Biology subjects

Chawla, P.

Publications and source records attributed to Chawla, P..

7 recordsLinked to original sources

bioRxiv2026

PDE3A-SLFN12 Molecular Glues Target Multiple KIT D816V Cell Types in Preclinical Models of Mast Cell Malignancies

A drug discovery approach was used to specifically target malignant cells with KIT D816V mutation, which is the predominant disease-causing mutation in clonal mast cell malignancies. To this end, KIT D816V cells derived from induced pluripotent stem cells (iPS cells) of KIT D816V patients were employed to screen a library of FDA approved and experimental drugs for specific killing of KIT D816V cells. We discovered the novel compound LDC 3416, which targets multiple malignant KIT D816V cell types, including hematopoietic stem/progenitor cells and mast cells. Importantly, by exploring the LDC 3416 targeting profile, we identified the phosphodiesterase 3A-Schlafen 12 (PDE3A-SLFN12) molecular glue pathway as a novel approach for specific targeting of malignant KIT D816V cells. We found that the KIT D816V mutant protein leads to increased expression of PDE3A and SLFN12 and thus confers a selective molecular vulnerability to PDE3A-SLFN12 molecular glues. Primary malignant mast cells of KIT D816V patients with indolent and advanced systemic mastocytosis also exhibit increased expression of PDE3A and SLFN12. We extended our study to include additional PDE3A-SLFN12 molecular glues and demonstrate their synergistic action with KIT D816V selective tyrosine kinase inhibitors (TKIs) in killing KIT D816V cells. Furthermore, the PDE3A-SLFN12 molecular glues also target KIT D816V megakaryocytes, a cell type that has been underestimated in malignant mast cell pathophysiology and molecular targeting. The identified molecular glues, along with their synergy with TKIs and their simultaneous targeting of multiple KIT D816V cell types, open novel treatment options for KIT D816V mast cell malignancies and other KIT D816V associated diseases.

cancer biology↗

bioRxiv2026

Pre-existing chromatin accessibility primes δ-cells for injury-induced endocrine plasticity

Adult zebrafish rapidly recover glucose homeostasis after {beta}-cell loss, but the cellular basis and regulatory mechanisms that enable this response remain unclear. Here we combine single-cell transcriptomics, single-cell chromatin accessibility profiling, paired multiome analysis and functional perturbation to define early pancreatic recovery after {beta}-cell ablation. We show that, during the first month after injury, insulin production is restored predominantly by sst1.1+ {delta}1-cells rather than by rapid reconstitution of canonical {beta}-cells. Following ablation, {delta}1-cells adopt a bihormonal hybrid state and induce metabolic, secretory and {beta}-cell-associated gene programs. Systematic comparison of chromatin accessibility across endocrine cell types reveals that these {delta}1-cells are uniquely close to {beta}-cells and exhibit open chromatin at {beta}-cell enhancers in the steady state. Moreover, hybrid-cell formation occurs without major chromatin remodeling, with {beta}-cell associated loci being already accessible in {delta}1-cells before {beta}-cell injury. A comparable permissive state is present in medaka but not in human {delta}-cells, suggesting that restricted insulin accessibility may represent a barrier to endocrine plasticity in the human pancreas. In zebrafish, {delta}1-cells also show evidence of metabolic remodeling after {beta}-cell loss, including rapid accumulation of neutral lipids. Gene regulatory network analysis and perturbation identify meis1a/b as required regulators of {delta}1 hybrid-cell formation after {beta}-cell loss in zebrafish, whereas meis1a/b are not upregulated following {beta}-cell ablation in medaka. Together, our results define pre-existing chromatin accessibility, metabolic remodeling and instructive transcriptional regulation as key features of early functional recovery after {beta}-cell loss in the adult zebrafish pancreas.

developmental biology↗

bioRxiv2026

Listeria monocytogenes prophage induction is activated by ppGpp and inhibited by c-di-AMP

