Department of Biological Sciences
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Item Cisplatin-induced oxidative stress regulates YAP to modulate epigenome promoting survival of osteosarcoma cells(2025-08) Chowdhury, Rajdeep; Chowdhury, Shibasish; Mukherjee, SudeshnaThe widely used chemotherapeutic drug cisplatin (CDDP) is an integral part of the pre-operative chemotherapy protocol for high-grade osteosarcoma (OS). However, despite an aggressive treatment regimen, drug refractoriness is a major hindrance to successful therapy. We previously identified key transcriptomic alterations essential for the survival of OS cells following CDDP exposure. In the present study, we further demonstrate that CDDP treatment resulted in a ROS-dependent enrichment of the repressive histone mark H3K27me3 at the upstream promoter regions of growth-promoting genes such as CCNA2, and on the promoter of the negative regulator of Yes-Associated Protein (YAP)-LATS1, thereby contributing to their transcriptional repression. This was associated with a growth arrest, and quenching of ROS with N-acetyl cysteine (NAC) reversed it. Importantly, repression of LATS1 led to an increased nuclear localization of YAP, while pharmacological or genetic ablation of YAP reduced CDDP-mediated induction of repressive marks. YAP was further found to co-localize and co-immunoprecipitate with the Polycomb Repressive Complex 2 (PRC2) catalytic member-the histone methyl transferase-EZH2, indicating its putative role in mediating transcriptional repression. In lieu of the above, inhibition of YAP or reversal of the repressive chromatin state using a histone deacetylase (HDAC) inhibitor sensitized OS cells to a low-dose CDDP treatment as well. Overall, the present study demonstrates an interplay between oxidative stress, epigenetics, and YAP in modulating OS cell fate post CDDP exposure.Item LncRNA YIYA enhances pancreatic cancer proliferation under high-glucose conditions through RAS–PKM2–mediated metabolic reprogramming that reinforces the Warburg phenotype(2025) Mukherjee, Sudeshna; Chowdhury, RajdeepDiabetes and the resulting hyperglycemia are metabolic complications frequently linked to pancreatic cancer (PC). In this study, we observe that the long non-coding RNA (lncRNA)-YIYA, which resides in a genomic region (1q32), frequently altered in various cancers, is overexpressed under conditions of chronic or intermittent high glucose (HG; 25 mM) compared to normal glucose (NG; 5.5 mM) in pancreatic ductal adenocarcinoma (PDAC) cells. It plays a pivotal role in regulating cellular metabolism-linked proliferation of PDAC cells, both under 2D and 3D conditions. Analysis of clinical datasets suggested that patients with elevated YIYA expression generally experience reduced survival in pancreatic cancer. Mechanistically, YIYA was found to regulate cellular energy metabolism and promote a Warburg phenotype, thereby facilitating the rapid proliferative status of PDAC cells. YIYA-mediated effects were found to be dependent on KRAS. Interestingly, the RIP assay revealed that YIYA interacts not only with KRAS but also with an important enzyme catalyzing the final step of the biochemical process, glycolysis, pyruvate kinase M2 (PKM2). YIYA was found to be predominantly localised in the cytoplasm, protecting the stability of the KRAS protein under a hyperglycaemic state. Importantly, YIYA knockdown enhanced autophagy-mediated degradation of KRAS. Our study is the first to identify YIYA as a glucose-responsive lncRNA in PDAC cells, and to reveal a novel YIYA-mediated connection between oncogenic KRAS signalling and metabolic reprogramming. Targeting YIYA represents a promising therapeutic strategy by disrupting the KRAS–PKM2–Warburg axis, thereby sensitizing PDAC cells.Item PGC1-α drives MFN2-linked mitochondrial fusion aiding glioblastoma cell survival under TMZ stress(Elsevier, 2026-01) Chowdhury, Rajdeep; Mukherjee, SudeshnaGlioblastoma Multiforme (GBM) is an extremely aggressive primary brain-tumor with a median-survival rate of <2 years. Higher risk in surgery has shifted the treatment paradigm towards combined chemotherapies. Interestingly, arduous dependency on chemotherapy has shown recurrence. Recent studies have portrayed the role of mitochondrial