ABSTRACT
BACKGROUND:In recent years, based on high-throughput molecular imaging, integration of genomics, proteomics and computer aided design and the application of correlative “technical chains” have achieved great achievements in the research of breast cancer, lung cancer, gastric cancer, colon cancer, ovarian cancer and melanin tumor. However, there are few researches on oral squamous cel carcinoma. OBJECTIVE:To detect the gene expression profile of the oral squamous cel carcinoma tissue and normal paracarcinoma tissue using DNA chip-based gene expression profile. METHODS:Two samples of oral squamous cel carcinoma tissue and normal paracarcinoma tissue of patients who received treatment at Stomatological Hospital of Guangdong Province of China in 2013 were included in this study. The gene expression profiles of oral squamous cel carcinoma and normal paracarcinoma tissue were determined by the Roche NimbleGen gene expression microarrays. RESULTS AND CONCLUSION: According to screening criteria of differential genes, 7 872 out of 32 448 detected genes were differentialy expressed genes of oral squamous cel carcinoma, which accounts for 24% of the total number of the screening genes. 3 800 genes were up-regulated, and 4 072 were down-regulated. The results confirm that through detection with the help of gene expression profile clip, 7 872 differentialy expressed genes were obtained through DNA chip-based gene expression profiles according to the screening criteria. Thus it can be concluded that the occurrence and development of the tumors are not a result of single or several genes. Previous experiments based on a single or several genes have great limitations. These findings also suggest that the occurrence of tumor is a result of mutual regulatory effects of many genes forming a network, moreover, the interactions of the network is quite complicated.
ABSTRACT
BACKGROUND:RACK1 is strongly associated with the occurrence and development of oral squamous cel carcinoma. However, the occurrence and development of tumor do not depend on a gene or protein, but a long-term complex process of a network structure of multiple genes and multiple molecules, multi-step, multi-stage joint action. Synergism between tumor genes promotes the formation and development of tumor cel s. Therefore, we cannot limit on a single gene or protein to discover the action mechanism of oral squamous cel carcinoma, but should pay attention on signaling network path related to differential protein or gene, investigate the alterations in related protein or gene expression in the whole signaling pathway, and analyze the action mechanism of the interaction of these molecules. OBJECTIVE:To screen differential genes related to oral squamous cel carcinoma, construct an interaction network through bioinformatics using STRING database, and provide clues for future tests. METHODS:In accordance with our previous classic proteomics results and microarray results of oral squamous cel carcinoma, genes with consistent expression and big differences were selected as differential genes. The differential genes were inputted into the database of STRING to find the possible relationship among the protein subunits and to construct network structure of their interaction. RESULTS AND CONCLUSION:The 19 differential proteins of oral squamous cel carcinoma construct a complicated net work, and the differential proteins interact through these networks. GNB2L1-encoded RACK1 is a node protein and interacts with other differential proteins via WD40 repeated protein (number COG2319) andβ-G protein subunit (number KOG0279). WD40 repeated protein (number COG2319) interacts with 5 differential proteins directly and constructs 10 interacting pathways.β-G protein subunit (number KOG0279) interacts with 8 differential proteins directly, which has 11 interacting pathways. We make a network structure picture based on the interaction of these 19 differential genes by the analysis of the STRING database. The results show that the two subunits of RACK1 protein have direct interaction with 8 differential proteins and have 18 interaction pathways on the picture. As a result, RACK1 is the core protein of the network, suggesting RACK1 is the key node protein in oral squamous cel carcinoma.