In silico analysis of hypermethylation of E-cadherin gene promoter in Nasopharyngeal carcinoma

Abstract

Background: DNA hypermethylation changes in CpG islands of promoter region of E-cadherin (E-cad) gene, one of the tumor suppressor genes, have been described to be involved the formation and progression of human nasopharyngeal carcinoma, which is the most common and highly incident cancer of head and neck cancer in Asian countries, especially in Vietnam. Purpose: In Vietnam, there is still no research about E-cad promoter methylation in NPC, thus, in current report, a systematic literature revision was carried out to summary the current evidences about the frequencies of Ecad gene promoter on NPC for further applied in Vietnamese population. Methods: A systematic literature analysis was conducted based on the comprehensive search of observational studies. Moreover, CpG islands of candidate gene and transcriptional factors were predicted by using many bioinformatics tools, such as Methprimer, TFsearch, etc. Results: Total of 9 previous published studies were identified and accessed for eligibility from the literature research and enrolled into systematic revision. The variants of E-cad hypermethylation frequency ranked from 11.0% to 64.55% were observed. Moreover, the average weight frequencies of methylated and unmethylated E-cad gene promoter were 55.46% and 40.78%, respectively. Moreover, by several bioinformatics tools, we were successful in predicting the CpG islands as well as identifing transcriptional factor binding sites, served as “hot spot” for ideal primer pick up, located in candidate gene promoter. Conclusion: Based on these data, it suggested that the hypermethylation of E-cad gene promoter was a significant characteristic of NPC, in which, it could be further applied in evaluation of E-cad gene promoter status in Vietnamese population.