissue was collected from mice in order to quantify changes in endocannabinoid levels and measure HFS-induced plasticity at corticostriatal synapses.ResultsOral administration of JZL184 significantly increased levels of 2-AG in striatal tissue. While JZL184 treatment had no impact on open field behavior, the treatment eliminated the difference in motor learning on the rotarod task between YAC128 and WT mice. Moreover, HFS-induced striatal plasticity in YAC128 mice was normalized to WT levels after JZL184 treatment.ConclusionsThese results suggest a novel target for mitigating early symptoms of HD and support the need for clinical trials of therapies that modulate the endocannabinoid system.

Supervised and unsupervised methods have emerged to address the complexity of single cell data analysis in the context of large pools of independent studies. Here, we present ClusterFoldSimilarity (CFS), a novel statistical method design to quantify the similarity between cell groups across any number of independent datasets, without the need for data correction or integration. By bypassing these processes, CFS avoids the introduction of artifacts and loss of information, offering a simple, efficient, and scalable solution. This method match groups of cells that exhibit conserved phenotypes across datasets, including different tissues and species, and in a multimodal scenario, including single-cell RNA-Seq, ATAC-Seq, single-cell proteomics, or, more broadly, data exhibiting differential abundance effects among groups of cells. Additionally, CFS performs feature selection, obtaining cross-dataset markers of the similar phenotypes observed, providing an inherent interpretability of relationships between cell populations. To showcase the effectiveness of our methodology, we generated single-nuclei RNA-Seq data from the motor cortex and spinal cord of adult mice. By using CFS, we identified three distinct sub-populations of astrocytes conserved on both tissues. CFS includes various visualization methods for the interpretation of the similarity scores and similar cell populations.

<h4>Background</h4>Sexual dysfunctions (SD) are highly prevalent in Chronic Liver Diseases (CLD). Whether Metabolic dysfunction-Associated Steatotic Liver Disease (MASLD) carries a higher risk of SD is unknown as is the role of dietary patterns or quality of Life (QoL).<h4>Aim</h4>to assess (1) prevalence of SD in CLD; (2) whether MASLD is a risk factor for SD; (3) the role of adherence to Mediterranean Diet (MD) or QoL.<h4>Methods</h4>Observational, cross-sectional study, 207 CLD patients (84 females and 123 males), median age 57 years (IQR:46-63); 96 (46.4%) MASLD; and 111 (53.6%) nonMASLD.<h4>Outcomes</h4>SD were assessed through Female Sexual Function Index (FSFI) and International Index of Erectile Function (IIEF) questionnaires. Adherence to MD was evaluated by the MD Score, QoL by SFHS-12 questionnaire evaluating physical [(ie, Physical Component Summary (PCS)] and mental [(ie, Mental Component Summary (MCS)] health. Multivariate analysis identified predictors of SD.<h4>Results</h4>(1) SD prevalence in CLD was 157/207 (75.8%); 80.9% females were at risk for SD, altered sexual desire/arousal and dyspareunia being the most common complaints, whereas 72.3% males had erectile dysfunction (ED); (2) prevalence of SD was higher in MASLD (89%) than in nonMASLD (64%) (<i>P</i> < 0.001); (3) in females, at univariate analysis, a negative correlation was found between FSFI and age, hypertension, or MASLD; (4) in males, at univariate analysis, IIEF-ED negatively correlated with age, DM2, or MASLD, whereas positively correlated with PCS and MCS; (5) in females, at multivariate analysis BMI (OR = 0.779,CI 95% = 0.640-0.948) and MCS (OR = 0.840,CI 95% = 0.741-0.953) were protective against SD, whereas age (OR = 1.115,CI 95% = 1.040-1.263) and DM2 (OR = 120.894,CI 95% = 1.396-10 741) were predictive of SD; (6) in males, at multivariate analysis, age (OR = 1088,CI 95% = 1032-1.148) and MASLD (OR = 4.075,CI 95% = 1.120-14.828) were risk factors for, whereas PCS (OR = 0,928,CI 95% = 0,865-0,995), and disease duration (OR = 0.393,CI 95% = 0.187-0.822) were protective against SD; 7) MD adherence, while higher in nonMASLD vs MASLD (<i>P =</i> 0.004), was not an independent protective factor against SD.<h4>Clinical implications</h4>SD should not be underestimated in CLD patients, in particular those with MASLD.<h4>Strengths and limitations</h4>Comprehensive study evaluating SD in a large cohort of CLD patients of both sexes, comparing MASLD vs nonMASLD. Due to its cross-sectional design, no conclusions can be drawn about cause and effect.<h4>Conclusions</h4>(1) CLD, in particular MASLD, have a high prevalence of SD which is not affected by MD adherence, whereas QoL seems to play a role; (2) CLD patients should be evaluated for SD, for early diagnosis and treatment.

Human induced pluripotent stem cells (hiPSCs) possess the ability to differentiate into a multitude of cell and tissue types but display heterogeneous propensity of differentiation into specific lineage. Characterization of the transcriptome of 11 hiPSC lines showed that activation of MIXL1 at the early stage of stem cell differentiation correlated with higher efficacy in generating definitive endoderm and advancing differentiation and maturation of endoderm derivatives. Enforced expression of MIXL1 in the endoderm-inefficient hiPSCs enhanced the propensity of endoderm differentiation, suggesting that modulation of key drivers of lineage differentiation can re-wire hiPSC to the desired lineage propensity to generate the requisite stem cell products.

Coffee is a globally popular beverage and a significant agricultural economic crop in planted countries and regions. To understand the influence of primary processing on coffee, the microbial communities and chemical compounds were analyzed using high-throughput sequencing and HPLC-MS/MS metabolomics to confirm the dynamic changes of them during the dry processing of <i>Coffea arabica</i> from Yunnan, China. The results showed that <i>Tatumella</i>, <i>Klebsiella</i>, <i>Gluconobacter</i>, <i>Brevundimonas</i>, and <i>Staphylococcus</i> at the bacterial general level and <i>Candida</i>, <i>Lachancea</i>, <i>Aschersonia</i>, <i>Cercospora</i>, and <i>Pichia</i> at the fungi general level were the predominant microorganisms in the dry processing. During the dry process, <i>Tatumella</i>, <i>Gluconobacter</i>, and <i>Candida</i> showed a trend of increasing firstly and decreasing subsequently, while <i>Klebsiella</i> and <i>Lachancea</i> reached the highest at the end of processing. In contrast, <i>Hannaella</i> decreased gradually. Meanwhile, 1551 chemical compounds coming from 15 superclasses were detected. Furthermore, 129 differentially changed compounds (DCCs) including 91 upregulated DCCs with VIP > 1.0, <i>p</i> < 0.05, and FC > 1.5 and 38 downregulated DCCs with VIP > 1.0, <i>p</i> < 0.05, and FC < 0.67 were determined in finished samples versus raw materials. Among them, cis-5-caffeoylquinic acid and sesamose were very significantly DCCs. Therefore, this study can provide useful information for understanding the dry processing of coffee beans and its impact on coffee's quality properties.

<h4>Purpose of review</h4>This review evaluates the known mechanisms of regulating erythroid regeneration via the sterile alpha motif protein-14 ( Samd14 ) enhancer, Samd14's role in stem cell factor/Kit and erythropoietin (Epo) signaling, possible SAMD14 functions beyond erythropoiesis, and extrapolation to other anemia-response pathways.<h4>Recent findings</h4>Samd14 expression is controlled by an anemia-activated E-box-GATA transcriptional enhancer required for erythroid regeneration, and the Samd14 protein is needed for acute anemia recovery. Samd14 interacts with actin capping proteins to elevate Kit signaling via MAPK and PI3K/Akt pathways in stress erythroid precursors and promotes Epo signaling at later stages. Whereas canonical cellular stress transcriptional mechanisms are involved in anemia (e.g. hypoxia-inducible HSF1, Nrf2, ATF4, and others), enhancers with sequence and molecular features resembling the Samd14 S14E cis -element - occupied by GATA1 and TAL1 - regulate anemia-activated proteins. Relative to physiological replacement of red blood cells, unique signaling cues are involved in erythroid regeneration at multiple stages.<h4>Summary</h4>Anemia-activated proteins coordinate an acute increase in red blood cell production from erythroid progenitors to regenerate lost cells and restore homeostasis. The Samd14 locus provides an exemplary examination of cell signaling - through both stem cell factor/Kit and Epo as well as transcriptional mechanisms involved in erythroid regeneration.

<b>Background:</b> Clear cell renal cell carcinoma (ccRCC) is marked by aggressive characteristics and a poor prognosis. The involvement of KCNJ2, an inward rectifying potassium channel, in the progression of ccRCC, along with its potential roles in immune modulation and metabolic pathways, remains unclear. <b>Methods:</b> The Cancer Genome Atlas (TCGA) database was utilized to analyze the gene expression, clinicopathological characteristics, and clinical relevance of KCNJ2. The prognostic value of KCNJ2 in ccRCC was evaluated with Kaplan-Meier survival analysis and receiver operating characteristic curve analyses. The TCGA-KIRC dataset was utilized to analyze tumor microenvironment (TME), focusing on tumor-infiltrating immune cells and immunomodulators. The biological functions of KCNJ2 were investigated in vitro using CCK-8, flow cytometry, wound healing, transwell, qRT-PCR, and Western blotting assays. <b>Results:</b> KCNJ2 expression was notably higher in ccRCC than in normal kidney tissues, with increased levels associated with advanced tumor stages. However, KCNJ2 did not exhibit obvious prognostic value. Coexpression analysis identified associations with genes implicated in energy metabolism. Analysis of the TME and immune profile indicated a link between KCNJ2 expression and immune cell infiltration, along with particular immune checkpoints. <i>In vitro</i> studies demonstrated that KCNJ2 overexpression enhanced cell proliferation, migration, invasion, glucose production, and ATP generation. <b>Conclusion:</b> KCNJ2 plays a crucial role in ccRCC progression through affecting glucose metabolism and immune responses. Our findings reveal the functional role of KCNJ2 in promoting tumor progression and metabolic reprogramming in ccRCC, highlighting its therapeutic potential as a novel target for ccRCC treatment. Further studies are essential to clarify the mechanisms by which KCNJ2 affects ccRCC biology and to evaluate its clinical relevance.

