Biology subjects

Zhang, W.

Publications and source records attributed to Zhang, W..

At least 145 records · Page 8Linked to original sources

bioRxiv2026

Distinct Chiral Nanostructures of Graphene Quantum Dots Govern Divergent Passive and Active Enantioselective Transport across Biological Membranes

Chirality in two-dimensional nanomaterials provides a powerful lever to control biological interfaces, yet the structural origins of nanoscale chirality remain poorly understood. Here, we systematically investigate chiral ligand modulated graphene quantum dots (GQDs) and reveal how ligand stereochemistry and edge chemistry modulate the formation of diverse chiral or achiral nanostructures. Spectroscopy, microscopy, and density functional theory with ring-puckering analysis identified six structural motifs, twisted-, twisted-boat, saddle-shaped, hybrid, unbuckled, and random. Among these, twisted-, twisted-boat, and saddle-shaped GQDs exhibited genuine nanoscale structural chirality, while unbuckled, hybrid, and random conformations lacked organized distortion. Importantly, structural chirality governed passive permeation into biological membrane (e.g. lipid membrane of extracellular vesicles), whereas achiral variants relied mainly on hydrophobic interactions. In contrast, active transport across biological membrane (e.g. endocytosis) is insensitive to nanoscale structural chirality but strongly influenced by chiral ligand identity and transporter recognition. Collectively, these results establish chiral ligand conjugation as a modular route to program both chiral and achiral motifs in graphene nanostructures and highlight nanoscale structural chirality as a design principle for engineering bio-nano interactions.

bioengineering↗

bioRxiv2026

Fully T2T pedigree assemblies reveal genetic stability and epigenetic plasticity of human centromeres across inheritance and cell-fate transitions

Centromeres are essential chromosome components yet remain poorly understood due to their highly repetitive sequence architecture. Using fully-phased telomere-to-telomere diploid assemblies from a three-generation pedigree integrated with long-read epigenomes from matched peripheral blood mononuclear cells, induced pluripotent stem cells, and neural progenitor cells, we generate allele-resolved single basepair resolution maps of centromere genetic and epigenetic dynamics across inheritance, reprogramming, and differentiation. We show that centromeric dip regions (CDRs), which define the functional core of centromeres, are positionally stable across generations and cell-fate transitions. In contrast, CDR epigenetic architecture is highly dynamic. Reprogramming markedly attenuates CDR hypomethylation, which is partially restored during differentiation in parallel with global hypomethylation of active alpha-satellite arrays and coordinated changes in nucleosome organization and protein occupancy. Centromeric remodeling is insulated from X-chromosome status, including Xa, Xi, and erosion. Finally, de novo mutations arising during reprogramming are enriched in centromeric regions but depleted within functional centromeric cores.

genomics↗

bioRxiv2026

TRIM32-UBQLN2-p62 axis promotes TDP-43 inclusion formation and amyloid aggregation through shuttle condensates

Aberrant protein aggregation is a hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD), which share overlapping genetic and pathological features. Similar aggregates are increasingly recognized in Alzheimers disease (AD) and limbic-predominant age-related TDP-43 encephalopathy (LATE). However, it remains unclear whether a shared molecular pathway drives this pathological aggregation. Here, we report that the E3 ubiquitin ligase TRIM32, together with the shuttle factor UBQLN2 and the autophagy adaptor p62/SQSTM1, form condensates that depend on E3 ligase activity and a network of intermolecular interactions. These condensates act as scaffolds that capture UBQLN2 client proteins, including TDP-43 and ANXA11, and modulate their mobility. A unique hydrophobic loop within TRIM32s substrate-binding domain mimics low-complexity motifs in ANXA11 and TDP-43, enabling selective retention via competitive binding mediated by UBQLN2 STI1 domain. Moreover, TRIM32 condensates promote amyloid aggregation of TDP-43, an effect that is exacerbated by pathogenic UBQLN2 mutation. In brains from individuals with diverse neurodegenerative diseases, TRIM32 co-localizes with pathological phospho-TDP-43 (pTDP-43) inclusions, supporting a model in which TRIM32-driven condensates function as selective proteostasis sorting compartments that broadly contribute to TDP-43 proteinopathy.

