Biology subjects

Mondal, P.

Publications and source records attributed to Mondal, P..

13 recordsLinked to original sources

bioRxiv2026

Rapid optogenetic manipulation of autophagy reveals that the nuclear pore complex is a robust autophagy substrate

Autophagy, a conserved recycling process, manages intracellular quality control to mitigate stress. To determine the rapid effects of autophagy perturbation, we developed the first optogenetic tool to rapidly inhibit autophagy, termed ASAP. Our approach leverages light-induced proteolytic cleavage to selectively inhibit autophagy within 5 minutes of light exposure, providing a precise and dynamic approach to study autophagy regulation. Proteomic profiling with ASAP revealed the most tightly regulated autophagy substrates along with novel, previously unidentified substrates, including nuclear pore complex (NPC) proteins. Interestingly, autophagy regulates quality control of cytoplasmic complexes of nucleoporins via specific LC3-interacting regions (LIRs), sparing nuclear pore complex proteins embedded in the nuclear envelope. Upon rapid autophagy inhibition, incomplete nucleoporin complexes accumulate and instead of undergoing autophagic degradation, cytoplasmic nucleoporin complexes aggregate in processing bodies (P bodies). Using ASAP, we demonstrate rapid and specific inhibition of autophagy, revealing that nuclear pore complex proteins are tightly regulated autophagy substrates.

cell biology↗

bioRxiv2025

Leveraging autophagy and pyrimidine metabolism to target pancreatic cancer

Autophagy inhibitors are promising compounds to treat pancreatic ductal adenocarcinoma (PDA) but their efficacy in patients is unclear, highlighting a need to understand mechanisms of resistance. We used a novel approach to uncover metabolic adaptations that bypass autophagy inhibition. Utilizing PDA cells with acquired resistance to different autophagy inhibitors, we found that severe autophagy depletion induces metabolic rewiring to sustain TCA intermediates and nucleotides for biosynthesis. Long-term autophagy inhibition results in altered pyruvate metabolism likely regulated by lower pyrimidine pools. Cells adapting to loss of autophagy preferentially salvage pyrimidines to replenish these pools instead of synthesizing them de novo. Exploiting this metabolic vulnerability, we found that acquired resistance to autophagy inhibition promotes increased salvage and therefore sensitivity to pyrimidine analogues, including gemcitabine and trifluridine/tipiracil leading to combinatory effects with autophagy inhibitors and pyrimidine analogs. These studies provide mechanistic insight defining how autophagy inhibition can be leveraged to treat pancreatic cancer.

cancer biology↗

bioRxiv2024

Frataxin deficiency in the astrocytes drives neurocognitive impairment in sickle cell disease mice

Individuals with sickle cell disease (SCD) suffer from a high burden of cerebrovascular lesions and cognitive impairment that vastly impact quality of life. Cerebrovascular lesions are characterized by microstructural neuroaxonal damage, but their pathogenesis has not been fully elucidated. Herein, we report that SCD mice (SS) have reduced expression of frataxin (FXN), a mitochondrial protein, in their astrocytes compared to control (AA) mice. Next, we generated chimeric mice with SS bone marrow and astrocyte-specific deletion of FXN (SSFXN-KO). Ex-vivo diffusion tensor magnetic resonance imaging and immunohistopathology of the brain showed that the SSFXN-KO mice have increased white matter neuroaxonal damage compared to the SS bone marrow chimera mice with wild-type FXN expression (SSFXN-WT). The SSFXN-KO mice also displayed poorer cognitive function as measured by the functional Y-maze and novel object recognition tests. Pharmacological induction of FXN by administration of insulin growth factor-1 improved cognitive function in the SSFXN-KO mice. Overall, our data demonstrate that FXN is a critical factor regulating neuroaxonal health and cognitive function in SCD mice. FXN may therefore be a novel pharmacologic target to prevent cerebrovascular complications in SCD.

