Biology subjects

Wei, R.

Publications and source records attributed to Wei, R..

At least 19 recordsLinked to original sources

bioRxiv2026

β4-integrins safeguard nuclear mechanics to suppress prostate cancer progression

Prostate cancer (PCa) progression is accompanied by profound alterations in cell-extracellular matrix (ECM) adhesion, nuclear architecture and mechanical adaptability, yet the molecular mechanisms linking these processes remain poorly understood. Hemidesmosomes (HDs), formed by 6{beta}4-integrins, anchor epithelial cells to the basement membrane and couple extracellular forces to the intermediate filament (IF) cytoskeleton. Here, we identify a previously unrecognized tumor-suppressive function of {beta}4-integrins in preserving nuclear integrity in prostate epithelial cells. Loss of {beta}4-integrins disrupted the cytokeratin-5 network and its coupling to the nucleus, leading to nuclear softening, lamin remodeling, reduced heterochromatin content and enhanced confined migration. Unexpectedly, proximity-labeling proteomics revealed that {beta}4-integrins engage nuclear pore complex (NPC) components in an 6-independent manner, particularly upon HD disassembly. Selected interactions were validated using proximity ligation and co-immunoprecipitation assays. {beta}4-integrin loss was associated with enlarged nuclear pores and aberrant nucleocytoplasmic transport, including nuclear accumulation of YAP1. Consistent with these findings, reduced {beta}4-integrin expression in a large PCa tissue cohort correlated with altered nuclear morphology, adverse clinicopathological features, metastatic progression, and poor patient survival. Collectively, our study establishes {beta}4-integrins as a critical molecular link between cell-ECM adhesion, nuclear mechanics and genome integrity.

cancer biology↗

bioRxiv2026

GALILEO: Embodied AI scientist for autonomous therapeutic discovery in dynamic membrane systems

Generalizable Agentic Laboratory Intelligence for Learning, Experimentation, and Optimization (GALILEO) closes the prediction-to-intervention gap in therapeutic peptide discovery. Unlike prior AI-scientist systems, GALILEO couples an Observation-Thought-Action-Summary (OTAS) reasoning loop with robotic peptide synthesis and multimodal phenotyping. Candidate peptides are retrieved from a clinically informed peptide prior (CPP) and locally edited through auditable operations. GALILEO autonomously prioritized LRRC8C and SLC25A1 branches and used wet-lab feedback to update target beliefs, sequence policies, assay choices, and mechanism hypotheses. Peptides generated under this framework blocked LRRC8C currents, perturbed osmolyte/redox homeostasis, and promoted tumor-dependent T-cell activation, while SLC25A1 peptides disrupted citrate-export metabolism, reduced extracellular acidosis, and enhanced CD8+ T-cell function. These results establish retrieval-and-editing-based physical learning as a route for auditable, experimentally grounded interventions and transferable membrane-blocker rules.

Molecular Biology↗

bioRxiv2026

Single-Cell Transcriptomic Mapping of PD-L1/TLR4 Remodeling Informs Topical Immunoprevention Timing in Skin Carcinogenesis

Cutaneous squamous cell carcinoma (cSCC) represents a growing public health burden, with incidence projected to increase 23-29% over the coming decade. Topical immunoprevention strategies targeting the PD-L1/PD-1 and TLR4 axes have demonstrated preclinical efficacy, yet optimal intervention timing in humans remains undefined. To address this gap, single-cell RNA sequencing was performed on matched sun-protected (SP), sun-damaged (SD), and actinic keratosis (AK) biopsies from the same individuals, along with independent cSCC cases. Immune checkpoint and innate inflammatory signals were detectable as early as SD skin, prior to histologically confirmed dysplasia. Monotonically increasing expression of CD274 (PD-L1), CTLA4, PDCD1, CD27, and STAT1, alongside progressive TLR4-MYD88 innate immune signaling, was revealed through pseudobulk data analysis, with earliest upregulation at the SD stage. Fuzzy c-means trajectory clustering identified cell-typespecific programs across dendritic cells, macrophages, T cells, fibroblasts, endothelial cells, and keratinocytes. Dendritic cells shifted from early inflammatory antigen-presenting programs toward late PD-L1/IFN-regulatory states; macrophages showed monotonically increasing TLR4-associated myeloid activation; and T cells defined a "hot but exhausted" microenvironment in established cSCC. These findings identify SD and AK as biologically active stages for topical immunoprevention and provide a cellular roadmap for PD-L1/PD-1 and TLR4 blockade strategies.

