Biology subjects

Yang, F.

Publications and source records attributed to Yang, F..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Claustrum-cortical reciprocal connections orchestrate allostatic responses following stress

Anxiety is an evolutionarily conserved response that supports threat detection and survival, yet dysregulated stress responses can drive its progression into pathological states. Here, we identify the claustrum (CLA) as a central hub that links acute stress responses to chronic affective dysfunction through cell-type-specific circuit dynamics. Acute social defeat stress robustly activated the CLA and induced anxiety-like behaviors in mice. Multimodal profiling revealed transcriptional and functional plasticity within CLA neurons, with Egr2-expressing excitatory and Gad2-expressing inhibitory populations exhibiting distinct adaptations to acute versus chronic stress. We further delineate a reciprocal CLA-anterior cingulate cortex (ACC) circuit that bidirectionally regulates stress responses in which glutamatergic CLAEgr2 [->] ACC projections promoted anxiety-like behaviors, whereas top-down ACC [->] CLAGad2inhibitory inputs constrained claustral output. Chronic stress induced hyperactivity in CLAGad2 inhibitory neurons and reshaped excitatory neuron dynamics, leading to increased intrinsic excitability, local circuit imbalance, and ultimately, depression-like phenotypes. These findings define a dynamic claustrum-centered circuit that governs the transition from adaptive anxiety to maladaptive affective states through balanced Egr2-Gad2 activity, and show that chronic-stress driven disruption of this excitatory-inhibitory equilibrium impairs stress coping and drives pathological behavioral outcomes. Graphic summaryAcute stress engages a claustrum (CLA)-centered network with activation of Egr2 excitatory neurons, promoting anxiety-like behaviors. Chronic stress drives CLAG142 neurons into a hyperactive state, enhancing local inhibition and suppressing excitatory output to induce depressive-like behaviors. A reciprocal CLAE7182[->]ACC feedforward and ACC[->]CLAG142 feedback circuit forms a state-dependent regulatory hub governing stress adaptation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/673892v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@75d664org.highwire.dtl.DTLVardef@4e5c31org.highwire.dtl.DTLVardef@86b5f2org.highwire.dtl.DTLVardef@135045_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

MALDI Deamidation Score (MDS): A Fast and Flexible Method for Assessing Deamidation in ZooMS Data and Its Application to the Denisova Cave Bone Assemblage

Estimating deamidation from MALDI-TOF MS spectra of bones has most frequently been achieved using the q2e method due to its high-throughput capacity and ease of use. Despite this accessibility, q2e is only capable of estimating deamidation at the peptide level on a fixed peptide list and does not generate a sample-wide summary. The introduction of the Parchment Glutamine Index (PQI) presented an alternative method for deamidation estimation. Initially designed for a large ZooMS dataset of parchment, it utilises weighted least squares and a linear mixed-effects model (LME) to generate deamidation estimation on both the peptide and sample level. To address the limitations of q2e and expand the applicability of PQI to a wider range of archaeological tissues and MALDI-derived data (such as ZooMS data on bone collagen), we developed the MALDI Deamidation Score (MDS), an iteration of the PQI method optimized for handling large-scale datasets. Compared to PQI, MDS is more streamlined for the analysis of multi-species data with customisable peptide lists, offering a dramatically decreased processing time while being able to normalise the peak intensity for higher accuracy. Through a case study on the published Denisova Cave ZooMS assemblage, we demonstrate that different peptides exhibit varying deamidation patterns over time, making the use of a single peptide to represent overall deamidation potentially biased. Such information is invaluable for investigating key questions such as protein preservation and site formation processes, especially when contextualized with other lines of archaeological evidence.

bioinformatics↗

bioRxiv2025

Endogenous Real Time Imaging Reveals Dynamic Chromosomal Mobility During Ligand-Mediated Transcriptional Burst Events

