Biology subjects

Zhou, X.

Publications and source records attributed to Zhou, X..

At least 181 records · Page 10Linked to original sources

bioRxiv2025

FMR1 KH0-KH1 Domains Coordinate m6A Binding and Phase Separation in Fragile X Syndrome

The Fragile X Mental Retardation Protein (FMR1) regulates neurodevelopment via m6A RNA interactions, but domain-specific roles of KH0 and KH1 in RNA binding and pathology remain unclear. Through mutagenesis and AlphaFold3 modeling, we demonstrate that KH1 serves as the primary m6A-binding interface, whereas the KH0 domain (e.g., Arg138) modulates liquid-liquid phase separation (LLPS). Pathogenic mutations in KH0 disrupt RNA binding and enhance LLPS aggregation, while m6A RNA suppresses LLPS at KH0. Structural simulations reveal synergistic cooperation between KH0 and KH1 through hydrophobic and electrostatic networks. These dual-domain interactions establish a mechanistic link between m6A dysregulation, aberrant phase separation, and Fragile X syndrome pathogenesis. Our findings propose KH0 as a therapeutic target for RNA-driven neurodevelopmental disorders.

cell biology↗

bioRxiv2025

An alternative framework for transcriptome-wide association studies to detect and decipher gene-trait associations

Transcriptome-wide association studies (TWAS) are widely used to uncover transcriptomic mechanisms underlying disease. Here, we present VINTAGE, an alternative TWAS framework designed to identify and decipher gene-trait associations through two complementary tests: a genetic variance test that generalizes TWAS and unifies it with SKAT, offering a clearer understanding of TWAS false signals when expression is not relevant to SNP-trait associations; and a local genetic correlation test that distinguishes it from TWAS by explicitly quantifying and testing the proportion of genetic effects on trait mediated through gene expression. Applied to eQTLGen and eighteen traits from UK Biobank, VINTAGE improved gene-trait association power by an average of 5% and 87% over SKAT and TWAS, respectively. VINTAGE is also the only method effective in assessing potential gene mediation effects, revealing that most genes lack detectable mediation effects (median = 12%), which explains the power advantage of VINTAGE and SKAT over TWAS. Notably, VINTAGE identified 61 genes with significant mediation, highlighting the role of expression in genetic influences on traits.

bioinformatics↗

bioRxiv2025

Stable hypermutators revealed by the genomic landscape of DNA repair genes among yeast species

Mutator phenotypes are short-lived due to the rapid accumulation of deleterious mutations. Yet, recent observations reveal that certain fungi can undergo prolonged accelerated evolution after losing DNA repair genes. Here, we surveyed 1,154 yeast genomes representing nearly all known yeast species of the subphylum Saccharomycotina to examine the relationship between reduced DNA repair repertoires and elevated evolutionary rates. We identified three distantly related lineages--encompassing 12% of species--with substantially reduced sets of DNA repair genes and the highest evolutionary rates in the entire subphylum. Two of these "faster-evolving lineages" (FELs)--a subclade within the order Pichiales and the Wickerhamiella/Starmerella (W/S) clade (order Dipodascales)--are described here for the first time, while the third corresponds to a previously documented Hanseniaspora FEL. Examination of DNA repair gene repertoires revealed a set of genes predominantly absent in these three FELs, suggesting a potential role in the observed acceleration of evolutionary rates. Genomic signatures in the W/S clade are consistent with a substantial mutational burden, including pronounced A|T bias and signatures of endogenous DNA damage. The W/S clade appears to mitigate UV-induced damage through horizontal acquisition of a bacterial photolyase gene, underscoring how gene loss may be offset by nonvertical evolution. These findings highlight how the loss of DNA repair genes gave rise to hypermutators that persist across macroevolutionary timescales, with horizontal gene transfer as an avenue for partial functional compensation.

evolutionary biology↗

bioRxiv2025

Ultrasonic Modulation of Astrocytic and Neuronal Calcium Dynamics in Mouse Cortex

