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Zhou, W.

Publications and source records attributed to Zhou, W..

At least 55 records · Page 3Linked to original sources

A ventral tegmental area GABAergic projection to the ventral pallidum regulates value-based decision making in mice

Activity of the mesolimbic system is essential for adaptive performance of reward-related behaviors. Within this system, dopaminergic (DAergic) neurons play a critical role in driving motivation to obtain rewards and encoding predictions and error signals during reinforcement learning. However, activity of DAergic neurons shifts from reward presentation to predictive cues following cue-reward learning, leaving open questions about the mechanism of subjective reward value representation. Our previous studies suggest that activity of a GABAergic circuit originating from the ventral tegmental area (VTA) and projecting to the ventral pallidum (VP) scales with unconditioned reward value, independent of effort or associative cue-reward learning. Here, we demonstrate that activity in this pathway consistently reflects unconditioned reward value across extended cue-reward training, unlike DA activity, which undergoes dynamic changes toward the cue and away from a predicted reward. VTA-to-VP GABA activity tracks internal-state-dependent reward value, showing minimal response to water drinking in sated mice and strong activity after overnight dehydration. In a two-option probabilistic operant reward task (PRT), optogenetic activation of this pathway upon reward consumption biased decision-making toward the stimulation-paired option, even when its reward was of lesser value. These findings identify a previously uncharacterized circuit that encodes reward value and contributes to value-based decision-making. Significance StatementAdaptive behavior depends on accurate representation of reward value. While dopamine (DA) signals shift from rewards to predictive cues during learning, the neural encoding of unconditioned reward value has remained elusive. We identify a GABAergic projection from the VTA to the VP that stably encodes unconditioned reward value across extended training, yet tracks changes in internal state such as thirst. Unlike DA activity, this pathway consistently reflects reward consumption and, when stimulated, biases choice toward otherwise less-preferred options. These findings uncover a stable but state-sensitive mechanism of reward value encoding, providing a new framework for understanding value-based decision-making and its disruption in neuropsychiatric disorders.

neuroscience↗

Genomic insights into rapid diversification and adaptive introgression in the earthworm Amynthas aspergillum

How species diversify in highly fragmented landscapes while maintaining genetic connectivity remains a central question in evolutionary biology. The megascolecid earthworm Amynthas aspergillum exemplifies this paradox, showing deeply divergent mitochondrial lineages despite extensive nuclear gene flow across southern China. We conducted whole-genome resequencing across its core distribution in the Guangxi karst region to elucidate the population structure and processes underlying this cytonuclear discordance. Genome-wide analyses identified three genetically distinct groups shaped by fine-scale karst isolation, alongside pervasive historical and contemporary introgression. Demographic modeling revealed rapid diversification during the Late Pleistocene ([~]0.14LJMa) with pronounced fluctuations in effective population size. Although isolation increased inbreeding and mutational load in some lineages, introgression persisted even among deeply divergent mitochondrial clades. Notably, several introgressed regions showed strong signatures of positive selection, including genes involved in mitochondrial function and metabolism.Together, these results demonstrate that gene flow can simultaneously mitigate the genomic costs of isolation and promote functional innovation via adaptive introgression, providing a genomic framework for diversification with gene flow in subterranean invertebrates inhabiting fragmented karst landscapes.

genomics↗

Integrated Multi-omics Analysis Identifies Molecular Signatures of Regular Physical Activity in Human Peripheral Blood

Regular physical activity is well established to protect against metabolic disorders and bolster immunity; yet, the underlying molecular and cellular mechanisms remain incompletely understood. We integrated plasma metabolomics and lipidomics with single-cell transcriptomic and chromatin accessibility profiles to decode the systemic impact of physical activity on human immunity and metabolism. Our data reveal that regular physical activity is linked to a coordinated metabolic signature marked by enhanced fatty acid oxidation and antioxidant defense. In circulating immune cells, regularly active individuals exhibited synchronous enhancement at both the chromatin accessibility and transcriptional levels for antigen presentation-related genes in antigen-presenting cells (APCs), particularly in classical monocytes, naive B cells, and switched memory B cells. Meanwhile, cytotoxic programs in CD8+ cytotoxic T and mature NK cells showed epigenetic pre-activation of effector function regulators. Intercellular communication analysis further revealed that regular exercise enhanced MHC-I/II signaling between APCs and T cells and suppressed inflammatory signaling networks. Together, these findings elucidate molecular mechanisms underlying the health benefits of regular exercise and offer a theoretical basis for enhancing public health and preventing chronic diseases.

