Assistant Professor, Division of Molecular Medicine
PhD: National Institute of Immunology, New Delhi, 2014
2019- 2022: DBT Ramalingaswmi Faculty, Scientist, University of Kalyani, West Bengal
2018-2019: DBT Ramalingaswmi Faculty, RGCB, Thiruvananthapuram
2014-2017: Visiting Fellow, National Cancer Institute, NIH, Bethesda
2013-2014: Post-Doctoral Scientist, George Washington University, Washington DC
Our laboratory works on the regulation of transcription factors in cancers. We study the ETS family of transcription factors that are known to cause various cancers including Prostate cancer, Triple-Negative Breast Cancer, and Leukemia.
1) Identify the mechanism of ETS transcription factors regulation for the detection and treatment of resistant cancer.
2). Study cross-talk between various post-translational modifications of ETS factors associated with hormone-dependent cancer and their role in therapeutic resistance.
3) Development of cost-effective high throughput screening platforms to test inhibitors/drugs/agents for undruggable cancers.
4) Use sequencing technology to screen patient samples for non-invasive biomarker discovery.
Division of Molecular Medicine
Unified Academic Campus
EN-80, Sector V
Kolkata - 700 091, India
Project: 1) Regulation of ETS transcription factor in refractory Prostate cancer model (Ramalingaswami Fellowship 2018)
My area of research is regulation of transcription factors in cancers. Till date no drug exists which can directly target transcription factors that are primary drivers of many cancers. The laboratory studies, ETS (E-Twenty-Six) family of transcriptional factors, a group of 27 family members with a conserved DNA binding ETS domain. ETS transcription factors are aberrantly over-expressed and mediate cancer progression through altered transcription of their target genes such as FLI1 in hematological malignancies, ERG in prostate cancer. Moreover, ETS factors generate oncogenic fusion genes through chromosomal translocation such as EWS-FLI1 fusion in Ewing sarcomas, TMPRSS2-ERG and TMPRSS2 ETV1 fusions in prostate cancer, which acts as drivers in these cancers. The lab will be studying posttranslational modifications (PTMs like phosphorylation, ubiquitination, acetylation, etc) within the ETS protein that are crucial for the stability and function of these protein and can provide excellent therapeutic targets even in the fusion counterpart. Currently, we are using prostate cancer to model our studies (Model 1 top).My area of research is regulation of transcription factors in cancers. Till date no drug exists which can directly target transcription factors that are primary drivers of many cancers. The laboratory studies, ETS (E-Twenty-Six) family of transcriptional factors, a group of 27 family members with a conserved DNA binding ETS domain. ETS transcription factors are aberrantly over-expressed and mediate cancer progression through altered transcription of their target genes such as FLI1 in hematological malignancies, ERG in prostate cancer. Moreover, ETS factors generate oncogenic fusion genes through chromosomal translocation such as EWS-FLI1 fusion in Ewing sarcomas, TMPRSS2-ERG and TMPRSS2 ETV1 fusions in prostate cancer, which acts as drivers in these cancers. The lab will be studying posttranslational modifications (PTMs like phosphorylation, ubiquitination, acetylation, etc) within the ETS protein that are crucial for the stability and function of these protein and can provide excellent therapeutic targets even in the fusion counterpart. Currently, we are using prostate cancer to model our studies (Model 1 below).
Most of our current studies will be based on two prostate cancer-specific ETS fusion transcription factor regulation; namely ETV1 and ERG. We are using the latest molecular biological techniques ranging from mass spectroscopy to sequencing as well as mouse based studies to figure out the role of these ETS factors during progression of prostate cancer. The project tends to capture various aspects of hormone independent resistance prostate cancer including metabolic reprogramming, clinical intervention, DNA damage and drug resistance, patient derived models of prostate cancer in future. Deliveribles: 1) ERG and ETV1 based Luciferase reporter systems will be developed as screening tools for screening efficiency of novel inhibitors against these ETS factors in prostate cancers (6-8 months). 2) Identification of key nodes in androgen-independent mechanism of prostate cancer progression altered steroid biosynthesis, drug-resistant metastasis (3-5 years). 3) Development of Low-Temperature sensitive lecithin (LTSL) coated drug formulations/capsules for ultrasound-assisted targeted delivery in mice models (3-4 years).
