Biology subjects

Zhou, C.

Publications and source records attributed to Zhou, C..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Single-Cell Spatial Proteomics Uncovers Molecular Interconnectivity among Hallmarks of Aging

Aging is accompanied by conserved hallmarks including genomic instability, epigenetic alterations, loss of proteostasis, and mitochondrial dysfunction, but how these processes emerge and become mechanistically linked remains unclear. Here we leverage a proteome-wide, single-cell, subcellular atlas of protein expression, localization, and aggregation across yeast replicative aging to map hallmark-linked remodeling in its spatial context. We identify hundreds of previously unappreciated molecular changes that underlie major hallmarks of aging and show that hallmark phenotypes frequently manifest as compartment-specific erosion of spatial confinement, relocalization, and aggregation. 91.6% human orthologs of these hallmark-linked yeast proteins also change during human aging. Integrating these spatial phenotypes reveals many molecular connections linking different hallmarks. Temporal analysis suggests that disorganization of nucleolar ribosome biogenesis, proteostasis decline, and mitochondrial dysfunction precede other hallmarks. Together, our findings substantially deepen the molecular underpinnings of aging hallmarks and provide a framework for linking them into a hierarchical sequence of cellular failures.

systems biology↗

bioRxiv2026

Drosophila melanogaster Nepl15 regulates lifespan, motor function, aging, heart rate, and cellular health in a sex-specific manner

Aging and obesity are characterized by comorbidities like declines in fertility, lifespan, gut barrier integrity, cardiac function, and motor activity, and an increase in oxidative stress due to altered nutrient and energy homeostasis. A study on Drosophila Neprilysin-like 15 (Nepl15) demonstrated that loss of Nepl15 gene significantly reduced glycogen and glycerolipid reserves in adult males and increased glycogen storage in adult females despite similar food consumption as controls. Therefore, we investigated the sex- and age-specific consequences of Nepl15 loss on cellular and physiological parameters associated with aging and obesity. We observed that egg production, rate of pupariation, and rate of adult fly eclosion were slightly better in the mutant flies. Interestingly, mutant females, but not males, exhibited significantly extended lifespan. Both sexes demonstrated improved locomotor performance, exercise endurance, gut barrier integrity, and preserved heart rate during progressive aging. At the cellular level, female mutants displayed reduced oxidative stress, elevated Sod2 expression, and increased ATP levels, all indicative of enhanced cellular health. Mutant males exhibited an increased mitochondrial membrane potential, indicating an enhanced capacity for rapid ATP production in response to enforced activity. Consistently, the energy-sensing kinase AMPK expression was reduced in the mutants. The lifespan extension of mutant females was supported by downregulation of mTOR and upregulation of Sirt6 expression. However, in mutant males, both mTOR and Sirt6 were downregulated, potentially contributing to improved physiological health without changing their lifespan. Collectively, our findings establish Nepl15 knockout mutation promotes anti-aging and anti-obesity health benefits, with stronger effects in female flies.

cell biology↗

bioRxiv2026

A Single-Cell Temporal Atlas of Mouse Nasal Embryonic Development

The mammals breathe and perceive odors through anatomically and functionally distinct respiratory and olfactory regions of the nose; however, how the early embryo endows this system remains largely unknown. Here, we present a temporal high-resolution single-cell RNA sequencing (scRNA-seq) atlas of mouse nasal development, comprising 183,247 cells collected from 20 embryos spanning embryonic day 10.5 (E10.5) to E18.5. We identified 7 major cell clusters and 52 molecularly defined subtypes, including previously unrecognized rare populations and niche-derived signaling components involved in progenitor cell maintenance. Lineage reconstruction of epithelial and mesenchymal compartments revealed dynamic cell fate transitions and highlighted candidate regulators of lineage specification, including Foxa1 as a regulator of nasal respiratory ciliated epithelium differentiation. Integration with adult nasal epithelium datasets further delineated transcriptional dynamics of olfactory stem cells. This study provides a molecular roadmap of nasal development and offers a valuable resource for future research into nasal biology and regenerative strategies.

