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Gao X, Zheng W, Ye L, Wen X, Wang S, Cao H, Liu X, Huang D, Wang F, Zhang S. Exploration of bladder cancer-associated methylated miRNAs by methylated DNA immunoprecipitation sequencing. Onco Targets Ther 2019; 12:6165-6174. [PMID: 31534349 PMCID: PMC6682176 DOI: 10.2147/ott.s192248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 05/20/2019] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The current study aimed to explore the association between two epigenomic components, miRNA and DNA methylation, in bladder cancer (BC). METHODS Eight paired samples of tumor tissue and matched adjacent normal tissues from BC patients were subjected to methylated DNA immunoprecipitation sequencing and sRNA-Seq for differentially methylated miRNA genes and differential miRNA analysis. The miRNAs regulated by DNA methylation were screened and their functions involved in BC were analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) as well as a miRNA-mRNA interaction network. RESULTS The methylation levels of 212 genes were different between tumors and normal tissues with specific enrichment at transcription initiation and termination sites. Among these genes, 154 were hypermethylated and 58 were hypomethylated. GO and KEGG pathway enrichment analysis indicated that differentially methylated miRNA genes were mainly enriched in tumor-associated GO terms and signaling pathways. Pairwise statistical analysis of MeDIP-Seq and sRNA-Seq data showed that there are 154 and 165 candidate methylation-regulated genes in tumors and normal tissues, respectively. Notably, an interaction network indicated that the miRNAs regulated by methylation regulated a broad range of mRNAs associated with cancer development and progression. In particular, the most differentially expressed miRNAs were validated by qRT-PCR, such that miR-145-5p was downregulated and miR-182-5p was upregulated in patients with bladder cancer. CONCLUSION A large number of miRNA genes were modified by methylation in BC. Identification of changes in the expression of these miRNAs provides a great deal of important information for BC diagnosis.
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Affiliation(s)
- Xin Gao
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| | - Wenwen Zheng
- Department of Clinical Laboratory, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou510655, Guangdong, People’s Republic of China
| | - Lili Ye
- Department of Clinical Laboratory, Jilin Provincial Tumor Hospital, Changchun130012, People’s Republic of China
| | - Xiaohong Wen
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| | - Shunlan Wang
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| | - Hui Cao
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| | - Xi Liu
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| | - Denggao Huang
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
| | - Fei Wang
- Department of Urology, People’s Hospital of Hainan Province, Haikou570311, Hainan, People’s Republic of China
| | - Shufang Zhang
- Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou570208, Hainan, People’s Republic of China
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