Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data
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 meta...
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Dove Medical Press
2016
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4818051/ |
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pubmed-48180512016-04-11 Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data Chang, Jing Huang, Liya Cao, Qing Liu, Fang Original Research 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. Dove Medical Press 2016-03-24 /pmc/articles/PMC4818051/ /pubmed/27069368 http://dx.doi.org/10.2147/OTT.S93338 Text en © 2016 Chang et al. This work is published by Dove Medical Press Limited, and licensed under Creative Commons Attribution – Non Commercial (unported, v3.0) License The full terms of the License are available at http://creativecommons.org/licenses/by-nc/3.0/. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Chang, Jing Huang, Liya Cao, Qing Liu, Fang |
| spellingShingle |
Chang, Jing Huang, Liya Cao, Qing Liu, Fang Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data |
| author_facet |
Chang, Jing Huang, Liya Cao, Qing Liu, Fang |
| author_sort |
Chang, Jing |
| title |
Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data |
| title_short |
Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data |
| title_full |
Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data |
| title_fullStr |
Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data |
| title_full_unstemmed |
Identification of colorectal cancer-restricted microRNAs and their target genes based on high-throughput sequencing data |
| title_sort |
identification of colorectal cancer-restricted micrornas and their target genes based on high-throughput sequencing data |
| description |
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. |
| publisher |
Dove Medical Press |
| publishDate |
2016 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4818051/ |
| _version_ |
1613561117003481088 |