Biology subjects

Li, Z.

Publications and source records attributed to Li, Z..

At least 271 records · Page 15Linked to original sources

bioRxiv2026

CTLA-4 inhibitors drive colitis through metabolic reprogramming-mediated Treg/Th17 imbalance

Immune checkpoint inhibitors (ICIs), especially CTLA-4 inhibitors (CTLA-4), exhibit a high incidence of colitis as an immune-related adverse event (irAE) during cancer treatment, severely limiting patient benefit. Clinically, both treatment interruption and existing intervention drugs for ICI-mediated colitis may compromise antitumor efficacy. However, there is inadequate research on the pathogenesis of ICI-mediated colitis, with findings often conflicting. Here, we first established multiple clinically relevant animal models, including an immuno-humanized ICI-mediated colitis model. Through time-series transcriptomics, we discovered that CTLA-4-induced colonic toxicity exhibits characteristics ranging from early metabolic reprogramming represented by glycolysis to later immune disorders represented by Th17 responses. By targeting colonic CTLA-4+ T cells, CTLA-4 blocked CD80/CD86-CTLA-4 interaction, thereby activating the PI3K-AKT-mTOR pathway. Subsequently, mTOR mediated metabolic reprogramming in T cells, shifting them from Treg-biased oxidative phosphorylation to Th17-biased glycolysis. The colonic toxicity of CTLA-4 has also been demonstrated to depend on the PI3K-AKT-mTOR pathway, glycolysis, and Th17 responses. Notably, metformin significantly relieved ICI-mediated colitis by inhibiting mTOR without impeding antitumor efficacy. Collectively, these findings highlighted the metabolic-immune axis in the colonic toxicity of ICI and provided a clinically superior intervention strategy.

pharmacology and toxicology↗

bioRxiv2026

Phosphorylation of KIN-G motor domain by Polo-like kinase negatively regulates centrin arm biogenesis in Trypanosoma brucei

The unicellular parasite Trypanosoma brucei assembles a motile flagellum that is required for locomotion, cell division plane placement, and cell-cell communication. Inheritance of the flagellum during the cell cycle relies on the faithful duplication/segregation of multiple flagellum-associated cytoskeletal structures, including a centrin-marked, bar-shaped structure termed centrin arm, which also determines the site for Golgi assembly. Biogenesis of the centrin arm requires the Polo-like kinase homolog TbPLK and the orphan kinesin KIN-G, but the mechanistic role of TbPLK in centrin arm biogenesis remains elusive. Here we report that TbPLK phosphorylates KIN-G, disrupts its microtubule-binding activity, and negatively regulates its function. TbPLK phosphorylates KIN-G in vitro at multiple residues, two of which are in vivo TbPLK phosphosites, including the Thr301 residue within one of the microtubule-binding motifs of the kinesin motor domain. Phosphorylation of Thr301 by TbPLK inhibits the microtubule-binding activity of KIN-G in vitro, and expression of a Thr301 phospho-mimic mutant in T. brucei disrupts centrin arm integrity, Golgi duplication, flagellum attachment zone elongation, flagellum positioning, and cell division plane placement. In wild-type T. brucei cells, Thr301 phosphorylation occurs on a small portion of the KIN-G population, suggesting that KIN-G undergoes phosphorylation/dephosphorylation cycles to regulate its activity. Together, these findings uncover a negative role of TbPLK-mediated phosphorylation of KIN-G in regulating centrin arm biogenesis in trypanosomes.

cell biology↗

bioRxiv2026

Functionally Mature Bioengineered Human Skeletal Muscle Tissues Capture Essential Aspects of Glucose Metabolism

