Biology subjects

Gao, X.

Publications and source records attributed to Gao, X..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Genome-wide CRISPR screen reveals PEX11B as a host restriction factor against ORFV through membrane fluidity regulation

Host-pathogen interactions are shaped by cellular restriction factors that direct antiviral defenses. We built the first ovine genome-wide CRISPR knockout library in sheep testis (OA3.Ts) cells, targeting all protein-coding genes. Using this platform, we identified PEX11B, a peroxisomal membrane regulatory protein, as a strong restriction factor against orf virus (ORFV) infection. Removing PEX11B increased viral susceptibility and triggered severe cytopathic effects with membrane fusion and syncytia formation. Mechanistic studies showed that PEX11B knockout harmed peroxisomal integrity and disrupted lipid metabolism. This led to greater plasma membrane fluidity, creating a proviral environment that allowed more viral entry and replication. These results reveal a new antiviral function for PEX11B in blocking viral infection and underscore the importance of peroxisomal regulation in host-virus interactions.

microbiology↗

bioRxiv2025

Efficient Identification of Short Tandem Repeats via Context-Aware Motif Discovery and Ultra-Fast Sequence Alignment

Tandem repeats (TRs) are highly polymorphic genomic elements, associated with diverse molecular traits and implicated in numerous human diseases. However, large-scale analysis of TRs has been limited by computational challenges, including motif recognition, detection in complex regions, and excessive computational cost. Here we present FastSTR, a computationally efficient tool for precise detection and characterization of TRs. FastSTR integrates a context-aware N-gram motif model with a segmented global alignment algorithm to enable accurate motif identification and boundary definition, even for repeat units up to 8 bp. Across 13 species, FastSTR achieved >90% recall and 99% precision, running several times faster than existing methods white outperforming them in both sensitivity and accuracy. Applied to the human genome, FastSTR uncovered previously unannotated HSATII elements, resolved population-specific TR demonstrate, and identified recurrent STR alterations in lung cancer. These results demonstrate FastSTR as a versatile framework for TR annotation and discovery, advancing studies of genome evolution, genetic diversity, and disease.

bioinformatics↗

bioRxiv2025

Integrated Bioinformatics analysis and Metabolomic Responses in finding novel therapeutic approach to treat viral myocarditis

BackgroundMyocarditis is one of the most common health problems in young people. Despite imaging techniques and endomyocardial biopsies advancing, there is still inadequate for myocarditis characterization. Some studies have shown that myocarditis is closely associated with mitochondrial dysfunction. Therefore, this study was aimed to identify mitochondrial-related biomarkers and gene regulatory networks in myocarditis and potential therapeutic targets. MethodsWe downloaded GSE95368 dataset from GEO to get myocarditis gene expression profiles, then used EdgeR and AI algorithm for bioinformatics analysis of DEGs functions. Established CVB3-induced mouse myocarditis model via intraperitoneal injection, and assessed energy metabolism differences using targeted metabolomics. CVB3 stimulus induced myocarditis in H9C2 cells. We assessed mitochondrial dysfunction (ATP, MMP) with commercial kits, MAPK8 release via ELISA, and MAPK8, p-PI3K, p-AKT levels by western blot. Furthermore, a total of 8 patients primarily diagnosed with myocarditis were enrolled, and levels of MAPK8 and CK in serum were detected. SP600125, an inhibitor of MAPK8, was administrated to CVB3-infected mice to study its potential protective effect in viral myocarditis. ResultsWe obtained 77 DEGs enriched in myocarditis. Analysis yielded 11 modules, MEpurple module genes linked to myocarditis progression were identified via WGCNA. MAPK8, NAMPT and ALB are associated with mitochondrial function. CVB3-infected mice showed cardiac inflammation and high MAPK8 expression in serum or heart tissues.The target metabolism results indicated altered central carbon metabolism distinguished CVB3 group from control, with higher D-Glucose-1-phosphate and D-Glucose-6-phosphate and lower L-Cystine, dCMP, IMP and Xylulose-5-phosphate levels. CVB3 treatment caused mitochondrial dysfunction in H9C2 cells (decreased ATP, MMP), and increased MAPK expression. Western blot showed MAPK8 consolidated the levels of p-PI3K and p-AKT. CK activity was notably higher in myocarditis patients than healthy individuals. MAPK8 levels in myocarditis patients serum also exceeded those in healthy individuals. Pearson analysis indicated that MAPK8 and CK may contribute to myocarditis progression via distinct mechanisms. In CVB3-infected mouse model with SP600125 treatment, cardiac inflammation and MAPK8, p-PI3k, p-AKT expression were reduced, confirming MAPK8s crucial role in viral myocarditis. ConclusionOur study identified MAPK8 as a key biomarker of myocarditis, and it may be a potential therapeutic target for myocarditis.

