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Synthetic Essentiality of Chromatin Remodelling Factor CHD1 in PTEN

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Synthetic Essentiality of Chromatin Remodelling Factor CHD1 in PTEN LETTER doi:10.1038/nature21357 Synthetic essentiality of chromatin remodelling factor CHD1 in PTEN-deficient cancer Di Zhao1, Xin Lu1*, Guocan Wang1*, Zhengdao Lan1, Wenting Liao1, Jun Li2, Xin Liang1, Jasper Robin Chen1, Sagar Shah1, Xiaoying Shang1, Ming Tang2, Pingna Deng1, Prasenjit Dey1, Deepavali Chakravarti1, Peiwen Chen1, Denise J. Spring1, Nora M. Navone4, Patricia Troncoso5, Jianhua Zhang2, Y. Alan Wang1 & Ronald A. DePinho1 Synthetic lethality and collateral lethality are two well-validated identifying functional interactions of components in specific pathways conceptual strategies for identifying therapeutic targets in cancers that show mutually exclusive patterns of genomic alterations. Such with tumour-suppressor gene deletions1–3. Here, we explore an epistatic patterns include components of the retinoblastoma (Rb) or approach to identify potential synthetic-lethal interactions by p53 pathways, in which alterations in one gene in the pathway typ- screening mutually exclusive deletion patterns in cancer genomes. ically alleviates genetic pressure to alter another driver in the same We sought to identify ‘synthetic-essential’ genes: those that are pathway, consistent with minimal additional selective advantage to occasionally deleted in some cancers but are almost always retained the cancer cell9,10. in the context of a specific tumour-suppressor deficiency. We also Using The Cancer Genome Atlas (TCGA) database, we sought to posited that such synthetic-essential genes would be therapeutic establish and validate an approach for identifying potential synthetic- targets in cancers that harbour specific tumour-suppressor lethal interactions in cancer by screening for mutually exclusive dele- deficiencies. In addition to known synthetic-lethal interactions, this tion patterns in the cancer genome. More specifically, we searched approach uncovered the chromatin helicase DNA-binding factor for genes that might occasionally be deleted in some cancers (that CHD1 as a putative synthetic-essential gene in PTEN-deficient is, non-essential genes) but that are always retained in the context of cancers. In PTEN-deficient prostate and breast cancers, CHD1 deletion of a specific tumour suppressor, reasoning that the retained gene depletion profoundly and specifically suppressed cell proliferation, might be required for executing the cancer-promoting actions in the cell survival and tumorigenic potential. Mechanistically, functional context of a specific tumour-suppressor deficiency (that is, a synthetic- PTEN stimulates the GSK3β-mediated phosphorylation of CHD1 essential gene). By extension, we posited that inhibition of these degron domains, which promotes CHD1 degradation via the synthetic-essential genes would impair the survival and tumorigenic β-TrCP-mediated ubiquitination–proteasome pathway. Conversely, potential of cancer cells harbouring the specific tumour-suppressor PTEN deficiency results in stabilization of CHD1, which in turn deficiency. Here, we focused on prostate cancer owing to the frequent engages the trimethyl lysine-4 histone H3 modification to activate and early deletion of the PTEN tumour suppressor and the paucity of transcription of the pro-tumorigenic TNF–NF-κB gene network. actionable ‘oncogene’ targets in prostate cancer. This study identifies a novel PTEN pathway in cancer and provides The well established synthetic-lethal interaction of BRCA1 and a framework for the discovery of ‘trackable’ targets in cancers that PARP1 provides a measure of validation for our approach, since a mutu- harbour specific tumour-suppressor deficiencies. ally exclusive deletion pattern of BRCA1 and PARP1 is readily observed Prostate cancer is the second leading cause of cancer-related death in the prostate cancer TCGA database (Extended Data Fig. 1a). for men in the United States, with 180,890 new cases and 26,120 deaths Similarly, consistent with preclinical and clinical studies suggesting that annually (NCI SEER 2016; http://seer.cancer.gov/csr/1975_2013/). PTEN deficiency sensitizes prostate, colorectal and endometrial cancer Up to 70% of primary prostate tumours show loss of heterozygosity at cells to PARP inhibitors11,12, we observed a synthetic-essential rela- the PTEN locus4. In mouse models, prostate-specific deletion of Pten tionship between PTEN and PARP1 (Extended Data Fig. 1b). Another (Ptenpc−/−) results in prostatic intraepithelial neoplasia, which may mutually exclusive deletion pattern in prostate cancer points to an inter- progress to high-grade