Biology subjects

Chen, W.

Publications and source records attributed to Chen, W..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

Targeting one-carbon metabolic vulnerabilities of metastasis with therapeutic potential

Evidence has shown that tumor progression is associated with the acquisition of growing autonomy and the creation of a complex signaling network through various signal pathways. Which particular signaling pathway is involved in the metastasis of a specific cancer is unclear. Here, we applied metastatic functional screening and identified that one-carbon and SSP metabolism pathways, as well as related genes, are associated with tumor metastasis inhibition. We engineered the cancer cells with poorly or highly metastatic potential to confirm the metabolism pathways regulating the ability to colonize different tissue sites. We also asked whether the restriction of the metabolism pathways by known inhibitors. We then identified three new compounds that can inhibit the expression of these genes and block tumor metastasis. Our findings uncovered a mechanism by which tumor cells reprogram their metabolism to promote migration, invasion, and survival at distant sites in tumor metastasis, offering a rational strategy to guide clinical treatment. The identified novel molecular proteins and pathways represent a promising therapeutic target for metastatic disease.

cancer biology↗

bioRxiv2026

CD28 Co-stimulation Is Organized by Signaling Condensates and Counteracted by PD-1

T cell activation relies on the coordinated integration of TCR and co-signaling pathways, yet how these signals are physically organized remains unclear. Here, we demonstrate that CD28 co-stimulation is driven by a phase-separation mechanism in which the CD28 intracellular domain (ICD) forms signaling condensates with the Src-family kinase Lck. Ligand engagement promotes the CD28 ICD accessibility, and triggers rapid CD28/Lck condensation, enhancing CD28 phosphorylation, cytoskeletal polarization, and cytokine production. We further identify PD-1 as a graded regulator of this process: monophosphorylated PD-1 is recruited into CD28/Lck condensates, whereas di-phosphorylated PD-1 competitively binds the CD28 ICD and dissolves these assemblies. CD28 and PD-1 ICDs also undergo condensation directly, revealing a dynamic and compositionally heterogeneous signaling system. Guided by this competitive phase-separation mechanism, we engineer CD28 ICD mutants that preserve Lck condensation while resisting PD-1-mediated disruption. Incorporation of these condensation-selective mutants into CAR constructs confers resistance to inhibitory signaling and enhances antitumor efficacy in vivo. These findings establish phase separation as a central organizing principle of CD28 co-stimulation and provide a biophysical framework for engineering more resilient therapeutic T cells.

immunology↗

bioRxiv2026

IBDkb: an AI-enhanced integrative knowledge base for inflammatory bowel disease research and drug discovery

IBDkb (Inflammatory Bowel Disease Knowledge Base; https://www.biosino.org/ibdkb) is a freely accessible, integrated web-based platform that systematically curates and harmonizes multi-source data related to inflammatory bowel disease (IBD). To address the fragmentation and therapeutic gaps in existing specialized resources, IBDkb establishes a unified framework featuring advanced full-text search, interactive visualizations, cross-module knowledge graphs, and AI-powered utilities for real-time literature retrieval, trend analysis, text/PDF interpretation, and domain-specific conversational assistance. The platform currently integrates 98,453 research articles, 3,390 clinical trials, 200 investigational drugs, 200,606 bioactive compounds, 103 therapeutic targets, 77 experimental models, 12 pathogenesis summaries, and 15 treatment strategies. These integrated tools facilitate efficient exploration of complex associations among drugs, targets, trials, and mechanisms, thereby accelerating hypothesis generation and translational research in IBD. The platform is openly available without registration and supports data downloads. A case study on structure-aware drug comparison further demonstrates its utility in facilitating cross-disease drug repositioning hypotheses.

bioinformatics↗

bioRxiv2026

The ZmHEAT1/ZmKAKU42-ZmNCH1 module regulates heat stress tolerance by modulating nuclear envelope structure in maize

Heat stress threatens maize production. Through a genome-wide association study using pollen viability decline rate as a phenotype, we identified ZmHEAT1, encoding the nuclear envelope protein ZmKAKU41, as a key regulator of thermotolerance. ZmHEAT1 positively regulates heat tolerance at seedling and reproductive stages, with its overexpression improving thermotolerance and its knockout reducing pollen viability and yield under high temperatures. ZmHEAT1 interacts with its homolog ZmKAKU42 and the nucleoskeleton protein ZmNCH1 to form a complex at the nuclear envelope. Mutants lacking ZmHEAT1 or ZmKAKU42 exhibit increased nuclear envelope damage under heat stress, along with repressed expression of key heat shock protein genes (e.g., HSP90-2, HSP17.4). This work establishes the ZmHEAT1/ZmKAKU42-ZmNCH1 complex as a critical guardian of nuclear integrity and heat response, providing a valuable genetic resource for breeding heat-tolerant maize varieties. One-sentence summaryModulation of the nuclear envelope structure in maize is involved in heat stress tolerance.