Enhancers serve as the major genomic elements regulating mammalian signal-dependent transcriptional programs, characterized by alternating periods of target gene "bursting" and "non-busting" that require investigation of induced enhancer condensates and locus motility in real time to provide dynamic insights into signal/ligand-dependent regulatory events. Here, endogenous live cell imaging has revealed the altered chromosomal dynamics/condensate formation occurring during estrogen receptor (ER)-dependent target gene bursting/post-bursting and chronic activation events. Simultaneous DNA/RNA endogenous live imaging reveals that an increased mobility of acutely ER-stimulated loci observed during the bursting phase is, unexpectedly, further increased in the subsequent non-burst phase. Single molecule tracking (SMT) of ER shows that the relatively high-burst, lower-mobility acute state was indeed enriched for high-viscosity, 1,6-hexanediol-sensative ER molecules in a low sub-diffusive confined state with enhanced condensate formation during burst activation. Consistent with this, blocking transcription with flavopiridol shifts DNA tracks into a non-confined state. Differential DNA kinetics during burst vs non-burst has provided a strategy to assess altered condensate formation during gene activation events. (165)

molecular biology↗

bioRxiv2025

Force Propagation in Active Cytoskeletal Networks

Conventional materials science establishes clear structure-function relationships: grain boundaries modulate strength by blocking dislocations, and defect density limits conductivity through electron scattering. Active matter presents a fundamentally different challenge, components continuously consume energy to generate forces, creating a dual identity as both structural elements and force-generating machines. This material-machine duality raises a fundamental question: which structural parameters govern functional behavior in systems where constituents actively generate forces rather than merely responding to external inputs? Here we demonstrate that percolation is the critical mechanism that transforms active cytoskeletal networks from energy-dissipating materials into work-performing machines. Using light-controlled microtubule-kinesin networks, we show that increasing bundle length from 0.9 {micro}m to 5 {micro}m triggers a percolation transition that enables global force organization. Networks below the threshold remain incapable of performing coordinated work, while networks above it develop correlation lengths exceeding 240 {micro}m, generate 25-fold stronger forces, and extract 1000-fold more mechanical work, powering transport of live cells across 800 {micro}m distances. Network simulations reveal that introducing just 5-10% longer bundles creates a connected component containing 90% of microtubules, establishing the precise threshold that drives this material-to-machine transition. Our findings establish percolation as the fundamental mechanism governing whether active matter systems function as passive materials or as coordinated machines--providing design principles for both synthetic and biological systems. increasing bundle length from 0.9 {micro}m to 5 {micro}m increasing bundle length from 0.9 {micro}m to 5 {micro}m

biophysics↗

bioRxiv2025

Scaling Molecular Representation Learning with Hierarchical Mixture-of-Experts

Recent advancements in large-scale self-supervised pretraining have significantly improved molecular representation learning, yet challenges persist, particularly when addressing distributional shifts (e.g., under scaffold-split). Drawing inspiration from the success of Mixture-of-Experts (MoE) networks in NLP, we introduce H-MoE, a hierarchical MoE model tailored for molecular representation learning. Since conventional routing strategies struggle to capture global molecular information--such as scaffold structures, which are crucial for enhancing generalization--we propose a hierarchical routing mechanism. This mechanism first utilizes scaffold-level structural guidance before refining molecular characteristics at the atomic level. To optimize expert assignment, we incorporate scaffold routing contrastive loss, ensuring scaffold-consistent routing while preserving discriminability across molecular categories. Furthermore, a curriculum learning approach and dynamic expert allocation strategy are employed to enhance adaptability. Extensive experiments on molecular property prediction tasks demonstrate the effectiveness of our method in capturing molecular diversity and improving generalization across different tasks.

bioinformatics↗

bioRxiv2025

Genomics of sable (Martes zibellina) x pine marten (Martes martes) hybridization

The sable (Martes zibellina) and pine marten (Martes martes) are two Palearctic mustelids with long-recognized hybrids (kidases), whose fertility was controversial for years. Early genetic studies confirmed hybrids beyond F1, but details remained unclear due to low-resolution methods. Both species were hunted for centuries, but anthropogenic pressures during the 20th-century caused severe bottlenecks in the sable followed by hunting bans and large-scale reintroduction programs across much of its range, including the sympatric zone, potentially affecting hybridization. We resequenced 30 individuals from most of the sables range and Eastern part of pine martens. Among samples, we found a broad spectrum of hybrid types with mosaic recombinant chromosomes that confirm hybrid fertility and indicate crossover is not suppressed in kidases. This necessitates re-evaluation of previous research, as we detected notable discrepancies between STR-based ancestry and whole-genome analysis. In pine martens, we revealed mitochondrial DNA introgression from sables, indicating displacement of native pine marten mitochondrial sequences. Pine marten heterozygosity is relatively low ([~]0.5-0.6 hetSNPs/kbp) while sable diversity ([~]1.5-1.8 hetSNPs/kbp) is unexpectedly high for a species with its demographic history, likely reflecting successful reintroduction programs. We dated species divergence at 1.52 (CI: 1.05-2.06) Mya and identified candidate genes associated with ecological, morphological, and dietary differences, as well as hybrid fertility issues. This study is the first to elucidate marten hybridization at the whole-genome level, opening new research directions for understanding hybridization among Holarctic martens, the genetic consequences of reintroduction programs, and comparative adaptomics.