neuroscience↗

bioRxiv2026

DIA-CLIP: a universal representation learning framework for zero-shot DIA proteomics

Data-independent acquisition mass spectrometry has increasingly emerged as a cornerstone for characterizing highly heterogeneous biological systems, such as single-cell proteomics, metaproteomics, and spatial proteomics, offering unparalleled identification depth and quantification reproducibility. Current DIA analysis frameworks, however, require semi-supervised training within each run for peptide-spectrum match (PSM) re-scoring, which is prone to overfitting and lacks generalizability across diverse species and experimental conditions. Here, we present {pi}DIA-CLIP, a generalized framework shifting the DIA analysis strategy from semi-supervised training to zero-shot cross-modal representation learning through integrating dual-encoder contrastive learning and encoder-decoder architectures to establish a unified, high-precision representation for spectral features and peptides. Notably, the generalized zero-shot nature of {pi}DIA-CLIP facilitates an inference-only architecture, streamlining the analysis to achieve exceptional computational efficiency. Extensive evaluations across five distinct benchmarks demonstrate that {pi}DIA-CLIP consistently outperforms existing tools, yielding an up to 44.6% increase in protein identification alongside a reduction in entrapment identifications reaching a maximal 52.5%. Furthermore, the enhanced identification depth facilitates the discovery of novel biomarkers and the elucidation of intricate cellular mechanisms.

bioinformatics↗

bioRxiv2026

Early developmental placental defects and pregnancy loss in lupus mice expressing human TLR8

Anti-phospholipid (APL) autoantibodies confer a high risk for adverse pregnancy outcomes, especially in Systemic Lupus Erythematosus (SLE). While human TLR8 (huTLR8) has been implicated in APL antibody-mediated placental injury in vitro, its in vivo role in pregnancy is unexplored. We report a novel mouse model of pregnancy loss in SLE-prone mice expressing huTLR8. Placental analysis revealed early developmental defects starting post-implantation, including a thin junctional zone, impaired vascularization, infarcts, and inflammation. Profound immune dysregulation was evident at E8.5 including increased myeloid cells and CD8 T cells and decreased uterine natural killer (uNK) cells. RNA sequencing revealed downregulated pregnancy-specific glycoproteins, reduced uNK cell-associated genes, and an upregulated myeloid cell signature. Bone marrow chimera studies demonstrated preferential activation of huTLR8-expressing placental Ly6C+ monocytes. Spatial transcriptomics at E9.5 confirmed uNK cell loss, decreased IL15 expression by both stromal and myeloid cells, and discrete inflammatory aggregates in the maternal layers containing myeloid cells and IFN{gamma}-expressing CD8 T cells. We propose that huTLR8, likely through myeloid cell activation and cytolytic T cell recruitment, drives placental injury in the context of SLE and APL autoantibodies. This model provides a valuable platform to dissect early pathogenic events in APL-associated pregnancy loss and identify new therapeutic targets.

immunology↗

bioRxiv2026

Film Recall Reveals Intact Event Memory but Impaired Sequence Memory in Temporal Lobe Epilepsy Patients

