Biology subjects

An, Y.

Publications and source records attributed to An, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

A Compact Regulatory Logic Governs Fibroblast Cell State Plasticity in Fibrosis

Fibroblast activation drives organ failure across human diseases, yet its regulatory basis remains largely undefined. Here, we repressed 280 conserved disease-activated enhancers using CRISPR droplet sequencing (CROP-seq) in ~550,000 fibroblasts, constructing a regulome of 15 gene programs governing the profibrotic state. Systematic TF perturbation converged on MEOX1 as a central regulator, and fibroblast-specific Meox1 deletion in mice improved cardiac function, reduced fibrosis, and rewired profibrotic fibroblasts toward quiescence in heart failure. Effector gene perturbation in human cardiac fibroblasts revealed distinct regulators of contractility, migration, and inflammatory signaling, and these programs were conserved across profibrotic states in human lung, liver, and skin. Simultaneous repression of just six enhancers using a multiplexed dCas12a-KRAB system collapsed the profibrotic network, suppressed migration and contraction, and rewired fibroblast paracrine signaling to attenuate macrophage inflammation. These findings define the regulatory logic of fibroblast plasticity and establish a new framework for reprogramming profibrotic cell states in disease.

genomics↗

bioRxiv2026

MINT: Predicting Enzyme-Cofactor Specificity by Multimodal Knowledge Transfer from Protein-Ligand Interactions

Protein-cofactor selectivity prediction is important for enzyme annotation, metabolic engineering, and biocatalyst discovery, but it remains challenging because experimentally supported associations are limited and unevenly distributed, and because biologically relevant differences can be subtler than those captured by general protein-ligand interaction models. Here, we present MINT (Multimodal Interaction Network with Teacher supervision), a multimodal framework for cofactor specificity prediction. MINT combines protein sequence features with cofactor sequence and graph representations and is trained with a gradual adaptation strategy that transfers useful information from a pretrained protein-ligand interaction model to the cofactor prediction task. On a fixed balanced held-out test set, MINT achieved the best overall performance among all compared methods (AUC = 0.932), and this ranking was reproduced in an independent family-stratified evaluation at the natural positive rate (pooled AUC = 0.939). Further analyses suggest that the pretrained model provides transferable structural information, while the gradual training scheme helps adapt that information to cofactor specificity. In a case study of the chemically near-identical NAD/NADP pair, MINT recovered 95.0-98.6% of true binders and resolved a single-phosphate-level distinction with direct relevance to engineering enzyme cofactor specificity. These results show that gradual transfer learning is an effective approach to cofactor specificity prediction when annotation is limited.

bioengineering↗

bioRxiv2026

Germline-encoded V(D)J gene usage does not impose strict constraints on the epitope-specificity of T cell receptors

The theoretical diversity of T cell receptors (TCRs), generated through V(D)J recombination, is enormous, yet the diversity of TCRs capable of recognizing the same epitope remains unknown. Defining this TCR solution space is essential for uncovering basic principles that govern TCR specificity. Using single-cell RNA and TCR sequencing, we generated ultra-deep (more than 4000 unique TCRs per epitope) epitope-specific TCR libraries derived from 560 immunized C57BL/6 mice, identifying over 27,000 unique epitope-reactive TCRs across three distinct CD8+ T cell epitopes presented by two major histocompatibility complex (MHC) class I alleles. Saturation analyses indicated that the solution space for all studied epitopes comprises many tens of thousands of unique TCRs. Despite highly skewed and peptide-dependent VJ-usage patterns, nearly the entire set of functional germline V/ and J/ segments was detected at least once within each epitope-specific repertoire. Therefore, diversity of epitope-specific TCRs is not limited by distinct germline combinations but rather can emerge from a near-to-complete combinatorial space of - and -chain, V and J segments paired with compatible CDR3 sequences.

immunology↗

bioRxiv2026

DextraDemixer enables accurate identification of antigen-specific T cells from pMHC multimer experiments

