Biology subjects

Liu, W.

Publications and source records attributed to Liu, W..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Cross-Species Insights from ART-D to Uncover Evolutionarily Conserved Oncogenic Mechanisms

Cancer arises from oncogenic clones, yet the dynamic mechanisms governing their stepwise evolution toward malignancy remain incompletely understood. Here, we establish the Atlas of Ras-driven Tumors in Drosophila (ART-D), a systematic, cross-species platform that dissects the molecular and phenotypic trajectories of tumorigenesis through ten genetically defined RasV12-driven models. By integrating longitudinal phenotypic profiling, we define three conserved stages of tumor development--initiation, promotion, and progression--distinguished by dynamic changes in tumor burden and tumor-induced cachexia. Transcriptomic dynamics reveal stage-specific signaling rewiring: early tumorigenesis is marked by co-activation of JAK/STAT, NF-{kappa}B/Toll, and MAPK pathways, whereas malignant progression is driven by Notch hyperactivation and Hippo pathway inactivation. Through integrative multi-omics and machine learning, we uncover an evolutionarily conserved pathogenic network involving coordinated JNK, NF-{kappa}B/Toll, Notch, and Hippo signaling that is functionally validated across species. ART-D provides a transformative resource that bridges Drosophila genetics and human cancer biology, offering a framework for decoding conserved oncogenic principles and enabling precision targeting of stage-specific vulnerabilities in RAS-driven cancers.

genetics↗

bioRxiv2025

H19 is a PERK-regulated long non-coding RNA that fine-tunes UPR signalling and inhibits endoplasmic reticulum stress-induced cell death

The endoplasmic reticulum (ER) responds to stimuli that disrupt its homeostasis by activating a signalling network known as unfolded protein response (UPR), that restores cellular balance and determines cell fate through three key sensors: IRE1, PERK, and ATF6. Emerging evidence suggests that the UPR regulates the expression of numerous long non-coding RNAs (lncRNAs), which play critical roles in modulating stress responses. Here we show that expression of lncRNA H19 is downregulated in response to ER stress in breast cancer cells. Using genetic and pharmacological approaches, we demonstrate that this downregulation is primarily mediated by the PERK arm of the UPR. Specifically, knockdown or chemical inhibition of PERK compromised the ER stress-mediated H19 repression, while PERK activation significantly reduced H19 expression. H19 overexpression promotes the optimal activation of ATF6 and PERK pathways, while it attenuates the signalling by IRE1-XBP1 axis of the UPR. Bioinformatic analyses across multiple breast cancer cohorts revealed that high H19 expression correlates with poor prognosis, particularly in basal-like subtypes. Furthermore, in triple-negative breast cancer (TNBC) cells, H19 was found to provide resistance to ER stress-induced apoptosis. Collectively, our findings establish H19 as a key regulatory node in the UPR network, where PERK-mediated repression of H19 shapes cellular outcomes under ER stress. These insights position H19 as a potential therapeutic target in breast cancer, especially in aggressive subtypes such as TNBC.

cancer biology↗

bioRxiv2025

A spatially-resolved human brain proteome atlas for understanding function and disease

While the brain performs specialized functions across distinct regions, the spatial organization of the human brain proteome remains largely uncharted. Here we present a comprehensive spatially-resolved proteome atlas of the human brain, analyzing over two thousand MRI- guided locations across four individuals. Proteome analysis integrated with transcriptomics reveals extensive post-transcriptional regulation, with cortical regions showing markedly higher protein diversity than transcript. Unsupervised molecular clustering defines distinct brain territories that transcend anatomical boundaries, instead reflecting metabolic demands and functional specialization patterns. Application to epilepsy brain tissue uncovered disrupted astrocyte metabolism, protein homeostasis and therapeutic targets including the seizure-associated purinergic receptor P2RX7. This resource bridges molecular and systems neuroscience to accelerate neurological drug discovery.

