Characteristics of miRNA interaction with mRNA candidate genes of esophageal adenocarcinoma
DOI:
https://doi.org/10.26577/eb-2019-3-b10Abstract
miRNAs is a class of nano-sized non-coding RNAs that regulate the expression of genes, and associated with many physiological and pathological processes, especially cancer. The expression of many genes is regulated by the binding of their mRNA with miRNA, so it is required to identify which candidate genes of oncogenesis and to what extent can interact with miRNA. The purpose of this work was to establish the characteristics of the interaction of known 3707 miRNA with mRNA of 38 candidate esophageal adenocarcinoma genes. It has been identified, that 84 miRNAs have binding sites in 31 mRNAs of genes at 5'UTR, CDS, and 3'UTR and the average free binding energy (ΔG) of miRNAs with mRNAs was -121 kJ/mole, -118 kJ/mole and -113 kJ/mole, respectively. 19 associations of miRNAs and mRNA of genes with a free energy of interaction more than -120 kJ/mole are recommended for the diagnosis of esophageal adenocarcinoma. The mRNAs of most genes containing two or more miRNA binding sites with overlapping of their nucleotide sequences form clusters. Based on the obtained results, associations of miRNA and mRNA of candidate genes are recommended to develop methods for early diagnosis of esophageal adenocarcinoma.
Key words: mRNA, miRNA, genes, oncological diseases, esophageal adenocarcinoma
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6. Hata A., Kashima R. (2016) Dysregulation of microRNA biogenesis machinery in cancer. Crit Rev Biochem Mol Biol., vol. 51, no. 3, pp. 121-34. DOI: 10.3109/10409238.2015.1117054
7. Hughes D., et al. (2009) MiRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus: Associations with survival. Clin Cancer Res., vol. 15, pp. 6192-6200.
8. Hvid-Jensen F., Pedersen L., Drewes A.M., Sørensen H.T., Funch-Jensen P. (2011) Incidence of adenocarcinoma among patients with Barrett's esophagus. N Engl J Med., vol. 365, pp. 1375-1383. DOI: 10.1056/NEJMoa1103042
9. Ivashchenko A. T., Niyazova R. Ye., Atambayeva Sh. A., Pyrkova A. Yu., Aisina D. E., Yurikova O. Yu., Kondybayeva A., Akimniyazova A., Bayzhigitova D., Bolshoy A. A. (2018) miRNA: achievements, misconceptions, perspectives. NEWS of NAS RK, vol. 4, no. 328, pp. 36-46.
10. Ivashchenko A., Berillo O., Pyrkova A., Niyazova R. (2014) Binding Sites of miR-1273 Family on the mRNA of Target Genes. Biomed Res Int., vol. 2014, pp. e11.
11. Ivashchenko A., Berillo O., Pyrkova A., Niyazova R., Atambayeva S. (2014) The properties of binding sites of miR-619-5p, miR-5095, miR-5096 and miR- 5585-3p in the mRNAs of human genes. Biomed Res Int., vol. 2014, p. 1-8.
12. Ivashchenko A.T., Pyrkova A.Y., Niyazova R.Y., Alybayeva A., Baskakov K. (2016) Prediction of miRNA binding sites in mRNA. Bioinformation, vol. 12, no. 4, pp. 237-240.
13. Karp X., Ambros V. (2005) Developmental biology. Encountering microRNAs in cell fate signaling. Science, vol. 310, no. 5752, pp. 1288–1289. DOI: 10.1126/science.1121566
14. Kool E.T. (2001) Hydrogen bonding, base stacking, and steric effects in DNA replication. Annu Rev Biophys Biomol Struct., vol. 30, pp. 1-22.
15. Leontis N.B., Stombaugh J., Westhof E. (2002) The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res., vol. 30, no. 16, pp. 3497-3531.
16. Londin E., Lohera P., Telonisa A.G., Quanna K., et al. (2015) Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs. PNAS USA, vol. 112, no. 10. - P. 1106-1115.
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21. Rustgi A.K., El-Serag H.B. (2014) Esophageal Carcinoma. New Engl J Med., vol. 371, pp. 2499-509. 10.1056/NEJMra1314530.
22. Smith E., Palethorpe H.M., Ruszkiewicz A.R., Edwards S., Leach DA., Underwood T.J., Need E.F., Drew P.A. (2016) Androgen Receptor and Androgen-Responsive Gene FKBP5 Are Independent Prognostic Indicators for Esophageal Adenocarcinoma. Dig Dis Sci., vol. 61, no. 2, pp. 433-43. DOI: 10.1007/s10620-015-3909-0
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27. Wu Y.R., Qi H.J., Deng D.F., Luo Y.Y., Yang S.L. (2016) MicroRNA-21 promotes cell proliferation, migration, and resistance to apoptosis through PTEN/PI3K/AKT signaling pathway in esophageal cancer. Tumor Biol., vol. 37, no. 9, pp. 12061–12070. DOI: 10.1007/s13277-016-5074-2
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29. Zhou Y., Li R., Yu H., Wang R., Shen Z. (2017) microRNA-130a is an oncomir suppressing the expression of CRMP4 in gastric cancer. Onco Targets Ther., vol. 10, pp. 3893-3905. doi: 10.2147/OTT.S139443
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How to Cite
Akimniyazova, A. N., & Ivashchenko, A. T. (2020). Characteristics of miRNA interaction with mRNA candidate genes of esophageal adenocarcinoma. Experimental Biology, 80(3), 106–116. https://doi.org/10.26577/eb-2019-3-b10
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МOLECULAR BIOLOGY AND GENETICS
