Biology subjects

Wang, J.

Publications and source records attributed to Wang, J..

At least 811 records · Page 45Linked to original sources

bioRxiv2025

Mechanism of biomimetic virus-like nanoparticles in triggering immune response elucidated by proteomics

The use of biomimetic nanoparticles (NPs) with virus-like morphology have recently attracted research interest as novel delivery platforms and immune adjuvants. However, the exact interactions between the nanoparticles and immune cells as well as the mechanism involved are not known in detail. This motivated us to develop virus-like mesoporous silica nanoparticles (VLP) to characterize their physicochemical properties, and to determine the immune pathways induced by the particles in mouse macrophages. The results showed inclusion of spikes mimicking virion structures on the surface increased cellular uptake and enhanced immune response as compared to spherical NPs. Proteomic analysis revealed that the RIG-I-like receptor signaling pathway, Chemokine signaling pathway, MAPK signaling pathway, NF-{kappa}B signaling pathway, Toll-like receptor signaling pathway, B cell receptor signaling pathway and Th1 and Th2 cell differentiation pathways were involved in regulating the immune response when macrophages interacted with VLP. When the spikes increased from 5 to 30 nm, the expression levels of immune-related proteins including TRAF6 and PIAS4 proteins enhanced. This study revealed the interaction pathways and key proteins in the activation of immune response with VLP, which may provide insights to develop novel immunotherapy for enhanced efficacy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/640536v3_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@395d6forg.highwire.dtl.DTLVardef@25238dorg.highwire.dtl.DTLVardef@41001borg.highwire.dtl.DTLVardef@16dfe2e_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Accurate identification of medulloblastoma subtypes from diverse data sources with severe batch effects by RaMBat

As the most common pediatric brain malignancy, medulloblastoma (MB) includes multiple distinct molecular subtypes characterized by clinical heterogeneity and genetic alterations. Accurate identification of MB subtypes is essential for downstream risk stratification and tailored therapeutic design. Existing MB subtyping approaches perform poorly due to limited cohorts and severe batch effects when integrating various MB data sources. To address these concerns, we propose a novel approach called RaMBat for accurate MB subtyping from diverse data sources with severe batch effects. Benchmarking tests based on 13 datasets with severe batch effects suggested that RaMBat achieved a median accuracy of 99%, significantly outperforming state-of-the-art MB subtyping approaches and conventional machine learning classifiers. RaMBat could efficiently deal with the batch effects and clearly separate subtypes of MB samples from diverse data sources. We believe RaMBat will bring direct positive impacts on downstream MB risk stratification and tailored treatment design.

bioinformatics↗

bioRxiv2025

Electromotility can be disassociated from gating charge movement in outer hair cells of conditional alpha2 spectrin knockout mice.

Electromotility in mammalian outer hair cells (OHC) is the mechanism underlying cochlear amplification. It is brought about by the piezoelectric-like property of the membrane protein prestin (Slc26a5) that lies in the OHCs lateral plasma membrane. Prestin connects to an underlying cytoskeletal network of circumferential actin filaments that bridge longitudinal spectrin filaments. This network, in turn, lies between the plasma membrane and a closely apposed ER-like tubular array of subsurface cisternae (SSC). Two previous papers examining spectrin knockouts in embryonic hair cells were confined to analyzing the effects on the apical cuticular plate and overlying stereocilia. In this paper, we examine the effects of conditional knockouts of alpha2 spectrin in postnatal OHCs. We find a significant auditory phenotype likely due to the novel disassociation of prestins gating charge movement from OHC electromotility. In addition, OHCs show enlargement in their SSC and plasma membrane-SSC space with preserved cuticular plates and overlying stereocilia, which contrasts with the findings in embryonic knockouts.