developmental biology↗

bioRxiv2026

Antibody-Dependent Heterotypic Syncytia Drive COVID-19 Inflammation and Disease Progression

Severe COVID-19 is characterized by profound immune dysregulation and excessive inflammation. Aberrant myeloid responses drive hyperinflammation, yet the precise mechanisms remain elusive. Here, we demonstrate that certain spike antibodies promote the formation of heterotypic syncytia between monocytes/macrophages and virus-infected pneumocytes, leading to excessive inflammatory cytokine release. This antibody-dependent syncytium formation requires Fc{gamma}RI (CD64) and ADAM10, as well as the assembly of the six-helix bundle by the spike S2 subunit. Notably, these syncytia exhibit a stronger proinflammatory signature compared to virus-infected epithelial cells. In vivo, sub-neutralizing antibody concentrations amplified inflammation and exacerbated disease in SARS-CoV-2-infected mice without increasing viral burden. Furthermore, scRNA-seq of postmortem lung tissues from COVID-19 patients implicated the monocyte/macrophage-derived syncytia as a key cellular source of inflammatory cytokines. Together, these findings define a novel mechanism of antibody-dependent enhancement of inflammation that helps explain the hyperinflammatory responses in severe COVID-19 and suggest new therapeutic opportunities targeting this pathway.

immunology↗

bioRxiv2026

Single-Cell and Spatial Transcriptomics Integration Identifies Mural Cell Oxidative Stress Genes Clu and Gria2 as Key Biomarkers in Ischemic Stroke

Oxidative stress (OS) is a key factor in ischemic stroke (IS), but the characterization of OS-related genes in IS remains largely unexplored. Identifying key OS-associated genes could improve our understanding of OS in IS. We analysed single-cell RNA sequencing datasets and utilized AUCell, Ucell, singscore, ssgsea, and AddModuleScore algorithms, along with correlation analysis, identified 167 OS-related genes potentially linked to IS. Furthermore, we used seven machine learning algorithms, including least absolute shrinkage and selection operator, XGBoost, Boruta, random forest, gradient boosting machines, decision trees, and support vector machine recursive feature elimination, to identify the optimal feature genes: Clusterin (Clu) and Glutamate Ionotropic Receptor AMPA Type Subunit 2 (Gria2). Bulk RNA-sequencing showed that Clu expression was upregulated and Gria2 expression was downregulated in IS tissues. Single-cell analysis further revealed that these expression changes predominantly occurred in mural cells, emphasizing their cell-specific roles in IS. Subsequently, we validated these findings through spatial transcriptomics (ST) analysis and animal model experiments. These results suggest that Clu and Gria2 may participate in the progression of IS by altering the OS activity of mural cells. However, further research is needed to validate its clinical efficacy and ensure its application in the treatment of IS.

neuroscience↗

bioRxiv2026

FluNexus: a versatile web platform for antigenic prediction and visualization of influenza A viruses

Influenza A viruses continuously undergo antigenic evolution to escape host immunity induced by previous infections or vaccinations, consequently causing seasonal epidemics and occasional pandemics. Antigenic prediction and visualization of influenza A viruses are crucial for precise vaccine strain selection and robust pandemic preparedness. However, a user-friendly online platform for these capabilities remains notably absent, despite widespread demand. Here, we present FluNexus (https://flunexus.com), the first-of-its-kind, one-stop-shop web platform designed to facilitate the prediction and visualization of the antigenic change in emerging variants. FluNexus features a data preprocessing module for hemagglutinin subunit 1 (HA1) and hemagglutination inhibition (HI) data across three major public health threat subtypes (H1, H3 and H5). Meanwhile, FluNexus provides an interactive interface for online antigenic prediction and offers practical guidance for researchers. Most notably, FluNexus offers the visualization of influenza A virus antigenic evolution, providing intuitive insights into its antigenic dynamics. Specially, FluNexus proposes a novel manifold-based method for positioning antigens and antisera, generating accurate antigenic cartographies even with sparse HI data. By alleviating the programming burden on biologists, FluNexus supports more informed decision-making in vaccine strain selection and strengthens surveillance and pandemic preparedness. HighlightsO_LIFluNexus features a data preprocessing module for HA1 and HI data spanning the H1, H3, and H5 subtypes. C_LIO_LIFluNexus facilitates online antigenic prediction utilizing ten state-of-the-art antigenic prediction tools, and offers practical guidance based on a comparative evaluation of their performance. C_LIO_LIFluNexus provides a visualization module for mapping antigenic evolution of influenza A viruses, incorporating a novel manifold-based method for antigenic cartography. C_LI

bioinformatics↗

bioRxiv2026

Harnessing FBXO31 with terminal amide-functionalized molecules for targeted protein degradation

