Biology subjects

Zhang, Z.

Publications and source records attributed to Zhang, Z..

At least 523 records · Page 29Linked to original sources

bioRxiv2025

Staining-free Visualization of Cell Boundaries in Sliced Tissues for Accurate Binning of Gene Expression in Spatial Transcriptomics

Overcoming the limitations of sparse expression data in high-resolution spatial transcriptomics remains a major challenge for dimensionality reduction and clustering analysis. Visualizing or inferring tissue cell boundaries using dye staining on the same slice can help assign capture spots on the chip to corresponding unit cells and enhance UMI counts and the number of detected genes. However, the staining process may disrupt tissue structures or degrade mRNA, leading to inaccurate spot assignment and cell annotation. In this study, we employed LysM-Cre mT/mG transgenic mice for spatial transcriptomic analysis, where cell boundaries were delineated by tdTomato signals, and myeloid cells were labeled with enhanced green fluorescent protein (EGFP). With the aid of these fluorescent markers, UMI counts and the number of detected genes per cell exceeded those obtained through naive binning with a square matrix. This staining-free approach for visualizing cell boundaries and landmark proteins provides a valuable framework for the studies of single-cell spatial transcriptomics.

bioengineering↗

bioRxiv2025

Endogenous structure of antimalarial target PfATP4 reveals new class of apicomplexan P-type ATPase modulators

The Plasmodium falciparum sodium efflux pump PfATP4 is a leading antimalarial target, but suffers from a lack of high-resolution structural information needed to identify functionally important features in conserved regions and guide rational design of next generation inhibitors. Here, we determine a 3.7[A] cryoEM structure of PfATP4 purified from CRISPR-engineered P. falciparum parasites, revealing a previously unknown, apicomplexan-specific binding partner, PfABP, which forms a conserved, likely modulatory interaction with PfATP4. The discovery of PfABP presents a new avenue for designing novel PfATP4 inhibitors.

microbiology↗

bioRxiv2025

Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement

Changes in gene expression are crucial for crop breeding, yet population genomics has primarily focused on sequence polymorphisms rather than gene expression diversity. The strategy of using single genome reference for RNA-seq analysis could not handle introgression bias, especially for hexaploidy wheat. Here, we conducted RNA-seq for 328 wheat lines, including representative diverse landraces and elite cultivars from China and the United States, to investigate the role of gene expression variation in shaping agronomic traits. Using pan-genome resources, we identified 20,615 more transcripts than using the Chinese Spring reference genome alone. We constructed a pan-gene atlas regulatory map through eQTL analysis, demonstrating that genes introgressed from wild relatives were under tight genetic control. Genes responding to environmental stress show higher activity after introgressed into the wheat genome, demonstrating how long-term breeding selection impacted the gene expression regulation of targeted introgression. Multi-omics modeling identified 231 high-confidence candidate genes for 34 field agronomic traits and the seedling resistance phenotypes of 8 powdery mildew isolates. More than one fifth of those candidates have no homolog in Chinese Spring reference genome. By utilizing the indexed KN9204 EMS library, 80% candidates showed significant trait difference between wild type and mutant lines. Furthermore, directional shifts in genes of which expression were changed by breeding improvement demonstrated distinct adaptations to local environments. Our study constructed a pan-gene atlas to correct the reference bias of reads mapping in RNA-seq studies and revealed the expression patterns of introgressed genes within the wheat genome and their regulatory mechanisms, which highlighted the impact of breeding selection on gene expression of the worlds most important crop.

plant biology↗

bioRxiv2025

BRCA1-A and LIG4 complexes mediate ecDNA biogenesis and cancer drug resistance

Extrachromosomal circular DNA (ecDNA) are commonly produced within the nucleus to drive genome dynamics and heterogeneity, enabling cancer cell evolution and adaptation. However, the mechanisms underlying ecDNA biogenesis remain poorly understood. Here using genome-wide CRISPR screening in human cells, we identified the BRCA1-A and the LIG4 complexes mediate ecDNA production. Following DNA fragmentation, the upstream BRCA1-A complex protects DNA ends from excessive resection, promoting end-joining for circularization. Conversely, the MRN complex, which mediates end resection and thus antagonizes the BRCA1-A complex, suppresses ecDNA formation. Downstream, LIG4 conservatively catalyzes ecDNA production in Drosophila and mammals, with patient tumor ecDNA harboring junctions marked by LIG4 activity. Notably, disrupting LIG4 or BRCA1-A in cancer cells impairs ecDNA-mediated adaptation, hindering resistance to both chemotherapy and targeted therapies. Together, our study reveals the roles of the LIG4 and BRCA1-A complexes in ecDNA biogenesis, and uncovers new therapeutic targets to block ecDNA-mediated adaptation for cancer treatment.