cancer biology↗

bioRxiv2026

Vgll2 and Tead1 Govern Generation of Mouse and Human Hypothalamic Hypocretin (Orexin) Neurons

The hypothalamic hypocretin (Hcrt; aka orexin) neuropeptide neurons are crucial for wakefulness and their malfunction results in narcolepsy; a devastating disorder without current cures. Transplantation of mouse Hcrt cells into mouse narcolepsy models is pointing to cell therapy as a potential treatment for narcolepsy. However, progress in this area requires decoding the developmental pathways generating human HCRT neurons and a deeper understanding of their diversity and physiology. Here, we identify the hypothalamic progenitor domain generating mouse Hcrt neurons and propose a conserved mouse/human genetic cascade driving Hcrt specification. This cascade involves the Vgll2 and Tead1 transcription factor partners, which we find are crucial for mouse Hcrt neuron generation. Conversely, co-misexpression of VGLL2 and TEAD1 in human stem cell derived hypothalamic organoids can induce HCRT neuron differentiation. These findings provide an important element for the development of human induced HCRT neurons for physiological studies and for cell therapy in narcolepsy.

neuroscience↗

bioRxiv2026

Engineering Pseudomonas putida KT2440 for open-loop upcycling of mixed plastics

Current mechanical and chemical recycling strategies address less than 10% of global plastic waste, necessitating alternative valorization routes. Biological upcycling via enzymatic depolymerization combined with microbial conversion of the resulting monomers offers a promising pathway to transform mixed plastic waste into valuable alternatives. Here, we employed a single engineered Pseudomonas putida KT2440 for simultaneous co-utilization of five plastic monomers including ethylene glycol, terephthalic acid, adipic acid, 1,4-butanediol, and L-lactic acid, which can be derived from enzymatic hydrolysis of polyethylene terephthalate (PET), polybutylene adipate-co-terephthalate (PBAT), polyester-polyurethanes (PUs), and polylactic acid (PLA). Continuous fermentation over 21 days with alternating mixed-monomer feeds achieved steady state growth and complete substrate depletion, yielding adaptive mutations that informed iterative strain improvement. Further engineering enabled the biosynthesis of (R)-3-hydroxybutyrate (R-3HB), and 0.70 g L-1 R-3HB was produced directly from enzymatic hydrolysates of blended PET, PBAT, and TPU. These results establish a viable bio-based approach for upcycling realistic mixed plastics into value-added bioproducts.

microbiology↗

bioRxiv2026

Spatial Decoding of Tertiary Lymphoid Structure Maturation in Non-Small Cell Lung Cancer Using Deep Neural Networks

Understanding the role of tertiary lymphoid structures (TLS) is crucial in non-small cell lung cancer (NSCLC), as they are associated with patient prognosis and treatment outcomes. Specific cellular ecosystems that originate anti-tumor activity or predict immunotherapy response remain poorly characterized. To this end, we developed a high-resolution, multimodal spatial atlas jointly profiling transcriptomics, proteomics, and histology to characterize TLS maturation in NSCLC alongside secondary lymph organs as a baseline. Using this atlas, we proposed a pathologist-in-the-loop framework that combines a variational graph autoencoder (VGAE) with diffusion pseudotime to refine human expert annotations and characterize TLS maturation. These spatial molecular representations were extended to H&E whole-slide images via a vision transformer-based foundation model. Next, we resolved cellular composition, spatial organization, and cell-cell interactions within these data and defined two divergent spatial ecosystems. Clinical evidence suggests that these ecosystems are associated with distinct patient outcomes: a mature germinal center niche with favorable prognoses, and a tumor-macrophage-fibroblast niche with unfavorable prognoses. In summary, our work decodes key components of TLS heterogeneity, identifies hallmark spatial patterns involved in NSCLC adaptive immunity, and provides a framework for translating spatial omics insights into clinical applications.

