Biology subjects

Zheng, H.

Publications and source records attributed to Zheng, H..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Extrusion-modulated DnaA activity oscillations coordinate DNA replication with biomass growth

Robust control of DNA replication is fundamental to bacterial proliferation. In Escherichia coli, replication initiation is thought to be regulated by oscillations in DnaA activity, driven by DnaA-chromosome interactions that differ among leading models. However, direct evidence linking these oscillations to replication initiation has been lacking, and existing models fail to explain the observed decoupling of replication initiation from dnaA expression. Here, we establish a direct link between DnaA activity and replication initiation by demonstrating robust oscillations in DnaA activity, which peak precisely at replication initiation across diverse growth conditions and genetic perturbations. Notably, these oscillations persist even when dnaA transcription remains constant, suggesting a regulatory mechanism that modulates DnaA activity independently of its expression. Additionally, we propose an extrusion model in which DNA-binding proteins sense biomass-DNA imbalance and extrude DnaA from the chromosome to trigger replication, overcoming limitations of existing models. Consistent with this model, perturbation of the nucleoid-associated protein H-NS modulates DnaA activity and replication timing, supporting its mechanistic validity.

microbiology↗

bioRxiv2025

A conserved immune dysregulation is associated with infection severity, risk factors prior to infection, and treatment response

Older age, being male, obesity, smoking, and comorbidities (e.g., diabetes, asthma) are associated with the increased risk for severe infections. We hypothesized that there is a conserved common immune dysregulation across these risk factors. We integrated single cell and bulk transcriptomic data and proteomic data from 12,026 blood samples across 68 cohorts to test this hypothesis. We found that our previously described 42-gene Severe-or-Mild (SoM) signature, is associated with each of these risk factors prior to infection. Furthermore, we found this conserved immune signature is modifiable using immunomodulatory drugs and lifestyle changes. The SoM score predicted patients with sepsis that would be harmed from hydrocortisone treatment, and patients with asthma that will not respond to monoclonal antibody treatment. Finally, the SoM score was associated with all-cause mortality. The SoM signature has the potential to redefine the immunologic framing of baseline immune state and response to chronic, subacute, and acute illnesses.

immunology↗

bioRxiv2025

Tnfrsf10 Signaling is Required to Maintain the Stem Cell Niche in the Zebrafish Lateral Line

Regenerative capacity varies significantly among species and across different organs. In mammals, the inner ear exhibits a limited ability to regenerate hair cells, whereas the lateral line sensory organ of zebrafish demonstrates apparently limitless capability to spontaneously regenerate hair cells following injury. However, the specific cell populations representing the stem cells in the neuromast and the mechanism of stem cell self-renewal remain unclear. In this study, we show that a mutation in tnfrsfa led to the depletion of neuromast sensory organs and impairment of hair cell regeneration in zebrafish. The decrease of cells peripheral to the neuromasts in tnfrsfa mutants indicates that these peripheral cells, particularly cells called "mantle cells", serve as the stem cells within the neuromast. Furthermore, our findings indicate that the ligands Tnfsf10 and Tnfsf10l3 (TRAIL) act through Tnfrsfa activating the NF-{kappa}B signaling pathway in the mantle cells in a non-cell-autonomous manner. NF-{kappa}B signaling is crucial for maintaining the stem cell identity of the mantle cells through activation or maintenance of sox2 expression. These findings demonstrate a critical role for TNF superfamily signaling in stem cell maintenance. HighlightsO_LIZebrafish tnfrsfa maintains the stem cell niche in neuromasts and is necessary for hair cell regeneration of the lateral line C_LIO_LITnfrsfa is essential for mantle cell proliferation during lateral line development and hair cell regeneration C_LIO_LITnfsf10 and Tnfsf10l3 signal through Tnfrsfa, activating NF-{kappa}B signaling and Sox2 expression in the mantle cells in a non-cell-autonomous manner C_LIO_LITnfrsfa regulates the development of neuromast independently of the Notch signaling pathway C_LI

developmental biology↗

bioRxiv2025

Tff2 marks gastric corpus progenitors that give rise to pyloric metaplasia/SPEM following injury