BackgroundAstrocytes are abundant in the brain and their calcium signaling is reported to have an important effect on neuronal activity in both physiological and pathological conditions. Low-frequency focused ultrasound (FUS) has recently emerged as a powerful noninvasive neuromodulation approach, yet its impact on astrocyte calcium dynamics in different brain states in vivo is poorly understood. ObjectiveThis study aimed to elucidate the effects of non-thermal FUS on astrocyte calcium dynamic with in vivo cellular-resolution and cell-type-specific recording and identify whether the influences of FUS on cortical astrocytes and neurons are distinctive and state dependent. MethodsHere we combined a customized 0.521MHz FUS transducer with two-photon microscopy, allowing simultaneous single-cell resoultion imaging and FUS stimulation at intensities of 0.91 or 1.5 W/cm2 to examine astrocyte and neuronal calcium responses in somatosensory cortex of both awake and lightly anesthetized mice. Functional clustering analysis was performed to identify calcium response activated or inhibited subpopulations. ResultsIn awake mice, FUS significantly enhanced the amplitude, frequency, and temporal integral of astrocyte calcium transients, while suppressing neuronal calcium activity and reducing the proportion of activated neuronal subpopulations. In contrast, lightly anesthetized mice displayed a blunted yet increased astrocyte response and negligible neuronal modulation under FUS, suggesting that baseline suppression from anesthesia partially masks FUS effects. ConclusionsOur study demonstrated that FUS elicited distinctive, state-dependent effects on cortical astrocytes and neurons, highlighting astrocytes as previously underappreciated targets of ultrasound neuromodulation. These findings will pave the way for FUS-based therapies targeting astrocyte-neuron interactions in conditions involving abnormal brain excitability. HighlightsO_LILow duty cycle low frequency focused ultrasound induced negligible heat effects. C_LIO_LIUltrasound markedly enhanced astrocyte calcium transients in awake mice. C_LIO_LIUltrasound suppressed neuronal calcium activity in awake mice. C_LIO_LIThe effects of ultrasound on both cell types were reduced under light anesthesia. C_LI

bioengineering↗

bioRxiv2025

Mesoderm-specific transcript reduces ciliary sphingomyelin levels to promote tendon stem/progenitor cells osteochondrogenesis in traumatic heterotopic ossification

Traumatic heterotopic ossification (tHO) is a musculoskeletal disorder characterized by ectopic bone formation in soft tissues following trauma. However, the etiology and mechanisms of tHO remain unknown, and no treatments are highly effective for tHO. Here, by performing single-cell RNA sequencing (scRNA-seq) on two tHO mouse models, we found that ciliary Hedgehog (Hh) and PI3K-Akt signaling in tendon stem/progenitor cells (TSPCs) is upregulated during tHO development, leading to the activation of GLI family zinc finger 2 (GLI2) transcription factor, which promotes mesoderm-specific transcript (MEST) gene expression. Untargeted lipidomics using liquid chromatography-tandem mass spectrometry (LC-MS/MS) on detached cilia indicated that MEST could reduce ciliary sphingomyelin (SM) levels by inhibiting SM synthesis in TSPCs, creating a positive feedback loop that amplified ciliary Hh signaling, enhancing TSPCs osteochondrogenesis and driving tHO formation. Targeting ciliary genes intraflagellar transport 88 (IFT88) or ADP ribosylation factor like GTPase 3 (ARL3) restored normal TSPCs osteochondrogenesis in vitro and attenuated ectopic bone formation in vivo by suppressing Hh and PI3K-Akt signaling. AAV-mediated MEST inhibition or exogenous SM administration in vivo also alleviates tHO progression. These findings may provide novel insights into tHO pathogenesis and potential therapeutic strategies.

