Research Article Chromosomal Breakpoints in Primary Colon Cancer Cluster at Sites of Structural Variants in the Genome Jordi Camps,1 Marian Grade,1,3 Quang Tri Nguyen,1 Patrick Ho¨rmann,1 Sandra Becker,1 Amanda B. Hummon,1 Virginia Rodriguez,2 Settara Chandrasekharappa,2 Yidong Chen,1 Michael J. Difilippantonio,1 Heinz Becker,3 B. Michael Ghadimi,3 and Thomas Ried1 1Genetics Branch, Center for Cancer Research, National Cancer Institute/NIH; 2Genome Technology Branch, National Human Genome Research Institute/NIH, Bethesda, Maryland; and 3Department of General and Visceral Surgery, University Medicine Go¨ttingen, Go¨ttingen, Germany Abstract 8q, 13, and 20q as well as losses of chromosomes 4q, 8p, 17p, and 18q (2). Genomic aberrations on chromosome 8 are common in colon cancer, and are associated with lymph node and distant Within the last decade, microarray technology has been metastases as well as with disease susceptibility. This extensively applied to survey the cellular transcriptome of common prompted us to generate a high-resolution map of genomic solid tumors, including colorectal cancer, and for colon cancers, imbalances of chromosome 8 in 51 primary colon carcinomas gene expression signatures were subsequently correlated with using a custom-designed genomic array consisting of a tiling clinical outcome (for reviews, see refs. 3–5). However, high- path of BAC clones. This analysis confirmed the dominant role resolution mapping of chromosomal copy number changes has of this chromosome. Unexpectedly, the position of the break- only recently been achieved using BAC or cDNA clone-based arrays points suggested colocalization with structural variants in the (6–10). human genome. In order to map these sites with increased Chromosome 8q is one of the most frequently gained resolution and to extend the analysis to the entire genome, chromosomal arms in colorectal cancers (2), and it is we analyzed a subset of these tumors (n = 32) by comparative conceivable that it contains more oncogenes than just the genomic hybridization on a 185K oligonucleotide array MYC oncogene, which maps to chromosome band 8q24.21. A potential role of chromosome 8q for the development of lymph platform. Our comprehensive map of the colon cancer genome confirmed recurrent and specific low-level copy number node metastases has been previously reported (11), and changes of chromosomes 7, 8, 13, 18, and 20, and unveiled overexpression of a gene, PRL-3, that maps to chromosome additional, novel sites of genomic imbalances including 8q24.3has been implied in the development of liver metastases amplification of a histone gene cluster on chromosome (12). Moreover, the 8q24 locus contains single nucleotide 6p21.1-21.33 and deletions on chromosome 4q34-35. The polymorphisms that are associated with an increased risk for systematic comparison of segments of copy number change the development of colon cancer (13–15). with gene expression profiles showed that genomic imbal- Recently, a new class of genetic variation among humans has ances directly affect average expression levels. Strikingly, we become recognized as a major source of genetic diversity. Termed observed a significant association of chromosomal break- structural variations, these polymorphisms can present themselves as copy number variants (CNV) and segmental duplications, points with structural variants in the human genome: 41% of all copy number changes occurred at sites of such copy which could be CNVs, but are not necessarily so (16–19). These À number variants (P < 2.2e 16). Such an association has not polymorphisms could induce chromosomal rearrangements (20). been previously described and reveals a yet underappreciated One of our previous analyses of chromosomal aberrations in cell plasticity of the colon cancer genome; it also points to lines established from different carcinomas indicated that genomic potential mechanisms for the induction of chromosomal copy number changes could be triggered by jumping trans- locations, many of which originated in the pericentromeric breakage in cancer cells. [Cancer Res 2008;68(5):1284–95] heterochromatin of several chromosomes (21). These regions frequently contain segmental duplications and other structural Introduction variants of the genome (22). Taken together, these data enticed us Colorectal cancer is the second leading cause of cancer death to systematically