dynamics for survival under drug-pressure leading to recurrence. However, such studies exploring the role of mitochondria in response to drug stress in GBM are limited. Here we show that PGC1α (Peroxisome Proliferator-activated Receptor Gamma coactivator-1 Alpha) upregulates Mfn2 (Mitofusin 2) enhancing mitochondrial-fusion in GBM cells contributing to survival under profound Temozolomide (TMZ) stress. The interaction of PGC1α with SET1 compass / compass-like complex induces H3K4me3 trimethylations at the promoter regions of Mfn2 leading to an open chromatin assisting Mfn2 upregulation. The latter is further involved in inducing mitochondrial fusion, promoting oxidative phosphorylation which supports cell survival under stress. Notably, this further corroborates with our observations in the patient samples and clinical data where upregulation of Mfn2 was concurrently observed with elevated levels of PGC1α simultaneously leading to poor prognosis. Thus, this study provides critical insights into the molecular regulation of mitochondrial dynamics-dependent survival mechanisms in GBM that could further be exploited to design future therapies.Item A switch from histone methyltransferase-EZH2 to demethylase KDM6A activity marks reinitiation of proliferation in cisplatin treated colorectal cancer cells(Elsevier, 2026-01) Chowdhury, Shibasish; Mukherjee, Sudeshna; Chowdhury, RajdeepColorectal cancer (CRC) is one of the deadliest cancers, ranking third in cancer incidence worldwide. These tumor cells often adopt unique strategies under chemotherapeutic stress to attain a reversible drug-tolerant state and evade cell death. However, the molecular adaptations associated with this transitory emergence of the drug-tolerant state remain elusive. Herein, epigenetic alterations often dictate such reversible dynamic changes, and this study aims to characterize the role of specific epigenetic modifiers governing CRC cell survival under cisplatin exposure and their subsequent relapse. We observed that under cisplatin-stress there is a drastic increase in the histone-repressive mark-H3K27me3, linked to an enhanced expression of EZH2, driving transcriptional inhibition of cell proliferation-associated genes and a proliferative arrest. Interestingly, cisplatin-induced oxidative stress increased the expression of P65 protein, which was found to interact with and regulate EZH2 expression. Quenching of ROS, cisplatin-rescue, or P65 inactivation compromised EZH2 activity, concurrent with a re-initiation of cell proliferation. Interestingly, this reversal to proliferative state was associated with an elevated activity of the histone lysine demethylase-KDM6A. The promoter elements of the proliferative genes were now occupied by KDM6A instead of EZH2. Accordingly, a genetic knockdown or pharmacological inhibition of KDM6A in vitro not only resulted in increased cell death but also prevented emergence of the re-proliferative CRC cells. Furthermore, KDM6A inhibition in combination with cisplatin, resulted in an increased tumor regression in vivo. Our study thus highlights the importance of KDM6A as a therapeutic target in preventing CRC growth and relapse which can have future therapeutic implications.Item DRP1-mediated mitochondrial dynamics orchestrate EMT in glioblastoma cells(2025-12) Chowdhury, Shibasish; Chowdhury, Rajdeep; Mukherjee, SudeshnaEpithelial to mesenchymal transition (EMT), a differentiation process, frequently imparts invasive properties in Glioblastoma Multiforme (GBM), which leads to a poor prognosis. Cells lose apical-basal polarity, cell-cell connections, and/or chemo-resistance during EMT, which can result in the spread of cancer and the acquisition of additional stem cell-like traits. It is unclear how organelle dynamics influence EMT in this respect. The interaction between cytoskeletal and mitochondrial regulators governing GBM cell EMT is explored in this article.Item Repurposing of CNS accumulating drugs Gemfibrozil and Doxylamine for enhanced sensitization of glioblastoma cells through modulation of autophagy(Springer Nature, 2025-07) Mukherjee, Sudeshna; Chowdhury, Rajdeep; Majumder, Syamantak; Chowdhury, Shibasish; Roy, AniruddhaGBM is one of the most aggressive malignancies, having the greatest fatality