Biology subjects

Hu, J.

Publications and source records attributed to Hu, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Lineage-Specific Neofunctionalization of Polyacetylene-Directing UGT76 Glycosyltransferases in Campanulaceae

Polyacetylene glycosides exhibit notable pharmacological activities, yet the glycosyltransferases acting on their polyacetylene scaffolds remain unknown. Here we report a telomere-to-telomere genome assembly of Codonopsis pilosula and, guided by spatial metabolomics, characterize three UDP-glycosyltransferases: CpUGT76BG1 and CpUGT76BG2 catalyze the direct glycosylation of lobetyol to lobetyolin, while CpUGT94BY2 performs subsequent sugar-sugar coupling to produce lobetyolinin, with each activity confirmed by in planta overexpression. Structural modeling reveals that CpUGT76BG1 and CpUGT76BG2 employ a deep hydrophobic tunnel to fully encase the linear polyacetylene chain, a binding architecture distinct from the shallow pockets used by canonical plant UGTs for planar aromatic substrates. Ancestral sequence reconstruction across eleven nodes partitions the UGT76 lineage into three functionally distinct evolutionary stages, tracing the trajectory from an ancestral shallow pocket to this specialized deep architecture. These findings establish the key glycosylation steps of polyacetylene glycoside biosynthesis, define a tunnel-based paradigm for non-planar substrate recognition, and reveal how tandem duplication-driven active site remodeling generates metabolic novelty.

evolutionary biology↗

bioRxiv2026

Bamsnap-LRS: an automated batch visualization tool for long-read sequencing alignments

SummaryLong-read sequencing (LRS) has become essential for genome assembly, structural variations (SVs) detection, haplotype phasing and transcript isoform characterization. However, these applications often require manual inspection of read alignment for validation. Existing visualization tools are either interactive genome browsers that are difficult to scale to large datasets or batch-oriented tools that are not optimized for the unique alignment patterns of long-read data. We developed Bamsnap-LRS, an automated command-line tool for high-throughput LRS alignment visualization. It supports long-read-specific features, phased SNP inspection, and publication-ready batch figure generation within a unified framework for genomic, transcriptomic, and haplotype-aware analyses. Availability and ImplementationAll codes and examples are freely available at https://github.com/comery/Bamsnap-LRS. ContactChentao Yang (yangchentao@genomics.cn) and Yang Zhou (zhouyang@genomics.cn). Supplementary informationSupplementary Table 1 and Supplementary Figures 1-8 are available at xxx online.

bioinformatics↗

bioRxiv2026

Multi-Omics Study of Ancestry in Adults with Intracranial Cancers Glioma (MOSAIC)