molecular biology↗

bioRxiv2026

Telomere-to-telomere gap-free and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres

Common tobacco (Nicotiana tabacum) is an economically important crop worldwide whose allotetraploid genome sequence remains incompletely assembled. We report a 4.2Gb telomere-to-telomere gap-free N. tabacum reference genome phased into two subgenomes (subS/subT) , revealing differential evolutionary trajectories between two subgenomes marked by a rapid divergence in paternal T-genome, especially for heterochromatic centromeric regions. To understand the evolutionary dynamics of tobacco centromeres following polyploidization, we characterize the centromere architecture in tetraploid N. tabacum and its diploid progenitors, demonstrating clear subgenomic diversification and repositioning of centromeres during speciation and allopolyploidization. These findings enrich our knowledge on centromere paradox in polyploid genomes.

genomics↗

bioRxiv2026

Evolutionary genomics of local adaptation, climate vulnerability, and linarin metabolism in Opisthopappus longilobus

Global climate change and human activities are posing substantial threats to biodiversity. The genus Opisthopappus (O. taihangensis and O. longilobus), endemic to Chinas Taihang Mountains, possesses great ecological, ornamental and medicinal value. However, it is confronted with the pressures of habitat fragmentation and climate change. Here, we present the first haplotype-resolved, chromosome-scale genome assembly of O. longilobus ([~]2.95 Gb) and re-sequence 115 individuals across its range. Comparative analyses show Opisthopappus is sister to Artemisia-Chrysanthemum, with Opisthopappus and Chrysanthemum diverging at 5.15-5.18 million years ago. A profound genetic divergence is evident between O. taihangensis and O. longilobus, resulting in two distinct lineages within each species, driven by geography and climate. Our analyses indicate restricted gene flow, low diversity, and recurrent demographic bottlenecks collectively contribute to their endangerment. By integrating population genomics and environmental variables, we identified 4,437 core adaptive genes linked to water deprivation, and metabolism. Genomic offset predicts higher maladaptation risk in populations under drastic climate change. Furthermore, diverged promoters of two O-methyltransferase genes, OMT250 and OMT310, likely underlie the differential acacetin/linarin accumulation between C. morifolium and O. longilobus. These findings advance understanding of Opisthopappus evolution and climate vulnerability, offering a model for genomics-guided biodiversity conservation.

plant biology↗

bioRxiv2026

Scalable Generation of Clinical-Grade Universal Human cDC1s Enables Potent Antitumor Immunotherapy

Despite decades of intensive clinical effort, monocyte-derived dendritic cell (DC) vaccines have not yet achieved sufficient clinical benefits in cancer therapy. Conventional type 1 DCs (cDC1s), a subset of antigen-presenting cells with superior cross-presentation capacity, are well established as pivotal mediators of antitumor immunity. However, their clinical translation has been hindered by the absence of scalable and efficient generation methods. Here, we develop a three-step strategy addressing this critical unmet need: a cost-effective, feeder cell-free, GMP-compatible approach enabling large-scale generation of cDC1s from human umbilical cord blood CD34+ hematopoietic stem and progenitor cells (CD34+ HSPCs). Starting from a single umbilical cord blood unit of CD34+ HSPCs, our method yields approximately 3.5x109 pure cDC1s--sufficient for over 700 therapeutic doses. These cDC1s exhibit robust antigen cross-presentation activity and substantial production of antitumor cytokines. Critically, in various humanized tumor mouse models, they elicit significantly stronger antitumor efficacy than either moDCs or PD-1 monoclonal antibody (mAb) alone, pronouncedly remodel the tumor microenvironment (TME), and synergize with PD-1 mAbs to achieve enhanced therapeutic effects. Furthermore, our system recapitulates the complete in vivo DC differentiation trajectory: from CD34+ HSPCs through early-pre-DCs and pre-DCs to mature subsets (cDC1s, cDC2s, DC3s, mregDCs, ASDCs). This platform thus provides a powerful tool to dissect the regulatory mechanisms governing human DC subset specification. Overall, this work overcomes a long-standing bottleneck in cDC1-directed cancer immunotherapy and accelerates the clinical translation of DC subset-selective immunotherapeutic strategies.

immunology↗

bioRxiv2026

Impacts of mutation accumulation and order on tumor initiation revealed by engineered murine colorectal cancer organoids