bioinformatics↗

Single-Cell Multi-Omics Insights into BMI-Mediated Immune-Related Disease Risk

This study is based on the Chinese Immune Multi-Omics Atlas (CIMA) cohort and performs an integrated single-cell multi-omics analysis of peripheral blood mononuclear cells (PBMCs) from 210 individuals aged 20-29, comprising 3,311,699 scRNA-seq cells and 1,839,860 scATAC-seq cells, to decipher immune characteristics across different body mass index (BMI) categories. By integrating gene regulatory network (GRN) and cell type-level molecular quantitative trait loci (xQTL) data, and conducting summary-data-based Mendelian randomization (SMR) analysis in conjunction with genome-wide association studies (GWAS) of BMI-mediated immune-related diseases, we identified key disease-associated cell types and molecular features. Using rheumatoid arthritis (RA) as an example, multi-omics evidence revealed that in MAIT-SLC4A10 cells of underweight individuals, increased chromatin accessibility at the CCR6 locus (chr6:167119627-167120128) and enhanced transcriptional activity of RORC/RORA collectively drive elevated CCR6 expression, which may represent a potential molecular mechanism underlying the higher risk of RA in underweight populations. Our study leverages single-cell multi-omics data to systematically dissect the molecular mechanisms by which different BMI categories mediate susceptibility to immune-related diseases through coordinated regulation of immune cell chromatin accessibility, transcription factor activity, and downstream gene expression.

bioinformatics↗

Molecular Mechanisms of Priming Innate Immunity by Small Extracellular Vesicles Released during Infection with Gram-negative Bacteria

Much still remains to understand about the underlying molecular mechanisms by which the trafficking of small extracellular vesicles (sEVs) modulates innate immune responses during infection with pathogenic Gram-negative bacteria. To address this significant gap in knowledge, we used two infection models to investigate innate immune regulation by the sEVs released from cells infected with either Yersinia pestis (Yp) or Burkholderia thailandensis (Bt), designated as EXi-Yp and EXi-Bt respectively. The EXi induced differentiation of naive human monocytes to macrophages and triggered robust pro-inflammatory cytokine release, including release of IL-6, mirroring direct bacterial infection effects. Comprehensive cell signaling analyses revealed that the EXi modulate a small set of host signaling proteins, with p38 activation being primarily responsible for the observed protective effects. EXi-induced p38 activation leads to increased IL-6 release, which in turn is responsible for decreased bacterial survival within recipient immune cells that are subsequently infected. Consistent with the in vitro results, mice administered with EXi-Yp exhibited elevated serum IL-6 levels and were protected from Yp infection. Furthermore, using our microfluidic chip platform that allows functional interrogation of EV effects under physiologically relevant conditions, we have demonstrated that EXi exchange between Yp-infected cells and naive recipient monocytes leads to differentiation of the recipient cells to macrophages. Together, our findings reveal a largely unexplored aspect of innate immunity and provide a mechanistic model in which EXi prime local and distant naive monocytes via p38-induced differentiation and IL-6 production to protect against infection with Gram-negative bacteria.

immunology↗

Shared TCRs in peripheral blood offer robust celiac disease classification independent of gluten Intake