adenocarcinoma after a long latency period5, action between PTEN and polo-like kinase 4 (PLK4) (Extended Data a pattern consistent with the loss of PTEN acting as a key initiation Fig. 1b). This observation aligns well with the single-agent anti-tumour event in prostate cancer development. To date, therapeutic targeting activity of the PLK4 inhibitor CFI-400945 and its capacity to induce of the PTEN–PI3K–AKT pathway has yielded meagre clinical ben- the regression of PTEN-deficient cancers, compared with PTEN-intact efit, prompting continued efforts to identify obligate effectors of this cancer cells13. Together, these circumstantial data prompted us to important pathway in order to identify effective therapeutic targets for speculate that druggable essential dependencies (synthetic-essential PTEN-deficient cancers. genes) of specific tumour-suppressor gene deficiencies might be uncov- The notion of targeting synthetic-lethal vulnerabilities in cancer has ered by scanning the patterns of cancer genome deletions. been validated in the treatment of cancers that harbour specific loss-of- Large-scale genomic analyses of TCGA and other prostate cancer function mutations1,6. One celebrated example is the effectiveness of databases identified CHD1 (5q21 locus) as a locus that is deleted in poly(ADP)-ribose polymerase (PARP) inhibitors in BRCA-deficient some human prostate cancer cases (7–10%)14–16, but is consistently tumours2,7. More recently, collateral lethality has emerged as another retained in PTEN-deficient prostate cancer (Fig. 1a and Extended target-discovery strategy for cancers harbouring tumour-suppressor Data Fig. 1c). In addition, the pattern of mutual exclusivity with PTEN gene deletions that also delete neighbouring genes encoding func- deletion was observed for CHD1 but not for other CHD homologues tionally redundant yet essential activities, thereby creating cancer- (Extended Data Fig. 1d). The PTEN–CHD1 relationship was reinforced specific vulnerabilities3,8. Genomic analyses have also been helpful in by the strong negative correlation observed between CHD1 and PTEN 1Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA. 2Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA. 3Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA. 4Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA. 5Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA. * These authors contributed equally to this work. 484 | NATURE | VOL 542 | 23 FEB RUARY 2017 © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. LETTER RESEARCH a Prostatee adenocarcinoma (TCGA,CGCGAAr, ref.reeff. 16) n = 333333 b Low CHD1 High CHD1 CHD1: 7% PTEN: 17% EGFR: 2% AKT1: 2% AKT2: 0% AKT3: 2% Pearson’s r = –0.301; P = 0.001 1000 High PIK3CA: 5% CHD1 80 Amplifcation Deep deletion Missense mutation Truncating mutation Low CHD1 60 c Pearson’s r = 0.290; P = 0.006 d PC-3 100 40 Ctrl #2 High shCHD1 #4 80 CHD1 CHD1 20 Low 60 of total cases Percentage 0 CHD1 β-actin 0 1 2 PTEN g DU145 Ctrl 40 ) 3 6600 DU145 shCHD1 m P = 0.5484 (NS) Percentage of cases Percentage 20 400 0 2 3 4 5 Ctrl #2 #4 Gleason grade e 200 1,00010 f Ki67 Tumour volume (mm Tumour 0 800 048121620242832 ) 3 Time (days) PC-3 Ctrl PC-3 shCHD1 #2 P < 0.0001 800 600 PC-3 shCHD1 #4 P < 0.0001 Ctrl ) 3 DU145 PTEN KO Ctrl 600 DU145 PTEN KO shCHD1 400 P = 0.0012** 400 Tumour volume (mm Tumour 200 200 shCHD1 0 volume (mm Tumour 0510 15 20 25 30 35 40 0 Time (days) 048121620242832 Time (days) Figure 1 | Knockdown of CHD1 inhibits tumour growth of PTEN-null shCHD1 #2 and #4. Representative data of triplicate experiments prostate cancer. a, Genomic alterations of CHD1 and genes in the are shown. e, Measurement of subcutaneous tumour growth of PTEN–AKT pathway in TCGA prostate cancer database (n = 333)16. CHD1-knockdown and control PC-3 cells. Control, n = 10; shCHD1 #2, b, Representative images of CHD1 expression, and the negative correlation n = 10; shCHD1 #4, n = 8. f, Representative images of Ki67 staining of between CHD1 and PTEN expression in human prostatic hyperplasia and subcutaneous tumour tissues generated from samples in e. g, Measurement cancer samples (n = 127). c, Distribution of CHD1 expression in human of subcutaneous tumour growth of CHD1-knockdown PTEN-intact or prostate cancer samples with different Gleason grades (n = 90). Pearson -deficient DU145 cells. PTEN-knockout (KO) shCHD1 n = 5; other groups correlation coefficient and two-tailed P value are shown. d, Immunoblots n = 6 for each. Error bars in e and g indicate s.d. P values were determined of lysates and colony-formation assays generated from shRNA-mediated by two-tailed t-test. NS, not significant. Scale bars, 50 m m (b, f). CHD1-knockdown and control (ctrl) PC-3
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