Tumorigenesis typically follows a multi-hit trajectory, driven by accumulating oncogenic mutations. Colorectal cancer (CRC) has long served as a paradigmatic model of multi-hit tumorigenesis, characterized by adenoma-carcinoma transition accompanied by acquisition of specific oncogene and tumor suppressor mutations. However, how the temporal order of early mutations influences CRC initiation remains poorly understood. To address this, we established a CRC tumorigenesis model using murine intestinal organoids. By introducing defined combinations of key CRC driver mutations (Kras, Apc, and Trp53) in distinct orders, we systematically investigated how the order of mutation accumulation affects tumor initiation. Our results reveal that the mutation accumulation confers growth advantages in both in vitro and in vivo models. Strikingly, mutation order also influenced the tumorigenic properties of the organoids. Whereas organoids with Trp53 loss before or after Apc loss similarly affected organoid phenotypes in vitro or tumorigenicity in immunodeficient mice, organoids with Trp53 loss preceding Apc inactivation exhibited reduced tumor-forming potential in immunocompetent mice, likely due to their distinct immunological features. Collectively, our study reveals a critical role of ordered mutation accumulation in CRC initiation, an insight that may hold clinical relevance.

cancer biology↗

bioRxiv2026

Proteolytic processing of Argonautes in multiphase condensates promotes transgenerational epigenetic inheritance

Epigenetic information can be memorized in perinuclear condenates to transmit across generations to modulate gene expression in descenent. Here, we identify a conserved N terminal proteolytic mechanism in Caenorhabditis elegans that is essential for small RNA-mediated transgenerational epigenetic inheritance (TEI) and for maintaining germline immortality. Two conserved, perinuclear germ granule subcompartments-enriched N-terminal processing peptidases, APP-1 and DPF-3, act cooperatively to trim N-terminal intrinsically disordered regions of the Argonaute proteins WAGO-1, WAGO-3, and WAGO-4. This processing shields these Argonautes from proteasome-mediated protein degradation, prevents the loss of their associated small RNAs, and promotes their accumulation in germ granules subcompartments. In contrast, unprocessed WAGOs are recognized and destabilized by the conserved E3 ubiquitin ligases RNF-1 and UBR-7. We propose that this cooperative proteolytic mechanism adds another layer of sspatiotemporal regulation over small RNA-directed epigenetic inheritance and may represents a broadly conserved strategy for regulating protein homeostasis and gene expression programs.

cell biology↗

bioRxiv2025

Comprehensive Mapping of the Virus and Host Factors that Guide the Paths of HIV-1 Escape from a Therapeutic

HIV-1 resistance to therapeutics can emerge through diverse mutational routes, yet the determinants guiding pathway selection in vivo remain unclear. Through comprehensive screening, we identified 18 mutations in the HIV-1 Env protein that enhance resistance to the FDA-approved small-molecule therapeutic temsavir. We then examined their occurrence in HIV-infected individuals who developed resistance on therapy. Only a subset of the resistance-enhancing mutations emerged in vivo. On-treatment mutation frequencies correlated with their spontaneous emergence rates in temsavir-untreated individuals, and were governed by two parameters: (i) Probability of mutation appearance, determined by number and type of nucleotide changes required, and (ii) Probability of mutation persistence, determined by Env functional and immune fitness. Notably, non-neutralizing antibodies commonly-elicited in HIV-infected individuals restricted emergence of multiple resistant forms, driving convergence to a narrow set of escape routes. These findings establish a quantitative framework for predicting therapeutic resistance and reveal how host-immunity constrains viral evolution during treatment.

microbiology↗

bioRxiv2025

Combined antagonism of Oncostatin M (OSM) and Interleukin 6 (IL-6) provides both anti-fibrotic and anti-inflammatory benefit in pulmonary fibrosis

Interstitial lung diseases (ILDs), including idiopathic pulmonary fibrosis (IPF) and systemic sclerosis-associated ILD (SSc-ILD), are irreversible fibrosing diseases with a mean survival time of less than 5 years for IPF. Poorly understood etiology and complex pathogenesis of these diseases have hampered the identification and development of effective therapeutics. Existing treatments can slow progressive fibrosis and lung function decline but do not stop it entirely, resulting in a minimal impact on patient survival. Thus, novel therapeutic interventions are needed. Tocilizumab, an anti-IL-6 receptor antibody, was recently approved by FDA for the treatment of SSc-ILD based on evidence demonstrating a reduction in the rate of lung function decline. In this study, we have characterized an IL-6-driven feed-forward myeloid axis contributing to lung inflammation providing a mechanistic hypothesis for tocilizumab. Concomitantly we have identified an oncostatin M (OSM) orchestrated lung injury response contributing to epithelial and endothelial cell disruption, myofibroblast activation and fibrosis. Despite dysregulated expression of IL11 in IPF, SSc-ILD, and murine models of fibrosis, we found no evidence for a pro-fibrotic role for IL-11 in vitro or in vivo. Instead, in pre-clinical models of IPF we demonstrate that antagonism of OSM alone, or to a greater degree in combination with IL-6, reduced lung fibrosis and inflammation. Translating these observations, we validated gp130:OSMR, rather than gp130:LIFR, as the dominant human receptor complex used by OSM, identifying OSMR as a potential therapeutic target to stall fibrosis.