molecular biology↗

bioRxiv2025

Genomic factors limiting the diversity of Saccharomycotina plant pathogens

The Saccharomycotina fungi have evolved to inhabit a vast diversity of habitats over their 400-million-year evolution. There are, however, only a few known fungal pathogens of plants in this subphylum, primarily belonging to the genera Eremothecium and Geotrichum. We compared the genomes of 12 plant-pathogenic Saccharomycotina strains to 360 plant-associated strains to identify features unique to the phytopathogens. Characterization of the oxylipin synthesis genes, a compound believed to be involved in Eremothecium pathogenicity, did not reveal any differences in gene presence within or between the plant-pathogenic and plant-associated strains. A reverse-ecological approach, however, revealed that plant pathogens lack several metabolic enzymes known to assist other phytopathogens in overcoming plant defenses. This includes L-rhamnose metabolism, formamidase and nitrilase genes. This result suggests that the Saccharomycotina plant pathogens are limited to infecting ripening fruits as they are without the necessary enzymes to degrade common phytohormones and secondary metabolites produced by plants.

genomics↗

bioRxiv2025

The 16p11.2 microdeletion influences how early-life microbiota perturbations affect hippocampal development and behavior throughout the lifespan

Neurodevelopmental disorders (NDDs) arise from interactions between genetic factors and environmental exposures, with infancy representing a critical period of vulnerability. This exploratory, preclinical study investigated whether the 16p11.2 microdeletion (16pDel), a NDD-associated genetic variant, exacerbates the effects of early-life therapeutic antibiotic exposure on the gut microbiome, hippocampal development, and behavior. Cefdinir, selected for its epidemiological association with NDD risk, acutely perturbed the gut microbiome, causing sustained reductions in Lachnospiraceae. These changes were followed by alterations in sociability, risk assessment, and associative learning. Notably, only cefdinir-exposed 16pDel mice exhibited altered hippocampal stem cell dynamics and gene expression, demonstrating genotype-dependent susceptibility. Increased intestinal permeability and alterations in arginine biosynthesis and glycerophospholipid metabolism implicate gut barrier dysfunction as a contributing factor. Our findings suggest that genetic composition can exacerbate neurodevelopmental consequences of early-life microbiome perturbations, identify metabolic pathways for potential interventions, and support cautious antibiotic use during infancy, especially in genetically vulnerable populations.

neuroscience↗

bioRxiv2025

A simple method for mapping the location of cross-β forming regions within protein domains of low sequence complexity

Protein domains of low sequence complexity are unable to fold into stable, three-dimensional structures. In test tube studies, these unusual polypeptide regions can self-associate in a manner causing phase separation from aqueous solution. This form of protein:protein interaction has been implicated in numerous examples of dynamic morphological organization within eukaryotic cells. In several cases, the basis for low complexity domain (LCD) self-association and phase separation has been traced to the formation of labile cross-{beta} structures. The primary energetic force favoring formation of these transient and reversible structures is enabled by polypeptide backbone interactions. Short, contiguous networks of peptide backbone amino groups and carbonyl oxygens are zippered together intermolecularly by hydrogen bonding as described by Linus Pauling seven decades ago. Here we describe a simple, molecular biological method useful for the identification of localized, self-associating regions within larger protein domains of low sequence complexity. SignificanceThis study describes a molecular biological method for analyzing protein domains of low sequence complexity in search of segments that mediate self-association and consequent phase separation both in vitro and in vivo. Small regions allowing for self-association correspond to sequences that specify the formation of labile cross-{beta} structural order. When juxtaposed to the C-terminus of GFP, cross-{beta} prone regions suppress fluorescence. A tiled scan of overlapping fragments of the low complexity domain (LCD) of the TDP-43 RNA binding protein pinpointed an evolutionarily conserved sequence of twenty amino acids essential for self-association, phase separation and the formation of nuclear speckles. The screening method described herein should be useful for the analysis of any LCD believed to function via homotypic self-association.

biochemistry↗

bioRxiv2025

CDK8 remodels the tumor microenvironment to resist the therapeutic efficacy of targeted KRASG12D inhibition in pancreatic ductal adenocarcinoma

