Manish Kumar Singh

Manish Kumar Singh

Assistant Professor
manish.kumar@mahindrauniversity.edu.in

Manish obtained his Ph.D. in Biotechnology from Calcutta University/Bose Institute, Kolkata in 2019. During his doctoral research in the laboratory of Prof. Basu, he studied the role of host microRNAs and transcription factors mediated regulation of Mycobacterium tuberculosis infection. Subsequently, he joined Dr. Altan-Bonnet’ lab at National Heart, Lung, and Blood Institute, National Institutes of Health, USA from 2019-2021, as a postdoctoral fellow to study Host-Virus dynamics and role of extracellular vesicles in virus transmission. He then moved to Dr. Vidigal’s lab at National Cancer Institute, National Institutes of Health, USA from 2022-2025 to explore the role of RNAi in disease and development. He joined Centre for Life Sciences as an Assistant Professor in 2025.

Ph.D.

  • Ph.D. in Biotechnology from Calcutta University/Bose Institute, Kolkata (2011-2019).

M.Sc.

  • M.Sc. in Biotechnology from Babasaheb Bhimrao Ambedkar University, Lucknow (2008-2010).

B.Sc.

  • B.Sc. in Applied Science from University of Allahabad, Allahabad (2005-2008).

2025- Present

  • 2025- Present Assistant Professor, Centre for Life Sciences, Mahindra University

2022-2025

  • 2022-2025- Postdoctoral Fellow, National Cancer Institute, NIH, USA.

2019-2021

  • 2019-2021- Postdoctoral Fellow, National Heart, Lung, and Blood Institute, NIH, USA.

Publications

Google scholar

2025

  • Manish Kumar, Andrea G. Maria, Mahendra Prajapat & Joana A. Vidigal. AGO2 slicing of a domesticated retrotransposon is necessary for normal vasculature development. bioRxiv, 2025.04. 02.646793. PMID: 40235999

2023

  • Manish Kumar & Joana A. Vidigal. AGO2 localizes to the nucleus in quiescence and represses transposon expression. Nature Structural & Molecular Biology. 2023, 30:1838-1839.
  • Laura Sala*, Manish Kumar* (equal contribution), Mahendra Prajapat*, Srividya Chandrasekhar, Rachel L. Cosby, Gaspare La Rocca, Todd S. Macfarlan, Parirokh Awasthi, Raj Chari, Michael Kruhlak, and Joana A. Vidigal. AGO2 silences mobile transposons in the nucleus of quiescent cells. Nature Structural & Molecular Biology. 2023, 30:1985-1995.
  • Pankaj Birari, Soumya Mal, Debayan Majumder, Arun K Sharma, Manish Kumar, Troyee Das, Zhumur Ghosh, Kuladip Jana, Umesh D Gupta, Manikuntala Kundu, Joyoti Basu, Nur77 influences immunometabolism to regulate the release of proinflammatory cytokines and the formation of lipid bodies during Mycobacterium tuberculosis infection of macrophages. Pathogens and Disease. 2023, 81: ftad033.
  • Lepcha, Thurbu, Manish Kumar, Arun Kumar Sharma, Soumya Mal, Debayan Majumder, Kuladip Jana, Joyoti Basu, and Manikuntala Kundu. Uncovering the role of microRNA671-5p/CDCA7L/monoamine oxidase-A signaling in Helicobacter pylori mediated apoptosis in gastric epithelial cells. Pathogens and Disease. 2023, 81: ftad006.

2022

  • Abhishek Pandeya, Raj Kumar Khalko, Sukhveer Singh, Manish Kumar, and Sunil Babu Gosipatala. Hcmv-miR-UL148D regulates the staurosporine-induced apoptosis by targeting the Endoplasmic Reticulum to nucleus signaling (ERN1). PLOS One. 2022, 17(9): e0275072.
  • Sourish Ghosh, Manish Kumar, Marianita Santiana, Ashish Mishra, Mengyang Zhang, ChiblyA.M., Hakashi Nakamura, Tsutomu Tanaka, John Chiorini, Matthew Hoffman, and Nihal Altan-Bonnet. Enteric viruses replicate in salivary glands and bypass the fecal-oral route of transmission. Nature. 2022, 607(7918): 345-350.