genomics↗

bioRxiv2025

B7-H4 Binds Galectin-9 Glycosylation-Dependently and Attenuates Galectin-9-Mediated CD28/AKT Activation and T Cell Death

B7-H4, a member of the B7 family, is broadly expressed on various cancer cells and has been implicated in negative immune regulation, particularly in suppressing anti-tumor immunity. However, the receptor for B7-H4 and the molecular mechanisms underlying its immunoinhibitory effects remain poorly understood. In this study, using peritoneal immune cells from mice adoptively transferred with OVA-expressing tumor cells and OVA-specific OT-1 T cells, we identified Galectin-9 (Gal-9) as a binding partner for B7-H4 and elucidated its role in modulating T cell responses through this interaction. We demonstrated that glycosylation in the IgC domain of B7-H4 is required for its binding to Gal-9; while the N-terminal carbohydrate recognition domain (N-CRD) of Gal-9, including the R65 residue in the N-CRD, is essential for this interaction. Additionally, we found that other B7 family members (B7.1, B7.2, B7-H2, and B7-DC) and immune cell surface receptors (CD28, 2B4, CD226, and SLAMF1) also bind to Gal-9 at comparable levels to B7-H4 and T cell immunoglobulin mucin receptor 3 (TIM-3). In vitro functional assays revealed that B7-H4 inhibits Gal-9-induced activation of CD28 downstream signaling and reduces Gal-9-mediated T cell death. In vivo, Gal-9 deficiency in mice resulted in a significant reduction in the proportion of splenic CD4+ T cells, whereas B7-H4 deficiency exhibited no observable phenotype. Furthermore, B7-H4 and Gal-9 double-knockout mice displayed no additional phenotype differences compared to Gal-9 single-knockout mice. Notably, tumor growth following tumor cell challenge was unaffected in all three knockout models (Gal-9 single-, B7-H4 single-, or double-knockout). Collectively, these findings suggest that B7-H4, other B7 family members, Gal-9, and T cell surface immune receptors form a complex regulatory network that modulates T cell activity and anti-tumor responses, although no single member exerts a major effect. This study provides a detailed molecular characterization of the interaction between B7-H4 and Gal-9 and identifies other previously unknown Gal-9 binding partners, offering valuable insights into the intricate regulatory network involving these molecules.

immunology↗

bioRxiv2025

BioinAI: a general bioinformatic framework for multi-level transcriptomic data analysis using multiple semi-agents

Clinical and biological insights from large-scale transcriptomic data are often limited by technical variability and analytical complexity. Here, we introduce BioinAI, a general bioinformatic framework designed for multi-level transcriptomic data analysis. As part of the BioinAI framework, two algorithms named DeepAdvancer and stNiche were developed to improve data integration and analytical efficiency. DeepAdvancer leverages a class-aware adversarial autoencoder to reconstruct gene-expression profiles from 49,738 samples across 131 skin conditions. These profiles revealed a conserved inflammatory axis and a transcriptomic continuum which link diverse diseases through shared immune responses and structural programs. stNiche leverages spatial graph networks and symmetry-aware matching to identify functional cellular niches and reveals microstructural alterations across development, homeostasis, and disease. For instance, it identified a fibroblast-immune niche surrounding hair follicles in healthy skin, which disappears in pathological states. In addition, BioinAI provides a user-friendly online analysis platform powered by multiple semi-agents (www.bioinai.com), significantly facilitating the extraction of biological insights to advance scientific research.