explore the genomic aberration profile and the in Europe and in the United States, with f300,000 new cases potential involvement of structural variants of the human genome and 200,000 deaths each year (1). Cytogenetic and molecular in the genesis of chromosomal aberrations in this common cancer. cytogenetic studies clearly established that the colorectal cancer We therefore established a high-resolution map of genomic copy genome is defined by a specific distribution of genomic imbalances, number changes in 51 primary colon carcinomas using compar- most prominently, gains of chromosomes and chromosome arms 7, ative genomic hybridization (CGH) on both a BAC-based genomic tiling array for chromosome 8 and, for a subset of those, using a 185K oligonucleotide platform for whole genome coverage. Note: Supplementary data for this article are available at Cancer Research Online (http://cancerres.aacrjournals.org/). Requests for reprints: Thomas Ried, Genetics Branch, Center for Cancer Materials and Methods Research, National Cancer Institute/NIH, Building 50, Room 1408, 50 South Drive, Bethesda, MD 20892. Phone: 301-594-3118; Fax: 301-435-4428; E-mail: riedt@mail. nih.gov. Patients and Sample Collection I2008 American Association for Cancer Research. The 51 patients included in this study were diagnosed with primary doi:10.1158/0008-5472.CAN-07-2864 adenocarcinomas of the colon, and treated at the Department of General Cancer Res 2008; 68: (5). March 1, 2008 1284 www.aacrjournals.org Downloaded from cancerres.aacrjournals.org on September 30, 2021. © 2008 American Association for Cancer Research. Chromosomal Breakpoints Cluster at Copy Number Variants Surgery, University Medicine Go¨ttingen, Go¨ttingen, Germany. All patients immediately after surgery and stored on ice for inspection by an experienced received standardized surgery and histopathologic workup, and tumor pathologist. Consistent with standard procedures, only samples with a staging was based on WHO criteria (23). Twenty-five tumors were associated tumor cell content of at least 70% were included in this study. Biopsies of with lymph node metastases [International Union Against Cancer (UICC)- normal adjacent mucosa were collected from some patients when possible. III], whereas 26 tumors were not (UICC-II). Tumor samples were obtained Table 1 summarizes the clinical data and experimental setup. Table 1. Clinical information and experimental setup Patient code Histopathology Chromosome 8 Gene expression 185K oligonucleotide BAC microarray microarray microarray ÂÂ Â CC-P1 pT3a pN0 (0/17) M0 R0 G2 ÂÂ CC-P2 pT3 pN0 (0/19) M0 R0 G2 ÂÂ CC-P3pT 3 pN0 (0/29) M0 R0 G2 ÂÂ CC-P4 pT3a pN0 (0/31) M0 R0 G3 ÂÂ Â CC-P6 pT4 pN0 (0/17) M0 R0 G3 ( ) ÂÂ CC-P7 pT3 pN0 (0/25) M0 R0 G2 ÂÂ Â CC-P8 pT3 pN0 (0/44) M0 R0 G2 ÂÂ Â CC-P9 pT3b pN0 (0/31) M0 R0 G1-2 ÂÂ Â CC-P10 pT3b pN0 (0/20) M0 R0 G2 Â ÂÂ CC-P11 pT3a pN0 (0/21) M0 R0 G2 ( ) ÂÂ Â CC-P12 pT3 pN0 (0/27) M0 R0 G2 ÂÂ CC-P13pT 3b pN0 (0/39) M0 R0 G2 ÂÂ Â CC-P14 pT3 pN0 (0/23) M0 R0 G2 ÂÂ Â CC-P15 pT3 pN0 (0/31) M0 R0 G3 ÂÂ Â CC-P16 pT3 pN0 (0/15) M0 R0 G2 ÂÂ Â CC-P19 pT4 pN0 (0/57) M0 R0 G2 ÂÂ Â CC-P20 pT3b pN0 (0/28) M0 R0 G2 ÂÂ Â CC-P21 pT3b pN0 (0/24) M0 R0 G2 ÂÂ Â CC-P22 pT3 pN0 (0/15) M0 R0 G2 ÂÂ Â CC-P23pT 3 pN0 (0/21) M0 R0 G3 ÂÂ Â CC-P24 pT3 pN0 (0/17) M0 R0 G2 ÂÂ CC-P26 pT3 pN0 (0/20) M0 R0 G2 ÂÂ CC-P27 pT3 pN0 (0/26) M0 R0 G2 ÂÂ CC-P28 pT3 pN0 (0/20) M0 R0 G2 ÂÂ CC-P30 pT3b pN0 (0/35) M0 R0 G2 ÂÂ CC-P32 pT3a pN0 (0/23) M0 R0 G2 ÂÂ CC-P34 pT3 pN1 (2/17) M0 R0 G2 ÂÂ CC-P35 pT4 pN1 (2/51) M0 R0 G2 ÂÂ CC-P36 pT3 pN2 (15/42) M0 R0 G2 ÂÂ CC-P37 pT3 pN1 (1/25) M0 R0 G2 ÂÂ Â CC-P38 pT2 pN1 (1/23) M0 R0 G2-3 ÂÂ Â CC-P39 pT3c pN1 (1/28) M0 R0 G2 ÂÂ Â CC-P42 pT3a pN1 (1/2) M0 R0 G2 ÂÂ Â CC-P44 pT1-3 pN1 (2/26) M0 R0 G2 ÂÂ Â CC-P45 pT4 pN2 (4/36) M0 R0 G2 ÂÂ CC-P46 pT3b pN2 (8/16) M0 R0 G3 Â ÂÂ CC-P47 pT3 pN2 (12/13) M0 R0 G2 ( ) ÂÂ Â CC-P48 pT3a pN2 (5/23) M0 R0 G2 Â ÂÂ CC-P49 pT4 pN2 (9/21) M0 R0 G2 ( ) ÂÂ Â CC-P51 pT3c pN2 (4/23) M0 R0 G2 Â ÂÂ CC-P53pT 4 pN2 (11/26) M0 R0 G2 ( ) Â ÂÂ CC-P54 pT3 pN1 (3/22) M0 R0 G2 ( ) ÂÂ Â CC-P56 pT3b pN1 (2/20) M0 R0 G2 ÂÂ CC-P58 pT3 pN2 (1/32) M0 R0 G2 ÂÂ Â CC-P60 pT3 pN1 (2/24) M0 R0 G2 ÂÂ Â CC-P65 pT3 pN1 (2/22) M0 R0 G2-3 ÂÂ CC-P66 pT2 pN2 (4/20) M0 R0 G2 ÂÂ CC-P68 pT3c pN2 (12/22) M0 R0 G3 ÂÂ CC-P70 pT3 pN2 (12/21) M0 R0 G2 ÂÂ Â CC-P71 pT3 pN1 (1/18) M0 R0 G3 ÂÂ Â CC-P72 pT2 pN1 (2/18) M0 R0 G3 NOTE: (Â), not included.