Antigen specificity of T cells defines the adaptive immune response, yet the vast majority of known T cell receptors (TCRs) lack annotated antigen targets. Single-cell peptide-MHC (pMHC) multimer assays offer a scalable approach to map TCR-antigen interactions. Still, their utility is limited by pervasive non-specific binding and severe overlap between signal and noise, which confound the accurate identification of antigen-specific cells. To address these limitations, we present DextraDemixer, a Bayesian hierarchical mixture model that disentangles antigen-specific T cells from background noise in pMHC multimer data. The model integrates information from negative controls and clonotype structure while providing calibrated uncertainty estimates for classification. We further introduce a dynamic thresholding scheme that enables credible interval-bounded control of the false discovery rate. Extensive benchmarking on simulated datasets and antigen-specific spike-in experiments demonstrated the models robustness and improved accuracy over established methods. In a longitudinal SARS-CoV-2 vaccine study, DextraDemixer identified antigen-specific TCRs characterized by high sequence similarity, elevated antigen-specificity prediction scores, and strong clonal purity. Annotations showed high concordance with external validation data and supported the identification of antigen-specific motifs. Overall, DextraDemixer provides a principled probabilistic framework for reliable identification of antigen-specific TCRs from single-cell pMHC-multimer assays.

bioinformatics↗

bioRxiv2026

Hyperactive STAT1 Promotes T Follicular Helper Type 1 Cell Differentiation to Trigger Autoimmunity

ABSTRACTSHeterozygous gain-of-function (GOF) mutations in signal transducer and activator of transcription 1 (STAT1) cause an inborn error of immunity characterized by immune dysregulation, recurrent infections and various autoimmune manifestations. However, the precise pathogenic mechanism by which STAT1 GOF contributes to autoimmunity remains elusive. In our cohort, STAT1-GOF patients exhibit biased circulating follicular helper T (cTfh) populations with CXCR3+ Tfh1-like features. Using a Stat1 GOF mouse model that spontaneously developed autoimmunity, we found that overactivated STAT1 promotes Tfh differentiation and disrupted T cell-dependent humoral responses with skewed immunoglobulin class switching towards IgG2. Furthermore, STAT1 GOF directly targets to Tfh and Th1 cell signature genes and thereby drives the development of Tfh1 cells with excessive IFN-{gamma} production, which implicated in autoantibody production and the development of autoimmunity. Notably, IFN-{gamma} neutralization significantly alleviated autoimmune cellular responses and autoantibody levels in mutant mice, highlighting IFN-{gamma} blockade as a promising targeted therapy for the STAT1-GOF patients with autoimmunity. Our findings suggest that proper regulation of STAT1 activity within a reasonable magnitude is crucial for ensuring optimal host-protective humoral immunity. One-sentence summaryOveractivated STAT1 promotes Tfh1 differentiation to drive autoimmunity.

immunology↗

bioRxiv2026

Functional activation reveals a repressor-gated fourth type VI secretion system in clinical Pseudomonas aeruginosa

Pseudomonas aeruginosa is a major opportunistic pathogen in which the type VI secretion system (T6SS) contributes to interbacterial competition and virulence. While most strains encode three T6SSs, we here functionally characterize a fourth system (H4-T6SS) in a clinical P. aeruginosa isolate. The H4-T6SS gene cluster is transcriptionally silent under laboratory conditions. By promoter rewiring, we demonstrate that the H4-T6SS assembles a contractile machine and mediates effector secretion and robust inter- and intraspecific antagonism. We identify a dominant pore-forming effector and its secretion pathway and a silent yet conserved nuclease effector. Genetic and biochemical analyses show that H4-T6SS expression is activated by an H4-encoded transcriptional regulator and repressed by H-NS family proteins. Analysis of over 1,200 clinical isolates reveals that the H4-T6SS is distributed across lineages and geographic regions. Finally, we observe functional crosstalk between H4- and H2-T6SSs. Together, these findings establish H4-T6SS as a functional and repressor-gated secretion system that expands the competitive arsenal of clinical P. aeruginosa.

microbiology↗

bioRxiv2025

TUPAD: A Tn5-Mediated, Pre-amplification/Adapter-Dimer-Free Platform for Ultra-Uniform, One-Step PGT Profiling with High Stability and Broad Compatibility