neuroscience↗

bioRxiv2024

Transcriptional Characterization of Resistance in Early Drug Response

Therapeutic resistance is a major cause of cancer treatment failure, with increasing evidence suggesting a non-genetic basis. This non-genetic resistance is often due to drug-resistant transcriptional cell states, either induced by treatment or pre-existing in some cells. However, the connection between early cellular drug response and long-term resistance is poorly understood. Moreover, it is unknown whether resistance-associated early transcriptional responses are evolutionarily conserved. Integrating long-term drug resistance and early drug response data across multiple cancer cell lines, bacteria, and yeast, our findings indicate that cancer states in drug-naive populations and shortly after treatment share transcriptional properties with fully resistant populations, some of which are evolutionarily conserved. CRISPR-Cas9 knockout of resistant states markers increased sensitivity to Prexasertib in ovarian cancer cells. Finally, early resistant state signatures discriminated therapy responders from non-responders across multiple human cancer trials, and distinguished premalignant breast lesions that progress to malignancy from those that do not.

cancer biology↗

bioRxiv2024

Structural basis for CCR6 modulation by allosteric antagonists

The CC chemokine receptor 6 (CCR6) is a potential target for chronic inflammatory diseases such as psoriasis and inflammatory bowel disease. Previously, we reported an active CCR6 structure in complex with its cognate chemokine CCL20, revealing the molecular basis of CCR6 activation mediated by CCL20. Here, we present two inactive CCR6 structures determined by cryo-EM in ternary complexes with different allosteric antagonists, CCR6/SQA1/OXM1 and CCR6/SQA1/OXM2. OXM1 and OXM2 are oxomorpholine (OXM) analogues which are highly selective for CCR6 and disrupt the molecular network critical for receptor activation by binding to an extracellular allosteric pocket within the transmembrane domain. A U-shaped conformation stabilized by intramolecular interactions was revealed by structural and NMR studies of active OXM analogues. SQA1 is a squaramide (SQA) derivative with close-in analogues that were previously reported to be antagonists of CCR6 and other chemokine receptors. Our structures reveal an intracellular pocket occupied by SQA1 that overlaps with the G protein binding site. In addition, SQA1 stabilizes a closed conformation of the intracellular pocket, a hallmark of the inactive state of GPCRs. Minimal communication was found between the two allosteric pockets. Overall, our work provides new evidence of the versatility of GPCR antagonism by small molecules, complementing previous knowledge on CCR6 activation, and sheds light on drug discovery approaches to target CCR6 for autoimmune disorders.

biochemistry↗

bioRxiv2024

A whole-genome CRISPR screen identifies the spindle accessory checkpoint as a locus of nab-paclitaxel resistance in pancreatic cancer cells

Pancreatic adenocarcinoma is one of the most aggressive and lethal forms of cancer. Chemotherapy is the primary treatment for pancreatic cancer, but resistance to the drugs used remains a major challenge. A genome-wide CRISPR interference and knockout screen in the PANC-1 cell line with the drug nab-paclitaxel has identified a group of spindle assembly checkpoint (SAC) genes that enhance survival in nab-paclitaxel. Knockdown of these SAC genes (BUB1B, BUB3, and TTK) attenuates paclitaxel-induced cell death. Cells treated with the small molecule inhibitors BAY 1217389 or MPI 0479605, targeting the threonine tyrosine kinase (TTK), also enhance survival in paclitaxel. Overexpression of these SAC genes does not affect sensitivity to paclitaxel. These discoveries have helped to elucidate the mechanisms behind paclitaxel cytotoxicity. The outcomes of this investigation may pave the way for a deeper comprehension of the diverse responses of pancreatic cancer to therapies including paclitaxel. Additionally, they could facilitate the formulation of novel treatment approaches for pancreatic cancer.

cancer biology↗

bioRxiv2024

Development of non-sedating antischistosomal benzodiazepines

The neglected tropical disease schistosomiasis infects over 200 million people worldwide and is treated with just one broad spectrum antiparasitic drug (praziquantel). Alternative drugs are needed in the event of emerging praziquantel resistance or treatment failure. One promising lead that has shown efficacy in animal models and a human clinical trial is the benzodiazepine meclonazepam, discovered by Roche in the 1970s. Meclonazepam was not brought to market because of dose-limiting sedative side effects. However, the human target of meclonazepam that causes sedation (GABAARs) are not orthologous to the parasite targets that cause worm death. Therefore, we were interested in whether the structure of meclonazepam could be modified to produce antiparasitic benzodiazepines that do not cause host sedation. We synthesized 18 meclonazepam derivatives with modifications at different positions on the benzodiazepine ring system and tested them for in vitro antiparasitic activity. This identified five compounds that progressed to in vivo screening in a murine model, two of which cured parasite infections with comparable potency to meclonazepam. When these two compounds were administered to mice that were run on the rotarod test, both were less sedating than meclonazepam. These findings demonstrate the proof of concept that meclonazepam analogs can be designed with an improved therapeutic index, and point to the C3 position of the benzodiazepine ring system as a logical site for further structure-activity exploration to further optimize this chemical series.

