Biology subjects

Padmanabhan, A.

Publications and source records attributed to Padmanabhan, A..

13 recordsLinked to original sources

bioRxiv2026

A Compact Regulatory Logic Governs Fibroblast Cell State Plasticity in Fibrosis

Fibroblast activation drives organ failure across human diseases, yet its regulatory basis remains largely undefined. Here, we repressed 280 conserved disease-activated enhancers using CRISPR droplet sequencing (CROP-seq) in ~550,000 fibroblasts, constructing a regulome of 15 gene programs governing the profibrotic state. Systematic TF perturbation converged on MEOX1 as a central regulator, and fibroblast-specific Meox1 deletion in mice improved cardiac function, reduced fibrosis, and rewired profibrotic fibroblasts toward quiescence in heart failure. Effector gene perturbation in human cardiac fibroblasts revealed distinct regulators of contractility, migration, and inflammatory signaling, and these programs were conserved across profibrotic states in human lung, liver, and skin. Simultaneous repression of just six enhancers using a multiplexed dCas12a-KRAB system collapsed the profibrotic network, suppressed migration and contraction, and rewired fibroblast paracrine signaling to attenuate macrophage inflammation. These findings define the regulatory logic of fibroblast plasticity and establish a new framework for reprogramming profibrotic cell states in disease.

genomics↗

bioRxiv2026

ZNF217 promotes receptor tyrosine kinase plasticity and AXL-ERK dependency in ovarian cancer

ZNF217 is a potent oncogene that drives ovarian cancer progression and therapeutic resistance. We show that ZNF217 overexpression markedly increases ERBB2 levels in ovarian cancer cells, suggesting its potential as a biomarker to identify ovarian tumors that will respond to ERBB2-targeted therapeutics. Unexpectedly, ZNF217-high ovarian cancer cells exhibit resistance to multiple ERBB2 inhibitors, revealing a disconnect between receptor abundance and drug sensitivity. Mechanistically, ZNF217 drives chemoresistance by elevating the expression of several key receptor tyrosine kinases, most notably AXL, that activates MAPK signaling. Further, ZNF217 also upregulates ERK1/2 levels in ovarian cancer cells. This induces rewiring of downstream signaling, promoting an ERK-dominant state that sustains survival despite ERBB2 inhibition. Therapeutic targeting of the AXL-ERK axis reduced cell viability and metastatic potential in vitro, while suppressing tumor burden and prolonging survival in xenograft models. Thus, by elevating the expression of several key signaling receptors and their downstream effectors in ovarian cancer cells, ZNF217 establishes signaling plasticity that defines a novel mechanism of chemoresistance. These findings identify ZNF217 as a key determinant of signaling state and drug response and provides rationale to evaluate targeting AXL and ERK signaling in ZNF217-high ovarian tumors.

cancer biology↗

bioRxiv2026

TOCA-2 regulates gonad development in C. elegans

The development of C. elegans gonad involves the coordinated action of diverse biochemical factors and physical forces. The precise roles and interconnections of these diverse components remain poorly understood. TOCA-2, the C. elegans ortholog of mammalian TOCA-1 (Transducer of CDC42 Dependent Actin Assembly) is an F-BAR domain protein known to play important roles in oocyte maturation and embryogenesis through membrane remodelling and regulation of actin cytoskeleton. Here we demonstrate that TOCA-2 is actively involved in maintaining the structural integrity and function of the C. elegans gonad. toca-2(null) animals exhibit pronounced architectural defects with particularly strong perturbations on the dorsal side of the gonad. Phalloidin staining and cytoplasmic particle velocity analysis revealed that the actomyosin corset surrounding the common rachis in the syncytial germline is severely disorganized in the mutants. This disorganization leads to significant disruptions in cytoplasmic flow across different regions of the syncytium. Together, our findings quantitatively highlight mechanisms underlying gonad morphogenesis and maintenance, establishing TOCA-2 as a key regulator of these processes. This work also provides a framework for positioning TOCA-2 within broader biochemical pathways governing organogenesis and other developmental processes dependent on actomyosin dynamics in C. elegans.

developmental biology↗

bioRxiv2025

Lifelong maintenance of locomotion by embryonically active dopamine neurons

Locomotor skills arise early in life and are maintained throughout an animals lifespan, yet how this continuity is achieved despite major neural remodeling remains unclear. Using Drosophila, which undergoes complete metamorphosis, we show that the activity of embryonically established dopamine neurons (DANs) is essential for locomotion across all developmental stages and adulthood. Through stage-specific behavioral assays, optogenetics, in vivo brain imaging, and fluorescent neuronal tracking, we identify a subset of ventral nervous system (VNS) DANs that modulate locomotor function throughout life. Transcriptomic analyses reveal that they maintain expression of developmental transcription factors. Knocking down these factors, particularly Antp and Pdm2, in post-mitotic VNS DANs reduces neurite arborization and impairs adult locomotion. These findings uncover a previously overlooked function for embryonic DANs and suggest that stable locomotion during nervous system maturation relies on persistent developmental regulator expression coupled with structural remodeling.