neuroscience↗

bioRxiv2025

A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex

The genetic and spatial determinants of cell type diversity in human cerebral cortices remain poorly defined. Here, we present a population-level single-cell spatial transcriptomic atlas of human cortices from 71 donors across the lifespan. We identified 906 layer-specific genes showing conserved and divergent laminar expression patterns between humans and other species. Spatial analysis revealed neuronal vulnerability and glial activation during aging, together with a decline in the proportion of superficial SST neurons and their interactions with other cells. Disease-associated genes exhibited high cell-type and layer-specific expression, implicating the pathogenic role of spatially specific gene expression. Spatial cis-eQTL analysis identified regulatory variants linked to genes related to diseases like Tourette syndrome. Cross-species comparison demonstrated glial expansion in the human cortex, accompanied by enhanced neuron-glia communication via the neuregulin signaling. Together, we provide a comprehensive single-cell atlas of the human cortex that is essential for understanding aging, evolution, and disease pathogenesis.

neuroscience↗

bioRxiv2025

Consistent Induction of Broadly Neutralizing HIV Antibodies by a Novel Two-Step Mechanism Informs Immunogen Design

A major obstacle confronting HIV-1 vaccine and cure research is the lack of an outbred animal model for rapid and consistent induction of broadly neutralizing antibodies (bNAbs). We designed an epitope-focused simian-human immunodeficiency virus (SHIV.5MUT) that elicited broad and potent V3-glycan-targeted antibodies within a year of infection in 14 of 22 macaques compared with 0 of 14 control animals. SHIV.5MUT elicited bNAbs by a novel two-step mechanism, inducing an initial wave of V1-directed antibodies that selected for Envs with shortened, hypoglycosylated V1 loops, which in turn primed V3-glycan bNAb precursors. Rhesus bNAbs were immunogenetically and structurally diverse, closely resembling human V3-glycan bNAbs. Env-bNAb coevolution revealed a diverse repertoire of bNAb precursors and the Env variants that matured them, yielding a molecular blueprint for vaccine design.

immunology↗

bioRxiv2025

A gap-free telomere-to-telomere pig reference genome provides insight in centromere evolution and breed-specific selection

The domestic pig is a key agricultural species and biomedical model, yet its reference genome has remained incomplete. Using PacBio HiFi, Oxford Nanopore reads, and Hi-C sequencing, we assembled the first telomere-to-telomere (T2T), gap-free pig genome (T2T-Sscrofa). Importantly, this assembly derives from the same individual pig that provided the original reference genome, thereby completing the long-standing foundation of pig genomics. This assembly resolves 274.8 Mb of previously unassembled sequence, including centromeres, segmental duplications, and ribosomal DNA arrays, and identifies 255 new protein-coding genes. Comparative analyses reveal a Robertsonian translocation in the western European wild boar and extensive structural variation across global pig populations. T2T-Sscrofa provides a comprehensive genomic foundation for agricultural, evolutionary, and biomedical research.

zoology↗

bioRxiv2025

NTX250: A Modular mRNA-Based Immunotherapy Platform for HPV-Associated Cancers with Broad Applicability.

Infection with high-risk human papillomavirus (HPV) is a key driver of multiple HPV-associated malignancies, including cervical intraepithelial neoplasia (CIN), oropharyngeal, head and neck, and anogenital cancers. Despite the high efficacy of prophylactic HPV vaccines, a substantial population remains at ongoing risk due to issues related to vaccine accessibility, awareness, or personal choice. Current treatments, such as the loop electrosurgical excision procedure (LEEP), address lesions but do not eliminate persistent HPV infection and are associated with potential complications. Moreover, individuals treated for HPV-related disease are at increased risk for subsequent HPV-associated malignancies. These factors underscore an urgent need for effective, non-invasive therapeutic strategies capable of targeting and eradicating persistent HPV infections. Here we introduce NTX250, an innovative mRNA-based therapeutic platform designed to deliver HPV type 16 (HPV16) E6-E7 antigens, combined with immunomodulators human interleukin-12 (IL-12) p70 and engineered human LIGHT (LIGHT). The mRNAs are co-delivered via lipid and ionizable peptoid nanoparticles referred to as Nutshell formulation for intralesional administration. Our preclinical evaluation demonstrates that localized delivery of NTX250 in HPV16-transformed tumor-bearing models results in complete tumor regression and the induction of durable, antigen-specific immune memory. Moreover, this modular mRNA nanoparticle approach combining tumor-specific antigens and immunomodulators is adaptable beyond HPV, with potential applications targeting neoepitopes or other tumor-associated antigens, thus offering a versatile platform for immunotherapy across a broad range of indications. These findings highlight the potential of this strategy as a broadly applicable, non-surgical immunotherapeutic capable of inducing robust and specific anti-tumor responses.