High-throughput sequencing stands as a cornerstone of clinical molecular diagnostics, particularly in preimplantation genetic testing (PGT)--a key application where the selection of chromosomally normal embryos is critical to enhancing in vitro fertilization (IVF) success rates. A fundamental challenge inherent to PGT, however, lies in the ultra-low gDNA input (typically <100 pg) from embryo biopsies. To mitigate this limitation, traditional workflows rely on whole genome amplification (WGA) technologies, such as MDA, PicoPlex, and MALBAC. Yet these WGA-based protocols inherently entail pre-amplification of gDNA prior to standard library construction---a step that introduces significant coverage bias and compromised uniformity. These are intrinsic flaws irreparable by downstream library preparation or bioinformatics analysis, ultimately leading to clinical uncertainty in the interpretation of copy number variations (CNVs). In this study, we developed TUPAD (Tn5-Mediated, Uniform Pre-amplification-free and Adapter-Dimer-Free Library preparation), a transformative technology that bypasses the limitations of traditional WGA. By engineering a novel adapter-dimer-free transposon system, TUPAD enables high-efficiency library construction from as little as 1 picogram (pg) of gDNA. This breakthrough allows for a pre-amplification-free workflow, effectively eliminating the primary source of amplification bias. Compared to existing WGA standards, these advantages are fully retained in embryo biopsy and positive sample testing, TUPAD consistently generates highly uniform library data, significantly enhancing the detection limit and accuracy of CNVs and other genomic variants. Beyond these performance advantages, TUPAD also cuts wet-lab processing time by 50%. Practical validation confirms TUPAD results are stable, reliable, with proven practical utility in PGT testing.

molecular biology↗

bioRxiv2025

Disrupted tRNA modification leads to intestinal mitochondrial dysfunction and microbial dysbiosis

Background and aimsTransfer RNA (tRNA) modifications determine translation fidelity and efficiency. It occurs through the action of specific enzymes that modify the nucleotides within the tRNA molecule. Our previous study demonstrated tRNA modopathies and altered queuine-related metabolites in inflammatory bowel diseases. Queuine tRNA-ribosyltransferase catalytic subunit 1 (QTRT1) and QTRT 2 co-localize in mitochondria and form a heterodimeric TGT participating in tRNA Queuosine (tRNA-Q) modification. Human body acquires Queuine/Vitamin Q from intestinal microbiota or from diet. However, the roles of tRNA-Q modifications in the maintenance of intestinal mitochondrial homeostasis and microbiome are still unclear. MethodsWe used publicly available human IBD datasets, QTRT1 knockout (KO) mice, QTRT1 intestinal epithelial conditional KO (QTRT1{Delta}IEC) mice, cultured cell lines with QTRT1-specific siRNA, and organoids from patients with IBD to investigate the mechanism of tRNA-Q modifications in intestinal mitochondrial homeostasis and therapeutic potential in anti-inflammation. ResultsIn single cell RNA sequencing datasets of human IBD, we identified significant reduced intestinal epithelial QTRT1 expression in the patients with Crohns Disease. Using publicly available datasets, we identified significantly changes of Vitamin Q-associated bacteria in human IBD, compared to the healthy control. Qtrt1-/- mice had significant reduction of Q-associated bacteria, e.g., Bacteroides. Alcian Blue and Mucin-2 staining revealed mucosal barrier damage and disrupted homeostasis, with reduced colonic cell proliferation. Intestinal tight junction integrity was impaired in QTRT1-KO mice, as evidenced by reduced ZO-1 and increased Claudin-10 expression. QTRT1{Delta}IEC mice also showed dysbiosis and disrupted TJs. ATP synthesis was significantly decreased in the colon of QTRT1-KO mice, accompanied by severe mitochondrial dysfunction: reduced mitochondrial quality, Cytochrome-C release, and mitochondrial DNA (mtDNA) leakage. Mitochondrial dysfunction contributed to colonic cell death, as shown by elevated expressions of Cleaved Caspase-3 and Cleaved Caspase-1, increased BAX/Bcl-2 ratio, and positive TUNEL signals. Elevated CDC42, CD14, and CD4 levels in QTRT1-KO colon suggested mucosal immune activation and tissue repair responses. QTRT1-deficient CaCO2-BBE cells showed mitochondrial dysfunction. Cytochrome-C and mito-DNA release leading to cell death characterized by elevated expressions of Cleaved Caspase-3 and Caspase-1, increased BAX/Bcl-2 ratio, and higher apoptosis rate. Organoids isolated from patients with IBD showed reduced levels of QTRT1 and dysfunctional mitochondria. Restoring mitochondrial function leads to enhanced QTRT1. ConclusionsThese findings underscore the critical role of QTRT1/Q-tRNA modification in maintaining intestinal and microbial homeostasis. Mechanistically, QTRT1 loss impacts mitochondrial integrity and mucosal homeostasis. Our study highlights the novel roles of tRNA-Q modification in maintaining mucosal barriers and innate immunity in intestinal health. What is already known about this subject?O_LIEukaryotes acquire queuine (q), also known as Vitamin Q, as a micronutrient factor from intestinal microbiota or from diet. C_LIO_LIVitamin Q is needed for queuosine (Q) modification of tRNAs for the protein translation rate and fidelity. C_LIO_LIQueuine tRNA-ribosyltransferase catalytic subunit 1 (QTRT1) is reduced in human IBD. C_LIO_LIHowever, health consequences of disturbed availability of queuine and altered Q-tRNA modification in digestive diseases remain to be investigated. C_LI What are the new findings?O_LIQTRT1 deficiency leads to altered microbiome and reduced Vitamin Q-associated bacteria in human IBD and a QTRT1 KO animal model. C_LIO_LIQTRT1 protects the host against losing intestinal integrity during inflammation. C_LIO_LIQTRT1 localizes in mitochondria and plays novel functions by maintaining intestinal mitochondrial function. QTRT1 loss impacts tRNA modification in the intestine, linking to mitochondrial integrity and mucosal homeostasis. C_LIO_LIHuman IBD showed reduced levels of QTRT1 and dysfunctional mitochondria. Restoring mitochondrial function leads to enhanced QTRT1. C_LI How might it impact on clinical practice in the foreseeable future?Targeting tRNA-Q modification in enhancing mitochondrial function will be a novel method to maintain intestinal health.

