My name is Deepankar, but I generally go by “Deep”. I am a PhD student at the University of Turku in Finland. At the moment, I am conducting research predominantly in the field of Cancer Genetics. I am actively involved in several projects which are aimed at understanding molecular mechanisms of different human Cancers and identifying opportunities for developing targeted therapeutics.
As my PhD project, I developed a new high-throughput screen to discern activating mutations in kinases by constructing a cDNA library encompassing all possible point-mutations in the said kinase. So far, the screen has been used to study the EGFR family of RTKs (EGFR, HER2, HER3, and HER4) and identify activating mutations and assess their druggability with TKIs. Using my screening workflow I am also investigating Therapeutic resistance to ERBB-targeted inhibitors.
Here’s a shorter version of my CV (PDF).
PhD in Medical Biochemistry and Genetics, 2015 - now
University of Turku, Finland
MSc in Bioinformatics, 2014
University of Turku, Finland
B.Tech in Biotechnology, 2012
Amity University, India
Conducting Functional Genetics research at the laboratory of Prof. Klaus Elenius. My responsibilities included:
Cancer tissues harbor thousands of mutations, and a given oncogene may be mutated at hundreds of sites, yet only a few of these mutations have been functionally tested. Here, we describe an unbiased platform for the functional characterization of thousands of variants of a single receptor tyrosine kinase (RTK) gene in a single assay. Our in vitro screen for activating mutations (iSCREAM) platform enabled rapid analysis of mutations conferring gain-of-function RTK activity promoting clonal growth. The screening strategy included a somatic model of cancer evolution and utilized a library of 7,216 randomly mutated epidermal growth factor receptor (EGFR) single-nucleotide variants that were tested in murine lymphoid Ba/F3 cells. These cells depend on exogenous interleukin-3 (IL-3) for growth, but this dependence can be compensated by ectopic EGFR overexpression, enabling selection for gain-of-function EGFR mutants. Analysis of the enriched mutants revealed EGFR A702V, a novel activating variant that structurally stabilized the EGFR kinase dimer interface and conferred sensitivity to kinase inhibition by afatinib. As proof of concept for our approach, we recapitulated clinical observations and identified the EGFR L858R as the major enriched EGFR variant. Altogether, iSCREAM enabled robust enrichment of 21 variants from a total of 7,216 EGFR mutations. These findings indicate the power of this screening platform for unbiased identification of activating RTK variants that are enriched under selection pressure in a model of cancer heterogeneity and evolution.
Courses and Conferences
Debian, Raspberry Pi
Shell, R, python
I ❤️ Primes!
Pihole, DNS resolvers, FOSS
Equities, ETFs, #Essentialism
The Office, Dark, Chuck