physiology↗

bioRxiv2025

Somatic repetitive element insertions Define New Biomarkers in Pan-cancer genome

Repetitive elements insertions (REIs), including tandem repeat insertions (TRIs) and transposable element insertions (TEIs), constitute >90% of large-scale (>50bp) somatic insertions and are linked to diseases and cancer biomarkers. However, the genomic landscape of large-scale REIs in pan-cancer has not been well-characterized due to short-read sequencing limitations. Here, we detected somatic REIs in 325 cancer genomes across 12 cancer types using long-read whole-genome sequencing and customized algorithms. The diverse sequence patterns of somatic TRIs and the insertion mechanisms of somatic TEIs were characterized across different cancer types. We identified 152 high-frequency somatic TRIs, with 10 showing pan-cancer characteristics, including TRIs in SHROOM2, PALMD, and the enhancer of PTPRZ1. The MHC class II gene cluster exhibited the highest somatic TEI abundance, affecting [~]40% tumors. Adenocarcinomas and squamous cell carcinomas exhibited differing TEI distributions within this region. Our study highlights REIs as important but under-explored markers for personalized cancer diagnosis and immunotherapy.

genomics↗

bioRxiv2025

Dissecting Force Transmission across SUN Proteins Using Nuclear Tension Sensors

Forces on the linker of the nucleoskeleton and cytoskeleton (LINC) complex control nuclear mechano-sensing and mechano-adaptation. However, the force transmission dynamics across the LINC complex are not fully understood, mainly because of the lack of imaging tools. We developed a set of genetically-encoded fluorescence resonance energy transfer (FRET)-based nuclear tension sensors (NuTS) that measure tension forces across SUN1/2 proteins in living cells with high sensitivity. SUN2-based NuTS (NuTS2) responded rapidly to mechanical changes in cell contractility and matrix stiffness. Notably, NuTS2 dynamically showed force transmission with high spatiotemporal resolution during cell adhesion, migration and squeeze. We also used NuTS2 to monitor tension force changes as the notochord matures in zebrafish development. NuTS2 detected a gradient tension force that increased from the posterior tail buds to the anterior as vacuoles expanded in notochord cells. Force reduction affected notochord maturation and zebrafish embryo development. Our results provide a biophysical cue for dissecting how force transmission on SUN2 protein regulates embryo development. TeaserNuclear tension sensor (NuTS) was developed for direct force measurement across SUN proteins in living cells and zebrafish.

biophysics↗

bioRxiv2025

SpaFun: Discovering Domain-specific Spatial Expression Patterns and New Disease-Relevant Genes using Functional Principal Component Analysis

SpaFun is a novel, non-model-based method developed to address limitations in existing spatially variable gene (SVG) detection techniques, particularly for large-scale spatially resolved transcriptomics (SRT) datasets. These limitations include computational inefficiency, limited statistical power with increasing data size, and the inability to capture spatial heterogeneity and co-expression patterns among genes. Built on functional principal component analysis (fPCA), SpaFun identifies domain-representative genes (DRGs) with significantly better computational efficiency and greater statistical power while accounting for spatial heterogeneity and co-expression patterns among genes. We applied SpaFun to three SRT datasets and demonstrated that SpaFun outperformed state-of-the-art algorithms for identifying representative genes for tumor regions (e.g., DESeq, edgeR, and limma), as well as recently developed novel algorithms designed for spatial omics to identify the representative genes (e.g., SPARK and CSIDE). This highlights SpaFuns ability to accurately identify genes most representative of each spatial domain (e.g., tumor, immune, or stroma regions). By uncovering novel disease-relevant genes overlooked by existing algorithms, SpaFun could provide insights into new molecular mechanisms and propose innovative therapeutic strategies to improve patient outcomes. Key PointsO_LISpaFun is the first method dedicated to identifying DRGs, capturing spatially representative expression patterns within annotated tissue regions, setting it apart from all traditional SVG detection methods. C_LIO_LIIt leverages fPCA to model gene expression as a function of spatial location, avoiding reliance on predefined spatial distribution assumptions. C_LIO_LIThe non-model-based framework ensures compatibility with different SRT platforms and experimental designs, making it a scalable and widely applicable tool for SRT research. C_LI

genomics↗

bioRxiv2025

Cloche/Npas4l is a pro-regenerative platelet factor during zebrafish heart regeneration

