Biology subjects

Zhang, I.

Publications and source records attributed to Zhang, I..

11 recordsLinked to original sources

bioRxiv2026

Human iPSC-Derived Cardiomyocytes Maladaptively Remodel to Cyclic Stretch in Hypoplastic Left Heart Syndrome

Background: Hypoplastic Left Heart Syndrome (HLHS) is a severe congenital heart defect characterized by underdevelopment of left-sided cardiac structures, requiring staged surgical palliation that establishes the right ventricle as the single ventricle maintaining systemic circulation. After surgery, patients remain highly susceptible to heart failure, possibly due to the increased hemodynamic load imposed on the single surviving ventricle. Because the etiology of HLHS remains poorly understood, elucidating the mechanisms that drive ventricular dysfunction requires model systems that capture both patient-specific genetics and the dynamic mechanical environment of the ventricle. Thus, our objective was to compare how induced pluripotent stem cell (iPSC)-derived cardiomyocytes (iPSC-CMs) from patients with HLHS differ from control in static culture and in response to cyclic stretch. Methods: Control iPSCs from two unaffected donors and iPSCs from four HLHS patients were differentiated into iPSC-CMs, engineered into aligned tissues, and cultured statically or exposed to cyclic 20% uniaxial stretch at 1 Hz for 48h. Sarcomere organization was quantified in static tissues using images of immunostained -actinin. Calcium transients at 1 Hz pacing frequency in static and stretched tissues were evaluated using Fluo-4 calcium indicator dye. Bulk RNA sequencing was performed to evaluate stretch-induced transcriptomic changes in control and HLHS iPSC-CMs. Results: In static culture, HLHS iPSC-CMs had modest defects in sarcomere organization and calcium transient morphology compared to control. In response to cyclic stretch, control iPSC-CMs exhibited calcium transients with quicker rise time, a response observed in only one of four lines of HLHS iPSC-CMs. Transcriptomic analysis revealed that all four lines of HLHS iPSC-CMs failed to upregulate calcium handling and sarcomere-associated genes in response to stretch, unlike control iPSC-CMs. Stretch also induced HLHS iPSC-CMs to exhibit pronounced activation of inflammatory signaling pathways, a response not observed in control iPSC-CMs. Conclusions: iPSC-CMs from HLHS patients demonstrate aberrant responses to cyclic stretch, including blunted adaptation of calcium transients and heightened inflammatory signaling. These findings implicate defective mechanoadaptation as a potential contributor to single ventricle failure and identify potential candidate biomarkers and new opportunities for therapeutic interventions for HLHS patients.

physiology↗

bioRxiv2026

Oxidized protein states define metastatic fitness in lung cancer

AbstractReactive oxygen species (ROS) are a pervasive feature of human cancers, yet the protein targets through which ROS-regulated cell states shape tumor biology remains poorly understood. Here, using cysteine chemical proteomics, we define signatures of protein states under distinct cellular ROS environments that capture protein oxidation and conformational changes. Quantifying these signatures in primary lung tumors and brain metastases revealed a surprising enrichment of oxidative states in metastasis. To determine how these states support fitness, we performed genome-wide CRISPR screens and identified the mitochondrial Complex I subunit NDUFA10 as a key oxidation-dependent vulnerability. Oxidation of NDUFA10*Cys253 supports Complex I function through a previously unrecognized nucleotide kinase activity that maintains mitochondrial DNA levels. Enforcing a reduced conformation in NDUFA10 disrupts brain metastatic colonization in vivo. These findings establish ROS regulated protein states as a functional layer of tumor fitness, providing a framework for identifying redox-dependent mechanisms that support cancer progression.

Cancer Biology↗

bioRxiv2024

Ecological dynamics explain modular denitrification in the ocean

Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is the multi-step denitrification, the dominant pathway for bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain only subsets ("modules") of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the observed prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when growth is limited by organic matter (OM), explaining the viability of populations respiring nitrite and N2O in a nitrate-filled ocean. Results predict denitrifier community succession along environmental gradients: shorter versus longer modules are favored when OM versus N limits growth, respectively, suggesting a niche for the NO3-{longrightarrow}NO2- module in free-living communities and for the complete pathway in organic particles, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3-{longrightarrow}NO2- module. Results also capture observations that nitrate is the dominant source of N2O. These results advance the mechanistic understanding of the relationship between microbial ecology and N loss, which is essential for accurately predicting the oceans future.