The serotonin (5-hydroxytryptamine) system represents a crucial neurotransmitter network that regulates mood, behavior, and cognitive functions, playing a significant role in the pathogenesis and progression of depression. Although this perspective faces significant challenges, the serotonin system continues to exert substantial modulatory effects on specific aspects of psychological functioning and actively contributes to multiple pathological processes in depression development. Therefore, this review systematically integrates interdisciplinary research advances regarding the relationship between the 5-hydroxytryptamine (5-HT) system and depression. By focusing on core biological processes including serotonin biosynthesis and metabolism, SERT gene regulatory networks, and protein molecular modifications, it aims to elucidate how 5-HT system dysregulation contributes to the development of depression, while providing novel research perspectives and therapeutic targets for innovative antidepressant drug development.

This study focuses on the proteomic analysis of cerebrospinal fluid (CSF) in a patient with stage III retinoblastoma (RB) with the aim to identify molecular changes associated with central nervous system (CNS) relapse. The child received systemic chemotherapy and intrathecal topotecan as CNS prophylaxis, along with enucleation of the left eye. After two chemotherapy cycles, CNS relapse occurred, evidenced by positive CSF findings and magnetic resonance imaging (MRI) showing leptomeningeal involvement at the anterior skull base. The child's condition deteriorated, and two months later, he died due to progressive CNS disease. The aim of the study was to analyze serial CSF samples collected at different stages of treatment, as well as a control sample, to identify differences in CSF protein expression profiles during CNS RB relapse. Using mass spectrometry, a total of 1,029 proteins were identified across all CSF samples, samples were analyzed in duplicate ensuring technical replication. An unsupervised heatmap revealed 46 differentially expressed proteins. Over-regulated proteins in CSF-RB samples were primarily involved in inflammation, extracellular matrix remodeling, epithelial mesenchymal transition initiation, migration, invasion, and cellular metabolism (PON1, RNPEP, MCAM, NEGR1, NID1, SERPINA1, FAT2, RELN, NEGR1, and SEZ6). These processes are key drivers of cancer progression and metastasis. Proteomic analysis could be valuable in identifying proteins modulated in CSF during disease progression in RB patients, offering potential for new prognostic biomarkers.

Rheumatoid Arthritis (RA) is a chronic inflammatory disease characterized by joint inflammation, progressive cartilage degradation, and bone erosion. Recent research has implicated ferroptosis not only in autoimmune hepatitis but also in the pathogenesis and progression of autoimmune disorders like RA. Consequently, numerous therapeutic strategies have begun to target the ferroptosis pathway, particularly in the design and development of nanodrug delivery systems (NDDSs). While previous reviews have comprehensively discussed the mechanisms of ferroptosis, related signaling pathways, and NDDS materials, recent studies have further elucidated the interplay between ferroptosis and various metabolic pathways, providing a robust theoretical basis for the design of NDDS-based ferroptosis strategies. This review focuses on investigating the role of ferroptosis in the development of RA, aiming to elucidate how targeting ferroptosis can offer novel therapeutic concepts and potential treatments for RA patients. Specifically, it summarizes the design strategies of ferroptosis-based NDDSs <i>via</i> different pathways and highlights the feasibility of RA treatment regimens based on the ferroptosis mechanism. Furthermore, the review critically discusses the current limitations of NDDSs and offers perspectives on future research directions in this field.

Cartilage is crucial for joints, and its damage can lead to pain and functional impairment, causing financial burden to patients. Due to its weak self-repair, cartilage injury control is a research focus. Cartilage injury naturally with age, but mechanical trauma, lifestyle factors and certain genetic abnormalities can increase the likelihood of symptomatic disease progression. Current treatments for cartilage injury include pharmacological and surgical interventions, but these lack the ability to stop the progression of disease and restore the regeneration of the cartilage. Biological therapies have been evaluated but show varying degrees of efficacy in cartilage regeneration long-term. The mesenchymal stem cell (MSC) therapy attracts attention as it is easily harvested and expanded. Once thought to repair via differentiation, MSCs are now known to secrete extracellular vesicles (EVs) paracrinely. These EVs, rich in bioactive molecules, enable cell communication, boost growth factor secretion, regulate the synthesis and degradation of extracellular matrix (ECM), and modulate inflammation, vital for cartilage repair. However, further research and clinical validation are still required for the application of MSC and MSC-EVs. This review highlights the current state of research on the use of MSC and MSC-EVs in the treatment of cartilage injury. It is hoped that the review in this paper will provide valuable references and inspiration for future researchers in therapeutic studies of cartilage repair.

Most women with ovarian cancer (OC) develop resistance to platinum chemotherapy, posing a significant challenge to treatment. Matrix metalloproteinase 3 (MMP3) is overexpressed in High-Grade Serous Ovarian Cancer (HGSOC) and is associated with poor survival outcomes; however, its role in platinum resistance remains underexplored. We evaluated the baseline and cisplatin-induced MMP3 transcript and protein levels in cisplatin-resistant OC cells, revealing significantly higher MMP3 levels in cisplatin-resistant cells than in cisplatin-sensitive cells. siRNA-mediated MMP3 knockdown in cisplatin-resistant OC cells significantly reduced viability, proliferation, and invasion, and these effects were further enhanced when combined with cisplatin treatment, indicating a possible synergistic impact on reducing cancer cell aggressiveness; however, chemical MMP3 inhibition did not replicate these effects. RNA sequencing of MMP3-siRNA-treated cisplatin-resistant HGSOC cells revealed 415 differentially expressed genes (DEGs) compared to the negative control, with an additional 440 DEGs identified in MMP3-siRNA HGSOC cells treated in combination with cisplatin. These DEGs were enriched in pathways related to cell cycle regulation, apoptosis, metabolism, stress response, and extracellular matrix organization. Co-immunoprecipitation-coupled mass spectroscopy (IP-MS) identified MMP3-interacting proteins that may contribute to cell survival and chemoresistance in cisplatin-resistant OC. While MMP3-siRNA monotherapy did not reduce tumor growth in vivo, its combination with cisplatin significantly inhibited tumor growth in a cisplatin-resistant HGSOC xenograft model. These findings underscore the multifaceted role of MMP3 in cisplatin resistance, suggesting its involvement in critical cellular processes driving chemoresistance and highlighting the challenges associated with direct MMP3 targeting in therapeutic strategies.

Stress may aggravate the development of inflammatory bowel disease and irritable bowel syndrome, in which the number of enterochromaffin (EC) cells and 5-hydroxytryptamine (5-HT) levels are abnormal, but the underlying mechanism remains largely unresolved. In this study, we discovered that restraint stress triggered the expression of Tph1, which led to 5-HT production. The 5-HT signaling then increased intestinal permeability, downregulated the expression of tight junction proteins, reduced the number of goblet cells and their ability to secrete mucin, promoted the expression of inflammatory cytokines, and ultimately damaged the intestinal mucosal barrier. Mechanistically, the 5-HT receptor HTR7 was highly expressed in the intestine. It interacted with 5-HT to initiate the Wnt/β-catenin signaling pathway, inducing an increase in intestinal EC cells and further promoting 5-HT secretion. Additionally, the activation of the Wnt/β-catenin signaling pathway could initiate the NF-κB signaling pathway and induce the expression of inflammatory cytokines. Blocking the 5-HT signal in mice inhibited the activation of the Wnt/β-catenin signal, thereby alleviating intestinal inflammation. Our findings revealed a novel role for 5-HT in intestinal inflammatory diseases and represent a potential new therapeutic target.

Glycosaminoglycans (GAGs) are key ligands for proteins involved in physiological and pathological processes. Specific GAG-binding patterns are rarely identified, with the heparin pentasaccharide as an Antithrombin-III ligand being the best characterized. Generating glycan-specific antibodies is difficult due to their size, pattern dispersion, and flexibility. Single-domain variable new antigen receptors (VNAR nanobodies) from nurse sharks are highly soluble, stable, and versatile. Their unique properties suggest advantages over conventional antibodies, particularly for challenging biotherapeutic targets. Here we have used VNAR semi-synthetic phage libraries to select high-affinity fondaparinux-binding VNARs that did not show cross-reactivity with other GAG species. Competition ELISA and surface plasmon resonance identified a single fondaparinux-selective VNAR clone. This VNAR exhibited an extraordinarily stable protein fold: the beta-strands are stabilized by a robust hydrophobic network, as revealed by heteronuclear NMR. Docking fondaparinux to the VNAR structure revealed a large contact surface area between the CDR3 loop of the antibody and the glycan. Fusing the VNAR with a human Fc domain resulted in a stable product with a high affinity for fondaparinux (Kd = 9.3 × 10^-8 M) that could efficiently discriminate between fondaparinux and other glycosaminoglycans. This novel glycan-targeting screening technology represents a promising therapeutic strategy for addressing GAG-related diseases.

<h4>Background</h4> Ferritin serves as a key marker of iron stores, and its levels are influenced by genetic, dietary, and physiological factors. However, racial disparities in ferritin levels among whole blood donors remain underexplored, despite their potential impact on donor health and transfusion practices. This study investigates racial differences in ferritin levels among whole blood donors at a single high-volume center to assess potential disparities and their implications for donor management.<h4>Methods</h4> A retrospective cross-sectional analysis was conducted on 26,130 whole blood donors from 2018 to 2021. Donor demographic data, including self-reported race and sex, were extracted from a centralized database. Serum ferritin levels were measured using a chemiluminescent immunoassay, and statistical comparisons were performed using Welch's t-test and ANOVA, with a significance threshold of p < 0.05.<h4>Results</h4> Significant racial disparities in ferritin levels were observed. Caucasian donors exhibited the lowest ferritin levels, while Asian donors had the highest levels. African American donors displayed relatively lower ferritin levels than expected based on prior literature. Across all racial groups, males had significantly higher ferritin levels than females (p < 0.05).<h4>Conclusion</h4> Racial disparities in ferritin levels suggest the need for race-conscious donor health strategies, including potential pre-donation ferritin screening and tailored donation intervals to mitigate iron depletion risks. Further research is warranted to assess the impact of donation frequency on these disparities.