neuroscience↗

bioRxiv2025

P. aeruginosa disrupts CDC-42/ARP-2/3 mediated F-actin organization to induce intestinal deformation in C. elegans

Apico-basal polarity is crucial for maintaining cortical actin organization and regulating secretory functions in intestinal epithelium. The opportunistic pathogen, Pseudomonas aeruginosa, exploits the interplay between cell polarity and cytoskeletal machineries to subvert host defenses. Mechanistic insights into such pathogen-induced cytoskeletal alterations have largely been derived from in-vitro epithelial monolayers, which may not capture the influences of multicellular physiology such as tissue mechanics, and innate immunity. Here, we show that the extracellular P. aeruginosa disrupts apical polarity in C. elegans enterocytes, leading to fragmentation of ARP-2/3 clusters and disorganization of apical F-actin. This disruption causes shedding of actin-rich vesicles into lumen and a pronounced apical deformation. Inhibition of CDC-42-ARP-2/3-mediated actin polymerization or PI3K-AKT signalling attenuated enterocyte deformation and extended the lifespan of C. elegans upon P. aeruginosa exposure. Our findings reveal a conserved strategy by which P. aeruginosa exploits cellular polarity machinery to disrupt host actin organization during extracellular infection of the intestinal epithelium.

cell biology↗

bioRxiv2025

Targeting RUNX1 in Macrophages Facilitates Cardiac Recovery

Despite advances in disease treatment, our understanding of how damaged organs recover and the mechanisms governing this process remain poorly defined. Here, we mapped the transcriptional and regulatory landscape of human cardiac recovery using single cell multiomics. Macrophages emerged as the most reprogrammed cell type. Deep learning identified the transcription factor RUNX1 as a key regulator of this process. Macrophage-specific Runx1 deletion recapitulated the human cardiac recovery phenotype in a chronic heart failure model. Runx1 deletion reprogrammed macrophages to a reparative phenotype, reduced fibrosis, and promoted cardiomyocyte adaptation. RUNX1 chromatin profiling revealed a conserved regulon that diminished during recovery. Mechanistically, the epigenetic reader BRD4 controlled Runx1 expression in macrophages. Chromatin activity mapping, combined with CRISPR perturbations, identified the precise regulatory element governing Runx1 expression. Therapeutically, small molecule Runx1 inhibition was sufficient to promote cardiac recovery. Our findings uncover a druggable RUNX1 epigenetic mechanism that orchestrates recovery of heart function.

immunology↗

bioRxiv2024

Single-nucleus RNA/ATAC-seq Reveals SWI/SNF complex activation and allele-specific non-myocyte activation in HCM mouse models

Hypertrophic cardiomyopathy (HCM) is associated with phenotypic variability. To gain insights into transcriptional regulation of cardiac phenotype, single-nucleus linked RNA-/ATAC-seq was performed in 5-week-old control mouse-hearts (WT) and two HCM-models (R92W-TnT, R403Q-MyHC) that exhibit differences in heart size/function and fibrosis; mutant data was compared to WT. Analysis of 23,304 nuclei from mutant hearts, and 17,669 nuclei from WT, revealed similar dysregulation of gene expression, activation of AP-1 TFs (FOS, JUN) and the SWI/SNF complex in both mutant ventricular-myocytes. In contrast, marked differences were observed between mutants, for gene expression/TF enrichment, in fibroblasts, macrophages, endothelial cells. Cellchat predicted activation of pro-hypertrophic IGF-signaling in both mutant ventricular-myocytes, and profibrotic TGF{beta}-signaling only in mutant-TnT fibroblasts. In summary, our bioinformatics analyses suggest that activation of IGF-signaling, AP-1 TFs and the SWI/SNF chromatin remodeler complex promotes myocyte hypertrophy in early-stage HCM. Selective activation of TGF{beta}-signaling in mutant-TnT fibroblasts contributes to genotype-specific differences in cardiac fibrosis.

bioinformatics↗

bioRxiv2023

Cortical F-actin filament organization corrals E-cadherin/HMR-1 during cytokinetic furrow ingression in C. elegans embryos