bioinformatics↗

bioRxiv2025

TIGAR DEFICIENCY ENHANCES CARDIAC RESILIENCE THROUGH EPIGENETIC PROGRAMMING OF PARKIN EXPRESSION

BACKGROUNDWhile mitochondrial dysfunction clearly drives cardiac deterioration in major heart diseases, the mechanisms controlling mitochondrial quality remain incompletely understood. This study investigated whether TIGAR (TP53-induced glycolysis and apoptosis regulator) deficiency influences cardiac protection through mitochondrial quality control pathways. METHODSWe generated both whole-body and cardiomyocyte-specific TIGAR knockout mice that were assessed for cardiac function following myocardial infarction (induced by left anterior descending coronary artery ligation) and diet-induced cardiomyopathy (using a 6-month high-fat diet protocol). Mitochondrial quality control was evaluated through mitophagy assays, subcellular fractionation, and molecular analyses. Epigenetic regulation was assessed using whole-genome bisulfite sequencing, chromatin immunoprecipitation, and CRISPR-mediated gene editing in multiple cell lines. RESULTSBoth whole-body (TKO) and cardiomyocyte-specific (hTKO) TIGAR knockout mice demonstrated cardioprotection following myocardial infarction. These animals maintained significantly better ejection fraction (43.35{+/-}17.76% vs 26.36{+/-}9.83% in wild-type controls, P<0.05) and displayed complete resistance to diet-induced cardiac hypertrophy, despite comparable weight gain. TIGAR deficiency led to dramatic increases in Parkin expression across multiple tissues, 6-fold increases in heart and muscle, and 5-fold increases in brain, which enhanced mitophagic responses during metabolic stress conditions including fasting and high-fat diet feeding. Generation of Parkin/TIGAR double knockout mice eliminated this protection, confirming Parkins essential role. Notably, adult manipulation of TIGAR through viral overexpression or knockdown failed to alter Parkin levels, suggesting developmental programming. Whole-genome bisulfite sequencing revealed reduced DNA methylation in a specific 3.2 kb region within Parkin gene intron 10, and CRISPR deletion of this regulatory region increased Parkin expression 10-fold in C2C12 myoblasts and 6-fold in 3T3-L1 fibroblasts. CONCLUSIONSThese findings reveal a novel TIGAR-Parkin regulatory axis operating through epigenetic mechanisms during cardiac development to establish lifelong cardioprotection via enhanced mitochondrial quality control. This discovery points toward new therapeutic approaches targeting developmental metabolic programming for heart disease prevention and identifies specific epigenetic targets for cardiovascular therapy. CLINICAL PERSPECTIVEO_ST_ABSWhat Is New?C_ST_ABSO_LITIGAR deficiency establishes lifelong cardiac protection through developmental epigenetic programming of Parkin expression. C_LIO_LIA novel 3.2 kb differentially methylated region in Parkin intron 10 regulates mitochondrial quality control in the heart. C_LIO_LIEarly metabolic programming during cardiac development can establish permanent cardioprotective phenotypes. C_LIO_LIThe TIGAR-Parkin axis provides protection against both acute ischemic injury and chronic metabolic cardiomyopathy. C_LI What Are the Clinical Implications?O_LITargeting the TIGAR-Parkin pathway could provide novel therapeutic approaches for preventing both ischemic heart disease and diabetic cardiomyopathy. C_LIO_LIEarly developmental interventions targeting cardiac metabolism might establish lifelong cardiovascular protection. C_LIO_LIEpigenetic modifications of mitochondrial quality control genes represent potential therapeutic targets. C_LIO_LIThe findings suggest optimal timing for cardiovascular preventive interventions may be during critical developmental windows. C_LI

molecular biology↗

bioRxiv2025

Host Microenvironment Reprogramming by Saccharides Overcomes Lung Barriers for mRNA Therapeutics