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths, primarily associated with liver cirrhosis from factors like hepatitis B virus (HBV), hepatitis C virus (HCV), alcohol abuse, metabolic syndrome, and genetic disorders. With the rising incidence of liver cancer, particularly in HBV-endemic regions, research into novel therapies like antibody-drug conjugates (ADCs) has gained momentum. ADCs target cancer cells by attaching cytotoxic drugs to antibodies, minimizing damage to healthy tissue. Recent clinical trials have demonstrated that ADCs targeting GPC3, such as GC33 and 32A9, show promising results in reducing tumor growth and improving patient outcomes in advanced HCC. These therapies offer a potential alternative to conventional chemotherapy, marking a significant advancement in precision oncology. This systematic review was implemented using various databases like PubMed, Google Scholar, Science Direct, EBSCO, and Public Library of Science (PLoS) using regular keywords and MeSH keywords. Eligibility criteria were restricted to free full texts in the English language, humans, and publications between 2019-2024. The exclusion criteria included languages other than English and publications before 2019. A total of 26 articles were identified, and 12 articles were selected after quality assessment.

<b>Background</b>: Advancements in pharmacogenomics, artificial intelligence (AI), and CRISPR gene-editing technology are revolutionizing precision medicine by enabling highly individualized therapeutic strategies. Artificial intelligence-driven computational techniques improve biomarker discovery and drug optimization while pharmacogenomics helps to identify genetic polymorphisms affecting medicine metabolism, efficacy, and toxicity. Genetically editing based on CRISPR presents a precise method for changing gene expression and repairing damaging mutations. This review explores the convergence of these three fields to enhance improved precision medicine. <b>Method</b>: A methodical study of the current literature was performed on the effects of pharmacogenomics on drug response variability, artificial intelligence, and CRISPR in predictive modeling and gene-editing applications. <b>Results</b>: Driven by artificial intelligence, pharmacogenomics allows clinicians to classify patients and select the appropriate medications depending on their DNA profiles. This reduces the side effect risk and increases the therapeutic efficacy. Precision genetic modifications made feasible by CRISPR technology improve therapy outcomes in oncology, metabolic illnesses, neurological diseases, and other fields. The integration of artificial intelligence streamlines genome-editing applications, lowers off-target effects, and increases CRISPR specificity. Notwithstanding these advances, issues including computational biases, moral dilemmas, and legal constraints still arise. <b>Conclusions</b>: The synergy of artificial intelligence, pharmacogenomics, and CRISPR alters precision medicine by letting customized therapeutic interventions. Clinically translating, however, hinges on resolving data privacy concerns, assuring equitable access, and strengthening legal systems. Future research should focus on refining CRISPR gene-editing technologies, enhancing AI-driven pharmacogenomics, and developing moral guidelines for applying these tools in individualized medicine going forward.

<b>Background/Objectives:</b> Acute myeloid leukemia (AML) is an aggressive malignancy marked by high relapse rates and molecular heterogeneity, necessitating the identification of novel therapeutic targets. T-complex protein 1 (TCP1), a chaperonin implicated in protein folding, remains underexplored in AML pathogenesis. This study investigates the functional role of TCP1 in AML progression and evaluates its therapeutic potential. <b>Methods:</b> Using successive generations of xenografted tumor models, we systematically assessed the correlation between TCP1 expression and AML tumorigenicity. Functional consequences of TCP1 silence were evaluated through in vitro proliferation assays and in vivo tumor growth monitoring. Two distinct inhibitory strategies were employed: miR-340-5p-mediated transcriptional silencing and FTY720-induced disruption of TCP1 chaperone activity. Mechanistic insights were derived from ubiquitin-proteasome pathway analysis, cell cycle profiling, and apoptosis assays. <b>Results:</b> High TCP1 expression correlated strongly with enhanced AML tumorigenicity. Knockdown of TCP1 significantly inhibited AML cell growth and induced degradation of AML1-ETO and PLK1 proteins through the ubiquitin-proteasome pathway. miR-340-5p effectively silenced TCP1 expression, exhibiting an inverse correlation with TCP1 levels. FTY720 disrupted TCP1's chaperone function, leading to cell cycle arrest, apoptosis, and reduced xenograft tumor growth in murine models. <b>Conclusion:</b> Our findings establish TCP1 as a promising therapeutic target for AML. Both miR-340-5p and FTY720 demonstrate potent anti-leukemic effects by suppressing TCP1 activity, highlighting their potential as novel strategies to inhibit AML proliferation and improve therapeutic outcomes.

Anaplastic multiple myeloma (AMM) is a rare, aggressive variant of multiple myeloma; liver involvement is even more exceedingly rare, with known poor response to conventional treatment. Diagnosis is challenging given the aggressive nature of the disease, with the majority of patients diagnosed postmortem. We present a 66-year-old female who presented with abnormal liver function tests and rapid progression to acute liver failure, with biopsy-proven AMM. To our knowledge, this is the second reported case of AMM of the liver.

<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, 2,000 fish were experimentally exposed by bath to IPNV and mortalities were monitored daily during 5 weeks. All fish were genotyped using a medium-density 57K SNP chip and imputed to high-density genotypes (665K SNP). <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 a few tens of SNP. In total, 25 QTL were mapped on 10 chromosomes. Among them, 7 were detected with very strong evidence on chromosomes 1, 14, 16 and 28. The most interesting QTL were associated to top SNP with mean survival rate differences over 20% between the beneficial and detrimental homozygous genotypes. Those SNP were all located within promising functional candidate genes on chromosome 1 ( uts2d , rc3h1 , ga45b ) and chromosome 16 ( irf2bp , eif2ak2) , all these genes being associated to the regulation of inflammatory pathways. A key factor of the genetic differences in susceptibility to IPNV among fish is PKR, the dsRNA-dependent serine/threonine-protein kinase encoded by the eif2ak2 gene. <h4>Conclusions</h4> All genes associated to 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 the IPN resistance in rainbow trout. These findings offer the possibility of marker-assisted selection for rapid dissemination of genetic improvement for IPN resistance.

<h4>Background</h4>There is significant overlap in clinical features between multisystem inflammatory syndrome in children (MIS-C) and Kawasaki disease (KD). We sought to compare the prevalence, severity, and associated factors for coronary artery (CA) involvement.<h4>Methods and results</h4>From January 1, 2020 through January 31, 2023, 1191 patients with MIS-C and 554 patients contemporaneously diagnosed with KD were enrolled into the International Kawasaki Disease Registry. Demographic and clinical features, laboratory values, maximum <i>Z</i> score in any CA branch at any time point, and worst left ventricular ejection fraction, were compared between groups. Factors associated with CA aneurysms (maximum <i>Z</i> score in any CA branch +2.5 or greater) were determined separately for each diagnosis using multivariable logistic regression analyses. The prevalence of CA aneurysms was lower for MIS-C versus KD (16% versus 25%, respectively; <i>P</i><0.001) and less severe by size category (1.2% with medium/large CA aneurysm versus 9.6%, respectively). Male sex and lower nadir hemoglobin levels were associated with greater odds of CA aneurysms for both groups. Additional associated factors for KD patients included age<6 months, fewer clinical KD criteria (more incomplete presentation), presentation with shock, and greater total days of fever. There were no additional associated factors for patients with MIS-C. Using exploratory splines, there was a trend of improvement in <i>Z</i> scores within 30 days of illness for both MIS-C and KD for CA involvement other than large aneurysms.<h4>Conclusions</h4>CA involvement for patients with MIS-C was less prevalent and milder in severity compared with contemporaneous patients with KD, with fewer associated factors, and a high prevalence of regression to a normal luminal dimension.

Cellular senescence is a cell fate triggered by stressful stimuli and displays a hypersecretory feature, the senescence-associated secretory phenotype (SASP). Senescent cell burden increases with aging and contributes to age-related organ dysfunction and multiple chronic disorders. In this study, a large scale screening of a natural product library for senotherapeutic candidates is performed. Apigenin, a dietary flavonoid previously reported with antioxidant and anti-inflammatory activities, exhibits capacity for targeting senescent cells as a senomorphic agent. This compound blocks the interactions between ATM/p38MAPK and HSPA8, preventing the transition of an acute stress-associated phenotype (ASAP) toward the SASP. Mechanistically, apigenin targets peroxiredoxin 6 (PRDX6), an intracellular redox-active molecule, suppressing the iPLA2 activity of PRDX6 and disrupting downstream reactions underlying SASP development. Apigenin reduces the severity of cancer cell malignancy promoted by senescent stromal cells in culture, while restraining chemoresistance when combined with chemotherapy in anticancer regimens. In preclinical trials, apigenin improves the physical function of animals with a premature aging-like state, alleviating physical frailty and cognitive impairment. Together, the study demonstrates the feasibility of exploiting a natural compound with senomorphic capacity to achieve geroprotective effects by modulating the SASP, thus providing a baseline for future exploration of natural agents for alleviating age-related conditions.

