Research Summary

Somatic Genetics of Human Cancer

The goal of Dutt laboratory is to develop a next generation of effective targeted therapies to improve treatment of cancer patients. Efforts involve genomic approaches using microarrays and advanced sequencing methodologies to interrogate somatic alterations in clinical cancer-specimens, with emphasis on carcinomas of the breast, lung and the head and neck. The group focuses on understanding the somatic genetic changes that occur in cancer, and what these genetic changes can tell us about how different cancers will behave. The major aspect of research involves:

Cancer Genomics: Using computational genomic approaches to uncover somatic genetic alterations in cancers, with a special focus on lung cancer, head and neck cancer, breast and cervical cancer; and, have pioneered many experimental and computational methods in cancer genomics.

Functional Genomics: The genome-discovery efforts are paired with biochemical and molecular experimental approaches, using tumor derived cell lines and transgenic mouse models. Specifically, the group focuses on to study FGFR3 and ERBB2 pathways that are subject to genomic alteration in lung cancers, in gallbladder cancer, respectively; and, those via the lineage specific oncogenes NOTCH1 in head and neck cancer.

Pathogen Discovery: The group has developed a computational pipeline, HPV Detector, to detect non-human DNA sequences in human clinical cancer samples. The researchers are currently expanding their investigations to  explore other possible pathogenic sequence present in the human cancer genome by developing, Cancer Pathogen Detector, and have recently discovered the presence of Non-typhoidal Salmonella in gallbladder cancer.

Figure Legend: The landscape of transcript fusion identified in early tongue tumors and HNSCC cell lines: Circos plot representation of high-quality candidate fusions transcripts identified in tongue tumors. From outside to inside: karyotype, Gene expression (TPM) and transcript fusions. Black lines track for gene expression, fusion transcripts arc colored by their chromosome of origin.