pharmacology and toxicology↗

bioRxiv2023

Molecular basis of VEGFR1 autoinhibition at the plasma membrane

Ligand-independent activation of VEGFR is a hallmark in diabetes and several cancers. Like most RTKs, the VEGFR2, the primary VEGF receptor, is activated spontaneously at higher receptor concentrations. An exception is VEGFR1, which remains constitutively inactive in the basal state. Ligand stimulation transiently phosphorylates VEGFR1 and induces weak kinase activation in endothelial cells. Recent studies, however, suggest that VEGFR1 signaling is indispensable in regulating various physiological or pathological events, which is puzzling. Why VEGFR1 is differentially regulated is an open question. Here we elucidate a mechanism of juxtamembrane inhibition that shifts the equilibrium more to the inactive state, rendering VEGFR1 an inefficient kinase. Our data suggest that a combination of tyrosine phosphatase activity and JM inhibition suppress the basal phosphorylation of VEGFR1. We conclude that a subtle imbalance in phosphatase activation or removing juxtamembrane inhibition is sufficient to induce basal activation of VEGFR1 and remodel tyrosine phosphorylation to be sustained.

biochemistry↗

bioRxiv2023

Cbl and Cbl-b Ubiquitin Ligases are Essential for Intestinal Epithelial Stem Cell Maintenance

Among the signaling pathways that control the stem cell self-renewal and maintenance vs. acquisition of differentiated cell fates, those mediated by receptor tyrosine kinase (RTK) activation are well established as key players. CBL family ubiquitin ligases are negative regulators of RTKs but their physiological roles in regulating stem cell behaviors are unclear. While hematopoietic Cbl/Cblb knockout (KO) leads to a myeloproliferative disease due to expansion and reduced quiescence of hematopoietic stem cells, mammary epithelial KO led to stunted mammary gland development due to mammary stem cell depletion. Here, we examined the impact of inducible Cbl/Cblb double-KO (iDKO) selectively in the Lgr5-defined intestinal stem cell (ISC) compartment. Cbl/Cblb iDKO led to rapid loss of the Lgr5Hi ISC pool with a concomitant transient expansion of the Lgr5Lo transit amplifying population. LacZ reporter-based lineage tracing showed increased ISC commitment to differentiation, with propensity towards enterocyte and goblet cell fate at the expense of Paneth cells. Functionally, Cbl/Cblb iDKO impaired the recovery from radiation-induced intestinal epithelial injury. In vitro, Cbl/Cblb iDKO led to inability to maintain intestinal organoids. Single cell RNAseq analysis of organoids revealed Akt-mTOR pathway hyperactivation in iDKO ISCs and progeny cells, and pharmacological inhibition of the Akt-mTOR axis rescued the organoid maintenance and propagation defects. Our results demonstrate a requirement for Cbl/Cblb in the maintenance of ISCs by fine tuning the Akt-mTOR axis to balance stem cell maintenance vs. commitment to differentiation.

cell biology↗

bioRxiv2023

Reversal of drug resistance by disruption of a Gain-of-Function mutant p53 and transcriptional co-activator PC4 interaction

