Molecular Biology Lab
visitors gallery
Prashant Kumar, Ph.D.
Faculty Scientist
DST-Ramanujan fellow
Institute of Bioinformatics
Discoverer Building, International Tech Park, Whitefield
Bangalore - 560 066
E-mail: prashant at ibioinformatics dot org
Phone: +91-80-28416140 Fax: +91-80-28416132
Ph.D. in molecular biology, Max Planck Institute for Infection Biology, Berlin, Germany, 2009
M.Sc. in Biotechnology, University of Allahabad, Allahabad, India, 2002

Positions Held

Faculty Scientist, Institute of Bioinformatics, Bangalore, June 2015 – present
Visiting Faculty at Institute of Health and Biomedical Innovation (IHBI) and Translational Research Institute (TRI), Queensland University of Technology (QUT), 37 Kent St Woolloongabba QLD 4102. Australia, 2017 – 2018
Research Scientist 'II', Institute of Molecular and Cell Biology (IMCB) A*STAR, Singapore, 2012 – 2015
Postdoctoral Research Associate, Department of Cancer Biology, University of Massachusetts Medical School, Worcester, USA, 2009 –2012
Junior Research Fellow, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India, 2003 – 2005

Honors and Awards

Ramanujan Fellowship awarded by Department of Science and Technology (DST), Government of India 2015
NIH-Fellowship (to pursue Post-Doctoral research at UMASS Medical School, Department of Cancer Biology, Worcester, USA) Oct 2009 to March 2012
International Max-Planck Fellowship (to pursue Ph.D. at Max Planck Institute for Infection Biology, Dept. Molecular Biology, Berlin, Germany) Feb 2005 to Sept 2009
Junior Research Fellowship, Indian Institute of Sciences, Bangalore, India, 2003 – 2005
Qualified Indian Council of Agricultural Research (ICAR) SRF/NET, 2001
Awarded a 6-month traineeship for the Biotech Industrial Training Program by the Biotech Consortium India Limited (BCIL), 2002 – 2003
Department of Biotechnology Fellowship, Government of India sponsored fellowship in M.Sc. Biotechnology after completing the All India Entrance Examination in Biotechnology conducted by Indian Institute of Technology (IIT), Roorkee, 1999 – 2001 (All India Rank-20)

Area of Specialization

Infection biology (H. pylori & Chlamydia)
High-throughput screening
Bladder cancer, breast cancer and gastric cancer
Circulating tumour cells (CTCs)


Dr. Prashant Kumar received his Ph.D. in 2009 from the Max Planck Institute for Infection Biology, Department of Molecular Biology, Berlin, Germany. Following this, Dr. Kumar received postdoctoral training in the laboratory of Prof. Karl Simin at the Department of Cancer Biology, University of Massachusetts (UMMS) Medical School, Worcester, USA, where he established a novel mouse model of malignant breast cancers that required improved therapeutic strategies, and was involved in studying the clinical impact of breast cancer. In his work, he showed that mammary tumors caused by the inactivation of the pRb family (pRbf) of proteins (pRb, p107, p130), together with Brca1 and p53 inactivation, mimicked several aspects of the most aggressive forms of breast cancer. This finding illustrated the compounding effect of acquiring multiple tumor suppressor mutations during tumor evolution and underscores the distinct requirements of each of these canonical tumor suppressor proteins. In June 2012, he moved to Singapore, continuing his research at the Institute of Molecular and Cell Biology (IMCB), A-STAR, in the laboratory of Prof. Jean Paul Thiery, a world renowned authority in the area of EMT (Epithelial-Mesenchymal Transition). During this period, the focus of his work took on a more translational aspect, and he was involved in the development of a novel point-of-care (POC) diagnostic platform for the detection of multiple protein bladder cancer biomarkers. He was also involved in the establishment of a culture method to assess breast cancer circulating tumor cells (CTCs) harvested from blood samples of patients undergoing neoadjuvant therapy. This new technique provides an opportunity to analyze CTC clonal heterogeneity and adapt therapeutic modalities in refractory breast cancer patients. At IOB, his work is now centred on biomarker discovery for bladder cancers, using state-of-the-art quantitative proteomics approaches. He is also interested in defining the molecular pathways that underlie the malignancy associated with bladder carcinoma, with an emphasis on the biological mechanisms and regulatory relationship of EMT in cancer progression.