genomics↗

bioRxiv2025

scMOBA: A conversational single-cell Multi-Omics Brain Agent across species

Single-cell and spatial multi-omics are revolutionizing our understanding of the complexity in the developmental, aging, and diseased brain, but integrating this knowledge across modalities and species remains challenging. To bridge this gap, we propose scMOBA, a conversational single-cell Multi-Omics Brain Agent established by a large language model, a gene encoder, and a cross-attention projector. The scMOBA was pre-trained on 130 million single-cell and spatial multi-omics data spanning the entire brain across diverse species, development, aging and diseases. The pre-training utilized a novel multi-omics Feature-Question-Answer (FQA) paradigm, enabling the model to generate biological answers from feature inputs and textual queries. This unique scheme facilitates superior zero-shot inference capabilities without requiring additional fine-tuning. We demonstrate that scMOBA achieves state-of-the-art performance in fine-grained cell type classification across different species and modalities, as well as in batch correction and multi-omics data integration. Furthermore, scMOBA significantly boosts the accuracy of kinds of critical downstream tasks, including cell-type specific aging clock construction and disease status prediction. Overall, scMOBA serves as a powerful scientific discovery engine for multi-omics brain research, advancing the precision prediction and early intervention of neurological aging and diseases.

bioinformatics↗

bioRxiv2025

Scalable integration and prediction of unpaired single-cell and spatial multi-omics via regularized disentanglement

Deciphering cellular states requires methods capable of integrating large-scale heterogeneous single-cell and spatial omics data. However, these data are typically unpaired due to destructive assays and further confounded by modality heterogeneity, technical noise, and immense scale. Here we present scMRDR, a scalable computational framework based on regularized disentangled representation learning for integrating fully unpaired single-cell and spatial multi-omics datasets. Built on a unified and structure-preserving architecture, scMRDR removes the need for pairing supervision while maintaining computational efficiency, enabling scaling to large datasets spanning multiple disparate omics modalities. Across diverse real-world benchmarks, scMRDR demonstrates strong performance in batch correction, modality alignment, and biological signal preservation. The framework further supports cross-modal translation across omics modalities and enables spatial coordinate imputation for non-spatial single-cell datasets using a reference atlas. The resulting spatial mapping allows spatially resolved analyses, including identification of spatially variable genes and characterization of epigenetic regulatory programs in their native tissue context. These capabilities position scMRDR as a scalable and versatile framework for large-scale multi-omics integration.

genomics↗

bioRxiv2025

COTree: A Statistical Framework for Deciphering Cell-Resolved Multi-Omics Trajectories

Recent advances in whole-cell modeling enable the computational tracking of the temporal evolution of thousands of molecular species across genomic, transcriptomic, proteomic, and metabolomic layers. These models provide a complementary perspective for studying cellular dynamics, offering continuous, system-wide observations that are difficult to obtain from experimental technologies, which are often destructive and yield only static measurements from limited modalities. While whole-cell models generate multi-omic simulation trajectories with high temporal resolution, analyzing and interpreting such complex data remains a major challenge that limits their potential to elucidate cellular dynamics. To address this challenge, we propose COTree, a statistical framework that learns integrated multi-omic representations and constructs a trajectory principal tree to summarize cellular progression patterns. COTree enables a broad range of downstream analyses, including cell classification, fate prediction, developmental time detection, and driver species identification, that provide new insights into how cells develop and differentiate. To demonstrate its practical utility, we apply COTree to a multi-omic trajectory dataset generated from the whole-cell model of JCVI-Syn3A, revealing cell types, characterizing long-term cellular dynamics, and identifying key driver species associated with cell death and replication.

bioinformatics↗

bioRxiv2025

Uncovering bacterial pseudaminylation with pan-specific antibody tools

Pseudaminic acids (Pse) are a family of carbohydrates found within bacterial lipopolysaccharides, capsular polysaccharides and glycoproteins that are critical for the virulence of human pathogens. However, a dearth of effective tools for detecting and enriching Pse has restricted study to only the most abundant Pse-containing glycoconjugates. Here, we devise a synthesis of - and {beta}-O-pseudaminylated glycopeptides to generate pan-specific monoclonal antibodies (mAbs) that recognise - and {beta}-configured Pse and its C8 epimer (8ePse) presented within glycans or directly linked to polypeptide backbones. Structural characterisation reveals the molecular basis of Pse recognition across a range of diverse chemical contexts. Using these mAbs, we establish a glycoproteomic platform to provide unprecedented depth in mapping the Pse glycome of Helicobacter pylori, Campylobacter jejuni, and Acinetobacter baumannii strains. Finally, we demonstrate that the mAbs recognise diverse capsule types in multidrug-resistant Acinetobacter baumannii and enhance phagocytosis to eliminate infections in mice.

