Identification of Gene Expression and Gene Ontology Classification by Differential Display RT-PCR in Human Cervical Squamous Cell Carcinoma

Seo, Min Je; Bae, Su Mi; Park, Kyoung Mi; Kim, Byung Hoon; Kim, Yong Wan; Seo, Kyuong Yun; Seo, Kyung A; Kim, Yong Wook; Hur, Soo Young; Ro, Duck Young; Lee, Joon Mo; Namkoong, Sung Eun; Kim, Chong Kook; Ahn, Woong Shick

Abstract

OBJECTIVE
The molecular pathology of cervical cancer associated with human papillomavirus infection is presently unclear. In an effort to clarify the multiple interactions of a number of genes involved in cervical carcinogenesis, the gene expression profiles and pathogenic cellular processes between human cervical squamous cell carcinoma and normal cervix were investigated by mRNA differential display and the Gene Ontology analysis.
METHODS
Cervical cancer biopsies were obtained from patients at the Department of Obstetrics and Gynecology, The Catholic University of Korea. The disease status was assigned according to the International Federation of Gynecology and Obstetrics. The squamous cell carcinoma tissue samples of 3 patients invasive cancer stage II (1), IV (2) were investigated by mRNA differential display. As a control, we used a common reference that was mixed with equal amount of RNA obtained from 17 normal cervix to obtain variation- independent control. Also, we constructed hierarchical functional structures using gene ontology. Then, the specific function groups were correlated with differential gene expression profiles. In addition, specific gene expression patterns in several tissue samples were investigated by using DDRT-PCR analysis.
RESULTS
Differentially expressed 191 genes were identified in tumor samples. Of these genes, 128 were up-regulated and 63 were down-regulated above 1.5-fold. The gene expression profiles were classified into 46 mutually dependent function sets and organized into sub-function sets depending on the cervical cancer pathway, suggesting the potentially significant genes of unknown function affected by carcinogenesis pathway. The genes related to metabolism, signal transduction, and chaperon activity were significantly up-regulated. In contrast, significant down-regulations were shown in nucleic acid binding activity, tumor suppressor and structural activity. Reliable gene expression data shows the validation of profiling method for studying the cervical cancer-specific pathway.
CONCLUSION
The specific functions assigned to each expressed gene were correlated with gene ontology for the establishment of a powerful cervical carcinogenesis pathway. The results suggest that the differentially regulated cellular process profiles have an important impact on discovery of pathogenic pathway in human cervical squamous cell carcinoma and provide the potentially significant genes of unknown function. Also, the gene ontology analysis can overcome the complexity of the expression profiles of mRNA differential display via a cellular process level approach. Thereby, a valuable prognostic candidate gene with real relevance to disease-specific pathogenesis can be found at the cellular process levels.