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Recurrent Deletion of CHD1 in Prostate Cancer with Relevance to Cell Invasiveness

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Recurrent Deletion of CHD1 in Prostate Cancer with Relevance to Cell Invasiveness Oncogene (2012) 31, 4164–4170 & 2012 Macmillan Publishers Limited All rights reserved 0950-9232/12 www.nature.com/onc SHORT COMMUNICATION Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness S Huang1, ZG Gulzar2, K Salari1, J Lapointe3, JD Brooks2 and JR Pollack1 1Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA; 2Department of Urology, Stanford University, Stanford, CA, USA and 3Division of Urology, Department of Surgery, McGill University, Montreal, Quebec, Canada Though prostate cancer is often indolent, it is nonetheless distinguishing indolent from aggressive cancer (to a leading cause of cancer death. Defining the underlying determine whether and how aggressively to treat), and molecular genetic alterations may lead to new strategies identifying effective therapies for later-stage castration- for prevention or treatment. Towards this goal, we recurrent prostate cancer (Damber and Aus, 2008). performed array-based comparative genomic hybridiza- Defining the full range of molecular genetic alterations tion (CGH) on 86 primary prostate tumors. Among the in prostate cancer should provide improved under- most frequent alterations not associated with a known standing and new targets for prevention and treatment. cancer gene, we identified focal deletions within 5q21 in 15 The molecular alterations underlying prostate cancer out of 86 (17%) cases. By high-resolution tiling array are partially understood (DeMarzo et al., 2003; Shen CGH, the smallest common deletion targeted just one and Abate-Shen, 2010). Common events include gene, the chromatin remodeler chromodomain helicase deletion of tumor suppressors, including CDKN1B (p27/ DNA-binding protein 1 (CHD1). Expression of CHD1 KIP1), RB1, TP53, PTEN and the prostate-specific was significantly reduced in tumors with deletion homeobox transcription factor NKX3-1. Amplification (P ¼ 0.03), and compared with normal prostate of the MYC oncogene is also frequent. In addition, (P ¼ 0.04). Exon sequencing analysis also uncovered oncogenic fusions driving ETS-family oncogenic tran- nonsynonymous mutations in 1 out of 7 (14%) cell lines scription factors (ERG, ETV1, ETV4 and ETV5), most (LAPC4) and in 1 out of 24 (4%) prostate tumors commonly as TMPRSS2-ERG, have been identified in surveyed. RNA interference-mediated knockdown of approximately half of prostate cancers. Androgen receptor CHD1 in two nontumorigenic prostate epithelial cell alterations, including amplification and rearrangement, lines, OPCN2 and RWPE-1, did not alter cell growth, but can also occur in castration-recurrent prostate cancer. promoted cell invasiveness, and in OPCN2-enhanced cell More recently, genomic profiling by comparative clonogenicity. Taken together, our findings suggest that genomic hybridization (CGH) and single-nucleotide CHD1 deletion may underlie cell invasiveness in a subset polymorphism arrays have provided comprehensive of prostate cancers, and indicate a possible novel role of views of DNA copy number alterations in prostate altered chromatin remodeling in prostate tumorigenesis. cancer (Lapointe et al., 2004; Kim et al., 2007; Robbins Oncogene (2012) 31, 4164–4170; doi:10.1038/onc.2011.590; et al., 2011), and have led to the nomination of new published online 19 December 2011 prostate cancer genes, for example, NCOA2 (Taylor et al., 2010). Next-generation genome sequencing is also Keywords: prostate cancer; genomic profiling; tumor now beginning to reveal the full landscape of somatic suppressor; chromatin remodeling; cell invasion rearrangements (Berger et al., 2011). Here, we have carried out genomic profiling by array CGH of a large collection of primary prostate tumors. Introduction Among our findings, we identify focal recurrent deletions within 5q21 targeting the chromatin remodeler Prostate cancer is the most frequently diagnosed cancer chromodomain helicase DNA-binding protein (CHD1), and the second leading cause of cancer death among whose loss we characterize to be a driver of cancer cell men in the United States (Jemal et al., 2010); approxi- invasiveness. mately one in six men will be diagnosed within their lifetime. Prostate cancer exhibits a range of clinical behaviors, from indolent growth to highly aggressive Results and discussion and metastatic disease. Key unmet clinical needs include To survey the landscape of DNA copy number Correspondence: Dr JR Pollack, Department of Pathology, Stanford alterations in prostate cancer, we profiled a collection University School of Medicine, 269 Campus Drive, CCSR-3245A, of 86 primary prostate tumors (clinicopathological Stanford, CA 94305-5176, USA. E-mail: [email protected] characteristics summarized in Supplementary Table S1) Received 12 July 2011; revised 4 November 2011; accepted 14 November using Agilent 44K CGH arrays (Agilent, Santa Clara, 2011; published online 19 December 2011 