OncoTargets and Therapy (Aug 2019)
Exploration of bladder cancer-associated methylated miRNAs by methylated DNA immunoprecipitation sequencing
Abstract
Xin Gao,1,* Wenwen Zheng,2,* Lili Ye,3 Xiaohong Wen,1 Shunlan Wang,1 Hui Cao,1 Xi Liu,1 Denggao Huang,1 Fei Wang,4 Shufang Zhang11Central Laboratory, Haikou People’s Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou 570208, Hainan, People’s Republic of China; 2Department of Clinical Laboratory, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510655, Guangdong, People’s Republic of China; 3Department of Clinical Laboratory, Jilin Provincial Tumor Hospital, Changchun 130012, People’s Republic of China; 4Department of Urology, People’s Hospital of Hainan Province, Haikou 570311, Hainan, People’s Republic of China*These authors contributed equally to this workBackground: 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.Keywords: DNA methylation, 5-methylcytidine, miRNA, bladder cancer