BACKGROUND AND OBJECTIVESPatients with epilepsy (PWE), especially temporal lobe epilepsy (TLE), experience impaired memory for personally experienced events. However, current assessments of episodic memory are limited in their ecological validity with a potential to miss detection of subtle cognitive decline. We conducted an exploratory study to determine whether a naturalistic film-viewing task with open-ended spoken recall could detect memory differences between TLE patients and healthy controls (HCs). METHODSTLE patients (ages 18-60, fluent in English, not legally blind) were recruited from a Level 4 Epilepsy Center (2018-2024). TLE diagnosis was based on seizure semiology, MRI Brain, and EEG. TLE patients scored [≥]22/30 on the Montreal Cognitive Assessment (MOCA); HCs scored [≥]26/30. Subjects watched 6 short films and then freely recalled film details. Spoken responses were recorded, transcribed, segmented, and scored for film- and event-level recall. Recall order was assessed using the Damerau-Levenshtein distance. Semantic and causal centrality were quantified using sentence embeddings and rater-identified causal links, respectively. Beta regression with cluster-robust standard errors assessed group and centrality effects on recall probability. Beta regression evaluated the influence of age, MOCA, and testing platform on sequence recall error. RESULTSWe recruited 51 subjects (27 TLEs; 24 HCs, 70.1% F, mean 29.9 {+/-}8.3 years). TLE patients and HCs showed similar recall of films (HC 89% {+/-}11% vs TLE 88% {+/-}18%, p = 0.54), coarse events (HC 50% {+/-}16% vs TLE 44% {+/-}18%, p = 0.19) and fine events (HC 25%{+/-}10% vs. TLE 22%{+/-}12%, p=0.17). Both groups recalled high causal centrality events better. For coarse event sequence recall, TLE patients showed a numerical trend toward greater sequence errors compared to HCs (HC 10.8% {+/-} 10.5% vs. TLE 19.5% {+/-} 18%, p = 0.06), although this difference did not reach statistical significance. However, TLE patients showed significantly greater fine event sequence errors at recall than HCs (HC 15% {+/-}13% vs 23% {+/-}18%, p = 0.02, Hedges g = 0.85, Cliffs {delta} = 0.51), with RTLE demonstrating more sequence errors than HCs (15%{+/-}13 vs. 29%{+/-}21% p = 0.021) Age, education, MOCA, and performance on standard verbal and visual memory tasks were unrelated to film, event, and sequence recall performance. DISCUSSIONWe demonstrate that a short film task with spontaneous spoken recall can identify sequence memory impairment in TLE patients despite intact film- and event-level recall. Sequence memory may represent a subtle manifestation of memory impairment that is not detected by standard cognitive testing. Key PointsO_LIWe asked whether a naturalistic film recall task could detect episodic memory impairment in a temporal lobe epilepsy cohort. C_LIO_LIPatients with temporal lobe epilepsy showed comparable film and event recall compared to healthy controls but were found to have impaired sequence memory. C_LIO_LISequential memory for temporal order is an overlooked aspect of episodic memory that may detect subtle memory decline. C_LI

neuroscience↗

bioRxiv2026

The genetic repertoire of the deep sea: from sequence to structure and function

The deep sea as the largest and maybe most hostile environment on Earth is still underexplored especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures, and used it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity, yet substantial structural conservation of proteins. Especially proteins involved in replication, recombination, and repair were identified to be under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as a unique evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.

bioinformatics↗

bioRxiv2026

A regulatory role of novel long non-coding RNA, BAZ1A-AS1, in vascular smooth muscle cell functions during neointima formation in human saphenous veins