immunology↗

bioRxiv2025

Fork Reversal Safeguards Epigenetic Inheritance during DNA Replication Under Stress

During DNA replication, epigenetic information carried by histone modifications is faithfully propagated and re-established on sister chromatids, ensuring cell identity. Chromatin reassembly is tightly coupled to DNA replication, therefore whether and how perturbations to DNA replication affects the fidelity of epigenetic inheritance remain poorly understood. In this study, we reveal a critical role for replication fork reversal in maintaining the transmission of epigenetic information under replication stress. We identify that cells defective in fork reversal exhibit reduced nucleosome density at replication forks, accompanied by the loss of parental histones during their transfer onto nascent DNA. Mechanistically, we demonstrate that PrimPol activation leads to single-stranded DNA gaps in fork reversal deficient cells, and that subsequent PARylation (poly ADP-ribosylation) and DNA-protein crosslinking on these gaps evicts nucleosomes. Our findings demonstrate that replication fork reversal, a widespread physiological process, is not only essential for preserving genome integrity but also for safeguarding epigenetic stability.

biochemistry↗

bioRxiv2025

Discovery of A Small Molecule non-IMiD Degrader of ZBTB7A for the Treatment of β-hemoglobinopathies

Sickle cell disease and {beta}-thalassemia, two major {beta}-hemoglobinopathies, pose significant clinical challenges globally. Current treatments often face limitations in efficacy and tolerability. The transcription factor ZBTB7A has emerged as a promising therapeutic target for reactivating fetal hemoglobin expression. Here, we report the discovery and characterization of SH6, a small molecule non-IMiD degrader of ZBTB7A. SH6 induces fetal hemoglobin in erythroid cell lines in a CRBN and ZBTB7A-dependent manner, and it is capable of inducing fetal hemoglobin expression in healthy donor, SCD and {beta}-thalassemia patient CD34+ cell derived erythroid cells. The efficacy of SH6 is confirmed in a xenotransplantation humanized mouse model. SH6 outperforms currently available therapeutic agents in vitro, and shows synergy with hypomethylating agents. SH6 exhibits a favorable in vivo toxicity profile. Our findings establish SH6 as a promising therapeutic lead candidate for further optimization towards clinical development for treatment of sickle cell disease and {beta}-thalassemia.

cell biology↗

bioRxiv2025

Sarbecovirus Rc-o319 S-Protein Structures Reveal Highly Specialized Adaptation to Rhinolophus cornutus ACE2

Bat sarbecoviruses often exhibit species-dependent ACE2 specificity. Understanding the determinants of receptor specificity enables better assessment of the cross-species transmission potential of sarbecoviruses. Here, we characterize the S-protein of Rc-o319, a sarbecovirus identified in Japanese Rhinolophus cornutus bats. Featuring an unusual 9-amino-acid deletion within its receptor binding motif (RBM), Rc-o319 S-protein utilizes its cognate R. cornutus ACE2 (bACE2R.cor) but not human ACE2 (hACE2), demonstrating highly restricted receptor specificity. Cryo-EM structures reveal two locked prefusion conformations of the Rc-o319 S-trimer and define a novel type-1b receptor-binding domain (RBD), featuring a distinct beta-loop (BL) within the RBM due to the RBM-deletion. The Rc-o319-RBD:bACE2R.cor complex structure reveals unique interactions mediated by the specialized BL and RBM-loop of Rc-o319-RBD and by a bACE2R.corglycan. Structure-guided mutagenesis demonstrates that changes in BL and RBM-loop within the Rc-o319 S-RBD must occur simultaneously to allow medium-to-high-affinity hACE2 binding. Comparative assays further show that the bACE2R.cor receptor supports only a subset of sarbecoviruses, highlighting its restricted sarbecovirus compatibility. Our findings establish the Rc-o319 S-protein as a structurally and functionally specialized adaptation to R. cornutus ACE2 and identify the structural constraints limiting its cross-species transmission potential. Author SummarySARS-related viruses are widely found in horseshoe bats. Some can bind the human ACE2 receptor with variable affinities, whereas others bind only bat ACE2 receptors. Understanding the basis for this difference is critical for assessing spillover risk. We studied the spike protein of a bat sarbecovirus, Rc-o319, isolated from Japanese Rhinolophus cornutus horseshoe bats. Although Rc-o319 is genetically related to SARS-CoV-2, it is unable to bind the human ACE2 receptor. Structural analyses and functional experiments revealed that the Rc-o319 spike protein possesses a distinct receptor-binding motif (RBM). This RBM features a specialized "beta-loop" that replaces the "large-loop" found in human-infecting sarbecoviruses. The beta-loop enables high-affinity binding to its cognate Rhinolophus cornutus bat ACE2 receptor while simultaneously preventing optimal interaction with human ACE2. We further found that acquisition of high affinity for the human ACE2 receptor would require coordinated changes across multiple regions of the RBM, including changing the beta-loop into a large-loop structure. Together, our findings demonstrate that the Rc-o319 spike protein is highly adapted to its cognate bat ACE2 receptor and faces substantial structural constraints that limit its ability to switch to binding human ACE2.