2021

  • Manish Kumar and Nihal Altan-Bonnet. Viral pores are everywhere. Molecular Cell. 2021,81(10): 2061-2063.
  • Mengyang Zhang, Sourish Ghosh, Manish Kumar, Marianita Santiana, Christopher K. E. Bleck, Natthawan Chaimongkol, Nihal Altan-Bonnet, and Danmeng Shuai. Emerging Pathogenic Unit of Vesicle-Cloaked Murine Norovirus Clusters is Resistant to Environmental Stresses and UV254 Disinfection. Environmental Science & Technology. 2021, 55(9):6197-6205.

2020

  • Manish Kumar, Debayan Majumdar, Soumya Mal, Sohini Chakraborty, Pushpa Gupta, Kuladip Jana, Umesh D. Gupta, Zhumur Ghosh, Manikuntala Kundu and Joyoti Basu. Activating transcription factor 3 modulates the macrophage immune response to Mycobacterium tuberculosis infection via reciprocal regulation of inflammatory genes and lipid body formation. Cell. Microbiol. 2020, 22(3): e13142.
  • Arijita Subuddhi, Manish Kumar, Debayan Majumder, Arijita Sarkar, Zhumur Ghosh, Madavan Vasudevan, Manikuntala Kundu and Joyoti Basu. Unraveling the role of H3K4 trimethylation lncRNA HOTAIR in SATB1 and DUSP4-dependent survival of virulent Mycobacterium tuberculosis in macrophages. Tuberculosis. 2020, 120:101897.

2019

  • Srijon Kaushik Banerjee, Suruchi Lata, Arun Kumar Sharma, Shreya Bagchi, Manish Kumar, Sanjaya Kumar Sahu, Pushpa Gupta, Kuladip Jana, Umesh D. Gupta, Ramandeep Singh, Sudipto Saha, Joyoti Basu and ManikuntalaKundu. The sensor kinase MtrB of Mycobacterium tuberculosis regulates hypoxic survival and establishment of infection. J. Biol. Chem. 2019, 294(52):19852- 19876.

2018

  • Chandreyee Datta, Arijita Subuddhi*, Manish Kumar* (equal contribution), Thurbu Lepcha, Sohini Chakraborty, Zhumur Ghosh, Asish kumar Mukhopadhyay, Joyoti Basu, and Manikuntala Kundu. Genome-wide mRNA- miRNA profiling uncovers a role of the microRNAmiR-29b-1-5p/PHLPP1 signaling pathway in Helicobacter pylori-driven matrix metalloproteinase production in gastric epithelial cells. Cell Microbiol. 2018, 11: e12859.
  • Ayan Chatterjee, Arun Kumar Sharma, Amar Chandra Mahatha, Srijon Kaushik Banerjee, Manish Kumar, Sudipto Saha, Joyoti Basu and Manikuntala Kundu. Global mapping of MtrA-binding sites links MtrA to the regulation of its targets in Mycobacterium tuberculosis. Microbiology. 2018, 164:99-110.

2017

  • Sanjaya Kumar Sahu*, Manish Kumar* (equal contribution), Sohini Chakraborty, Srijon Kaushik Banerjee, Ranjeet Kumar, Pushpa Gupta, Kuladip Jana, Umesh D. Gupta, Zhumur Ghosh, Manikuntala Kundu, and Joyoti Basu. miR-26a/KLF4 and CREB-C/EBP-β regulate innate immune signaling, the polarization of macrophages, and the trafficking of Mycobacterium tuberculosis to lysosomes during infection. PLOS Pathogens. 2017, 13(5): e1006410.

2016

  • Srijon Kaushik Banerjee, Manish Kumar, Reshma Alokam, Arun Kumar Sharma, Ayan Chatterjee, Ranjeet Kumar, Sanjaya Kumar Sahu, Kuladip Jana, Ramandeep Singh, Perumal Yogeeswari, Dharmarajan Sriram, Joyoti Basu and Manikuntala Kundu. Targeting multiple response regulators of Mycobacterium tuberculosis augments the host immune response to infection. Sci. Reports. 2016, 6: 25851.
  • Ranjeet Kumar, Sanjaya Kumar Sahu, Manish Kumar, Kuladip Jana, Pushpa Gupta, Umesh D. Gupta, Manikuntala Kundu and Joyoti Basu. MicroRNA-17-5p regulates autophagy in Mycobacterium tuberculosis-infected macrophages by targeting Mcl-1 and Stat3. Cell. Microbiol. 2016, 18(5): 679-691.

