Biology subjects

Zhou, W.

Publications and source records attributed to Zhou, W..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Organism-wide cellular dynamics and epigenomic remodeling in mammalian aging

To investigate organism-wide cellular alterations and epigenomic dynamics during aging, we constructed a single-cell chromatin accessibility atlas spanning 21 mouse tissues across three age groups and both sexes. We found that around one quarter of 536 organ-specific cell types and 1,828 finer-grained subtypes exhibited significant age-related population shifts. Cellular states from broadly distributed lineages displayed synchronized dynamics with age, indicating systemic signals that coordinate these changes. Molecular analyses identified both intrinsic regulators (chromatin peaks, transcription factor activity) and extrinsic factors (cytokine programs) underlying these shifts. Moreover, [~]40% of aging-associated population dynamics were sex-dependent, with tens of thousands of peaks altered exclusively in one sex. Together, these findings present a comprehensive framework for how aging reshapes the chromatin landscape and cellular composition across diverse tissues.

genomics↗

bioRxiv2025

EnrichSci: Transcript-guided Targeted Cell Enrichment for Scalable Single-Cell RNA Sequencing

Large-scale single-cell atlas efforts have revealed many aging-or disease-associated cell types, yet these populations are often underrepresented in heterogeneous tissues, limiting detailed molecular and dynamic analyses. To address this, we developed EnrichSci--a highly scalable, microfluidics-free platform that combines Hybridization Chain Reaction RNA FISH with combinatorial indexing to profile single -nucleus transcriptomes of targeted cell types with full gene-body coverage. When applied to profile oligodendrocytes in the aging mouse brain, EnrichSci uncovered aging-associated molecular dynamics across distinct oligodendrocyte subtypes, revealing both shared and subtype-specific gene expression changes. Additionally, we identified aging-associated exon-level signatures that are missed by conventional gene-level analyses, highlighting post-transcriptional regulation as a critical dimension of cell-state dynamics in aging. By coupling transcript-guided enrichment with a scalable sequencing workflow, EnrichSci provides a versatile approach to decode dynamic regulatory landscapes in diverse cell types from complex tissues.

genomics↗

bioRxiv2025

Spatiotemporal profiling reveals the impact of caloric restriction on mammalian brain aging

Aging induces functional declines in the mammalian brain, increasing its vulnerability to cognitive impairments and neurodegenerative disorders. Among various interventions to slow the aging process, caloric restriction (CR) has consistently demonstrated the ability to extend lifespan and enhance brain function across different species. Yet the precise molecular and cellular mechanisms by which CR benefits the aging brain remain elusive, especially at region-specific and cell type-specific resolution. In this study, we performed spatiotemporal profiling of mouse brains to elucidate the detailed mechanisms driving the anti-aging effects of CR. Utilizing highly scalable single-nucleus genomics and spatial transcriptomics platforms, EasySci and IRISeq, we profiled over 500,000 cells from 36 mouse brains across three age groups and conducted spatial transcriptomic analysis on twelve brain sections from aged mice under CR and control conditions. This comprehensive approach allowed us to explore the impact of CR on over 300 cellular states and assess region-specific molecular alterations. Our findings reveal that CR effectively modulates key aging-associated changes, notably by delaying the expansion of inflammatory cell populations and preserving cells critical to the neurovascular system and myelination pathways. Moreover, CR significantly reduced the expression of aging-associated genes involved in oxidative stress, unfolded protein stress, and DNA damage stress across various cell types and regions. A notable reduction in senescence-associated genes and restoration of circadian rhythm genes were observed, particularly in ventricles and white matter. Furthermore, CR exhibited region-specific restoration in genes linked to cognitive function and myelin maintenance, underscoring its targeted effects on brain aging. In summary, the integration of single-nucleus and spatial genomics provides a novel framework for understanding the complex effects of anti-aging interventions at the cellular and molecular levels, offering potential therapeutic targets for aging and neurodegenerative diseases.

