Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles

Bülent Arman Aksoy, Emek Demir, Ozgun Babur, Weiqing Wang, Xiaohong Jing, Nikolaus Schultz, Chris Sander

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Motivation: Somatic homozygous deletions of chromosomal regions in cancer, while not necessarily oncogenic, may lead to therapeutic vulnerabilities specific to cancer cells compared with normal cells. A recently reported example is the loss of one of the two isoenzymes in glioblastoma cancer cells such that the use of a specific inhibitor selectively inhibited growth of the cancer cells, which had become fully dependent on the second isoenzyme. We have now made use of the unprecedented conjunction of large-scale cancer genomics profiling of tumor samples in The Cancer Genome Atlas (TCGA) and of tumor-derived cell lines in the Cancer Cell Line Encyclopedia, as well as the availability of integrated pathway information systems, such as Pathway Commons, to systematically search for a comprehensive set of such epistatic vulnerabilities. Results: Based on homozygous deletions affecting metabolic enzymes in 16 TCGA cancer studies and 972 cancer cell lines, we identified 4104 candidate metabolic vulnerabilities present in 1019 tumor samples and 482 cell lines. Up to 44% of these vulnerabilities can be targeted with at least one Food and Drug Administration-approved drug. We suggest focused experiments to test these vulnerabilities and clinical trials based on personalized genomic profiles of those that pass preclinical filters. We conclude that genomic profiling will in the future provide a promising basis for network pharmacology of epistatic vulnerabilities as a promising therapeutic strategy.

Original languageEnglish (US)
Pages (from-to)2051-2059
Number of pages9
JournalBioinformatics
Volume30
Issue number14
DOIs
StatePublished - Jul 15 2014
Externally publishedYes

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Vulnerability
Genomics
Cancer
Cells
Prediction
Cell
Neoplasms
Isoenzymes
Tumors
Therapeutics
Tumor
Line
Atlas
Genes
Profiling
Atlases
Deletion
Pathway
Drugs
Genome

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. / Aksoy, Bülent Arman; Demir, Emek; Babur, Ozgun; Wang, Weiqing; Jing, Xiaohong; Schultz, Nikolaus; Sander, Chris.

In: Bioinformatics, Vol. 30, No. 14, 15.07.2014, p. 2051-2059.

Research output: Contribution to journalArticle

Aksoy, Bülent Arman ; Demir, Emek ; Babur, Ozgun ; Wang, Weiqing ; Jing, Xiaohong ; Schultz, Nikolaus ; Sander, Chris. / Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. In: Bioinformatics. 2014 ; Vol. 30, No. 14. pp. 2051-2059.
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