A.Data from recent publications indicating a novel function for transcription factor ERG in prostate cancer: From Dhara, A., Aier, I., Paladhi, A. et al. PGC1 alpha coactivates ERG fusion to drive antioxidant target genes under metabolic stress. Commun Biol 5, 416 (2022). https://doi.org/10.1038/s42003-022-03385-x
We are currently planning for NGS on Indian prostate cancer samples, which will provide evidence of altered pathways in patients.
Significance: Prostate cancer (PCa) is the second most frequently diagnosed cancer in men worldwide resulting in thousands of death each year (Ferlay et al, 2010). Previously, PCa was considered rare in India but data from national cancer registry program (http://www.ncrpindia.org/ALL_NCRP_REPORTS/TREND_REPORT_1982_2010/ ) shows that incidence of PCa have significantly increased in last 20 years making prostate, among the top 10 leading sites for cancer according to population based cancer registry (PBCRs). Surprisingly, PCa incidences are higher in metropolitan cities (Delhi, Mumbai, Kolkata, Chennai, Bangalore, Jain et al 2014) thus indicative of future challenges the Indian population will face from hormone resistance PCa.
Project 2) Regulation of ETS1-driven metastasis in Triple-negative breast cancer (ECR awards, DST)
Recently, ETS1 expression was shown to be associated with only Triple negative breast cancer (TNBC) but not the hormone dependent cancers. One of the most prevalent cancer in India women, TNBC tends to be resistant to hormone and chemotherapy, resulting in high mortality rates. The major pathology for the later stages of TNBC related complications is metastasis. A few studies have implicated ETS1 to be associated with breast cancer metastasis without clear mechanism. Pilot studies from my laboratory indicate ETS1 driven metastatic signatures in TNBC cell lines but not the hormone responsive lines. Specific Kinase inhibitors tend to lower the expression of ETS1 in TNBC cells resulting in growth inhibition and less colony formation. I plan to study the breast to lung metastasis model using specific kinase inhibitors that target ETS1 expression. Deliverables: 1) Identifying upstream regulatory kinases of ETS1 that can be altered to modulate ETS1 driven metastasis. 2) Development of peptide mimetic based on strategic phosphorylation sites (based on kinase inhibitor studies) that target ETS1 expression and metastasis progression in mice models. Significance: TNBC have been shown to relapse within the first 3 years after the initial treatment of the disease with the majority of deaths occurring in the first 5 years and a significantly shorter survival rate is observed after the diagnosis of metastatic disease. Till date, there are no drugs that directly modulate metastasis in TNBC resulting in favorable outcomes. Breast cancer ranks the top tier in national cancer registry for female population in India. Although extensive data regarding breast cancer subtypes in India is lacking, recent studies show that TNBC is prevalent in India. Interestingly, recent meta-analysis studies involving large patient cohorts revealed that prevalence of TNBC in India is >32%, which is higher than the observed prevalence in western population. Rate of survival for TNBC patients is low compared to hormone sensitive cancers since drugs are limited to systemic chemotherapy, indicating a need for alternative drug targets for metastatic. We are currently using exom sequencing to discover noninvasive biomarker from TNBC samples in collaboration with AIIMS, Kalyani
B. Pilot Data from the TNBC project indicating expression of ETS1 in TNBC and associated hazard ratio of ETS1 with PIKK kinases in TCGA patient data sets.
C. Drug development strategy for hormone refractive cancers in the future using Low-temperature sensitive Liposomes (LTSL)/Nano based designs, etc.
