Co-modulated Behavior and Effects of Differentially Expressed MiRNA in Colorectal Cancer

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2014 Feb 26

PMID 24564330

Citations 8

Authors

Wei-Shone Chen

Ting-Wen Chen

Tzu-Hsien Yang

Ling-Yueh Hu

Hung-Wei Pan

Chung-Man Leung

Sung-Chou Li

Meng-Ru Ho

Chih-Wen Shu

Pei-Feng Liu

Shou-Yu Yu

Ya-Ting Tu

Wen-Chang Lin

Tony T Wu

Kuo-Wang Tsai

Affiliations

Soon will be listed here.

Abstract

Background: MicroRNAs (miRNAs) are short noncoding RNAs (approximately 22 nucleotides in length) that play important roles in colorectal cancer (CRC) progression through silencing gene expression. Numerous dysregulated miRNAs simultaneously participate in the process of colon cancer development. However, the detailed mechanisms and biological functions of co-expressed miRNA in colorectal carcinogenesis have yet to be fully elucidated.

Results: The objective of this study was to identify the dysfunctional miRNAs and their target mRNAs using a wet-lab experimental and dry-lab bioinformatics approach. The differentially expressed miRNA candidates were identified from 2 miRNA profiles, and were confirmed in CRC clinical samples using reported target genes of dysfunctional miRNAs to perform functional pathway enrichment analysis. Potential target gene candidates were predicted by an in silico search, and their expression levels between normal and colorectal tumor tissues were further analyzed using real-time polymerase chain reaction (RT-PCR).

Conclusion: Fifteen dysfunctional miRNAs were engaged in metastasis-associated pathways through comodulating 7 target genes, which were identified by using a multi-step approach. The roles of these candidate genes are worth further exploration in the progression of colon cancer, and could potentially be targets in future therapy.

Citing Articles

Long Noncoding RNA LOC550643 Acts as an Oncogene in the Growth Regulation of Colorectal Cancer Cells.

Wu H, Lu T, Lo Y, Tu Y, Chen Y, Lee M Cells. 2022; 11(7).

PMID: 35406629 PMC: 8997465. DOI: 10.3390/cells11071065.

Myosin Motors: Novel Regulators and Therapeutic Targets in Colorectal Cancer.

Naydenov N, Lechuga S, Huang E, Ivanov A Cancers (Basel). 2021; 13(4).

PMID: 33670106 PMC: 7916823. DOI: 10.3390/cancers13040741.

Downregulation of microRNA-126 is inversely correlated with insulin receptor substrate-1 protein expression in colorectal cancer and is associated with advanced stages of disease.

Ye S, Yu C, Zhang G, Shi F, Chen Y, Yang J Oncol Lett. 2020; 20(3):2411-2419.

PMID: 32782558 PMC: 7400408. DOI: 10.3892/ol.2020.11796.

TACCO, a Database Connecting Transcriptome Alterations, Pathway Alterations and Clinical Outcomes in Cancers.

Chou P, Liao W, Tsai K, Chen K, Yu J, Chen T Sci Rep. 2019; 9(1):3877.

PMID: 30846808 PMC: 6405743. DOI: 10.1038/s41598-019-40629-z.

Aberrantly Expressed Genes and miRNAs in Slow Transit Constipation Based on RNA-Seq Analysis.

Zhao S, Chen Q, Kang X, Kong B, Wang Z Biomed Res Int. 2018; 2018:2617432.

PMID: 30186855 PMC: 6112260. DOI: 10.1155/2018/2617432.

References

Lai V, Ashraf M, Jiang S, Haider K . MicroRNA-143 is a critical regulator of cell cycle activity in stem cells with co-overexpression of Akt and angiopoietin-1 via transcriptional regulation of Erk5/cyclin D1 signaling. Cell Cycle. 2012; 11(4):767-77. PMC: 3318108. DOI: 10.4161/cc.11.4.19211. View

Monzo M, Navarro A, Bandres E, Artells R, Moreno I, Gel B . Overlapping expression of microRNAs in human embryonic colon and colorectal cancer. Cell Res. 2008; 18(8):823-33. DOI: 10.1038/cr.2008.81. View

Akao Y, Nakagawa Y, Naoe T . MicroRNA-143 and -145 in colon cancer. DNA Cell Biol. 2007; 26(5):311-20. DOI: 10.1089/dna.2006.0550. View