BackgroundMost genomic studies of adult-type diffuse gliomas have focused on predominantly European ancestry populations, limiting the generalizability of molecular classifications and precision medicine approaches. We assembled a multi-institutional glioma cohort of diverse patients to investigate how germline ancestry, molecular subtypes, and mutational processes shape tumor biology and clinical outcomes. MethodsWe analyzed 1,102 adults with WHO 2021-classified diffuse gliomas (IDH-mutant, 1p/19q-codeleted oligodendroglioma; IDH-mutant astrocytoma; IDH-wildtype glioma) from seven U.S. institutions. Whole-exome sequencing (WES) of FFPE tumors identified somatic alterations and COSMIC SBS v3.2 mutational signatures. Genetic ancestry was estimated from WES using 1000 Genomes reference populations. Overall survival was assessed using Kaplan-Meier and multivariable models. ResultsThe cohort included 66.9% European (EUR), 21.1% Admixed American/Hispanic (AMR), 10.3% Admixed African (AFR), and 1.6% Asian (AS) ancestry. Survival followed expected molecular hierarchy (median overall survival: oligodendroglioma 15.7 years, astrocytoma 10.6 years, IDH-wildtype glioma 1.9 years). Within oligodendroglioma, AMR patients showed improved survival versus EUR (HR 0.67, 95% CI 0.48-0.94; p=0.011), with similar trends across subtypes. Somatic profiling confirmed canonical subtype-defining alterations and revealed higher ATRX alterations in AFR and AMR IDH-wildtype tumors compared with EUR. ATRX alterations were associated with improved survival only in AFR (p=0.003). Mutational signature analysis identified subtype-specific signatures, including therapy-associated signatures. Chemotherapy-related signatures were more frequent in EUR and AMR than in AFR. ConclusionsThis ancestrally diverse glioma cohort confirms established molecular classifications and identifies ancestry-associated differences in survival, somatic alterations, and mutational processes, indicating the critical need for broad representation to inform precision neuro-oncology. Key PointsO_LIA multi-institutional glioma cohort validates subtype and survival patterns across ancestries. C_LIO_LITherapy-associated mutational signatures differ by ancestry, suggesting distinct treatment-related mutational processes. C_LIO_LIAdmixed American patients show improved survival, particularly in oligodendroglioma. C_LI Importance of the StudyMost genomic studies of adult-type diffuse glioma have focused on populations of predominantly European ancestry which limits the ability to examine variation in tumor biology and clinical outcomes across populations. In this study, we assembled one of the largest ancestrally diverse cohorts of molecularly characterized adult diffuse gliomas, integrating germline ancestry inference with tumor whole-exome sequencing and mutational signature analysis. We confirm that established molecular classifications and survival hierarchies remain robust across ancestry groups. However, we also identified ancestry-associated differences in survival within specific tumor subtypes, higher ATRX alteration frequencies in African American and admixed American patients with IDH-wildtype tumors, and variation in therapy-associated mutational signatures across ancestry groups. These findings highlight the importance of incorporating population differences into genomic studies of glioma and provide a resource for future multi-ancestry investigations of glioma risk, tumor evolution, and treatment response, ultimately supporting more inclusive precision neuro-oncology.

bioinformatics↗

bioRxiv2026

A Stress-Adaptive Lipid Kinase Axis Defines Metabolic Vulnerabilities in Neuroendocrine Prostate Cancer

Neuroendocrine prostate cancer (NEPC) persists in a profoundly hypoxic microenvironment, yet the mechanisms enabling tumor adaptation to this metabolically challenging niche remain undefined. Here, we identify the lipid kinase PIKfyve as overexpressed in NEPC, functioning as a central node in a stress-lipid kinase axis that drives adaptation to persistent endoplasmic reticulum (ER) stress. Mechanistically, NEPC requires PIKfyve-mediated lysosomal degradation and lipid recycling to maintain metabolic homeostasis under hypoxia. PIKfyve inhibition disrupts lysosomal function, leading to ER stress accumulation and activation of a compensatory, sterol regulatory element-binding protein (SREBP)-dependent de novo lipogenesis program essential for NEPC survival. This stress-lipid axis creates a synthetic vulnerability between PIKfyve and fatty acid synthase (FASN), where dual inhibition synergistically amplifies ER stress, triggers the terminal unfolded protein response, and induces tumor cell death. These findings reveal a metabolic adaptation in NEPC and provide preclinical evidence that co-targeting PIKfyve and FASN can overcome hypoxia-associated stress adaptation.

cancer biology↗

bioRxiv2026

A Dual-Locus-Targeting Strategy to Enhance CRISPR/Cas9-mediated CFTR Replacement via Helper-Dependent Adenoviral vector in porcine genome

Gene therapy has been the subject of extensive research following the advent of gene-editing technologies. Genetic disorders with difficult-to-target tissues, such as cystic fibrosis (CF), still face many challenges in developing efficacious gene therapy. The potential universal approach of gene replacement involves inserting a functional CFTR gene after generating DNA double strand breaks using gene editors such as CRISPR/Cas9. However, this strategy has not achieved clinical significance, as CRISPR/Cas9-mediated integration of CFTR is limited primarily by the infrequent activity of the homology-directed repair (HDR) pathway. To circumvent this limitation and improve CFTR transgene integration and expression, we explored a method of adding a second integration site, which we termed the dual-locus-targeting method. Using a helper-dependent adenoviral vector (HDAd)-delivered CRISPR/Cas9 system in porcine epithelial cells, we found that sequential delivery of two vectors, one targeting the CFTR locus and the other the genomic safe harbour site GGTA1, enhanced the integration efficiency of lacZ and CFTR donor genes to 16.5% and 3.4%, respectively. These results demonstrated a potential strategy to improve the efficacy of CFTR replacement for the development of a universal and permanent gene therapy treatment for CF lung disease. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/731381v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@14c8583org.highwire.dtl.DTLVardef@d1862eorg.highwire.dtl.DTLVardef@1c0594eorg.highwire.dtl.DTLVardef@1271c10_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2026