AbstractOvercoming biological barriers remains the paramount challenge for pulmonary mRNA therapeutics. Conventional approaches focus exclusively on passively optimizing formulation quality without controlling dynamic host barriers. Here, we pioneer a host-centric strategy by leveraging sugar that actively reprograms the airway microenvironment to boost IVT-mRNA transfection. Utilizing machine learning-accelerated screening of a chemically diverse saccharide library, we identify D-glucose as the best-performing candidate. Glucose assisted-delivery within lipid nanoparticles (Glu-LNP) achieves robust, lung-specific protein expression (up to 131.21-fold increase) across diverse preclinical models with reduced inflammation. In lung carcinoma models, Glu-LNP-encapsulated IL-12 mRNA reduced tumor burden by approximately 59.12% and improved survival by 2.5-fold compared to the LNP group. Mechanistically, glucose orchestrates a dual-pathway cascade: metabolic reprogramming via the Warburg effect elevates ATP, fueling endocytosis and translation; ATP further activates the P2Y2-IP3 signaling axis that triggers Ca2+ release and subsequent CLCA1/TMEM16A-dependent chloride/bicarbonate efflux, which remodels mucus barriers and enhances nanoparticle penetration. This bioenergetic and mucolytic host intervention strategy presents a broadly applicable paradigm to transcend delivery limitations for respiratory mRNA therapeutics.

bioengineering↗

bioRxiv2025

Methyl gallate Attenuates Post-Stroke Emotional and Cognitive Symptoms by Promoting Hippocampal Neurogenesis via PI3K/GSK3 and AMPK Signaling

Restoring hippocampal neurogenesis is an effective strategy for post-stroke recovery. Methyl gallate (MET) exhibits neuroprotective properties. However, the effect of MET in improving brain functional recovery in the post-stroke depression (PSD) model and its underlying mechanism remains unknown. Single-cell data analysis showed that the cell types and molecular characteristics of PSD are similar to those of primary depression but exhibit weaker synaptic plasticity and stronger inflammatory signals. In addition, molecular docking studies revealed that MET exhibits a significant binding capacity with AMPK/GSK3, suggesting that MET mediates the neuroprotective effects of both. In this study, we created a post-stroke depression (PSD) model by performing physical restraint after ischemia and tested the treatment effects of MET. We observed that MET significantly attenuated PSD-induced depressive-/anxiety-behaviors associated with a reduction of stress hormone corticosterone and ACTH levels. Morris water maze and recognition task results indicate that MET can also alleviate cognitive impairments in the PSD model. In the hippocampus of the PSD model, MET improved the proliferation and differentiation of neural stem/progenitor cells (NSPCs). MET treatment significantly enhanced the activity of AMPK and decreased the activity of GSK3{beta}. Furthermore, in primary neural progenitors under hypoxia, both the PI3K inhibitor LY294002 and the AMPK inhibitor compound C blocked the effects of MET to promote neural development. Animal experiments also confirmed that LY294002/compound C treatment could reduce the effects of MET in antidepressant behaviours. Taken together, our results indicate that PI3K, as well as AMPK-mediated adult neurogenesis, is restored by MET to improve brain functions in the PSD model.

neuroscience↗

bioRxiv2025

Measure Sodium Transport in Cells with NMR

Sodium ions (Na+) are fundamental to numerous physiological functions, such as maintaining electrolyte balance, enabling nerve impulse transmission, and facilitating muscle contraction. Dysregulation of Na+ transport across cell membranes is implicated in a range of health issues, including metabolic syndromes, neurological conditions, and cardiovascular diseases. However, current methods for assessing cellular Na+ activity often face limitations; they can be invasive or fail to capture dynamic changes. In this study, we introduce a non-invasive 23Na nuclear magnetic resonance (NMR) methodology designed to directly quantify the transport rate of sodium ions in living cells. Our technique integrates relaxation exchange spectroscopy (REXSY) with a multi-site exchange model, enabling the investigation of Na+ transport dynamics on a timescale of sub-seconds. A key advantage is its ability to differentiate between intracellular and extracellular Na+ pools based on the endogenous NMR relaxation difference, thereby avoiding the need for potentially disruptive exogenous reagents. Experiments conducted on human cell lines successfully demonstrated the techniques capacity to distinguish between various physiological states, such as when ion channels are pharmacologically blocked or activated. The resulting measurements of Na+ transport rates and intracellular Na+ fractions show a clear correlation with cellular metabolic activity, offering valuable quantitative markers for monitoring transmembrane ion dynamics in vitro.