microbiology↗

bioRxiv2025

GSDME unlocks astrocyte-driven neurotoxicity in Alzheimer's Disease

Astrocytic calcium dysregulation and reactivity precede A{beta} deposition in amyloid-{beta} deposition in Alzheimers disease (AD) but the neurotoxic mechanisms remain unclear. We show that GSDME acts as a switch, linking MAM-mediated calcium release to astrocyte-driven neurotoxicity. Specifically, A{beta}-activated microglial signals activate astrocytic GSDME, releasing its N-terminal fragment, which targets MAMs and triggers ER calcium efflux. This induces biphasic CaMKII phosphorylation, initially boosting NRF2 defenses, then activating NF-{kappa}B-driven inflammation, shifting astrocytes from protective to toxic states. GSDME activation also drives astrocyte-derived exosomes (ADEs) to carry neurotoxic tau, proinflammatory miRNAs, and toxic lipids, propagating toxicity. GSDME deletion in AD mice reduces A{beta} burden, restores NF-{kappa}B/NRF2 balance, reprograms astrocytes and ADEs to protective states, and rescues cognition. Multi-omics profiling of serum ADEs from AD patients reveals a disease-specific signature with central neurotoxicity and peripheral immune regulation. These findings position GSDME as a promising dual diagnostic and therapeutic target for early AD invention.

neuroscience↗

bioRxiv2025

An integrated multi-tissue atlas of epigenomic landscapes and regulatory elements in the bovine genome

Deciphering the regulatory syntax of the genome is essential to understand the genetic and molecular architecture of complex traits, as most trait-associated variants lie in non-coding regions. Yet, functional annotation of the bovine genome remains limited, hindering our ability to unravel the mechanisms underpinning complex traits of economic and ecological importance in cattle. Here, we present a comprehensive epigenetic atlas comprising 1,138 genome-wide epigenetic profiles, including chromatin accessibility, six histone modifications, CCCTC-binding factor (CTCF) transcription factor binding, DNA methylation, chromatin conformation, and transcriptomes across 53 adult tissues, five fetal tissues, and seven primary cell types. This atlas-level data enables us to annotate around 45% of the genome as putative regulatory elements exhibiting tissue- or cell-specific regulatory activity. Leveraging sequence-to-function deep learning models, we discovered 301 sequence motifs and predicted the functional impact of genetic variants through in silico mutagenesis, thereby facilitating the decoding of the regulatory syntax of the cattle genome and fine-mapping of GWAS loci for 22 complex traits. Cross-species analysis further revealed evolutionarily conserved features of regulatory architecture and provided evolutionary insights into complex traits and diseases in humans. Together, this atlas offers a foundational resource for advancing cattle functional genomics, sustainable breeding, and studies of regulatory evolution.

genomics↗

bioRxiv2025

Time-Resolved Mapping in Calves Reveals BoHV-1 Shift From Mucosal Replication to Trigeminal Neuroinvasion and IFN-α-bPML Antagonism