Mutations in KRAS are a dominant driver of pancreatic ductal adenocarcinoma (PDAC), with over 40% of PDAC patients presenting with KRASG12D mutations. The recent development of small molecule inhibitors targeting KRASG12D has enabled targeting of mutant KRAS signaling and suppression of PDAC; however, the contribution of the tumor microenvironment (TME) to the sustained therapeutic efficacy of KRASG12D inhibition and mechanism/s of resistance to KRASG12D suppression remain to be elucidated. Here, we employed spatial transcriptomics, single cell RNA sequencing, and CODEX-based spatial proteomics to evaluate cancer cell intrinsic and extrinsic responses to KRASG12D inhibition with MRTX1133. While KRASG12D inhibition initially increases CD11c+ cells with impactful T cell infiltration within proximity to cancer cells, long-term treatment with MRTX1133 resulted in reversal of the immune responses leading to KRASG12D therapy resistance promoted by CDK8, a multiprotein mediator complex associated kinase. CDK8 imparts resistance in part through induction of downstream CXCL2 chemokine secretion, inhibition of FAS expression, and remodeling of the TME to promote immune evasion. Targeting CDK8 by itself and in combination with CTLA-4 immunotherapy overcomes resistance to KRASG12D inhibition with prolonged survival with translational implications.

cancer biology↗

bioRxiv2025

FastCCC: A permutation-free framework for scalable, robust, and reference-based cell-cell communication analysis in single cell transcriptomics studies

Detecting cell-cell communications (CCCs) in single-cell transcriptomics studies is fundamental for understanding the function of multicellular organisms. Here, we introduce FastCCC, a permutation-free framework that enables scalable, robust, and reference-based analysis for identifying critical CCCs and uncovering biological insights. FastCCC relies on fast Fourier transformation-based convolution to compute p-values analytically without permutations, introduces a modular algebraic operation framework to capture a broad spectrum of CCC patterns, and can leverage atlas-scale single cell references to enhance CCC analysis on user-collected datasets. To support routine reference-based CCC analysis, we constructed the first human CCC reference panel, encompassing 19 distinct tissue types, over 450 unique cell types, and approximately 16 million cells. We demonstrate the advantages of FastCCC across multiple datasets, most of which exceed the analytical capabilities of existing CCC methods. In real datasets, FastCCC reliably captures biologically meaningful CCCs, even in highly complex tissue environments, including differential interactions between endothelial and immune cells linked to COVID-19 severity, dynamic communications in thymic tissue during T-cell development, as well as distinct interactions in reference-based CCC analysis.

bioinformatics↗

bioRxiv2025

A niche-dependent redox rheostat regulates epithelial stem cell fate in the distal colon

The niche environment surrounding intestinal stem cells (ISCs) varies along the length of intestine and provides key cues that regulate stem cell fate. Here, we investigated the role of cellular redox balance in colonic ISC function. We show that hypoxia and Wnt signaling synergize to restrict the reactive oxygen species (ROS) generating enzyme NADPH oxidase 1 (NOX1) to the crypt base in the distal colon. NOX1 function maintains a more oxidative cell state that licenses cell cycle entry, altering the balance of asymmetric stem cell self-renewal and directing lineage commitment. Mechanistically, cell redox state directs a self-reinforcing circuit that connects hypoxia inducible factor 1 (HIF1)-dependent signaling with regulation of the metabolic enzyme isocitrate dehydrogenase 1 (IDH1). Our studies show that cellular redox balance is a central and niche-dependent regulator of epithelial homeostasis and regeneration and provide a basis for understanding disease propensity in the distal large intestine. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/634856v2_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@107798aorg.highwire.dtl.DTLVardef@1bc9013org.highwire.dtl.DTLVardef@96d56aorg.highwire.dtl.DTLVardef@95268d_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIThe balance of cycling intestinal stem cells (ISCs) versus committed epithelial cells in the uniquely hypoxic niche of the distal colon is regulated by NADPH oxidase 1 (NOX1) dependent H2O2 both at homeostasis and during regeneration. C_LIO_LIPhysiological increase in cellular H2O2 favors maintenance of glycolysis in ISCs for self-renewal through regulation of isocitrate dehydrogenase 1 activity. C_LIO_LIMaintenance of the increased cellular oxidative state stabilizes HIF1 through a re-enforcing metabolic circuit. C_LIO_LIA shift from a relatively oxidative to a reductive cell environment in distal colonic ISCs leads to decreased progression through the cell cycle and altered cell fate determination. C_LI

cell biology↗

bioRxiv2025

Vaccination with mRNA-encoded membrane-bound HIV Envelope trimer induces neutralizing antibodies in animal models