BackgroundNeointimal proliferation (NP) is a major cause of stenosis and occlusion in arteries and veins. Human saphenous veins (HSV), often used for coronary artery bypass grafting, frequently fail in part due to NP. Long non-coding RNAs (lncRNAs) have emerged as critical regulators of vascular smooth muscle cell (VSMC) phenotype, yet lncRNAs governing NP in human veins remain largely uncharacterized. Methods and ResultsUsing an ex vivo model of NP in human SV, we performed bulk RNA sequencing on SV tissues with and without NP. Among differentially expressed lncRNAs, we identified a previously uncharacterized transcript, Bromodomain Adjacent to Zinc Finger A1 antisense 1 (BAZ1A-AS1), and its predicted cis-regulatory partner gene BAZ1A, as markedly upregulated during NP and predominantly enriched in VSMCs. Both transcripts were induced by genotoxic stimuli, with BAZ1A-AS1 showing transient induction preceding sustained BAZ1A upregulation, consistent with a priming role in the DNA damage response. Silencing of either BAZ1A-AS1 or BAZ1A attenuated VSMC proliferation and migration, accompanied by upregulation of contractile markers and suppression of proliferative and inflammatory transcriptional programs. ChIRP-qPCR demonstrated that BAZ1A-AS1 physically interacts with 3' distal exons of BAZ1A at the DNA level while selectively engaging CNN1, CCND1, and IL6 mRNAs, indicating mechanistically distinct chromatin- and RNA-level regulatory functions. Baz1a haploinsufficiency attenuated neointima formation and preserved VSMC contractile identity in a mouse carotid artery ligation model. ConclusionsWe identify BAZ1A-AS1 and BAZ1A as stress-responsive regulators of VSMC phenotype, operating through dual mechanisms of cis-regulatory chromatin interaction and selective mRNA engagement, and demonstrate a novel role for the BAZ1A-AS1/BAZ1A axis in promoting NP.

physiology↗

bioRxiv2026

Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia

The basal ganglia play essential roles in motor control, emotion, learning and reward processing. Their dysfunction contributes to many neurological and psychiatric disorders. However, the gene regulatory programs defining basal ganglia cell-type identity and function remain poorly understood, limiting interpretation of disease-associated non-coding variants. Here, we present the first single-cell multiome atlas of histone modifications and transcriptomes across eight basal ganglia regions from neurotypical adult human donors. Joint profiling reveals cell-type-specific deployment of active and repressive cis-regulatory elements and gene regulatory networks, and suggests a combinatorial homeobox transcription factor code underlying cell identity. Integration with matched spatial transcriptomic MERFISH data uncovers regional heterogeneity of epigenomic landscapes. Comparative analysis between human and mouse medium spiny neurons uncovers conservation of core gene regulatory features. This atlas interprets non-coding risk variants of neuropsychiatric disorders and supports the development of a deep learning model to predict gene regulation and functional effects of disease-associated variants. HIGHLIGHTSO_LIJoint single-cell profiling of transcriptomes and three histone modifications across eight human basal ganglia regions characterizes active and repressive chromatin states at cell-type resolution. C_LIO_LICell-type-specific gene regulatory programs decode combinatorial homeobox TF grammar governing the identity and diversification of basal ganglia neurons. C_LIO_LIIntergrative analyses link noncoding neuropsychiatric risk variants to specific cell types, regulatory elements, and candidate target genes. C_LIO_LIA sequence-to-function deep-learning model predicts gene regulation from DNA sequence and prioritizes functional disease-associated variants. C_LI

genomics↗

bioRxiv2026

PRDM1 Drives Chemoradiotherapy-associated Enrichment of Adaptive NK Cells in Cervical Cancer

Chemoradiotherapy (CRT) induces not only direct tumor cell death but also extensive remodeling of the tumor immune microenvironment. Adaptive natural killer (aNK) cells, initially characterized in chronic viral infection, are increasingly recognized as functionally relevant immune populations in solid tumors, where they may contribute to antitumor immunity and immune memory. However, how aNK cells dynamically respond to chemoradiotherapy and the regulatory mechanisms underlying their activation in solid tumors remain poorly defined. To address this, we analyzed single-cell RNA sequencing data from cervical cancer patients collected before CRT, after the first CRT fraction, and after the second fraction. Single-cell profiling revealed a significant enrichment of aNK cells following CRT. Differential gene expression and pathway enrichment analyses demonstrated that CRT-associated aNK cells exhibit enhanced virus-defending programs with increased cytotoxicity. Among the differentially expressed genes, the transcription factor PRDM1 was consistently and robustly upregulated in aNK cells after both the first and second rounds of CRT. To investigate the functional role of PRDM1, we applied in silico perturbation analyses using scTenifoldKnk and CellOracle. Virtual knockout of PRDM1 resulted in a marked attenuation of effector programs and disruption of metabolic networks in aNK cells. Moreover, PRDM1 perturbation altered inferred cellular trajectories, reversing the progression toward the aNK cell state, suggesting a requirement for PRDM1 in maintaining aNK identity and functional maturation within the CRT-conditioned tumor microenvironment. Together, these findings identify PRDM1 as a key regulatory factor associated with the enrichment, functional activation, and trajectory stabilization of aNK cells following CRT in cervical cancer, providing insight into innate immune remodeling during CRT and highlighting PRDM1 as a potential target for enhancing radiotherapy-induced antitumor immunity.