cancer biology↗

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

A non-catalytic role for MLL2 in controlling chromatin organisation and mobility during the priming of pluripotent cells for differentiation

How the chromatin regulator MLL2 (KMT2B) influences cell differentiation remains poorly understood. MLL2 is the main histone 3 lysine 4 (H3K4) trimethyltransferase acting at bivalent promoters in embryonic stem cells (ESCs) and is required for ESCs to differentiate into neuroectoderm. We show here that this requirement occurs during exit from naive pluripotency, days before neuroectoderm differentiation is impaired. Although MLL2 knockout has only a subtle effect on transcription during exit, reducing the expression of a few important neuroectodermal transcription factors, it substantially remodels chromatin architecture, disrupting 3D chromatin loops associated with bivalent promoters. The enzymatic activity of MLL2 is not needed for stabilising these loops or for neuroectoderm differentiation. This non-catalytic function of MLL2 in stabilising 3D chromatin loops has implications for lineage specification. Because MLL2 shares features with all four MLLs, chromatin tethering, rather than H3K4 methylation, may represent the primary function of MLL proteins during lineage commitment.

cell biology↗

bioRxiv2025

High-throughput, unbiased single-molecule displacement mapping with deep learning reveals spatiotemporal heterogeneities in intracellular diffusivity

Single-molecule displacement/diffusivity mapping (SMdM) has revolutionized the study of molecular motion in live cells by providing high spatial resolution insights. However, its utility is restricted by measurement biases and low throughput, making it challenging to capture temporal dynamics of intracellular diffusivity. Here we report a high-throughput single-molecule diffusivity microscopy approach (Hi-SMdM) that rapidly and unbiasedly maps nanoscale heterogeneities in molecular motion inside mammalian cells, enabling time-resolved imaging of local diffusivity dynamics. Hi-SMdM employs a self-supervised deep-learning denoising framework with a general noise model to effectively restore the scarce signals of fast-moving single molecules, while eliminating artifact motions without relying on spatial redundancies or temporal correlations. It then provides unbiased estimations of nanoscale diffusion coefficient and improve both throughput and temporal resolution by up to an order of magnitude. We demonstrate the versatility of Hi-SMdM through time-resolved mapping of the spatially heterogeneous diffusivity of free proteins in the cytoplasm. Hi-SMdM also unveils the temporal dynamics of intracellular diffusion under hypotonic conditions in live cells. Additionally, Hi-SMdM tracks the spatiotemporal dynamics of intraorganellar diffusivity during rapid rearrangements of the ER network and functional activities of mitochondria. Overall, Hi-SMdM provides exceptional opportunities for high-throughput and unbiased single-molecule diffusivity mapping with excellent spatiotemporal resolution.

biophysics↗

bioRxiv2025

Hypoxia-Induced Cardiopulmonary Remodeling and Recovery: Critical Roles of the Proximal Pulmonary Artery, Macrophages, and Exercise

Hypoxemia impairs cardiopulmonary function. We investigated pulmonary artery remodeling in mice exposed to chronic hypoxia for up to five weeks and quantified associated changes in cardiac and lung function, without or with subsequent normoxic recovery in the absence or presence of exercise or pharmacological intervention. Hypoxia-induced stiffening of the proximal pulmonary artery stemmed primarily from remodeling of the adventitial collagen, which resulted in part from altered inter-cellular signaling associated with phenotypic changes in the mural smooth muscle cells and macrophages. Such stiffening appeared to precede and associate with both right ventricular and lung dysfunction, with changes emerging to similar degrees regardless of the age of onset of hypoxia during postnatal development. Key homeostatic target values of the wall mechanics were recovered by the pulmonary arteries with normoxic recovery while other values recovered only partially. Overall cardiopulmonary dysfunction due to hypoxia was similarly only partially reversible. Remodeling of the cardiopulmonary system due to hypoxia is a complex, multi-scale process that involves maladaptations of the proximal pulmonary artery.