Major Research Areas

In vivo mouse model and clinical impact associated with bladder/breast/head and neck/gastric cancer(s)

Translational research and in development of novel point-of-care (POC) diagnostic platform for the detection of multiple protein cancer biomarkers
Targeting pathways contributing to Epithelial-Mesenchymal Transition (EMT) in malignancy associated with carcinoma
Ex vivo culture of circulating tumor cells for individualized testing of drug susceptibility


Research papers: 16; Book chapters: 1; Patents: 2


Saha, M., Kumar, S., Bukhari, S., Balaji, S. A., Kumar, P., Hindupur, S. K., Rangarajan, A (2018). AMPK-AKT double negative feedback loop in breast cancer cells regulates their adaptation to matrix deprivation. Cancer Research. In press

Khan, A. A., Advani, J., Patel, K., Nanjappa, V., Datta, K. K., Solanki, H. S., Kumar, P., Mathur, P. P., Nair, B. P., Prasad, T. S. K., Chatterjee, A and Gowda, H. (2018). Chronic exposure of cigarette smoke and chewing tobacco alters expression of microRNAs in esophageal epithelial cells. MicroRNA. In press

Nanjappa, V., Sathe, G.J., Jain, A. P., Rajagopalan, P., Raja, R, Subbannayya, T., Patil, A. H., Kumar, P., Prasad, T. S. K., Mathur, P. P., Sidransky, D., Gowda, H., Chatterjee, A. (2017). Investigation of curcumin mediated signaling pathways in head and neck squamous cell carcinoma. Translational Research in Oral Oncology. In press

Solanki, H. S., Advani, J., Kumar, M., Kumar, P., Bhagat, H., Prasad, T. S. K., Sidransky, D., Gowda, H., Chatterjee, A. (2017) miRNA profiling of bladder cells chronically exposed to cigarette smoke condensate and its vapor. Research Reports. In press

Leonard, J. L., Leonard, D. M., Wolfe, S. A., Liu, J., Rivera, J., Yang, M., Leonard, R. T., Johnson, J. P. S., Kumar, P., Liebmann, K. L., Tutto, A. A., Mou, Z., Simin, K. J. (2017). The Dkk3 gene encodes a vital intracellular regulator of cell proliferation. PLoS One. 12, e0181724. [PubMed]

Yadavalli, S., Jayaram, S., Manda, S. S., Madugundu, A. K., Nayakanti, D. S., Tan, T. Z., Bhat, R., Rangarajan, A., Chatterjee, A., Gowda, H., Thiery, J. P. and Kumar, P.* (2017). Data-Driven Discovery of Extravasation Pathway in Circulating Tumor Cells. Scientific Reports. 7, 43710. [PubMed] (*Corresponding Author)

Radhakrishnan, A., Nanjappa, V., Raja, R., Sathe, G. J., Chavan, S., Nirujogi, R. S., Patil, A., Solanki, H., Renuse, S., Sahasrabuddhe, N. A., Mathur, P. P., Prasad, T. S. K., Kumar, P., Califano, J. A., Sidransky, D., Pandey, A., Gowda, H. and Chatterjee, A. (2016). Dysregulation of splicing proteins in head and neck squamous cell carcinoma. Cancer Biology and Therapy. 17, 219-29. [PubMed]

Wu, F†., Kumar, P†., Lu, C., El Marjou, A., Qiu, W., Lim, C. T., Thiery, J. P. and Liu, R. (2015). Homophilic Interaction and Deformation of E-cadherin and Cadherin 7 Probed by Single Molecule Force Spectroscopy. Archives of Biochemistry and Biophysics. 587, 38-47. [PubMed] 
†These authors contributed equally to this project

Khoo, B. L†., Lee, C. S†., Kumar, P†., Tan, Z. T., Warkiani, E. M., Ow, GW. S., Nandi, S., Lim, T. C. and Thiery, P. J. (2015). Short-term expansion of breast circulating cancer cells predicts response to anti-cancer therapy. Oncotarget. [PubMed] 
†These authors contributed equally to this project

Kumar, P., Nandi. S., Tan, Z. T., Ler, G. S., Seng, K. C., Yen, W. L., Vordos, D., laTaille, D. A., Raida, M., Beyer, B., Ricci, E., Colombel, M., Chong, W. T., Chiong, E., Soo, R., Park, K. M., Ha, K. H., Gunaratne, J. and Thiery, P. J. (2015). Highly sensitive and specific novel biomarkers for the diagnosis of transitional bladder. Oncotarget. 6:13539-49. [PubMed] 