Human skeletal muscle is a major regulator of whole-body metabolic homeostasis, yet mechanistic insight into human muscle plasticity is limited by the lack of in vitro models with adult-like metabolic and functional maturity. Here, we develop a workflow for generating bioengineered human skeletal muscle tissues that undergo coordinated structural, molecular, and functional maturation and stabilize in an adult-like state by day 21. Time-resolved RNA-seq and protein profiling reveal consolidation of contractile programs alongside progressive metabolic maturation, including increased mitochondrial electron transport chain content, mature mitochondrial network organization, and upregulation of glucose- and glycogen-handling proteins as well as muscle-enriched AMPK isoforms. Functionally, the tissues develop physiological force-frequency behavior, post-tetanic potentiation, and reproducible fatigue responses that are exacerbated by hypoxia and glucose withdrawal. Exercise-like chronic stimulation increases force and endurance with hypertrophy-like remodeling, and these adaptations reverse with detraining. The model also captures pharmacological responsiveness. {beta}2-adrenergic stimulation activates canonical signaling, increases force, limits disuse-related decline, and improves endurance in a glucose-dependent manner. Under physiological insulin and IGF-1 conditions, tissues show robust insulin-stimulated glucose uptake and glycogen synthesis, with punctate glucose transporter 4 (GLUT4) localization. Finally, knockdown of muscle glycogen synthase (GYS1) preserves peak tetanic force but impairs endurance and force recovery under fuel stress, indicating that glycogen metabolism is a key determinant of human muscle resilience.

cell biology↗

bioRxiv2026

Joint Segmental Duplication Co-option Drives Human-specific Transcriptional Readthrough and Expression Fine-tuning of NPEPPS-TBC1D3

Segmental duplication (SD) is a major driver of functional changes in evolution and disease. Many genes embedded within SDs, such as NPEPPS and TBC1D3, display substantial copy number variation (CNV) across individuals. Yet, the precise identification of the functional copies and their transcriptional outputs remains largely unstudied. Focusing on NPEPPS and TBC1D3, we illustrate human-specific expression fine-tuning mechanisms associated with readthrough transcripts. We identified a human-specific NPEPPS-TBC1D3 digenic genomic structure that originated from a joint SD pair and became fixed across populations. Experiments demonstrate that this structure generates NPEPPS-TBC1D3 readthrough transcripts, which are the predominant isoforms of TBC1D3 expression in various cell types, fine-tuning its protein level. Furthermore, a human-specific hypomethylation signal within an upstream CpG island of NPEPPS precisely pinpoints the expressed TBC1D3 paralog. Moreover, we reveal transcriptional readthrough events are [~]3-fold enriched for joint-SD-associated transcriptional readthrough (JSDTR) and identify 109 JSDTR gene pairs, including neurodevelopmentally important pairs and clinically interesting SERF1A/B-SMN1/2. Taken together, our findings comprehensively describe an example of how a joint SD event shaped evolution and suggest that JSDTR is a broad mechanism for the emergence of new functions.

genetics↗

bioRxiv2026

Hidden stop codons orchestrate mRNA fate by ambushing ribosomal frameshifting associated with codon usage

In eukaryotes, the mRNA stability is generally shaped by codon usage bias, the uneven preferences for synonymous codons, in a translation-dependent manner. However, the conserved mechanism linking codon to mRNA decay remains elusive. Hidden stop codons (HSCs), defined as stop codons located in the +1 or -1 frame relative to canonical ORF, are widespread across all genomes but largely uncharacterized. Here, we demonstrate that in both fungi and human cells, HSCs play an conserved and mechanistic role in promoting mRNA decay by rapidly terminating out-of-frame translation promoted by nonoptimal codons, primarily through +1 ribosomal frameshifting. In the filamentous fungus Neurospora crassa, partially deleting HSCs via synonymous substitutions in the clock gene frequency increases mRNA stability and disrupts circadian rhythmicity. In human cells, acute depletion of translation termination factor eRF1 impairs recognition of HSCs, leading to global stabilization of mRNAs enriched in nonoptimal codons and HSCs. In both Neurospora and humans, these mRNAs are in part degraded through the NMD pathway via UPF1. Collectively, these findings suggest that in eukaryotes, HSCs serve as surveillance elements to monitor ribosomal frameshifting and out-of-translation promoted by nonoptimal codons, thereby initiating mRNA decay through NMD.

molecular biology↗

bioRxiv2026

Enhancing volumetric microscopy with blind computational correction of spatially variant aberrations using neural field representation

