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Dr. Soumen Basak

Research Interest:

In a multidisciplinary research program, we are using systems biology tools to characterize regulatory cell circuitries that enable crosstalk between various immune activating and homeostatic signals.In sum, we are interested in understanding physiological and patho-physiological consequences of such cross-regulations in the context of

i) Inflammatory immune response and inflammatory diseases
ii) Neoplastic disorders

Summary of Research:

A multitude of biochemical processes links the intracellular signaling pathways in a network. Importantly, this interlinked signaling network, and not the individual pathways, eventually shapes cellular responses. Because of the complexity of the signaling network, assigning specific interactions between signaling modules to distinct immune functions has remained challenging.Our research interest lies in exploring the crosstalk between these “dedicated” signaling pathways and understanding the implications of such interdependent regulations in physiology and patho-physiology.

In particular, the NF-kappaB system has the remarkable capacity to process signals from a variety of extracellular as well as intracellular cues, those include pathogen derived substances, host-derived cytokines, cell-differentiating and developmental cues, reactive oxygen species or metabolic substances.The NF-κB systemtransduces these signals through either the canonical or the non-canonical module to activate an overlapping set of close to a dozen of transcription factors.In our laboratory, we have considered this pleiotropic NF-κB systemas a potential playerin mediating signaling crosstalk in varied physiological context. In a multidisciplinary research program that combines biochemistry, molecular biology, cell biology, mouse genetics and computational modeling, we aim to biochemically characterize the cross-regulatory elementsembedded within the NF-κB system that enable crosstalk between immune activating and homeostatic cues. By simulating a computational model describing the NF-κB system, we generatein silico predictions on pathway crosstalks. Using biochemical assays, such as Immunoblot analysis, EMSA, Real Time PCR etc., and genetic tools, including a panel of knockout cells,we then test signaling crosstalk ex vivo. Finally, we examine potential physiological or pathophysiological ramification of pathway crosstalks in vivo in murine model.One long-term objective of our research program is to eventually define connectivities between the NF-κB system and other important immunesignaling pathways, such as type-1 IFN pathway.

Our systems based approach not only promises new mechanistic insights into the dynamic control of immune responses but also has therapeutic importance. Our finding bears promises for disease-specific interventions in inflammation-associated diseases that target the crosstalk motif delinking inflammatory module from the integrated network.

Group Members:
Yashika Ratra, Uday Aditya Sarkar, Manti Kumar Saha, Alvina Deka, Naveen Kumar, Chandrima Bharadwaj, Shivani Rajoriya and Gayathri Devi, (Ph.D. students); Syed Yusuf Mian (Research Associate); Birendra Kumar and Vijendra Kumar (Technical help)

• 2021 : Elected Fellow of the Indian Academy of Sciences (IASc).
• 2021 : Elected Fellow of the National Academy of Science India (NASI).
• 2019 : Shanti Swarup Bhatnagar Award for Research Excellence in Biological Sciences.
• 2018 : Received the National Bioscience Award for Career Development in recognition of the research in the area of immunology and cell signaling.
• 2017 : Elected as a member of the Guha Research Conference.
• 2010-2015 : Intermediate Fellowship, Wellcome Trust-DBT India Alliance.
• 2010 : Ramachandran fellowship, National Institute of Immunology, Department of Biotechnology, India.
• 2003 : Young Scientist Award from the Indian Science Congress Association (ISCA).

James Gomes and Manidipa Banerjee from IIT-Delhi, Shailly Tomar from IIT-Roorkee, Guruprasad R. Medigeshi from THSTI-Faridabad, Sunil K. Raghav from ILS-Bhubaneswar, Abhyudai Singh from Univ. of Delaware,Vineet Ahuja from AIIMS, and Subhra K. Biswas from Singapore.

  • Meenakshi Chawla, Tapas Mukherjee, Alvina Deka, Budhaditya Chatterjee, Uday Aditya Sarkar, Amit K. Singh, Saurabh Kedia, Josephine Lum, Manprit Kaur, Balaji Banoth, Subhra K Biswas, Vineet Ahuja, Soumen Basak# An epithelial Nfkb2 pathway exacerbates intestinal inflammation by supplementing latent RelA dimers to the canonical NF-κB module. #corresponding author, Proceedings of the National Academy of Sciences USA. 2021 Jun 22;118(25).
  • Tapas Mukherjee*, Yashika Ratra*, Balaji Banoth, Alvina Deka, Smarajit Polley, Soumen Basak# A kinase assay for measuring the activity of the NIK-IKK1 complex induced in the noncanonical NF-κB pathway. #corresponding author, *contributed equally, Methods in Molecular Biology - NF-κB Transcription Factors, edited by Guido Franzoso and Francesca Zazzero, vol: 2366: 165-181, July 2021.
  • Meenakshi Chawla, Payel Roy, Soumen Basak# Role of the NF-κB system in context-specific tuning of the inflammatory gene response. #corresponding author, Current Opinion in Immunology, 68:21-27, Sep 2020.
  • Bais SS, Ratra Y, Khan NA, Pandey R, Kushawaha PK, Tomar S, Medigeshi G, Singh A, Basak S# Chandipura virus utilizes the pro-survival function of RelA NF-κB for its propagation. #corresponding author, Journal of Virology. 2019 Jun 28; 93(14).
  • Budhadittya Chatterjee*, Payel Roy*, Uday Aditya Sarkar, Mingming Zhao, Yashika Ratra, Amit Singh, Meenakshi Chawla, Supriyo De, James Gomes,  Ranjan Sen, Soumen Basak# Immune Differentiation Regulator p100 Tunes NF-κB Responses to TNF. # corresponding author, *contributed equally, Frontiers in Immunology. 2019 May 7; 10:997.
  • Tapas Mukherjee, Budhadittya Chatterjee, Atika Dhar, Sachendra S. Bais, Meenakshi Chawla,  Payel Roy, Anna George, Vineeta Bal, Satyajit Rath, Soumen Basak# A TNF-p100 pathway subverts LTβR-mediated noncanonical NF-κB signaling and restricts naïve lymphocyte ingress in inflamed secondary lymphoid organs. # corresponding author, EMBO J. 2017 Dec 1;36(23):3501-3516.
  • Budhaditya Chatterjee*, Balaji Banoth*, Bharath Vijayaragavan, Tapas Mukherjee, James Gomes, Soumen Basak# Late-phase synthesis of IκBα insulates the TLR4-activated canonical NF-κB pathway from noncanonical NF-κB signaling in macrophages. # corresponding author, *contributed equally, Science Signaling, 2016 Dec 6, 9 (457):ra 120


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