Characteristics of miRNA interaction with mRNA candidate genes of esophageal adenocarcinoma
DOI:
https://doi.org/10.26577/eb-2019-3-b10Аннотация
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
Библиографиялық сілтемелер
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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
2. Cheng A.M., Byrom M.W., Shelton J., Ford L.P. (2005) Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis. Nucleic Acids Res., vol. 33, no. 4, pp. 1290–1297. DOI: 10.1093/nar/gki200
3. Desai TK., Krishnan K., Samala N., et al. (2012) The incidence of oesophageal adenocarcinoma in non-dysplastic Barrett’s oesophagus: a meta-analysis. Gut, vol. 61, pp. 970-976. DOI: 10.1136/gutjnl-2011-300730
4. Du Y., Liu P., Zang W., Wang Y., Chen X., Li M., Zhao G. (2015) BTG3 upregulation induces cell apoptosis and suppresses invasion in esophageal adenocarcinoma. Mol Cell Biochem., vol. 404, no. 1-2, pp. 31-8. doi: 10.1007/s11010-015-2363-9
5. Garofalo M., Croce C.M. (2011) microRNAs: Master regulators as potential therapeutics in cancer. Annu Rev Pharmacol Toxicol., vol. 51, pp. 25–43.
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.
17. Mikhail S., Albanese C., Pishvaian MJ. (2015) Cyclin-dependent kinase inhibitors and the treatment of gastrointestinal cancers. Am J Pathol., vol. 185, no. 5, pp. 1185-97. doi: 10.1016/j.ajpath.2015.01.008
18. Ou Y.H., Chung P.H., Hsu F.F., Sun T.P., Chang W.Y., Shieh S.Y. (2007) The candidate tumor suppressor BTG3 is a transcriptional target of p53 that inhibits E2F1. EMBO J., vol. 26, no. 17, pp. 3968-80. DOI: 10.1038/sj.emboj.7601825
19. Poy M.N., Eliasson L., Krutzfeldt J., et al. (2004) A pancreatic islet-specific microRNA regulates insulin secretion. Nature, vol. 432, no. 7014, pp. 226–230. DOI: 10.1038/nature03076
20. Rath S.N., Das D., Konkimalla V.B., Pradhan S.K. (2016) In silico study of miRNA based gene regulation, involved in solid cancer, by the assistance of Argonaute protein. Genomics Inform., vol. 14, no. 3, pp. 112-124. DOI: 10.5808/GI.2016.14.3.112
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
23. Streppel M.M., Lata S., DelaBastide M., Montgomery E.A., Wang J.S., Canto M.I., Macgregor-Das A.M., Pai S., Morsink FHM, Offerhaus G.J., et al. (2014) Next-generation sequencing of endoscopic biopsies identifies ARID1A as a tumor-suppressor gene in Barrett’s esophagus. Oncogene, vol. 33, pp. 347–57. doi: 10.1038/onc.2012.586
24. Wang Z., Zhao Z., Yang Y., Luo M., Zhang M., Wang X., Liu L., Hou N., Guo Q., Song T., Guo B., Huang C. (2018) MiR-99b-5p and miR-203a-3p Function as Tumor Suppressors by Targeting IGF-1R in Gastric Cancer. Sci Rep., vol. 8, no. 1, pp. 10119. doi: 10.1038/s41598-018-27583-y
25. Wani S., Puli SR., Shaheen NJ., et al. (2009) Esophageal adenocarcinoma in Barrett's esophagus after endoscopic ablative therapy: a meta-analysis and systematic review. Am. J. Gastroenterol., vol. 104, pp. 502–513. DOI: 10.1038/ajg.2008.31
26. Wu R.C., Wang T.L., Shih IeM. (2014) The emerging roles of arid1a in tumor suppression. Cancer Biol Ther., vol. 15, no. 6, pp. 655–664.
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
28. Zeng H., Zheng R., Zhang S., Zuo T., Xia C., Zou X., Chen W. (2016) Esophageal cancer statistics in China, 2011: Estimates based on 177 cancer registries. Thorac Cancer., vol. 7, pp. 232–237. doi: 10.1111/1759-7714.12322
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
Жүктелулер
Как цитировать
Akimniyazova, A. N., & Ivashchenko, A. T. (2020). Characteristics of miRNA interaction with mRNA candidate genes of esophageal adenocarcinoma. ҚазҰУ Хабаршысы. Биология сериясы, 80(3), 106–116. https://doi.org/10.26577/eb-2019-3-b10
Шығарылым
Бөлім
МОЛЕКУЛЯРНАЯ БИОЛОГИЯ И ГЕНЕТИКА
