In silico analysis of hypermethylation in CpGislands of UCHL1 gene’s promoter in nasopharyngeal carcinoma

• Main Authors: Lao Duc Thuan, Thieu Hong Hue, Hoang Van Nam, Nguyen Hoang Danh, Le Huyen Ai Thuy, Ngo Dong Kha, Nguyen Hoang Anh Tuan
• Format: Article
• Language: English
• Published: HO CHI MINH CITY OPEN UNIVERSITY JOURNAL OF SCIENCE 2018-08-01
• Series: Ho Chi Minh City Open University Journal of Science - Engineering and Technology
• Subjects: methylation; msp; npc; uchl-1 gene
• Online Access: https://journalofscience.ou.edu.vn/index.php/tech-en/article/view/333
• ISSN: 2734-9330; 2734-9608

Background and Objective: The methylation of Ubiquitin C-Terminal Hydrolase L1 (UCHL1) gene has been reported in many human cancers including nasopharyngeal carcinoma (NPC). In Vietnam, the methylation of UCHL1 gene’s promoter in NPC has not been demonstrated yet. In this study, a systematic literature revision was carried out to summarize the current evidences about the frequencies of UCHL-1 gene’s promoter methylation in NPC for further application in Vietnamese population. Methods: A systematic literature analysis was conducted based on the comprehensive studies. Moreover, many bioinformatic tools such as Methprimer, TFsearch, IDT OligoAnalyzer 3.1 were used to predict the CpG islands, transcriptional factors, and to pick up the MSP (Methylation-Specific PCR) primers. Results: Total of three previous studies were summarized and accessed for eligibility from literature research. As the results, the average weight methylated frequencies were 72.4% and 13.0% for NPC and non-cancerous samples, respectively. The significant association between UCHL-1 promoter methylation and NPC with the OR of 10.459 (95% CI = 4.915 – 22.254, p < 0.001) and RR of 4.117 (95% CI = 1.958 – 6.645, p < 0.0001) based on the random effects model, was observed. Moreover, we were successful in predicting the CpG islands as well as identifying transcriptional factor binding sites which served as “hot spot” for ideal primer pick up and located in gene promoter. Conclusion: The methylation of UCHL-1 gene promoter was significantly associated and contributed to NPC developmentin which it could be further applied in evaluation of UCHL-1 gene promoter status in Vietnamese population.