immunology↗

bioRxiv2025

Human and AI voice identities evoke shared neural signatures during speaker recognition across changes in speech content and prosody

Both biologically-produced human voices and algorithmically-generated AI speech manifest speaker identity. Critically, prosodic variations modulate the acoustic dimensions (e.g., fundamental frequency) that also shape individual speaker identity representations. So far it remains unclear whether listeners process speaker identities in human and AI voices through neurologically equivalent mechanisms, nor how prosodic cues might influence these cognitive processes. We examined event-related potentials during old/new speaker discrimination after name-based identity learning, and further analyzed correctly recognized old speakers comparing trials where prosody matched vs. mismatched between learning and testing. For old/new discrimination, multivariate pattern analysis (MVPA) revealed three significant late windows (662-1498 ms) with Pz as the primary contributor for AI voices, yet none for human voices. Univariate analyses revealed that human voices showed earlier widespread discrimination (N250: 200-280 ms), while both voice types converged on Pz as the strongest contributor based on effect size rankings for late old/new effects (400-800 ms). These old/new effects emerged across completely different speech content between learning and testing, addressing a gap in prior literature. For speaker-specific prosodic expectation effects in the 500-900 ms window, unexpected prosody elicited late positivity for human voices compared to the prosody used during learning, whereas AI voices elicited late negativity. The late positivity resembles P600 components observed for communicative style expectancy violations, while the late negativity likely reflects effortful reprocessing of prosodic violations within atypical synthetic signals, analogous to accented speech processing. Our study advances understanding of voice identity in cognitive neuroscience and offers implications for AI voices in human-computer interaction. [Word count: 250]

neuroscience↗

bioRxiv2025

Mapping Core Components of Membrane-less Organelles in Living Cells by Phase-APEX2 Proximity Labeling

Membrane-less organelles (MLOs), formed via liquid-liquid phase separation, are crucial for organization of biomacromolecules and cellular processes, yet their dynamic nature challenges compositional analysis. Conventional proximity labeling methods lack the specificity to overcome high background and systematic biases inherent in studying these condensates. Here we introduce Phase-APEX2, a three-input AND-gate strategy that dramatically enhances labeling specificity. By integrating a split-APEX2 system with a light-controlled H2O2 generator, we developed Phase-APEX2 platforms for two application contexts: Phase-APEX2-MS for proteomics and Phase-APEX2-seq for genomics. Our analyses revealed not only the core interactomes of the nucleolus and stress granules with high accuracy but also uncovered distinct "molecular grammars" governing their assembly and a surprising link between nucleolar dynamics and the transcriptional regulation of mitosis-related genes. This highly specific and adaptable platform opens new avenues for exploring the composition and function of diverse biomolecular condensates.

cell biology↗

bioRxiv2025

Whole-brain connectomics of Drosophila reveals a robust, distributed architecture for the suppression of feeding during escape

Survival demands instant prioritization of escape over maintenance. To decode the dynamic logic embedded in the static Drosophila connectome (FlyWire v783), we simulated the conflict between predator-evasion, feeding, and grooming to uncover the logic of this switch. We show that escape is a holistic state defined by distributed robustness: it is reliably triggered by only a fraction of visual inputs (LC4/LPLC2) and induces a system-wide pause on behaviors like feeding and grooming. Within this global suppression, we identify a specialized, fail-safe architecture for arresting feeding. A redundant ensemble of neurons (DNge031/CB0565) targets the premotor center Roundup, effectively disfacilitating motor output. Crucially, this inhibition is modular, anatomically distinct from grooming suppression, and relies on additive logic to ensure suppression even if individual components fail. Our results demonstrate how connectome topology implements robust, survival-critical control through distributed neural architecture.