Background and AimsCeliac disease (CeD) is a chronic digestive autoimmune disorder affecting approximately 1% of the worldwide population. It is driven by T cells activated by specific HLA-DQ2 or HLA-DQ8 molecules leading to the destruction of intestinal villi. We aimed to characterize shared CeD-specific T cells in patients on and off a gluten-free diet (GFD) from a large cohort of cases and controls. MethodsWe performed bulk TCR{beta} immune sequencing of the peripheral blood of 1,604 biopsy-confirmed CeD patients (1,339 on GFD, 265 on normal diet) and 1,100 controls. We identified over 300 TCR{beta}s enriched in CeD cases versus controls in an HLA-aware manner, controlling for CeD risk alleles. ResultsCeD-associated TCR{beta}s were found to be more predictive of disease than previously characterized gliadin and glutenin-binding TCRs in a validation cohort. Furthermore, the clonal breadth of these TCR{beta}s was associated with increased intestinal damage. Immune sequencing of the peripheral blood also uncovered repertoire-level differences between CeD patients and controls. CeD patients displayed significantly higher productive clonality compared to age-matched controls as well as expansion of TCR{beta}s specific to cytomegalovirus (CMV) and Epstein-Barr Virus (EBV). ConclusionsThese findings underscore the value of unbiased immune repertoire sequencing to identify novel biomarkers for autoimmune disease and to discover new disease mechanisms which can improve both diagnosis and treatment of disease.

immunology↗

Nuclear N-Glycosylation Redefines the Glycoscape and Directs Cell Identity

Glycans modify nucleic acids, proteins and lipids in fundamental biological processes, but have long been considered confined to the secretory pathway and cell surface. Here, we challenge this view with evidence that N-glycosylation, a ubiquitous glycan modification, occurs within cell nuclei across tissues and species, exhibiting cell type-dependent abundance and localization patterns. Using a multi-faceted approach, we show that numerous classical membrane and secreted glycoproteins localize to the nucleus with N-glycan modifications, exemplified by the cell adhesion molecule L1CAM. Mechanistically, we show that the N-glycosylated L1CAM is transported to the nucleus by KPNB1, where it transcriptionally modulates neuronal differentiation. Moreover, this nuclear N-glycosylation event contributes to neurodevelopmental disorders and is pharmacologically reversible. These findings revise the cellular geography of N-glycosylation and expand the known routes of protein trafficking, and highlight nuclear N-glycosylation pathways as potential therapeutic entry points for developmental disorders.

cell biology↗

Bypassing the Batch Effects to Improve the Reusability of RAD-seq Data: A Case Study of Recurrent Hybridization in the Japanese Torreya Species Complex

Understanding the evolutionary effects of natural hybridization in gymnosperms remains limited due to their large genome sizes and frequent reliance on sparce molecular data. In this study, we reassessed the evolutionary history and taxonomy of the Japanese Torreya species complex (T. nucifera) by integrating the morphological characteristics, environmental niches, and molecular evidence. We developed RADADOR version 2 to overcome allele dropout (ADO) issues in RAD-seq data sets. This version of RADADOR enabled us to recover ADO loci using low-coverage whole genome sequencing (lc-WGS) data ([~]5-10X coverage). We integrated previously generated plastome and RAD-seq data with whole genome data to build robust, genome-wide phylogenies. Subsequently, we employed PhyloNet to detect hybridization events in Torreya and utilized a fossilized birth-death model to estimate the formation times of Japanese Torreya species. Our phylogenetic results indicated conflicting nuclear and plastome topologies and suggested two historical hybridization events in Japanese Torreya. One ancient hybridization between T. nucifera and a North American lineage likely contributed to the origin of T. fruticosa, while a more recent event may have generated a putative hybrid in regions where their distributions overlap. Integrating the lc-WGS data and RAD-seq data in a reproducible framework revealed the complex reticulate evolution of Torreya in Japan and underscores the repeated contribution of inter-specific hybridization to the evolution of gymnosperms.

evolutionary biology↗

Graded Hair Cell Ablation Reveals Functional Redundancy in the Mature Mouse Vestibular System

