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Woo BJ, Moussavi-Baygi R, Karner H, Karimzadeh M, Garcia K, Joshi T, Yin K, Navickas A, Gilbert LA, Wang B, Asgharian H, Feng FY, Goodarzi H. Integrative identification of non-coding regulatory regions driving metastatic prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.14.535921. [PMID: 37398273 PMCID: PMC10312451 DOI: 10.1101/2023.04.14.535921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Large-scale sequencing efforts of thousands of tumor samples have been undertaken to understand the mutational landscape of the coding genome. However, the vast majority of germline and somatic variants occur within non-coding portions of the genome. These genomic regions do not directly encode for specific proteins, but can play key roles in cancer progression, for example by driving aberrant gene expression control. Here, we designed an integrative computational and experimental framework to identify recurrently mutated non-coding regulatory regions that drive tumor progression. Application of this approach to whole-genome sequencing (WGS) data from a large cohort of metastatic castration-resistant prostate cancer (mCRPC) revealed a large set of recurrently mutated regions. We used (i) in silico prioritization of functional non-coding mutations, (ii) massively parallel reporter assays, and (iii) in vivo CRISPR-interference (CRISPRi) screens in xenografted mice to systematically identify and validate driver regulatory regions that drive mCRPC. We discovered that one of these enhancer regions, GH22I030351, acts on a bidirectional promoter to simultaneously modulate expression of U2-associated splicing factor SF3A1 and chromosomal protein CCDC157. We found that both SF3A1 and CCDC157 are promoters of tumor growth in xenograft models of prostate cancer. We nominated a number of transcription factors, including SOX6, to be responsible for higher expression of SF3A1 and CCDC157. Collectively, we have established and confirmed an integrative computational and experimental approach that enables the systematic detection of non-coding regulatory regions that drive the progression of human cancers.
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Affiliation(s)
- Brian J Woo
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Ruhollah Moussavi-Baygi
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Heather Karner
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Mehran Karimzadeh
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
- Vector Institute, Toronto, ON, Canada
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada
- Arc Institute, Palo Alto 94305, USA
| | - Kristle Garcia
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Tanvi Joshi
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Keyi Yin
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Albertas Navickas
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Luke A. Gilbert
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
- Arc Institute, Palo Alto 94305, USA
| | - Bo Wang
- Vector Institute, Toronto, ON, Canada
- Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada
| | - Hosseinali Asgharian
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, US
| | - Felix Y. Feng
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California, USA
| | - Hani Goodarzi
- Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, California, USA
- Department of Urology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, US
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