cell biology↗

bioRxiv2025

A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex

The genetic and spatial determinants of cell type diversity in human cerebral cortices remain poorly defined. Here, we present a population-level single-cell spatial transcriptomic atlas of human cortices from 71 donors across the lifespan. We identified 906 layer-specific genes showing conserved and divergent laminar expression patterns between humans and other species. Spatial analysis revealed neuronal vulnerability and glial activation during aging, together with a decline in the proportion of superficial SST neurons and their interactions with other cells. Disease-associated genes exhibited high cell-type and layer-specific expression, implicating the pathogenic role of spatially specific gene expression. Spatial cis-eQTL analysis identified regulatory variants linked to genes related to diseases like Tourette syndrome. Cross-species comparison demonstrated glial expansion in the human cortex, accompanied by enhanced neuron-glia communication via the neuregulin signaling. Together, we provide a comprehensive single-cell atlas of the human cortex that is essential for understanding aging, evolution, and disease pathogenesis.

neuroscience↗

bioRxiv2025

Contralateral-Ipsilateral Segregation as a Conserved Principle of the Visual Corpus Callosum

How the brain maintains distinct information streams within dense white matter is a fundamental question. We investigated whether the visual corpus callosum transmits information via segregated "parallel wires" or mixed pathways. This distinction is critical: a mixed architecture would render the signals origin ambiguous, whereas a segregated arrangement implies that spatial position tracks the direction of information flow. Using high-field fMRI and Bayesian modeling in humans, we demonstrate a segregated architecture featuring distinct contralateral and ipsilateral channels. This functional segregation mirrors a precise anatomical arrangement in mice, where dual-color viral tracing and light-sheet microscopy reveal that callosal axons remain spatially segregated in distinct laminae after crossing the midline. Our findings establish a conserved "parallel wires" principle of callosal organization, providing a new framework to decode directional information flow and assess pathway-specific damage in neurological disease.

neuroscience↗

bioRxiv2025

High-fidelity CRISPR genome editing of single-nucleotide mutation with near-complementary guide RNA via enhanced target binding kinetics