Inner ear hair cells are mechanoreceptors critical for hearing and balance. Damage to vestibular hair cells causes balance impairment, yet it is unclear whether hair cell loss correlates with vestibular dysfunction. In this study, we ablated hair cells in Pou4f3DTR/+ mice with diphtheria toxin (DT), and found a dose-dependent decrease in hair cell survival in both the macula and crista ampullaris, including loss of type I and II hair cells in the striolar/central and extrastriolar/peripheral regions. Responses to linear acceleration, measured by the translational vestibulo-ocular reflex (tVOR) and vestibular sensory evoked potential (VsEP), were intact with 25% or more hair cell survival in the macula, and diminished only when hair cell survival decreased further. By contrast, rotational vestibulo-ocular reflex (rVOR) responses were significantly reduced with [~]31% hair cell survival in the cristae. Further, single-unit recordings of vestibular afferents from cristae and maculae showed more irregular and reduced firing rates, but only those corresponding to cristae displayed reduced sensitivity to head rotation. Limited hair cell regeneration was observed in the extrastriolar/peripheral regions of both maculae and cristae 6 months post ablation, although no significant recovery of the VORs was observed. Thus, the adult mouse vestibular end organs display different degrees of redundancy, demonstrating robust responses to head rotation and linear acceleration despite loss of most hair cells.

neuroscience↗

Single-Cell Multi-Omics Dissects Transcript Isoform and Immune Repertoire Dynamics in Human Immunosenescence

Immunosenescence, a major hallmark of systemic aging, refers to the progressive functional decline of the immune system. This decline not only compromises host defense and immunological memory but also fuels chronic inflammation and tissue degeneration (collectively known as inflammaging). While single-cell RNA sequencing (scRNA-seq) has revealed transcriptomic alterations in immune aging, analyses restricted to transcript abundance fail to capture deeper regulatory layers, such as transcript isoform diversity and the remodeling of immune receptor repertoires. To address this, we present the human peripheral immune single-cell multi-omics atlas that integrates gene expression, transcript isoforms diversity, and immune receptor repertoires. By combining single-cell full-length transcriptome sequencing (scCycloneSEQ), short-read scRNA-seq, and single-cell immune receptor sequencing (scTCR/BCR-seq), we systematically profiled peripheral blood mononuclear cells (PBMCs) from healthy young and elderly donors. Our analyses uncovered extensive age-related remodeling of immune cell composition, functional states, and TCR/BCR diversity. Notably, we identified in CD4 effector memory T cells exhibited widespread differential isoform usage (DIU), 3'UTR length variation, and a marked reshaping of cytotoxic T lymphocyte (CTL) clonotypes--all closely associated with aging-related inflammation and cellular senescence. This multi-omics atlas delineates key molecular features of immunosenescence and provides a high-resolution resource for deciphering the regulatory architecture underlying immune aging.

immunology↗

A unified language model bridging de novo and fragment-based 3D molecule design delivers potent CBL-B inhibitors for cancer treatment

The rational design of small molecules is central to drug discovery, yet current artificial intelligence (AI) methodologies for generating three-dimensional (3D) molecules are often siloed, focusing on either de novo design or fragment-based design. The lack of a holistic framework limits AIs application across the complex and multi-step pipeline spanning from novel scaffold identification to lead compound optimization, and prevents AI from effectively learning from the entire process. Here, we introduce UniLingo3DMol, a language model for 3D molecular generation, empowered by fragment permutation-capable molecular representation alongside multi-stage and multi-task training strategy. This integrated design enables UniLingo3DMol to seamlessly span both de novo and fragment-retained molecular design, demonstrating superior performance over existing generation models in in silico evaluations across more than 100 diverse biological targets. We further leveraged UniLingo3DMol in the design of inhibitors targeting CBL-B, a crucial immune E3 ubiquitin ligase and attractive immunotherapy target. This strategy led to a lead compound demonstrating excellent in vitro activity and robust in vivo anti-tumor efficacy. Our findings establish UniLingo3DMol as a generalized and powerful platform, showing the strong potential to advance AI-driven drug discovery.