Bovine herpesvirus 1 (BoHV-1) causes huge cattle losses, yet the transition from mucosal replication to neuroinvasion is poorly resolved. Using a controlled calf model, we integrated quantitative virology and transcriptomics to map pathogenesis and define the role of promyelocytic leukemia protein (PML). Calves inoculated intranasally/ocularly (1.4x10^6 pfu/head) were sampled daily (1-14 dpi) for gB-qPCR; tissues at 4 and 14 dpi were analyzed for viral DNA and trigeminal ganglia (TG) mRNA-seq. Shedding peaked at 3-6 dpi (nasal > ocular >> rectal) and declined by 10-14 dpi. Tonsils bore the highest burden at 4 dpi; TG was low-positive at 4 dpi but remained positive at 14 dpi, indicating neuroinvasion. TG programs shifted from early proteostasis priming (4 dpi) to immune/ECM activation with synaptic repression (14 dpi). In MDBK/Vero cells, IFN- increased bovine PML (bPML) and enlarged PML nuclear bodies (PML-NBs), reducing very-early viral DNA, whereas BoHV-1 disrupted PML-NB integrity. bPML isoforms diverged (bPML1/6 pro-viral; bPML3/4/5 antiviral). Cross-species STRING mapped a conserved PML-SUMO1-UBE2I-DAXX-SP100 core. These data delineate the mucosal-to-neuronal trajectory, establish PML as both effector and viral target, and nominate SUMO/ubiquitin-linked proteostasis as a tractable antiviral leverage point.

microbiology↗

bioRxiv2025

Structural insights on the ligand selectivity of the mouse trace amine-associated receptor TAAR7e

Trace amine-associated receptors (TAARs), a subclass of G protein-coupled receptors involved in detecting volatile amines, are co-expressed with odorant receptors in the main olfactory epithelium. Although many behaviorally relevant amines have been identified for olfactory TAARs, the molecular mechanisms underlying their selectivity for amines with varying carbon chain lengths and degrees of amine substitution remain unclear. In this study, we used mTAAR7e as a model to investigate these mechanisms. Homology modeling revealed a conserved ligand-binding pocket, supported by sequence-structure covariance analysis across TAARs. Structure-activity relationship profiling revealed key chemical determinants integral to mTAAR7e-mediated odorant recognition and provided, for the first time, a structural explanation for its selective preference toward longer carbon chains and tertiary amines. Computationally predicted interactions between mTAAR7e and the representative ligand N,N-dimethylcyclohexylamine (DMCHA) were validated through site-directed mutagenesis. Furthermore, conformational dynamics of mTAAR7e during receptor activation were characterized, providing insights into activation-related structural rearrangements. Together, these findings offer novel insights into the molecular logic of TAAR ligand selectivity and may advance our understanding of how TAARs mediate both olfactory and systemic aminergic signaling.

molecular biology↗

bioRxiv2025

High-throughput 3D super-resolution ultrasound imaging

Capturing fast hemodynamics in deep organs is essential for understanding microvascular regulation of organ responses to physiological demands and pathological stress. However, non-invasive three-dimensional (3D) imaging of these microscale processes remains challenging due to trade-offs between spatial resolution, imaging speed, and penetration depth. Here, we present fluctuation-based high-order super-resolution acoustic microscope (FLAME), a tracking-free 3D ultrasound imaging technology capable of fast microvascular angiography and flow measurement. Using as few as 30 volumes, FLAME improves 3D ultrasound resolution by 8-fold ([~]50 m) and shortens data acquisition time by over two orders of magnitude, from tens of seconds to tens of milliseconds, compared with conventional tracking-based super-resolution approaches1-6. This high-throughput capability supports high-fidelity imaging of tissue functions under flexible experimental settings. FLAME achieves an unprecedented 3D super-resolution frame rate of [~]40 Hz, capturing transient hemodynamic responses to various physiological and pathological stimuli in different mouse organs, from the microvascular level to the whole-body scale. With open-sourced implementation, FLAME provides an accessible platform for real-time, in-depth hemodynamic monitoring across diverse biomedical applications and clinical translation.

bioengineering↗

bioRxiv2025

Ex vivo and in vivo CRISPR/Cas9 screenings identify the roles of protein N-glycosylation in regulating T-cell activation and functions