pathology↗

bioRxiv2025

Carbohydrate adaptation drives liver-brain axis maturation

Mammalian postnatal life requires adaptation to a carbohydrate-rich diet, yet how metabolic programs are coordinated within and across organs is unclear. Using time-resolved transcriptomic and metabolomic analyses from the neonatal period through adulthood, we show that mouse liver rapidly acquires oxidative and detoxification capacity after weaning. This transition enables the brain to establish energy-sufficient, low-toxicity metabolic environment for neuronal development. This maturation process is marked by progressive activation of the hepatic electron transport chain (ETC), with the mitochondrial RNA endoribonuclease LACTB2 acting as a key regulator. LACTB2 prevents the accumulation of mitochondrial RNAs and sustains expression of mtDNA-encoded ETC subunits, thereby preserving mitochondrial competence for oxidative metabolism. LACTB2 is postnatally induced in hepatocytes, and its loss causes defective glucose utilization, systemic metabolic toxicity, and impaired brain metabolism and myelination, leading to prepubertal lethality, particularly in males. Restoring ETC function through liver-targeted expression of yeast NADH dehydrogenase NDI1, inhibiting the integrated stress response or ammonia scavenging improved survival. Our findings identify LACTB2-dependent hepatic mitochondrial maturation as a central mechanism that aligns carbohydrate adaptation with the liver-brain metabolic coordination to support early-life development.

developmental biology↗

bioRxiv2025

Rank- and Threat-Dependent Social Modulation of Innate Defensive Behaviors

Fear and defense are among the most fundamental survival behaviors and are profoundly influenced by the social environment in group-living animals. However, it remains poorly understood how social context--and particularly dominance hierarchy, a defining feature of many social species--modulates defensive strategies under ethologically relevant conditions. To address this question, we investigated the social modulation of innate fear in mice exposed to two ethologically relevant threats: a transient visual looming stimulus and a sustained predatory threat posed by a live rat. We found that social presence alleviated threat-induced stress and modulated defensive behaviors in a rank- and threat-specific manner. During looming exposure, it reduced immediate defensive responses and alleviated post-looming anxiety, with dominants showing greater benefit. During rat exposure, it promoted a shift from passive to active defense, again most prominently in dominants. These behavioral changes were accompanied by reorganization of transitions between defensive states, indicating that social hierarchy shapes both the expression and temporal organization of innate defensive behaviors. Conversely, threat exposure strengthened social engagement, with dominant mice exhibiting more proactive social behaviors and subordinate mice responding more readily to dominant social initiations. Together, these findings demonstrate how dominance hierarchy modulates defensive responses to distinct naturalistic threats and, in turn, how threat experience shapes social behavior, providing a behavioral framework for probing the neural basis of socially modulated innate fear.