The CRISPR-Cas9 system is a powerful genome editing tool capable of precisely recognizing and cleaving specific DNA sequences, and has been extensively investigated as a strategy for correcting mutations associated with genetic diseases and cancer. However, conventional CRISPR genome engineering often fail to discriminate single-nucleotide mutations from wild-type alleles when the mutation is located outside the protospacer adjacent motif (PAM) sequence. To address this limitation, we developed a RNA engineering approach for designing near-complementary single guide RNA (sgRNA) that contain intentional mismatches within the seed region of the sgRNA. Single molecule kinetic analyses showed that the near-complementary sgRNA selectively reduces the binding affinity of CRISPR ribonucleoprotein complex by via differentiated increment in the dissociation rates to the wild-type target DNA compared to the mutant allele. The engineered kinetic characteristics of near-complementary sgRNAs enable highly specific genome editing of single-base mutations without reliance on PAM proximity. We demonstrate the application of the strategy to the a cancer-specific single-nucleotide G228A (-124C > T) mutation in the TERT promoter, frequently found in glioblastomas and other tumors, that does not generate a canonical PAM sequence. Our near-complementary sgRNA successfully induced selective editing of the mutant allele while sparing the wild-type sequence. Furthermore, single-molecule fluorescence resonance energy transfer (smFRET) analyss revealed distinct differences in binding kinetics between mutant and wild-type DNA, providing kinetic insight into the discrimination process. We conclude that the near-complementary sgRNA CRISPR editing strategy facilitates precise PAM-independent targeting of single-nucleotide mutations without protein engineering and offers a molecular framework for expanding the specificity and applicability of CRISPR-based genome and epigenome editing technologies.

biochemistry↗

bioRxiv2025

A PBD-dimer containing antibody drug conjugate targeting CCRL2 for high-risk MDS/AML

Patients with myelodysplastic syndrome (MDS)/acute myeloid leukemia (AML) with high-risk features including TP53 mutations and deletions have poor outcomes due to lack of effective therapies. The atypical chemokine surface receptor C-C motif chemokine receptor-like 2 (CCRL2) is overexpressed in MDS and secondary AML (sAML) compared to healthy hematopoietic cells and we recently found that TP53-mutated MDS/AML and AML with erythroid features express the highest levels of this receptor across MDS/AML subtypes. To illustrate the therapeutic potential of CCRL2 as a therapeutic target, we developed an anti-CCRL2 antibody-drug conjugate (ADC) by conjugating an anti-CCRL2 antibody with the cytotoxic drug pyrrolobenzodiazepine (PBD), which causes DNA double-strand breaks leading to cancer cell death. The anti-CCRL2 ADC demonstrated strong CCRL2-selective cytotoxicity against cell lines derived from MDS/AML patients with TP53 mutations and erythroid features, surpassing the cytotoxic effects observed with gemtuzumab and PBD-conjugated anti-CD33 and anti-CD123 ADCs. It also induced apoptosis and suppressed the clonogenicity of primary MDS/AML bone marrow samples without affecting the survival, differentiation and clonogenicity of healthy hematopoietic stem and progenitor cells. This agent also suppressed the leukemic growth of TP53-mutated MDS/AML cell line xenografts, improving mice survival and decreasing the leukemic burden in patient-derived TP53-mutated MDS/AML xenografts. In conclusion, our study introduces CCRL2 as a potential new therapeutic target in high-risk MDS/AML. Statement of significancePyrrolobenzodiazepine(PBD)-conjugated anti-CCRL2 ADC shows anti-leukemic effect in MDS/AML models including TP53-mutated disease without affecting healthy hematopoietic cells supporting that it is a promising candidate for single-agent or combination therapies in high-risk MDS/AML.

