Deepankar Chakroborty

PhD student (Turku Doctoral Programme of Molecular Medicine)

Hi!!

I am Deepankar, but I usually go by the shorter version: “Deep”. I did my PhD research at the University of Turku in Finland (public defense scheduled in February 2023). I was actively involved in several projects, predominantly in the field of Cancer Genetics, which were aimed at understanding molecular mechanisms of different human cancers and identifying opportunities for developing targeted therapeutics.

During the PhD, 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 various TKIs. Using my screening workflow I am also investigating therapeutic resistance to ERBB-targeted inhibitors.

I have also developed a collection of webtools using R and shiny, some of which are publicly hosted at https://eleniuslabtools.utu.fi

Here is my detailed CV in a PDF format.

Interests

Kinases & Kinase inhibitors
Receptor Tyrosine Kinases
Targeted therapeutics
Therapeutic resistance
Predictive biomarkers
Somatic mutations in Cancer

Education

PhD (Medical Biochemistry and Genetics), 2015 - 2022
Institute of Biomedicine, University of Turku, Finland
MSc (Bioinformatics), 2012 - 2014
Turku Centre for Biotechnology, University of Turku, Finland
B.Tech in Biotechnology, 2008 - 2012
Amity Institute of Biotechnology, Amity University, India

Experience

PhD student

University of Turku

Jan 2015 – Dec 2022 Turku, Finland

Conducting Functional Genetics research at the laboratory of Prof. Klaus Elenius. My responsibilities included:

Planning and conducting Functional Genetics experiments
Mammalian cell culture & dose-response analysis (Kinase inhibitors)
Analysis of next-generation sequencing data

Research Assistant

University of Turku

Jun 2014 – Dec 2014 Turku, Finland

While working at the laboratory of Prof. Klaus Elenius. I cloned and tested some retroviral mammalian expression constructs. I also evaluated different methods of random mutagenesis.

Master’s thesis student

Turku Centre for Biotechnology

Nov 2013 – May 2014 Turku, Finland

Under supervision of Prof. Laura Elo, my project was to investigate an embryonic stem cell marker and its interaction partners in gene expression datasets from different cancer types.

Summer Internship

Turku Centre for Biotechnology

Jun 2013 – Jul 2013 Turku, Finland

During the internship (supervised by Prof. Laura Elo) my primary task was mining cancer databases (like Oncomine, GEO, ArrayExpress, etc.) and summarizing the data by performing bioinformatics analyses.

Featured Publication

Deepankar Chakroborty, Veera K. Ojala, Anna M. Knittle, Jasmin Drexler, Mahlet Z. Tamirat, Regina Ruzicka, Karin Bosch, Johanna Woertl, Susanne Schmittner, Laura L. Elo, Mark S. Johnson, Kari J. Kurppa, Flavio Solca, Klaus Elenius

January 2022 Cancer Research Communications research article

An Unbiased Functional Genetics Screen Identifies Rare Activating ERBB4 Mutations

ERBB4 is a member of the ERBB family of oncogenes (with EGFR, HER2 & HER3). ERBB4 is frequently mutated in different cancers, but the functional impact of its somatic mutations remains unknown. Here, in an unbiased functional genetics screen, we analyzed the function of over 8,000 ERBB4 variants that were generated by random mutagenesis. The data indicate the presence of rare activating ERBB4 mutations in cancer, with potential to be targeted with clinically approved pan-ERBB inhibitors.

Recent Publications

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Database of recurrent mutations (DORM), a web tool to browse recurrent mutations in cancers

There is an abundance of recurrent (n > 1) but infrequent somatic mutations in cancer. We built a database to list all the recurrent mutations identified from genome-scale DNA sequencing of cancer samples spanning 38 primary sites sourced from the COSMIC cancer registry.

Deepankar Chakroborty, Ilkka Paatero, Kari J. Kurppa, Klaus Elenius

Database of recurrent mutations (DORM), a web tool to browse recurrent mutations in cancers

An Unbiased Functional Genetics Screen Identifies Rare Activating ERBB4 Mutations

ERBB4 is a member of the ERBB family of oncogenes (with EGFR, HER2 & HER3). ERBB4 is frequently mutated in different cancers, but the functional impact of its somatic mutations remains unknown. Here, in an unbiased functional genetics screen, we analyzed the function of over 8,000 ERBB4 variants that were generated by random mutagenesis. The data indicate the presence of rare activating ERBB4 mutations in cancer, with potential to be targeted with clinically approved pan-ERBB inhibitors.

Deepankar Chakroborty, Veera K. Ojala, Anna M. Knittle, Jasmin Drexler, Mahlet Z. Tamirat, Regina Ruzicka, Karin Bosch, Johanna Woertl, Susanne Schmittner, Laura L. Elo, Mark S. Johnson, Kari J. Kurppa, Flavio Solca, Klaus Elenius