Biology subjects

Zhang, H.

Publications and source records attributed to Zhang, H..

At least 271 records · Page 15Linked to original sources

bioRxiv2025

Minute-scale control of ubiquitin-mediated degradation reveals dynamics of bacterial secreted effector-functions

Precise temporal control of protein abundance is essential for dissecting dynamic cellular processes. While degron-based systems enable rapid protein depletion in eukaryotic cells, comparable tools are lacking for bacterial effectors delivered into host cells during infection. Here, we establish AIDE (Auxin-Inducible Degradation of Effectors), a host-directed degradation platform that harnesses the ubiquitin-proteasome system to selectively eliminate secreted bacterial proteins, including membrane-integrated effectors. By integrating a minimal auxin-inducible degron (AID) tag into effector genes, AIDE enables rapid, reversible, and spatially confined degradation while preserving native expression and secretion. Applied to Chlamydia trachomatis, AIDE revealed that the membrane-integrated deubiquitinase Cdu1 suppresses autophagy early and later promotes developmental transitions, whereas the integral membrane fusogen IncA is continuously required for inclusion integrity. This AIDE platform provides minute-scale, spatiotemporal control over bacterial effector activity, offering a broadly applicable framework for dissecting virulence mechanisms and host-pathogen interactions across diverse secretion-dependent pathogens.

microbiology↗

bioRxiv2025

MAAD: Multidimensional Antiviral Antibody Database

Antibodies have emerged as central components of therapeutic strategies against viral infectious diseases, functioning as key effectors in both prevention and treatment. While traditional antibody discovery has relied heavily on high-throughput screening, the field is now shifting toward rational antibody design, which requires integrative insights into sequence-structure-function relationships. However, the absence of a standardized and well-annotated antibody database integrating these multidimensional features hampers systematic exploration, cross-pathogen comparison, and rational antibody design. Here, we introduce a "Multidimensional Antiviral Antibody Database" (MAAD; http://www.xxx), a curated platform dedicated to antibody nanobody and single-chain variable fragment targeting three high-impact RNA virus families, Coronaviridae (SARS-CoV-1, SARS-CoV-2, MERS-CoV), Orthomyxoviridae (influenza virus), and Pneumoviridae (respiratory syncytial virus, human metapneumovirus), due to the large, high-quality datasets accumulated in recent years. MAAD further incorporates a suite of interactive analysis modules, including CDR annotation, similarity-based CDR3 sequence analysis, V/J gene usage profiling, sequence-based clustering and structure-based antigen-antibody interfaces residues with per-site entropy and mutation rate profiling. These features enable in-depth exploration of antibody sequence characteristics, thereby facilitating functional and structural insights for rational antibody design. Together, by bridging antibody sequence, structure and function, MAAD offers an open and standardized platform that advances comparative antiviral research and supports therapeutic antibody discovery.

bioinformatics↗

bioRxiv2025

The cloacal outgrowth orchestrates co-development of the bladder and umbilical arteries

The urinary bladder is an innovation of eutherian mammals to manage liquid wastes. However, bladder development and its embryonic function remain poorly understood. Here, we report that in both humans and mice the bladder emerges from the cloaca as the rostral outgrowth, which is flanked by the umbilical arteries. Arrest of the outgrowth, as seen in Shh-null mouse embryos, causes bladder agenesis and unexpected severe defect of the umbilical arteries, suggesting that the outgrowth epithelial signal Shh coordinates development of both the bladder and umbilical arteries. Wnt2 signaling molecule is restricted to the rostral outgrowth mesenchyme; and its expression is dramatically down-regulated in Shh-null mutants. Furthermore, Wnt2-null mutants develop small bladder and single umbilical artery defects. Findings here uncover an unexpected co-development mechanism of the bladder and umbilical arteries orchestrated by the cloacal outgrowth signals. The co-development paradigm offers a conceptual framework to understand evolution and development of the bladder. Significance StatementThe urinary bladder is found in the eutherian mammals but largely absent from other vertebrates. Innovation of the bladder has been viewed as a necessity to manage liquid metabolic wastes on dry land. In this study, we report that the bladder emerges from the rostral outgrowth of the cloaca. We also report an unexpected developmental link between the bladder and umbilical arteries and, demonstrate that their co-development is orchestrated by the outgrowth epithelial signal Shh and mesenchymal signal Wnt2. Findings here highlight a possibility that, in addition to managing metabolic wastes, normal bladder development is required for growth of mammalian embryos by supporting development of the umbilical arteries.