genomics↗

bioRxiv2025

Uncovering Convergent Cell State Dynamics Across Divergent Genetic Perturbations Through Single-Cell High-Content CRISPR Screening

High-throughput genomic studies have uncovered associations between diverse genetic alterations and disease phenotypes; however, elucidating how perturbations in functionally disparate genes give rise to convergent cellular states remains challenging. Here, we present PerturbFate, a high-throughput, cost-effective, combinatorial-indexing single-cell platform that enables systematic interrogation of massively parallel CRISPR perturbations across the full spectrum of gene regulation, from chromatin remodeling and nascent transcription to steady-state transcriptomic phenotypes. Using PerturbFate, we profiled over 300,000 cultured melanoma cells to characterize multi-modal phenotypic and gene regulatory responses to perturbations in more than 140 Vemurafenib resistance-associated genes. We uncovered a shared dedifferentiated cell state marked by convergent transcription factor (TF) activity signatures across diverse genetic perturbations. Combined inhibition of cooperative TF hubs effectively reversed cellular adaptation to Vemurafenib treatment. We further dissected phenotypic responses to perturbations in Mediator Complex components, linking module-specific biochemical properties to convergent gene activations. Together, we reveal common regulatory nodes that drive similar phenotypic outcomes across distinct genetic perturbations. We also delineate how perturbations in functionally unrelated genes reshape cell state. PerturbFate thus establishes a versatile platform for identifying key molecular regulators by anchoring multi-modal regulatory dynamics to disease-relevant phenotypes.

genomics↗

bioRxiv2025

Complement receptor C3ar1 deficiency does not alter brain structure or functional connectivity across early life development

Genetic deletion of the complement C3a anaphylatoxin chemotactic receptor (C3ar1), a key component of the innate immune response, is reported to induce behavioural phenotypes consistent with psychiatric symptomatology in mice, but when and where C3ar1 is needed in the brain is unresolved. These questions are significant because, as a G-protein-coupled receptor, human C3AR1 serves as a potential therapeutic target for disorders associated with complement dysregulation, such as schizophrenia. To provide a brain-wide (where) assessment of developmental C3ar1 activity, we used longitudinal (when) tensor-based morphometry, diffusion-weighted magnetic resonance imaging (MRI) and blood oxygen-level dependent functional MRI in male and female C3ar1-deficient mice and wild-type littermates, with behavioural assessment in adulthood. Unexpectedly, we did not find a robust C3ar1-dependent phenotype in any of these measures. Therefore, our study does not support neurodevelopmental hypotheses for C3ar1, which is encouraging for therapeutic strategies targeting this receptor since interventions are unlikely to disrupt brain development.

neuroscience↗

bioRxiv2025

ER-tethering directs TREX1 penetration of a BAF-dependent barrier at micronuclei

Micronuclei are membrane-encapsulated nuclear aberrations that form following chromosome segregation errors. Micronuclear membrane collapse permits access of the pattern recognition receptor cGAS and its antagonist, the TREX1 exonuclease. TREX1 carboxy-terminal domain mediated endoplasmic reticulum tethering association is essential for invasion into ruptured micronuclei, however the mechanisms underlying this dependency are unknown. Here, we identify barrier-to-autointegration nuclear assembly factor 1 (BAF) as a key regulator of TREX1 activity at micronuclei. BAF accumulates on micronuclei following membrane collapse and augments TREX1 recruitment in a manner that depends on BAF interactions with membrane-associated LEM-domain proteins. Despite delayed entry, TREX1 exhibits enhanced micronuclear DNA degradation and independence from ER-tethering in BAF-deficient cells. In accordance, recombinant BAF protein inhibits TREX1-mediated DNA degradation in vitro in a manner that depends on BAF DNA-binding. BAF similarly outcompetes cGAS for micronuclear DNA interaction and reduces cGAS activation at micronuclei. These findings reveal, a BAF-dependent protective barrier to diffusive entry of DNA binding proteins at ruptured micronuclei, explaining the requirement of TREX1 ER-tethering for micronuclear localization and suppression of productive cGAS DNA substrate interactions that activate innate immune responses in chromosomally unstable cells.

