|
1
|
Zhang Z, Zhou C, Li X, Barnes SD, Deng S, Hoover E, Chen CC, Lee YS, Zhang Y, Wang C, Metang LA, Wu C, Tirado CR, Johnson NA, Wongvipat J, Navrazhina K, Cao Z, Choi D, Huang CH, Linton E, Chen X, Liang Y, Mason CE, de Stanchina E, Abida W, Lujambio A, Li S, Lowe SW, Mendell JT, Malladi VS, Sawyers CL, Mu P. Loss of CHD1 Promotes Heterogeneous Mechanisms of Resistance to AR-Targeted Therapy via Chromatin Dysregulation. Cancer Cell 2020; 37:584-598.e11. [PMID: 32220301 PMCID: PMC7292228 DOI: 10.1016/j.ccell.2020.03.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 11/04/2019] [Accepted: 02/28/2020] [Indexed: 12/25/2022]
Abstract
Metastatic prostate cancer is characterized by recurrent genomic copy number alterations that are presumed to contribute to resistance to hormone therapy. We identified CHD1 loss as a cause of antiandrogen resistance in an in vivo small hairpin RNA (shRNA) screen of 730 genes deleted in prostate cancer. ATAC-seq and RNA-seq analyses showed that CHD1 loss resulted in global changes in open and closed chromatin with associated transcriptomic changes. Integrative analysis of this data, together with CRISPR-based functional screening, identified four transcription factors (NR3C1, POU3F2, NR2F1, and TBX2) that contribute to antiandrogen resistance, with associated activation of non-luminal lineage programs. Thus, CHD1 loss results in chromatin dysregulation, thereby establishing a state of transcriptional plasticity that enables the emergence of antiandrogen resistance through heterogeneous mechanisms.
Collapse
MESH Headings
- Androgen Antagonists/pharmacology
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Cell Proliferation
- Chromatin/genetics
- Chromatin/metabolism
- DNA Helicases/antagonists & inhibitors
- DNA Helicases/genetics
- DNA-Binding Proteins/antagonists & inhibitors
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Drug Resistance, Neoplasm/genetics
- Gene Expression Regulation, Neoplastic
- High-Throughput Screening Assays
- Humans
- Male
- Mice
- Prostatic Neoplasms, Castration-Resistant/drug therapy
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/pathology
- RNA, Small Interfering/genetics
- Receptors, Androgen/chemistry
- Receptors, Androgen/genetics
- Transcription Factors/metabolism
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Zeda Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chuanli Zhou
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaoling Li
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Spencer D Barnes
- Bioinformatics Core Facility of the Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Su Deng
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabeth Hoover
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chi-Chao Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Young Sun Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, La Jolla, CA, USA
| | - Choushi Wang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lauren A Metang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chao Wu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Nickolas A Johnson
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - John Wongvipat
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Zhen Cao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Danielle Choi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chun-Hao Huang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA
| | - Eliot Linton
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xiaoping Chen
- Department of Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yupu Liang
- Center for Clinical and Translational Science, Rockefeller University, New York, NY 10065, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Elisa de Stanchina
- Department of Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Amaia Lujambio
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sheng Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Joshua T Mendell
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Venkat S Malladi
- Bioinformatics Core Facility of the Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Ping Mu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|