rate and average life years lost. The current standard medicine, temozolomide (TMZ), is ineffective, requiring the development of new treatments. However, identifying and introducing a novel medicine takes time and money. In this context, repurposing FDA-approved drugs can be a novel yet efficient alternative method. Here, we, therefore, investigated the differential expression signatures of genes of patients suffering from GBM from publicly available GEO datasets and constructed a connectivity map. Functional annotation and KEGG pathway analysis showed dysregulated molecular activities and pathways. Based on their gene ontologies, putative key genes and hub genes linked with the disease were identified, and the C-MAP database was scanned for FDA-approved medicinal compounds that could alter hub gene expression or associated pathways. Our in-silico investigation showed that Gemfibrozil (Gem) and Doxylamine (Doxy) might reverse GBM disease patterns by deregulating GBM-related genes. Evaluation of the GBM inhibitory potential of these drugs through in-vitro and three-dimensional spheroid assay showed promising results. These drugs were more cytotoxic than TMZ; however, they synergised with TMZ as well. Interestingly, the cellular homeostatic process autophagy which has been implicated significantly in GBM pathogenesis and therapy resistance, was found to be inhibited by the drugs Gemfibrozil and Doxylamine, signifying their prospective potential. Therefore, in this study, we, for the first time, identify drugs with the ability to cross the blood brain barrier (BBB), with potential cytotoxic effects beyond TMZ, and with autophagy inhibitory potential, which can be further explored for repurposing against GBM.Item Chloroquine attenuates hypoxia-mediated autophagy to curb thrombosis- an ex vivo and in vivo study(2024-04) Mukherjee, Sudeshna; Majumder, Syamantak; Chowdhury, Shibasish; Chowdhury, RajdeepHypoxia can trigger the activation of blood platelets, leading to thrombosis. If not addressed clinically, it can cause severe complications and fatal consequences as well. The current treatment regime for thrombosis is often palliative and includes long-term administration of anticoagulants, which has the risk of over-bleeding in injury and other secondary effects as well. This demands a deeper understanding of the process and exploration of an alternative therapeutic avenue. Interestingly, recent studies demonstrate that platelets though atypical and enucleated, possess components of autophagy machinery. This cellular homeostatic process though well-studied in non-platelet cells, is under-explored in platelets.Item Metal-free, visible-light-mediated synthesis of tetracyclic benzimidazole: regioselective c–h functionalization with in vitro and computational study of anti-breast cancer compounds(ACS, 2025-02) Murugesan, Sankaranarayanan; Mukherjee, SudeshnaGlobally, breast cancer is the leading cause of mortality. Within the field of antibreast cancer drug design by several compound docking studies, eight new N-containing nonsteroid tetracyclic derivatives have been synthesized via regioselective intramolecular C–H functionalization by visible light. The adopted methodology is highly efficient, green, and sustainable to unload a new pathway with excellent yield. It offers a rapid, low-cost, catalyst-free method for creating physiologically active molecules from easily accessible substrates. The synthesized substances were described using spectroscopic methods like HRMS, 1HNMR, 13CNMR, and XRD analysis. This study explores the cytotoxic potential of novel compounds against human MCF-7 breast cancer cells. This study includes in vitro experiments to assess the effect of our compounds on cells. These experiments include cytotoxicity assessment by cell cycle, apoptosis, MTT test analysis by flow cytometry, reactive oxygen species (ROS) production assessment, etc. Among the novel compounds, compound 2e exhibited the most potent cytotoxic activity, with an inhibitory concentration (IC50) of 40 nM, surpassing the efficacy of established drugs such as exemestane (IC50 24.97 micromolar) and tamoxifen (IC50 5.45 μM). Compound 2e also significantly induced apoptosis and cell cycle arrest in the G1 phase, increasing the