cancer biology↗

bioRxiv2025

Targeting RUNX1 in Macrophages Facilitates Cardiac Recovery

Despite advances in disease treatment, our understanding of how damaged organs recover and the mechanisms governing this process remain poorly defined. Here, we mapped the transcriptional and regulatory landscape of human cardiac recovery using single cell multiomics. Macrophages emerged as the most reprogrammed cell type. Deep learning identified the transcription factor RUNX1 as a key regulator of this process. Macrophage-specific Runx1 deletion recapitulated the human cardiac recovery phenotype in a chronic heart failure model. Runx1 deletion reprogrammed macrophages to a reparative phenotype, reduced fibrosis, and promoted cardiomyocyte adaptation. RUNX1 chromatin profiling revealed a conserved regulon that diminished during recovery. Mechanistically, the epigenetic reader BRD4 controlled Runx1 expression in macrophages. Chromatin activity mapping, combined with CRISPR perturbations, identified the precise regulatory element governing Runx1 expression. Therapeutically, small molecule Runx1 inhibition was sufficient to promote cardiac recovery. Our findings uncover a druggable RUNX1 epigenetic mechanism that orchestrates recovery of heart function.

immunology↗

bioRxiv2025

Cancer-like fragmentomic characteristics of somatic variants in cell-free DNA

Cell-free DNA (cfDNA) in plasma consists of short DNA fragments resulting from a non-random fragmentation process, with distinct "fragmentomic" characteristics that are related with their cellular origins. Despite the wealth of low-pass whole genome sequencing data from recent cancer liquid biopsy studies, somatic variants within this data have often been overlooked without detailed characterization. Here, we reported that in low-pass sequencing data, somatic variant signatures in cfDNA markedly differ between non-cancerous controls and cancer patients, indicating that tumor-associated signals are retained in these variants. Surprisingly, our investigation into cfDNA fragmentomics showed that even in controls, cfDNA molecules harboring somatic variants exhibit cancer-like traits, such as reduced size, decreased DNA methylation, and altered end motif usages and distributions in the nucleosome structure. Importantly, these somatic variants-associated fragmentomic aberrations are more pronounced in cancer patients, enabling cancer diagnosis. In a large pan-cancer cohort, we utilized artificial intelligence to integrate genomic, fragmentomic, and epigenomic features, developing diagnostic models named FreeSV (Fragmentomic and epigenomic examinations of Somatic Variants in cfDNA) and FreeSV-m. Leveraging somatic variant-associated features alone, the FreeSV model achieved area under the ROC curves (AUCs) between 0.81-0.92 across cancer types; however, when genomewide features were also included, the AUCs of FreeSV-m model substantially increased to 0.93-0.99 across cancer types, highlighting the significance of integrative genomic and fragmentomic analyses in cfDNA for cancer liquid biopsy.

cancer biology↗

bioRxiv2025

Mitochondrial dysfunction in Machado Joseph disease: insights from a multi-model system

Spinocerebellar ataxia type-3 (SCA3), also known as Machado Joseph disease, MJD) is a fatal, neurodegenerative disease belonging to the polyglutamine repeat disease family, caused by inheritance of an abnormal form of the ATXN3 gene, carrying a longer than usual trinucleotide repeat sequence. Within this study we explored mitochondrial function in a range of different experimental models of MJD, including transgenic zebrafish, mice and neuronal cells, to gain an understanding of mitochondrial function in the disease, and possible mechanisms of any dysfunction. Firstly, we examined the transgenic CMVMJD135 mouse model that develops impaired movement, neurodegeneration and decreased survival. We performed proteomic analysis on brain lysates extracted from a cohort of male and female WT and MJD mice, for analysis of differences in male and female mice separately. We identified that a major difference predicted by Ingenuity Pathway Analysis to be in both male and female MJD mice was related to impaired oxidative phosphorylation and mitochondrial dysfunction. We examined primary neuron cultures obtained from CMVMJD135 mice, validating the findings of the proteomic analysis, and finding changes to mitochondrial morphology, as well. We further examined a transgenic zebrafish model of MJD that expresses EGFP fused human ataxin-3 with short or long polyQ stretches (23 or 84Q, respectively) in neurons (expression driven under the elav/HuC promoter). The MJD zebrafish also exhibit altered mitochondrial electron transport chain complex protein levels, together with enhanced sensitivity to rotenone administration, which may be a valuable readout for treatment investigation studies in the future. Together, this study confirms, and extends on, the growing body of evidence suggesting that mitochondrial dysfunction plays a role in MJD, warranting investigation for therapeutic intervention.

