Biology subjects

Zhang, C.

Publications and source records attributed to Zhang, C..

At least 235 records · Page 13Linked to original sources

bioRxiv2025

Intratumoral Treg ablation is sufficient to mediate tumor control systemically without autoimmunity

Regulatory T cells (Tregs) infiltrate most tumors, yet whether they suppress immune responses directly within tumor tissues is not clear. We used intratumoral (IT) delivery of diphtheria toxin (DT) in Foxp3DTR mice to deplete IT Tregs while leaving peripheral Tregs intact. IT delivery of DT reduced Treg frequencies in the tumor, which promoted potent tumor control without autoimmunity. Interestingly, this control was principally mediated by CD4+ T cells, whereas CD8+ T cells only contributed when CD4+ T cells were absent. While conventional dendritic cells (cDCs) were required to clear tumors, Batf3+ cDC1s were dispensable. Distant secondary tumors, mimicking metastases, were also controlled by IT Treg ablation. Mechanistically, IT Tregs suppressed antitumor T cell responses by blocking the acquisition of tumor antigen by cDC2s. Importantly, similar mechanisms of control were observed using a clinically translatable IT Treg-depleting anti-CCR8 antibody and reveal a distinct therapeutic strategy that leverages cDC2s and CD4+ T cells.

cancer biology↗

bioRxiv2025

Intra-Tumoral Treg Ablation Unleashes NK Cell-Mediated Control of CD8 T Cell-Resistant Tumors

Cancer cells frequently lose MHC I to evade CD8+ T cell recognition. While Natural Killer (NK) cells are poised to target MHC I-deficient cancer cells, MHC I loss alone is often insufficient to unleash fully effective NK cell responses. Here we show that selective intra-tumoral (IT) ablation of regulatory T (Treg) cells elicited potent antitumor NK cell responses that controlled MHC I-deficient and even MHC I+ cancers. Tregs controlled the activation, maturation, and anti-tumor cytotoxic activity of NK cells within the tumor microenvironment. Mechanistically, IT Tregs prevented the cDC2-dependent induction of IL-2 production by CD4+ Tconv cells that was necessary for NK cell activation. Systemically administered antibodies that selectively depleted IT Tregs similarly empowered NK- dependent tumor control. These findings expand the breadth of Treg-mediated cancer immunosuppression to encompass antitumor NK cells and suggest that targeting Tregs in tumors can control CD8+ T cell-resistant cancers. One Sentence SummaryIT Treg ablation drives NK cell tumor control via CD4+ Tconv-derived IL-2, eliminating MHC I+/MHC I- cancers without systemic toxicity.

immunology↗

bioRxiv2025

Male-Biased Cyp17a2 Governs Antiviral Sexual Dimorphism in Fish via STING Stabilization and Viral Protein Degradation

Differences in immunity between males and females in living organisms are generally thought to be due to sex hormones and sex chromosomes, and it is often assumed that males have a weaker immune response. Here we report that in fish, males exhibit stronger antiviral immune responses, the male-biased gene cyp17a2 as a critical mediator of this enhanced response. First, we observed that male zebrafish exhibit enhanced antiviral resistance compared to females, and notably, zebrafish lack sex chromosomes. Through transcriptomic screening, we found that cyp17a2 was specifically highly expressed in male fish. Cyp17a2 knockout males were equivalent to wild-type males in terms of sex organs and androgen secretion, but the ability to upregulate IFN as well as antiviral resistance was greatly reduced. Then, Cyp17a2 is identified as a positive IFN regulator which located at endoplasmic reticulum, and specifically interacts with and enhances STING mediated antiviral responses. Mechanistically, Cyp17a2 stabiles STING expression by recruiting the E3 ubiquitin ligase bloodthirsty-related gene family member 32 (btr32), which facilitates K33-linked polyubiquitination. The capacity of IFN induction of Cyp17a2 was abolished when STING is knockdown. Meanwhile, Cyp17a2 also attenuates viral infection directly to strengthen the antiviral capacity as an antiviral protein, Cyp17a2 degrades the spring viremia of carp virus (SVCV) P protein by utilizing USP8 to reduce its K33-linked polyubiquitination. These findings reveal a sex-based regulatory mechanism in teleost antiviral immunity, broadening our understanding of sexual dimorphism in immune responses beyond the conventional roles of sex chromosomes and hormones.

