title: Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data.
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-450-b-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.
authors.affiliation: Department of Gerontology, Xinhua Hospital Affiliated to Jiaotong University School of Medicine, Shanghai, People's Republic of China.
authors.forename: Jing
authors.initials: J
authors.lastname: Chang
authors.affiliation: Department of Gerontology, Xinhua Hospital Affiliated to Jiaotong University School of Medicine, Shanghai, People's Republic of China.
authors.forename: Liya
authors.initials: L
authors.lastname: Huang
authors.affiliation: Department of Gerontology, Xinhua Hospital Affiliated to Jiaotong University School of Medicine, Shanghai, People's Republic of China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Cao
authors.affiliation: Department of Gerontology, Xinhua Hospital Affiliated to Jiaotong University School of Medicine, Shanghai, People's Republic of China.
authors.forename: Fang
authors.initials: F
authors.lastname: Liu
keywords: colorectal cancer; differentially expressed genes; differentially expressed microRNAs; oncogenes; tumor suppressor genes