In BriefTu et al. show that Tff2+ corpus isthmus cells are TA progenitors, and they, not chief cells, are the primary source of SPEM following injury. Upon Kras mutation, these progenitors directly progress to dysplasia, bypassing metaplasia, highlighting them as a potential origin of gastric cancer. HighlightsO_LITff2+ corpus cells are TA progenitors that give rise to secretory cells. C_LIO_LITff2+ progenitors, not chief cells, are the primary source of SPEM after injury. C_LIO_LIKras-mutant Tff2+ progenitors progress directly to dysplasia, bypassing metaplasia. C_LIO_LIMulti-omics analysis reveals distinct trajectories for SPEM and gastric cancer. C_LI O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/647847v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@48a2d1org.highwire.dtl.DTLVardef@b96642org.highwire.dtl.DTLVardef@1e89a4dorg.highwire.dtl.DTLVardef@1ea6a86_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG Pyloric metaplasia, also known as spasmolytic polypeptide-expressing metaplasia (SPEM), arises in the corpus in response to oxyntic atrophy, but its origin and role in gastric cancer remain poorly understood. Using Tff2-CreERT knockin mice, we identified highly proliferative Tff2+ progenitors in the corpus isthmus that give rise to multiple secretory lineages, including chief cells. While lacking long-term self-renewal ability, Tff2+ corpus progenitors rapidly expand to form short-term SPEM following acute injury or loss of chief cells. Genetic ablation of Tff2+ progenitors abrogated SPEM formation, while genetic ablation of GIF+ chief cells enhanced SPEM formation from Tff2+ progenitors. In response to H. pylori infection, Tff2+ progenitors progressed first to metaplasia and then later to dysplasia. Interestingly, induction of KrasG12D mutations in Tff2+ progenitors facilitated direct progression to dysplasia in part through the acquisition of stem cell-like properties. In contrast, Kras-mutated SPEM and chief cells were not able to progress to dysplasia. Tff2 mRNA was downregulated in isthmus cells during progression to dysplasia. Single-cell RNA sequencing and spatial transcriptomics of human tissues revealed distinct differentiation trajectories for SPEM and gastric cancer. These findings challenge the conventional interpretation of the stepwise progression through metaplasia and instead identify Tff2+ progenitor cells as potential cells of origin for SPEM and possibly for gastric cancer.

cell biology↗

bioRxiv2025

AlphaFold3 in Drug Discovery: A Comprehensive Assessment of Capabilities, Limitations, and Applications

Accurate prediction of protein-ligand interactions remains a cornerstone challenge in drug discovery. AlphaFold3 (AF3), a recent breakthrough Diffusion Transformer model, holds significant promise for structural biology, but its performance across diverse pharmaceutical applications requires systematic evaluation. In this study, we comprehensively benchmark AF3s capabilities using carefully curated datasets, examining its performance in binary protein-ligand complexes, apo/holo structural variations, GPCR-ligand conformations, ternary systems, and inhibitor affinity prediction. Our analysis reveals that AF3 excels at predicting static protein-ligand interactions with minimal conformational changes, significantly outperforming traditional docking methods in side-chain orientation accuracy. However, we identify critical limitations: AF3 struggles with protein-ligand complexes involving significant conformational changes (>5[A] RMSD), demonstrates a persistent bias toward active GPCR conformations regardless of ligand type, performs poorly on ternary complex prediction, and lacks reliable affinity ranking capability. Notably, AF3s performance declined significantly on structures released after its training cutoff date, suggesting potential memorization rather than physical understanding of molecular interactions. We explored AF3s practical utility through applications in chemoproteomics data interpretation, drug resistance mutation prediction, and kinome profiling simulation. AF3 demonstrated value as a "true-hit binary interaction modeler," capable of generating reliable structural models for experimentally validated binding pairs. However, its ranking metrics showed minimal correlation with experimental binding affinities and limited ability to differentiate across the kinome, highlighting the need for integration with physics-based scoring methods. Our findings indicate that while AF3 represents a significant advancement in protein-ligand structure prediction, it requires complementary approaches to address its limitations in conformational sampling, affinity ranking, and complex system modeling. Recent developments like YDS Ternoplex suggest that enhanced sampling techniques can overcome some of these limitations. The optimal strategy for leveraging AF3 in drug discovery likely involves its integration into hybrid computational pipelines that combine AI-based prediction with physics-based refinement and experimental validation.