bioinformatics↗

Mutant p53 binds RNA to drive mitochondrial dysfunction

Tumor suppressor protein 53 (p53) is a transcription factor that is deregulated in 50% of cancers. Often termed the guardian of the genome, p53 is responsible for maintenance of genomic stability, cell cycle arrest, DNA repair, senescence, and apoptosis. In cancer cells, deregulation of p53 often occurs through mutations in the DNA binding domain which lead to a loss of the transcriptional activity. While 100s of somatic mutations in the DNA binding domain are known, a small number of mutants are enriched in cancer, suggesting a gain-of-function role. Here we deploy an intein-based approach to localize {micro}Map photoproximity labeling to p53 to define novel interactions contributing to the loss and gain of function roles of 5 separate hotspot mutants. These data revealed that G245S and R273H binds to RNA through its C-terminal domain. We show through CLIP experiments that mutant p53 has an RNA binding motif that conserved across mutants and is enriched in 3UTRs, promoting ribosomal localization and labeling of proteins at the mitochondrial surface. We further demonstrate that the RNA binding ability of mutant p53 promotes altered miRNA processing and mitochondrial dysfunction providing mechanistic rationale for historically reported but poorly understood phenotypes.

molecular biology↗

FlAsH-ID: A short peptide tag for live cell photoproximity labeling

Methods to determine how biomolecules interact in a cellular context has led to significant advances in our understanding of biology. Of these, proximity labeling has emerged as a valuable tool for the interrogation protein-protein and protein-RNA interactions. Almost all proximity labeling methods are deployed via large fusion proteins, which while powerful in many contexts, can disrupt native biology or obscure important epitopes on the protein under study. This challenge is especially prominent for small transcriptionally active proteins where the protein cistrome is vital for correct localization and function. Here, we have developed a photoproximity labeling method that is localized to a short 6 amino acid peptide sequence that employs the combination of the Tsien tetracysteine tag with FlAsH dye for localized singlet oxygen generation that we term FlAsH-ID. We demonstrate this method is non toxic and can be employed to label several cellular compartments, and generate high quality interactomics data around H3.1. Furthermore, we show that FlAsH-ID can be used to probe dynamic chnages in protein movement in response to immune stimuli, identifying several RNA-binding protiens that are trafficked to the nucleus following poly(I:C) treatment. Finally we demonstrate FlAsH-ID can be used for proximity proteomics in primary CD8+ T cells by focusing on the transcription factor RUNX3. RUNX3-tetracysteine, but not RUNX3-TurboID, recaptiulated the function of wildtype RUNX3 and rescued the phenotype of Runx3-deficeint CD8+ T cells in response to viral infection in vivo. In primary CD8+ T cells, FlAsH-ID identified RUNX3 in proximity to the nucleosome remodeler ARID1A and we show that both factors act concertedly during initial naive CD8+ T cell activation to drive chromatin accessibility in cis-regulatory regions that induce differentiation of effector and long-lived memory CD8+ T cells. Our results suggest this technique will expand the field of proximity labeling to small, functionally sensitive proteins in primary cells without perturbing their function.

molecular biology↗

A Druggable Tumor Suppressor and Leukemic Stem Cell Marker

Withdrawal StatementThe authors have withdrawn this preprint because the co-authors were not in agreement about posting the work in its current form. The authors request that this work not be cited. Please contact the corresponding author (Dr. Xunlei Kang, kangxu@health.missouri.edu) with questions.

cancer biology↗

DEEPReditor-CMG: A deep-learning-based predictive RNA editor for crop mitochondria genomes