neuroscience↗

bioRxiv2025

Widespread gray and white matter microstructural alterations in dual cognitive-motor impairment

INTRODUCTIONDual cognitive-motor impairment in aging is a strong predictor of dementia, yet its effects on vulnerable gray matter regions microstructure remain unexplored. METHODSThis study classified 582 individuals aged 36-90 into cognitive-motor impairment, isolated cognitive or motor impairment, and control groups. Microstructural differences in 27 temporal and motor-related gray matter regions and white matter tracts were assessed using DTI and mean apparent propagator (MAP-MRI), a technique well-suited for gray matter analysis. RESULTSWe found widespread microstructural alterations in gray and white matter among individuals with dual cognitive-motor impairment. These changes were not observed in isolated cognitive or motor impairment after multiple comparisons correction. DISCUSSIONDual cognitive-motor impairment is associated with reduced cellular density in temporal gray matter, decreased fiber coherence, and potential demyelination in white matter tracts, suggesting widespread microstructural disruption. These findings could help understand brain aging and facilitate interventions to slow neurodegeneration and delay dementia onset.

neuroscience↗

bioRxiv2025

Presence of Hepatitis B virus infection in colon cancer

Hepatitis B virus (HBV) infection affects [~]300 million people worldwide, which population is at an elevated risk of various cancers, such as gastrointestinal cancer, while the matter behind is largely unclear. In this study, we analyzed 10 colonic specimens from 6 colon cancer patients who were also chronic HBV carriers through Fluorescence-activated Cell Sorting and Immunofluorescence assay to inspect the expression of HBsAg (HBV surface antigen), NTCP (current known cellular receptor of HBV) and CD45 (common marker for immune cells) proteins in single-cell resolution. We found that presence of HBsAg in colonic cells was observed in specimens from all patients, and the proportions of HBV-infected cells were higher in tumors than normal tissues. Strikingly, HBsAg in both immune cells and NTCP-negative cells were also observed in all the patients. In vitro experiments further demonstrated that colonic cells expressing NTCP were indeed highly suspectable to HBV infection. Hence, HBV could infect colonic cells (including immune ones) and may play roles during tumorigenesis in colon cancer.

cancer biology↗

bioRxiv2025

Single-cell spatial transcriptome reveals pathological features of human hippocampus with sclerosis

More than half of epileptic patients ultimately turned to intractable epilepsy. Mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS), the most common type of intractable epilepsies, whose pathological mechanism remains elusive. Here, using 42 human hippocampal samples from surgical donors of MTLE (32 with and 10 without HS) through single-cell resolution Stereo-seq and histologcial experiments, we revealed spatially pathological changes of gene expression and cell type composition with HS systematically. After precise parcellation of hippocampal subregions and differentially expressed gene (DEG) analysis between each region with and without sclerosis, we found Cornu Ammonis (CA) subregions with higher number of DEGs were vulnerable to sclerosis, especially CA1 and CA3. Within CA1, we found that CA1-superficial and proximal areas were more vulnerable than CA1-deep and distal areas in sclerosis. Meanwhile, after analyzing 350,795 segmented cells from Stereo-seq, we found dramatically increasing density of astrocyte accompanied with significantly decreasing density of excitatory neurons in CA1, especially superficial and proximal CA1, and CA3 in sclerosis. In these two vulnerable subregions, proliferative astrocyte (P_astrocyte) and reactive astrocyte (R_astrocyte) were found to be enriched whereas apoptotic subtype of astrocyte (A_astrocyte), related with apoptotic pathway, was mainly located in alveus, which strengthened cell communication with reactive microglia (R_microglia) in HS, revealing the novel pathological feature in our work. The pseudotime analysis indicated that CA excitatory neurons underwent synaptic impairment, energy dysfunction, aging, and finally losing cell identity until death through autophagy or apoptosis. Besides, we also found a resilient subtype, EX_CA2-4.3, highly expressed extracellular matrix related genes including PDYN, and was increasing the interaction of BDNF-NTRK, NFASC-CNTN1 to withstand the damage from sclerosis. Together, our study provided a reference of human hippocampus with and without HS caused by MTLE, and highlighted the potential pathological mechanism on molecular and cellular level of MTLE-HS.

neuroscience↗