physiology↗

bioRxiv2025

Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies

Chimeric antigen receptor-engineered macrophages (CAR-Ms) hold great promise for solid tumor immunotherapy. The intracellular domains (ICDs) of CARs determine the phenotypic output of therapeutic macrophages but remain largely unexplored. Here, we constructed a CAR library containing 131 unique signaling domains derived from native immune receptors and identified 17 ICDs that enhance macrophage phagocytosis, inflammatory responses, or tumor infiltration in vitro and in vivo. We further developed a scalable 3 barcode technology, CARode, to uniquely label and trace ICD variants within large-scale combinatorial CAR library and applied it to single-cell RNA sequencing and single-cell CAR analysis to assess the synergetic effects of ICD combinations on macrophage activation. Our approach uncovered a novel CD40-LY9-FCRL1 chimeric receptor that modulates the tumor microenvironment and improves solid tumor clearance. In conclusion, our findings demonstrate that pooled screening can accelerate the discovery of complex ICD constructs, providing a powerful platform for engineering macrophage-based immunotherapies.

bioengineering↗

bioRxiv2025

Few-shot in-context learning with large language models for antibody characterization

Large language models (LLMs) can learn new tasks by in-context learning (ICL), but it is unknown whether this ability reliably transfers to biological sequence classification. Here, we systematically evaluate how demonstration selection, shot count, and prompting strategies affect performance across 20 general-purpose LLMs. Using antibody characterization as a representative test case, we compare zero-shot, few-shot, and chain-of-thought (CoT) ICL on three classification tasks: humanness, antigen specificity, and isotype. Our results reveal a clear performance hierarchy: while zero-shot prompting performs near chance, few-shot prompting with randomly selected demonstrations improves performance, showing that LLMs can perform ICL using biological sequences from minimal supervision. However, matching protein-language model (pLM)-based classifier accuracy is only achieved when using label-diverse demonstrations drawn from antibodies similar to the query sequence. To leverage this insight, we introduce Sim-ICL, a framework that automatically retrieves such demonstrations. Using only 32-shot prompting, Sim-ICL achieves performance competitive with pLM-based classifiers, matching or outperforming them in two of the three tasks. Furthermore, reasoning-oriented prompts yield marginal gains and often produce fluent but biologically incorrect rationales, suggesting that current CoT explanations function as after-the-fact rationalizations rather than capturing mechanistic determinants of antibody properties. From these experiments, we derive practical design principles for ICL on biological sequences: use similarity-based, label-diverse demonstrations and modest shot counts, and treat reasoning prompts primarily as post hoc narratives rather than drivers of performance. Sim-ICL implements these principles in a streamlined, prompt-based framework for antibody sequence classification and, in principle, could be adapted to other biological sequence tasks.

bioinformatics↗

bioRxiv2025

TAC-C uncovers open chromatin interaction in crops and SPL-mediated photosynthesis regulation

Cis-regulatory elements (CREs) direct precise gene expression for development and environmental response, yet their spatial organization in crops is largely unknown. We introduce Transposase-Accessible Chromosome Conformation Capture (TAC-C), a method integrating ATAC-seq and Hi-C to capture fine-scale chromatin interactions in four major crops: rice, sorghum, maize, and wheat. TAC-C reveals that chromatin interaction frequency aligns with genome size and gene expression, exhibiting distinct loop structures between C3 and C4 plants, particularly in C4-specific enzymes coding genes. Integrating chromatin structure with population genetics data highlights that chromatin loops connect distal regulatory elements to phenotypic variation. Asymmetrical open chromatin interactions among subgenomes, driven by transposon insertions and sequence variations, contribute to biased homoeolog expression. Furthermore, TaSPL7/15 regulate photosynthesis-related genes through chromatin interactions, with enhanced photosynthetic efficiency and starch content in Taspl7&15 mutant. TAC-C provides new insights into the spatial organization of regulatory elements in crops, especially for SPL-mediated photosynthesis regulation in wheat. TeaserTAC-C Reveals Chromatin Interactions and SPL-Mediated Photosynthesis Regulation in Crops.

plant biology↗

bioRxiv2025

Partially differentiated enterocytes in ileal and distal-colonic human F508del-CF-enteroids 1 secrete fluid in response to forskolin and linaclotide.

