Transcription factor activities enhance markers of drug sensitivity in cancer

Luz M Garcia-Alonso, Francesco Iorio, Angela Matchan, Nuno A Fonseca, Patricia Jaaks, Gareth Peat, Miguel Pignatelli, Fiammetta Falcone, Cyril H Benes, Ian Dunham, Graham R Bignell, Simon McDade, Mathew J Garnett, Julio Saez-Rodriguez

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Transcriptional dysregulation induced by aberrant Transcription factors (TFs) is a key feature of cancer, but its global influence on drug sensitivity has not been examined. Here we infer the transcriptional activity of 127 TFs through analysis of RNA-seq gene expression data newly generated for 448 cancer cell lines, combined with publicly available datasets to survey a total of 1,056 cancer cell lines and 9,250 primary tumors. Predicted TF activities are supported by their agreement with independent shRNA essentiality profiles and homozygous gene deletions, and recapitulate mutant-specific mechanisms of transcriptional dysregulation in cancer. By analysing cell line responses to 265 compounds, we uncovered numerous TFs whose activity interacts with anti-cancer drugs. Importantly, combining existing pharmacogenomic markers with TF activities often improves the stratification of cell lines in response to drug treatment. Our results, which can be queried freely at, offer a broad foundation for discovering opportunities to refine personalised cancer therapies.

Original languageEnglish
Pages (from-to)1-35
JournalCancer Research
Issue number3
Early online date11 Dec 2017
Publication statusEarly online date - 11 Dec 2017


  • Journal Article


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