developmental biology↗

bioRxiv2025

Global Mapping of circRNA-Target RNA Interactions Reveals P-Body-Mediated Translational Repression

Circular RNAs (circRNAs) are primarily produced through pre-mRNA back-splicing, yet their target repertoire and functional mechanisms remain elusive. Here, we present circTargetMap, a computational framework for globally mapping circRNA targets using RNA-RNA interactomes obtained via RNA in situ conformation sequencing (RIC-seq) in the hippocampus and ten human cell lines. This approach identified 117,163 high-confidence circRNA-target RNA interactions, with 83% of target mRNAs bound by multiple circRNAs. Functionally, CDR1as and circRMST repress target mRNA translation by sequestering them into processing bodies (P-bodies)--membraneless granules--through sequence-specific base-pairing, probably independent of AGO2, DICER, and miRNAs. To directly capture granule-associated interactions, we developed granule RIC-seq (GRIC-seq) method, revealing the broad role of circRNA-target RNA interactions in translational repression. Moreover, pathogenic variants are significantly enriched around circRNA-target RNA interaction sites, suggesting potential roles in disease. Our study provides valuable resources for circRNA functional exploration and a framework for investigating RNA-RNA interactions within membraneless organelles.

molecular biology↗

bioRxiv2025

Autolamellasomes: An Autophagy-Dependent Parallel Pathway for Bulk ER Degradation and Lysosome Biogenesis

Lysosomes containing multilamellar membrane whorls are a hallmark of cellular aging and storage disorders, yet the biogenesis of these structures has remained elusive for decades. Here, we identify a distinct form of endoplasmic reticulum (ER) remodeling, termed autolamellasomes, which mediates bulk ER degradation under chronic mTOR inhibition. Unlike canonical ER-phagy, autolamellasomes are concentric ER stacks that form via an autophagy-dependent but receptor-independent mechanism. Using Cryo-ET, CLEM, and a reconstituted cell-free system, we demonstrate that these structures arise from the cytosolic compaction of fragmented ER membranes, driven by the core autophagy machinery. We find that autolamellasomes accumulate in senescent cells and fibroblasts from patients with Hutchinson-Gilford progeria syndrome, linking sustained mTOR suppression to lysosomal membrane homeostasis. Our results resolve the origin of intralysosomal whorls and define a conserved pathway that couples nutrient sensing to membrane turnover and cellular aging.

cell biology↗

bioRxiv2025

Modular mRNA lipid nanoparticle platform rescues diverse genetic male infertility

Genetic male infertility arises from diverse mutations that disrupt spermatogenesis, yet therapeutic strategies capable of restoring germ-cell function remain limited. Messenger RNA (mRNA) therapeutics offer a programmable and non-integrating approach, but their functional compatibility in structured and immune-privileged tissues remains unclear. Here we identify a temporal mismatch between mRNA delivery kinetics and the progression of spermatogenesis as a key barrier to functional rescue. We show that delivery efficiency does not predict outcome: formulations with high peak expression but short duration fail to support spermiogenesis, whereas sustained expression aligned with developmental timing enables recovery. Guided by this principle, we establish a testis-targeted mRNA delivery platform that restores spermatogenesis across multiple genetic models and generates functional sperm capable of supporting embryo development and multigenerational inheritance. The approach is modular, extends to human seminiferous tubules ex vivo, and is supported by comprehensive safety analyses. Together, these findings define a design constraint for RNA therapeutics in structured tissues: functional rescue requires temporal alignment between delivery kinetics and the therapeutic window defined by tissue-specific biological programs.

bioengineering↗

bioRxiv2025

Discovery and optimization of antimicrobial peptides from extreme environments on global scale