Targeted protein degradation (TPD) is a powerful strategy for controlling protein abundance. Here, we establish FBXO31 as a TPD-competent E3 ligase by exploiting its recognition of C-terminal amide-bearing degrons. Using an amidated Ala-Phe motif as a chemical recruiter, multiple small-molecule binders can be transformed into FBXO31-dependent degraders that induce rapid and potent target degradation. Mechanistic studies confirm FBXO31-mediated ternary complex formation and identify key residues in FBXO31 required for recruiter engagement and target degradation. We further show that an FBXO31-based multi-kinase degrader exhibits a distinct and broader degradation profile than a CRBN-based degrader, highlighting a potentially expanded degradable target space beyond CRBN.

biochemistry↗

bioRxiv2026

Decoding the cell intrinsic and extrinsic roles of PRC2 in early embryogenesis

Early embryogenesis is accompanied by dynamic epigenetic modifications. While such dynamics are important in cell intrinsic regulation of gene expression, their extrinsic roles in mediating intercellular communication during early embryogenesis is less understood. Using the dTAG system, here we reveal previously underappreciated stage-specific functions of PRC2 in regulating pre-implantation and primordial germ cell (PGC) development. We demonstrate that PRC2 plays important roles in regulating maternal to zygotic transition (MZT), and epiblast (EPI) formation. By systematically analyzing H3K27me3 and H3K4me3 dynamics, we redefine the timing of bivalency establishment and uncover a stepwise mechanism governing bivalency acquisition in early embryogenesis. Moreover, PRC2 regulates proper PGC numbers in the EPI by controlling Esrrb expression in the extraembryonic ectoderm (ExE). Thus, our study uncovers a previously unknown cell-autonomous function of PRC2 in preimplantation development and its non-cell-autonomous impact in PGC number regulation, both through interplays between epigenetic-epigenetic and epigenetic-TFs networks.

developmental biology↗

bioRxiv2026

RNA Structure Coordinates Translation Across the Meiotic Program

mRNA structure clearly modulates translation efficiency for individual transcripts, yet its role in coordinating translation across many transcripts remains poorly defined. Meiosis offers a compelling test case, involving large-scale gene expression changes coordinated across hundreds of mRNAs under conditions where transcription is constrained by chromosome condensation. We profiled mRNA structures across yeast meiosis, generating a high-resolution structurome encompassing ~70% of annotated mRNAs, including multi-time-point measurements for 2,084 transcripts. Transcripts upregulated during meiosis generally adopt flexible structures that enhance translation, whereas mRNAs with complex 5' UTR and coding-region structures show suppressed translation, indicating that RNA structure globally shapes meiotic translation. We further observed a high-low-high oscillation in cytoplasmic RNA helicase levels across meiosis. Together, these findings support a model in which RNA structure and helicase expression act jointly to program stage-specific translation of hundreds of mRNAs, with highly structured transcripts selectively translated at late stages. Consistent with this model, disrupting the structure of the abundant transcript CCW22, or altering Ded1p helicase levels, impaired meiotic progression in an RNA structure-dependent manner. Our study reveals that the concerted action of RNA structure and helicases coordinates cell-wide translation dynamics to meet stage-specific demands, especially critical when transcription is limited during meiotic divisions.

genomics↗

bioRxiv2026

HIF-1 regulated TPM3 links hypoxia to motility and invasion beyond the hypoxic fraction in triple-negative breast cancer

