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Korean Journal of Obstetrics & Gynecology 2006;49(9):1881-1891.
Published online September 1, 2006.
Genomic gain and loss of cervical cancer using BAC Chip.
Guo Hua Ding, Su Mi Bae, Sun Young Kwak, Hyun Jin Min, Aery Lee, Hee Jeong Yu, Jeong Namkoong, Eun Kyeong Oh, Jae Eun Shin, Ji Hyang Choe, Seo Yun Tong, Sung Jae Shin, Yong Wan Kim, Jong Chul Shin, Byoung Don Han, Chong Kook Kim, Woong Shick Ahn
1Catholic Research Institute of Medical Science, The Catholic University of Korea.
2Department of Obstetrics and Gynecology, College of Medicine, The Catholic University of Korea. ahnws@catholic.ac.kr
3Koma Biotech Research Center, Seoul, Korea.
4College of Pharmacy, Seoul National University, Korea.
Cervical cancer has long been linked to the sexually transmitted human papillomavirus (HPV), and the oncoproteins E6 and E7 disrupt the functions of tumour suppressor genes, resulting in genetic alteration. It was shown that loss of heterozygosity at 6p is a common genetic alteration in cervical cancer. However, the molecular genetics of cancer have only recently been understood, and for the development of cervical cancer additional genetic alterations in host cell genes are required. The present study has identified the differential changes of the cervical cancer-associated genetic alterations by a genome-wide array based comparative genomic hybridization (array-CGH). METHODS: We analyzed 15 cases of cervical cancer from St. Mary's hospital of The paraffin-fixed tissue samples were microdissected under microscope and DNA was extracted by the procedures of proteinase K digestion and chloroform extraction. Array-based CGH and genomic PCR were carried out with statistical analyses such as hierarchical clustering and Gene Ontology. The BAC array used in this study consisted of 1,440 human BACs, the space among the clones were approximately 2.08 megabase (Macrogen, Seoul, Korea). RESULTS: All of 15 cases of cervical cancer showed specific gains and losses. The analysis limit of average gains and losses was 53%. A significant positive correlation was found between 1p36.32, 3p14.2, 3q27.1, 7p21.1, 8q24.3 and 11q13.1 changes through the cervical carcinogenesis. The high-level of gain regions, BAC clones encoded GSDMDC1, RECQL4, TP73, ABCF3, ALG3, HDAC9, ESRRA and RPS6KA4 genes. Frequently gained BAC clones encoded genes were PRSS8, FUS, COL18A1, PCOLN3, MAFG and ASPSCR1. The genes encoded by frequently lost BAC clones were PTPRG, GRM7, ZDHHC3, EXOSC7, LRP1B and NR3C2. Also, hierarchical clustering of the expression data readily distinguished genomic alterations in cervical cancer. A subset of cellular processes from each gene was clustered by Gene Ontology database. CONCLUSION: Using Array-CGH, genomic alterations related to cervical cancer were identified to determine whether induction of chromosomal imbalances occurs prior to carcinogenesis. The high resolution of array-CGH combined with human genome database would give a chance to find out possible target genes present in the gained or lost clones.
Key Words: Cervical squamous cell carcinoma, BAC Chip (bacterial artificial chromosome chip)

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