Zebrafish has full capacity of heart regeneration, but little is known about how blood cells, especially platelets, are involved in this regenerative process. Here we report that cloche/npas4l is a pro-regenerative platelet factor for heart regeneration. We found that haploinsufficiency of npas4l disrupted cardiomyocyte (CM) and endothelial cell (EC) proliferation and heart regeneration after injury. A single-cell transcriptomic atlas revealed that npas4l was dynamically expressed in platelets after heart injury and regulated robust interactions between platelets-CMs or -ECs. Decreasing platelets by either nitroreductase-mediated platelet depletion or platelet-deficient mutant mpl impaired CM and EC proliferation, and over-expression of npas4l in platelets sufficiently induced CM and EC proliferation in uninjured hearts, as well as rescued CM and EC proliferation defects in cloche mutants. Mechanistically, Npas4l positively regulated a panel of ligands expression including bmp6 in platelets to fine-tune CM proliferation and heart regeneration. Therefore, this work unveils a novel platelet Npas4l signaling and presents mechanisms on how platelets modulate CM/EC proliferation via ligand-receptor network during zebrafish heart regeneration.

cell biology↗

bioRxiv2025

China Autism Brain Imaging Consortium: Charting Brain Growth in Chinese Children with Autism

Autism Spectrum Disorder (ASD) is a lifelong neurodevelopmental condition characterized by atypical brain growth. While advances in neuroimaging and openly sharing large-sample datasets such as the Autism Brain Imaging Data Exchange (ABIDE) have improved understanding of ASD, most studies focus on adolescents and adults, with early brain development-critical for diagnosis and intervention-remaining underexplored. Existing research predominantly involves Western samples, offering limited insight and generalizability into non-Caucasian populations. We introduce the China Autism Brain Imaging Consortium (CABIC) (https://php.bdnilab.com/resources/), a grassroots effort by researchers across the country to aggregate previously collected multi-site structural MRI datasets and phenotypic information from 1,451 autistic children and 1,119 typically developing children, covering an age range from early childhood to school age (1.0 - 12.92 years). Here, we present this resource and depict brain growth charts to push forward a more comprehensive understanding of the brain development in Chinese autism children. We constructed brain growth charts that reveal a developmental shift in autistic children, transitioning from early overgrowth to delayed maturation. Regional analyses identified distinct atypical trajectories across specific brain regions. Individual deviation scores quantified inter-subject variability, characterizing the heterogeneity of brain development in ASD. Comparative analyses between CABIC and ABIDE highlighted differences potentially attributable to ethnicity and culture, advancing our understanding of cross-population neurodevelopmental diversity. CABIC MRI datasets will be shared publicly to foster investigation of the potential neural mechanisms underlying ASD in non-Western populations and support efforts toward precision medicine for autistic individuals across diverse backgrounds.

neuroscience↗

bioRxiv2025

panHiTE: a comprehensive and accurate pipeline for TE detection in large-scale population genomes

Transposable elements (TEs) are key drivers of genomic variation and species evolution. Advances in high-throughput sequencing have enabled whole-genome sequencing of individuals or subspecies, facilitating the identification of population-specific variations. Detecting population-specific TE insertions at scale is crucial for understanding species-specific phenotypic traits. However, tools for constructing comprehensive pan-TE databases remain limited. To address this gap, we develop panHiTE, a population-scale TE detection and annotation tool with several core innovations. panHiTE features a deep learning-based long terminal repeat retrotransposon (LTR-RT) detection algorithm, outperforming existing tools in both sensitivity and precision. It also introduces a novel de-redundancy algorithm, which eliminates highly divergent redundant TE instances, significantly reducing the size of the TE library. Additionally, panHiTE can detect low-copy TEs, which are overlooked in individual genome analyses and absent from existing databases due to their rarity. Furthermore, panHiTE allows for TE-gene association analysis, enabling comprehensive insights into TE-driven phenotypic variation. panHiTE, powered by a Nextflow pipeline, enables efficient and scalable TE detection in large plant genomes and has successfully been applied to hundreds of plant population genomes, demonstrating its effectiveness and scalability.