biochemistry↗

bioRxiv2025

Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell

Macromolecular complexes in the genetically minimized bacterium, JCVI-syn3A, support gene expression (RNA polymerase, ribosome, degradosome), metabolism (ABC transporters, ATP synthase) and chromosome dynamics. In this work, we further incorporate the assembly of 21 unique macromolecular complexes into the existing whole-cell kinetic model of Syn3A. The synthesis and translocation of protein subunits in membrane complexes occur through distinct pathways. A range of 2D association rates for membrane complexes were considered to guarantee a high yield of assembly given the existing time scales of gene expression. By alleviating the undesired kinetically trapped intermediates in ATP synthase assembly, the efficiency was improved. The assembly of RNA polymerase, ribosome, and degradosome influence the speed and efficiency of protein synthesis. Collectively, this model predicted time-dependent cellular behaviors consistent with experiments. A machine learning analysis of the time-dependent metabolomics and metabolic fluxes highlighted the effect of introducing complex assembly into our whole-cell model.

biophysics↗

bioRxiv2025

Impaired envelope integrity in the absence of SanA is linked to increased Lipid II availability and an imbalance of FtsI and FtsW activities

In Gram-negative bacteria, the outer membrane (OM) acts in conjunction with the peptidoglycan (PG) cell wall as a barrier against physical, osmotic, and chemical environmental stressors including antibiotics. SanA, an inner membrane protein in Escherichia coli K-12, is required for vancomycin resistance at high temperatures (>42 {degrees}C) and impacts sodium dodecyl sulfate (SDS) resistance during stationary phase reached from carbon limitation. However, its function remains unknown. Here, we show that {Delta}sanA has a synthetic genetic interaction with {Delta}wecA, a mutation that increases the availability of the isoprenoid carrier for PG synthesis. Specifically, the {Delta}sanA {Delta}wecA strain demonstrated heightened SDS-EDTA sensitivity, activation of the Rcs stress response, and increased cell length. Further investigation tied the SDS-EDTA sensitivity to increased lipid II available for PG synthesis. Spontaneous suppressor mutants of this phenotype harbored point mutations in prc, which encodes tail specific protease, or ftsI, which encodes the cell division DD-transpeptidase, a target of Prc. We focused on the ftsI mutations and demonstrated that the ftsI mutations had increased cell length but nevertheless enhanced PG incorporation at the septum compared to the {Delta}sanA mutant, returning PG incorporation to wild-type levels. Moreover, other mutations affecting septal PG synthesis, but not divisome assembly, also suppressed the SDS-EDTA sensitivity. These findings suggest that, in the absence of SanA, increased lipid II availability perturbs the balance between septal PG synthesis, lateral PG elongation, and other envelope biogenesis pathways, which leads to increased OM permeability. IMPORTANCEThe Gram-negative cell envelope is a barrier that protects the cell from environmental stress. Therefore, the synthesis of each layer of this envelope needs to be closely coordinated throughout growth and division. Here, we investigated SanA, a protein in Escherichia coli K-12 that affects envelope permeability under cellular stress, including nutrient limitation and high temperature. We found that SanA plays a key role in maintaining the permeability barrier when precursor levels for peptidoglycan (PG) synthesis are elevated, linking envelope integrity to balanced septal PG production during cell division. Our results suggest that SanA modulates substrate availability to preserve envelope function, and that in its absence, imbalanced substrate flux to septal PG synthesis disrupts septum formation and compromises barrier integrity.

microbiology↗

bioRxiv2025

Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution

The intestinal epithelium is often a site of pathology, such as in inflammatory bowel disease (IBD), and its maintenance is highly modulated by interactions with the microenvironment. However, a systematic understanding of how the myriad of niche cues impact distinct epithelial cell types in a diseased context is still lacking. To address this gap, we first benchmarked diverse human colonic organoid injury models against IBD tissue, and established a disease-relevant model of epithelial inflammation using TNF, IFN{gamma}, and IL1{beta}. Using this system, we built a dictionary of epithelial responses to 81 secreted niche factors at single cell resolution via donor-pooled, multiplexed single cell RNA-sequencing (scRNA-seq). The comprehensive nature of our atlas allowed us to map relationships between perturbations, infer the function of less well-characterized ligands, and identify cell type-specific perturbed pathways. Finally, we established the relevance of organoid-derived gene programs by mapping them to single cell and spatial atlases of human IBD tissue. Our resource offers a global view of epithelial responses to microenvironmental cues in a physiologically relevant disease context and generates new hypotheses for signaling factors that may be involved in epithelial homeostasis and repair.