neuroscience↗

bioRxiv2025

Universal super-resolution for subcellular fluorescence imaging

Super-resolution fluorescence microscopy has emerged as an essential instrument for investigating subcellular structures and monitoring intracellular physiology. Despite rapid advances driven by deep learning, most existing approaches are modality specific and exhibit limited generalizability, restricting their practical applicability. Here we introduce universal super-resolution (UniSR), a framework that operates across microscopes and subcellular structures without optical modifications or prior sample knowledge. UniSR is initially pre-trained on simulated image pairs to establish mappings from low-to high-resolution features and subsequently fine-tuned with only one experimental image pair, reducing data demand and acquisition time. Across wide-field and point-scanning modalities, UniSR enhances resolution to match structured illumination, single-molecule localization, or stimulated emission depletion microscopy. Applied to diverse biological samples, it reveals nanoscale structures, dynamic processes, and organelle interactions with high spatiotemporal fidelity. UniSR provides a practical and broadly generalizable tool for super-resolution imaging in live-cell research.

bioinformatics↗

bioRxiv2025

Asymmetric Spring and Autumn Phenology Control Growing Season Length in Temperate Deciduous Forests

Forest phenological responses to climatic variation among species and populations across broad spatial scales remain poorly understood. Here, we quantify four decades of phenological dynamics for 10 major deciduous tree species by compiling a unique dataset that integrates high spatial resolution remote sensing with extensive field inventory data across the Northeastern and Midwestern United States. We found that spring and autumn phenology impose asymmetric controls on growing season length, with spring regulating interannual variation and autumn driving long-term trends. Spring phenology across all species was primarily controlled by temperature, while autumn phenology was influenced by spring phenology and an interacting suite of species-specific environmental factors. Our study demonstrates the promise of combining high resolution remote sensing with forest inventory data to investigate phenological dynamics over large regions. More importantly, our results provide new insights into how species-specific sensitivities to environmental drivers regulate growing season length in temperate forests.

ecology↗

bioRxiv2025

Division Asymmetry Drives Cell Size Variability in Budding Yeast

Cell size variability within proliferating populations reflects the interdependent regulation of cell growth and division as well as intrinsically stochastic effects. In budding yeast, the G1/S transition exerts strong size control in daughter cells, which manifests as the inverse correlation between how big a cell is when it is born and how much it grows in G1. However, mutations affecting this size control checkpoint only modestly influence population-wide size variability, often altering the coefficient of variation (CV) only by [~]10%. To resolve this paradox, we combine computational modeling and live-cell imaging to identify the principal determinants of cell size variability. Using an experimentally validated stochastic model of the yeast cell cycle, we perform parameter sensitivity analysis and find that division asymmetry between mothers and daughters is the dominant driver of CV, outweighing the effects of G1/S size control. Experimental measurements across genetic perturbations and growth conditions confirm a strong correlation between mother-daughter size asymmetry and population CV. These findings reconcile previous observations and show how asymmetric division operates in concert with G1/S size control to govern cell size heterogeneity.

cell biology↗

bioRxiv2025

Engineering Treg-mediated immune tolerance via foxp3a overexpression to evade allograft transplantation barriers in zebrafish

In mammals, regulatory T cells (Treg) cells have been utilized to enhance tolerance in organ transplantation. Although transplanting germline stem cells (GSCs) or gonadal primordia into immunodeficient zebrafish have shown to be an important technique which can bypass the juvenile phase and expedite gamete generation, it remains challenging to raise the immunodeficient fish. Here, we achieved in vivo induction of Tregs by overexpressing the key transcription factor Foxp3a, generating transgenic zebrafish with robust immune tolerance. This was characterized by a significant downregulation of T cell development and homing-related genes, accompanied by a marked upregulation of immunosuppressive factors. Using these immune-tolerant fish as hosts for subcutaneous gonadal primordium transplantation (SGPT) and intraperitoneal GSC transplantation (IGCT), we markedly accelerated germ cell maturation and efficiently established stable transgenic lines. Transcriptomic analyses demonstrated that transgenic hosts demonstrated a phenotypic profile characterized by delayed immune activation, attenuated responsiveness, and enhanced graft survival. Thus, we present a Treg-induction-based approach in fish that resolves the intrinsic conflict between high embryonic transgenesis efficiency and early lethality, while significantly improving overall transgenesis success rates. Moreover, it offers a practical alternative to immunodeficient recipients, avoiding the challenges of complex husbandry and compromised fertility.