genomics↗

bioRxiv2025

Structural basis of ATP release and ion selectivity in Pannexin1 channels

This study investigated the structural basis of adenosine triphosphate (ATP) release and ion selectivity by Pannexin1 (Panx1). The microinjection of active SRC tyrosine kinase increased Panx1-mediated currents in Panx1-expressing oocytes. Furthermore, a mutation mimicking phosphorylation at Y308 turned Panx1 into a constitutively open ATP-releasing channel with broad ion permeability. Cryogenic electron microscopy showed that for most maps, the channel alternated between wide and narrow conformations. However, in the map of the phosphomimetic Y308E mutation, Panx1 remains in a wide ATP-releasing conformation. The pore-lining residues, W74 and R75, are flexible and create, in concert with the sequestered N-terminal helix, a path for ATP. The data point to phosphorylation as a reversible switch that activates ATP permeability by stabilizing Panx1 in the ATP-releasing conformation, which is crucial for developing modulators for diseases such as cancer and chronic pain.

biophysics↗

bioRxiv2025

Themis dominates T cell exhaustion by regulation of TCR and PD-1 signaling

T cell exhaustion is important to protect the host from immunopathology during chronic viral infection, but it also impairs T cell anti-tumor immunity1-5. A fundamental unresolved question is whether and how T cell exhaustion is determined at the onset of TCR signaling6-8. Here we report an unexpected role of Themis, a TCR-proximal signaling molecule9, in T cell exhaustion. Chronic viral infection in mice usually leads to T cell exhaustion and survival of the host. Surprisingly, Themis T-cell conditional knockout mice died from severe CD8+-dependent lung immunopathology in chronic viral infection, showing Themis importance in establishing T cell exhaustion. We found that Themis-deficient CD8+ T cells were hyperactivated at the single-cell level - producing more TNF and IFN{gamma} compared to wild-type counterparts - but defective in population-level expansion. Moreover, TCF-1 and TOX expression were inhibited in Themis-deficient CD8+ T cells, thereby impairing differentiation of exhausted T cell precursors (T-pex) and maintenance of terminally exhausted T cells (T-ex), respectively. Mechanistically, Themis initially promotes TCR signaling to induce PD-1 expression and subsequently mediates PD-1 signaling. In the latter, Themis binds to PD-1 and promotes PD-1 phosphorylation and its recruitment of SHP2, thereby acting as a negative regulator to inhibit T cell effector functions. Without Themis, the orderly regulation of TCR and PD-1 signaling, and therefore exhaustion, is disrupted. Thus, our results unequivocally demonstrate that Themis-mediated early TCR signaling plays a decisive role in T cell exhaustion and provide a novel mechanism of PD-1 signaling through Themis.

immunology↗

bioRxiv2025

CRISPR-based shuttle cloning of 1,397 human genes into UAS vectors

The construction of genome-wide DNA libraries from publicly available resources is essential for leveraging functional genomics to investigate complex biological systems. However, all existing high-throughput cloning methods for transferring DNA fragments between vectors require PCR amplification of the DNA fragments, rendering the construction of genome-wide DNA libraries labor-intensive and time-consuming. By introducing a concept of CRISPRshuttle cassette, we herein present a method named CRISPR-based shuttle cloning (CRISPRshuttle cloning). This method enables the high-throughput transfer of numerous DNA fragments from original plasmids with identical backbones to a different vector background without the need for PCR amplification of the DNA fragments. The procedure comprises two-step test tube reactions followed by bacterial transformation. Using CRISPRshuttle we successfully generated a library of GAL4/UAS-based UAS-ORF plasmids covering 1,397 human genes conserved in Drosophila. This library may serve as a valuable resource for gain-of-function screening in cultured cells and for the creation of a transgenic UAS-ORF library in Drosophila.

molecular biology↗

bioRxiv2025

p16 expression confers sensitivity to CDK2 inhibitors

Blocking the cell cycle is a promising avenue for cancer therapy, with Cyclin-Dependent Kinase 2 (CDK2) emerging as a key target. However, in multiple cell types, CDK4/6 activity compensates for CDK2 inhibition and sustains the proliferative program, enabling CDK2 reactivation. Thus, we hypothesized that sensitivity to CDK2 inhibition is linked to the absence of this CDK4/6-mediated compensatory mechanism. Here we show that Cyclin E1-driven ovarian cancers often co-express the tumor suppressor p16, which inhibits CDK4/6. We show that ovarian cancer cells expressing p16 exhibit heightened sensitivity to CDK2 inhibitors and that depletion of p16 renders them significantly more resistant. Multiplexed immunofluorescence of 225 ovarian patient tumors reveals that at least 18% of tumors express high Cyclin E1 and high p16, a group that we expect to be particularly sensitive to CDK2 inhibition. Thus, p16 may be a useful biomarker for identifying the patients most likely to benefit from CDK2 inhibitors.