biochemistry↗

bioRxiv2025

A reference genome assembly of the alpine forage grass Elymus nutans

Elymus nutans Griseb. (Poaceae: Triticeae, 2n=6x=42) is a dominant perennial plant species in the Qinghai-Tibetan Plateau in China, which is an important forage resource in high-altitude and cold regions and is the most popular species used for high yield artificial grassland planting because of its rich nutritional value and good palatability for herbivorous ruminant animals. In this study, using advanced sequencing technology, we generated an allohexaploid reference genome for E. nutans, representing the three sets of chromosomes (subgenomes St, Y, and H). This is the first study to our knowledge to confirm the origin of the Y subgenome, which shares a close relationship with the V subgenome. We predict that E. nutans arose via two-step hybridization and that its speciation occurred [~]3.16 MYA. The whole genome in this study will update the Triticeae family genomics information and provide theoretical basis for the evolutionary of its related speicies.

plant biology↗

bioRxiv2025

The Golgi Rim is a Precise Tetraplex of Golgin Proteins that Can Self-Assemble into Filamentous Bands

Golgin proteins have long been suspected to be organizers of the Golgi stack. Using three-dimensional super-resolution microscopy, we comprehensively localize the human golgin family at the rim of the Golgi apparatus at 10-20 nm resolution in situ. Unexpectedly, we find that the golgins are precisely organized into a tetraplex with four discrete layers, each containing a specific set of rim golgins. We observe no golgins inside the stack between its membrane-bound cisternae. Biochemically characterizing most of the golgins as isolated proteins, we find that they form anti-parallel dimers and further self-assemble into bands of multi-micron-long filaments. Based on our findings, we propose an "outside-in" physical model, the Golgin Organizer Hypothesis, in which the Golgi stack of cisternae and its overall ribbon morphology directly result from bending circumferential bands of rim golgin filaments onto a membrane surface, explaining stack formation without the need for special "stacking proteins."

cell biology↗

bioRxiv2025

Joint imputation and deconvolution of gene expression across spatial transcriptomics platforms

Spatially resolved transcriptomics (SRT) technologies measure gene expression across thousands of spatial locations within a tissue slice. Multiple SRT technologies are currently available and others are in active development with each technology having varying spatial resolution (subcellular, single-cell, or multicellular regions), gene coverage (targeted vs. whole-transcriptome), and sequencing depth per location. For example, the widely used 10x Genomics Visium platform measures whole transcriptomes from multiple-cell-sized spots, while the 10x Genomics Xenium platform measures a few hundred genes at subcellular resolution. A number of studies apply multiple SRT technologies to slices that originate from the same biological tissue. Integration of data from different SRT technologies can overcome limitations of the individual technologies enabling the imputation of expression from unmeasured genes in targeted technologies and/or the deconvolution of ad-mixed expression from technologies with lower spatial resolution. We introduce Spatial Integration for Imputation and Deconvolution (SIID), an algorithm to reconstruct a latent spatial gene expression matrix from a pair of observations from different SRT technologies. SIID leverages a spatial alignment and uses a joint non-negative factorization model to accurately impute missing gene expression and infer gene expression signatures of cell types from ad-mixed SRT data. In simulations involving paired SRT datasets from different technologies (e.g., Xenium and Visium), SIID shows superior performance in reconstructing spot-to-cell-type assignments, recovering cell-type-specific gene expression, and imputing missing data compared to contemporary tools. When applied to real-world 10x Xenium-Visium pairs from human breast and colon cancer tissues, SIID achieves highest performance in imputing holdout gene expression. A PyTorch implementation of SIID is available at https://github.com/raphael-group/siid.