molecular biology↗

bioRxiv2025

The Role of N-acetylcysteine Amide in Acute Graft-versus-host Disease Mouse Model

Graft-versus-host disease (GvHD) remains one of the major complications following allogeneic hematopoietic cell transplantation (allo-HCT), resulting in reduced quality of life, morbidity, and mortality in transplanted patients. Clinical strategies to prevent GvHD are frequently associated with off-target effects and dose-related toxicity. Given that oxidative stress is elevated in allo-HCT recipients and contributes to the pathogenesis of GvHD, the current study aims to characterize the role of N-acetylcysteine amide (NACA), a novel antioxidant, as the prophylactic treatment for acute GvHD. Using a murine GvHD model, we found that oral administration of NACA significantly reduced GvHD severity, prolonged survival, and improved the clinical manifestations and integrity of target organs compared to saline or N-acetylcysteine (NAC) treatment. NACA modulated splenic T cells differentiation with an increase in the regulatory (Treg) subset and a decrease in the cytotoxic (CD8+) subset. Moreover, inflammatory mediators, such as ROS and pro-inflammatory cytokines were downregulated by NACA treatment. In addition, NACA hindered donor T-cell proliferation in the recipients, and restrained Th1 and Th17, but not Th2 polarization. Importantly, NACA did not influence full donor engraftment in bone marrow and spleen. Taken together, our findings provide a new candidate for GvHD prophylactic treatment by targeting oxidative stress that can be easily translated to clinical use. Key PointsO_LINACA provides superior prophylactic effect against aGvHD compared to NAC in an allogeneic transplantation mouse model. C_LIO_LINACA treatment neither showed systemic toxicity nor altered the engraftment of the donor cells. C_LI

pharmacology and toxicology↗

bioRxiv2025

SLC44A1 deficiency impedes myelin development in the central nervous system

Axon-wrapping myelin sheath is essential for the proper functioning of the central nervous system (CNS). Defects in myelination occur in various neurodevelopmental disorders. Human deficiency of the solute carrier 44A1 (SLC44A1) causes a new type of childhood-onset neurodegeneration with leukoencephalopathy. Currently, there is no effective treatment for this devastating disease, and little is known about its pathological mechanisms. In this study we identified that SLC44A1 is enriched in oligodendrocytes and required for myelin development in the CNS of zebrafish and rodents, which is crucial for normal motor coordination and cognitive function. Defective oligodendroglial maturation and myelinogenesis can be visualized by in vivo time-lapse imaging in the spinal cord of zebrafish with Slc44a1b deficiency. Mechanistically, SLC44A1 deficiency disrupts the expression of genes involved in phosphatidylcholine production pathway, and subsequently inhibiting phospholipid biosynthesis and disturbing the lipid composition of myelin sheaths. More importantly, supplementation with citicoline, a natural choline metabolite, restores developmental myelination in SLC44A1-deficient animals. These findings demonstrate that SLC44A1 is essential for CNS myelination and citicoline supplementation represents a potential therapeutic strategy to address the developmental hypomyelination.

neuroscience↗

bioRxiv2025

Unveiling Gene Modules at Atlas Scale through Hierarchical Clustering of Single-Cell Data