2015

  • Manish Kumar*, Sanjaya Kumar Sahu*, Ranjeet Kumar* (equal contribution), Arijita Subuddhi, Ranjan Kumar Maji, Kuladip Jana, Pushpa Gupta, Johanna Raffetseder, Maria Lerm, Zhumur Ghosh, Geert Van Loo, Rudi Beyaert, Umesh D. Gupta, Manikuntala Kundu and Joyoti Basu. MicroRNA let-7 modulates the immune response to Mycobacterium tuberculosis infection via control of A20, an inhibitor of the NF-κB pathway. Cell Host & Microbe. 2015, 17(3): 345-356.

2012

  • Ranjeet Kumar, Priyanka Halder, Sanjaya Kumar Sahu, Manish Kumar, Mandavi Kumari,Kuladip Jana, Zhumur Ghosh, Pawan Sharma, Manikuntala Kundu and Joyoti Basu. Identification of the novel role of ESAT-6-dependent miR-155 induction during infection of macrophages with Mycobacterium tuberculosis. Cell. Microbiol. 2012, 14(10): 1620-1631.
  • Nisha Singh, Manish Kumar, and Rakesh Kumar Singh. Leishmaniasis: Current status of available drugs and new potential drug targets. Asian Pac. J. Trop. Med. 2012, 5(6): 485-497.

Book Chapter

2019

  • Manish Kumar, Manikuntala Kundu and Joyoti Basu. The role of microRNAs in bacterial infections. AGO-Driven Non-Coding RNAs. 2019, pages 57-71. Published by Academic Press.

Research concept

Welcome to our research laboratory dedicated to Innate Immunity & Extracellular Vesicles (EVs), where we explore the host’s defense mechanisms in the context of infectious diseases. The ability of innate immune system to sense pathogenic organisms and respond appropriately to control infection is paramount for our survival. To achieve this, innate immune system identify invading pathogens and respond by initiating inflammation. Macrophages, vital components of innate immunity are found in various tissue and play a crucial role in coordinating inflammatory responses and eliminating invading microorganisms. Macrophage derived extracellular vesicles also play crucial role in immune surveillance, inflammation, and intercellular communication, in addition to its direct microbes killing ability. Our primary goal is to combat specific pathogens by harnessing the body’s natural defense mechanism, rather than relying on antibiotics that bacteria can quickly develop resistance to.

Research projects 

  1. Exploring macrophage biology in the context of pathogenic infections
    Our goal is to develop a nuanced understanding of epigenetic, transcriptional, and post-transcription regulation of innate immune cell signaling pathways in order to identify therapeutic targets that are mediated by the host.
  1. Exploring the role of EVs in modulating immune responses
    We are exploring the contents of EVs derived from macrophages and other immune cells, focusing on their role in cellular communication and their impact on the establishment or resolution of infection.
  1. Development of EVs- based diagnostics and therapeutics for infectious diseases
    We are identifying membrane-displayed antigens on EVs during infection and utilizing these antigens to develop, optimize, and evaluate detection assays. Additionally, we are engineering EVs for the targeted delivery of RNAi therapeutics.

Research approaches

          We are using multidisciplinary approaches to validate our hypothesis like:

  • Molecular biology & Immunology techniques
  • Cellular biology & advanced imaging techniques
  • High-throughput omics
  • EV engineering using CRISPR and advanced EV isolation
  • In vitro and in vivo immune models

We are seeking enthusiastic Ph.D. candidates in accordance with Mahindra University guidelines. Master students interested in pursuing dissertations are also welcome to apply.

Postdoctoral candidates with their own research grants, such as NPDF, ICMR, DBT etc are encouraged to apply. We are also open to discussing project proposals to help secure these fellowships.

If our research excites you, feel free to write manish.kumar@mahindrauniversity.edu.in or visit our lab by contacting us in advance.