immunology↗

bioRxiv2025

EVODEX: A Mechanistic Framework for Extracting, Structuring, and Predicting Enzymatic Reactivity

Accurately modeling enzymatic reactivity is essential for synthesis planning, mass spectrometry interpretation, and biochemical knowledge extraction, but existing reaction datasets are often incomplete or inconsistently annotated. EVODEX introduces two abstractions to address this: partial reactions, which isolate atom-mapped substrate-product transformations from complex biochemical reactions, and Electronic Reaction Operators (EROs), which encode the bonding and orbital environment of atoms undergoing change. From 349,458 curated reactions in EnzymeMap, EVODEX constructs over 186,000 partial reactions and mines a core set of 1,404 EROs, each supported by at least 10 examples. Together, these explain 91 percent of test reactions at the formula level and 62 percent at the mechanistic level. A further filtered synthesis subset of 436 one-to-one operators that exclude ubiquitous metabolites provides a compact and generalizable vocabulary of single-step enzymatic transformations. EVODEX operators are auditable, reusable, and available as part of an open-source Python package with datasets, Jupyter notebooks, and a browsable website.

bioinformatics↗

bioRxiv2025

Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae

Orchidaceae (orchids) is commonly known as one of the largest families of seed plants, and grow in an extensive range of habitats worldwide. In the present study, we generated chromosome-level reference genomes for two orchids using a combination of PacBio, Illumina, and Hi-C sequencing, Cypripedium singchii has the largest genome and chromosomes among the sequenced species so far, with a genome size of 43.19 Gb (1C) with ten chromosomes, and Apostasia fujianica has the smallest known genome and chromosomes in Orchidaceae, with a genome size of 340.90 Mb (1C) with 35 chromosomes. We predicted a total of 32,412 and 21,724 protein-coding genes for C. singchii and A. fujianica, respectively. The overall BUSCO score was 85.01% for C. singchii and 91.80% in A. fujianica. Based on protein-coding sequences from 55 conserved single-copy families across 21 plant species, we constructed a high-confidence phylogenetic tree and estimated the divergence times. The high-quality genomes of super-giga and tiny orchids offer key insight for future evolutionary researches.

genomics↗

bioRxiv2025

PPIKB: A Comprehensive Knowledge Base and Analysis Platform for Protein Peptide Interactions Based on Literature and Patents

Protein-protein interactions (PPIs) underpin a multitude of fundamental biological processes and represent critical therapeutic targets. Peptide compounds--owing to their structural flexibility, high target specificity, and the combined advantages of small molecules and biologics--have emerged as powerful modulators of these interactions. However, the exponential growth of scientific publications and patent filings poses a significant challenge for the systematic integration of protein-peptide interaction (PPepI) data. To address this, we implemented a high-throughput extraction pipeline powered by large language models (LLMs) to harvest affinity data from both research articles and patents, followed by rigorous manual curation. Applying this approach to 4,241 research papers and 483 patents published between 1972 and 2025, we compiled 21,760 manually validated quantitative affinity entries encompassing 2,013 unique protein targets derived from human, mouse, rat, viral, bacterial, and other species. In parallel, we consolidated 18,005 structural entries of protein-peptide complexes from the Protein Data Bank and associated literature. Leveraging these comprehensive datasets, we developed PPIKB, a user-friendly database and analysis platform that enables efficient querying, visualization, and in-depth analysis of protein-peptide interactions. PPIKB also provides a suite of tools tailored to facilitate peptide-based drug discovery, protein engineering, and systems-level biological research. By combining state-of-the-art text-mining technologies with expert validation, PPIKB sets a new standard for accessibility and utility in the field of protein-peptide interaction data resources. Access PPIKB at: https://ppikb.duanlab.ac

bioinformatics↗

bioRxiv2025

Glis3 is a modifier of cyst progression in autosomal dominant polycystic kidney disease