Knowledge of the genetic factors in normal pressure hydrocephalus (NPH) is rapidly evolving, with significant advances in recent years. We conducted a systematic review examining genetic contributions to NPH risk. Ovid Embase, Ovid Medline, Web of Science, and Cochrane Central were searched from inception through October 14, 2024, for human studies in English reporting familial NPH cases, genetic variants associated with NPH, and associations with other neurogenetic disorders and exploring transcriptomics. Studies on secondary, obstructive, and congenital hydrocephalus were excluded, and findings were reported narratively. Of 2562 titles and abstracts screened, 56 met inclusion criteria, predominantly involving European populations. More than 30 familial cases were identified, and two cohorts found that 10%-16% of patients with NPH had relatives with NPH symptoms. Whole-genome/exome sequencing, copy-number variant analyses, and genome-wide association studies showed risk variants enriched in NPH cohorts in or near CFAP43, SFMBT1, CWH43, AK9, RXFP2, PRKD1, HAVCR1, OTOG, MYO7A, NOTCH1, SPG11, MYH13, FOXJ1, AMZ1/GNA12, and C16orf95, alongside protective variants near SLCO1A2 and MLLT10. These genes are associated with blood-brain and blood-cerebrospinal fluid barriers, cilia, and ependymal function. In addition, higher rates of pathological C9orf72 repeat expansions were observed in an NPH cohort compared with controls. NPH was also more prevalent in frontotemporal dementia cohorts without this expansion and co-occurred with myotonic dystrophy type 1 in several cases. Despite heterogeneity in outcome measures, this review highlights the genetic contribution to NPH risk. Future research should encourage collaborations for big data generation, identify genetic variants addressing diversity, and integrate clinical, environmental, and shunt-response data. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

Vertebrate extracellular fluids lie below the threshold for spontaneous calcium phosphate (Ca-P_i) precipitation; yet, they remain supersaturated enough to foster crystal growth if unchecked. Calciprotein particles (CPP) and their smaller precursor calciprotein monomers (CPM) have emerged as fast-acting "mineral buffers" that mitigate abrupt local oversaturation. Although these complexes typically contain only trace amounts of Ca-P_i relative to total plasma levels, they exhibit remarkably high turnover kinetics, with clearance from the circulation within minutes, far outpacing hormonal loops that operate on timescales of hours to days. By forming ephemeral colloidal assemblies, CPM/CPP help maintain fluid-phase stability and avert uncontrolled crystallization "accidents" in microenvironments such as the intestine or bone-remodeling sites. However, under chronic mineral stress, such as in chronic kidney disease, multiple inhibitory factors (e.g., fetuin-A, pyrophosphate) can become deficient, enabling persistent generation of more advanced, crystalline CPP species. These "modified" CPP can adsorb additional ligands (e.g., apolipoproteins, microbial remnants, growth factors) and have been linked to inflammatory and pro-calcific changes in vascular and immune cells. Despite their minor quantitative contribution, these rapidly mobilized colloids may exert outsized influence on vascular and skeletal homeostasis, underscoring the need to clarify their origins, biological roles, and potential therapeutic targeting in disorders of mineral metabolism.

Risk of cardiovascular disease (CVD) in women increases with the menopausal transition. Using a chemical model (4-vinylcyclohexene diepoxide; VCD) of accelerated ovarian failure, we previously demonstrated that menopausal females are more susceptible to CVD compared with peri- or premenopausal females like humans. Yet, the cellular and molecular mechanisms underlying this shift in CVD susceptibility across the pre- to peri- to menopause continuum remain understudied. In this work using the VCD mouse model, we phenotyped cellular and molecular signatures from hearts at each hormonally distinct stage that included transcriptomic, proteomic, and cell biological analyses. The transcriptional profile of premenopausal hearts clustered separately from perimenopausal and menopausal hearts, which clustered more similarly. Proteomics also revealed hormonal clustering; perimenopausal hearts grouped more closely with premenopausal than menopausal hearts. Both proteomes and transcriptomes showed similar trends in genes associated with atherothrombosis, contractility, and impaired nuclear signaling between pre-, peri-, and menopausal murine hearts. Further analysis of posttranslational modifications (PTMs) showed hormone-dependent shifts in the phosphoproteome and acetylome. To further interrogate these findings, we triggered pathological remodeling using angiotensin II (Ang II). Phosphorylation of AMP-activated protein kinase (AMPK) signaling and histone deacetylase (HDAC) activity were found to be dependent on hormonal status and Ang II stimulation. Finally, knockdown of anti-inflammatory regulatory T cells (Treg) exacerbated Ang II-dependent fibrosis implicating HDAC-mediated epigenetic suppression of Treg activity. Taken together, we demonstrated unique cellular and molecular profiles underlying the cardiac phenotype of pre-, peri-, and menopausal mice supporting the necessity to study CVD in females across the hormonal transition.<b>NEW & NOTEWORTHY</b> Cycling and perimenopausal females are protected from cardiovascular disease (CVD) whereas menopausal females are more susceptible to CVD and other pathological sequalae. The cellular and molecular mechanisms underlying loss of CVD protection across the pre- to peri- to menopause transition remain understudied. Using the murine 4-vinylcyclohexene diepoxide (VCD) model of menopause we highlight cellular and molecular signatures from hearts at each hormonally distinct stage that included transcriptomic, proteomic, and cell biological analyses.

<b><i>Introduction:</i></b> Hypoglycemia is prevalent among patients postbariatric surgery, but its clinical implications remain unclear. The purpose of this study was to examine the longitudinal associations of hypoglycemia (<i>i.e.,</i> occurrence in the past 3 months, frequency in the past 7 days, number of severe episodes in the past 3 months, and symptoms) with depressive symptoms, quality of life (QoL), work productivity, and weight loss over an 84-month follow-up period after bariatric surgery. <b><i>Methods:</i></b> This secondary analysis used data from the Longitudinal Assessment of Bariatric Surgery-2 study. Hypoglycemia, depressive symptoms, QoL, and work productivity were self-reported. Weight was primarily based on objective measures. Linear mixed modeling with time-lagged techniques was used for analysis, adjusting for potential covariates such as age and gender. <b><i>Results:</i></b> Across the 84-month follow-up, 20%-30% of participants (<i>N</i> = 552) reported experiencing hypoglycemia in the past 3 months. Hypoglycemia occurrence was positively associated with depressive symptoms [β = 2.4; 95% confidence interval (CI): 1.7, 3.0] and negatively associated with physical (β = -4.2; 95% CI: -5.1, -3.3) and mental QoL (β = -3.4; 95% CI: -4.4, -2.4). These associations became stronger with increased frequency of hypoglycemia, a higher number of severe episodes, and the presence of symptoms. Additionally, hypoglycemia occurrence was associated with several domains of work productivity, including presenteeism (β = 5.8; 95% CI: 3.4, 8.2), work productivity loss (β = 5.6; 95% CI: 2.6, 8.6), and activity impairment (β = 8.8; 95% CI: 6.0, 11.6), with the strength of these associations increasing with greater hypoglycemic frequency. <b><i>Conclusions:</i></b> This study highlights the critical role of hypoglycemia in patients' physical and psychosocial well-being postbariatric surgery. Future studies employing more rigorous measures of hypoglycemia and expanded outcomes (<i>e.g.</i> cognitive function) are needed to fully understand its clinical relevance.

<h4>Background/aims</h4>Information about the association of glucagon-like peptide-1 receptor (GLP-1RA) with liver and non-liver complications is insufficient in patients with type 2 diabetes (T2D) and metabolic dysfunction-associated steatotic liver disease (MASLD). We conducted a target trial emulation study to evaluate whether GLP-1RA decreases the risk of liver and non-liver outcomes.<h4>Methods</h4>Patients with T2D and MASLD initiating GLP-1RA or dipeptidyl peptidase-4 inhibitor (DPP-4i) were included from 2013 to 2022 in Merative™ Marketscan® Research Databases. Primary outcomes included incidences of (1) hepatocellular carcinoma (HCC) and cirrhosis, and (2) cardiovascular disease (CVD), chronic kidney disease (CKD), and non-liver cancer. Inverse probability of treatment weighting was applied to balance baseline characteristics and Cox regression models were conducted to estimate hazard ratio (HR) and 95% confidence interval (CI).<h4>Results</h4>In the intention-to-treat design, GLP-1RA, compared with DPP-4i, had a significantly lower incidence (per 1,000 person-years) of HCC (0.8 vs. 1.7; HR 0.53, 95% CI 0.39-0.71), of cirrhosis (29.3 vs. 32.9; HR 0.91, 95% CI 0.86-0.96), of CVD (57.2 vs. 73.9; HR 0.90, 95% CI 0.86-0.95), of CKD (4.5 vs. 6.8; HR 0.73, 95% CI 0.64-0.84), and of non-liver cancer (16.9 vs. 22.9; HR 0.82, 95% CI 0.77-0.89). In the per-protocol design, significant inverse associations for these study outcomes still were observed, with HR 0.60-0.77.<h4>Conclusion</h4>In this emulated target trial of nationwide patients with T2D and MASLD, GLP-1RA use, when compared with DPP-4i, was associated with a significantly lower risk of liver and non-liver complications.

Decreased expression of sirtuin 1 (SirT1) has been implicated in Alzheimer's disease (AD), and as we previously reported, is related to transcriptional repression by the major risk factor for sporadic AD, apolipoprotein E4 (ApoE4). Herein we describe the discovery of an orally brain-permeable small-molecule, DDL-218, that enhanced SirT1 in ApoE4-expressing neuronal cells and a murine AD model. DDL-218 increased the transcription factor NFYb resulting in upregulation of PRMT5. Mechanistic and modeling studies show that binding of ApoE4 to the SirT1 gene promoter can be displaced by PRMT5 leading to increased SirT1 transcription. DDL-218 treatment elicited improvement in memory in the AD model, suggesting that DDL-218 enhancement of neurotrophic SirT1 in the brain has potential to modulate neuronal activity that may clinically provide an improvement in cognitive function and complement the current anti-Aβ antibody monotherapy. Our findings support further development of DDL-218 as a novel ApoE4-targeted therapeutic candidate for AD.

Development and lineage choice are driven by interconnected transcriptional, epigenetic and metabolic changes. Specific metabolites, such as α-ketoglutarate (αKG), function as signalling molecules affecting the activity of chromatin-modifying enzymes. However, how metabolism coordinates cell-state changes, especially in human pre-implantation development, remains unclear. Here we uncover that inducing naive human embryonic stem cells towards the trophectoderm lineage results in considerable metabolic rewiring, characterized by αKG accumulation. Elevated αKG levels potentiate the capacity of naive embryonic stem cells to specify towards the trophectoderm lineage. Moreover, increased αKG levels promote blastoid polarization and trophectoderm maturation. αKG supplementation does not affect global histone methylation levels; rather, it decreases acetyl-CoA availability, reduces histone acetyltransferase activity and weakens the pluripotency network. We propose that metabolism functions as a positive feedback loop aiding in trophectoderm fate induction and maturation, highlighting that global metabolic rewiring can promote specificity in cell fate decisions through intricate regulation of signalling and chromatin.