immunology↗

bioRxiv2026

AADAT-Driven Metabolic Control of Malate and CoQ10 Shapes Immune Evasion in Triple-Negative Breast Cancer

Compared to other subtypes of breast cancer, triple-negative breast cancers (TNBC) have fewer treatment options and exhibit a worse prognosis. Through integrated transcriptomic, metabolomic, immunohistochemical, spatial, and clinical analyses, we identify the mitochondrial enzyme, -aminoadipate aminotransferase (AADAT) as a previously unrecognized metabolic immune checkpoint in TNBC. AADAT mRNA and protein were significantly upregulated in human TNBC, and high AADAT expression was associated with reduced intra-tumoral CD8 T-cell density and inferior survival. Genetic silencing of AADAT in orthotopic murine TNBC models curtailed primary tumor growth and distant metastasis in a CD8 T-cell-dependent manner, enhanced effector T-cell activation, and sensitized tumors to dual PD-1/CTLA-4 blockade. Mechanistically, unbiased metabolomics showed increased malate levels after AADAT knockdown. Additionally, 4-hydroxyphenylpyruvate, an essential precursor for coenzyme Q10(CoQ10) biosynthesis, decreased following AADAT knockdown, suggesting an impaired mitochondrial electron transport chain. CoQ10 supplementation restored metabolic balance and reversed malate accumulation caused by AADAT knockdown, indicating that AADAT helps maintain CoQ10-supported redox homeostasis, thereby preventing malate buildup and export. Notably, malate addition directly boosted CD8 T-cell oxidative metabolism, increased the NAD/NADH ratio and reactive oxygen species, and augmented TNF- and IFN-{gamma} production. In vivo, malate supplementation in drinking water phenocopied AADAT knockdown, restored the response to paclitaxel plus anti-PD-1 therapy in multiple independent syngeneic TNBC models with de novo or acquired resistance to immunotherapy, reduced tumor burden, and prolonged survival. In patient cohorts, higher spatially clustered intra-tumoral malate is associated with co-localization of functional CD8 T cells, decreased exhausted T-cell neighborhoods, and superior post-chemotherapy outcomes. These data position AADAT as a central metabolic orchestrator of immune escape in TNBC and nominate oral malate as a readily translatable adjuvant to reverse chemo-immunotherapy resistance in TNBC. Statement of SignificanceAADAT defines a metabolic-immune axis driving immune evasion and therapy resistance in triple-negative breast cancer. Blocking AADAT or administering oral malate reactivates CD8 T-cell immunity and sensitizes chemo-immunotherapy-resistant tumors to these agents. These findings uncover a readily translatable metabolic vulnerability with potential to improve outcomes for patients with aggressive breast cancer subtypes.

cancer biology↗

bioRxiv2026

The RNA Editome of Esophageal Squamous Cell Carcinoma Identifies an ADAR1-CDK13 Editing Feedback Loop Mediating cGAS-STING Activation in Early Tumorigenesis