A protective vaccine against HIV will likely need to induce broadly neutralizing antibodies (bnAbs) that engage relatively conserved epitopes on the HIV envelope glycoprotein (Env) trimer. Nearly all vaccine strategies to induce bnAbs require the use of relatively complex immunization regimens involving a series of different immunogens, most of which are Env trimers. Producing protein-based clinical material to evaluate such relatively complex regimens in humans presents major challenges in cost and time. Furthermore, immunization with HIV trimers as soluble proteins induces strong non-neutralizing responses to the trimer base, which is normally occluded on the virion. These base responses could potentially detract from the induction of nAbs and the eventual induction of bnAbs. mRNA vaccine platforms offer potential advantages over protein delivery for HIV vaccine development, including increased production speed, reduced cost, and the ability to deliver membrane-bound trimers that might facilitate improved immuno-focusing to non-base epitopes. We report the design of mRNA-delivered soluble and membrane-bound forms of a stabilized native-like Env trimer (BG505 MD39.3), initial immunogenicity evaluation in rabbits that triggered clinical evaluation, and more comprehensive evaluation of B cell, T cell, and antibody responses in non-human primates. mRNA-encoded membrane-bound Env immunization elicited reduced off-target base-directed Env responses and stronger neutralizing antibody responses, compared with mRNA-encoded soluble Env. Overall, mRNA delivery of membrane-bound Env appears promising for enhancing B cell responses to subdominant epitopes and facilitating rapid translation to clinical testing, which should assist HIV vaccine development. One Sentence SummaryHIV envelope trimer mRNA enables membrane-bound expression and represents a functional immunogen in pre-clinical mammalian models.

immunology↗

bioRxiv2025

A method for inducing a senescence trend in mesenchymal stem cells using D-galactose

The aging of the body is accompanied by a decline in tissue function, and this decline mainly stems from the aging of tissue stem cells. Therefore, they play a crucial role in the aging of the body.This study explores the biological characteristics of senescent hUCMSCs by establishing a replicative senescence model of hUCMSCs and a rapid senescence model induced by D - galactose (D-Gal), and analyzing the proliferative capacity, cell viability, cell cycle, pluripotency, and reactive oxygen species (ROS) levels of senescent hUCMSCs.

cell biology↗

bioRxiv2025

Sequencing-based Spatial Transcriptomics with scRNA-seq Sensitivity

The advent of spatial transcriptomics has dramatically expanded our ability to study the vast network of cell-cell interactions at the molecular level in tissue. Among current methods, sequencing-based approaches have great potential in discovering because of its unbiased capture. In the last couple of years, the spatial resolution for the capture addresses has been significantly improved from 100 m to <1 m, well below the size of a mammalian cell. However, the capture efficiency has always been a pain point, [~]one order of magnitude lower than that of single cell RNA sequencing (scRNA-seq). The low capture efficiency limits the depth and breadth of its applications in the study of complex biological systems and diseases. Here, we introduce Salus Spatial transcriptomic system (Salus-STS), which provides [~]1 m capture resolution and a capture efficiency [~]1 order of magnitude higher than other current methods. Analysis with sub-cellular resolution becomes practical for sequencing-based spatial transcriptomics.

molecular biology↗

bioRxiv2025

Preclinical Evaluation of P4B-2412 as Phosphodiesterase 4B Radioligand for Positron Emission Tomography Imaging