Bacteriophages, particularly temperate prophages that integrate directly into the host genome, are crucial drivers of bacterial evolution and act as fundamental architects of microbial communities. Listeria monocytogenes 10403S has two phage elements - prophage {Phi}10403S and monocin element. In this study, we found that c-di-AMP, a crucial second messenger in L. monocytogenes, regulates phage production. C-di-AMP accumulation down-regulates the gene expression of prophage and monocin gene loci and inhibits phage production, both spontaneous phage production as well as under phage induction through mitomycin-C treatment. We found that in genetically heterogenous cultures, super-infection of non-lysogenic strains with phage-containing strains can significantly amplify spontaneous prophage production. Using these cultures as an induction system, we found other inducers of spontaneous phage production. We found that ppGpp accumulation and nutrient starvation acts as an inducer of the spontaneous prophage production in L. monocytogenes. H2O2 can also play a role in inducing spontaneous phage production. Moreover, {Phi}10403S prophage production is suppressed in co-cultures of L. monocytogenes 10403S with L. monocytogenes F2365 and L. innocua CLIP11262. ImportanceMost Listeria and L. monocytogenes strains are lysogens, although the impact of phage genes on bacterial host metabolism or host fitness during bacterial competition is still unexplored. Bacteriophages have been shown to influence the evolution of their host and, in several cases, have a major effect on environmental fitness, pathogenicity and/or virulence of bacterial pathogens, either by regulating expression of critical genes or encoding beneficial genes. Prophages provide their hosts with a competitive edge through lysogenic conversion-- introducing novel toxins and defense systems--while simultaneously maintaining a molecular trigger, in the form of lysogenic-to-lytic switch, capable of initiating population-wide lysis in response to environmental stress. In the human pathogen Listeria monocytogenes, these prophages are near-ubiquitous and studies by other groups have described them as critical regulators of the bacteriums SOS pathways and its pathogenic lifestyle. This study identifies important novel regulators of phage induction in Listeria monocytogenes - c-di-AMP, ppGpp and H2O2, and how phage induction and production can shape the dynamics of bacterial competition of its host.

microbiology↗

bioRxiv2025

Small molecule intervention of actin-binding protein profilin1 reduces tumor angiogenesis in renal cell carcinoma

Angiogenesis plays a key role in the development and progression of renal cell carcinoma (RCC). Actin-binding protein profilin-1 (Pfn1) is overexpressed in clear cell RCC predominantly in tumor-associated vascular endothelial cells (ECs). We previously demonstrated that that EC-selective (over)expression of Pfn1 accelerates RCC progression, and conversely, genetic loss of EC-Pfn1 dramatically inhibits tumor angiogenesis impeding tumor initiation and/or progression in RCC, suggesting that Pfn1 could be an actionable therapeutic target in RCC. In this study, we demonstrate that 4,4-((4-bromophenyl)methylene)bis(3,5-dimethyl-1H-pyrazole), a small molecule that we had previously identified as an inhibitor of Pfn1-actin interaction, directly binds to Pfn1 and attenuates tumor angiogenesis when directly administered into subcutaneous RCC tumors. Next, we undertook a chemical optimization approach to design and synthesize 4,4-((4-(trifluoromethyl)phenyl)methylene)bis(3,5-dimethyl-1H-pyrazole), a structural analog of our originally identified inhibitor, that exhibits improved anti-angiogenic efficacy in vitro and in vivo. Finally, we demonstrate that Pfn1 inhibitor is amenable to lipid microbubble encapsulation and release in the tumor microenvironment (TME) by ultrasound-mediated disruption of circulating microbubbles to achieve anti-angiogenic and anti-tumor benefit. In summary, our findings suggest that tumor-localized release of Pfn1 inhibitor could be a potential therapeutic strategy in RCC.

cell biology↗

bioRxiv2023

MRTF activity in breast cancer cells promotes osteoclastogenesis through a paracrine action of CTGF

