Identification of High-Frequency Methylation Sites in RNF180 Promoter Region Affecting Expression and Their Relationship with Prognosis of Gastric Cancer
Received 22 January 2020
Accepted for publication 14 April 2020
Published 13 May 2020 Volume 2020:12 Pages 3389—3399
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Editor who approved publication: Dr Seema Singh
Fang Han,1,2,* Shuang Liu,1,3,* Jingjing Jing,1 Hao Li,1 Yuan Yuan,1 Li-Ping Sun1
1Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, Shenyang 110001, People’s Republic of China; 2Hepatobiliary and Pancreatic Surgery, Minimal Invasive Surgery, Zhejiang Provincial People’s Hospital, Hangzhou Medical College, Hangzhou 310014, People’s Republic of China; 3Department of Oncology, Shanxi Provincial Tumor Hospital, Xi’an 710076, People’s Republic of China
*These authors contributed equally to this work
Correspondence: Li-Ping Sun; Yuan Yuan Email email@example.com; firstname.lastname@example.org
Background: Ring finger protein 180 (RNF180) is a tumor suppressor gene regulated by promoter methylation. We previously demonstrated that the RNF180 promoter methylation could be a risk factor for gastric cancer (GC); and eight high-frequency hypermethylated CpG sites were associated with GC. However, it is not clear whether these key sites can affect gene expression and involve in prognosis. The aim of this study was to investigate the effects of above CpG sites on the gene expression and prognosis of GC.
Patients and Methods: A total of 164 GC tissues were enrolled and followed up. Tissue samples were used for DNA and RNA isolation. Methylation status of RNF180 was detected using bisulfite sequencing PCR (BSP). Expression levels of RNF180 were detected using quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR). JASPAR and PROMO databases were used to predict the transcription factors (TFs) binding to the CpG site.
Results: The methylation in RNF180 promoter region increased and mRNA expression decreased in GC tissue. Correlation analysis revealed that the average methylation rate (AMR) and four CpG sites methylation rate were negatively related to RNF180 expression, including M3(− 165)(Chr5:64165942), M5(− 148)(Chr5:64,165,959), M7(− 133)(Chr5:64,165,974) and M8(− 130)(Chr5:64,165,977). Furthermore, the methylation rate of M5(− 148)(Chr5:64,165,959) and M27(− 26)(Chr5:64,166,081) above 0.3 indicated poor prognosis (PM5 = 0.008, PM27 = 0.003, HRM5(− 148) = 2.000 (1.201,3.332), HRM27(− 26)=2.389 (1.336,4.271)), which could be independent factors of prognosis.
Conclusion: By focusing on the methylation sites in the RNF180 promoter region, we identified two high-frequency methylation sites, M5(− 148)(Chr5:64,165,959) and M27(− 26)(Chr5:64,166,081), which could affect gene expression and predict the prognosis of GC. In the future, the possible molecular mechanism involved needs to be further studied.
Keywords: gastric cancer, RNF180, methylated CpG sites, prognosis, methylation
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