ecology↗

bioRxiv2024

The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube

The vertebrate neural tube generates a large diversity of molecularly and functionally distinct neurons and glia from a small progenitor pool. While the role of spatial patterning in organising cell fate specification has been extensively studied, temporal patterning, which controls the timing of cell type generation, is equally important. Here we define a global temporal programme operating in progenitors throughout the vertebrate nervous systems that governs cell fate choices by regulating chromatin accessibility. Perturbation of this cis-regulatory programme affects sequential cell fate transitions in neural progenitors and the identity of their progeny. The temporal programme operates in parallel to spatial patterning, ensuring the timely availability of regulatory elements for spatial determinants to direct cell-type specific gene expression. These findings identify a chronotopic spatiotemporal integration strategy in which a global temporal chromatin programme determines the output of a spatial gene regulatory network resulting in the temporally and spatially ordered allocation of cell type identity.

developmental biology↗

bioRxiv2023

Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex

Relative alchemical binding free energy calculations are routinely used in drug discovery projects to optimize the affinity of small molecules for their drug targets. Alchemical methods can also be used to estimate the impact of amino acid mutations on protein:protein binding affinities, but these calculations can involve sampling challenges due to the complex networks of protein and water interactions frequently present in protein:protein interfaces. We investigate these challenges by extending a GPU-accelerated open-source relative free energy calculation package (Perses) to predict the impact of amino acid mutations on protein:protein binding. Using the well-characterized model system barnase:barstar, we describe analyses for identifying and characterizing sampling problems in protein:protein relative free energy calculations. We find that mutations with sampling problems often involve charge-changes, and inadequate sampling can be attributed to slow degrees of freedom that are mutation-specific. We also explore the accuracy and efficiency of current state-of-the-art approaches--alchemical replica exchange and alchemical replica exchange with solute tempering--for overcoming relevant sampling problems. By employing sufficiently long simulations, we achieve accurate predictions (RMSE 1.61, 95% CI: [1.12, 2.11] kcal/mol), with 86% of estimates within 1 kcal/mol of the experimentally-determined relative binding free energies and 100% of predictions correctly classifying the sign of the changes in binding free energies. Ultimately, we provide a model workflow for applying protein mutation free energy calculations to protein:protein complexes, and importantly, catalog the sampling challenges associated with these types of alchemical transformations. Our free open-source package (Perses) is based on OpenMM and available at https://github.com/choderalab/perses.

biophysics↗

bioRxiv2022

Sinking diatom aggregates provide carbon to drive microscale denitrification in a bulk oxygenated ocean

Sinking marine particles drive the biological gravitational pump that naturally sequesters carbon dioxide from the atmosphere. Ubiquitous throughout the ocean, these particles are largely composed of phytoplankton that aggregate together or are repackaged by zooplankton into pellets that sink to the deep. Despite their small size, the compartmentalized nature of these particles promotes intense localized metabolic activity by the bacteria lucky enough to colonize them. Due to their sheer numbers, these microscale interactions can change the chemistry of the bulk ocean and impact global biogeochemical budgets. As soon as phytoplankton-derived particles are exported from the surface ocean, the fate of the carbon depends on the lability and availability of the carbon, the diffusive supply of oxidants from the bulk, and the development of microbial communities throughout the aggregate. Here we show with a model experimental system that aggregates composed of marine diatoms -- important primary producers substantially contributing to global carbon export -- can support active denitrification even among bulk oxygenated water ill-conducive to anaerobic metabolisms. We further show the primary nitrite maximum could be formed, in part, due to dissimilatory reduction of nitrate and nitrite occurring at anoxic microsites within such particles. Particle-based denitrification and other anaerobic metabolisms can change the global budget of elemental cycles important for life and climate across the oceans.

microbiology↗

bioRxiv2022

Developmental cell fate choice employs two distinct cis regulatory strategies

In many developing tissues the patterns of gene expression that assign cell fate are organised by secreted signals functioning in a graded manner over multiple cell diameters. Cis Regulatory Elements (CREs) interpret these graded inputs to control gene expression. How this is accomplished remains poorly understood. In the neural tube, a gradient of the morphogen Sonic hedgehog allocates neural progenitor identity. Here, we uncover two distinct ways in which CREs translate graded Shh signaling into differential gene expression. In the majority of ventral neural progenitors a common set of CREs are used to control gene activity. These CREs integrate cell type specific inputs to control gene expression. By contrast, the most ventral progenitors use a unique set of CREs. These are established by the pioneer factor FOXA2, paralleling the role of FOXA2 in endoderm. Moreover, FOXA2 binds a subset of the same sites in neural and endoderm cells. Together the data identify distinct cis regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for FOXA2-mediated regulatory strategy across tissues.

developmental biology↗

bioRxiv2022

Porous marine snow differentially benefits chemotactic, motile, and non-motile bacteria