Hypoxia is a defining feature of triple-negative breast cancer (TNBC), driving invasion, metastasis, and therapy resistance. Understanding the molecular effectors of hypoxia is essential to identify new therapeutic targets. Here, we investigated tropomyosin 3 (TPM3), an actin-binding protein that regulates filament stability. TPM3 is significantly upregulated in breast cancer, including in TNBC, where elevated levels correlate with poor overall survival. Using validated hypoxia signatures and TNBC cell models, we show that TPM3 is induced in physiologically relevant hypoxic conditions in a HIF-1-dependent manner. Both mRNA and protein levels of TPM3 increased in response to hypoxia, and TPM3 colocalised with F-actin, supporting cytoskeletal organisation. Functional assays demonstrated that depletion or inhibition of TPM3 impaired cell morphology, motility, and invasion in hypoxic TNBC cells, while not affecting viability. Notably, TPM3 inhibition synergised with Paclitaxel and Doxorubicin, enhancing therapeutic efficacy. In addition, TPM3 was incorporated into extracellular vesicles (EVs), with hypoxia increasing EV-mediated transfer of TPM3 to normoxic cells and promoting their motility. These findings establish TPM3 as a hypoxia-inducible, HIF-1-regulated effector of cytoskeletal dynamics and intercellular communication, underscoring its potential as a therapeutic target to limit TNBC aggressiveness and improve treatment outcomes.

cancer biology↗

bioRxiv2025

Structural Basis of Inhibition and Desensitization in Heteromeric Kainate Receptors

Kainate receptors (KARs) mediate excitatory synaptic transmission and regulate neurotransmitter release. In the central nervous system, KARs predominantly exist as heterotetramers comprising low-affinity (GluK1-3) and high-affinity (GluK4-5) subunits, with GluK2/GluK5 being the most abundant. To elucidate their conformational transitions, we determined the cryo-electron microscopy (cryo-EM) structures of GluK2/GluK5 KARs in the apo and distinct ligand-bound states. The apo structure revealed compact packing with extensive inter-subunit interactions between the ligand-binding domains (LBDs) beyond the conserved D1-D1 upper-lobe contacts. The glutamate-bound structure exhibited enhanced packing that stabilized the desensitized conformation through increased intersubunit contacts relative to the homomeric KARs, indicating that the heterotetramers were conformationally less dynamic. To investigate subtype-specific antagonism, we engineered GluK2 and GluK5 mutants with altered affinities for the competitive antagonist UBP310. Structural analysis of these mutants revealed distinct UBP310 binding modes on the GluK2 versus the GluK5 subunits. Furthermore, we demonstrated that targeting GluK5 was more effective than targeting GluK2. Specifically, blocking GluK5 locked the receptor in a pore-occluded conformation, whereas antagonizing GluK2 retained structural flexibility above the pore. These findings provide a structural framework for understanding the distinct contributions of the GluK2 and GluK5 subunits to KAR function. TeaserCryo-EM structures of heteromeric kainate receptors reveal unique assembly and regulation mechanisms.

biophysics↗

bioRxiv2025

Covalent Reprogramming of Kinase Binders to Modulate Protein Homeostasis

Small molecules that modulate protein abundance through induced proximity have expanded the landscape beyond traditional inhibition. Here, we explore how introducing covalent or latent electrophilic groups into a multi-kinase binder scaffold can reprogram protein homeostasis within the kinase family. Using the broad-spectrum kinase ligand TL13-87 as a template, we synthesized analogs bearing -chloroacetamide, acrylamide, or terminal amine groups. Quantitative proteomics revealed that while most analogs had minimal global impact, MKI-AA uniquely stabilized the mitotic kinase AURKA, a protein often destabilized by ATP-competitive inhibitors. Mechanistic studies showed that MKI-AA acts post-translationally to suppress AURKA ubiquitination and proteasomal degradation. Proteomic mapping of MKI-AA-induced AURKA interactors revealed changes in protein associations upon treatment, providing mechanistic insights into how MKI-AA influences AURKA stability. Intriguingly, adding a short linker to MKI-AA converted it from a stabilizer into a degrader, highlighting how subtle structural variations can invert functional outcomes. These findings demonstrate that electrophilic ligand design can modulate kinase stability and reveal a previously unrecognized mode of covalent proximity-driven protein stabilization.