Studying biological processes across multi-millimeter scales requires imaging systems that combine high spatial resolution with a large field of view (FOV). However, optical aberrations degrade image quality, particularly in large-FOV systems where distortions gradually worsen toward the periphery. Existing methods for correcting field-dependent aberrations are limited and often impractical. Hardware-based solutions such as adaptive optics demand additional components and sample manipulation, increasing system complexity and experimental burden. Computational approaches, while promising, typically rely on exhaustive point spread function (PSF) calibration or large training datasets, restricting their applicability. We introduce a self-supervised algorithm that simultaneously estimates spatially varying aberrations and reconstructs 3D sample structure from a single blurred image--without PSF calibration or training data. Our method was implemented on optically cleared mouse hippocampal neurons and cortical vasculature imaged with oblique plane microscopy (OPM), as well as in vivo mouse retinal vasculature captured with adaptive optics scanning laser ophthalmoscopy (AOSLO), where PSF calibration is infeasible. The algorithm predicts and corrects aberrations across multi-millimeter FOVs, enhances contrast in low signal-to-noise regions, and reveals critical structural details in neuronal and vascular systems that are obscured in raw images. This approach enables high-resolution, large-scale imaging without hardware modifications, expanding the accessibility of advanced microscopy techniques.

bioinformatics↗

bioRxiv2026

Amplified genome editing by in vivo editor production

Genome editing enzymes have vast therapeutic potential. However, achieving sufficient delivery in vivo remains a major challenge, because editing machinery is confined to the subset of transfectable cells in a tissue. Here, we tested the possibility that genome editing could be amplified in vivo by enabling transfected cells to transfer editing enzymes to neighboring cells. Our data show that this NANoparticle-Induced Transfer of Enzyme (NANITE) strategy quadrupled editing efficiency in cultured cells relative to non-spreading controls. A single intravenous injection of the NANITE plasmid into mice induced ~3-fold higher levels of liver editing at the transthyretin (Ttr) locus relative to non-spreading controls, with corresponding reductions in serum TTR levels. Spreading therapeutic enzymes offers a nonviral and non-infectious strategy to boost therapeutic effects after delivery.

bioengineering↗

bioRxiv2026

Dynamic Mechanical Loading Reprograms Meniscus Cell-Derived Extracellular Vesicles to Enhance Their Regenerative Potency

The meniscus is a fibrocartilaginous tissue critical for knee stability and load distribution, but its poor healing capacity makes regeneration after injury a major clinical challenge. Extracellular vesicles (EVs) are emerging as promising cell-free therapeutics for tissue regeneration. However, their clinical translation remains limited by low yield and variable bioactivity. Here, we investigated how dynamic mechanical loading regulates the production, composition, and function of meniscus fibrochondrocyte-derived EVs (MFC-EVs). Using a custom bioreactor system, cells were subjected to physiologically relevant cyclic tensile loading. Mechanical stimulation significantly increased EV production and secretion, likely through the ESCRT-independent pathway, without altering vesicle size or tetraspanin expression. Functionally, "mechanically primed" EVs enhanced aggrecan expression in recipient mesenchymal stromal cells (MSCs), mirroring the loading-response phenotype of their source cells. Proteomic profiling identified 380 unique proteins across all EV groups, with loaded EVs enriched in extracellular matrix- and cytoskeleton-associated proteins, as well as pathways related to tissue morphogenesis, cell migration, and cartilage development. Together, these findings demonstrate that physiologic mechanical loading enhances both the yield and regenerative potency of MFC-EVs by enriching their cargo with matrix- and development-associated proteins, providing a scalable and biologically inspired approach for engineering high-efficacy EV therapeutics for meniscus repair and musculoskeletal regeneration.

bioengineering↗

bioRxiv2026

Adult human ex vivo brain slices for dissecting glial biology and multicellular communication

Glial cells are critical modulators of brain function in health, aging, and disease, emerging as promising therapeutic targets. However, exploring their roles and therapeutic potential is limited by the lack of experimental systems that faithfully capture the repertoire of mature human glial cells while permitting controlled perturbations. Here, we establish a robust ex vivo platform for cell-type specific interrogation of glial responses and multicellular crosstalk, based on adult human organotypic brain slice cultures, obtained from neurosurgical resections. We show that slice cultures preserve tissue architecture, maintain all major cell types and mature cellular identities over weeks in culture. These cultures elicit robust, stimulus-specific transcriptional programs to diverse stressors and inflammatory stimuli, demonstrating sensitivity to distinguish closely related signals and reproducibility despite biological and technical variation. Moreover, we resolved coordinated glial cell type-specific responses to TNF, a key mediator of neuroinflammation, uncovering distinct and physiologically relevant functional roles validated in postmortem human brains. Network analyses discovered balanced pro- and anti-inflammatory loops among microglia and astrocyte cells, which notably also involved oligodendrocyte precursor cells (OPCs), confirming their suggested role in regulation of the tissue level inflammatory response in human brains. We experimentally validated that glial activation in slice cultures is orchestrated not only by direct stimulation but also through intercellular signaling across cell types, mirroring natural multicellular dynamics in brain tissue. Together, organotypic brain slice cultures emerge as a sensitive and robust platform for dissecting adult human glial biology, paving the way for deeper mechanistic insights and advanced drug-screening applications.