Constipation causes significant morbidity in Cystic Fibrosis (CF) patients. Using CF patient (F508del) derived ex vivo ileal and distal colonic/rectal enteroids as a model and the Forskolin Induced Swelling Assay (FIS), we compared CFTR mediated fluid secretion in human enterocytes across the crypt-villus axis. CFTR expression and FIS decreased as enterocytes differentiated from crypt to become partially differentiated and then mature villus cells. While there was no FIS response in undifferentiated (crypt enterocytes) F508del-CF enteroids, partially differentiated F508del-CF enteroids had a swelling response to forskolin (cAMP) and linaclotide (cGMP) which was [~]48%, and [~]67% of the response in healthy enteroids, respectively and was prevented by a CFTR inhibitor. Also, linaclotide and a general PDE inhibitor independently enhanced combined CFTR-modulator-induced FIS response from partially differentiated F508del-CF enteroids. These findings demonstrate that partially differentiated ileal and distal colonic F508del-CFTR enteroids can be stimulated to secrete fluid by cAMP and cGMP.

physiology↗

bioRxiv2025

Beyond RNA Structure Alone: Complex-Aware Feature Fusion for Tertiary Structure-based RNA Design

Tertiary structure-based RNA design plays a crucial role in synthetic biology and therapeutics. While existing methods have explored structure-to-sequence mappings, they focus solely on RNA structures and overlook the role of complex-level information, which is crucial for effective RNA design. To address this limitation, we propose tthe Complex-Aware tertiary structure-based RNA Design model, CARD, that integrates complex-level information to enhance tertiary structure-based RNA sequence design. To be specific, our method incorporates protein features extracted by protein language model (e.g., ESM-2), enabling the design model to generate more accurate and complex relevant sequences. Considering the biological complexity of protein-RNA interactions, we introduce a distance-aware filtering for local features from protein representation. Furthermore, we design a high-affinity design framework that combines our CARD with an affinity evaluation model. In this framework, candidate RNA sequences are generated and rigorously screened based on affinity and structural alignment to produce high-affinity RNA sequences. Extensive experiments demonstrate the effectiveness of our method with an improvement of 5.6% compared with base model without our complex-aware feature integration. A concrete case study for 2LBS further validates the superiority of our CARD.

bioinformatics↗

bioRxiv2025

Tracking mobilization uncovers an evolutionarily conserved mechanism in suppressing transpositions during somatic development

Transposon mobilizations could cause gene mutations and even genomic instability, whose aberrant activation is tightly linked with cancer, neurodegenerative disorder and other pathologies. However, the precise suppression mechanisms of transposon mobilizations during somatic development throughout evolution remain largely obscure. Here, by spatiotemporally monitoring transpositions with single-cell resolution, we determined a highly conserved mechanism in suppressing transposon mobilizations. We identified that Cramp1 safeguards the genomic integrity in both Drosophila hindgut regeneration and mouse embryonic erythropoiesis through silencing transposon mobility. Cramp1 is characterized as a major hallmark that specifically binds to the DNA sequences of histone gene cluster to initiate transcription of linker histone H1, which subsequently promotes H3K36me2-established heterochromatin for transposon silencing. Our finding highlights that with the endless arms race between hosts and transposons during evolution, the core mechanisms will also evolve to suppress transposon mobilizations during somatic development. One-sentence abstractCramp1 plays an evolutionarily conserved role in specifically initiating linker histone H1 transcription and triggering H1-H3K36me2-established heterochromatin to suppress transposon mobilizations and maintain genome integrity during somatic development.

genetics↗

bioRxiv2025

Dietary quorum quenching AHL lactonase impairs the adaptation of commensal bacterium to host innate immunity

Quorum sensing (QS) is the communication system of bacteria that depends on QS signals. Quorum quenching (QQ) enzymes degrade QS signals and are promising alternatives of antibiotics to treat bacterial infections. Here, we found that dietary QQ N-acyl homoserine (AHL) lactonase led to microbiota dysbiosis in zebrafish, with reduction of Aeromonas and enrichment of Plesiomonas. Through gnotobiotic zebrafish colonized with a minimal microbiota, we found that QQ-mediated microbial alteration relies on host Myd88 signaling and neutrophil elastase. Mechanistically, quorum quenching increased the susceptibility of commensal Aeromonas to host neutrophil elastase by impairing bacterial lateral flagellar system, leading to reduced colonization of Aeromonas and subsequent enrichment of Plesiomonas due to ecological competition of the two species. Together, we found that dietary QQ lactonase led to microbiota alteration by impairing the adaptation of commensal Aeromonas to host innate immunity, which provided novel insight in the role of quorum sensing in host-microbiota interaction.