biochemistry↗

bioRxiv2025

Systematic characterization of cancer-associated SPOP mutants reveals novel and reprogrammable degradative activities

Speckle-type POZ protein (SPOP) functions as the substrate adaptor of the Cullin3-RING ligase (CRL3) complex and is recurrently mutated in multiple cancer types. Among these, F102C and F133L are frequent prostate cancer mutations within the substrate-binding domain, yet their biochemical consequences remain incompletely understood. Using quantitative proteomics, we show that SPOP-F133L, unlike SPOP-F102C, retains degradative activity toward the nuclear basket proteins NUP153 and TPR, indicating substrate-dependent loss-of-function. Moreover, SPOP-F133L induces partial down-regulation of p53 through a CRL-dependent, post-translational mechanism, revealing a potential neo-substrate relationship. Finally, we demonstrate that both SPOP-F102C and SPOP-F133L support targeted protein degradation (TPD) in an engineered cellular system. These findings define the degradative capacities of SPOP mutants and highlight opportunities to repurpose these variants as mutant-selective E3 ligases for therapeutic applications.

biochemistry↗

bioRxiv2025

Transcriptomic insights into developmental toxicity of per- and poly-fluoroalkyl substances (PFAS) in Caenorhabditis elegans: The potential key role of xenobiotic detoxification pathway

Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants known to induce developmental toxicity across multiple species, yet the molecular mechanisms are still not fully understood. This study aims to evaluate the developmental toxicity of four long-chain legacy PFAS (PFOA, PFOS, PFNA, PFDA) and one short-chain alternative (PFBA) at environmentally relevant concentrations (1-5 M) using the model organism Caenorhabditis elegans, with a focus on elucidating the underlying molecular mechanisms. Phenotypic analysis indicated that PFDA and PFOS significantly delayed development of worms, and reduced the number of fertilized eggs in the uterus. RNA-seq and subsequent bioinformatic analysis revealed strong impacts of PFDA and PFOS on physiological age. A core set of xenobiotic detoxification genes (e.g., cyp-13A4, cyp-13A6, and cyp-13A7), which were found to be primarily regulated by nuclear hormone receptors (NHR-102, NHR-85, NHR-28), showed consistent up-regulation upon PFAS exposure. Gene co-expression network analysis (WGCNA) further linked this detoxification gene signature to developmental impairment. Cross-species comparison using public databases identified several evolutionarily conserved detoxification genes that are associated with PFAS-induced developmental toxicity, among which CYP3A4 and its orthologs appear to be emerging biomarkers of PFAS exposure. Our findings demonstrate that activation of conserved xenobiotic detoxification pathways is a central transcriptomic signature of PFAS exposure, providing mechanistic insights into the structure-dependent developmental toxicity of this kind of pervasive pollutant. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/689658v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@c50b2borg.highwire.dtl.DTLVardef@605b6dorg.highwire.dtl.DTLVardef@125fa8org.highwire.dtl.DTLVardef@464d34_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

pharmacology and toxicology↗

bioRxiv2025

Prognosis prediction using autophagy gene expression in osteosarcoma

Defining the transition from localized to metastatic osteosarcoma (OS) before overt dissemination is fundamental for improving survival. However, effective early diagnostic tools remain scarce, largely due to limited exploitation of the pre-metastatic tumor microenvironments own record of molecular barcode exposures encoded in cell-intrinsic stress states. We analyzed autophagy-dependent transcriptional datasets from 139 individuals to develop Auto-RS, a computational classifier that can integrate age and sex to deliver individualized risk management. The prognosis-interpretable features of Auto-RS recapitulate established molecular trajectories of metastasis at the single-cell level, capturing tumor cells intrinsic shift from proliferative to invasive states and revealing cooperative programs among cancer-associated fibroblasts and immune cells. More significantly, Auto-RS can expose chemotherapy vulnerabilities of newer drugs, providing a framework to prioritize therapeutics without direct testing in children. This framework brings a potential inflection point, where metastasis prediction and therapeutic stratification may converge to improve OS outcomes.