cell biology↗

bioRxiv2025

GABA-independent activation of GABAB receptor by mechanical forces

The heterodimeric GABAB receptor, composed of GB1 and GB2 subunits, is a metabotropic G protein-coupled receptor (GPCR) activated by the neurotransmitter GABA. GABA binds to the extracellular domain of GB1 to activate G proteins through GB2. Here we show that GABAB receptors can be activated by mechanical forces, such as traction force and shear stress, in a GABA-independent manner. This GABA-independent mechano-activation of GABAB receptor is mediated by a direct interaction between integrins and the extracellular domain of GB1, indicating that GABAB receptor and integrin form a novel type of mechano-transduction complex. Mechanistically, shear stress promotes the binding of integrin to GB1 and induces an allosteric re-arrangement of GABAB receptor transmembrane domains towards an active conformation, culminating in receptor activation. Furthermore, we demonstrate that shear stress-induced GABAB receptor activation plays a crucial role in astrocyte remodeling. These findings reveal a previously unrecognized function of GABAB receptor in mechano-transduction, uncovering a novel ligand-independent activation mechanism for GPCRs.

neuroscience↗

bioRxiv2025

Single-cell Characterization of DNA Hydroxymethylation of the Mouse Brain During Aging

DNA methylation dynamics, including 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC), critically regulate brain function, yet conventional methods cannot distinguish these modifications, obscuring their distinct roles in gene regulation and aging. We present Joint- Cabernet, a bisulfite-free single-cell platform enabling simultaneous profiling of 5hmC, 5mC, and transcriptomes. Applying Joint-Cabernet to 84,071 nuclei from adult and aged mouse brains, we resolved cell-type-specific DNA hydroxymethylation landscapes, revealing elevated 5hmCG and 5hmCH levels in transcriptionally active genes across neuronal subtypes and spatial gradients in cortical layers. During aging, 5hmCG accumulates globally but is selectively enriched at open chromatin loci, aligning with the upregulation of cell-type-specific genes in distinct brain cell types. This single-cell DNA methylation brain cell atlas provides a framework for studying methylation- driven mechanisms in brain aging and neurodegenerative diseases.

genetics↗

bioRxiv2025

NUSAP1 regulates mitotic processes via KIF2C interaction and AURKA phosphorylation in primary microcephaly

Primary microcephaly (PM) is a neurodevelopmental disorder characterized by a significantly smaller head than normal. Despite the identification of several genes associated with PM subtypes, the etiology remains unclear in a significant proportion of patients. Here, we reported two de novo nonsense mutations in the NUSAP1 gene identified in two independent PM families: c.1209 C>G (p.Tyr403*) and c.1213C>T (p.Gln405*). Nusap1-edited mouse models, designed to mimic Human NUSAP1 mutations, replicated the microcephaly phenotype, characterized by a small brain and thinner cerebral cortex. We demonstrated that Nusap1 was specifically expressed in neural stem/progenitor cells (NSPCs), and the number of NSPCs was significantly reduced in Nusap1-edited mice. In vitro experiments revealed that NUSAP1 mutations disrupted mitotic metaphase chromosome alignment, increased polyploidy, induced cell cycle arrest, and promoted apoptosis. Co-IP confirmed direct interactions between NUSAP1 and KIF2C, and showed that truncating mutations impaired their binding. Furthermore, NUSAP1 rescued the cell cycle arrest and increased apoptosis caused by KIF2C overexpression in NUSAP1 KO HEK293T cells, whereas the mutant truncated protein failed to exert such a rescue effect. We also uncovered an interaction between NUSAP1 and Aurora kinase A (AURKA). Intriguingly, subsequent experiments revealed that AURKA-mediated phosphorylation of NUSAP1 modulates its binding affinity to KIF2C. In conclusion, our findings established NUSAP1 as a novel pathogenic gene for PM. We proposed a model in which AURKA-mediated phosphorylation of NUSAP1 regulates its interaction with KIF2C, balancing spindle microtubule stability and depolymerization to ensure proper sister chromatid segregation. Disruptions in this pathway impair NSPCs mitosis, thereby affecting neocortical development.

genetics↗

bioRxiv2025

scTransMIL Bridges Patient-Level Phenotypes and Single-Cell Transcriptomics for Cancer Screening and Heterogeneity Inference