BackgroundAutosomal dominant polycystic kidney disease (ADPKD) is caused by mutations affecting polycystin-1 (PC1) or -2 (PC2). The existence of a cilia-dependent cyst activation (CDCA) pathway has been identified by demonstrating that structurally intact primary cilia are crucial for cyst growth following loss of polycystins. We previously used translating ribosome affinity purification (TRAP) RNA-Seq on pre- cystic mouse kidneys to determine the translatome that meet the criteria for CDCA and identified Glis2 as an early effector of polycystin signaling. Here, we investigate the potential role of Glis3 in ADPKD, which, while not transcriptionally altered, encodes a cilia-localized transcription factor belonging to the same family of genes as Glis2. MethodsWe used live cell confocal imaging to study the subcellular localization of Glis3 in the presence or absence of Pkd1. We used Glis3 conditional knockout mice to investigate the genetic interaction between Glis3 and Pkd1. Changes in gene expression and chromatin accessibility were assessed by RNA-Seq and ATAC-Seq on an allelic series of Glis3 and Pkd1 kidney selective inactivation models at 7-weeks age to evaluate the function of Glis3. ResultsThe ciliary localization of Glis3 is not affected by Pkd1 mutation status. Kidney selective Glis3 by itself does not affect kidney structure or function, but dual inactivation of Glis3 and Pkd1 significantly worsen polycystic kidney disease. Integration of transcriptomic profiling and chromatin accessibility assays suggested that kidney tubule specific Glis3 inactivation results in dysregulated fatty acid metabolism and circadian. ConclusionsGlis3 is a primary cilium localized transcription factor that genetically interacts with Pkd1 and modifies kidney epithelial cell metabolism and circadian function.

genetics↗

bioRxiv2025

Quantifying Protein-Protein Interaction with a Spatial Attention Kinetic Graph Neural Network

Accurate prioritisation of near-native protein-protein interaction (PPI) models remains a major bot-tleneck in structural biology. Here we present SAKE-PP, a physics-inspired, spatial-attention equivariant graph neural network that directly regresses interface RMSD (iRMSD) without any native references. Trained on docking decoys generated through our novel hierarchical sampling strategy applied to PDB-Bind dataset, SAKE-PP combines force-field-like attention with Laplacian-eigenvector orientation to couple local interaction forces with global topology. On the 2024PDB benchmark comprising 176 het-erodimers, SAKE-PP demonstrates effective optimization and selection of AF3 decoys, achieving improvements of 13.75% based on iRMSD statistics and 12.5% based on DockQ scores. It consistently outperforms the AF3 ranking score in multiple metrics, including overlap, hit rate, and correlation. In zero-shot evaluation of 139 antibody-antigen complexes, SAKE-PP improves the score-iRMSD correlation by 0.4. By unifying geometric deep learning with physics-based realism, SAKE-PP provides a robust, plug-and-play scoring function that streamlines reliable PPI evaluation and accelerates downstream structure-guided drug-design workflows.

bioinformatics↗

bioRxiv2025

Designing a broad-spectrum four-helix bundle targeting different strains of SARS-CoV-2 Spike Receptor Binding Domains with ACE2-like binding interface

One major strategy for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to evade antibody drugs or preventive vaccines is high mutation rate of the spike receptor binding domain (RBD). Because variable RBDs of different SARS-CoV-2 strains must bind to the same human receptor angiotensin-converting enzyme 2 (hACE2) for viral cell entry and infection, we hypothesize that designing a protein with the same or very similar hACE2 binding interface might have a broad-spectrum effect against various SARS-CoV-2 strains. The designed protein binds specifically to the WT-RBD (with micromolar affinity) but not to RBDs from other SARS-CoV-2 strains. However, two rounds of the E. coli display and Magnetic Cell Sorting (MACS) selection are sufficient to yield a protein named CYN1 with nanomolar binding affinities not only to the WT-RBD but also to those of Omicron BA.1, XBB.1.16, and JN.1. Molecular dynamics simulations and free-energy hotspot analysis revealed that CYN1s broader spectrum capability stems from its engagement of essentially all ACE2 hotspot residues critical for WT-RBD binding, unlike the designed protein. The discovery of CYN1, differing by only four mutations from the designed protein, confirms that targeting the small interface of human viral receptors--rather than the entire receptor--offers a viable strategy for developing broad-spectrum inhibitors. This approach minimizes potential off-target effects arising from receptor multifunctionality.

molecular biology↗

bioRxiv2025

TGF-beta coordinates changes in Keratin gene expression during complex tissue regeneration.