cell biology↗

bioRxiv2025

Drosophila melanogaster model of RVCL-S demonstrates age dependent disease progression

Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (RVCL-S) is a disease that causes deterioration of small vessels, affecting various organs: eyes, brain, liver, and others. The RVCL-S carriers have lower life expectancy. There is no cure available to date. The disease has been linked to mutations in TREX1 gene disrupting its cytoplasmic localization. To facilitate the disease mechanism investigation, we employed model organism D. melanogaster, identified human TREX1 ortholog cg3165, and confirmed its vital significance to flies. Then, we expressed human TREX1 and its mutant form TREX1 V235Gfs in flies and used optical coherence microscopy (OCM) to monitor the dynamics of flies vascular system. We detected the relapse of fly dorsal vessel, movement impairment, and reduced longevity in TREX1 V235Gfs-expressing transgenic animals. Vascular deterioration and shorter life span recapitulate the RVCL-S manifestations in humans. We have established a robust quantitative Drosophila RVCL-S phenotypic system that can potentially serve as a screening platform for drug discovery and drug targets identification.

genetics↗

bioRxiv2025

Engineered Promoter System Enables High-efficiency Transgenic CRISPR Editing in Malaria Transmitting Mosquito Anopheles sinensis

The CRISPR/Cas9 system deployed through crosses of transgenic lines expressing Cas9 and gRNA facilitates efficient mutagenesis. However, its application in non-model insects remains limited, primarily due to a lack of well-characterized promoters capable of driving robust and stable expression of Cas9 and gRNA. In the malaria mosquito Anopheles sinensis, we evaluated several ovary-biased promoters--Asvasa2, Aszpg, and Asnanos--for driving Cas9 expression. Notably, the Asvasa2 promoter mediated mutagenesis in nearly 60% of G0 individuals following microinjection of gRNAAswhite. Among four RNA polymerase III promoters derived from AsU6 genes, AsU6-1 yielded the highest gRNA transcriptional output, enabling 62% editing efficiency in G0 offspring. In addition, hybrid crosses between established transgenic lines demonstrated that the Asvasa2-Cas9 and AsU6-1-gRNA combination enabled complete germline editing penetrance, where all F2 progeny inherited the intended mutations. This work provides a essential genetic toolkit for synthetic biology applications in Anopheles mosquitoes and a scalable framework for engineering other non-model insects.

genetics↗

bioRxiv2025

3D-printing-assisted, microfabricated devices reveal hierarchical and temporal mechanosensing in high-density fibroblast culture

Understanding how cells integrate mechanical forces across multiple directions, length scales, and timescales remains a fundamental challenge in mechanobiology. Deciphering how cells integrate this information is particularly important in the context of wound healing, where the timing and duration of the fibroblast-to-myofibroblast transition can determine healing outcomes. Here, we discovered that fibroblasts in engineered tissues respond to directional anisotropy in stress through a hierarchical temporal cascade, with individual cell elongation (24 hr) preceding collective alignment (40 hr), which then drives -smooth muscle actin expression and myofibroblast transition (96h). To enable this discovery, we developed a modified hydrogel-assisted stereolithographic elastomer (HASTE) prototyping platform to incorporate a detergent that improves wettability of template agar hydrogels by poly(dimethylsiloxane) elastomer. HASTE allowed rapid prototyping of intricate 3D micropost arrays that provides isotropic (8-post) versus anisotropic (4-post) boundary conditions. Fibroblasts sensed and responded to stress directionality before bulk tissue reorganization occurs. Computational modeling predicted steady-state activation patterns based on initial stress anisotropy rather than magnitude, and our experiments reveal that reaching this state requires sequential mechanosensitive processes operating across distinct timescales. This temporal hierarchy persists even when extensive cell-cell contacts might be expected to mask matrix-mediated mechanical signals. Our findings demonstrate that fibroblast mechanosensing involves adaptive responses encoded through progressive cell and tissue reorganization. Results provide insight into how nanoscale mechanosensing scales up to direct tissue-level organization, with implications for understanding wound healing, understanding fibrosis, and engineering functional tissue replacements.

bioengineering↗