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Biology subjects

Mallick, M.

Publications and source records attributed to Mallick, M..

6 recordsLinked to original sources

Polyphosphate synthesis in mast cell granules relies on V-ATPase activity supported by IP6K1

Polyphosphate (polyP), a linear polymer of orthophosphate residues, is enriched in secretory granules in specialised mammalian cell types including platelets and mast cells. Although polyP released during activation and degranulation of these cells has been shown to promote blood clotting and inflammation, little is known about the mechanisms governing polyP synthesis in these granules. In mice, the loss of IP6K1, an enzyme that catalyses the production of 5-InsP7, has been shown to result in depletion of platelet polyP and impaired hemostasis. Here, we use the rat mast cell line RBL-2H3 as a model to study the regulation of polyP synthesis in secretory granules. By monitoring real-time polyP synthesis in isolated mast cell granules, we demonstrate that ATP is the substrate fuelling granule polyP production. By the use of inhibitors, we show that accumulation of polyP in granules requires an intact transmembrane proton gradient maintained by vacuolar H+ATPase (V-ATPase). In RBL-2H3 cells, depletion of IP6K1 led to a substantial reduction in cellular polyP levels and defective accumulation of polyP, serotonin, and tryptase inside granules. Cells with reduced IP6K1 showed a profound loss of granule acidification, correlating with downregulated levels of V1 subunits of V-ATPase. Adding back active or catalytically inactive IP6K1 rescued the expression of V-ATPase V1 subunits, reversed granule deacidification, and restored polyP levels in IP6K1-depleted cells. Together, these data unveil a role for IP6K1 in maintaining granule pH and thereby supporting polyP synthesis in mammals.

biochemistry↗

Workload-induced changes to cell state contribute to β-cell failure in diabetes

Insufficient insulin secretion relative to insulin demand is a key feature of type 2 diabetes (T2D). While the defects of insulin-producing {beta}-cells in T2D are well defined, little is known about how {beta}-cells progress from the functionally normal state to the decompensated state during the natural history of this disease. Here, we provide evidence that workload-induced {beta}-cell overstimulation precipitates {beta}-cell failure in T2D. We employ scRNA-seq to define workload-induced changes to {beta}-cell transcriptional states, identifying a novel compensating state that is distinct from the stressed state of decompensated {beta}-cells. We demonstrate a key role for the chromatin-modifying enzyme Lysine-specific demethylase 1 (Lsd1) in restraining workload-induced {beta}-cell state transitions, indicating epigenomic control of {beta}-cell state. Experimental manipulations that promote the compensating state accelerate {beta}-cell failure in mouse models of diabetes. Altogether, these findings show that the compensatory response of the {beta}-cell to increased workload becomes maladaptive over time and contributes to the pathogenesis of T2D.

physiology↗

FRAPPe - a novel FRET-based biosensor to detect inorganic polyphosphates

Inorganic polyphosphate (polyP), a linear polymer of orthophosphate residues, is involved in a range of cellular processes, including phosphate storage, blood clotting, chromatin remodeling, RNA processing, and mitochondrial function. Despite its significance, tools for monitoring polyP with specificity and in real time are lacking, limiting insights into its dynamics. Here, we present FRAPPe (FRET-based Ratiometric Analysis of Polyphosphate), a FRET-based sensor for polyP. FRAPPe consists of an eCFP-eYFP FRET pair flanking CHAD, a polyP-binding domain. The sensor remains unresponsive to nucleic acids and other polyanions, while polyP binding induces a significant decrease in FRET, allowing quantitative estimation of polyP. We further show that FRAPPe can qualitatively estimate polyP levels from crude cell extracts, supporting its utility in high-throughput genetic and pharmacological screens to identify regulators of polyP metabolism and signaling.

biochemistry↗

Functional implications of the interaction of the SARS-CoV-2 Nucleocapsid protein with factors involved in nonsense-mediated mRNA decay

The RNA genome of the SARS-CoV-2 virus encodes for four structural proteins, 16 non- structural proteins and nine putative accessory factors. A high throughput analysis of interactions between human and SARS-CoV-2 proteins identified multiple interactions of the structural Nucleocapsid (N) protein with RNA processing factors. The N-protein, which is responsible for packaging of the viral genomic RNA was found to interact with two RNA helicases, UPF1 and MOV10 that are involved in nonsense-mediated mRNA decay (NMD). Using a combination of biochemical and biophysical methods, we investigated the interaction of the SARS-CoV-2 N-protein with NMD factors at a molecular level. Our studies led us to identify the core NMD factor, UPF2, as an interactor of N. The viral N-protein engages UPF2 in multipartite interactions and can negate the stimulatory effect of UPF2 on UPF1 catalytic activity. N also inhibits UPF1 ATPase and unwinding activities by competing in binding to the RNA substrate. We further investigate the functional implications of inhibition of UPF1 catalytic activity by N in mammalian cells. The interplay of SARS-CoV-2 N with human UPF1 and UPF2 does not affect decay of host cell NMD targets but might play a role in stabilizing the viral RNA genome.

biochemistry↗

Integration of single-cell multiomic measurements across disease states with genetics identifies mechanisms of beta cell dysfunction in type 2 diabetes

Altered function and gene regulation of pancreatic islet beta cells is a hallmark of type 2 diabetes (T2D), but a comprehensive understanding of mechanisms driving T2D is still missing. Here we integrate information from measurements of chromatin activity, gene expression and function in single beta cells with genetic association data to identify disease-causal gene regulatory changes in T2D. Using machine learning on chromatin accessibility data from 34 non-diabetic, pre-T2D and T2D donors, we robustly identify two transcriptionally and functionally distinct beta cell subtypes that undergo an abundance shift in T2D. Subtype-defining active chromatin is enriched for T2D risk variants, suggesting a causal contribution of subtype identity to T2D. Both subtypes exhibit activation of a stress-response transcriptional program and functional impairment in T2D, which is likely induced by the T2D-associated metabolic environment. Our findings demonstrate the power of multimodal single-cell measurements combined with machine learning for identifying mechanisms of complex diseases.

systems biology↗

Engineered vasculature induces functional maturation of pluripotent stem cell-derived islet organoids

Blood vessels play a critical role in pancreatic islet health and function, yet current culture methods to generate islet organoids from human pluripotent stem cells (SC-islets) lack a vascular component. Here, we engineered 3D vascularized SC-islet organoids by assembling SC-islet cells, human primary endothelial cells (ECs) and fibroblasts both in a non-perfused model and a microfluidic device with perfused vessels. Vasculature improved stimulus-dependent Ca2+ influx into SC-{beta}-cells, a hallmark of {beta}-cell function that is blunted in non-vascularized SC-islets. We show that an islet-like basement membrane is formed by vasculature and contributes to the functional improvement of SC-{beta}-cells. Furthermore, cell-cell communication networks based on scRNA-seq data predicted BMP2/4-BMPR2 signaling from ECs to SC-{beta}-cells. Correspondingly, BMP4 augmented the SC-{beta}-cell Ca2+ response and insulin secretion. These vascularized SC-islet models will enable further studies of crosstalk between {beta}-cells and ECs and can serve as in vivo-mimicking platforms for disease modeling and therapeutic testing.

cell biology↗