Zebrafish larval tail regeneration can be broadly broken down into three phases: wound repair, initiation of regeneration and redevelopment of the tail. We and others have shown that activation of the Hedgehog and TGF-beta signalling pathways is required to initiate tail regeneration. In this study we initially focus on these two pathways to better understand their role regeneration. We have found that Hedgehog signalling acts upstream of the TGF-beta pathway by activating transcription of the TGF-beta ligand tgfb1a. We have identified differentially expressed genes that are regulated after tail excision as well as those that are dependent upon TGF-beta signalling. From this analysis we found that Keratin genes fall into categories of co-expression: one set that is upregulated by TGF-beta signalling after injury (krtup) and a second set that is downregulated (krtdown). To see whether these two sets show co-expression more broadly, we analysed single cell RNA sequencing data and found that krts fall into the same categories during zebrafish development. We have mapped the expression of a representative member of krtup (krt97) and krtdown (krt5) sets during development and regeneration and show that krt97 is found in epithelia that is moving and krt5 is expressed in epithelia that is stationary. Based upon our results we propose that the krtup set allows for collective epithelial migration while the krtdown set inhibits mobility. These results reveal one mechanism by which TGF-beta may initiate regeneration and could help to explain how changes in cytoskeletal composition influence cell movement during development and repair.

developmental biology↗

bioRxiv2025

Biocompatible Multi-functional Polymeric Material for Mineralized Tissue Adhesion

This study developed a biocompatible multifunctional thiol-ene resin system for adhesion to dentin mineralized tissue. Adhesive resins maintain the strength and longevity of dental composite restorations through chemophysical bonding to exposed dentin surfaces after cavity preparations. Dental pulp cells are exposed to residual monomers transported through dentinal tubules. Monomers of conventional adhesive systems may result in inhomogeneous polymer networks and the release of residual monomers that cause cytotoxicity. In this study, we develop a one-step multi-functional polymeric resin system by incorporating trimethylolpropane triacrylate (TMPTA) and bis[2-(methacryloyloxy)ethyl] phosphate (BMEP) to enhance both mechanical properties and adhesion to dentin. Molecular dynamics simulations identified an optimal triacylate:trithiol ratio of 2.5:1, which was consistent with rheological and mechanical tests that yielded a storage modulus of ~30 MPa with or without BMEP. Shear bond tests demonstrated that the addition of BMEP significantly improved dentin adhesion, achieving a shear bond strength of 10.8 MPa, comparable to the commercial primer Clearfil SE Bond. Nanoindentation modulus mapping characterized the hybrid layer and mechanical gradient of the adhesive resin system. Further, the triacrylate-BMEP resin showed biocompatibility with fibroblasts in vitro. These findings suggest the triacrylate-trithiol crosslinking and chemophysical bonding of BMEP provide enhanced bond strength and biocompatibility for dental applications.

bioengineering↗

bioRxiv2025

Multi-spectral optoacoustic microscopy driven by gas-filled hollow-core fiber laser pulses

Multi-spectral optoacoustic microscopy (MS-OAM) requires high-performance light sources capable of delivering multiple intense spectral lines precisely matched to the absorption characteristics of selected biomolecules. We present a gas-filled anti-resonant hollow-core fiber (ARHCF) laser source optimized for near-infrared (NIR) MS-OAM. The hydrogen (H2)-filled ARHCF laser emits multiple spectral lines with high pulse energy and narrow linewidths (<0.1 nm) across a broad spectral range ([~]1100 nm to [~]2200 nm). Several Raman laser lines were generated to overlap with key biomolecular absorption bands, including lipids (1210 nm and 1700 nm), collagen ([~]1540 nm), and water ([~]1400 nm and [~]1900 nm). We demonstrate the systems performance by mapping absorbers in the first and second overtone regions of hair, pig tissue, and collagen samples. This work aims to bring the gas-filled fiber technology in MS-OAM applications and paves the way for high-resolution, label-free bio-imaging across extended infrared and ultraviolet regimes.