bioinformatics↗

bioRxiv2025

SurfNet: Reconstruction of Cortical Surfaces via Coupled Diffeomorphic Deformations

To achieve fast and accurate cortical surface reconstruction from brain magnetic resonance images (MRIs), we develop a method to jointly reconstruct the inner (white-gray matter interface), outer (pial), and midthickness surfaces, regularized by their interdependence. Rather than reconstructing these surfaces separately without taking into consideration their interdependence as in most existing methods, our method learns three diffeomorphic deformations jointly to optimize the midthickness surface to lie halfway between the inner and outer cortical surfaces and simultaneously deforms it inward and outward towards the inner and outer cortical surfaces, respectively. The surfaces are encouraged to have a spherical topology by regularization terms for non-negativeness of the cortical thickness and symmetric cycle-consistency of the coupled surface deformations. The coupled reconstruction of cortical surfaces also facilitates an accurate estimation of the cortical thickness based on the diffeomorphic deformation trajectory of each vertex on the surfaces. Validation experiments have demonstrated that our method achieves state-of-the-art cortical surface reconstruction performance in terms of accuracy and surface topological correctness on large-scale MRI datasets, including ADNI, HCP, and OASIS.1

neuroscience↗

bioRxiv2025

Cryo-EM structures reveal the PP2A-B55α and Eya3 interaction that can be disrupted by a peptide inhibitor

We have previously shown that Eya3 recruits PP2A-B55 to dephosphorylate pT58 on Myc, increasing Myc stability and enhancing primary tumor growth of triple-negative breast cancer (TNBC). However, the molecular details of how Eya3 recruits PP2A-B55 remain unclear. Here we determined the cryo-EM structures of PP2A-B55 bound with Eya3, with an inhibitory peptide B55i, and in its unbound state. These studies demonstrate that Eya3 binds B55 through an extended peptide in the NTD of Eya3. The Eya3 peptide and other PP2A-B55 substrates and protein/peptide inhibitors including B55i bind to a similar area on the B55 surface but the molecular details of the binding differ. We further demonstrated that the B55i peptide inhibits the B55 and Eya3 interaction in vitro. B55i peptide expressed on a plasmid increases pT58 and decreases Myc protein level in TNBC cells, suggesting the potential of B55i or similar peptides as therapies for TNBC.

molecular biology↗

bioRxiv2025

Aberrant Modular Dynamics of Functional Networks in Schizophrenia and Their Relationship with Neurotransmitter and Gene Expression Profiles

IntroductionNumerous studies have emphasized the time-varying modular architecture of functional brain networks and its relevance to cognitive functions in healthy participants. However, how brain modular dynamics change in schizophrenia and how these alterations relate to neurotransmitter and transcriptomic signatures have not been well elucidated. MethodsWe harmonized resting-state fMRI data from a multi-site sample including 223 patients and 279 healthy controls and applied the multilayer network method to estimate the regional module switching rate (flexibility) of functional brain connectomes. We examined aberrant flexibility in patients relative to controls and explored its relations to neurotransmitter systems and postmortem gene expression. ResultsCompared with controls, patients with schizophrenia had significantly higher flexibility in the somatomotor and right visual regions, and lower flexibility in the left parahippocampal gyrus, right supramarginal gyrus, right frontal-operculum-insula, bilateral precuneus posterior cingulate cortex, and bilateral inferior parietal gyrus. These alterations were associated with multiple neurotransmitter systems and weighted gene transcriptomic profiles. The most relevant genes were preferentially enriched for biological processes of transmembrane transport and brain development, specific cell types, and previously identified schizophrenia-related genes. ConclusionsThis study reveals aberrant modular dynamics in schizophrenia and its relations to neurotransmitter systems and schizophrenia-related transcriptomic profiles, providing insights into the understanding of the pathophysiology underlying schizophrenia.

neuroscience↗

bioRxiv2025

Overturning circulation structures the microbial functional landscape of the South Pacific