The escalating crisis of global antimicrobial resistance (AMR) necessitates the discovery of novel antibiotics. Antimicrobial peptides (AMPs), particularly those from under-explored extreme environments, represent a promising therapeutic class. Here, we introduce SEGMA (Structure-aware Extremophile Genome Mining for Antimicrobial peptides), a computational framework that integrates structure information to systematically mine AMPs from extremophile genomes on a global scale. By analyzing 60,461 extremophile metagenome-assembled genomes (MAGs) from diverse habitats, SEGMA identified 3,298 novel AMPs (termed "extremocins"), which exhibit unique amino acid profiles and physicochemical properties. Leveraging a beam search-guided optimization strategy, we further enhanced selected extremocins to achieve broad-spectrum antimicrobial activity. Experimental validation confirmed potent in vitro efficacy against clinically relevant pathogens. This study underscores the value of structure-aware mining and extremophile microbiomes in expanding the antibiotic arsenal against AMR. HighlightsO_LISEGMA, a structure-aware deep learning framework, mines 3,298 novel antimicrobial peptides (extremocins) from 60,461 extremophile genomes on global scale. C_LIO_LIExtremocins exhibit unique sequence features, and expand known antibiotic space, few of which shows homology to existing AMP databases. C_LIO_LIA beam search-guided optimization strategy enhanced selected extremocins to achieve broad-spectrum activity against clinically relevant pathogens. C_LIO_LIExperimental validation confirmed that candidate extremocins exhibit potent in vitro and in vivo antimicrobial activity, highlighting their therapeutic potential. C_LI

bioinformatics↗

bioRxiv2025

FGF13 is not secreted from neurons

FGF13, a noncanonical fibroblast growth factor (FGF) and member of the fibroblast growth factor homologous factor (FHF) subset, lacks a signal sequence and was previously reported to remain intracellular, where it regulates voltage-gated sodium channels (VGSCs) at least in part through direct interaction with the cytoplasmic C-terminus of VGSCs. Recent reports suggest that FGF13 is secreted and regulates neuronal VGSCs through interactions with extracellular domains of integral plasma membrane proteins, yet supportive data are limited. Using rigorous positive and negative controls, we show that transfected FGF13 is not secreted from cultured cells in a heterologous expression system nor is endogenous FGF13 secreted from cultured neurons. Further, employing multiple unbiased screens including proximity protein proteomics, our results suggest FGF13 remains within membranes and is unavailable to interact directly with extracellular protein domains.

neuroscience↗

bioRxiv2025

Phage-encoded factor stimulates DNA degradation by the Hna anti-phage defense system

Prokaryotic organisms have evolved unique strategies to acquire immunity against the constant threat of bacteriophage (phage) and mobile genetic elements. Hna is a broadly distributed anti-phage immune system that confers resistance against diverse phage by eliciting an abortive infection response. Using a combination of biochemistry, cryo-electron microscopy, and single-molecule fluorescence imaging, we reveal that Hna functions as a 3--5 single-stranded DNA exonuclease that forms an auto-inhibited dimer under physiological ATP concentrations. We observed that Hna autoinhibition can be overcome by incorporation of a phage-encoded single-stranded DNA binding protein (SSB), stimulating unregulated Hna nuclease activity. Furthermore, phage escape mutants encode SSB variants that evade Hna surveillance by adopting higher order stoichiometries with enhanced DNA binding affinity. Our work establishes the molecular basis of Hna-mediated anti-phage activity and provides novel insights into how phage-encoded proteins can directly stimulate a bacterial immune response.

biochemistry↗

bioRxiv2025

Parsing auditory neural code into maximum-entropy packets

Deciphering the neural code requires identifying its fundamental symbols or code-words. Neural activity is usually interpreted either as a rate code - based on average spike counts - or as a temporal code, which distinguishes patterns with identical counts. Yet, the symbols of the code remain undefined. Here we show that the symbols can be clearly defined by parsing auditory spike trains into variable-duration "packets", within which precise spike timing is irrelevant. Because packets vary in duration, this is not a rate code. A single neuron could encode very different stimuli depending on the number of spikes it produced per packet. The packet-based code enables real-time readout upon packet completion due to its instantaneous code structure and maximizes information capacity at both single-neuron and population levels.

neuroscience↗

bioRxiv2025

An InDel Genomic Variant within a Bifunctional Super-Enhancer for LINC00636 and CD47 Regulation in Breast Cancer

Highly accessible genomic super-enhancers often drive tumor-promoting programs, yet the impact of genomic variation within these regulatory elements remains unclear. Here, we identified a bifunctional super-enhancer that regulates the expression of cancer-promoting genes LINC00636 and CD47 in breast cancer. We discovered that a common germline insertion variant within the super-enhancer is associated with reduced chromatin accessibility at the super-enhancer locus. Deletion of the insertion in breast cancer cells increased chromatin accessibility, leading to upregulation of LINC00636 and CD47, enhanced resistance to nutrient-deprivation-induced apoptosis (mediated by CD47), activation of senescence (driven by elevated LINC00636), delayed cell death, and reduced infiltration of CD80 pro-inflammatory macrophages, changes that represent tumor-promoting features. Together, our findings uncover a common insertion-deletion variant that fine-tunes the regulatory activity of a bifunctional super-enhancer, suggest a protective role for the insertion allele, and establish a novel function for LINC00636 in senescence and breast cancer.

