Deepankar Chakroborty

PhD student (Turku Doctoral Programme of Molecular Medicine)

Hi!!

I am Deepankar, but I usually go by the shorter version: “Deep”. I am a PhD student enrolled at the University of Turku in Finland. I am actively involved in several projects, predominantly in the field of Cancer Genetics, which are aimed at understanding molecular mechanisms of different human cancers and identifying opportunities for developing targeted therapeutics.

During my 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 hosted at https://eleniuslabtools.utu.fi.

Here’s a shorter version of my CV (PDF).

Interests

Kinases & Kinase inhibitors
Receptor Tyrosine Kinases
Mutations in EGFR family
Targeted therapeutics
Therapeutic resistance
Predictive biomarkers

Education

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

Experience

PhD student

University of Turku

Jan 2015 – Present 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 that is frequently mutated in different cancer types but the functional impact of its somatic mutations remains unknown. Here, we have analyzed the function of over 8,000 randomly mutated ERBB4 variants in an unbiased functional genetics screen. 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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An Unbiased Functional Genetics Screen Identifies Rare Activating ERBB4 Mutations

ERBB4 is a member of the ERBB family of oncogenes that is frequently mutated in different cancer types but the functional impact of its somatic mutations remains unknown. Here, we have analyzed the function of over 8,000 randomly mutated ERBB4 variants in an unbiased functional genetics screen. 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

Identification of Predictive ERBB Mutations by Leveraging Publicly Available Cell Line Databases

Marika K. A. Koivu, Deepankar Chakroborty, Mahlet Z. Tamirat, Mark S. Johnson, Kari J. Kurppa, Klaus Elenius

L1TD1 - a prognostic marker for colon cancer

Deepankar Chakroborty, Maheswara Reddy Emani, Riku Klén, Camilla Böckelman, Jaana Hagström, Caj Haglund, Ari Ristimäki, Riitta Lahesmaa, Laura L. Elo

An unbiased in vitro screen for activating epidermal growth factor receptor mutations

Deepankar Chakroborty, Kari J. Kurppa, Ilkka Paatero, Veera K. Ojala, Marika Koivu, Mahlet Z. Tamirat, Jussi P. Koivunen, Pasi A. Jänne, Mark S. Johnson, Laura L. Elo, Klaus Elenius