Genomic Alterations Detected in Colon Cancer Cell Lines by Using Array-Comparative Genomic Hybridization

Kim, Mi Jin; Park, Soo Yeun; Hann, Hoo Jae

Abstract

Cancer development is accompanied by genetic events like losses, gains and amplification of certain chromosome regions or alterations of chromatin structure. Array-based CGH (Array-CGH) is a highly comprehensive, sensitive and fast technique to allow investigation of general changes in target oncogenes and tumor suppressor genes. Recently, the prevalence of colon cancer is rapidly increasing in Korea and now it is the fourth leading cause of cancer death. So, the purpose of this study is to examine genomic alterations in colon cancer cell lines and to search novel genes which might be related to the development of colon cancer. In this study, genomic alterations are analyzed by using array-CGH in three colon cell lines from Korean, SNU-81, SNU-407 and SNU-1047. We observed numerous chromosomal imbalances from all cell lines. The common chromosomal gains were observed in 1p36.33, 1q22, 1q32.1, 2q35, 8p12, 8q22.3, 14q32.33, 16p13.3, and 16q24. Common chromosomal losses were found in 4q22.1, 9q13, 14q21.1, 14q32.33, 20p12.1, Xq21.1, and Yq11.223. Gains of 1p, 2q, 8p, and 8q or losses of 4q, 14q and 20p are already known to be associated with the colon cancer development. For gene alterations, we could see gains of some genes such as ELF3 and AAMP, which were already reported to be associated with colon cancer. Also, we could find some gene alterations which were known to be associated with other cancer types. These genes were GON4L, RNPEP, TMBIM1, TIMM17A, GPBAR1, PPP1R13B and SOX8. Besides, we found alterations of new genes such as PKND and LEPROTL1. The association of these genes with colon cancer is first demonstrated here. These genes may be the novel candidate genes functioning in the development of colon cancer. In conclusion, array-CGH demonstrated the complexity of genetic aberrations in several colon cell lines. These data about the patterns of genomic alterations could be a basic step for understanding more detailed genetic events in the carcinogenesis and also provide information about possible target genes for diagnosis and treatment in colon cancer.