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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

An Unbiased Functional Genetics Screen Identifies Rare Activating ERBB4 Mutations

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

This work stems from my M.Sc. Thesis Project, which led us to study L1TD1, an embryonic stem cell marker, in the context of colorectal cancer. With the meta-analysis of 900+ clinical samples, we uncovered that L1TD1 is a prognostic marker in colon cancer. We discovered that a higher L1TD1 expression associates with a prolonged disease-free survival (despite adjusting for various clinical parameters like Stage, KRAS/TP53 mutation status, etc.). We subsequently filed a patent based on our findings.

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

Here, we established a screening platform using EGFR as a model gene, where in high-throughput experiment, thousands of variants of a gene can be functionally characterized using a phenotypic assay (here, cell proliferation).

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

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

Different responses of colorectal cancer cells to alternative sequences of cetuximab and oxaliplatin

Elli Narvi, Katri Vaparanta, Anna Karrila, Deepankar Chakroborty, Sakari Knuutila, Arto Pulliainen, Maria Sundvall, Klaus Elenius

Receptor tyrosine kinase profiling of ischemic heart identifies ROR1 as a potential therapeutic target

Juho Heliste, Anne Jokilammi, Ilkka Paatero, Deepankar Chakroborty, Christoffer Stark, Timo Savunen, Maria Laaksonen, Klaus Elenius

Transcriptional Repressor HIC1 Contributes to Suppressive Function of Human Induced Regulatory T Cells

Ubaid Ullah, Syed Bilal Ahmad Andrabi, Subhash Kumar Tripathi, Obaiah Dirasantha, Kartiek Kanduri, Sini Rautio, Catharina C. Gross, Sari Lehtimäki, Kanchan Bala, Johanna Tuomisto, Urvashi Bhatia, Deepankar Chakroborty, Laura L. Elo, Harri Lähdesmäki, Heinz Wiendl, Omid Rasool, Riitta Lahesmaa

The L1TD1 protein interactome reveals the importance of post-transcriptional regulation in human pluripotency

Maheswara Reddy Reddy Emani, Elisa Närvä, Aki Stubb, Deepankar Chakroborty, Miro Viitala, Anne Rokka, Nelly Rahkonen, Robert Moulder, Konstantin Denessiouk, Ras Trokovic, Riikka Lund, Laura L. L. Elo, Riitta Lahesmaa