ObjectiveRNA adenosine-to-inosine (A-to-I) editing, catalyzed by adenosine deaminases acting on RNA (ADARs), is a pervasive post-transcriptional mechanism that expands transcriptomic and proteomic diversity. However, the global landscape of RNA A-to-I editing, as well as its functional and clinical significance in esophageal squamous cell carcinoma (ESCC), remains largely unexplored. This study aimed to systematically characterize the RNA editome of ESCC and elucidate its biological and clinical significance. MethodsWhole-transcriptome sequencing was performed on 121 primary ESCC tumors, with or without lymph node metastasis, together with matched normal tissues, to construct a high-resolution RNA editome. ADAR1-regulated RNA editing events were identified, and their functional consequences were investigated using integrated transcriptomic, phosphoproteomic, and RNA immunoprecipitation sequencing (RIP-seq) analyses. Associations between CDK13 editing, cGAS-STING-interferon-stimulated gene (ISG) signaling, and patient survival were further evaluated. ResultsA total of 222,020 high-confidence RNA editing sites were identified, of which approximately 98% were A-to-I events, including 124,486 ESCC-specific edits predominantly enriched in introns, 3' untranslated regions, and non-coding RNAs, highlighting a pervasive post-transcriptional regulatory layer. RNA A-to-I editing was extensively remodeled and globally up-regulated in non-metastatic ESCC, whereas only minimal changes were observed during lymph node metastasis, indicating that RNA editing alterations predominantly occur during early tumorigenesis. CDK13 emerged as a recurrent ADAR1 target, with RNA editing inversely correlated with CDK13 expression. ADAR1-mediated CDK13 editing established a positive feedback loop associated with enhanced interferon-stimulated gene (ISG) signaling and poorer survival in non-metastatic ESCC. Mechanistically, partial attenuation of CDK13 induced chronic, tumor cell-intrinsic activation of the cGAS-STING-ISG pathway. Integrated multi-omics analyses further revealed that CDK13 regulates phosphorylation networks governing cytoskeleton organization, intracellular trafficking, RNA homeostasis, and immune signaling. ConclusionRNA A-to-I editing represents a dynamic regulatory mechanism driving early ESCC progression and remodeling tumor cell-intrinsic immune signaling. ADAR1-mediated editing of CDK13 provides a mechanistic link between RNA editing and cGAS-STING-ISG pathway activation, revealing potential therapeutic vulnerabilities and supporting its utility as an early prognostic biomarker in ESCC.

cancer biology↗

bioRxiv2026

An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia

The basal ganglia regulate motor, cognitive, and affective behaviors, and their dysfunction underlies diverse neurological and psychiatric disorders. Comprehensive, accessible multi-omics resources are needed to understand the regulatory mechanisms governing basal ganglia cell types. Here we present an open, interactive web-based platform for exploring single-cell multi-omics datasets from basal ganglia, generated using 10X Multiome, snm3C-seq, and Paired-Tag technologies from the BICAN (NIH BRAIN Initiative Cell Atlas Network) consortium. The platform is available at https://basalganglia.epigenomes.net/ and enables integrated visualization of gene expression, chromatin accessibility, DNA methylation, histone modifications, and chromatin conformation across cell types and human, macaque, marmoset, and mouse species, with direct genome browser support and comparative epigenomic functionality. Representative analyses demonstrate cell-type-specific regulatory landscapes, conserved and species-specific regulatory elements, and links between epigenomic regulation and transcription. This resource provides a scalable, community-oriented foundation for advancing basal ganglia biology and interpreting regulatory mechanisms relevant to brain function and disease. HighlightsO_LIIntegrated single-cell epigenomic resource for basal ganglia C_LIO_LIInteractive genome browser enables multi-omics and cross-species exploration C_LIO_LIReveals cell-type-specific and species-specific regulatory landscapes C_LIO_LISupports community access to complex brain epigenomic datasets C_LI

genomics↗

bioRxiv2026

Riboflavin Deficiency-Induced Angular Stomatitis and Conjunctivitis in Associated with Gut Microbiota Dysbiosis