genomics↗

bioRxiv2025

A multi-tissue atlas of genetic regulatory effects in sheep

Characterizing the impact of genomic variants on genome function and ultimately complex traits in livestock is essential for the development of sustainable precision agriculture and comparative genomics. Here, as part of the Farm animal Genotype-Tissue Expression (FarmGTEx) project, we present the pilot phase of the SheepGTEx resource through analyzing 6,761 RNA-sequencing samples of 51 primary tissues in a multi-breed population of sheep. We identify millions of regulatory variants associated with seven types of molecular phenotypes, and fine-map 322,468 primary and 114,017 non-primary effects, revealing a high degree of regulatory allelic heterogeneity. We systematically characterize the pleiotropic effects of these variants on molecular phenotypes, assess their context-specific regulatory patterns across tissues, breeds, sexes, and developmental stages, as well as explore their evolutionary constraints across mammals. Finally, we demonstrate the substantial potential of the SheepGTEx resource (https://sheepgtex.farmgtex.org), by providing examples of regulatory mechanisms underpinning 34 complex traits, population divergence between European and Asian breeds, and adaptive evolution in sheep over the past ten millennia.

genomics↗

bioRxiv2025

End-to-end high-throughput single-cell proteomics via SPRINT and dual-spray LC-MS

Single-cell proteomics (SCP) enables direct measurement of protein heterogeneity but remains constrained by throughput and limited applicability to primary tissues. Here, we present an integrated workflow developed to address both challenges. We engineered SPRINT, an AI-powered bioprinting platform that prepares more than 10,000 single cells per day, over tenfold faster than existing systems, while maintaining stability and enabling identification of over 6,000 proteins from individual HeLa cells. To expand analytical capacity, we further designed a dual-spray tandem direct injection (TDI) LC system that parallelizes non-analytical steps with peptide separation, doubling MS utilization efficiency and enabling 168 label-free SCP runs per day without sensitivity loss. Together with optimized tissue-dissociation protocols, this integrated workflow enabled creation of the first mouse tissue-derived SCP atlas, profiling >1,000 single cells across six organs. These advances establish SCP as a scalable platform ready for broad biological and biomedical applications.

systems biology↗

bioRxiv2025

The transcriptional regulatory circuit as a driver and therapeutic target in CML blast crisis

Patients with blast crisis in chronic myeloid leukemia (CML) exhibit an extremely poor prognosis, with median survival of only a few months and limited therapeutic options. Dysregulated transcriptional regulation plays a pivotal role in driving blast crisis progression. In this study, we performed histone modification and transcriptomic high-throughput sequencing on bone marrow cells derived from chronic and blast-phase CML patients, identifying a CML blast-specific transcriptional regulatory circuit comprising MEF2C, MYB, MEIS1, and ZEB2. These transcription factors (TFs) form protein complexes that co-bind to shared enhancers or promoters, reciprocally enhancing each others transcriptional activity and that of their downstream targets. Mechanistically, this circuit synergistically reprograms chromatin accessibility and transcriptional landscapes in blast cells, parallel activation of purine metabolism and Rho GTPase signaling pathways which exhibit functional crosstalk. Functional validation demonstrated that silencing components of this circuit or its downstream core targets significantly suppressed CML blast progression in vitro and in vivo. Notably, mebendazole (MBZ), a clinically approved inhibitor targeting MYB protein stability, recapitulated these inhibitory effects. Our findings establish the MEF2C-MYB-MEIS1-ZEB2 transcriptional circuit as a central driver of CML blast crisis and position MBZ as a high-potential translational strategy for targeting this lethal phase of the disease. Key PointsO_LIMEF2C, MYB, MEIS1, and ZEB2 form the CML blast-crisis transcriptional circuit, synergistically reprogramming chromatin and transcription. C_LIO_LIMebendazole inhibits CML blast progression by impairing the circuit, offering a rapid translational strategy for this lethal phase. C_LI

cancer biology↗

bioRxiv2025

Delivery of collagen-encoding mRNA to the skin for cosmetic applications

Collagens, the predominant structural proteins in mammalian, maintain tissue integrity through its unique triple-helical conformation. Traditionally, cosmetic collagens have been administered as hydrolyzed peptides derived from animal sources, which exhibit poor bioavailability and functional efficacy due to limited skin penetration and disrupted tertiary/quaternary structures. To overcome these limitations, we developed a novel system for in vivo collagen expression. This system utilizes the topical application of in vitro synthesized, AI-designed mRNAs encoding types I, III, and XVII collagens to improve human skin condition. Significant upregulation of target collagen expression was observed in dermal fibroblasts, leading to improved skin condition through in situ assembly of collagens in natural conformation.