A major challenge in scRNAseq analysis is how to recover the biologically meaningful cell ontology tree and conserved gene modules across datasets. Data integration and batch-effect correction have been the key to effectively analyze multiple datasets, but often fail to disentangle cell states in heterogeneous samples, such as in cancer and the immune system. Here we present super single cell clustering (SuperSCC), a novel algorithm that utilizes machine-learning models to discover cell identities and gene modules from multiple datasets without the need of data integration. Of note, SuperSCC can be implemented both in cell lineage and cell state level, thereby building the hierarchy of cell programs with specific cell identity and gene modules. Such information has the great potential to identify the shared rare populations across datasets regardless of batch effect and benefits label transfer for mapping cell labels from reference to query. We used SuperSCC to perform atlas level data analysis on more than 90 datasets and build a cell state map of complex tissue in healthy and diseased stages, such as human lung. We show that SuperSCC outperforms existing approaches in identifying cellular context, has better annotation accuracy, and outlines gene modules that indicate conserved immune cell status in lung microenvironments.

bioinformatics↗

bioRxiv2025

The hollow truth: ethylene-triggered ROS, PCD, senescence, and autophagy drive hollow stem formation

Hollow stems have independently evolved multiple times across the plant kingdom, and play crucial roles in plant development and various environmental adaptations. However, the mechanisms underlying stem hollowness remain poorly understood. Water spinach (Ipomoea aquatica) is one of the few hollow-stemmed plants in the Convolvulaceae family, and its hollow stems are essential for thriving in aquatic environments. Using histochemical staining and transcriptome analysis, we identified programmed cell death (PCD) is involved in cavity formation of water spinach shoot tips. Single-cell transcriptome analysis further revealed that ethylene and reactive oxygen species (ROS) drive and regulate this process by activating transcription factors IaNAC074, IaNAC087, IaNAC029, IaNTL9, and IaTGA9, which initiate PCD, senescence, and autophagy, collectively controlling cell death. These findings were validated through treatments with ethylene and ROS reagents in water spinach and transient expression in tobacco. Additionally, transcriptomic data suggest that these mechanisms may also play a role in hollow stem formation in bamboo, highlighting the conservation of PCD regulatory mechanisms in plant development. This work not only fills a major knowledge gap in the adaptive mechanisms of hollow stem formation but also opens new avenues for agricultural and ecological applications, offering strategies to enhance crop tolerance to flooding and accelerate crop growth.

plant biology↗

bioRxiv2025

Estimating the cis-heritability of gene expression using single cell expression profiles controls false positive rate of eGene detection

For gene expression traits, cis-genetic heritability can quantify the strength of genetic regulation in particular cell types, elucidating the cell-type-specificity of disease variants and genes. To estimate gene expression heritability, standard models require a single gene expression value per individual, forcing data from single cell RNA-sequencing (scRNA-seq) experiments to be "pseudobulked". Here, we show that applying standard heritability models to pseudobulk data overestimates gene expression heritability and produces inflated false positive rates for detecting cis-heritable genes. Therefore, we introduce a new method called scGeneHE (single cell Gene expression Heritability Estimation), a Poisson mixed-effects model that quantifies the cis-genetic component of gene expression using individual cellular profiles. In simulations, scGeneHE has a consistently well-calibrated false positive rate for eGene detection and unbiasedly estimates cis-heritability at many parameter settings. We applied scGeneHE to scRNA-seq data from 969 individuals, 11 immune cell types, and 822,552 cells from the OneK1K cohort to infer cell-type-specificity of genetic regulation at risk genes for immune-mediated diseases and trace the fluctuation of cis-heritability across cellular populations of varying resolution. In summary, we developed a new statistical method that resolves the analytical challenge of estimating gene expression cis-heritability from native scRNA-seq data.

genetics↗

bioRxiv2025

Repeatable phenotypic but not genetic response to selection on body size in the black soldier fly