neuroscience↗

bioRxiv2026

Ploidy-dependent modulation of DNA replication kinetics in Xenopus

DNA replication in multicellular organisms follows a tightly regulated spatio-temporal program. Although the mechanisms underlying this replication program remain only partially understood, studies in model systems such as Xenopus laevis have highlighted the importance of titrating low-abundance replication factors. Whole-genome duplications as a consequence of polyploidization introduce additional layers of complexity, yet comparative analyses of replication programs across closely related polyploid species are scarce. Here, we developed an interspecies in vitro replication system using X. laevis egg extracts and sperm nuclei from three Xenopus species with varying ploidy: diploid (X. tropicalis), tetraploid (X. laevis), and dodecaploid (X. eysoole). Replication in diploid X. tropicalis was faster than in tetraploid X. laevis nuclei, due to higher fork density and speed. Surprisingly, dodecaploid X. eysoole replication was also accelerated compared to tetraploid nuclei, suggesting that higher ploidy does not necessarily extend S phase. Since replication genes are highly conserved between these species, these results imply dynamic tuning of replication programs across polyploid species and shed light on the evolutionary adaptability of DNA replication in response to genome duplication.

molecular biology↗

bioRxiv2026

GraphESMStable: A Deep Learning Framework for Protein Stability Prediction Fusing Pre-trained Sequence Models and Graph Neural Networks

Predicting protein stability is fundamental, yet existing computational methods often face limitations in generalization, reliance on single data modalities, and challenges with complex multi-point mutations. To address these, we propose GraphESMStable, a novel deep learning framework for predicting protein mutation-induced thermal stability changes. GraphESMStable integrates rich evolutionary context from a frozen pre-trained protein sequence language model with fine-grained three-dimensional structural geometry captured by a trainable Graph Neural Network. A sophisticated residue-level cross-attention mechanism facilitates the deep fusion of these distinct modal representations. The framework features a dedicated prediction head capable of predicting an entire single-point mutation landscape in a single forward pass, and an Epistasis Decoder explicitly modeling non-additive effects for multi-point mutations. Trained exclusively on a large-scale dataset, GraphESMStable achieves state-of-the-art performance, outperforming baselines across a diverse suite of independent evaluation benchmarks. This includes superior generalization on multiple stability datasets, cross-metric generalization to thermal melting prediction, and a significant lead in predicting double mutation epistatic effects. Furthermore, it demonstrates robust performance in predicting human pathogenic mutation stability and achieves substantial improvements in low-sample fitness prediction tasks. Our ablation studies confirm the synergistic benefits of this cross-modal fusion. GraphESMStable represents a significant advancement towards building highly generalizable and efficient foundational models for protein stability prediction, offering broad applicability in protein design and biomedical research.

bioengineering↗

bioRxiv2026

A mediterranean-mimicking diet harnesses gut microbiota-derived 3-IAA to rejuvenate T cell

Diet profoundly shapes the tumor microenvironment through metabolite modulation, yet the mechanisms linking diet, gut microbiota, and antitumor immunity remain unclear. Here, we demonstrate that a mediterranean-mimicking diet (MedDiet) suppresses tumor growth by orchestrating a microbiota-metabolite-immune axis. MedDiet selectively enriched Bacteroides thetaiotaomicron (B. thetaiotaomicron) in the gut, whose administration recapitulated tumor suppression. Both MedDiet and B. thetaiotaomicron elevated plasma levels of the tryptophan metabolite indole-3-acetic acid (3-IAA). Mechanistically, 3-IAA enhanced CD8+ T cell cytotoxicity and alleviated exhaustion by inhibiting the integrated stress response, sustaining antitumor immunity in vivo. Importantly, 3-IAA synergized with anti-PD-1 therapy to further restrain tumor progression. Finally, we developed a MedDiet Score to predict patient survival and response to immunotherapy. These findings reveal that dietary modulation of gut microbiota can reshape systemic metabolites to potentiate T cell-mediated antitumor responses. Our study identifies 3-IAA as a metabolite-based adjuvant for immune checkpoint therapy and highlights the translational potential of diet-driven immunomodulation in cancer treatment.