β-Catenin Drives Apical-Basal Polarization to facilitate TE lineage commitment In Vitro and In Vivo

Embryo polarization is critical for the first cell fate segregation. While mechanisms underlying its initiation have been described, the intrinsic signaling pathways that regulate this process remain poorly understood. Here, we show that mouse embryonic stem cells, when aggregated under defined conditions, recapitulate the first lineage segregation to generate trophectoderm (TE)-like cell populations and undergo self-organized morphogenesis into blastocyst-like structures. In the blastoid-forming medium, we identify CHIR99021 is essential for the generation of blastoids from both ESCs and totipotent-like cells. CHIR99021 promotes cell polarization and TE differentiation by activating the WNT/{beta}-catenin pathway and upregulating associated genes. Consistent with this, genetic ablation of {beta}-catenin abolished the cell polarization and disrupted blastoid formation from ESCs, a defect that was restored by {beta}-catenin overexpression. Moreover, {beta}-catenin depletion compromised cell polarization in natural embryos. Collectively, this study establishes the Wnt/{beta}-catenin as a critical regulator initiating polarization in vitro and in mouse early embryo development.

developmental biology↗

bioRxiv2026

X-Gutor: a high-fidelity in vitro platform for long-term gut microbiome recovery

In vitro gut microbiome-culturing models are essential for studying host-microbe interactions, yet achieving high microbial recovery and long-term stability remains a long-standing challenge. Here we devise X-Gutor, an ecologically designed in vitro platform that recapitulates the monogastric digestive system with precise control of pH, redox potential, and a mucin-based biofilm matrix. Using an integrated assessment framework, microbial source tracking, a curated gut metabolism database (GutDB), and short-chain fatty acid profiling, we benchmarked gut community recovery. Building on this platform, HanGutor and PigGutor were developed to recover 96.27{+/-}4.92% and 90.48{+/-}5.95% of human and swine gut microbiota, respectively. Ecological fine-tuning revealed that redox potential drives the Prevotella-Bacteroides trade-off and that spatial biofilm structure suppresses cheater (Succinivibrio) growth. The X-Gutor provides a scalable, modular platform for gut microbiome engineering, dietary intervention, and microbiota-targeted therapy development.

microbiology↗

bioRxiv2026

A horizontally transferred fungal deubiquitinase facilitates insecticides resistance in whitefly

Horizontal gene transfer (HGT) has enabled insects to acquire novel genetic material that can fuel adaptation to environmental change. However, the role of HGT in the evolution of insecticide resistance remains poorly characterised. Here, we identify BtUCH19, a fungal gene that has integrated into the genome of the global pest Bemisia tabaci and functions as a deubiquitinating enzyme (DUB). We show that compared to endogenous DUB, BtUCH19 specifically removes K63-linked ubiquitin chains from a cytochrome P450, CYP4C64, thereby stabilizing this key detoxification enzyme in vivo. Sustained CYP4C64 abundance enhances metabolic detoxification of two commonly used insecticides thiamethoxam (TMX) and clothianidin (CLO) to their low-toxicity products TMX-Urea and CLO-Urea. Consequently, BtUCH19 drives insecticide resistance through a novel "HGT-PTM-Metab" axis. Our work reveals the instrumental role of a HGT in orchestrating ubiquitin-proteasome system (UPS)-mediated protein level regulation of a key detoxification pathway. These findings offer new insights into the intricate mechanisms underlying co-evolutionary biology, and provide a new molecular target for Integrated Pest Management (IPM).

zoology↗

bioRxiv2026

Plant growth forms shaping biodiversity patterns can guide conservation planning on the Qinghai-Tibet Plateau