neuroscience↗

bioRxiv2025

Preclinical immunogenicity of the LP.8.1-adapted BNT162b2 COVID-19 vaccine

SARS-CoV-2 evolution toward antigenically distinct lineages drives escape from host immunity. JN.1 lineage derivatives have recently dominated the global epidemiologic landscape. In preclinical models, an LP.8.1-adapted BNT162b2 vaccine elicited higher serum neutralizing antibody responses against contemporary, circulating JN.1 sublineages, including the currently dominant XFG, as compared to JN.1-, KP.2- and XEC-adapted vaccines. These findings supported the selection of an LP.8.1-adapted vaccine for the composition of the 2025-26 COVID-19 vaccine formula.

immunology↗

bioRxiv2025

RAFTER: a releasing factor tethered RNA editing system for quantifying mRNA translation

Measurement of mRNA translational efficiency has heavily relied on quantifying the amount of polysome-associated RNAs which would not always reflect the efficient translation. To address this, we developed RAFTER, which combined RNA editing enzyme with translation releasing factor to selectively label successfully translated RNAs. The translational efficiency estimated based on RAFTER correlated well with that by Ribo-seq and Polysome-seq, but with greatly simplified workflow, which enables it for single-cell analysis.

genomics↗

bioRxiv2025

Identification of SASP-associated biomarkers and regulatory mechanisms in diabetic foot ulcers based on transcriptomics and experimental validation

BackgroundDiabetic foot ulcers (DFU) constitute a major complication arising from diabetes mellitus. Emerging research findings have underscored the pivotal contribution of cellular senescence to the pathophysiological development of wounds exhibiting delayed healing; nevertheless, the molecular regulatory networks governing this process in DFU pathogenesis remain incompletely elucidated MethodsDFU-related transcriptomic datasets were acquired from public databases. Biomarkers were identified through machine learning algorithms combined with expression validation. To evaluate the diagnostic predictive capacity of identified biomarkers for DFU, a nomogram prediction model was developed and validated. Further analyses included Gene Set Enrichment Analysis (GSEA), molecular network regulation, immune infiltration profiling, and drug prediction. Subsequently, the expression profiles of these biomarkers were quantitatively assessed through reverse transcription quantitative PCR (RT-qPCR) methodology. ResultsFour feature genes were identified using machine learning. Among them, CXCR2 and SIGLEC7 passed expression validation and were significantly up-regulated in DFU groups across two datasets (p < 0.05), confirming their potential as biomarkers. A nomogram constructed based on these two biomarkers demonstrated high discriminative accuracy and good calibration (decision curve net benefit > 0, AUC = 0.99). GSEA indicated that CXCR2 and SIGLEC7 were both enriched in the cytokine-cytokine receptor interaction pathway as well as other functionally associated pathways. Molecular regulatory network analysis indicated that both CXCR2 and SIGLEC7 were predicted to be regulated by transcription factors (TFs) such as SOX2. Immune infiltration analysis showed a significant strong positive correlation between CXCR2 and activated mast cells (correlation coefficient (cor) = 0.72, p < 0.001), and between SIGLEC7 and macrophages M0 (cor = 0.71, p < 0.001). Drug prediction identified 12 drugs targeting CXCR2 (e.g., Indoprofen) and one drug targeting SIGLEC7 (N-acetyl-alpha-D-glucosamine). Validation through Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR) revealed that CXCR2 and SIGLEC7 expression levels were markedly increased in the DFU group, showing statistically significant differences (p<0.05), which aligned with the bioinformatics analysis outcomes ConclusionThis study identified CXCR2 and SIGLEC7 as SASPRG-related biomarkers in DFU through bioinformatic analysis, providing new theoretical support and a basis for early diagnosis and treatment of DFU.

genomics↗

bioRxiv2025

3' to 5' Translation of Circular RNAs?

For decades, the 5[->]3 direction of translation has been a central dogma of molecular biology(1). Here we present evidence that eukaryotic circular RNAs (circRNAs) can serve as templates for 3[->]5 backward translation (BT), yielding polypeptides with distinct sequence and structural features not found in canonical proteomes. Mining of more than 6,000 multi-omics datasets identified [~]1 million candidate BT proteins across eukaryotes, including 59,000 high-confidence human BT proteins supported by mass spectrometry. Genetic combinatorial experiments (KO and KI) and cell-free translation of synthetic circRNAs establish BT as a conserved mechanism. Loss-of-function studies of hs.circCAPN15 in human and dm.circROLS in Drosophila underscore the functional importance of BT-derived proteins. Our work challenges the long-standing unidirectional translation paradigm, expands the functional landscape of the genetic code, and reveals a hitherto hidden layer of proteomic complexity with broad implications for biology and therapeutics.

molecular biology↗