Department of Biological Sciences

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Author: search.filters.author.Chowdhury, ShibasishStart date: 2023

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    Cisplatin-induced oxidative stress regulates YAP to modulate epigenome promoting survival of osteosarcoma cells
    (2025-08) Chowdhury, Rajdeep; Chowdhury, Shibasish; Mukherjee, Sudeshna
    The 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.
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    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, Rajdeep
    Colorectal 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.
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    DRP1-mediated mitochondrial dynamics orchestrate EMT in glioblastoma cells
    (2025-12) Chowdhury, Shibasish; Chowdhury, Rajdeep; Mukherjee, Sudeshna
    Epithelial 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.
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    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, Aniruddha
    GBM 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.
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    Chloroquine attenuates hypoxia-mediated autophagy to curb thrombosis- an ex vivo and in vivo study
    (2024-04) Mukherjee, Sudeshna; Majumder, Syamantak; Chowdhury, Shibasish; Chowdhury, Rajdeep
    Hypoxia 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.
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    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, Rajdeep
    Background 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 pathogenesis
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    Inhibition of autophagy in platelets as a therapeutic strategy preventing hypoxia induced thrombosis
    (Springer Nature, 2025-02) Mukherjee, Sudeshna; Majumder, Syamantak; Chowdhury, Shibasish; Chowdhury, Rajdeep
    Hypoxia 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.
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    Fink’s Integrated Course Design and Taxonomy: The Impact of Their Use in an Undergraduate Introductory Course on Bioinformatics
    (Springer, 2024-03) Chowdhury, Shibasish; Sharma, Pankaj Kumar
    The Integrated Course Design (ICD), using Fink’s taxonomy of significant learning, popularly known as ICD/SL, is a handy way to create a better learning environment for students. It is a learner-centered approach with the desired end-product, but at the same time, it upgrades the teaching by improving the instructors’ delivery mechanism. Our goal of this study was to see whether ICD/SL affects students’ class participation and academic performance in the “Introduction to Bioinformatics” course offered at the Department of Biological Science, BITS Pilani, Pilani campus, India. Three class groups were chosen for this purpose: 2019–2020 (51 students), 2020–2021 (77 students), and 2021–2022 (72 students). The control group, 2019–2020, received no ICD/SL instruction; the remaining two groups, 2020–2021 and 2021–2022, received ICD/SL instruction that included revised learning goals based on Fink’s taxonomy and new teaching and evaluation activities. A Likert scale was utilized to assess students’ academic feedback using the Kruskal–Wallis test to determine the P-value. The findings showed that the treatment groups had higher class participation and academic performance in the summative assessment of final grades. In the experimental groups, the class participation was 23 to 27% higher compared to the control group. The absenteeism rate on the course decreased from 14% in 2019–2020 to 9% in 2020–2021 and 4% in 2021–2022. Also, in the treatment groups, 83 to 90% of students were in the High to Excellent category, compared to 74% in the control group. The failure rate of the course decreased from nearly 18 to 10% in 2021–2022 and only 6% in 2020–2021. There were significant differences between the treatment and control groups in class participation and academic performance (P < 0.05). This study has shown that the use of ICD/SL has the potential to improve students’ class participation and academic performance.
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    Epigenetic adaptations in drug-tolerant tumor cells
    (Elsevier, 2023) Chowdhury, Rajdeep; Chowdhury, Shibasish; Mukherjee, Sudeshna
    Traditional chemotherapy against cancer is often severely hampered by acquired resistance to the drug. Epigenetic alterations and other mechanisms like drug efflux, drug metabolism, and engagement of survival pathways are crucial in evading drug pressure. Herein, growing evidence suggests that a subpopulation of tumor cells can often tolerate drug onslaught by entering a “persister” state with minimal proliferation. The molecular features of these persister cells are gradually unraveling. Notably, the “persisters” act as a cache of cells that can eventually re-populate the tumor post-withdrawal drug pressure and contribute to acquiring stable drug-resistant features. This underlines the clinical significance of the tolerant cells. Accumulating evidence highlights the importance of modulation of the epigenome as a critical adaptive strategy for evading drug pressure. Chromatin remodeling, altered DNA methylation, and de-regulation of non-coding RNA expression and function contribute significantly to this persister state. No wonder targeting adaptive epigenetic modifications is increasingly recognized as an appropriate therapeutic strategy to sensitize them and restore drug sensitivity. Furthermore, manipulating the tumor microenvironment and “drug holiday” is also explored to maneuver the epigenome. However, heterogeneity in adaptive strategies and lack of targeted therapies have significantly hindered the translation of epigenetic therapy to the clinics. In this review, we comprehensively analyze the epigenetic alterations adapted by the drug-tolerant cells, the therapeutic strategies employed to date, and their limitations and future prospects.
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    Transcriptomic analysis reveals differential adaptation of colorectal cancer cells to low and acute doses of cisplatin
    (Elsevier, 2023-05) Chowdhury, Rajdeep; Chowdhury, Shibasish; Mukherjee, Sudeshna
    Over the years, the landscape of cisplatin-based cancer treatment options has undergone continuous transitions. Currently, there is much debate over the optimum dose of cisplatin to be administered to cancer patients. In clinical practice, it can extend from repeated low sub-toxic doses to a few cycles of acute high drug doses. Herein, the molecular understanding of the overall cellular response to such differential doses of cisplatin becomes crucial before any decision making; and it has been a grey area of research. In this study, colorectal cancer (CRC) cells were treated with either- a low sub-toxic dose (LD; 30 µM) or a ten times higher acute dose (HD; 300 µM) of cisplatin, and thereafter, the cellular response was mapped through RNA sequencing followed by transcriptomic analysis. Interestingly, we observed that the tumor cells’ response to varying doses of cisplatin is distinctly different, and they activate unique transcriptional programs. The analysis of differentially regulated or uniquely expressed transcripts and corresponding pathways revealed a preferential enrichment of genes associated with chromatin organization, oxidative stress, senescence-associated signaling, and developmentally-active signaling pathways in HD; whereas, modulation of autophagy, protein homeostasis, or differential expression of ABC transporters was primarily enriched in LD. This study is the first of its kind to highlight cellular transcriptomic adaptations to different doses of cisplatin in CRC cells. Consequently, since, protein homeostasis was found to be deeply affected after cisplatin treatment, we further analyzed one of the primary cellular protein homeostatic mechanisms- autophagy. It was activated upon LD, but not HD, and served as a pro-survival strategy through the regulation of oxidative stress. Inhibition of autophagy improved sensitivity to LD. Overall, our study provides a holistic understanding of the distinct molecular signatures induced in CRC cells in response to differential cisplatin doses. These findings might facilitate the design of tailored therapy or appropriate drug dose for enhanced efficacy against CRCs.