Bottom-up, integrated -omics analysis identifies broadly dosage-sensitive genes in breast cancer samples from TCGA

Bobak D. Kechavarzi, Huanmei Wu, Thompson N. Doman

Research output: Contribution to journalArticle

Abstract

The massive genomic data from The Cancer Genome Atlas (TCGA), including proteomics data from Clinical Proteomic Tumor Analysis Consortium (CPTAC), provides a unique opportunity to study cancer systematically. While most observations are made from a single type of genomics data, we apply big data analytics and systems biology approaches by simultaneously analyzing DNA amplification, mRNA and protein abundance. Using multiple genomic profiles, we have discovered widespread dosage compensation for the extensive aneuploidy observed in TCGA breast cancer samples. We do identify 11 genes that show strong correlation across all features (DNA/mRNA/protein) analogous to that of the well-known oncogene HER2 (ERBB2). These genes are generally less well-characterized regarding their role in cancer and we advocate their further study. We also discover that shRNA knockdown of these genes has an impact on cancer cell growth, suggesting a vulnerability that could be used for cancer therapy. Our study shows the advantages of systematic big data methodologies and also provides future research directions.

Original languageEnglish (US)
Article numbere0210910
JournalPLoS ONE
Volume14
Issue number1
DOIs
StatePublished - Jan 1 2019

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Gene Dosage
Atlases
breast neoplasms
Genes
Genome
Breast Neoplasms
neoplasms
genome
dosage
Neoplasms
genes
genomics
sampling
proteomics
Proteomics
Messenger RNA
DNA
Cell growth
Gene Knockdown Techniques
oncogenes

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

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Bottom-up, integrated -omics analysis identifies broadly dosage-sensitive genes in breast cancer samples from TCGA. / Kechavarzi, Bobak D.; Wu, Huanmei; Doman, Thompson N.

In: PLoS ONE, Vol. 14, No. 1, e0210910, 01.01.2019.

Research output: Contribution to journalArticle

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