PurposeRiboflavin deficiency causes ariboflavinosis, and the purpose of this study is to investigate the potential biological factors underlying its occurrence. MethodsMale F344 rats were randomly assigned to R6 and R0 groups. The healthy controls (R6 group) was fed a riboflavin-normal diet (6 mg/kg riboflavin), while the R0 group was fed a riboflavin-deficient diet (0 mg/kg riboflavin) for 16 weeks. Following this period, the R0 group was switched to a riboflavin replenishment diet (6 mg/kg riboflavin) for an additional 4 weeks (weeks 17-20). The bacterial communities were analyzed using high-throughput 16S rRNA gene sequencing. ResultsRiboflavin deficiency induces ariboflavinosis in rats (66.7%), characterized by angular stomatitis and conjunctivitis. With riboflavin replenishment, ariboflavinosis was completely resolved. Riboflavin deficiency altered the gut microbiota co-occurrence network and composition. The potential mechanism is predicted to involve an increase in glycan biosynthesis and metabolism within the gut microbiota, particularly in lipopolysaccharide biosynthesis pathways. ConclusionsThese findings suggest that riboflavin deficiency induces ariboflavinosis by altering the gut microbiota, providing new insights into the mechanisms of riboflavin deficiency and its association with chronic inflammation. Clinical perspectivesRiboflavin is an essential nutrient that must be obtained through the diet, as the human body cannot synthesize it. Since riboflavin is not stored in the body, regular dietary intake is necessary. Riboflavin deficiency is prevalent worldwide and can lead to ariboflavinosis. However, the specific mechanisms underlying riboflavin deficiency-induced ariboflavinosis remain unclear. This study demonstrates that riboflavin deficiency causes ariboflavinosis (characterized by angular stomatitis and conjunctivitis) in rats and reveals a close relationship between riboflavin deficiency and alterations in gut microbiota composition. Gut dysbiosis appears to be a hallmark of ariboflavinosis and may serve as a promising diagnostic biomarker and therapeutic target for the condition.

microbiology↗

bioRxiv2026

Multimodal Behavior Scoring quantifies depression-like severity across chronic stress models and identifies stress-resilient mice

IntroductionRodent chronic-stress models are central to preclinical depression research, yet behavioral phenotypes are often assessed assay-by-assay, which can reduce cross-cohort comparability and mask heterogeneity across symptom domains (e.g., anhedonia, anxiety-like behavior, and behavioral despair). An integrative behavioral index may provide a more robust and interpretable measure of overall stress-induced severity and facilitate stratification of susceptible versus resilient individuals. MethodsWe developed the Multimodal Behavior Scoring (MBS) algorithm to integrate outcomes from standard assays--sucrose preference test (SPT), open field test (OFT), and forced swim test (FST)--into a unified severity score. MBS was evaluated in two independent paradigms, chronic unpredictable mild stress (CUMS) and chronic social defeat stress (CSDS), quantifying group discrimination, reproducibility (intraclass correlation coefficient, ICC), and phenotypic stratification. ResultsMBS robustly separated stressed from control mice (CUMS: +39.8%, p<0.0001; CSDS: +121.8%, p<0.0001) and showed high cross-cohort reproducibility (ICC>0.88). MBS further identified stress-resilient subpopulations and uncovered paradigm-specific behavioral signatures, with despair-dominant patterns in CUMS (FST-MBS, r=0.61) and anxiety-centric patterns in CSDS (OFT-MBS, r=-0.74). Excluding TST did not reduce discrimination performance. ConclusionMBS provides an integrative framework for quantifying depression-like behavioral severity and heterogeneity, enabling streamlined protocols and improving the translational utility of preclinical cohorts for biomarker discovery and antidepressant screening.

animal behavior and cognition↗

bioRxiv2026

Circuit-Specific Resting-State fMRI Signatures for Stratifying First-Episode Major Depressive Disorder and Predicting Recurrence Risk