Single-cell sequencing technology has revolutionized cancer research by revealing unprecedented insights into tumor heterogeneity. However, reliably connecting patient-level cancer phenotypes with single-cell transcriptomic profiles remains challenging, due to technical constraints and labeling ambiguity. This further hinders the precise cancer screening and intensive study of tumor mechanism based on single-cell sequencing. To bridge this gap, we introduce scTransMIL, a scRNA-seq Transformer-based Multi-Instance Learning framework that learns whole-genome context to deliver comprehensive cancer insights at the sample, cell, and gene levels across three biological scales: (1) accurate patient-level cancer phenotype prediction, (2) precise single-cell disease scoring (validated on 4 million single cells), and (3) genome-wide biomarker discovery. Benchmark experiments demonstrate scTransMILs exceptional performance, including robust out-of-distribution generalization and clinically relevant prediction of metastatic tissue-of-origin, a crucial capability for identifying cancers of unknow primary. At single-cell resolution, scTransMIL identified both known and novel biomarkers for tumor B cells that conventional differential expression analysis failed to detect while maintaining consistent concordance with malignant cell annotations. scTransMILs adaptability is exemplified in acute myelocytic leukemia, where minimal fine-tuning with only a few patient sample labels enabled: (i) discovery of novel disease subtypes with distinct clinical outcomes, (ii) reconstruction of differentiation trajectories at the single-cell resolution, and (iii) identification of subtype-specific gene signatures. In summary, by systematically linking cellular and molecular profiles with clinical disease phenotypes, scTransMIL emerges as a transformative tool poised to advance both basic cancer research and precision oncology applications.

bioinformatics↗

bioRxiv2025

LPS/TLR4-Activating Exosomes from M1-Polarized Avian Macrophages Enhances IBV Vaccine-Induced Protective Immunity in Chickens

Infectious bronchitis virus (IBV) presents a substantial economic burden to poultry production due to extensive serotypic diversity and limited cross-protection afforded by conventional vaccines. This study evaluated exosomes derived from M1-polarized chicken macrophages (HD11M1-exo) as a novel adjuvant for IBV vaccination. HD11M1-exo, isolated from LPS-activated HD11 macrophages via ultracentrifugation, demonstrated significant immunomodulatory properties across multiple experimental systems. In vitro analyses revealed HD11M1-exo enhanced macrophage phagocytosis and cellular immune activation via the LPS/TLR4 signaling pathway. In embryonated eggs, HD11M1-exo pre-treatment induced TNF- upregulation, enhanced viral resistance, and reduced pathological damage. In chickens, HD11M1-exo administration elevated CD80/CD86 and TGF-{beta}4 expression in respiratory tissues and increased secretory IgA in lacrimal fluid. When combined with H120 vaccine, HD11M1-exo significantly augmented both humoral immunity (elevated serum IgY and mucosal IgA) and cellular responses (increased CD80/CD86 expression), surpassing commercial adjuvants in efficacy. Following viral challenge, HD11M1-exo+H120 immunized chickens exhibited significantly reduced viral loads and attenuated histopathology compared to controls. These data collectively suggest that exosome-based formulations may serve as effective adjuvants for enhancing poultry vaccine immunogenicity and protective efficacy.

immunology↗

bioRxiv2025

Altered laminin signaling destinates melanocyte reprogramming in vitiligo

Vitiligo is an acquired depigmenting skin disorder characterized by progressive melanocyte loss, but the cellular mechanisms driving this process remain unclear. Here, we identify melanocyte dedifferentiation as a central and reversible pathogenic mechanism in vitiligo. In healthy human skin, melanocytes reside within a basement membrane niche defined by dystroglycan-laminin-211 adhesion. In contrast, vitiligo lesions exhibit aberrant extracellular matrix remodeling, leading to an adhesion switch to integrin 3{beta}1-laminin-332 interactions. This shift promotes melanocyte dedifferentiation via Rho-F-actin-dependent activation of Hippo and MAPK pathways, resulting in c-Jun-mediated transcriptional changes. Dedifferentiated melanocytes lose their pigment-producing identity and acquire neural crest-like features with multilineage potential. Importantly, this process is reversible. Pharmacological inhibition of involved pathways restores melanocyte differentiation and induces repigmentation in both vitiligo mouse models and ex vivo patient skin. Notably, JAK inhibitors also promote redifferentiation independently of immune modulation. These findings uncover melanocyte dedifferentiation as a fundamental driver of vitiligo and a tractable therapeutic target, offering new opportunities for therapeutic intervention.

cell biology↗