biophysics↗

bioRxiv2025

Aptamer-Enabled Discovery and Clinical Analysis of Exosomal Surface Biomarkers in Hepatocellular Carcinoma

Exosomal membrane proteins hold promise as cancer biomarkers but face detection challenges due to low abundance and conformational sensitivity. We developed AptEx-ID, a microbead-displayed aptamer platform enabling high- throughput screening of hepatocellular carcinoma (HCC)-specific exosomal surface proteins. Aptamers, selected via competitive binding to tumor-derived versus healthy exosomes, demonstrated high affinity and specificity. Clinical validation using 50 HCC and 30 control plasma samples identified a 7-aptamer panel via machine learning, achieving 93.75% accuracy and 0.95 ROC-AUC. These aptamers further revealed HCC-associated biomarkers (e.g., IMPDH1, ASCC3, GTSE1), validated by siRNA knockdown and biophysical assays. Post-treatment monitoring showed aptamer signal reduction in responsive patients, highlighting their prognostic utility. This platform integrates biomarker discovery, diagnostics, and therapeutic monitoring, offering a robust approach for HCC management through exosomal surface proteome profiling.

molecular biology↗

bioRxiv2025

Hepatocyte-specific CLSTN3B ablation impairs lipid droplet maturation and alleviates diet-induced steatohepatitis in mice

Excessive lipid accumulation in hepatocytes, a hallmark of metabolic dysfunction-associated steatotic liver disease (MASLD), can lead to progressive liver damage. Understanding the molecular mechanisms governing lipid storage in hepatocytes is essential for identifying therapeutic targets to halt MASLD progression. Here, we show a pivotal role for the protein calsyntenin 3{beta} (CLSTN3B) in promoting lipid droplet (LD) maturation and lipid storage in hepatocytes. Previously characterized as an endoplasmic reticulum (ER)-LD contact protein that facilitates LD maturation in adipocytes, we now show that CLSTN3B expression is strongly induced in mouse hepatocytes by peroxisome proliferator-activated receptor gamma (PPAR{gamma}) in response to dietary caloric excess. Hepatocyte-specific deletion of CLSTN3B in mice significantly increases energy expenditure, reduces metabolic efficiency, and protects against diet-induced hepatic steatosis and fibrosis. Mechanistically, CLSTN3B deficiency causes reduced LD phospholipid coverage and increased lipase recruitment. This results in enhanced fatty acid oxidation driven by a futile cycle of lipolysis and re-esterification. Notably, human clinical data reveal a positive correlation between hepatic CLSTN3B expression and MASLD severity and progression, emphasizing its relevance to human disease. Together, our findings establish CLSTN3B as a key regulator of hepatocyte lipid storage and metabolic efficiency and highlight its potential as a therapeutic target in MASLD.

physiology↗

bioRxiv2025

Identification and Characterization of PLUTO-201, a Novel Long Non-Coding RNA Associated with Poor Outcomes in Prostate Cancer

Background: Despite extensive investigation, the factors promoting aggressive prostate cancer are poorly understood. In particular, despite a few prominent examples, the role of long non-coding RNAs (lncRNAs) is largely unknown. Methods: We performed a comprehensive analysis of whole-genome transcriptome data to identify differential expression across 1,567 patients with prostate cancer, then correlated differential expression with risk of metastatic recurrence. We characterized the lncRNA most associated with metastasis in vitro and in vivo to investigate the mechanism by which it promotes aggressive prostate cancer. Results: We have identified a novel lncRNA, Prostate Cancer Associated hnRNPK Interacting Transcript (PCAHIT), which is strongly associated with metastasis and poor overall survival in men with prostate cancer. We find that overexpression/knockdown of PCAHIT in pre-clinical models of prostate cancer modulates proliferation rates and markers of an aggressive phenotype through regulation of steroid biosynthesis and expression of the MHC class I complex, driving increased growth in androgen-depleted conditions and decreased susceptibility to T cell-mediated cytotoxicity. We further find that the heterogeneous nuclear ribonucleoprotein hnRNPK directly binds PCAHIT and is indispensable for its activity. Conclusions: Overall, our findings indicate that PCAHIT is a driver of aggressive prostate cancer phenotypes and poor clinical outcomes through suppression of the immune response and increased androgen-independent cancer growth. PCAHIT is a potential biomarker of aggressive disease.