bioengineering↗

bioRxiv2025

Long-term Locus Coeruleus Stimulation Exacerbates Tau Pathology in PS19 Mice

BackgroundAlzheimers disease (AD) is the most common form of dementia, characterized by the accumulation of amyloid-{beta} (A{beta}) plaques and hyperphosphorylated Tau tangles. The locus coeruleus (LC) is among the first brain regions to show degeneration and Tau pathology during the early stages of AD. Previous studies have demonstrated that short-term chemogenetic LC stimulation can improve memory performance in the TgF344-AD rat model, while long-term norepinephrine (NE) reuptake inhibition can worsen memory deficits in the ADLPTau mouse model. However, the effects of long-term LC stimulation in Tau mouse models on memory, synaptic plasticity, and tauopathy remain unclear. ObjectiveTo evaluate the impact of long-term locus coeruleus stimulation on memory, synaptic plasticity, and tauopathy in PS19 mice using behavioral paradigms, electrophysiological recordings, and immunohistochemical analysis. MethodsThe radial arm water maze and fear conditioning test were conducted to assess memory performance in PS19 mice with and without long-term LC stimulation. Hippocampal long-term potentiation was recorded to evaluate the effect of long-term LC stimulation on synaptic plasticity. Immunohistochemistry was employed to examine Tau phosphorylation, neurodegeneration, and neuroinflammation. ResultsLong-term LC stimulation in PS19 mice exacerbated spatial memory deficits in the water maze, impaired contextual fear memory, reduced hippocampal LTP, and increased AEP expression, Tau hyperphosphorylation, and astrocyte activation. ConclusionLong-term LC stimulation may exacerbate memory deficits in PS19 mice by impairing synaptic plasticity and increasing neural degeneration in the hippocampus. Elevated norepinephrine levels resulting from long-term LC stimulation may increase AEP expression, contributing to Tau hyperphosphorylation in the LC.

pathology↗

bioRxiv2025

ProAffinity++

Proteins are essential biological macromolecules that play a crucial role in living organisms. Protein-protein interactions, which govern various biological processes such as signal transduction, cell metabolism, and cell growth, are key aspect of protein function. The strength of these interactions, characterized by protein-protein binding affinity({Delta}G), is a critical thermodynamic property of protein complexes. Accurate prediction of protein-protein binding affinity is meaningful for understanding the mechanisms of biological systems and improving the speed of binding affinity determination. However, current methods are limited in their accuracy and are primarily designed for binary complexes. To address these limitations, we propose ProAffinity++, an end-to-end algorithm that predicts binding affinities using a combined representation of sequence and structure. The core idea of ProAffinity++ is to model the binding regions of protein complexes and utilize graph neural networks to capture the local microenvironment of residues. Our experimental evaluations demonstrate that ProAffinity++ outperforms state-of-the-art methods in predicting protein-protein binding affinities. Moreover, it exhibits remarkable performance in challenging scenarios, such as antigen-antibody interactions and missense mutation problems, where existing methods have limitations.

bioinformatics↗

bioRxiv2025

Excitatory neurons as the default fate in bifurcation of excitatory and inhibitory neuron lineages

In the brain, a precise excitation-inhibition balance underpins every neural operation. Strikingly, across the vertebrate CNS, excitatory and inhibitory neurons often emerge from common progenitors (termed EX-IN lineage), yet how such dichotomous fates diverge has remained enigmatic. Here, exploiting spinal v2a (excitatory)-v2b (inhibitory) and retinal bipolar (excitatory) - amacrine (inhibitory) lineages as EX-IN lineage paradigm, we report a single, conserved genetic program: excitatory neural fate is the default state when sibling-cell communication is silenced; progenitor- and excitatory neuron-expressed homeobox genes actively repress the inhibitory program, while Notch signaling releases this repression to unleash inhibitory identity. Thus, we define a unifying principle governing EX-IN lineage divergence that generate the fundamental dichotomy of neural circuits.

developmental biology↗