genetics↗

bioRxiv2025

A Fkh1/2 binding site array in the WHI5 promoter drives sub-scaling transcription

Cells typically regulate their size within a relatively tight range by coupling growth to the cell division cycle using a dedicated set of molecular mechanisms. In budding yeast, cells are born with a similar amount of the G1/S inhibitor protein Whi5 that is then diluted by growth throughout G1. As cells grow, Whi5 concentration decreases and cells become more likely to enter the cell cycle. Cells are born in G1 with similar amounts of Whi5 because of the size-independent (sub-scaling) expression of WHI5 mRNA during S/G2/M phases and the equal partitioning of Whi5 protein at division. While the latter is known to be achieved by association with chromatin before anaphase, the mechanism for the former is poorly understood. Through systematic mutations of the WHI5 promoter, we discovered that WHI5s core promoter region located -126 to -75 base pairs upstream of the start codon is responsible for sub-scaling expression. This sequence contains a repeating array of binding sites for the transcription factors Fkh1 and Fkh2. Mutation of any of these sites, deletion of either FKH1 or FKH2, or preventing Fkh1 or Fkh2 dimerization weakens the sub-scaling of WHI5 transcription. Taken together with structural predictions and a mathematical model of cooperative Fkh-DNA binding, we conclude that WHI5s sub-scaling transcription is regulated by a Fkh1/2 heteropolymer binding an array of sites in its core promoter.

cell biology↗

bioRxiv2025

STRIDE: A Sequencing Depth-Insensitive Metric for Robust Comparison between Sparse Chromosome Conformation Capture Data

The study of three-dimensional (3D) genome organization has been revolutionized by high-throughput chromatin conformation capture technologies (Hi-C) or its derivatives. However, the dependency on sequencing depth severely restricts the reliability and accuracy of existing Hi-C tools, especially in single-cells. To address this issue, we introduce a novel computational framework based on the mean first passage time (MFPT) in Markov chain theory, which transforms chromatin contact matrices into a robust, distance-based representation. We demonstrate that MFPT representation is inherently insensitive to sequencing depth. Leveraging this transformation, we develop STRIDE (Spatial Topological Representation of Interaction Distance Evaluation), a parameter-free metric for library similarity. STRIDE is resilience to sparse and noisy data, insensitive to technical variabilities, and facilitates unsupervised embedding from single-cell Hi-C, enabling accurate delineation of cellular states and developmental trajectories. In conclusion, as a reliable computational framework for sparse and noisy data, STRIDE may serve as a base for wide range single-cell 3D genome analysis that used to be inconceivable.

bioinformatics↗

bioRxiv2025

Lineage Tracing Reveals a Shared Cellular Origin for Supraclavicular Brown and Inguinal Beige Adipocytes

The metabolic importance of brown adipose tissue (BAT) has been recognized, but the origins of BAT, particularly supraclavicular BAT (scBAT), are less clear. Here, we traced the origin of scBAT to Mef2c-anterior heart field (AHF)-marked cells. Mef2c-AHF-marked cells isolated from scBAT can spontaneously differentiate into brown adipocytes, express mesenchymal stem cell markers, and can be isolated from the stromal-vascular fraction (SVF) of wild-type scBAT as [CD31-CD45-SCA-1+CD29+CD34-CD24-] (CD34-) cells. Mef2c-AHF-marked cells substantially overlap with Prrx1-marked cells in scBAT, which also contribute to beige adipocytes in inguinal white adipose tissue (iWAT) during development. Similarly, CD34- cells isolated from the SVF of iWAT can spontaneously differentiate into beige adipocytes in vitro. Using intersectional tracing, we revealed that common progenitors of Mef2c-AHF- and Prrx1-marked cells in scBAT emerge from the developing heart. Thus, these studies reveal a common origin for scBAT and cardiac tissue and a close lineage relationship between scBAT and beige adipocytes of the iWAT.