apoptotic cell population to 65.97%. Additionally, the compound led to a marked rise in the level of ROS generation, implicating oxidative stress in its mechanism of action. Molecular docking and dynamic simulation further supported the vigorous anticancer activity of compound 2e, demonstrating its promise as an effective breast cancer treatment.Item LncRNA HULC augments high glucose-associated pancreatic cancer progression and drug resistance by enhancing YAP activity and autophagy(Wiley, 2024-07) Mukherjee, Sudeshna; Chowdhury, Shibasish; Chowdhury, RajdeepBackground Information: One of the confounding factors in pancreatic cancer (PC) pathogenesis is hyperglycemia. The molecular mechanism by which high glucose (HG) influences PC severity is poorly understood. Our investigation delved into the impact of lncRNA highly upregulated in liver cancer (HULC) and its interaction with yes-associated protein (YAP) in regulating the fate of pancreatic ductal adenocarcinoma cells (PDAC) under HG-induced conditions. PDAC cells were cultured under normal or HG conditions. We thereafter measured the effect of HG on the viability of PDAC cells, their migration potential and drug resistance properties. The lncRNAs putatively dysregulated in PC and diabetes were shortlisted by bioinformatics analysis followed by wet lab validation of function. Results: HG led to enhanced proliferation and drug refractoriness in PDAC cells. HULC was identified as one of the major deregulated lncRNAs following bioinformatics analysis. HULC was found to regulate the expression of the potent transcriptional regulator – YAP through selective histone modifications at the YAP promoter. siRNA-mediated ablation of HULC resulted in a concurrent decrease in YAP transcriptional activity. Importantly, HULC and YAP were found to co-operatively regulate the cellular homeostatic process autophagy, thus inculcating drug resistance and proliferative potential in PDAC cells. Moreover, inhibition of autophagy or YAP led to a decrease in HULC levels, suggesting the existence of an inter-regulatory feedback loop. Conclusions: We observed that HG triggers aggressive properties in PDAC cells. Mechanistically, up-regulation of lncRNA HULC resulted in activation of YAP and differential regulation of autophagy coupled to increased proliferation of PDAC cells. Significance: Inhibition of HULC and YAP may represent a novel therapeutic strategy for PDAC. Furthermore, this study portrays the intricate molecular interplay between HULC, YAP and autophagy in PDAC pathogenesisItem Inhibition of autophagy in platelets as a therapeutic strategy preventing hypoxia induced thrombosis(Springer Nature, 2025-02) Mukherjee, Sudeshna; Majumder, Syamantak; Chowdhury, Shibasish; Chowdhury, RajdeepHypoxia triggers activation of platelets, leading to thrombosis. If not addressed clinically, it can cause severe complications and fatal consequences. The current treatment regime for thrombosis is often palliative and include long-term administration of anticoagulants, causing over-bleeding risk and other secondary effects as well. This demands a molecular understanding of the process and exploration of an alternative therapeutic avenue. Interestingly, recent studies demonstrate that platelets exhibit functional autophagy. This cellular homeostatic process though well-studied in non-platelet cells, is under-explored in platelets. Herein, we report autophagy activation under physiologically relevant hypoxic condition (10% O2; associated with high altitude) in ex-vivo platelets and in vivo as well. We show that autophagy inhibition using chloroquine (CQ), a repurposed FDA-approved drug, can significantly reduce platelet activation, both in ex-vivo and in-vivo settings. Further, surgical ligation of inferior vena cava (IVC) was performed to induce thrombus formation. Interestingly, CQ pre-treated rats showed reduced clotting ability in surgical animals as well. Importantly, thrombosis inhibitory dose of CQ was considerably lower than the currently used drug-acetazolamide; CQ was also found to be non-toxic to the tissues. Hence, we propose that repurposing of CQ can attenuate hypoxia-induced thrombosis through inhibition of autophagy and can be explored as an effective therapeutic alternative.