cancer biology↗

bioRxiv2025

Mapping Anhedonia-Related Damage Network: Insights for TMS Treatment

BackgroundMany studies have explored anhedonia-related functional connectivity (FC), but the findings remain inconsistent. There is a gap in identifying a consistent anhedonia-related damage network and applying it to TMS treatment. MethodsWe systematically reviewed studies on anhedonia-related functional connectivity and identified anhedonia-related brain damage locations. Using a novel functional connectivity network mapping approach applied to a large normative connectome dataset, we mapped these damage locations to anhedonia-related damage networks. Subsequently, transcriptomic analysis was conducted to uncover underlying molecular mechanisms. Additionally, we investigated the application of the anhedonia-related damage network in transcranial magnetic stimulation (TMS) treatment, focusing on changes in FC within this network following TMS treatment and its association with anhedonia improvement, as well as predicting TMS treatment efficacy based on baseline FC within the anhedonia-related damage network. ResultsA total of eight experiments from seven studies using the nucleus accumbens (NAc) as the seed were eligible for functional connectivity network mapping analysis. This study identified an anhedonia-related damage network, primarily characterized by disrupted functional connectivity between the NAc and the default mode network. Transcriptomic analysis revealed gene enrichment associated with synaptic signaling, neuronal development, ion transport, and actin cytoskeleton regulation. TMS treatment increased NAc functional connectivity within the anhedonia-related damage network in the response group, with these changes correlating with improvements in anhedonia. Furthermore, baseline NAc FC within this network demonstrated predictive potential for TMS treatment efficacy. ConclusionThe anhedonia-related damage network was identified, emphasizing its underlying mechanisms and predictive value for TMS in treating anhedonia.

neuroscience↗

bioRxiv2025

Infectome Analysis of Small Mammals in Southern China Reveals Ecological Associations and Emerging Threats from Diverse Pathogens

Small mammals harbor a diverse array of zoonotic pathogens. To date, however, metagenomic surveys of these species have primarily focused on viral diversity, with limited attention paid to bacteria and eukaryotic pathogens. Additionally, the ecological determinants of pathogen diversity within these mammals have not been systematically examined. Herein, we employed a metatranscriptomics approach to survey the pathogen infectome of 2,408 individual samples, representing lung, liver, and gut tissues from 858 animals collected throughout Guangdong province, China, with a study design that accounted for host species, tissue, season, and geographic location. We identified 76 pathogen species, including 29 RNA viruses, 12 DNA viruses, 5 bacteria, and 30 eukaryotic pathogens, 33 of which were newly discovered. Tissue distribution analysis revealed distinct organotropisms, suggesting varied transmission routes, while host distribution analysis showed that each animal carried an average of one pathogen, with 10 pathogens widely distributed among mammalian orders. Our characterization of the geographic and seasonal patterns revealed that pathogen richness was primarily influenced by region, host species, and season, while pathogen composition was largely shaped by host genetic distance. Collectively, these data provide the first comprehensive insight into the dynamics of the pathogen infectome in these key mammalian disease reservoirs, highlighting the major factors driving pathogen diversity and transmission.

microbiology↗

bioRxiv2025

Classification of skin transcriptome reveals two molecular subtypes in hidradenitis suppurativa