Akalay, I., Tan, T. Z., Kumar, P., Janji, B., Mami-Chouaib, F., Charpy, C., Vielh, P., Larsen, A. K., Thiery, J. P., Sabbah, M. and Chouaib, S. (2015). Targeting WNT1-inducible signaling pathway protein 2 alters human breast cancer cell susceptibility to specific lysis through regulation of KLF-4 and miR-7 expression. Oncogene. 34:2261-2271. [PubMed]

Johnson, J. P., Kumar, P., Koulnis, M., Patel, M. and Simin, K. (2014). Crucial and Novel Cancer Drivers in a Mouse Model of Triple-Negative Breast Cancer. Cancer Genomics Proteomics. 11:115-126. [PubMed]

Goel, L. H., Pursell, B., Chang, C., Shaw, L., Mao, J., Simin, K., Kumar, P., Kooi, C., Shultz, L., Greiner, D., Norum, J., Toftgard, R., Kuperwasser, C. and Mercurio, M. A. (2013). GLI1 regulates a novel neuropilin-2/a6�1 integrin based autocrine pathway that contributes to breast cancer initiation. EMBO Mol Med 5:488-508. [PubMed]

Kumar, P., Mukherjee, M., Johnson, J. P., Patel, M., Huey, B., Albertson, D. G. and Simin, K. (2012). Cooperativity of Rb, Brca1, and p53 in Malignant Breast Cancer Evolution. PLoS Genet. 8. [PubMed]

Singh, D. D., Saikrishnan, K., Kumar, P., Surolia, A., Sekar, K. and Vijayan, M. (2005). Glycobiology. Unusual sugar specificity of banana lectin from Musa paradisiaca and its probable evolutionary origin. 15:1025-1032. [PubMed]

Singh, D. D., Saikrishnan, K., Kumar, P., Dauter, Z., Sekar, K., Surolia, A. and Vijayan, M. (2004). Purification, crystallization and preliminary X-ray structure analysis of the banana lectin from Musa paradisiaca. Acta Crystallogr D Biol Crystallogr 60:2104-2106. [PubMed]


Book Chapters

Khoo, L, B., Kumar, P. and Thiery, P. J. (2014). Current cancer series: Fundamental studies of CTC "Genesis of Circulating Tumor Cells (CTCs) through Epithelial-Mesenchymal Transition (EMT) as a mechanism for distant dissemination". Springer publication, USA


Biomarker Discovery in the urine of early stage Bladder cancer patients (Singapore Patent Application No: 201308203-7), 2013 Jean Paul Thiery, Prashant Kumar, Jayantha Gunaratne
US Provisional Patent Application No: IMC/P/07991/00/SG PCT extension USA October 2014 Jean Paul Thiery, Prashant Kumar, Jayantha Gunaratne


Editorial Boards
Editorial board member of American Journal of Cancer Prevention (2013-2017): An editorial board member of American Journal of Cancer Prevention, Science and Education Publishing
Editorial board member of Trends Journal of Sciences Research (TJSR, 2013-2017)
A reviewer of a peer-reviewed scientific journal, Scientific Reports, 2017
A reviewer of a peer-reviewed journal, Oncotarget, 2016-2017
A reviewer of a peer-reviewed journal, Proteomics, 2016-2017
A reviewer of a peer-reviewed journal, Clinical Proteomics, 2016-2017
A reviewer of a peer-reviewed journal, Cancer Research, 2016-2017
A reviewer of a peer-reviewed journal, PLOS ONE, 2014-2017
Member of European Association of Urology, EAU- Research Foundation (EAURF)
Member of Proteomic Society, India (PSI)