Hepatocellular carcinoma (HCC) is the third major cause of cancer death worldwide, with more than a doubling of incidence over the past two decades in the United States. Yet, the survival rate remains less than 20%, often due to late diagnosis at advanced stages. Current HCC screening approaches are serum alpha-fetoprotein (AFP) testing and ultrasound (US) of cirrhotic patients. However, these remain suboptimal, particularly in the setting of underlying obesity and metabolic dysfunction-associated steatotic liver disease/steatohepatitis (MASLD/MASH), which are also rising in incidence. Therefore, there is an urgent need for novel biomarkers that can stratify risk and predict early diagnosis of HCC, which is curable. Advances in liver cancer biology, multi-omics technologies, artificial intelligence, and precision algorithms have facilitated the development of promising candidates, with several emerging from completed phase 2 and 3 clinical trials. This review highlights the performance of these novel biomarkers and algorithms from a mechanistic perspective and provides new insight into how pathological processes can be detected through blood-based biomarkers. Through human studies compiled with animal models and mechanistic insight in pathways such as the TGF-β pathway, the biological progression from chronic liver disease to cirrhosis and HCC can be delineated. This integrated approach with new biomarkers merit further validation to refine HCC screening and improve early detection and risk stratification.

<h4>Background</h4>Integration of immune checkpoint inhibitors (ICIs) with non-immune therapies relies on identifying combinatorial biomarkers, which are essential for patient stratification and personalized treatment.<h4>Methods</h4>We analyzed genomic and transcriptomic data from pretreatment tumor samples of 342 melanoma patients treated with ICIs to identify mutations and expression signatures associated with ICI response and survival. External validation and mechanistic exploratory analyses were conducted in two additional datasets to assess generalizability.<h4>Results</h4>Responders were more likely to have received anti-PD-1 therapy rather than anti-CTLA-4 and exhibited a higher tumor mutation burden (both P < 0.001). Mutations in the dynein axonemal heavy chain (DNAH) family genes, specifically DNAH2 (P = 0.03), DNAH6 (P < 0.001), and DNAH9 (P < 0.01), were enriched in responders. The combined mutational status of DNAH 2/6/9 effectively stratified patients by progression-free survival (hazard ratio [HR]: 0.69; 95% confidence interval [CI] 0.51-0.92; P = 0.013) and overall survival (HR: 0.58; 95% CI 0.43-0.78; P < 0.001), with consistent association observed in the validation cohort (HR: 0.28; 95% CI 0.12-0.61; P < 0.001). DNAH-altered melanomas exhibited upregulation of chemokine signaling, cytokine-cytokine receptor interaction, and cell cycle-related pathways, along with elevated expression of immune-related signatures in interferon signaling, cytolytic activity, T cell function, and immune checkpoints. Using LASSO logistic regression, we identified a 26-gene composite signature predictive of clinical response, achieving an area under the curve (AUC) of 0.880 (95% CI 0.825-0.936) in the training dataset and 0.725 (95% CI 0.595-0.856) in the testing dataset. High-risk patients, stratified by the expression levels of a 13-gene signature, demonstrated significantly shorter overall survival in both datasets (HR: 3.35; P < 0.001; HR: 2.93; P = 0.002).<h4>Conclusions</h4>This analysis identified potential molecular determinants of response and survival to ICI treatment. Insights from melanoma biomarker research hold significant promise for translation into other malignancies, guiding individualized anti-tumor immunotherapy.

<h4>Background</h4>Myelophil is a standardized ethanol extract of Astragali Radix and Salviae Miltiorrhizae Radix, which has been developed based on clinical experience in traditional Korean medicine practices for patients with unexplained chronic fatigue, including myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Our previous studies demonstrated Myelophil's clinical efficacy in ME/CFS, as well as its brain-related activities in animal models. However, the underlying pharmacological mechanisms remain unclear. Recently, we identified serotonergic hyperactivity as a key pathophysiological factor in central fatigue, such as ME/CFS. Therefore, in the present study, we aimed to investigate the mechanisms by which Myelophil exerts its effects, particularly in the context of a 5-HTergic hyperactivity model.<h4>Method</h4>To verify the action mechanisms of Myelophil on serotonergic hyperactivity condition, we herein assessed its anti-central fatigue properties using a fluoxetine-treated mice model. Male C57BL/6 N mice (9 weeks old) were subjected to periodic intraperitoneal (IP) injections of fluoxetine for 4 weeks and the mice were simultaneously oral administered Myelophil (0, 50, or 100 mg/kg) or ascorbic acid (100 mg/kg).<h4>Result</h4>Four-week injection of fluoxetine notably increased serotonin (5-hydroxytryptamine, 5-HT) activity, as evidenced by immunofluorescence staining and Western blot assays in the raphe nuclei (RN), and induced central fatigue-like behaviors in the nest building test, wheel running test, rota-rod test, plantar test, and open field test. Meanwhile, Myelophil (100 mg/kg) administration significantly ameliorated those fatigue-related behaviors including pain sensitivity. Furthermore, the anti-fatigue effects of Myelophil were corroborated by changes in serotonin-related parameters (serotonin transporter; 5-HTT and vesicular monoamine transporter 2; VMAT2), as well as neurotrophic markers including c-Fos and brain-derived neurotrophic factor (BDNF) in the RN.<h4>Conclusion</h4>These results provide experimental evidence suggesting the potential mechanisms by which Myelophil may alleviate central fatigue associated with hyper-5-HTergic activity.<h4>Clinical trial number</h4>Not applicable.

Understanding the relative influences of age, pubertal development, and sex assigned at birth on brain development is a key priority of developmental neuroscience given the complex interplay of these factors in the onset of psychopathology. Previous research has investigated how these factors relate to static (time-averaged) functional connectivity (FC), but little is known about their relationship with dynamic (time-varying) FC. The present study aimed to investigate the unique and overlapping roles of these factors on dynamic FC in children aged approximately 9 to 14 in the ABCD Study using a sample of 5122 low-motion resting-state scans (from 4136 unique participants). Time-varying correlations in the frontolimbic, default mode, and dorsal and ventral corticostriatal networks, estimated using the Dynamic Conditional Correlations (DCC) method, were used to calculate variability of within- and between-network connectivity and of graph theoretical measures of segregation and integration. We found decreased variability in global efficiency across the age range, and increased variability within the frontolimbic network driven primarily by those assigned female at birth (AFAB). AFAB youth specifically also showed increased variability in several other networks. Controlling for age, both advanced pubertal development and being AFAB were associated with decreased variability in all within- and between-network correlations and increased variability in measures of network segregation. These results potentially suggest advanced brain maturation in AFAB youth, particularly in key networks related to psychopathology, and lay the foundation for future investigations of dynamic FC.

Solid-tubulocystic variant of intrahepatic cholangiocarcinoma (ST-iCCA) is newly described entity characterized by two distinct histologic growth patterns: (1) solid sheets of tumor cells with focal necrosis giving pseudopapillary appearance and (2) tubular or pseudoglandular structures containing pink, colloid-like material. Tumor cells are inhibin-positive and harbor NIPBL::NACC1 fusion gene. To date, only 28 cases of ST-iCCA have been documented. While prior molecular studies provided insights into ST-iCCA, genetic profiles of individual histologic components have not been explored. This study presents first transcriptomic analysis comparing the solid/pseudopapillary and pseudoglandular components of ST-iCCA. Two cases of histologically confirmed ST-iCCA were identified for RNA sequencing which was performed on solid/pseudopapillary component, pseudoglandular component, and normal tissue. Analysis revealed distinct gene expression profiles for each pattern. Solid/pseudopapillary component uniquely overexpressed DMRTA1, NEXMIF, PRDM6, SORCS3, and NALF, while pseudoglandular component exhibited unique overexpression of HRG, ITIH3, TAT, APOA2, CP, ALDOB, CPS1, F2, KHG1, SERPINC1, HPX, C9, ADGRF1, MUC21, SAA2, SPRR2A, SAA1, FGL1, CFHR1, and LBP. These findings establish unique gene signatures for these variants of ST-iCCA, providing potential biomarkers for differential diagnosis, prognosis and targeted therapy. The distinct genetic profiles may also uncover novel therapeutic targets to address the aggressive nature of ST-iCCA.

<h4>Background</h4>Hepatocellular carcinoma (HCC) is the most common primary liver cancer worldwide, and early pathological diagnosis is crucial for formulating treatment plans. Despite the widespread attention to pathology in the treatment of HCC patients, a large amount of information contained in pathological images is often overlooked.<h4>Methods</h4>We retrospectively collected clinical data and pathological slide images from (a) 331 HCC patients at Qingdao University Affiliated Hospital between January 2013 and December 2016 and (b) 180 HCC patients from The Cancer Genome Atlas (TCGA). After data screening, precise quantification of various cell types was achieved using QuPath software. Key factors related to the survival prognosis of pathologically confirmed HCC patients were identified through Cox regression and neural network models, and potential therapeutic targets were screened.<h4>Results</h4>Our study showed that tumour-infiltrating lymphocytes (TILs) had a protective effect. We quantified the TILs index by machine learning and built a neural network model to predict the prognostic risk of patients (ROC = 0.836 for training set ROC validation set). 95% CI [0.7688-0.896], and there was a significant difference in prognosis in the high-low risk group predicted by the model (<i>p</i> = 2.6e-18, HR = 0.18, 95% CI [0.12-0.27], and TNFSF4 was identified as a possible immunotherapy target.<h4>Conclusion</h4>This study included a total of 511 patients, divided into a training cohort of 331 cases (from Qingdao University Hospital between January 2013 and December 2016) and a validation cohort of 180 cases (TCGA). The results revealed that tumor-infiltrating lymphocytes (TILs) have a protective effect and successfully predicted the survival risk of liver cancer patients using machine learning and neural network technology. The discovery of TNFSF4 provides a new potential target for immunotherapy.

