Biology subjects

Bhagwate, A.

Publications and source records attributed to Bhagwate, A..

5 recordsLinked to original sources

bioRxiv2026

ARID5A Is a PERK-Dependent Effector of the Endoplasmic Reticulum Stress Response That Protects Against Steatohepatitis

Lipotoxic endoplasmic reticulum (ER) stress is a fundamental feature of metabolic dysfunction-associated steatohepatitis (MASH). ER stress activates adaptive signaling processes that aim to restore ER homeostasis. Yet, depending on the duration, magnitude, and cellular context, sustained ER stress becomes maladaptive and leads to cell death. The regulatory pathways that determine adaptive versus maladaptive ER stress outcomes remain incompletely understood. Here we integrated transcriptomic and chromatin-accessibility analyses in complementary models of proteotoxic and lipotoxic ER stress to identify previously unrecognized regulators of the ER stress response. These analyses identified the dual DNA- and RNA-binding protein AT-rich interaction domain 5A (ARID5A) as an ER stress-responsive gene. ARID5A protein was abundantly expressed in hepatocytes, and ARID5A mRNA and protein were upregulated in palmitate-induced lipotoxic ER stress across multiple hepatocyte models. Using complementary genetic and pharmacological approaches, we demonstrated that ARID5A induction was independent of IRE1 and ATF6 signaling and was attenuated by inhibition of the PERK pathway. To determine the functional relevance of ARID5A in MASH, we employed hepatocyte-directed AAV9-mediated ARID5A overexpression in mice fed a MASH-inducing diet. ARID5A overexpression attenuated steatohepatitis, inflammation, and fibrosis. Together, these findings identify ARID5A as a previously unrecognized PERK-dependent effector of the hepatocyte ER stress response and demonstrate that increasing hepatocyte ARID5A is protective in experimental MASH. This work provides a foundation for defining the mechanisms by which ARID5A regulates hepatocyte stress responses and MASH severity.

cell biology↗

bioRxiv2026

ACLY integrates metabolism and chromatin accessibility to enable B Cell activation and humoral immunity

B cell activation and differentiation into antibody-secreting cells require extensive metabolic and epigenetic remodeling, yet the molecular mechanisms that integrate these programs remain incompletely understood. ATP-citrate lyase (ACLY) links glucose metabolism to acetyl-CoA production, supporting lipid biosynthesis and protein acetylation. However, its role in humoral immunity has not been fully defined. Here, using genetic and integrated multi-omics approaches, we show that B cell activation is accompanied by coordinated metabolic, transcriptional, and epigenetic reprograming. Although ACLY is dispensable for B cell development and homeostasis, it is required to establish chromatin accessibility programs in activated B cells, with a more pronounced impact on the epigenetic landscape than on transcriptional output. ACLY-deficient B cells exhibit profound defects in TLR and BCR elicited activation, survival and metabolic fitness ex vivo. In vivo, B cell-intrinsic loss of ACLY results in impaired antigen-specific antibody production, associated with reduced germinal center and plasmablast formation, but normal homeostatic proliferation. Deletion of ACLY after B cell activation reduces plasmablast generation in vivo, indicating a continued requirement for ACLY beyond the initial activation phase. Together, these findings identify ACLY as a central regulator that links metabolism to epigenetic programing that supports B cell activation and humoral immunity.

immunology↗

bioRxiv2025

Intestinal Stem Cells Retain an Epigenetic Memory of Prior Inflammation

Intestinal epithelial damage and impaired repair are hallmarks of ulcerative colitis (UC), even after inflammation resolves. Intestinal stem cells (ISCs) can retain stable epigenetic changes after inflammation, highlighting the potential for long-lived epithelial memory in the gut. Inflammatory injury in barrier tissues induces epigenetic memory in epithelial stem cells, and the tendency of UC to relapse at previously inflamed sites led us to hypothesize that ISCs from IBD patients acquire lasting memory of prior inflammation. To test this, we derived colonic organoids from inflamed and uninflamed regions of the same UC patients and propagated in long-term culture. Chromatin profiling revealed 2,252 accessible regions unique to prior-inflamed (PI) organoids, associated with stress response, repair, and inflammatory genes. Although these regions remained accessible, [~]95% of associated genes were not upregulated in PI organoids, indicating a primed state. Upon inflammatory or injury re-challenge, PI organoids exhibited heightened transcriptional responses and accelerated wound closure, despite reduced clonogenicity and impaired barrier function, indicating a retained inflammatory memory program. Our findings demonstrate that human ISCs retain a chromatin-based memory of inflammation that persists in the absence of immune cues and shapes future responses to injury. While this may support epithelial adaptation to secondary insults, it may predispose tissue to relapse in patients with UC.

molecular biology↗

bioRxiv2021

In vivo lentiviral vector gene therapy to cure hereditary tyrosinemia type 1 and prevent development of precancerous and cancerous lesions

Conventional therapy for hereditary tyrosinemia type-1 (HT1) with 2-(2-nitro-4-trifluoromethylbenzoyl)-1,3-cyclohexanedione (NTBC) delays and in some cases fails to prevent disease progression to liver fibrosis, liver failure, and activation of tumorigenic pathways. Here we demonstrate for the first time a cure of HT1 by direct, in vivo administration of a therapeutic lentiviral vector targeting the expression of a human fumarylacetoacetate hydrolase (FAH) transgene in the porcine model of HT1. This therapy was well tolerated and provided stable long-term expression of FAH in pigs with HT1. Genomic integration displayed a benign profile, with subsequent fibrosis and tumorigenicity gene expression patterns similar to wild-type animals as compared to NTBC-treated or diseased untreated animals. Indeed, the phenotypic and genomic data following in vivo lentiviral vector administration demonstrate comparative superiority over other therapies including ex vivo cell therapy and therefore support clinical application of this approach.

cell biology↗

bioRxiv2019

Use of FFPE-Derived DNA in Next Generation Sequencing: DNA extraction methods

Archival tissues represent a rich resource for clinical genomic studies, particularly when coupled with comprehensive medical records. Use of these in NGS is a priority. Nine formalin-fixed paraffin-embedded (FFPE) DNA extraction methods were evaluated using twelve FFPE samples of varying tissue types. Quality assessment included total yield, percent ds DNA, fragment analysis and multiplex PCR. After assessment, three tissue types from four FFPE DNA methods were selected for NGS downstream evaluation, whole exome (WES) and targeted sequencing. In addition, two low input library protocols were evaluated for WES. Analysis revealed average coverage across the target regions for WES was ~20-30X for all four FFPE DNA methods. For the targeted panels, the highest molecular tag coverage was obtained with the Kingfisher FFPE extraction method. The genotype concordance was 99% for the commonly called variant positions between all four extraction methods with the targeted PCR NGS panel and 96% with WES.

molecular biology↗