Global overturning circulation partitions the deep ocean into regions with unique physicochemical characteristics, but the extent to which these water masses represent distinct ecosystems remains unknown. Here, we integrate extensive genomic information with hydrography and water mass age to delineate microbial taxonomic and functional boundaries across the South Pacific. Prokaryotic richness steeply increases with depth in the surface ocean, forming a "phylocline", below which richness is consistently high, dipping slightly in highly aged water. Reconstructed genomes self-organize into six spatially-distinct taxonomic cohorts and ten functionally-distinct biomes that are primarily structured by wind-driven circulation at the surface and density-driven circulation at depth. Overall, water physicochemistry, modulated at depth by water age, drives microbial diversity and functional potential in the pelagic ocean.

microbiology↗

bioRxiv2024

dFCExpert: Learning Dynamic Functional Connectivity Patterns with Modularity and State Experts

Characterizing brain dynamic functional connectivity (dFC) patterns from functional Magnetic Resonance Imaging (fMRI) data is of paramount importance in imaging neuroscience and medicine. Recently, many graph neural network (GNN) models, combined with transformers or recurrent neural networks (RNNs), have shown great potential for modeling the dFC patterns. However, these methods face challenges in effectively characterizing the modularity organization of brain networks and capturing varying dFC state patterns. To address these limitations, we propose dFCExpert, a novel method designed to learn robust representations of dFC patterns in fMRI data with modularity experts and state experts. Specifically, the modularity experts optimize multiple experts to characterize the brain modularity organization during graph feature learning process by combining GNN and mixture of experts (MoE), with each expert focusing on brain nodes within the same functional network module. The state experts aggregate temporal dFC features into a set of distinctive connectivity states using a soft prototype clustering method, providing insight into how these states support diverse brain functions and how they vary across brain conditions. Experiments on three large-scale fMRI datasets have demonstrated the superiority of our method over existing alternatives. The learned dFC representations not only enhance interpretability but also hold promise for advancing our understanding of brain function across a range of conditions, including development, sex difference, and Autism Spectrum Disorder. Our code is publicly available at MLDataAnalytics/dFCExpert1.

neuroscience↗

bioRxiv2024

Highly dynamic supernumerary mini-chromosomes in a Magnaporthe oryzae strain

Magnaporthe oryzae (syn. Pyricularia oryzae), the causative agent of devastating crop diseases, exhibits remarkable genomic plasticity that contributes to its adaptability and pathogenicity. Individual M. oryzae strains may contain supernumerary mini-chromosomes, which are dispensable and highly repetitive. Here, we explored the stability of two mini-chromosomes of a Lolium strain isolated in the US, TF05-1, in which one mini-chromosome contains sequences nearly identical to the mini-chromosome of the wheat isolate B71 from Bolivia. The discordance of their phylogenetic relationships based on genomic polymorphisms in core chromosomes and polymorphisms in mini-chromosomes indicated horizontal transfer of the mini-chromosome. Karyotyping analysis and genome sequencing analysis found variation in numbers and sizes of mini-chromosomes among asexual monoconidial progeny of TF05-1. Rearrangement within mini-chromosomes occurred frequently in the TF05-1 progeny. We characterized an intrachromosomal rearrangement presumably mediated by a palindrome repeat. The rearrangement resulted in a 300-kb deletion and a 900-kb duplication. The susceptibility to structural variation in mini-chromosomes may be associated with repetitive features and the high activity of transposable elements in mini-chromosomes, in which many intact retrotransposons were recently inserted, largely unmethylated, and likely have yet to be silenced by fungal genome defense mechanisms such as repeat-induced point mutation.

genomics↗

bioRxiv2024

SegCSR: Weakly-Supervised Cortical Surfaces Reconstruction from Brain Ribbon Segmentations

Deep learning-based cortical surface reconstruction (CSR) methods heavily rely on pseudo ground truth (pGT) generated by conventional CSR pipelines as supervision, leading to dataset-specific challenges and lengthy training data preparation. We propose a new approach for reconstructing multiple cortical surfaces using weak supervision from brain MRI ribbon segmentations. Our approach initializes a midthickness surface and then deforms it inward and outward to form the inner (white matter) and outer (pial) cortical surfaces, respectively, by jointly learning diffeomorphic flows to align the surfaces with the boundaries of the cortical ribbon segmentation maps. Specifically, a boundary surface loss drives the initialization surface to the target inner and outer boundaries, and an inter-surface normal consistency loss regularizes the pial surface in challenging deep cortical sulci. Additional regularization terms are utilized to enforce surface smoothness and topology. Evaluated on two large-scale brain MRI datasets, our weakly-supervised method achieves comparable or superior CSR accuracy and regularity to existing supervised deep learning alternatives.

