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Dhingra P, Martinez-Fundichely A, Berger A, Huang FW, Forbes AN, Liu EM, Liu D, Sboner A, Tamayo P, Rickman DS, Rubin MA, Khurana E. Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network. Genome Biol 2017; 18:141. [PMID: 28750683 PMCID: PMC5530464 DOI: 10.1186/s13059-017-1266-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 06/27/2017] [Indexed: 11/22/2022] Open
Abstract
We report a novel computational method, RegNetDriver, to identify tumorigenic drivers using the combined effects of coding and non-coding single nucleotide variants, structural variants, and DNA methylation changes in the DNase I hypersensitivity based regulatory network. Integration of multi-omics data from 521 prostate tumor samples indicated a stronger regulatory impact of structural variants, as they affect more transcription factor hubs in the tissue-specific network. Moreover, crosstalk between transcription factor hub expression modulated by structural variants and methylation levels likely leads to the differential expression of target genes. We report known prostate tumor regulatory drivers and nominate novel transcription factors (ERF, CREB3L1, and POU2F2), which are supported by functional validation.
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Affiliation(s)
- Priyanka Dhingra
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Alexander Martinez-Fundichely
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Adeline Berger
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Franklin W Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
- Cancer Program, The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
| | - Andre Neil Forbes
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Eric Minwei Liu
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
| | - Deli Liu
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
- Department of Urology, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Andrea Sboner
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, 10065, USA
| | - Pablo Tamayo
- Cancer Program, The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA, 02142, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - David S Rickman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, 10065, USA.
- Meyer Cancer Center, Weill Cornell Medical College, New York, New York, 10065, USA.
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, 10065, USA
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, 10065, USA
- Meyer Cancer Center, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Ekta Khurana
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA.
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, 10021, USA.
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, 10065, USA.
- Meyer Cancer Center, Weill Cornell Medical College, New York, New York, 10065, USA.
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