Plant growth forms effectively reflect profound evolutionary adaptations that underpin ecosystem functioning; however, how their biogeographic disparities influence conservation prioritization remains poorly understood. We here integrate a comprehensive phylogeny with high-resolution distribution data for 14,468 vascular plant species across the Qinghai-Tibet Plateau, showing that growth-form identity decouples the spatial patterns of taxonomic and phylogenetic diversity, with distinct forms exhibiting marked differences in geographic range sizes and elevational optima (2,200-3,300 m). Although herbs dominate plant assemblages across spatial scales, their proportional abundance decreases along a northwest-to-southeast aridity gradient, yielding to structurally complex, non-herbaceous forms in humid, species-rich regions. Consequently, priority conservation areas derived for individual growth forms exhibit low spatial similarity. Despite this divergence, we identify trees and climbers as highly effective umbrella growth forms: prioritizing these functional groups captures [≥]75% of the multidimensional diversity of all other growth forms within a minimal spatial footprint. Our findings demonstrate that accounting for growth-form-based functional identity is essential for maximizing conservation efficacy, providing a scalable framework for biodiversity hotspots worldwide.

ecology↗

bioRxiv2026

Circular RNA aptamers act as superb sub-stoichiometric chaperones to prevent cytosolic TDP-43 condensation

Pathological protein misfolding and aggregation underlie many devastating human diseases, yet strategies to selectively neutralize aggregation-prone protein states without perturbing their normal functions remain limited. Here we identify loosely structured circular RNA (cRNA) aptamers, circT3 and its minimized 116-nt variant circT3-M3, as superb sub-stoichiometric RNA chaperones that suppress pathological assembly of TAR DNA-binding protein 43 (TDP-43), a defining feature of amyotrophic lateral sclerosis and frontotemporal dementia, in vitro and in cells. Rather than acting through simple stoichiometric sequestration, these cRNA aptamers engage TDP-43 transiently and iteratively through functionally and pathologically important residues in the RRM1 domain. Such interaction enables a single cRNA aptamer to promote rapid and multiple RRM1-dependent homomeric assembly, thereby stabilizing TDP-43 in a soluble oligomeric state to outcompete the C-terminal prion-like domain-driven condensation and supersaturation. Together, our findings establish cRNA aptamers as highly efficient subcellular RNA chaperones with exceptionally potent low-dose activity and highlight their promise as next-generation RNA therapeutics for certain protein-aggregation disorders.

molecular biology↗

bioRxiv2026

From unsupervised clustering to atlas-guided annotation in cohort-scale spatial omics with HiCAT

Pathologist-annotated tissue regions provide a fundamental reference for examining spatial omics data, yet such annotations are available for a limited number of samples due to the substantial manual effort required. Moreover, these annotations are derived from morphology within individual histology images, which can overlook molecularly defined regions and obscure intra-sample heterogeneity. To address these limitations, we present HiCAT, a machine-learning framework that automatically generates pathologist-informed region annotations and characterizes regional heterogeneity in spatial omics data. Across seven datasets, HiCAT consistently outperforms state-of-the-art methods, achieving a median relative improvement of 107% in accuracy. Beyond transferring pathologist annotations, HiCAT uncovers molecularly informed regional heterogeneity not captured by original annotations, including tumor subregions associated with clinical outcomes and brain subregions aligned with spatiotemporal disease progression. By generating consistent, highly granular, and biologically informative region annotations across large cohorts, HiCAT enables scalable downstream analysis and provides training labels for foundation models in spatial biology.

genomics↗

bioRxiv2026

Cell-type-specific transposable element transcription tracks symbiosis and calcification programs in the reef-building coral Acropora hemprichii

Transposable elements (TEs) are pervasive components of eukaryotic genomes and major drivers of genome evolution, yet their contribution to cell-type-specific regulatory landscapes remains poorly understood, particularly in non-model marine invertebrates. Here, we integrated single-cell RNA sequencing with pseudo-aligned TE expression profiling to examine how TE transcription relates to cell type identity in the reef-building coral Acropora hemprichii. We constructed a cell atlas comprising 4,716 cells across eight major cell types. Notably, TE expression alone was sufficient to accurately resolve all major cell types, indicating that cell-type-specific transcriptional states are robustly reflected in TE activity patterns. We identified 9,759 expressed TEs, of which 333 exhibited strong cell-type-specific activity. These differentially expressed TE features were associated with nearby expressed genes and transcription factor loci, suggesting a relationship between cell-type-specific TE activity and local gene regulatory programs. Genes associated with cell-type-specific TEs were enriched for core coral physiological processes, including calcification, metabolite transport, and symbiosis-related functions. Together, these findings indicate that TE transcription is structured along coral cell-type identity and physiological specialization. Our study provides a single-cell-resolved framework for investigating TE-gene relationships in early-diverging metazoans and a community resource for future functional interrogation in reef-building corals.