In metazoan cells, the delicate equilibrium between proliferative cell division and inter-cellular adhesion is crucial for achieving growth while maintaining tissue integrity and homeostasis. The transmembrane adhesion receptor, E-cadherin, not only facilitates cell-cell adhesion but modulates cytokinesis by impeding cortical F-actin flow and inhibiting actomyosin contractility. In the C. elegans zygote, newly established cell-cell interfaces following cytokinesis lack E-cadherin/HMR-1 (Padmanabhan et al., 2017b). The mechanisms responsible for the spatial exclusion of HMR-1, however remain elusive. Here, we show that HMR-1 is actively prevented from entering the cytokinetic furrow zone during early embryonic divisions in C. elegans. The compact alignment of unbranched F-actin filaments polymerized by the formin/CYK-1 restricts HMR-1 from entering the ingressing furrow. This corralling phenomenon depends on the physical association between HMR-1 and F-actin mediated via the {beta}- and - catenins, HMP-2 and HMP-1, respectively. Our findings reveal a previously unknown reciprocal regulatory relationship between cell adhesion and cell division machineries, ensuring the precise orchestration of the cytokinesis during embryonic development.

cell biology↗

bioRxiv2023

Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis

Chronic inflammation and tissue fibrosis are common stress responses that worsen organ function, yet the molecular mechanisms governing their crosstalk are poorly understood. In diseased organs, stress-induced changes in gene expression fuel maladaptive cell state transitions and pathological interaction between diverse cellular compartments. Although chronic fibroblast activation worsens dysfunction of lung, liver, kidney, and heart, and exacerbates many cancers, the stress-sensing mechanisms initiating the transcriptional activation of fibroblasts are not well understood. Here, we show that conditional deletion of the transcription co-activator Brd4 in Cx3cr1-positive myeloid cells ameliorates heart failure and is associated with a dramatic reduction in fibroblast activation. Analysis of single-cell chromatin accessibility and BRD4 occupancy in vivo in Cx3cr1-positive cells identified a large enhancer proximal to Interleukin-1 beta (Il1b), and a series of CRISPR deletions revealed the precise stress-dependent regulatory element that controlled expression of Il1b in disease. Secreted IL1B functioned non-cell autonomously to activate a p65/RELA-dependent enhancer near the transcription factor MEOX1, resulting in a profibrotic response in human cardiac fibroblasts. In vivo, antibody-mediated IL1B neutralization prevented stress-induced expression of MEOX1, inhibited fibroblast activation, and improved cardiac function in heart failure. The elucidation of BRD4-dependent crosstalk between a specific immune cell subset and fibroblasts through IL1B provides new therapeutic strategies for heart disease and other disorders of chronic inflammation and maladaptive tissue remodeling.

molecular biology↗

bioRxiv2022

Single Cell Epigenetics Reveal Cell-Cell Communication Networks in Normal and Abnormal Cardiac Morphogenesis

Communication between myriad cell types during organ formation underlies proper morphogenesis1. In cardiac development, reciprocal signaling between mesoderm progenitors and neural crest cells is essential, and its disruption leads to congenital heart malformations, the most common human birth defect. However, mechanistic interrogation of temporal gene networks and cis regulatory elements in this crosstalk is limited2,3. Here, we integrated single cell chromatin accessibility and transcriptomics to establish an unbiased and temporal epigenomic map of the embryonic mouse heart over multiple stages and developed machine learning models to predict enhancers for heart and neural crest. We leveraged these advances to determine the consequences of dysregulated signaling at single cell resolution caused by deletion of TBX1, a transcription factor that causes morphogenetic defects of the cardiac outflow tract in humans and functions non-cell autonomously in cardiac mesodermal progenitors to direct pharyngeal neural crest differentiation4-6. Loss of Tbx1 in mice led to broad closure of chromatin regions enriched in cardiac progenitor transcription factor motifs within a narrow subset of cardiac mesodermal progenitors and correlated with diminished expression of numerous members of the fibroblast growth factor, retinoic acid, Notch and Semaphorin pathways. In affected progenitors, ectopic accessibility and expression of posterior heart field factors in the anterior heart field suggested impaired axial patterning. In response, a subset of cardiac neural crest cells displayed epigenomic and transcriptional defects, indicating a failure of differentiation corresponding to dysregulation of the anterior-posterior gradient of pharyngeal Hox gene expression. This study demonstrates that single-cell genomics and machine learning can generate a mechanistic model for how disruptions in cell communication selectively affect spatiotemporally dynamic regulatory networks in cardiogenesis.

developmental biology↗

bioRxiv2022

Single Cell Multimodal Analyses Reveal Epigenomic and Transcriptomic Basis for Birth Defects in Maternal Diabetes