<h4>Background</h4>Alzheimer's disease (AD) is characterized by complex molecular alterations that complicate its pathogenesis and contribute to the lack of effective treatments. Mesenchymal stem cell-derived extracellular vesicles (EVs) have shown promise in AD models, but results across different EV subpopulations remain inconsistent.<h4>Objectives</h4>This study investigates proteomic and transcriptomic data from publicly available postmortem AD brain datasets to identify molecular changes at both the gene and protein levels. These findings are then compared with the proteomes of various EV subpopulations, differing in size and distribution, to determine the most promising subtype for compensating molecular degeneration in AD.<h4>Design</h4>We conducted a comprehensive analysis of 788 brain samples, including 481 AD cases and 307 healthy controls, examining protein and mRNA levels to uncover AD-associated molecular changes. These findings were then compared with the proteomes of different EV subpopulations to identify potential therapeutic candidates.<h4>Methods</h4>A multi-omics approach was employed, integrating proteomic and transcriptomic data analysis, miRNA and transcription factor profiling, protein-protein network construction, hub gene identification, and enrichment analyses. This approach aimed to explore molecular changes in AD brains and pinpoint the most relevant EV subpopulations for therapeutic intervention.<h4>Results</h4>We identified common alterations in the cAMP signaling pathway and coagulation cascade at both the protein and mRNA levels. Distinct changes in energy metabolism were observed at the protein level but not at the mRNA level. A specific EV subtype, characterized by a broader size distribution obtained through high-speed centrifugation, was identified as capable of compensating for dysregulated mitochondrial proteostasis in AD brains. Network biology analyses further highlighted potential regulators of key therapeutic proteins within this EV subtype.<h4>Conclusion</h4>This study underscores the critical role of proteomic alterations in AD and identifies a promising EV subpopulation, enriched with proteins targeting mitochondrial proteostasis, as a potential therapeutic strategy for AD.

The reported frequencies of perineural invasion (PNI) in human cervical cancer, ranging from 7.0% to 35.1%, may underestimate the significant role that nerves play in cervical cancer progression. Neurosecretory factors can promote tumor migration and invasion, even in cases classified as "PNI-negative". This study aimed to clarify whether tumor innervation influences tumor progression and cervical cancer patient outcomes. We first evaluated the gene signatures of human myelinating Schwann cells (SCs) using the Inferring Pathway Activity and Suppression (IPAS) scoring system to predict the degree of tumor innervation in 304 cervical cancer patients from The Cancer Genome Atlas (TCGA) database. Subsequently, we constructed a myelin-associated risk prognostic signature using LASSO regression analysis. Finally, we obtained a risk score using a quantitative formula and categorized all samples into high- and low-risk score groups. Our results indicated that tumor innervation in cervical cancer is associated with poor patient survival. Higher levels of innervation were correlated with an impaired immune response and reduced expression of immune checkpoints, including PD-L1. The prognostic model demonstrated excellent consistency between predicted and actual survival outcomes. Overall, tumor innervation plays a crucial role in regulating cervical cancer prognosis. The identified prognostic risk signatures offer a valuable tool for risk stratification and prognostic prediction in clinical practice.

A groundbreaking milestone in oncology has been the recognition and targeted elimination of malignant cells through cancer immunotherapy, which harnesses the body's immune system to attack cancer [...].

A well-regulated metabolism is crucial for optimal oocyte development and embryonic health. However, the metabolic framework governing oocyte maturation remains poorly understood. Using bovine oocytes as a model, we examined metabolomic and transcriptomic alterations during the transition from the germinal vesicle (GV) to the metaphase II (MII) stage. Our findings reveal distinct metabolic shifts, including suppressed β-oxidation combined with the accumulation of long-chain fatty acids (LCFAs). Notably, progesterone emerged as a key regulator of meiotic resumption through its influence on cAMP levels. We also observed enhanced glycolysis, moderate activation of the citric acid cycle (TCA cycle), and suppression of oxidative phosphorylation (OXPHOS), alongside reduced urea cycle flux and shifts in amino acid metabolism favoring glutamate synthesis. Intriguingly, discrepancies between metabolic and transcriptional activities in pathways such as the TCA cycle and nucleotide metabolism suggest asynchronous regulation. These findings provide a comprehensive multi-omics resource, advancing our understanding of the dynamic metabolic and transcriptional landscape during bovine oocyte maturation.

<h4>Background/objectives</h4>Iron is necessary for bodily function, but abnormal levels can increase the risk of chronic diseases. Studies of leukocyte telomere length suggest blood iron levels are positively associated with cellular senescence and accelerated aging. However, associations between blood iron and more robust metrics of biological aging, specifically those based on DNA methylation, have not been examined.<h4>Methods</h4>In a random sample of women from the Sister Study (<i>n</i> = 1260) with measured serum iron (ferritin, iron, transferrin saturation), we used linear regression models to assess cross-sectional associations between standardized serum iron and three methylation-based biological aging metrics (GrimAgeAccel, PhenoAgeAccel, and DunedinPACE), with and without adjustment for smoking, alcohol, menopause status, education, time since menopause, exercise, and diet.<h4>Results</h4>In adjusted models, a one standard deviation increase in serum ferritin was positively associated with higher standardized levels of DunedinPACE, GrimAgeAccel, and PhenoAgeAccel (DunedinPACE: 0.05, (0.00, 0.10); PhenoAgeAccel: 0.06 (0.00, 0.11); GrimAgeAccel: 0.06 (0.01, 0.11)). In contrast, higher serum iron and transferrin saturation were inversely associated with the biological aging metrics (serum iron, DunedinPACE: -0.02, (-0.07, 0.03); PhenoAgeAccel: -0.04 (-0.10, 0.01); GrimAgeAccel: -0.05 (-0.10, -0.01); transferrin saturation (DunedinPACE: -0.01, (-0.06, 0.05); PhenoAgeAccel: -0.01 (-0.06, 0.05); GrimAgeAccel: -0.05 (-0.10, -0.01))).<h4>Conclusions</h4>The positive association with ferritin is consistent with the proposed role of oxidative stress in accelerated aging associated with high iron exposure. However, the observed inverse associations with serum iron and transferrin saturation are not consistent with this common explanation, and future studies are needed to examine potential explanations.

<h4>Background</h4>The immune tolerance of the tumor immune microenvironment (TIME) restricts the response to immune checkpoint inhibitors (ICIs). Targeted activation of dendritic cells (DCs) in the TIME seems to be a scheme for improving the therapeutic effect of ICIs treatment. The purpose of this study was to utilize nanotechnology to reprogram the immunosuppressive tumor immune microenvironment <i>in situ</i>, improving the response of ICIs to lung cancer.<h4>Methods</h4>In this study, a folic acid (FA)-modified nanoassembly (NA) loaded with low-dose paclitaxel (PTX) (FA-PTX NA), self-assembled by distearoylphosphatidylethanolamine-methoxy polyethylene glycol 2000-folic acid (DSPE-mPEG2000-FA) and PTX, was designed to reprogram the DC function of the TIME to sensitize cells to cancer immunotherapy. The characteristics of FA-PTX NAs were studied, and the cytotoxicity, cellular uptake, and DC stimulation of FA-PTX NAs were evaluated <i>in vitro</i> using a Lewis lung carcinoma (LLC) cell line and bone marrow-derived cells (BMDCs). Following this, the effect of the reprogrammed TIME and on the sensitization to immunotherapy <i>in vivo</i> were examined in a C57BL/6 mouse LLC subcutaneous xenograft model.<h4>Results</h4>The prepared FA-PTX NAs exhibited a slightly negative surface charge, appropriate size and shape, good drug release profiles, and high drug encapsulation efficiency and blood compatibility. The FA-PTX NAs were effectively uptaken by bone BMDCs, increasing the activation and expression of the costimulatory factor of BMDCs <i>in vitro</i>. In the LLC xenograft model treated with intravenous injection of FA-PTX NAs, the numbers of CD4⁺ and CD8⁺ T cells in the TIME increased significantly, the killing activity of tumor-specific cytotoxic T lymphocytes (CTLs) was significantly enhanced, and at the same time, the concentration of transforming growth factor β (TGF-β) decreased significantly. Furthermore, the infiltrated CD8⁺ T cells in TIME were mainly distributed in the tumor parenchyma. The combination of FA-PTX NAs and ICIs effectively inhibited the growth of LLC xenograft tumor, demonstrating a greater effect than that of ICIs alone. Moreover, it was found that apoptosis induction, increase in CD4⁺ and CD8⁺ T-cell infiltration, and improvement in the distribution of CD8⁺ T cells were involved in the anticancer mechanism of this combination treatment.<h4>Conclusions</h4>The NA loaded with low-dose PTX can reprogram the DC function in the TIME and exert a synergistic anticancer effect with ICIs in lung cancer treatment. Increased sensitization to ICI therapy as stimulated by PTX-enhanced NAs has potential applications in lung cancer immunotherapy.

<b>Importance:</b> Genomic sequencing enables the rapid identification of a breadth of genetic variants. For clinical purposes, sequencing for small genetic variations is considered a solved problem, while challenges remain for structural variants, given the lower sensitivity and specificity. Interest has recently risen among governing bodies in developing protocols for population-wide genetic screening. However, usefulness is constrained when the probability of being affected by a rare disease remains low, despite a positive genetic test. This is a common scenario in neurodegenerative disorders. The problem is recognised among statisticians and statistical geneticists but is less well-understood by clinicians and researchers who will act on these results, and by the general public who might access screening services directly without the appropriate support for interpretation. <b>Observations:</b> We explore the probability of subsequent disease following genetic screening of several variants, both single nucleotide variants (SNVs) and larger repeat expansions, for two neurological conditions, Huntington's disease (HD) and amyotrophic lateral sclerosis (ALS), comparing these results with screening for phenylketonuria, which is well-established. The risk following a positive screening test was 0.5% for <i>C9orf72</i> in ALS and 0.4% for <i>HTT</i> in HD when testing repeat expansions, for which the test had sub-optimal performance (sensitivity = 99% and specificity = 90%), and 12.7% for phenylketonuria and 10.9% for ALS <i>SOD1</i> when testing pathogenic SNVs (sensitivity = 99.96% and specificity = 99.95%). Subsequent screening confirmation via PCR for <i>C9orf72</i> led to a 2% risk of developing ALS as a result of the reduced penetrance (44%). <b>Conclusions and Relevance:</b> We show that risk following a positive screening test result can be strikingly low for rare neurological diseases, even for fully penetrant variants such as <i>HTT</i>, if the test has sub-optimal performance. Accordingly, to maximise the utility of screening, it is vital to prioritise protocols with very high sensitivity and specificity, and a careful selection of markers for screening, giving regard to clinical interpretability, actionability, high penetrance, and secondary testing to confirm positive findings.