neuroscience↗

bioRxiv2024

In situ Membrane Protein Expression by Efficient Recruitment of mRNA to the Membranes of Synthetic Cells

The synthesis of artificial cells is crucial for understanding the origins of life. In synthetic cells, however, the absence of membrane-bound organelles and auxiliary proteins severely limits the efficient expression and precise localization of membrane proteins using cell-free expression systems. Here we introduce a robust method that significantly enhances membrane protein synthesis by recruiting mRNA to phospholipid membranes. This is achieved through the use of cholesterol-modified, single-stranded DNA that anchors to the membrane and pairs with the mRNAs untranslated region. This strategic placement facilitates the assembly of protein expression machinery, promoting direct co-translational folding at the membrane. Our approach not only ensures correct protein topology and functionality but also demonstrates broad applicability for the in situ expression of various membrane proteins. It effectively addresses the challenges of membrane protein localization and assembly in synthetic cells, showcasing its versatility for synthesizing a wide array of membrane proteins.

synthetic biology↗

bioRxiv2024

International multi-cohort analysis identifies novel framework for quantifying immune dysregulation in critical illness: results of the SUBSPACE consortium

Progress in the management of critical care syndromes such as sepsis, Acute Respiratory Distress Syndrome (ARDS), and trauma has slowed over the last two decades, limited by the inherent heterogeneity within syndromic illnesses. Numerous immune endotypes have been proposed in sepsis and critical care, however the overlap of the endotypes is unclear, limiting clinical translation. The SUBSPACE consortium is an international consortium that aims to advance precision medicine through the sharing of transcriptomic data. By evaluating the overlap of existing immune endotypes in sepsis across over 6,000 samples, we developed cell-type specific signatures to quantify dysregulation in these immune compartments. Myeloid and lymphoid dysregulation were associated with disease severity and mortality across all cohorts. This dysregulation was not only observed in sepsis but also in ARDS, trauma, and burn patients, indicating a conserved mechanism across various critical illness syndromes. Moreover, analysis of randomized controlled trial data revealed that myeloid and lymphoid dysregulation is linked to differential mortality in patients treated with anakinra or corticosteroids, underscoring its prognostic and therapeutic significance. In conclusion, this novel immunology-based framework for quantifying cellular compartment dysregulation offers a valuable tool for prognosis and therapeutic decision-making in critical illness.

immunology↗

bioRxiv2024

GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors

Precise identification of transcription factor (TF) binding sites is a long standing challenge in human regulatory genomics: TF binding motifs are short and degenerate, while the genome is large. Motif scans, therefore, often produce excessive binding site predictions. By surveying 179 TFs across 25 families using >1,500 cyclic in vitro selection experiments with fragmented, naked, and unmodified genomic DNA - a method we term GHT-SELEX (Genomic HT-SELEX) - we find that many human TFs possess much higher sequence specificity than anticipated. Moreover, genomic binding regions from GHT-SELEX are often surprisingly similar to those obtained in vivo (i.e., ChIP-seq peaks). Contrary to conventional wisdom, we find that high specificity can also be obtained from motif scans, but performance is highly dependent on the derivation and use of the motifs, including accounting for multiple local matches. We also observe alternative engagement of multiple DNA-binding domains within the same protein: long C2H2 zinc finger proteins often utilize modular DNA recognition, engaging different subsets of their DNA-binding domain (DBD) arrays to recognize multiple types of distinct target sites, frequently evolving via internal duplication and divergence of one or more DBDs. Thus, it is common for TFs to possess sufficient intrinsic specificity to delineate a large fraction of in vivo genomic targets, independently of other cellular factors.

genomics↗