Cytotoxic CD8+ T-cells play central roles in tumor immunotherapy. Understanding mechanisms that regulate development, differentiation, and functions of cytotoxic CD8+ T-cells leads to development of better immunotherapies. By combining primary T-cell culture and a syngeneic mouse tumor model with both genome-wide and custom CRISPR/Cas9 screenings, we systematically identified genes and pathways that regulate PD-1 expression and functions of CD8+ T-cells. Among them, inactivation of a key enzyme in glycoconjugate biosynthesis, beta 1, 4-galatosyltransferase 1 (B4GALT1), leads to significantly enhanced T-cell receptor (TCR) activation and functions of CD8+ T-cell. Interestingly, suppression of B4GALT1 enhances functions of TCR-T-cells, but has no effect on chimeric antigen receptor T (CAR-T) cells. We systematically identified the substrates of B4GALT1 on CD8+ T-cell surface by affinity purification and mass spectrometry analysis, which include protein components in both TCR and its co-receptor complexes. The galactosylation of TCR and CD8 leads to reduced interaction between TCR and CD8 that is essential for TCR activation. Artificially tethering TCR and CD8 by a TCR-CD8 fusion protein could bypass the regulation of B4GALT1 in CD8+ T-cells. Finally, the expression levels of B4GALT1 normalized to tumor infiltrated CD8+ T-cells in tumor microenvironment are significant and negatively associated with prognosis of human patients. Our results reveal the important roles of protein N-glycosylation in regulating functions of CD8+ T-cells and prove that B4GALT1 is a potential target for tumor immunotherapy.

immunology↗

bioRxiv2025

Executive control in Obsessive-Compulsive Disorder: A worldwide mega-analysis of task-based functional neuroimaging data of the ENIGMA-OCD consortium

ObjectiveObsessive-compulsive disorder (OCD) is associated with impaired executive function and altered activity in associated neural circuits, contributing to reduced goal-directed behavior. To investigate neural activation during executive control, we conducted a mega-analysis in the ENIGMA-OCD consortium pooling individual participant data from 475 individuals with OCD and 345 healthy controls across 15 fMRI tasks collected worldwide. MethodsIndividual participant data was uniformly processed using HALFpipe to construct voxelwise statistical images of executive control and task load contrasts. Parameter estimates extracted from regions of interest were entered into multilevel Bayesian models to examine regional and whole-brain effects of diagnosis, and, within OCD, the influence of medication status, symptom severity, and age of onset on task activation. ResultsWe observed a robust task activation pattern across individuals with OCD and control participants in executive control regions across tasks. Relative to controls, individuals with OCD showed moderate to very strong evidence of weaker activation of the dorsolateral prefrontal cortex, precuneus, frontal eye fields, and inferior parietal lobule during executive control (all positive posterior probabilities [P+]<0.1). Individuals with OCD also showed stronger activation in regions of the default mode network during executive function relative to controls. We found little evidence for differential activation during executive control in task- positive regions related to disease onset, severity and medication status. ConclusionIn the first mega-analysis of fMRI studies of executive function in OCD, we found strong evidence of weaker frontoparietal activation during executive control tasks. Our findings also suggest a failure of default mode network regions to appropriately disengage during task performance in OCD.

neuroscience↗

bioRxiv2025

Low-dimensional brain-symptom associations delineate depression phenotypes with distinct connectivity biomarkers and symptom profiles

Depression is neurobiologically and clinically heterogeneous. New approaches using resting-state functional MRI (rs-fMRI) functional connectivity (FC) data have modeled the neural basis of depression heterogeneity and revealed unique neural phenotypes. Yet, no studies have identified depression phenotypes from electrophysiological magnetoencephalography (MEG) data although MEG measures human brain dynamics at millisecond precision. We demonstrate here unique depression phenotypes based on MEG-oscillation FC. We collected resting-state MEG, MRI, and clinical symptom data from 263 patients with unipolar depression and 75 healthy controls. We assessed MEG-FC with two oscillatory coupling-mode measures that are fundamental for information processing. To define normative phenotypes, we computed their latent-space low-dimensional brain-symptom associations, and used these components to identify phenotypes using unsupervised machine learning. We identified five stable depression phenotypes that were characterized by unique symptom profiles and distinct spectral patterns. Our results demonstrate new neural underpinnings of depression heterogeneity and reveal unique neural phenotypes with potential personalized diagnostic value.

neuroscience↗