bioengineering↗

bioRxiv2025

SpatialAgent: An Autonomous AI Agent for Spatial Biology

Advances in AI are transforming scientific discovery, yet spatial biology, a field that deciphers the molecular organization within tissues, remains constrained by labor-intensive workflows. Here, we present SpatialAgent, an autonomous AI agent for spatial biology research. SpatialAgent couples large language models with a Plan-Act-Conclude architecture, dynamic tool and skill retrieval, multimodal interpretation, and verification modules that audit generated claims. It supports the full discovery loop, from gene-panel design and multimodal annotation to trajectory inference, cell-cell communication analysis, imputation, and hypothesis generation. Across human and mouse brain, heart, tonsil, colon, and prostate datasets, SpatialAgent outperformed established computational baselines and matched or surpassed expert scientists in key tasks. In open-ended case studies, it recovered known tissue organization and generated spatially grounded hypotheses. In a prospective mouse prostate cancer Xenium study, it designed a compact 100-gene add-on panel that profiled 4.2 million cells across 21 samples, improved cell-type and malignant-state prediction, and captured spatially structured tumor and microenvironment programs. SpatialAgent establishes a framework for autonomous and collaborative discovery in spatial biology.

bioinformatics↗

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

Spacer Extension Reconciles Specificity and Activity in High-Fidelity Cas9 Genome Editing

AbstractEngineering high-fidelity CRISPR enzymes often leads to reduced cleavage activity, creating a significant hurdle in balancing nuclease specificity and efficiency for clinical applications. Here, we demonstrate that extending the spacer to 21 or 22 nucleotides restores the impaired cleavage activity of SuperFi-Cas9, an engineered high-fidelity Cas9 variant with seven mutations at the PAM-distal region. Structural and mutational analyses reveal that the spacer extension strengthens additional interactions at the PAM-distal end, stabilizing the nuclease- sgRNA-DNA complex, which appears to be disturbed due to the seven mutations. This approach not only provides a high-fidelity Cas9 with uncompromised efficiency but also introduces a novel strategy to enhance CRISPR complex stability. Our findings offer a promising avenue for precise and efficient genome editing, crucial for advancing CRISPR technologies toward clinical translation.

genomics↗

bioRxiv2024

Enalapril mitigates aging by targeting antioxidative genes via phosphorylated Smad1/5/9

Aging increases the risk of a myriad of chronic diseases, which are expensive and difficult to treat owing to their various risk factors. Repurposing existing medications has accelerated the development of therapies aimed at slowing aging. In this study, we revealed that enalapril, a drug widely prescribed for hypertension, can improve both cellular senescence and individual health. Mechanistically, phosphorylated Smad1/5/9 act as pivotal mediators of the anti-senescence properties of enalapril. It stimulates downstream genes involved in cell cycle regulation and antioxidative defense, facilitating cell proliferation and diminishing the production of reactive oxygen species (ROS), thus increasing the antioxidative ability of enalapril. At the organismal level, enalapril has been shown to bolster the physiological performance of various organs; it notably enhances memory capacity and renal function and relieves lipid accumulation. Our work highlights the potential of enalapril to augment antioxidant defenses and combat the effects of aging, thereby indicating its promise as a treatment strategy for aging-associated diseases and its use for healthy aging.

cell biology↗

bioRxiv2024

Improved split prime editors enable efficient in vivo genome editing

Prime editor (PE) is a precise genome-editing tool that enables all 12 possible base-to-base conversions, as well as insertions and deletions, that does not require DSBs or donor DNA. The efficient delivery of prime editors in vivo is critical for realizing the full potential of prime editing in disease modeling and therapeutic correction. Although PE has been divided into two halves and delivered using dual adeno-associated viruses (AAVs), editing efficiency at different gene loci varies among split sites, and efficient split sites within Cas9 nickase are limited. In this study, by screening multiple split sites, we demonstrated that 1115 (Asn) is an efficient split site when delivering PE by dual-AAV. Besides, we utilized a feature reported by others recently that RNase could be detached from the Cas9n and designed split sites in the first half of Cas9n. We found that split-PE-367 enabled high prime editing efficiency with Rma intein. To test the editing efficiency in vivo, dual-AAV split-ePE3-367 was packaged in AAV9 and delivered by tail vein injection in mice, achieving 24.4% precise genome editing 4 weeks after injection. Our findings establish an alternative split-PE architecture that could achieve robust gene editing efficiency, facilitating the potential utility both in model organisms and as a therapeutic modality.

genomics↗