Background and AimsHidradenitis suppurativa (HS) is an understudied chronic inflammatory skin disease that is characterized by painful bumps and abscesses. Adalimumab and secukinumab are the only two approved biologics for the treatment of HS. Despite these advances in the treatment of disease, there remains significant unmet medical need, with many patients only achieving moderate improvements in disease, or continuing to experience flares. This suggests that there may be distinct patient subsets with unique molecule drivers of disease. The aim of this study is to identify and characterize the molecular subtypes of HS patients to further understand its heterogeneity. MethodsSix public datasets with a total of 100 skin lesional samples were integrated to identify molecular subtypes and build a 36-gene classifier, which was validated by three independent lesional skin datasets. Two out of six training datasets generated from patients treated with adalimumab were used to identify the relationship between subtypes and response status. ResultsTwo molecular subtypes were identified from the training datasets, in which subtype S1 had a higher response rate of adalimumab than subtype S2 in the two adalimumab treatment datasets. Subtype S1 was characterized by three gene modules associated with keratinization, development, and metabolism, and six cell types related to sebocytes, smooth muscle cells, endothelial cells, schwann cells, basal cells, and proliferating cells. Subtype S2 was associated with three modules related to immune response, wound healing, keratinization, and cell cycle, and three cell types related to T lymphocytes, dendritic cells, and fibroblasts. The two subtypes were replicated in three additional independent datasets. ConclusionsThis study discovered and validated two HS subtypes with different molecular mechanisms and drug response, which may aid interpretation of heterogeneous molecular and clinical information in HS patients.

immunology↗

bioRxiv2025

scCompare: a web app for single-cell RNA sequencing dataset comparisons across multiple auto-immune diseases

MotivationSingle-cell RNA sequencing (scRNA-seq) datasets have been widely used to identify the cell types and marker genes with pivotal roles in driving pathogenesis and progression of auto-immune diseases. Comparative analysis of different cell types or diseases across multiple scRNA-seq datasets can reveal the homogeneous and heterogeneous pathogenesis, and a comprehensive web-based comparison tool that could streamline this process is not yet available. ResultsWe introduce scCompare, a web-based platform for scRNA-seq comparisons in autoimmune diseases. scCompare includes 2,125 differential gene lists from 100 scRNA-seq datasets in 22 auto-immune diseases and a query system supporting 170 standardized keywords from four attributes (disease, cell type, tissue, and treatment). scCompare also provides three modules enabling several comparative analysis and visualization options. geneQuery supports comparisons of queried genes across differential gene lists identified from multiple scRNA-seq datasets. DEGEnricher performs cell-type-specific enrichment analysis across studies based on a user-input gene list. DEGCompare allows interactive comparisons of multiple differential gene lists of many studies and performs pathway enrichment analyses. Using two case studies as examples, we demonstrated that scCompare represents a unique platform for biologists to identify, compare and validate the pathogenesis at the single-cell levels among auto-immune diseases. Availability and implementationscCompare is freely available at https://sccompare.shinyapps.io/main/. The source code is available at https://github.com/abbviegrc/scCompare.

bioinformatics↗

bioRxiv2025

Cryo-EM reveals a new allosteric binding site at the M5 mAChR

The M5 muscarinic acetylcholine receptor (M5 mAChR) represents a promising therapeutic target for neurological disorders. However, the high conservation of its orthosteric binding site has posed significant challenges for drug development. While selective positive allosteric modulators (PAMs) offer a potential solution, a structural understanding of the M5 mAChR and its allosteric binding sites has remained limited. Here, we present a 2.8 [A] cryo-electron microscopy structure of the M5 mAChR complexed with heterotrimeric Gq protein and the agonist iperoxo, completing the active-state structural characterization of the mAChR family. To identify the binding site of M5-selective PAMs, we implemented an integrated approach combining mutagenesis, pharmacological assays, structural biology, and molecular dynamics simulations. Our mutagenesis studies revealed that selective M5 PAMs bind outside previously characterized M5 mAChR allosteric sites. Subsequently, we obtained a 2.1 [A] structure of M5 mAChR co-bound with acetylcholine and the selective PAM VU6007678, revealing a novel allosteric pocket at the extrahelical interface between transmembrane domains 3 and 4 that was confirmed through mutagenesis and simulations. These findings demonstrate the diverse mechanisms of allosteric regulation in mAChRs and highlight the value of integrating pharmacological and structural approaches to identify novel allosteric binding sites.

pharmacology and toxicology↗