Polygenic traits are expected to show high genetic redundancy and therefore low repeatability in the genomic response to selection. We tested this prediction by selecting for large body size in the black soldier fly (Hermetia illucens). Over three replicate experiments selected for large body size, we found a strong and repeatable phenotypic response, with a mean 15% increase in body size. Selected lines also increased in larval growth rate (+19%) and average protein content (+14%), suggesting that selection on large body size does not result in strong trade-offs. In contrast to the predictability of the phenotypic response across replicates, whole genome sequencing identified a highly polygenic and non-repeatable genomic response. We identified 120, 301 and 157 outlier genomic regions in the three replicates, but high redundancy with only four shared regions. Among 12 candidate genes found in these regions, the insulin-like receptor gene (HiInR) was confirmed as regulating larval growth using a CRISPR knockout experiment. In summary, polygenic quantitative traits show high genetic redundancy, even where the phenotypic response to selection is highly repeatable.

evolutionary biology↗

bioRxiv2025

Graph-based Contrastive Learning Enables Unified Integration and Niche Transfer Across Single-Cell and Spatial Multi-Omics

The rapid growth of single-cell and spatial omics has outpaced computational methods capable of unifying these data into a cohesive framework for tissue atlas construction and cross-sample analysis. A critical bottleneck lies in the inability of existing tools to co-embed cells from diverse technologies--spanning transcriptomics, epigenomics, and proteomics--into a shared reference space while preserving spatial architecture and molecular specificity. Here, we present Garfield (Graph-based Contrastive Learning Enables Fast Single-Cell Embedding), a geometric deep-learning framework that addresses these challenges through spatially or molecularly aware cell embedding. Leveraging a graph contrastive learning framework, Garfield learns a shared embedding space for data generated by diverse technologies, enabling seamless construction and querying of spatial reference atlases. Our results show that Garfield consistently outperforms state-of-the-art benchmark models in identifying spatial niches across multiple datasets. We further demonstrate Garfields versatility by applying it to multi-modal spatial data, including gene expression and chromatin accessibility, where it successfully identifies distinct niches in the mouse brain. Notably, Garfield reveals tumor microenvironment heterogeneity in non-small cell lung cancer and breast cancer, uncovered conserved, barrier-like immune niches at tumor margins orchestrating CD80-mediated T cell-B cell-dendritic cell interactions and IFN-/B cell activation pathways, forming spatially coordinated immune surveillance hubs. These findings underscore Garfields potential to advance spatial omics research by offering a robust, scalable solution for integrating and interpreting complex spatial data across diverse tissue types and modalities.

bioinformatics↗

bioRxiv2025

Specific neuroblast-derived signals control both cell migration and fate in the rostral migratory stream

Functional neuronal circuits require neuroblasts migrate to appropriate locations and then differentiate into neuronal subtypes. However, it remains unknown how neuroblasts in the subventricular zone (SVZ) are guided through the rostral migratory stream (RMS) to the olfactory bulb (OB). Here we define EphB2 as a neuroblast-derived cue that controls migration along the RMS and helps to determine cell fate. Within the RMS, EphB2 is expressed selectively in, kinase-active in, and required for the migration of neuroblasts. As neuroblasts enter the OB and differentiate, EphB kinase activity is down-regulated, and in the granule cell layer (GCL), EphB2 expression is down-regulated. Blocking EphB kinase activity or knocking down EphB2 results in defects in migration and premature cellular differentiation in the RMS. Unexpectedly, premature loss of EphB2 expression causes neuroblasts to stop migrating and differentiate into astrocyte-like cells. Thus, EphB2 kinase activity and expression are linked to migration and specification of neuroblast fate.

neuroscience↗

bioRxiv2025

Single-Cell Genomics Elucidates Molecular Variations and Regulatory Mechanisms in Circulating Immune Cells

