NIBMG Fellows

Research

Cancer Epigenomics

To investigate the role of enhancer RNAs (eRNAs) and epigenomic modification in Pancreatic Cancer.

Summary

Pancreatic cancer is an extremely lethal disease. The symptoms are often non-specific, which means that the patients are often present at advanced stages of cancer leading to death. Pancreatic cancer comprises mostly of pancreatic ductal adenocarcinoma (PDAC), which involves progressive accumulations of driver mutations, including the oncogene KRAS and tumour suppressor gene TP53. KRAS and TP53 mis-regulation can induce several different epigenetic changes in cancer cells. 

Moreover, the cis-acting DNA elements, known as enhancers, serve as critical regulatory elements for transcriptional programs by directing development, homeostasis and disease states. A reliable epigenetic feature of active enhancers is the production of enhancer-directed transcripts (eRNAs). Here, we will identify the differentially expressed eRNAs in pancreatic cancer cells by GRO-seq and ChIP-seq analysis and investigate the functional role of those eRNAs in pancreatic cancer progression.

• Received grant from NIBMG-IGIB conclave on functional roles of eRNA. Duration: 2023-2025
  
  

Antiviral Epigenetics

To investigate the role of epigenetic modification driven trained immunity in anti-viral immune response.

Immune response is often heterogeneous and varies between individuals. Here, we will investigate the role of differential epigenetic modifications in disease severity during viral infection. We will also explore whether the unique epigenetic modification can be used as efficient antiviral drug targets against RNA viruses.

Extramural Funding

• Received Start-up Research Grant (SRG) from DST-SERB on antiviral epigenomics. Duration: 2022-2024
• Received Core Research Grant (CRG) from DST-SERB on Anti-viral drug designing. Duration: 2023-2026 

CV

Professional Appointments

• Associate Professor, Adamas University, Barasat, West Bengal, India (11/2020- 05/2021)
• Post-Doctoral Researcher, University of California San Diego, CA, USA (10/2019 –10/2020)
• Post-Doctoral Fellow, University of California Los Angeles, CA, USA (06/2017- 10/2019)
• Post-Doctoral Researcher, University of California San Diego, CA, USA (12/2014 - 05/2017)

Professional Memberships

Life member of Society of Biological Chemists (India).

Life member of All India Cell Biology Society.

Awards/Honors

• Received Keystone Symposia Future of Science Fund Scholarship to present poster in the Keystone Symposia RNA Silencing Meeting held from 31st Jan to 5th Feb 2014 at Seattle, WA, USA.

• Qualified National Eligibility Test (NET) and received fellowship as Junior research Fellow (2008-2010) and as Senior research fellow (2010-2013) from Council of Scientific and Industrial Research (CSIR), India.

• Qualified Graduate Aptitude Test (GATE) in 2007.

Invited/Special lectures

The role of epigenetic modifications in antiviral immune response. Faculty Development Program, Guru Nanak Institute of Technology, Kolkata, India, 2021.

Selected presentations

• A transient reversal of miRNA-mediated repression on the onset of pro-inflammatory immune response in activated macrophage. 7th All India RNA Meeting, 2013.

• Modulation of immune response by small regulatory RNA in mammalian macrophages. Department of Biochemistry, University of Calcutta, 2013.

• The NF-kB subunit RelB controls p100 processing by competing with NIK/IKK1 for binding to p100. Signalling Systems lab, Department of Microbiology, Immunology and Molecular Genetics, UCLA, 2017.

Past Major Projects

• The role of enhancer RNA (eRNA) in colon cancer disease progression.
• The combinatorial control of transcription factor dynamics in innate immune response.
• Regulation of non-canonical NF-kB signalling.
• Modulation of immune response by miRNA in Bacterial infection or Leishmania parasite infection.

Publications

1. Divergent mutations of Delta and Omicron variants: key players behind differential viral attributes across the COVID‑19 waves. Amrita Panja, Jayita Roy, Anup Mazumder* Sujata Maiti Choudhury*. VirusDisease, 10 May 2023. doi.org/10.1007/s13337-023-00823-0 (*Co-Corresponding author).

2. Emergence of a unique SARS-CoV-2 Delta sub-cluster harboring a constellation of co-appearing non-spike mutations. Banerjee A.*, Mazumder A.*, Roy J., Das J., Majumdar A., Chatterjee A., Biswas NK, Chawla-Sarkar M., Das S., Dutta S., Maitra A. Journal of Medical Virology 2022 December 21. doi.org/10.1002/jmv.28413 (*Co-First author)

3. Contrasting Distribution of SARS-CoV-2 Lineages across Multiple Rounds of Pandemic Waves in West Bengal, the Gateway of East and North-East States of India. Singh AK, et. al. Microbiology Spectrum. 2022 Jul 19:e0091422. doi:10.1128/spectrum.00914-22.

4. Identifying the combinatorial control of signal-dependent transcription factor. Wang N, Lefaudeux D, Mazumder A, Li JJ, Hoffmann A. Plos Computational Biology, 2021June 24; 17(6): e1009095. PMID: 34166361

5. MicroRNA Exporter HuR Clears the Internalized Pathogens by Promoting Pro-inflammatory Response in Infected Macrophages. Goswami A*, Mukherjee K*, Mazumder A*, Ganguly S*, Mukherjee I, Chakraborty S, Roy S, Sundar S, Chattopadhyay K and Bhattacharyya SN. EMBO Molecular Medicine 2020 Mar 6;12(3): e11011. PMID 32031337. (*Co-first Author)

6. Structural basis for activation of IKK1/α. Polley S, Passos D. O., Huang D-B, Mulero M. C., Mazumder A, Biswas T, Verma I. M., Lyumkis D, Ghosh G. Cell Reports. 2016; 17(8):1907-1914. PMID: 27851956

7. The NF-kB subunit RelB controls p100 processing by competing with the kinases NIK and IKK1 for binding to p100. Fusco A. J. *, Mazumder A*, Wang V. Y-F, Tao Z, Ware C, Ghosh G. Science Signaling. 2016; 9(447): ra 96. PMID: 2767822. (*co-first Author)

8. A transient reversal of miRNA-mediated repression on the onset of pro-inflammatory immune response. Mazumder A, Bose M, Chakraborty A, Chakrabarti S, Bhattacharyya SN. EMBO Reports. 2013; 14(11):1008-16. PMID: 24030283 

Lab members

Ph.D. Student:

1. Ms. Jayita Roy, UGC-SRF [Jointly with Dr. Srikanta Goswami]

2. Mr. Sadananda Kumbhakar, UGC-JRF [Jointly with Dr. Sagar Sengupta]

Project Personnel:

1. Mr. Bikram Bhakat, Project-JRF

Integrated MS-Ph.D. student:

1. Mr. Aniket Kumar

Alumni:

1. Mr. Dipjit Basak

2. Ms. Tarasa Shami

3. Ms. Brati Chakraborty

4. Mr. Sabyasachi Baksi

5. Ms. Moubani Dutta

6. Mr. Sunit Chakraborty