C-to-U RNA editing is a pervasive phenomenon in crop mitochondria, playing a pivotal role in the processing of functional proteins encoded by mitochondrial genes and serving as a crucial regulatory mechanism for nuclear control over mitochondrial gene expression. However, identifying editing sites across the mitochondrial genome with high precision remains a formidable challenge. To address this challenge and uncover the potential regulatory patterns of C-to-U RNA editing, this study compiled a comprehensive dataset of mitochondrial genome sequences from 13 crops, including Arabidopsis thaliana, Lactuca sativa var. Capitata, Oryza sativa Japonica, and Zea mays, among others, annotated with editing sites from NCBI. Utilizing TensorFlow 2.0, we constructed a rigorous hyperparameter optimization framework, which facilitated the development of the DEEPReditor-CMG model, demonstrating superior predictive capabilities. Based on the DEEPReditor-CMG model and three interspecies relationship indices, we discovered that species with closer phylogenetic relationships exhibit more similar C-to-U RNA editing mechanisms, providing valuable insights into the evolutionary conservation of RNA editing mechanisms. We further developed executable programs for predicting C-to-U RNA editing sites in crop mitochondrial genomes, leveraging the conserved nature of the crop RNA editing machinery to maximize prediction reliability and uncover new editing sites with great potential. This research not only deepens our understanding of C-to-U RNA editing and post-transcriptional regulatory mechanisms in crop mitochondria but also paves a novel avenue for investigating RNA editing mechanisms. Experimental data, computational code, and applications are publicly accessible at https://github.com/Qinsidong/DEEPReditor-CMG. HighlightsHigh-precision prediction model for C-to-U RNA editing in crops--DEEPReditor-CMG Three interspecies relationship indices describing C to U RNA editing Prediction tools based on the conservation of crop RNA editing mechanisms Open-sourced experimental data, computational code, and applications

bioinformatics↗

Pharmacological Induction of Irreversible Senescence in Drug-Tolerant Persister Cells Prevents Tumor Relapse

Despite substantial advances in targeted therapies, most patients with advanced cancers ultimately relapse. This relapse is frequently seeded by drug-tolerant persister cells (DTPs), which persist as minimal residual disease (MRD) by adopting a reversible quiescent state and later reacquire proliferative capacity under ongoing treatment. To address this, we sought to convert quiescent DTPs into an irreversible, non-proliferative state by pharmacologically inducing senescence. Through large-scale chemical screening and combination optimization, we identified SAHA plus tilorone dihydrochloride (SIC) as a regimen that robustly induces senescence in melanoma DTPs and abolishes their proliferative potential in vitro. Mechanistically, SAHA relieves HDAC1-mediated repression of HMGA2, a key senescence driver, while tilorone synergistically inhibits autophagy to promote a fully senescent state. In a melanoma xenograft mouse model receiving MAPK-targeted therapy, SIC treatment significantly suppressed MRD progression. Importantly, SIC also induced robust senescence across diverse DTP models irrespective of tumor origin, mutational background, or prior treatment. Collectively, these findings provide proof-of-concept that converting DTPs from reversible quiescence to permanent senescence represents an effective strategy to prevent relapse under targeted therapy and position SIC as a broadly applicable pharmacological approach for durable control of residual disease in advanced cancers.

cancer biology↗

Global Mapping of Combinatorial Chromatin Regulatory Events Using Hi-Plex CUT&Tag

Epigenetic modulators, transcription factors, and chromatin-associated proteins collaboratively regulate essential genomic functions, such as transcription, repression, and DNA damage repair. However, the intricate cross-talk or the interaction between these chromatin regulatory factors (CRFs) remains poorly understood, largely due to limitations in experimental methods, which traditionally interrogate the genomic locations of only one CRF. Although the latest methods can study multiple CRFs simultaneously, they cannot examine the interaction between these factors. Inferring biological interactions often requires integrating data from multiple experiments, which can be labor-intensive and imprecise since the measurement is not from the same DNA molecule. To address these challenges, we developed Hi-Plex CUT&Tag, an advanced technology that enables the robust detection of co-localization events across over 600 pairs of CRFs using 36 barcoded monoclonal antibodies (mAbs), while minimizing background signals and cross-contamination. Hi-Plex CUT&Tag facilitates comprehensive pairwise analysis of epigenetic modifiers, including histone post-translational modifications (PTMs), writers, and transcription factors (TFs). Each Tn5 tagmentation fragment provides detailed insights, capturing the identities of two co-localized events, the underlying genomic sequences, and the molecular distance between them. For the first time, numerous novel bivalent events, epigenetic-context-dependent transcriptional regulation, and specific chromatin mark combinations with significant impacts on gene regulation can be detected in a single experiment. Furthermore, single-cell Hi-Plex CUT&Tag enables the analysis of synergistic interactions between CRF pairs at the single-cell level, providing unprecedented resolution for studying chromatin dynamics.

genetics↗