bioinformatics↗

bioRxiv2026

An N-terminal amphipathic helix governs activity and conformational dynamics of Nramp metal transporters

Nramps are a family of proton-coupled divalent metal ion transporters that play critical roles in maintaining homeostasis of essential metals. In humans, Nramp2 (DMT1) mediates iron uptake to support both cellular and systemic iron homeostasis, whereas Nramp1 exports metals from phagosomes, contributing to antimicrobial defense. A survey of experimentally solved Nramp structures reveals that an N-terminal helix (A) immediately preceding TM1 is folded only in the outward-facing or outward-facing occluded states, raising the question of its role in Nramp transport. Here, we combined mutagenesis, transport assays, and molecular dynamics simulations to investigate A. Our results show that deletion or substitution of conserved residues in A markedly reduces Fe2+ transport. Simulations indicate that A behaves as an amphipathic helix in the outward-facing state and preferentially stabilizes this conformation over the inward-facing state, thus acting as a key player in controlling conformational equilibrium. This study provides new insights into structural dynamics of Nramps and potentially sheds light on other LeuT-fold transporters.

biochemistry↗

bioRxiv2026

Symmetry Analysis and Ancestral Sequence Reconstruction Reveal a Symmetrical Translocation Pathway and Activity Determinants of ZIP Metal Transporter

Membrane transporters frequently exhibit internal structural symmetry, reflecting evolutionary origins through gene duplication and fusion events, and this feature has been widely used to infer transport mechanisms. Yet its application to the ZIP (Zrt-/Irt-like protein) family of divalent metal transporters, which are crucial for trace metal homeostasis, has not been fully explored. Here, we apply combined symmetry analysis and ancestral sequence reconstruction to study the ZIP family. We show that internal symmetry is broadly present across prokaryotic ZIPs and is more prominent in reconstructed ancestral sequences, supporting an evolutionary pathway in which the modern 8-transmembrane (TM) ZIP fold arose from duplication, domain rearrangement, and fusion of an ancestral 4-TM protein. Leveraging this symmetry framework, we identify a continuous and symmetric metal translocation pathway composed of symmetric entrance, transport, and exit sites in the ZIP fold, and define gates that ensure alternating access. Application of this structural model to human ZIP4 enables identification of the gate-forming residues, and functional studies reveal that two residues (T529 and V533) in the external gate play a crucial role in controlling metal transport. In addition, comparison with ancestral sequences uncovers a set of LIV-1 subfamily-specific metal chelating residues (D504, E541, and D544) that break the symmetry in the ancestral sequences. Functional studies showed that these residues play distinct roles in transport. Together, our study demonstrates that combining internal symmetry analysis and ancestral sequence reconstruction for the ZIP family facilitates elucidation of metal translocation mechanism and identification of the subfamily-specific features that confer functional specialization.

biochemistry↗

bioRxiv2026

Functional screening of ZIP8 naturally occurring variants identifies pathogenic mutations and trafficking defects

The rapid expansion of human genomic data has revealed a large number of naturally occurring variants, creating a major challenge for functional annotation. The human metal transporter SLC39A8 (ZIP8) is a clinically important, promiscuous divalent metal transporter, yet most of its documented variants remain uncharacterized. Here, we developed a workflow to functionally evaluate ZIP8 variants by integrating laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS) with scaled-up cell-based transport assays. Using this method, we systematically analyzed 33 naturally occurring missense variants located in the extracellular domain (ECD) of ZIP8. The assay enables direct quantification of intracellular metal accumulation with substantially improved throughput ([~]150 samples per hour). Functional screening identified 14 potential pathogenic variants with significantly reduced transport activity. Comparison with computational predictions revealed a moderate correlation between activity and AlphaMissense pathogenicity scores (R2 = 0.423), while an error rate of [~]20% underscores the need for experimental validation. Flow cytometry analysis showed that most loss-of-function variants exhibit impaired trafficking of the protein to the cell surface possibly due to mutation-caused protein misfolding or instability. Structural mapping of activity-compromised variants, together with functional assessment of the ZIP8-ECD, highlights the importance of this domain in ZIP8 expression and intracellular trafficking. Together, this work establishes a scalable approach for functional screening of metal transporter variants and provides new insights into the structure-function relationships of ZIP8.