1) Aiindrila Dhara, Imlimaong Aier, Ankush Paladhi, Pritish Kumar Varadwaj, Sumit Kumar Hira, Nirmalya Sen (corresponding author). PGC1 alpha coactivates ERG fusion to drive antioxidant target genes under metabolic stress. Communication Biology (Nature) Article no: 5:416, 1-11, May 2022
2) Dhara A, Ghosh S, Sen N (corresponding). Regulation of ETS family of transcription factors in cancer. Journal of Cancer Biology. ;3(1):33-49. 2022
3) Imlimaong Aier, Rahul Semwal, Aiindrila Dhara, Pritish Kumar Varadwaj, Nirmalya Sen (Co-corresponding author). An integrated epigenome and transcriptome analysis identifies PAX2 as a master regulator of drug resistance in high grade pancreatic ductal adenocarcinoma. PLoS One. 2019 Oct 17;14(10):e0223554, PMID: 31622355
4) Nirmalya Sen, Allison M. Cross, Philip L. Lorenzi, Javed Khan, Berkley E. Gryder, Suntae Kim, Natasha J. Caplen. EWS-FLI1 reprograms the metabolism of Ewing sarcoma cells via positive regulation of glutamine import and serine glycine biosynthesis. Molecular Carcinogenesis,;57(10):1342-1357, 2018 Oct
5) Berkley E. Gryder , Marielle E. Yohe , Nirmalya Sen , Hsien-Chao Chou , Xiaohu Zhang , Joana Marques , Marco Watchte , Beat Schaefer , Alberto Gualtieri , Silvia Pomella , Rossella Rota , Young K. Song , Abigail Cleveland , Xinyu Wen , Mr. Sivasish Sindiri , Jun S. Wei , Frederic G. Barr , Rajarshi Guha , Madhu Lal-Nag , Marc Ferrer , Thorkell Andresson , Jack F. Shern , Keji Zhao , Craig J. Thomas, Javed Khan. PAX3-FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability. Cancer Discovery, Volume 7, Issue 8, p884-899, August 1, 2017.
6) Patrick J. Grohar, Suntae Kim, Guillermo O. Rangel Rivera, Nirmalya Sen, Sara Haddock, Matt L. Harlow, Nichole K. Maloney, Jack Zhu, Maura O’Neill, Tamara L. Jones, Konrad Huppi, Magdalena Grandin, Kristen Gehlhaus, Carleen A. Klumpp-Thomas, Eugen Buehler, Lee J. Helman, Scott E. Martin, and Natasha J. Caplen. Functional Genomic Screening Reveals Splicing of the EWS-FLI1 Fusion Transcript as Vulnerability in Ewing Sarcoma. Cell Reports, Volume 14, Issue 3, p598–610, 26 January 2016
7) Nirmalya Sen, Gui Bin, Rakesh Kumar. Role of MTA1 in cancer progression and metastasis. Cancer Metastasis Rev. 2014 Dec;33(4):879-89.
8) Nirmalya Sen, Gui Bin, Rakesh Kumar. Physiological functions of MTA family of proteins. Cancer Metastasis Rev. 2014 Dec;33(4):869-77.
9) Rajni Kumari, Nirmalya Sen and Sanjeev Das. Tumour suppressor p53: understanding the molecular mechanisms inherent to cancer. Current Science, Vol. 107, August 2014
10) Nirmalya Sen, Rajni Kumari, Manika Inderjit Singh and Sanjeev Das. HDAC5, a Key Component in Temporal Regulation of p53-Mediated Transactivation in Response to Genotoxic Stress. Molecular Cell, Volume 52, Issue 3, 406-420, 10 October 2013.
11) Nirmalya Sen, Yatendra Kumar Satija and Sanjeev Das. p53 and metabolism: Old player in a new game. Transcription, Volume 3, Issue 3, 119 – 123, May/June 2012.
12) Nirmalya Sen, Yatendra Kumar Satija and Sanjeev Das. PGC-1α, a Key Modulator of p53, Promotes Cell Survival upon Metabolic Stress. Molecular Cell, Volume 44, Issue 4, 621-634, 18 November 2011View More
- DBT Ramalingaswami Fellow, 2016-17
- DST-SERB ECR Award, 2019
|Debkumar Pal||Junior Research Fellow||Division of Molecular Medicine||Unifiedfirstname.lastname@example.org|