Bone is a frequent site for breast cancer metastasis. The vast majority of breast cancer-associated metastasis is osteolytic in nature, and RANKL (receptor activator for nuclear factor {kappa}B)-induced differentiation of bone marrow-derived macrophages (BMDMs) to osteoclasts (OCLs) is a key requirement for osteolytic metastatic growth of cancer cells. In this study, we demonstrate that Myocardin-related transcription factor (MRTF) in breast cancer cells plays an important role in paracrine modulation of RANKL-induced osteoclast differentiation. This is partly attributed to MRTFs critical role in maintaining the basal cellular expression of connective tissue growth factor (CTGF), findings that align with a strong positive correlation between CTGF expression and MRTF-A gene signature in the human disease context. Luminex analyses reveal that MRTF depletion in breast cancer cells has a broad impact on OCL-regulatory cell-secreted factors that extend beyond CTGF. Experimental metastasis studies demonstrate that MRTF depletion diminishes OCL abundance and bone colonization breast cancer cells in vivo, suggesting that MRTF inhibition could be an effective strategy to diminish OCL formation and skeletal involvement in breast cancer. In summary, this study highlights a novel tumor-extrinsic function of MRTF relevant to breast cancer metastasis. SIGNIFICANCE STATEMENTO_LIMRTF, a transcriptional coactivator of SRF, is known to promote breast cancer progression through its tumor-cell-intrinsic function. Whether and how MRTF activity in tumor cells modulates other types of cells in the tumor microenvironment are not clearly understood. C_LIO_LIThis study uncovers a novel tumor-cell-extrinsic function of MRTF in breast cancer cells in promoting osteoclast differentiation partly through CTGF regulation, and further demonstrates MRTFs requirement for bone colonization of breast cancer cells in vivo. C_LIO_LIOur studies suggest that MRTF inhibition could be an effective strategy to diminish osteoclast formation and skeletal involvement in metastatic breast cancer. C_LI

cancer biology↗

bioRxiv2022

Differential representation of natural and manmade images in the human ventral visual stream

AO_SCPLOWBSTRACTC_SCPLOWThe human visual cortex processes visual stimuli hierarchically. Early visual areas (V1, V2) of the ventral visual stream feed crude visual features (like orientation and edges) into later visual areas (V4, lateral occipital (Lat Occ), inferior temporal (IT)) that then encode complex visual features (like object form). Previous studies have reported a difference in fMRI responses between natural and urban landscapes in certain parts of the brain. Here we asked if this distinction in the representation of complex natural and man-made visual stimuli extends to the ventral visual stream and if state-of-the-art convolutional neural networks (CNN) provide a map to this categorical distinction. To assess this, we used an open source fMRI data set of V1-4 and LatOcc BOLD responses to 1750 passively viewed natural and man-made grayscale images. The same images were fed into the pre-trained CORnet-S, a CNN designed to model hierarchical human visual processing layer-wise. To identify differences in representations within and between the human visual cortex and the CNN, we computed representational dissimilarity matrices. The BOLD response to the manmade and natural images shows correlation differences for the two categories, which increase across V4 and LatOcc. Such differences were also observed in the model CORnet-S for the layers V4 and IT. Our results suggest that the human visual cortex processes natural and manmade images differently starting from V4 and that this representational difference is modeled in CORnet-S. In both, categorical representation is progressively established in the later processing stages. This might indicate that the brain has perhaps developed two-distinct systems for their representations which can be directed through evolution. Further analysis may elucidate the contributory role of evolution towards this paradigm.

neuroscience↗

bioRxiv2021

A single-cell atlas of de novo β-cell regeneration reveals the contribution of hybrid β/δ cells to diabetes recovery in zebrafish

Regeneration-competent species possess the ability to reverse the progression of severe diseases by restoring the function of the damaged tissue. However, the cellular dynamics underlying this capability remain unexplored. Here, we use single-cell transcriptomics to map de novo {beta}-cell regeneration during induction and recovery from diabetes in zebrafish. We show that the zebrafish has evolved two distinct types of somatostatin-producing {delta}-cells, which we term {delta}1- and {delta}2-cells. Moreover, we characterize a small population of glucose-responsive islet cells, which share the hormones and fate-determinants of both {beta}- and {delta}1-cells. The transcriptomic analysis of {beta}-cell regeneration reveals that {beta}/{delta} hybrid cells constitute a prominent source of insulin-expression during diabetes recovery. Using in vivo calcium imaging and cell tracking, we further show that the hybrid cells form de novo and acquire glucose-responsiveness in the course of regeneration. The overexpression of dkk3, a gene enriched in hybrid cells, increases their formation in the absence of {beta}-cell injury. Finally, interspecies comparison shows that plastic {delta}1-cells are partially related to PP-cells in the human pancreas. Our work provides an atlas of {beta}-cell regeneration and indicates that the rapid formation of glucose-responsive hybrid cells contributes to the resolution of diabetes in zebrafish

developmental biology↗