cancer biology↗

bioRxiv2026

Discovery of potent oligopeptides for various metabolic diseases using deep learning

Artificial intelligence (AI)-based methods are increasingly critical in peptide drug discovery, but their applications are limited in a narrow scope such as antimicrobial peptides. For indications where peptide therapy inherently excels, such as metabolism, endocrinology, and tissue regeneration, AI-based pipeline for therapeutic peptide discovery is long awaited but still unmet. Here, we propose a deep learning-based pipeline, Deepeptide, capable of identifying therapeutic oligopeptides for various metabolism-related indications. Leveraging the intrinsical relationship of disease indication -- biological processes -- molecular functions, Deepeptide discovers oligopeptides with indication-ameliorating-related molecular functions as lead candidates for indication of interest. Deepeptide was applied in five representative indications of metabolism, endocrinology, and tissue regeneration: angiogenesis, lipid metabolism, osteogenesis, glucose metabolism, and anti-angiogenesis. Overall, 62% of the identified oligopeptide candidates demonstrated significant bioactivity in vitro, with most of them showing comparable potency to the first-line drugs. Notably, the heptapeptide AP7 exhibited angiogenic potency comparable to VEGF in excisional wound splinting mouse model by promoting cell migration rather than proliferation, and hexapeptide TP6 showed significant dual-efficacy against hyperlipidemia and obesity in high-fat diet mice by inhibiting lipid synthesis and regulating gut microbiota. These findings highlight the potential and generalizability of Deepeptide in therapeutic oligopeptide discovery for metabolic diseases.

bioinformatics↗

bioRxiv2026

Targeting matrix metalloproteinase-14 disrupts DNA repair and reduces viability in adrenocortical carcinoma

BackgroundAdrenocortical carcinoma (ACC) is a rare and aggressive endocrine cancer with limited treatment options and poor prognosis. Identifying novel therapeutic targets requires understanding the molecular drivers of ACC progression and establishing translational models for preclinical validation. ResultsMatrix metalloproteinase-14 (MMP-14) is the most highly expressed MMP in ACC, and high MMP-14 expression is associated with worse overall and disease-free survival. We demonstrate that MMP-14 is essential for ACC cell survival and serves an unexpected role in maintaining genome stability. Genetic silencing or pharmacologic inhibition of MMP-14 significantly reduced viability in both NCI-H295R cells and patient-derived tumor organoids (PTOs). MMP-14 knockdown induced CHK1 activation and S-phase checkpoint arrest. Mechanistically, MMP-14 translocates to the nucleus and binds to chromatin following DNA damage induced by ionizing radiation or cisplatin. Loss of MMP-14 resulted in accumulation of DNA double-strand breaks, as evidenced by increased {gamma}H2AX foci, and impaired non-homologous end joining (NHEJ)-mediated repair. ConclusionsThese findings reveal a novel nuclear function for MMP-14 in DNA repair and identify MMP-14 as a promising therapeutic target in ACC. Targeting MMP-14 may sensitize ACC tumors to DNA-damaging chemotherapy by impairing the repair of therapy-induced lesions.