Phosphodiesterase 4B (PDE4B) plays a critical role in cAMP hydrolysis and is highly expressed in brain regions associated with neuroinflammation and neurodegenerative disorders. Selective PDE4B radioligands hold significant potential for elucidating disease mechanisms and enabling target occupancy measurements. In this study, we developed [18F]P4B-2412, a novel PDE4B-selective radioligand, and evaluated its utility for PET imaging. [18F]P4B-2412 was synthesized with high radiochemical yield (27.2%), excellent radiochemical purity (99%), and favorable molar activity (66.2 {+/-} 2.5 GBq/mol). In vitro autoradiography revealed high PDE4B binding, while dynamic PET imaging demonstrated high in vivo specificity for PDE4B in rodent brain regions. Notably, [18F]P4B-2412 exhibited excellent metabolic stability in vitro and in vivo. These findings establish [18F]P4B-2412 as a promising PET probe for imaging PDE4B in vivo, offering a valuable tool for investigating neuroinflammation and advancing CNS drug development.

neuroscience↗

bioRxiv2025

ATP-sensitive isoforms of P2X5: A reevaluation of its function across species

The P2X receptor family comprises ATP-gated non-selective cation channels central to physiological processes across the nervous, immune, cardiovascular, respiratory, and reproductive systems. While P2X1, P2X2, P2X3, P2X4, and P2X7 are well-established as ATP-sensitive, P2X5 isoforms and transcript variants (TVs) have traditionally been considered ATP-insensitive, limiting their functional exploration. This study identifies previously overlooked ATP-sensitive P2X5 isoforms across diverse species. Through gene profiling and next-generation sequencing (NGS), we found that the zfP2X5TV2 isoform dominates ATP-sensitive forms in zebrafish. In mice, ATP-sensitive mP2X5G317 (mP2X5.1) comprises [~]90% of transcripts, while in rats, exon 3-containing rP2X5F191 accounts for over 70%. In human cell lines, ATP-sensitive isoforms retaining exons 3, 7, and 10 represent [~]15-30% of P2X5 transcripts. RNA-seq from human tissues confirms frequent retention of exons 3 and 7 and polymorphic exon 10 expression. ATP-sensitive P2X5 variants were also identified in chickens, bullfrogs, dogs, cows, and naked mole-rats. These findings challenge the prevailing assumption of ATP-insensitivity, highlighting the need to reassess P2X5s roles in physiological and pathological contexts.

physiology↗

bioRxiv2025

Dynamic face-related eye movement representations in the human ventral pathway

Multiple brain areas along the ventral pathway have been known to represent face images. Here, in a magnetoencephalography (MEG) experiment, we show dynamic representations of face-related eye movements in the ventral pathway in the absence of image perception. Participants followed a dot presented on a uniform background, the movement of which represented gaze tracks acquired previously during their free-viewing of face and house pictures. We found a dominant role of the ventral stream in representing face-related gaze tracks, starting from the orbitofrontal cortex (OFC) and anterior temporal lobe (ATL), and extending to the medial temporal and ventral occipitotemporal cortex. Our findings show that the ventral pathway represents the gaze tracks used to explore faces, by which top-down prediction of face category in OFC and ATL may guide, via the medial temporal cortex or directly, face perception in the ventral occipitotemporal cortex.

neuroscience↗

bioRxiv2025

Non-mutated human tau stimulates Alzheimer's disease-relevant neurodegeneration in a microglia-dependent manner

The accumulation of abnormal, non-mutated tau protein is a key pathological hallmark of Alzheimers disease (AD). Despite its strong association with disease progression, the mechanisms by which tau drives neurodegeneration in the brain remain poorly understood. Here, we selectively expressed non-mutated or mutated human microtubule-associated protein tau (hMAPT) in neurons across the brain and observed neurodegeneration in the hippocampus, especially associated with non-mutated human tau. Single-nuclei RNA sequencing confirmed a selective loss of hippocampal excitatory neurons by the wild-type tau and revealed the upregulation of neurodegeneration-related pathways in the affected populations. The accumulation of phosphorylated tau was accompanied by cellular stress in neurons and reactive gliosis in multiple brain regions. Notably, the lifelong absence of microglia significantly and differentially influenced the extent of neurodegeneration in the hippocampus and thalamus. Therefore, our study established an AD-relevant tauopathy mouse model, elucidated both neuron-intrinsic and neuron-extrinsic responses, and highlighted critical and complex roles of microglia in modulating tau-driven neurodegeneration.

neuroscience↗