CA, USA). Genomic Identification of Significant Targets CHD1 deletion in prostate cancer S Huang et al 4165 3q21.3 7p22.2 8p23.3 8q21.11 9q34.11 11q13.2 17q21.32 10-4.1 MYC 10-2.3 10-1.4 10-1.0 10-0.82 -0.71 0.011 10 0.25 1 2 3 4 5 67 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 q-value G-score 0.024 0.25 10-1.2 10-1.8 10-3.1 RYBP ZBTB16 SHQ1 PIK3R1 10-5.7 RGMB CDKN1B TP53 CHD1 PTEN 10-10 TMPRSS2-ERG NKX3.1 RB1 10-21 3p13 8p22 2q22.1 5q13.1 5q21.1 6q16.1 1p31.1 1q42.13 11q23.2 12p13.1 13q14.3 13q22.1 16q23.2 17p13.1 18q22.3 21q22.2 10q23.31 17q21.31 22q13.31 Figure 1 Landscape of copy number alterations in prostate cancer. Genomic Identification of Significant Targets in Cancer (GISTIC) plot identifies significant DNA copy number alterations (by consideration of both frequency and amplitude, and in comparison with randomly permuted data). Gains and losses are depicted in red and blue, respectively, and ordered by genome position. The significance threshold (false discovery rate, o0.25) is indicated, as are selected known cancer genes. Prostate tumors were obtained from radical prostatectomy cases performed at the Stanford University Hospital, with the Institutional Review Board approval and patient informed consent. Freshly-frozen specimens were cryostat sectioned and scalpel macrodissected to enrich tumor nuclei to 480%. Genomic DNA (and total RNA) were isolated using Qiagen Allprep DNA/RNA Mini Kits (Qiagen, Valencia, CA, USA). Tumor DNA and normal male reference DNA (pooled from eight donor leukocyte preparations) were respectively labeled with Cy5 and Cy3, as described (Kwei et al., 2008), then co-hybridized onto Agilent Human Genome CGH 44K arrays. Microarrays were scanned using an Agilent G2505C Microarray Scanner System, and normalized fluorescence ratios obtained using Feature Extraction 9.5.3 (Agilent). DNA gains and losses were called by Circular Binary Segmentation (Olshen et al., 2004) and significant alterations defined by GISTIC (Beroukhim et al., 2007). Array CGH data are accessible through the Gene Expression Omnibus (GSE29229). in Cancer analysis (Beroukhim et al., 2007) was applied CHD1 is a member of the chromodomain helicase to identify loci with significantly recurrent copy number DNA-binding (CHD) family, a group of ATP-depen- alteration, which included 19 deletions and 7 amplifica- dent chromatin remodelers that use the energy from tions (Figure 1). Deletions of known tumor suppressors ATP hydrolysis to alter histone–DNA contacts within included (ordered by chromosome) NKX3-1 (8p21.2) nucleosomes to modulate gene expression (Hall and (occurring in 38% of tumors), PTEN (10q23.31) (22%), Georgel, 2007; Marfella and Imbalzano, 2007). All CDKN1B (12p13.1) (20%), RB1 (13q14.2) (40%) and CHD family proteins (CHD1–9) have two tandem TP53 (17p13.1) (21%). Deletion of 21q22.2 (29%) also chromo (chromatin organization modifier) domains at defined intrachromosomal rearrangements generating the N-terminus and a SNF2-related helicase/ATPase TMPRSS2-ERG. Frequent gains included those on domain in the central region; CHD1 and CHD2 also chromosomes 7 (12%) and 8 (9%), the latter spanning have a C-terminal DNA-binding domain (Hall and MYC (8q24.21), and 9 (10%). Georgel, 2007). Intriguingly, other CHD family members Among the most significant deletions not associated have been linked to cancer, most notably CHD5 deletions with a known tumor suppressor (and therefore in neural-associated tumors (Bagchi and Mills, 2008). presumably pinpointing a novel candidate), we noted Consistent with a possible tumor-suppressor role, deletions at 5q21.1 in 15 out of 86 (17%) prostate CHD1 transcript levels (measured by microarray) were tumors. To more precisely map the boundaries of these significantly decreased (1.4-fold on average) in the deletions, we designed a custom high-density Agilent subset of prostate tumors with 5q21 deletion (P ¼ 0.03, 15K CGH array, with probes covering 6.5 Mb within two-tailed Mann–Whitney U-test), and in comparison 5q15–q21.1 and tiled every 500 bp. Profiling eight with normal prostate tissue (P ¼ 0.04) (Figure 2b). samples with informative deletions, we could delimit a Neither CHD1 deletion nor decreased expression was smallest common region of deletion of 120 kb significantly associated with specific clinicopathological (Figure 2a). Remarkably, the commonly deleted region features, including preoperative serum prostate-specific targeted just one gene, CHD1. antigen levels, tumor Gleason grade, tumor stage or Oncogene CHD1 deletion in prostate cancer S Huang et al 4166 538* 453 184 362* 248 490 45 166 184 248 237 366 S07866b 538 405 343 19 490 453 362 501 45 166 93.5 Mb 98 Mb 15.3 15.1 14 RGMB 13 12 11.2 CHD1 13 14 15 21 22 23 31 32 33 34 35 chr 5 104 Mb 99 Mb -1.50 1.5 -1.0 0 1.0 loss gain loss gain 1.5 P=0.04 ratio) 1.0 2 P=0.03 0.5 0 n=52 n=30 -0.5 -1.0 n=11 CHD1expression (log -1.5 Tumors with Tumors without Normal adjacent 5q21 deletion 5q21 deletion prostate Oncogene CHD1 deletion in prostate cancer S Huang et al 4167 biochemical recurrence (Supplementary Table S2).
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