The human peripheral blood displays diverse molecular characteristics across populations, understanding the drivers and underlying mechanisms of which remains challenging. Here, we introduce the Chinese Immune Multi-Omics Atlas (CIMA), elucidating sex-, age-, and genetic-related molecular variations by analyzing multi-omics data from 428 adults with over 10 million immune cells. CIMA generated an enhancer-driven gene regulatory network, identifying 237 high-quality regulons and revealing cell type-specific regulatory mechanisms. Additionally, 11,521 lead cis-expression quantitative trait loci (eQTLs) and 46,339 chromatin accessibility QTLs (caQTLs) were identified at cell type level. CIMA also uncovered pleiotropic associations among immune-related disease risk loci, eQTLs, and caQTLs in a cell type-specific manner. Lastly, a novel cell language model, CIMA-CLM, was developed to predict chromatin accessibility and noncoding variant effects using chromatin sequences and gene expressions. This work represents a population-scale multi-omics resource of human immune cells, providing a valuable reference for future investigation of immune-related diseases.

immunology↗

bioRxiv2025

Isolation of a novel plant growth-promoting Dyella sp. from a Danish natural soil

Environmental soils are natural reservoirs of unexplored microbes, including potentially beneficial microbes to improve plant performance. Here, we isolated 75 bacterial strains from surface-sterilized roots of Arabidopsis thaliana (Arabidopsis) grown in a natural soil derived from an alder swamp. Culture-dependent isolation of individual strains from the roots followed by monoassociation-based screening identified seven bacteria that promoted Arabidopsis seedling weight. Of those, we identified a new species from the Dyella genus which increased biomass of tomato and Arabidopsis seedlings in agar as well as the shoot biomass of Arabidopsis grown in both the alder swamp soil and potting soil. Dyella sp. A4 specifically promoted the elongation of lateral roots without affecting lateral root number and primary root elongation. The new Dyella sp. A4 expands the toolbox of biostimulants for plant growth promotion via modulating root architecture.

plant biology↗

bioRxiv2025

SMTdb: A comprehensive spatial meta-transcriptome resource in cancer

Microbes have been found in various tumors and the research of tumor microbiome has been garnering increased attention. However, it remains challenge to investigate the microbiome in cancer at spatial resolution. The rapid advent of spatially resolved transcriptomics techniques has given rise to map transcripts at single-cell resolution in various types of cancer. Here, we constructed a comprehensive spatial meta-transcriptome resource by manually curating 203 fresh frozen (FF) slices from 20 cancers encompassing 334,253 spots and 1,908,646 cells. SMTdb (http://bio-bigdata.hrbmu.edu.cn/SMTdb/) was constructed to provide comprehensive insights into the abundance, distribution and enriched TME regions of 1218 microbiota in spatial tissue slices. SMTdb enables vast interactive data exploration of spatial distribution and expression of microbiota, host gene modules associated with certain microbiota and co-occurrence between microbiota and immune cells within tumor microenvironment. The atlas resource serves as a one-stop and time-effective platform to investigate the interactions among microbial ecosystems and hosts in cancer.

bioinformatics↗

bioRxiv2025

Single cell resolved spatial immune repertoire unveils spatial heterogeneity of lymphoid aggregates in human immune disorders

Adaptive immunity, mediated by T and B cell responses, is essential for defending against infections and cancers while also being implicated in autoimmune diseases. Tracking T and B cell repertoires in situ at single-cell resolution is essential for understanding adaptive immune responses. To address the lack of tools for in situ single-cell T/BCR (XCR) sequencing, we developed Stereo-XCR-seq, an efficient strategy for retrieving and sequencing TCR and BCR from Stereo-seq cDNA libraries at subcellular resolution. Stereo-XCR-seq provides unbiased full-length XCR reads alongside spatial transcriptomics, enabling the identification of heterogeneous lymphoid aggregates with distinct clonal activities in cancers and inflammatory bowel disease (IBD). We identified plasma cell aggregates that differ from tertiary lymphoid structures (TLSs) in both transcriptomic profiles and clonal activities, with spatial positioning potentially mediating unique immune responses. Collectively, Stereo-XCR-seq enables in situ single-cell profiling of T and B cell clonal activities within tissue microenvironments, providing insights into lymphocyte adaption to environmental stimuli. This technology provides potential for advancing our understanding of tissue immunity and the development of therapeutic strategies for immune disorders.

immunology↗