cancer biology↗

bioRxiv2025

AlphaFold3 for Non-canonical Cyclic Peptide Modeling: Hierarchical Benchmarking Reveals Accuracy and Practical Guidelines

Despite the revolutionary impact of AlphaFold3 on structural biology, this models capability in predicting non-canonical cyclic peptides remains unexplored. Given the clinical significance of cyclic peptides containing unnatural residues as a therapeutic modality, we present the first systematic evaluation of AlphaFold3 for this class of molecules. To facilitate benchmarking, we developed an automated input pipeline to streamline AlphaFold3 predictions for cyclic peptides. Our study aims to: (1) quantify the hierarchical accuracy (all-atoms, C atoms, and atoms of unnatural residue levels) of AlphaFold3 in predicting both non-canonical cyclic peptide monomers and complexes; (2) assess the reliability of AlphaFold3s confidence metrics; (3) evaluate the influence of multiple sequence alignment (MSA) and structural templates; and (4) identify systematic biases in AlphaFold3s predictions. Based on these analyses, we provide practical guidelines for applying AlphaFold3 in cyclic peptide structure prediction for facilitating the related research of bioactive cyclic peptides.

bioinformatics↗

bioRxiv2025

From Structure to Immunogenicity: Decoding Correlated Dynamics atthe Peptide MHC interface to Understand TCR Recognition

The interaction between a class I peptide-major histocompatibility complex (pMHC) and a T cell receptor (TCR) plays a central role in the elicitation of CD8+ T cell immune responses. As a result, considerable effort has been invested in understanding the structural, dynamic, and biophysical parameters that govern this recognition event, including designing altered peptide ligands (APLs) which seek to modulate the downstream signaling outcomes. However, dynamic links between modified peptide positions and distant residues have until yet been ill resolved. Using an integrative approach combining crystallographic ensemble and single models with atomistic molecular dynamics simulations and correlational analysis, we have established an approach that allows us to identify coupled dynamics between spatially distant residues at the pMHC interface. Furthermore, we constructed a network encoding the inter-residue couplings observed throughout the simulations. This computational workflow corroborates well with experimental data and leads to novel insights regarding the differential immunogenicity of the closely related peptides analyzed in this study. Ultimately, we present an intuitive and comprehensive strategy for decoding the linked dynamics at the pMHC interface allowing for mechanistic insights into the biophysical bases governing immunogenicity. One Sentence SummaryThe dynamics at the pMHC interface can be encoded as a biophysically relevant network to yield molecular insights into immunogenicity

immunology↗

bioRxiv2025

Testicular mRNA-LNP Delivery: A Novel Therapy for Genetic Spermatogenic Disorders

Uniform testicular maturation arrest is a severe form of male infertility characterized by the presence of germ cells that do not complete spermatogenic development. It is usually caused by meiotic arrest with genetic variants and difficult to treat via drugs or surgery. mRNA-lipid nanoparticle (LNP) delivery is a promising therapeutic option for maturation arrest with monogenic variants via protein replacement therapy. Herein, a spermatocytes-tropic LNP (Pool1-LNP3) was identified via a library of 30 ionizable lipids screening. And in vivo delivery of this novel LNP composition using rete testis microinjection was showed to be high spermatocytes targeting with high transfection efficiency. Thereafter, it was revealed that in vivo delivery of Pool1-LNP3 encapsulating Msh5 mRNA could promote crossover formation and restore spermatogenesis in Msh5D486Y/D486Y mouse models with DSB recombination defects. Notably, the offspring without genomic integration was born using intracytoplasmic sperm injection (ICSI) derived from rescue of Msh5D486Y/D486Ymouse and embryo transfer. Furthermore, no obvious inflammation and histologic damage in any tissue were detected after in vivo delivery of mRNA-LNP. In addition, it was demonstrated that Maps mRNA-LNP3 recovered spermatogenesis in Maps KO mouse with meiotic arrest. Altogether, these findings suggested that this spermatocytes-tropic mRNA-LNP delivery could become a viable and broad applicable strategy for treatment of spermatogenic disorders with genetic defects, providing a foundation for future clinical application.

molecular biology↗