BackgroundDepression is biologically heterogeneous, and first-episode depression (FED) carries a high risk of recurrence that is poorly captured by symptom-based assessment. Early identification of patients likely to relapse, as well as reliable identification of those unlikely to relapse, is needed to support personalized intervention and efficient allocation of care. MethodsWe developed a neurocomputational framework to infer recurrence risk from resting-state fMRI functional connectivity. The framework combines a Convolutional Filtering Autoencoder (CFAE) with a k-medoids clustering algorithm (FED-kMC) to derive neurofunctional FED subtypes, followed by a Manifold Sheaves-based Ensemble Support Vector Machine (MST-LVSVM) to estimate individual-level recurrence risk and define an interpretable decision boundary. Circuit-level analyses were then used to localize connectivity pathways associated with high relapse risk. ResultsThe framework identified two neurofunctionally distinct FED subtypes with divergent recurrence trajectories and achieved an external validation accuracy of 82.61% for recurrence risk prediction. Circuit analyses highlighted dysfunction within the Medial Superior Frontal Gyrus-Hippocampus and Angular Gyrus-Precuneus pathways as neural correlates of high relapse risk, together with a decision boundary enabling early-stage risk stratification. ConclusionsIntegrating connectome-derived, circuit-level information with subtype-aware machine learning may support proactive identification of FED patients at elevated recurrence risk and facilitate targeted early interventions, bridging connectome-level analysis and clinical decision-making.

neuroscience↗

bioRxiv2026

The endoderm cell trajectory of urochordate Styela clava reveals the dual developmental origin and evolution of digestive tract

The digestive system exhibits extensive diversity in developmental mechanisms and morphology across metazoans, yet the evolutionary origins underlying its organ differentiation remain unclear. Here, single-cell RNA sequencing was employed to investigate endodermal cell lineage specification during metamorphosis in the urochordate Styela clava, a newly established model for chordate evolution. By profiling 26,099 cells across five stages, we identified 21 major cell clusters and reconstructed the endodermal differentiation trajectories. Our analysis reveals two larval endodermal progenitor populations with distinct differentiation potentials. Pseudotime and RNA velocity analyses indicate that these progenitors give rise to stomach and intestinal lineages, respectively. Cross-species comparisons reveal putative homologous relationships between ascidian endodermal lineages and mouse definitive and visceral endodermal lineages, suggesting dual origins of digestive tract in chordates. We also identified conserved TGF-{beta} and FGF regulatory programs in digestive organ patterning and highlight earlier fate restriction of stomach and intestinal progenitors in ascidians compared to vertebrates. These findings provide insights into how chordate digestive organs evolved from ancestral endodermal patterning programs.

evolutionary biology↗

bioRxiv2026

Polymer-lipid hybrid nanoparticle enhances mRNA delivery and T cell-mediated immunity

mRNA vaccines have transformed prophylactic immunization against infectious diseases as well as therapeutic interventions for cancer. However, their effectiveness against emerging viral variants and a range of malignancies continues to be hindered by suboptimal induction of T cell-mediated immunity. To overcome this limitation, here we developed a polymer-lipid hybrid nanoparticle (PLNP) platform engineered to improve mRNA delivery to antigen-presenting cells (APCs) and to potentiate T cell responses. Relative to conventional mRNA lipid nanoparticle (LNP) vaccines, mRNA PLNP vaccines demonstrated markedly improved lymph node targeting, APC activation, Th1-biased pro-inflammatory cytokine response, and antigen-specific T cell expansion while retaining robust humoral immunity. Remarkably, mRNA-PLNP vaccines generated approximately 50% more antigen-specific CD8+ T cells than mRNA-LNP vaccines across multiple antigens, including SARS-CoV-2 spike, influenza hemagglutinin, and ovalbumin. In prophylactic applications, mRNA PLNP vaccine provided complete protection against SARS-CoV-2 variants. As a therapeutic approach in a melanoma model, mRNA PLNP vaccination resulted in enhanced tumor control and significantly prolonged survival compared to LNP-based formulations. Collectively, these results establish PLNP as a versatile and broadly applicable platform for augmenting mRNA vaccine efficacy through improved mRNA delivery and T cell priming, offering promising implications for infection prevention and cancer immunotherapy.

immunology↗