biochemistry↗

bioRxiv2026

Neural Dynamics of Belief and Value Computations Guiding Strategic Social Decisions

Successful strategic behavior must be grounded in beliefs about the opponent and her intentions. While many potential models have been proposed to explain choices in such situations, the neural mechanisms that govern learning and choice in complex strategic contexts remain poorly understood. Here, we use a computational model that combines dynamic learning and choice mechanisms to explain both choices and response times of human participants engaged in a competitive strategic task. Using electroencephalography (EEG), we identify temporally structured stages of neural processing that support an evolving value-based decision process, corresponding to first- and second-order belief updates and evidence accumulation related to the comparison of action values. Gamma-band phase coupling between central and parietal EEG signals varied with individual winning rate, suggesting that strategic behavior involves coordinated information transfer across spatially remote areas. Together, our data characterize the temporally evolving neural dynamics of belief and valuation processes that underlie strategic choice and provide neural validation for assumptions embedded in computational models of this behavior.

neuroscience↗

bioRxiv2026

Large-scale activity analysis of gut prophages reveals significantly active lineages in the human gut

Prophages dominate the human gut virome and their transition from lysogeny to lytic replication profoundly affects gut microbial community structure. However, the global activity landscape of gut prophages remains largely uncharted. Here, we developed a workflow to assess prophage activity across more than 30,000 gut bacterial isolates cultured in vitro under standard conditions. Using this approach, 4,033 prophages, corresponding to a small fraction (7.5%) of the overall prophage reservoir, were detected as active, indicating a high-lysogeny, low-activity landscape. Prophage activity varied markedly across host taxa, with Bacillota exhibiting notably elevated active rates. Active prophages derived from 183 viral families (vFAMs), 55 of which were assigned as significantly active (SA-vFAMs), including: SA-vFAM7, a novel, hyper-prevalent lineage with expanded host range into Tannerellaceae and substantial intra-lineage diversity; and Candidatus Mubacviridae (SA-vFAM1), a newly defined, hankyphage-inclusive, highly active Mu-like transposable phage family infecting Bacteroidales, characterized by conserved MuA-MuB operons and cross-family host range. Together, this work provides a large-scale, activity-integrated atlas of human gut prophages, demonstrating that prophage activity is driven by both host phylogeny and viral lineage identity, and establishing a foundational resource for understanding prophage ecology.

microbiology↗

bioRxiv2026

Genetic suppression of myeloid receptor Clec7a attenuates microglia neuroinflammation and promotes microglial phagocytosis to delay disease progression in ALS models

Microglial activation has been closely associated with accelerated ALS disease progression. However, specific microglial pathways that regulate microglial activation and ALS disease progression remain limitedly understood. Here, we determined the role of Clec7a (or Dectin-1), a core signature gene of disease-associated microglia (DAM) in ALS, in regulating microglial activation and ALS disease progression. Our spinal cord scRNA-Seq results found that Clec7a deficiency specifically attenuated microglial neuroimmune gene expression in SOD1G93A mice and human ALS. In addition, in vivo two-photon imaging of human (h) TDP43 phagocytosis by microglia in the cortex showed that Clec7a deficiency promotes microglial phagocytosis of pathological hTDP43 by enhancing microglial process dynamics. Subsequent survival analysis further showed that selective deletion of Clec7a in microglia mitigates motor neuron degeneration and delays disease progression in SOD1G93A ALS mice. Together, our results establish that Clec7a is a key regulator in shaping disease microglial functions and promotes disease progression in ALS.

neuroscience↗