developmental biology↗

bioRxiv2025

Water body size shapes body size evolution via subgenomic selection in allopolyploid fish

Allopolyploidization is a major force in species evolution, and studying allopolyploids in diverse environments provides insights into their genetic mechanisms. Here, we investigated how water body size variation influences body size in allopolyploid fish. We used a nascent allopolyploid lineage derived from goldfish (Carassius auratus) and common carp (Cyprinus carpio) and established two populations in small and large water bodies for two generations. Genomic, transcriptomic, and epigenomic analyses revealed that the larger population had higher genetic diversity in subgenome R, while the smaller population had higher diversity in subgenome C. Potential selection regions were associated with growth regulatory genes, suggesting a role for gene regulation in body size adaptation. Dynamic gene expression patterns in various tissues indicated potential mechanisms underlying muscle development and adaptation to smaller water bodies. Furthermore, selection regions were linked to changes in chromatin accessibility, with subgenome R being more susceptible to these changes during genetic divergence. Our findings demonstrate that water body size variation drives body size in allopolyploid fish through subgenomic selection, impacting genetic variation, gene regulation, and epigenetic mechanisms.

genomics↗

bioRxiv2025

Dietary methionine restriction primes T cell metabolism for activation and tumor inhibition and enhances the efficacy of immune checkpoint blockade

The proliferation of many cancer cells is methionine dependent and dietary methionine restriction (MR) has shown anti-tumor effects in a wide variety of immunodeficiency preclinical models. Yet, whether MR exerts an anti-tumor effect in the presence of an immune-competent background remains inconclusive. Accumulating evidence has shown an essential role of methionine in immune cell differentiation and function. Thus, competition for methionine between tumor cells and immune cells in the tumor microenvironment may drive tumor growth and tumor response to therapy. Here, we aim to define the impact of MR on tumor growth and associated immunity. We first assessed the effect of MR in a series of immunocompetent mouse models of melanoma, colorectal cancer, breast cancer, and lung. MR led to a broad tumor inhibition effect across these models and such tumor inhibition was not sex-or genetic background-dependent but appears to be fully or partially immune-dependent. Through flow cytometry analysis, we found a consistent increase in intratumoral activated CD8+ T cells across different tumor models and depletion of CD8+ T cells partially or completely reversed MR-induced tumor inhibition in a model dependent manner. Interestingly in young healthy non-tumor-bearing mice, MR increased spleen CD3+ and CD8+ T cell populations. Metabolomics and RNAseq analysis of spleen-derived CD8+ T cells revealed significant increase in purine metabolism and amino acid metabolism and that are in line with the metabolic feature of activated T cells. Furthermore, MR improved the efficacy of anti-PD1 immune checkpoint blockade. Together, MR primes T cell metabolism for its anti-tumor effect and improves the efficacy of anti-PD1 checkpoint blockade.

cell biology↗

bioRxiv2025

The Hypothalamic-Pituitary-Adrenal Axis Orchestrates Energy Homeostasis during Cold Exposure

Cold exposure stimulates the sympathetic nervous system (SNS) to activate brown fat thermogenesis and maintain optimal body temperature, while simultaneously triggering compensatory hyperphagia to restore energy balance. The mechanisms coordinating energy expenditure and intake, however, remain unclear. Here, we reveal that the hypothalamic-pituitary-adrenal (HPA) axis plays a dual role in this process: endogenous adrenocorticotropic hormone (ACTH) directly stimulates the melanocortin-2 receptor (MC2R) in brown adipocytes to promote thermogenesis, whereas glucocorticoids drive cold-induced hyperphagia and act permissively to enhance ACTH-mediated energy expenditure. These findings uncover previously unrecognized functions of the HPA axis and a delicate hormonal interplay that orchestrates energy homeostasis during cold stress. Targeting these pathways may offer novel strategies to mitigate hyperphagic responses associated with increased energy expenditure, with potential implications for obesity treatment. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/677113v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@1ac072forg.highwire.dtl.DTLVardef@10bc88corg.highwire.dtl.DTLVardef@9b9b5corg.highwire.dtl.DTLVardef@1f4e276_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIThe HPA axis orchestrates cold adaptation. C_LIO_LIACTH activates brown fat thermogenesis in vitro and in vivo via activating MC2R. C_LIO_LIGlucocorticoids drive cold-induced hyperphagia. C_LIO_LIGlucocorticoids have a permissive effect on ACTH function in brown adipocytes. C_LI