Invited Lectures

An invited speaker in Lung Cancer Consortium Asia Annual Meeting: Lecture delivered on "Short term ex vivo expansion of CTCs in lung cancer predicts response to anti-cancer therapy" ITC Parel, Mumbai; 15th December, 2017
An invited lecture on "Circulating tumor cells: their utility in cancer management and predicting outcomes" Kokilaben Dhirubhai Ambani hospital and medical research Institute, Mumbai; 14th December, 2017
An invited speaker in First Indo-Australian Symposium on Epithelial-Mesenchymal TransitionNew advances in cancer development: Lecture delivered on "Extravasation Pathway Discovery and Integrated Regulatory Network for Epithelial-Mesenchymal Transition"
An invited lecture on "Liquid Biopsies and the Early Diagnosis of Cancer" Nizam's Institute of Medical Sciences, Hyderabad, India; 17th May, 2017
An invited lecture on "Liquid Biopsy: The Future of Cancer Treatment and Detection" Mahavir Cancer Institute and Research Centre, Patna, India; 12th April, 2017
An invited lecture on "Highly sensitive and specific novel biomarkers: Potential Diagnostic and Therapeutic Strategies" Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), New Delhi, India; 5th April, 2017
An invited lecture on "Bioengineering and Clinical Utility of Biomarkers: A Quest for Noninvasive Detection" Gandhi Medical College and Hospital, Hyderabad, India; 25th February, 2017
An invited lecture on "Clinical Utility of Biomarkers: A Quest for Noninvasive Detection" Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India; 24th February, 2017
An invited speaker in Next Generation Sequencing conference on "Data-Driven Discovery of Extravasation Pathway and Integrated Regulatory Network for Epithelial-Mesenchymal Transition in Circulating Tumor Cells" IICT auditorium, Hyderabad, India; 23rd February, 2017
An invited lecture on "Circulating Tumor Cells: current challenges and new directions for Liquid Biopsy" Kidwai Memorial Institute of Oncology, Infosys Hall, Bangalore, India; 5 October, 2016
An invited speaker in Molecular Diagnostics Europe meeting: Lecture delivered on "Expansion of Breast Circulating Cancer Cells Predicts Response to Anti-Cancer Therapy" Lisbon, Portugal; 4-7 April, 2016
An invited speaker in National Seminar on "Drug Discovery and Cancer therapy" (DDCT-2016), Pondicherry University; Lecture delivered on "Emerging Bladder cancer Biomarker: Potential Diagnostic and Therapeutic Strategies" 25th Feb, 2016
An invited lecture on "Basics of mass spectrometry-based proteomics" Karunya University, Coimbatore, Tamil Nadu, India 21st August, 2015
Scientific Meetings
EMBO Gold MEDALLIST SYMPOSIUM, 11-13 May, 2015, Biopolis, Singapore
IMCB 30th Anniversary Mini-Symposium, 7 May, 2015, Singapore
Merck-Singapore, Drug Discovery and Translational Medicine Symposium. 3-5 March, 2015
NUS-Kanagawa Prefecture Urology Symposium 19-20 January, 2015, Centre for Life Sciences Auditorium, 28 Medical Drive, Singapore
A*STAR-DxD Hub-HAS, Regulatory Framework on Medical device Development: 28 November, 2014
Frontiers in Cancer Science 2014, 3-5 November, 2014, The Academia, 20 College Road, Singapore
Frontiers in Cancer Science 2013, 5-7 November, 2013, Matrix @ Biopolis, Singapore
21st Meeting of the EAU Section of Urological Research (ESUR), 25-27 September, 2013, Dresden, Germany
Next Generation Dx Summit Moving Assays to the clinic, 20-22 August, 2013, Hyatt Regency on Capitol Hill Washington, DC
2013 Omics in the Clinic Conference Series, 12 April. 2013, Grand Park City Hall, Singapore
Stem Cell Society Singapore iPSC Symposium, 14 December, 2012
The Frontiers in Cancer Science (FCS) 2012, 4th annual meeting will be held on 5-8 November, 2012, at the UCC Theatre at the University Cultural Centre, National University of Singapore in Singapore
2nd Singapore Ovarian Cancer Symposium 15 June, 2012
Annual Cancer biology training Program retreat, May 17, 2011, Hoagland-Pincus Conference center, Shrewsbury, Worcester, MA, USA
Poster presentation at Signal Transduction Society (STS), 10th Joint Meeting at Weimar, Germany, November 2006. Functional profiling of pathogen-induced signaling pathways based on high throughput RNAi Screens
A discussion meeting of the RNA group (The first symposium on RNA research in India), February, 2003, Dept. of Microbiology and Cell biology, Indian Institute of Science (IISc), Bangalore, India
GLYCO XVII International Symposium on Glycoconjugates, Indian Institute of Science (IISc), Bangalore, India, 12-16, 2003
Workshop on Circulating Tumor Cells and Cancer Stem Cells from Research to Clinic: Next Generation Dx Summit Moving Assays to the Clinic, August 20-22, 2013 Washington, DC (Moderator: Marek Malecki, M.D., Ph.D., President, Phoenix Biomolecular Engineering Foundation; Visiting Professor, University of Wisconsin, Madison Instructors: Minetta C. Liu, M.D., Associate Professor, Department of Oncology and Department of Laboratory Medicine and Pathology, Mayo Clinic Cancer Center Avraham Rasooly, Ph.D., Special Assistant for Cancer Technologies and Translational Research, Division of Cancer Biology, NCI NIH Abraham Tzou, Medical Officer, FDA CDRH)