microbiology↗

bioRxiv2025

Dynamic Proximal Interactomics and Chemical Genetic Screening Reveal CCR4-NOT Sequestration in Stress Granules as a Mechanism for Transcript Stabilization

Cells adapt to stress by rewiring their post-transcriptional gene regulation. Stress granules--biomolecular condensates composed of polyadenylated RNAs and RNA-binding proteins--are implicated in this process, yet their precise functional roles remain debated. To address this, we mapped the dynamic proteomic landscapes of stress granules formed under oxidative and hyperosmotic stress using multi-bait BioID proximity profiling coupled with quantitative mass spectrometry. This analysis revealed context-specific remodeling of proximal interaction networks and identified a conserved, stress-dependent shift in association with the CCR4-NOT deadenylase complex. A complementary genome-wide chemical genetic screen further implicated CCR4-NOT in stress granule biology, showing that reduced CCR4-NOT activity bypassed lipoamide-mediated inhibition of stress granule assembly. Microscopy showed sequestration of the CCR4-NOT complex into stress granules, and global transcriptomic analyses revealed that this relocalization promotes poly(A) tail lengthening and increased abundance of stress-induced survival transcripts. Together, integration of proteomics, chemical genetics, and transcriptomics uncovers a spatial mechanism by which stress granule assembly promotes cellular adaptation to stress through sequestration of CCR4-NOT from the cytosol and consequent remodeling of post-transcriptional regulation.

cell biology↗

bioRxiv2025

Mouse Cortical Cellular Diversification Through Lineage Progression of Radial Glia

Cortical radial glia (RGs) sequentially generate pyramidal neurons (PyNs) and glia. In this study, we investigated the cell intrinsic programs underlying cortical cellular diversification using time-series scRNA-seq and snATAC-seq on purified mouse cortical progenitors across embryonic and postnatal stages. Our data revealed that RGs transition from early to late over time, sequentially producing intermediate neuronal progenitors (INPs) and intermediate glial progenitors (IGPs). While INPs expand exclusively to generate PyNs, IGPs progress from young to old, sequentially producing cortical astrocytes, oligodendrocytes, and olfactory bulb interneurons. We constructed comprehensive molecular maps that reflect cell lineage progression. In particularly, we found that chromatin accessibility drives cortical cellular diversification by restricting broadly expressed transcription factors to specific stages and cell types. Developmental changes in chromatin accessibility confine Lhx2-induced neurogenesis to early-stage RGs, leading to the loss of neurogenic competence and the acquisition of gliogenic competence as corticogenesis progresses.

neuroscience↗

bioRxiv2025

Symmetry as a Fundamental Principle in Defining Gene Expression and Phenotypic Traits

Symmetry refers to properties that remain invariant upon mathematical transformations. The principles of symmetry have guided numerous important discoveries in physics and chemistry but not in biology and medicine. Here, we aim to explore the presence of symmetry relationships at the gene expression level as a mean to distinguish between healthy and disease states. We deployed Learning-Based Invariant Feature Engineering - LIFE, a hybrid machine learning approach implemented with two symmetric invariant feature functions (IFFs) to identify Invariant Feature Genes (IFGs), which are gene pairs whose IFF single-value outputs remain invariant across individual samples in a given biological phenotype. Our multiclass classification results across the transcriptomes of 25 normal organs, 25 cancer types, and blood samples obtained from 4 different types of neurodegenerative diseases revealed the presence of unique phenotype-specific IFGs. We constructed networks using these IFGs (IF-Nets) and intriguingly, we demonstrated that the hubs could serve as information encoders, capable of reconstructing sample-wise expression values in relation to their counterpart genes. More importantly, we found that hubs of cancer IF-Nets were enriched with both approved and clinical trial drugs, highlighting "symmetry breaking" as a novel approach for treating diseases.

systems biology↗