Li X, Zhang G, Luo F, Ruan J, Huang D, Feng D . Identification of aberrantly expressed miRNAs in rectal cancer. Oncol Rep. 2012; 28(1):77-84. DOI: 10.3892/or.2012.1769. View

Callari M, Dugo M, Musella V, Marchesi E, Chiorino G, Mello Grand M . Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues. PLoS One. 2012; 7(9):e45105. PMC: 3441572. DOI: 10.1371/journal.pone.0045105. View

Hou J, Lin L, Zhou W, Wang Z, Ding G, Dong Q . Identification of miRNomes in human liver and hepatocellular carcinoma reveals miR-199a/b-3p as therapeutic target for hepatocellular carcinoma. Cancer Cell. 2011; 19(2):232-43. DOI: 10.1016/j.ccr.2011.01.001. View

Gusev Y . Computational methods for analysis of cellular functions and pathways collectively targeted by differentially expressed microRNA. Methods. 2007; 44(1):61-72. DOI: 10.1016/j.ymeth.2007.10.005. View

Chen C, Ridzon D, Broomer A, Zhou Z, Lee D, Nguyen J . Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 2005; 33(20):e179. PMC: 1292995. DOI: 10.1093/nar/gni178. View

Chen W, Leung C, Pan H, Hu L, Li S, Ho M . Silencing of miR-1-1 and miR-133a-2 cluster expression by DNA hypermethylation in colorectal cancer. Oncol Rep. 2012; 28(3):1069-76. DOI: 10.3892/or.2012.1899. View

10.

Honda N, Jinnin M, Kajihara I, Makino T, Makino K, Masuguchi S . TGF-β-mediated downregulation of microRNA-196a contributes to the constitutive upregulated type I collagen expression in scleroderma dermal fibroblasts. J Immunol. 2012; 188(7):3323-31. DOI: 10.4049/jimmunol.1100876. View

11.

Schetter A, Harris C . Alterations of microRNAs contribute to colon carcinogenesis. Semin Oncol. 2011; 38(6):734-42. PMC: 3217180. DOI: 10.1053/j.seminoncol.2011.08.009. View

12.

Joung J, Hwang K, Nam J, Kim S, Zhang B . Discovery of microRNA-mRNA modules via population-based probabilistic learning. Bioinformatics. 2007; 23(9):1141-7. DOI: 10.1093/bioinformatics/btm045. View

13.

Tran D, Satou K, Ho T . Finding microRNA regulatory modules in human genome using rule induction. BMC Bioinformatics. 2008; 9 Suppl 12:S5. PMC: 2638145. DOI: 10.1186/1471-2105-9-S12-S5. View

14.

Krek A, Grun D, Poy M, Wolf R, Rosenberg L, Epstein E . Combinatorial microRNA target predictions. Nat Genet. 2005; 37(5):495-500. DOI: 10.1038/ng1536. View

15.

Dong Y, Wu W, Wu C, Sung J, Yu J, Ng S . MicroRNA dysregulation in colorectal cancer: a clinical perspective. Br J Cancer. 2011; 104(6):893-8. PMC: 3065287. DOI: 10.1038/bjc.2011.57. View

16.

Juhila J, Sipila T, Icay K, Nicorici D, Ellonen P, Kallio A . MicroRNA expression profiling reveals miRNA families regulating specific biological pathways in mouse frontal cortex and hippocampus. PLoS One. 2011; 6(6):e21495. PMC: 3120887. DOI: 10.1371/journal.pone.0021495. View

17.

Kim S, Choi M, Cho K . Identifying the target mRNAs of microRNAs in colorectal cancer. Comput Biol Chem. 2008; 33(1):94-9. DOI: 10.1016/j.compbiolchem.2008.07.016. View

18.

Pan H, Li S, Tsai K . MicroRNA dysregulation in gastric cancer. Curr Pharm Des. 2012; 19(7):1273-84. DOI: 10.2174/138161213804805621. View

19.

Anglim P, Galler J, Koss M, Hagen J, Turla S, Campan M . Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer. Mol Cancer. 2008; 7:62. PMC: 2483990. DOI: 10.1186/1476-4598-7-62. View

20.

Liang H, Li W . MicroRNA regulation of human protein protein interaction network. RNA. 2007; 13(9):1402-8. PMC: 1950750. DOI: 10.1261/rna.634607. View