physiology↗

bioRxiv2025

Unify: Learning Cellular Evolution with Universal Multimodal Embeddings

Integrating single-cell RNA-sequencing (scRNA-seq) data across species is hindered by evolutionary divergence, technical batch effects, and the reliance on one-to-one orthologs. We present Unify, a transfer learning methodology that learns universal cell embeddings by defining functionally coherent, multi-modal macrogenes. This is achieved by combining RNA expression with embeddings from protein language models and general-purpose language models. Unify transcends species boundaries, enabling cross-species comparisons beyond strict gene-level homology. Unify corrects batch effects while preserving conserved biological signals across vast evolutionary distances and enables more accurate prediction of perturbation responses across species, such as from mouse to human. Applied to species separated by over 700 million years, Unify reconstructs more accurate multi-species cell-type evolutionary trees and uncovers convergent gene programs. Together, these results establish Unify as a powerful method for comparative single-cell genomics and evolutionary biology.

bioinformatics↗

bioRxiv2025

A Generative Foundation Model for Antibody Design

Antibodies are indispensable components of the immune system, yet the design of high-affinity antibodies remains a time-consuming and experimentally intensive process. To address this challenge, we present IgGM, a novel generative foundation model designed to accelerate high-affinity antibody engineering. IgGM learns the complex relationships underlying the binding interactions between antigens and antibodies, as well as the mapping between antibody sequences and structures. By conditioning on different inputs, IgGM supports a wide range of antibody design tasks, including complex structure prediction, inverse design, affinity maturation, framework optimization, humanization, and de novo antibody design. It is compatible with both conventional antibodies and nanobodies, and allows user-defined CDR loop lengths for flexible design. To prioritize candidates, we introduce a frequency-based computational screening strategy that enhances design efficiency. Extensive evaluation through both in silico benchmarks and in vitro experiments across diverse antigens such as PD-L1, Protein A, TNF-, IL-33, SARS-CoV-2 RBD and its variants demonstrates that IgGM consistently generates antibodies or nanobodies with high measured affinity. These results underscore IgGMs versatility and effectiveness as a powerful tool for next-generation antibody discovery and optimization.

bioinformatics↗

bioRxiv2025

Mechanical Memory Primes Cells for Confined Migration

When migratory cells move from one stiffness niche to another in vivo, they are exposed to highly confined spaces imposed by dense extracellular matrix (ECM) networks and inter-tissue boundaries. Cells that originate from one niche possess distinct mechanosensitive adaptations that influence their response to their new niche, a concept known as mechanical memory. However, the mechanisms by which this memory is acquired, and the degree to which it influences migratory potential and decision-making processes in confinement remain poorly understood. Here, we combine stiffness priming using polyacrylamide hydrogels with a confinement platform to screen mechanical memory across healthy and transformed cells. Using a dose-and- passage approach, we find that in stiffness-sensitive cells primed on soft substrates navigate confinement more efficiently. Bulk RNA sequencing identifies NFATC2 as a transcription factor that mediates mechanical memory by reprogramming gene expression in stiffness-sensitive cells. siRNA-induced knockdown of NFATC2 in memory-sensitive cells confirmed its necessity for mechanical memory acquisition and subsequent confined migration enhancement. Interestingly, highly invasive cancer cells exhibit minimal sensitivity to prior mechanical priming, suggesting differential adaptation strategies. These findings reveal mechanical memory as a cell-intrinsic property shaped by past mechanical environments and highlight potential implications for controlling migration in wound repair, fibrosis, and disease progression.

cell biology↗