The positive coactivator 4 or PC4 is a chromatin-associated protein whose role in gene regulation by wild-type p53 is now well-known. During tumorigenesis, p53 is often mutated resulting in its loss of function. A sub-class of these mutants gain new pro-proliferation properties which occur largely due to the upregulation of many pro-proliferation genes. Little is known about the roles of PC4 in tumor cells bearing mutant p53 genes. In this article, we show that PC4 associates with one of the tumor-associated gain-of-function p53 mutants, R273H. This association drives its recruitment to two promoters, UBE2C, and MDR1, known to be responsible for imparting aggressive growth and resistance to many drugs. A previously reported peptide that disrupts PC4-wild-type p53 interaction also disrupts the PC4-R273Hp53 protein-protein interaction. The introduction of this peptide to tumor cells bearing the R273HTP53 gene resulted in a lowering of MDR1 expression and abrogation of drug resistance. Interestingly, cells bearing another gain-of-function mutant R248W do not show the same type of response, suggesting that the action of PC4 on mutant p53s may differ for different GOF mutants. The results presented here suggest that PC4-R273H interaction may be a promising target for reducing proliferation and tumor drug resistance.

molecular biology↗

bioRxiv2022

Arsenic induced alteration of neuroregulatory gene expression in Macrobrachium lamarrei: a neurotoxicological approach to grooming behaviour

Arsenic is a highly active neuromodulator which can induce neurological disorders in invertebrates. The present study is a neurotoxicological approach to assess the toxicity of arsenic trioxide, where grooming behaviour is considered as a behavioural biomarker of arsenic induced stress in the prawns. Non-lethal exposure to arsenic trioxide, manipulates the expression pattern of neuroregulatory marker genes in a freshwater prawn, Macrobrachium lamarrei and induces symptoms of autism spectrum disorders (ASDs) in a short time.

pharmacology and toxicology↗

bioRxiv2019

Hyperinsulinemia promotes HMGB1 release leading to inflammation induced systemic insulin resistance: An interplay between pancreatic beta-cell and peripheral organs

Insulin resistance results from several pathophysiologic mechanisms, including chronic tissue inflammation and defective insulin signaling. Pancreatic {beta}-cells hypersecretion (hyperinsulinemia), is a central hallmark of peripheral insulin resistance. However, the underlying mechanism by which hyperinsulinemia perpetuates towards the development of insulin resistance remains unclear and is still a bigger therapeutic challenge. Here, we found hyperinsulinemia triggers inflammation and insulin resistance by stimulating TLR4-driven inflammatory cascades. We show that hyperinsulinemia activates the TLR4 signaling through HMGB1, an endogenous TLR4 ligand emanating from hyperinsulinemia exposed immune cells and peripheral organs like adipose tissue and liver. Further, our observation suggests hyperinsulinemia ensuring hyperacetylation, nuclear-to-cytoplasmic shuttling and release of HMGB1 into the extracellular space. HMGB1 was also found to be elevated in serum of T2DM patients. We found that extracellular HMGB1 plays a crucial role to promote proinflammatory responses and provokes systemic insulin resistance. Importantly, in-vitro and in-vivo treatment with naltrexone, a TLR4 antagonist led to an anti-inflammatory phenotype with protection from hyperinsulinemia mediated insulin resistance. In-vitro treatment with naltrexone directly enhanced SIRT1 activity, blocked the release of HMGB1 into extracellular milieu, suppressed release of proinflammatory cytokines and ultimately led to insulin-sensitizing effects. These observations elucidate a regulatory network between pancreatic {beta}-cells, macrophage and hepatocytes and assign an unexpected role of TLR4 - HMGB1 signaling axis in hyperinsulinemia mediated systemic insulin resistance.\n\nGraphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

physiology↗

bioRxiv2019

Repurposing protein degradation for optogenetic modulation of protein activities

Non-neuronal optogenetic approaches empower precise regulation of protein dynamics in live cells but often require target-specific protein engineering. To address this challenge, we developed a generalizable light modulated protein stabilization system (GLIMPSe) to control intracellular protein level independent of its functionality. We applied GLIMPSe to control two distinct classes of proteins: mitogen-activated protein kinase phosphatase 3 (MKP3), a negative regulator of the extracellular signal-regulated kinase (ERK) pathway, as well as a constitutively active form of MEK (CA MEK), a positive regulator of the same pathway. Kinetics study showed that light-induced protein stabilization could be achieved within 1 minute of blue light stimulation. GLIMPSe enables target-independent optogenetic control of protein activities and therefore minimizes the systematic variation embedded within different photoactivatable proteins. Overall, GLIMPSe promises to achieve light-mediated post-translational stabilization of a wide array of target proteins in live cells.

bioengineering↗