Birth defects occur in [~]6% of all live births and can be caused by combinations of genetic and environmental influences1. Large-scale DNA sequencing efforts are revealing genetic influences2,3, but investigations into the contributions of environmental factors have largely been limited to association studies with limited mechanistic insight. Hyperglycemia present in pre-gestational diabetic mothers is among the most frequent environmental contributor to congenital defects and results in an increased incidence of congenital heart defects and craniofacial anomalies4. However, the cell types involved and underlying mechanisms by which maternal hyperglycemia affects these regions are unknown. Here, we utilized multi-modal single cell analyses to reveal that maternal diabetes affects the epigenomic and transcriptomic state of specific subsets of cardiac and craniofacial progenitors during embryogenesis. A previously unrecognized subpopulation of anterior heart field progenitors expressing Alx3 acquired a more posterior identity in response to maternal hyperglycemia, based on gene expression and chromatin status. Similarly, a sub-population of neural crest-derived cells in the second pharyngeal arch, which contributes to craniofacial structures, also displayed abnormalities in cell specification and patterning. Analysis of differentially accessible chromatin regions demonstrated that disrupted patterning was associated with increased intrinsic retinoic acid signaling in affected cell types in response to maternal diabetes and hyperglycemia. This work demonstrates how an environmental insult can have highly selective epigenomic consequences on discrete cell types leading to developmental patterning defects.

developmental biology↗

bioRxiv2020

A Transcriptional Switch Governing Fibroblast Plasticity Underlies Reversibility of Chronic Heart Disease

In diseased organs, stress-activated signaling cascades alter chromatin, triggering broad shifts in transcription and cell state that exacerbate pathology. Fibroblast activation is a common stress response that worsens lung, liver, kidney and heart disease, yet its mechanistic basis remains poorly understood1,2. Pharmacologic inhibition of the BET family of transcriptional coactivators alleviates cardiac dysfunction and associated fibrosis, providing a tool to mechanistically interrogate maladaptive fibroblast states and modulate their plasticity as a potential therapeutic approach3-8. Here, we leverage dynamic single cell transcriptomic and epigenomic interrogation of heart tissue with and without BET inhibition to reveal a reversible transcriptional switch underlying stress-induced fibroblast activation. Transcriptomes of resident cardiac fibroblasts demonstrated robust and rapid toggling between the quiescent fibroblast and activated myofibroblast state in a manner that directly correlated with BET inhibitor exposure and cardiac function. Correlation of single cell chromatin accessibility with cardiac function revealed a novel set of reversibly accessible DNA elements that correlated with disease severity. Among the most dynamic elements was an enhancer regulating the transcription factor MEOX1, which was specifically expressed in activated myofibroblasts, occupied putative regulatory elements of a broad fibrotic gene program, and was required for TGF{beta}-induced myofibroblast activation. CRISPR interference of the most dynamic cis-element within the enhancer, marked by nascent transcription, prevented TGF{beta}-induced activation of Meox1. These findings identify MEOX1 as a central regulator of stress-induced myofibroblast activation associated with cardiac dysfunction. The plasticity and specificity of the BET-dependent regulation of MEOX1 in endogenous tissue fibroblasts provides new trans- and cis- targets for treating fibrotic disease.

molecular biology↗

bioRxiv2020

BRD4 Interacts with GATA4 to Govern Mitochondrial Homeostasis in Adult Cardiomyocytes

Gene regulatory networks control tissue plasticity during basal homeostasis and disease in a cell-type specific manner. Ubiquitously expressed chromatin regulators modulate these networks, yet the mechanisms governing how tissue-specificity of their function is achieved are poorly understood. BRD4, a member of the BET (Bromo- and Extra-Terminal domain) family of ubiquitously expressed acetyl-lysine reader proteins, plays a pivotal role as a coactivator of enhancer signaling across diverse tissue types in both health and disease, and has been implicated as a pharmacologic target in heart failure. However, the cell-specific role of BRD4 in adult cardiomyocytes remains unknown. Here, we show that cardiomyocyte-specific deletion of BRD4 in adult mice leads to acute deterioration of cardiac contractile function with mutant animals demonstrating a transcriptomic signature enriched for decreased expression of genes critical for mitochondrial energy production. Genome-wide occupancy data show that BRD4 enriches at many downregulated genes and preferentially co-localizes with GATA4, a lineage determining cardiac transcription factor not previously implicated in regulation of adult cardiac metabolism. Co-immunoprecipitation assays demonstrate that BRD4 and GATA4 form a complex in a bromodomain-independent manner, revealing a new interaction partner for BRD4 that has functional consequences for target transactivation and may allow for locus and tissue specificity. These results highlight a novel role for a BRD4-GATA4 module in cooperative regulation of a cardiomyocyte specific gene program governing bioenergetic homeostasis in the adult heart.

molecular biology↗