cancer biology↗

bioRxiv2026

TRPV4 Inhibition by a Natural Product Mediates Analgesia

The transient receptor potential vanilloid 4 (TRPV4) channel, a polymodal calcium-permeable cation channel, is activated by diverse stimuli, including hyposmolarity, moderate heat, mechanical stress, and acidic pH. TRPV4 plays a critical role in the onset and progression of pain and is implicated in multiple pathological conditions, positioning it as an attractive therapeutic target. However, the development of TRPV4-targeted therapeutics has been hindered by limited mechanistic understanding of its inhibition. Here, the natural product (R)-1-(3-ethylphenyl)ethane-1,2-diol (AH001) is identified as a potent, subtype-selective TRPV4 inhibitor. A potential gating mechanism of TRPV4 inhibition is proposed through a combination of structural analyses and site-directed mutagenesis. Electrophysiological studies and cryo-electron microscopy (cryo-EM) further reveal that AH001s glucuronide metabolite, AHP, retains robust TRPV4 inhibitory activity, providing a critical structural basis for rational optimization of AH001 as a lead compound. Notably, AH001 demonstrated significant efficacy in reducing neuronal hyperexcitability in dorsal root ganglia (DRGs) and produced pronounced analgesic effects across multiple pain models, highlighting its therapeutic potential in pain relief. This study offers critical structural and mechanistic insights into TRPV4 inhibition and lays the groundwork for the structure-based design of TRPV4-targeted therapeutics.

biochemistry↗

bioRxiv2026

Bioarchaeological evidence for commensal brown rats (Rattus norvegicus) in early Neolithic China

Due to its commensal relationship with humans, facilitating its dispersal from its natural range in East Asia, the brown rat (Rattus norvegicus) is now one of the most cosmopolitan and invasive mammals. Brown rats are also vectors of human pathogens and the most commonly used mammalian model (after mice) for biomedical research. Despite their major role in biodiversity loss and medicine, our understanding of a likely origin for their commensal relationship with humans in China still relies on modern population genetics, without a reliable timeframe of localisation. In this research, we have tried to fill this gap using direct information from the archaeological remains of rats collected by Chinese colleagues in several archaeological sites dated between 9000 and 3500 BP. Thanks to high-resolution morphometrics and direct 14C dating, we have identified the occurrence of the brown rat (Rattus norvegicus) within the domestic area deposits of the early Neolithic site of Jiahu by 7500 cal BP, suggesting a tentative link between rice agriculture and an early commensal behaviour of this species.

zoology↗

bioRxiv2026

Leveraging Human Pangenome for Improved Somatic Variant Detection

Somatic variant detection is technically challenging due to low variant allele fractions, the confounding presence of germline variation, and reference bias. Linear references such as GRCh38 miss sample-specific variation, causing misalignments and incorrect variant calls. Although telomere-to-telomere donor-specific assemblies (DSAs) accurately represent individual genomes, their application is limited by cost and technical barriers. Alternatively, the graph-based human pangenome provides a scalable framework to improve read alignment and perform genome inference. Here, we benchmarked somatic variant detection using GRCh38, graph-based pangenomes, and pangenome-inferred DSAs with a HapMap mixture dataset and the COLO829 melanoma cell line. Pangenome-guided alignment improves read mapping and somatic variant calling accuracy. Furthermore, personalized pangenomes partially reconstruct donor-specific genomic content, improving accuracy, reducing germline contamination, and enabling detection of events in loci absent or poorly represented in GRCh38. These findings demonstrate that graph-based and personalized pangenomes are effective strategies for enhancing somatic variant detection compared with GRCh38.

genomics↗

bioRxiv2026

Progenitor Diversity and Architecture of the Human Ganglionic Eminences Shaping the Basal Ganglia

The embryonic medial and lateral ganglionic eminences (MGE, LGE) are the principal sources of most neurons and glia for the basal ganglia. In primates, the MGE has a distinctive cytoarchitecture characterized by doublecortin enriched cellular nests (DENs), yet the architectonic organization underlying DEN formation, the molecular heterogeneity of ganglionic eminence progenitors and their lineage relationships, remain poorly understood. Here, using paired single-nucleus transcriptomics and chromatin accessibility profiling of the three GEs, we identify distinct progenitor populations, delineate their gene regulatory networks, and reconstruct their lineage trajectories. Live imaging reveals a unipolar outer radial glia-like population (GE-oRG) that undergoes mitotic somal translocation. Spatial transcriptomics identifies a distinct CRABP1+/ANGPT2+ domain within the MGE. Integrated spatial and electron microscopy demonstrates a periphery-to-center gradient of differentiation in the MGE. Leveraging DEN-forming MGE organoids derived from PCDH19 knockout human pluripotent stem cell lines, we identify the protocadherin, PCDH19, as a key regulator of DEN formation.

neuroscience↗