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Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data

Authors Chang J, Huang L, Cao Q, Liu F

Received 29 July 2015

Accepted for publication 23 October 2015

Published 24 March 2016 Volume 2016:9 Pages 1787—1794


Checked for plagiarism Yes

Review by Single-blind

Peer reviewers approved by Prof. Dr. Haijun Zhang

Peer reviewer comments 3

Editor who approved publication: Dr Faris Farassati

Jing Chang, Liya Huang, Qing Cao, Fang Liu

Department of Gerontology, Xinhua Hospital Affiliated to Jiaotong University School of Medicine, Shanghai, People’s Republic of China

Abstract: To identify potential key microRNAs (miRNAs) and their target genes for colorectal cancer (CRC). High-throughput sequencing data of miRNA expression and gene expression (ID: GSE46622) were downloaded from Gene Expression Omnibus, including matched colon tumor, normal colon epithelium, and liver metastasis tissues from eight CRC patients. Paired t-test and NOISeq separately were utilized to identify differentially expressed miRNAs (DE-miRNAs) and genes. Then, target genes with differential expression and opposite expression trends were identified for DE-miRNAs. Combined with tumor suppressor gene, tumor-associated gene, and TRANSFAC databases, CRC-restricted miRNAs were screened out based on miRNA-target pairs. Compared with normal tissues, there were 56 up- and 37 downregulated miRNAs in metastasis tissues, as well as eight up- and 30 downregulated miRNAs in tumor tissues. miRNA-1 was downregulated in tumor and metastasis tissues, while its target oncogenes TWIST1 and GATA4 were upregulated. Besides, miRNA-let-7f-1-3p was downregulated in tumor tissues, which also targeted TWIST1. In addition, miRNA-133b and miRNA-4458 were downregulated in tumor tissues, while their common target gene DUSP9 was upregulated. Conversely, miRNA-450b-3p was upregulated in metastasis tissues, while its target tumor suppressor gene CEACAM7 showed downregulation. The identified CRC-restricted miRNAs might be implicated in cancer progression via their target genes, suggesting their potential usage in CRC treatment.

Keywords: colorectal cancer, differentially expressed microRNAs, differentially expressed genes, oncogenes, tumor suppressor genes

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