Damage to mitochondrial DNA (mtDNA) results in defective electron transport system (ETS) complexes, initiating a cycle of impaired oxidative phosphorylation (OXPHOS), increased reactive oxygen species (ROS) production, and chronic low-grade inflammation (inflammaging). This culminates in energy failure, cellular senescence, and progressive tissue degeneration. Rapamycin and metformin are the most extensively studied longevity drugs. Rapamycin inhibits mTORC1, promoting mitophagy, enhancing mitochondrial biogenesis, and reducing inflammation. Metformin partially inhibits Complex I, lowering reverse electron transfer (RET)-induced ROS formation and activating AMPK to stimulate autophagy and mitochondrial turnover. Both compounds mimic caloric restriction, shift metabolism toward a catabolic state, and confer preclinical-and, in the case of metformin, clinical-longevity benefits. More recently, small molecules directly targeting mitochondrial membranes and ETS components have emerged. Compounds such as Elamipretide, Sonlicromanol, SUL-138, and others modulate metabolism and mitochondrial function while exhibiting similarities to metformin and rapamycin, highlighting their potential in promoting longevity. The key question moving forward is whether these interventions should be applied chronically to sustain mitochondrial health or intermittently during episodes of stress. A pragmatic strategy may combine chronic metformin use with targeted mitochondrial therapies during acute physiological stress.

Schizophrenia is a chronic and severe psychiatric disorder affecting approximately 1% of the global population, characterized by disrupted synaptic plasticity and brain connectivity. While substantial evidence supports its classification as a neurodevelopmental disorder, non-canonical neurodegenerative features have also been reported, with increasing attention given to astrocytic dysfunction. Overall, in this study, we explore the role of astrocytes as a structural and functional link between neurodevelopment and neurodegeneration in schizophrenia. Specifically, we examine how astrocytes contribute to forming an aberrant substrate during early neurodevelopment, potentially predisposing individuals to later neurodegeneration. Astrocytes regulate neurotransmitter homeostasis and synaptic plasticity, influencing early vulnerability and disease progression through their involvement in Ca²⁺ signaling and dopamine-glutamate interaction-key pathways implicated in schizophrenia pathophysiology. Astrocytes differentiate via nuclear factor I-A, Sox9, and Notch pathways, occurring within a neuronal environment that may already be compromised in the early stages due to the genetic factors associated with the 'two-hits' model of schizophrenia. As a result, astrocytes may contribute to the development of an altered neural matrix, disrupting neuronal signaling, exacerbating the dopamine-glutamate imbalance, and causing excessive synaptic pruning and demyelination. These processes may underlie both the core symptoms of schizophrenia and the increased susceptibility to cognitive decline-clinically resembling neurodegeneration but driven by a distinct, poorly understood molecular substrate. Finally, astrocytes are emerging as potential pharmacological targets for antipsychotics such as clozapine, which may modulate their function by regulating glutamate clearance, redox balance, and synaptic remodeling.

<h4>Background</h4>Chronic inflammatory conditions are among the leading causes of disability and mortality. Although therapies have been significantly improved with the introduction of target-specific biologics, many chronic inflammatory conditions can be only moderately controlled by inhibition of individual cytokines.<h4>Objective</h4>We sought to compare individual versus simultaneous blockade of TNF-α and OX40L in controlling inflammation.<h4>Methods</h4>Analysis was conducted of the murine xenograft graft-versus-host disease model, a novel cynomolgus monkey model of simultaneous T cell-dependent antibody response (TDAR) and delayed-type hypersensitivity (DTH) skin reaction, and samples of patients with hidradenitis suppurativa (HS).<h4>Results</h4>Compared with individual inhibition, combined targeting of TNF-α and OX40L using mAbs more potently suppressed TDAR and DTH in cynomolgus monkey. We therefore created SAR442970, a bispecific pentavalent Nanobody containing 2 domains each binding to OX40L and TNF-α and 1 domain binding serum albumin to extend half-life. In xenograft graft-versus-host disease, disease control by SAR442970 was superior compared with treatment with monospecific anti-TNF-α or anti-OX40L Nanobodies. In cynomolgus monkey, SAR442970 potently suppressed TDAR and DTH. The transcriptional signature of inflamed monkey skin showed similarities to that of lesional skin of patients with atopic dermatitis and, even more so, HS and was inhibited by SAR442970 treatment. Increased numbers of cells expressing OX40 were observed in HS lesions, and bioinformatics analyses of single-cell and bulk RNA sequencing data identified cells expressing OX40 as T cells with a highly mobile phenotype.<h4>Conclusion</h4>OX40-OX40L interaction is a key pathogenetic feature in HS, and patients with HS might benefit from combined TNF-α/OX40L blockade by SAR442970, which is currently investigated in a clinical phase 2 trial.

Predictive genetic testing for major depressive disorder (MDD) has become a widespread technological advancement to aid the process of early diagnosis and treatment selection. Despite these tests' growing accessibility to the public, scant attention has been given to the behavioural changes that test-takers experience in response to undergoing the procedure and learning about their predisposition to MDD. The current paper aimed to be the first literature review to compile and evaluate the existing evidence demonstrating both the desirable and potentially harmful psychological responses following these tests. Studies portray a complicated picture, including desirable changes in the domains of felt stigma, lifestyle habits, and beliefs in treatment efficacy; as well as noteworthy deteriorations in perceived agency, fatalistic thoughts, and negativity bias in retrospective memory. In light of these findings, our review concludes that clear psychoeducation before testing is crucial to ensure that behavioural changes are predominantly beneficial for test-takers.

<h4>Background and objectives</h4>The lack of approved therapies for N-methyl-d-aspartate receptor (NMDAR) encephalitis has contributed to substantial variability in treatment. Inebilizumab is a humanized anti-CD19 monoclonal antibody that can be administered intravenously. Inebilizumab may be an efficacious treatment for patients with NMDAR encephalitis, with the potential to achieve early robust and sustained suppression CD19⁺ plasmablasts, some plasma cells, and NMDAR autoantibodies, with the potential to improve short-term and long-term outcomes in patients with NMDAR encephalitis.<h4>Methods</h4>The ExTINGUISH trial is a multisite, phase 2B, randomized, double-blind, placebo-controlled trial designed to evaluate the safety and efficacy of inebilizumab 300 mg for the acute treatment of participants with moderate-to-severe NMDAR encephalitis. ExTINGUISH will randomize 116 patients across the United States and Europe. Participants will receive standard first-line immunotherapies (intravenous steroids and intravenous immunoglobulins and/or plasma exchange) before randomization (1:1). In addition, cyclophosphamide rescue therapy will be offered to participants with persistent moderate-to-severe disease 6 weeks after randomization. Primary outcomes will be measured 16 weeks from randomization using the change in the adapted ExTINGUISH modified Rankin scale and accepted safety measures in 32 weeks. Secondary outcomes will be measured up to 96 weeks and include comprehensive neuropsychological tests, bedside cognitive screening tools, and quality-of-life/functional indices. Clinical data will be combined with blood and CSF biomarkers of immune activation to inform putative biologic contributors to outcomes (exploratory outcomes). Study operations are supported by the National Institute of Neurological Disorders and Stroke-supported Network for Excellence in Neuroscience Clinical Trial (NeuroNEXT) infrastructure.<h4>Discussion</h4>The ExTINGUISH trial will determine the safety and efficacy of inebilizumab as a treatment of NMDAR encephalitis while evaluating the utility of clinical, cognitive, and quality-of-life outcome measures and supporting standardized collection and measurement of biofluid biomarkers. These innovations will inform development of future treatments and trials for patients with NMDAR encephalitis and other types of autoimmune encephalitis. The ExTINGUISH trial opened to enrollment of adult patients (older than 18 years) in 2022 and pediatric patients (older than 12 years) in 2024; enrollment is ongoing.

<b>Background and Clinical Significance</b>: Neonatal hemochromatosis is a rare iron overload disorder that causes severe liver injury in newborns, typically with extrahepatic siderosis. Diagnosis of neonatal hemochromatosis is usually confirmed through a biopsy and MRI, demonstrating deposition of iron and liver failure. However, in severe patients who are not able to undergo biopsy, the diagnostic and management method remains unknown. <b>Case Presentation</b>: We present an unusual case of neonatal hemochromatosis without extrahepatic iron deposition in a 9-day-old male who showed signs of liver failure and respiratory distress. This case suggests that when the risks of biopsy outweigh its benefits, a diagnosis may be reached based on clinical evaluation and MRI findings. Early high-dose intravenous immunoglobulin therapy improved liver function and led to recovery, highlighting the need for early therapeutic intervention in neonatal hemochromatosis. <b>Conclusions</b>: This case highlights that the absence of extrahepatic siderosis cannot exclude a diagnosis of neonatal hemochromatosis, and high doses of IVIG should be administered promptly when neonatal hemochromatosis is suspected to maximize therapeutic effectiveness.

BACKGROUND Simultaneous liver-kidney transplantation (SLKT) is a complex procedure essential for patients with end-stage liver and kidney disease. Most SLKT outcome reports originate from large transplant centers in developed countries, with limited data from Latin America. This study aimed to describe SLKT outcomes at a high-complexity center in Colombia to assess their comparability with existing literature. MATERIAL AND METHODS A retrospective, single-center study included adult and pediatric patients who underwent SLKT between January 2005 and December 2023. Data on demographics, perioperative status, in-hospital course, and follow-up outcomes were collected from hospital databases and medical records. Kaplan-Meier survival analysis and descriptive statistics were utilized. RESULTS During the study, 41 SLKTs were performer - 31 in adults and 10 in children - accounting for 4.18% of liver transplants and 5.73% of kidney transplants. Alcoholic cirrhosis was the primary indication for adult liver transplants (38.7%), while congenital hepatic fibrosis was prevalent in children (50%). Diabetic nephropathy was the leading cause of adult kidney disease (48.3%), with nephronophthisis and polycystic kidney disease common in pediatric cases (30% each). All adult grafts were from deceased donors; 50% of pediatric cases used living donors. No intraoperative dialysis was required. Four early postoperative deaths occurred due to sepsis and multiple organ failure. Survival rates at 1, 3, and 5 years were 92.6%, 80.4%, and 75.6%, respectively. CONCLUSIONS SLKT outcomes at the institution are satisfactory and comparable to other series, though pediatric patients face a higher risk of early septic complications.