Particulate organic carbon settling through the marine water column is a key process that regulates global climate by sequestering atmospheric carbon. The initial colonization of marine particles by heterotrophic bacteria represents the first step in recycling this carbon back to inorganic constituents - setting the magnitude of vertical carbon transport to the abyss. Here, we demonstrate experimentally that bacterial motility is required for particle colonization and chemotaxis specifically benefits at higher settling velocities. We further explore the role of particle microstructure on the colonization efficiency of bacteria with different motility traits. We highlight that non-motile cells benefit disproportionally from the porous microstructure and are relatively enriched in the particle wake due to the efficient particle colonization of chemotactic and motile cells. Our results imply that although the chemotactic and motile bacteria benefit from the high nutrient availability when colonizing the particles, scavenging of these cells benefits the often oligotrophic, non-motile cells common among the planktonic community. Significance statementBacteria in the ocean rely on ephemeral nutrient patches from sinking marine particles, but attaching to these structures is challenging as particle settling rates often exceed bacterial swimming velocities and the numerically dominant marine bacteria are non-motile - posing an interesting paradox about the prominence of particle foraging. Here, we quantify the importance of chemotaxis and motility for the efficient colonization of marine particles and find that although chemotaxis provides a clear advantage, motility is the basic requirement for particle colonization. We expand this analysis to consider highly heterogeneous particle structures and find a disproportionate benefit for non-motile cells by facilitating a direct encounter with the particle surface and enriching non-motile microbes in the nutrient-rich particle plume.

microbiology↗

bioRxiv2022

IL-13-programmed airway tuft cells produce PGE2, which promotes CFTR-dependent mucociliary function

Chronic type 2 (T2) inflammatory diseases of the respiratory tract are characterized by mucus overproduction and disordered mucociliary function, which are largely attributed to the effects of IL-13 on common epithelial cell types (mucus secretory and ciliated cells). The role of rare cells in airway T2 inflammation is less clear, though tuft cells have been shown to be critical in the initiation of T2 immunity in the intestine. Using bulk and single cell RNA sequencing of airway epithelium and mouse modeling, we find that IL-13 expands and programs airway tuft cells towards eicosanoid metabolism, and that tuft cell deficiency leads to a reduction in airway prostaglandin E2 (PGE2) concentration. Allergic airway epithelia bear a signature of prostaglandin E2 activation, and PGE2 activation leads to CFTR-dependent ion and fluid secretion and accelerated mucociliary transport. Together these data reveal a role for tuft cells in regulating epithelial mucociliary function in the allergic airway.

immunology↗

bioRxiv2021

Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape

An ideal anti-SARS-CoV-2 antibody would resist viral escape1-3, have activity against diverse SARS-related coronaviruses4-7, and be highly protective through viral neutralization8-11 and effector functions12,13. Understanding how these properties relate to each other and vary across epitopes would aid development of antibody therapeutics and guide vaccine design. Here, we comprehensively characterize escape, breadth, and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD), including S3094, the parental antibody of the late-stage clinical antibody VIR-7831. We observe a tradeoff between SARS-CoV-2 in vitro neutralization potency and breadth of binding across SARS-related coronaviruses. Nevertheless, we identify several neutralizing antibodies with exceptional breadth and resistance to escape, including a new antibody (S2H97) that binds with high affinity to all SARS-related coronavirus clades via a unique RBD epitope centered on residue E516. S2H97 and other escape-resistant antibodies have high binding affinity and target functionally constrained RBD residues. We find that antibodies targeting the ACE2 receptor binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency, but we identify one potent RBM antibody (S2E12) with breadth across sarbecoviruses closely related to SARS-CoV-2 and with a high barrier to viral escape. These data highlight functional diversity among antibodies targeting the RBD and identify epitopes and features to prioritize for antibody and vaccine development against the current and potential future pandemics.

microbiology↗

bioRxiv2020

Temporal patterning of the central nervous system by a shared transcription factor code

The molecular mechanisms that ensure the reproducible generation of neuronal diversity in the vertebrate nervous system are incompletely understood. Here we provide evidence of a temporal patterning program consisting of cohorts of transcription factors expressed in neurons generated at successive developmental timepoints. This program acts in parallel to spatial patterning, diversifying neurons throughout the nervous system and in neurons differentiated in-vitro from stem cells. We demonstrate the TGF{beta} signalling pathway controls the pace of the temporal program. Furthermore, targeted perturbation of components of the temporal program, Nfia and Nfib, reveals their requirement for the generation of late-born neuronal subtypes. Together, our results provide evidence for the existence of a previously unappreciated global temporal program of neuronal subtype identity and suggest that the integration of spatial and temporal patterning programs diversifies and organises neuronal subtypes in the vertebrate nervous system.

developmental biology↗