<h4>Abstract</h4>Anti-IgLON5 disease is an evolving entity that lies at the confluence of autoimmunity and neurodegeneration. Reports from India remain sparse. In this series, we describe seven Indian patients with anti-IgLON5-related disease. Patients presented across the fifth to eighth decades with a mean duration of illness of 16 months. All had movement disorders, which included gait ataxia, parkinsonism, and chorea. Six patients had sleep disturbances. Five had a frontal dysexecutive dementia phenotype. Two had epilepsy. Bulbar involvement was present in four, and one had amyotrophic lateral sclerosis (ALS)-like features. Magnetic resonance imaging was abnormal in two cases. Positron emission tomography of the brain also contributed to diagnosis. Combination immunotherapies were used in most of the patients, with three showing a sustained response and two deaths reported due to sepsis-related complications. It is important to recognize the increasing spectrum of IgLON5-related disease to enable timely initiation of immunotherapy before marked degeneration occurs.

Homologous recombination deficiency (HRD) leads to genomic instability, and patients with HRD can benefit from HRD-targeting therapies. Previous studies have primarily focused on identifying HRD biomarkers using data from a single technology. Here we integrated features from different genomic data types, including total copy number (CN), allele-specific copy number (ASCN) and single nucleotide variants (SNV). Using a semi-supervised method, we developed HRD classifiers from 1404 breast tumours across two datasets based on their BRCA1/2 status, demonstrating improved HRD identification when aggregating different data types. Notably, HRD-positive tumours in ER-negative disease showed improved survival post-adjuvant chemotherapy, while HRD status strongly correlated with neoadjuvant treatment response. Furthermore, our analysis of cell lines highlighted a sensitivity to PARP inhibitors, particularly rucaparib, among predicted HRD-positive lines. Exploring somatic mutations outside BRCA1/2, we confirmed variants in several genes associated with HRD. Our method for HRD classification can adapt to different data types or resolutions and can be used in various scenarios to help refine patient selection for HRD-targeting therapies that might lead to better clinical outcomes.

<h4>Background</h4>Firefighters are at an increased risk of cancer and other health conditions compared with the general population. However, the specific exposures and mechanisms contributing to these risks are not fully understood. This information is critical to formulate and test protective interventions.<h4>Objective</h4>The purpose of the Fire Fighter Cancer Cohort Study (FFCCS) is to conduct community-engaged research with the fire service to advance the evaluation and reduction of firefighter exposures, along with understanding and mitigating effects leading to an increased risk of cancer and other health conditions. This involves establishing a long-term (>30 years) firefighter multicenter prospective cohort study.<h4>Methods</h4>The structure of the FFCCS includes a fire service oversight and planning board to provide guidance and foster communication between researchers and fire organizations; a data coordinating center overseeing survey data collection and data management; an exposure assessment center working with quantitative exposure data to construct a firefighter job exposure matrix; and a biomarker analysis center, including a biorepository. Together, the centers evaluate the association between firefighter exposures and toxic health effects. Firefighter research liaisons are involved in all phases of the research. The FFCCS research design primarily uses a set of core and project-specific survey questions accompanied by a collection of biological samples (blood and urine) for the analysis of biomarkers of exposure and effect. Data and samples are collected upon entry into the study, with subsequent collection after eligible exposures, and at intervals (eg, 1-2 years) after enrollment. FFCCS data collection and analysis have been developed to evaluate unique exposures for specific firefighter groups; cancer risks; and end points in addition to cancer, such as reproductive outcomes. Recruitment is carried out with coordination from partnering fire departments and eligible participants, including active career and volunteer firefighters in the United States.<h4>Results</h4>The FFCCS protocol development was first funded by the US Federal Emergency Management Agency in 2016, with enrollment beginning in February 2018. As of September 2024, >6200 participants from >275 departments across 31 states have enrolled, including recruit and incumbent firefighters. Biological samples have been analyzed for measures of exposure and effect. Specific groups enrolled in the FFCCS include career and volunteer structural firefighters, women firefighters, trainers, fire investigators, wildland firefighters, firefighters responding to wildland-urban interface fires, and airport firefighters. Peer-reviewed published results include measurement of exposures and the toxic effects of firefighting exposure. Whenever possible, research results are provided back to individual participants.<h4>Conclusions</h4>The FFCCS is a unique, community-engaged, multicenter prospective cohort study focused on the fire service. Study results contribute to the evaluation of exposures, effects, and preventive interventions across multiple sectors of the US fire service, with broad implications nationally.<h4>International registered report identifier (irrid)</h4>DERR1-10.2196/70522.

<h4>Purpose</h4>Depression often occurs in the males with semen abnormalities. Evidence suggested a genetic correlation between depression and the pathogenesis of abnormal sperm parameters, whereas the mechanisms remained unclear.<h4>Methods</h4>Genomic datasets of major depressive disorder (MDD) and abnormal sperm parameters were obtained from the Gene Expression Omnibus database. After screening the datasets, differentially expressed genes (DEGs) were identified. GO and pathway enrichment analyses, a protein-protein interaction network, and receiver operator characteristic curve analysis were conducted. Then, MDD-related DEGs (MDRGs), the external validation, immunological, and translational regulation analysis were performed. Moreover, tissue expression of MDRGs was explored.<h4>Results</h4>A total of 249 overlapped MDRGs were discovered in the MDD and abnormal sperm parameters gene sets. MDRGs had a tight relationship with adhesion-associated and PI3 K-Akt-associated biological signaling. The protein-protein interaction module showed the enriched pathways involved in neuron differentiation and cell adhesion. Drug prediction revealed ten pharmacologic candidates. Finally, two hub MDRGs were identified and validated with good diagnostic values. Immunological and translational results showed three closely correlated kinds of CD8 + T lymphocytes, neutrophils, and macrophages, 19 transcription factor-MDRGs, and 71 miRNA-MDRGs interactions. Furthermore, expression signatures of Carnosine Dipeptidase 2 (CNDP2) and Galectin 3 Binding Protein (LGALS3BP) were displayed in cortex and testis.<h4>Conclusion</h4>Our study discovered the genetic profiles in abnormal sperm parameters and MDD and elucidated enriched pathways and molecular associations between hub genes and immune infiltration. These findings provide novel insights into the common pathogenesis of both diseases as well as the potential biomarkers for MDD-associated abnormal sperm parameters.

Huntington's disease (HD) is a devastating neurodegenerative disorder that manifests from an N-terminal polyQ-expansion (>35) in the Huntingtin (HTT) gene leading to axonal degeneration and significant neuronal death. Despite evidence for a scaffolding role for HTT in membrane-related processes such as endocytosis, vesicle transport, and vesicle fusion, it remains unclear how polyQ-expansion alters membrane binding during these processes. Using quantitative Mass Spectrometry-based proteomics on HTT-containing light vesicle membranes isolated from healthy and HD iPSC-derived neurons, we found significant changes in the proteome and kinome of signal transduction, neuronal translation, trafficking, and axon guidance-related processes. Through a combination of in vitro kinase assays, Drosophila genetics, and pharmacological inhibitors, we identified that GSK3β and ERK1 phosphorylate HTT and that these events play distinct and opposing roles during HD with inhibition of GSK3β decreasing polyQ-mediated axonal transport defects and neuronal cell death, while inhibition of ERK enhancing these phenotypes. Together, this work proposes two novel pathways in which GSK3β phosphorylation events exacerbate and ERK phosphorylation events mitigate HD-dependent neuronal dysfunction highlighting a highly druggable pathway for targeted therapeutics using already available small molecules.

Dual-task composed of gait or stepping tasks combined with cognitive tasks has been well-established as valuable tools for detecting neurocognitive disorders such as mild cognitive impairment and early-stage Alzheimer's disease. We previously developed a novel dual-task system with high accuracy for differentiating patients with neurocognitive disorders from healthy controls. In this study, we aimed to elucidate whether the output value obtained through artificial intelligence assumptions has clinical meaning other than diagnosis labelling. This is a retrospective cross-sectional study. Patients with Alzheimer's disease dementia, dementia with Lewy bodies, or mild cognitive impairment who participated in our previous dual-task experiment and completed all routine neuropsychological assessments at our hospital within one year of the experimental date were eligible for inclusion in the neurocognitive disorders group. Participants in the healthy control group were recruited from community-dwelling older adults. The correlation between the output value, "y-value", and each neuropsychological test: Mini-Mental State Examination (MMSE), Addenbrook's Cognitive Examination, Logical Memory tests, Frontal Assessment Battery, and digit span were assessed by Pearson's correlation coefficient. We also evaluated the correlation between the MMSE and those neurocognitive tests. To elucidate the diagnostic availability of the dual-task system and the MMSE on this dataset, we conducted a receiver operating characteristic analysis. We enrolled 97 participants in the neurocognitive disorders group: 42 with Alzheimer's disease dementia, 11 with dementia with Lewy bodies, and 44 with mild cognitive impairment. Additionally, 249 participants were included in the healthy control group. Although the y-value showed significant correlations with several tests, the MMSE demonstrated much stronger significant correlations with a broader range of cognitive tests. Meanwhile, its sensitivity and specificity were 0.969 and 0.912, respectively, and the area under the curve was 0.981, which was higher than the 0.934 of the MMSE. Our new AI-driven dual-task system has a high ability to predict neurocognitive disorders. However, the clinical significance of its output values is limited to screening for neurocognitive disorders and does not extend to estimating cognitive function. When using this system in clinical practice, it is essential to understand its limitations and select the appropriate usage scenarios.