Характеристики взаимодействия miRNA c mRNA кандидатных генов немелкоклеточного рака легкого
DOI:
https://doi.org/10.26577/eb-2018-3-1341Аннотация
Рак легких является одним из наиболее распространенных злокачественных заболеваний. В развитии немелкоклеточного рака легкого предполагается участие более 200 кандидатных генов. Целью исследования было изучить характеристики взаимодействия 137 кандидатных генов немелкоклеточного рака легкого и miRNA. Полученные данные показывают, что значительное число генов являются мишенями двух и более miRNA. mRNA некоторых генов содержат сайты связывания нескольких miRNA с наложением нуклеотидных последовательностей, которые были названы кластерами. Впервые изучены свойства кластеров генов немелкоклеточного рака легкого, содержащие сайты связывания нескольких miRNA. Рассмотрены свойства кластеров с большим числом сайтов связывания miRNA в 5'UTR. mRNA генов CHKA, E2F1, HMGA2, PTEN, HTRA2, ING1, MTA3, SMARCA4, NFATC2 содержат кластеры сайтов связывания для наибольшего количества miRNA. Несколько кластеров имеется в CDS mRNA генов CEBPA, NOTCH3, TRIO, LATS2, RB1 и ZBTB7A. 32 гена являются мишенями 49 miRNA, сайты связывания с которыми локализованы на участке 3'UTR. Гены CDK6 и IRS1 обладают кластерами с наибольшим числом сайтов связывания miRNA. В генах AKT1, EMP и HMGA2 имеются кластеры длиной 34 нт, 40 нт and 41 нт, соответственно, из сайтов связывания трёх miRNA. Каждая mRNA генов BCAR1, ITGA11, MYLK, PTK6, PXN, SOX2 и SSX2 имеют кластеры из сайтов связывания двух miRNA. Предполагается что экспрессия рассмотренных генов будет зависеть в большей степени от miRNA взаимодействующей с mRNA с большей свободной энергией связи.
Ключевые слова: miRNA, mRNA, немелкоклеточный рак легкого, гены мишени.
Библиографические ссылки
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22. Leontis N.B., Stombaugh J., Westhof E. The non-Watson- Crick base pairs and their associated isostericity matrices // Nucleic Acids Research. - 2002. - Vol. 30, No. 16. - P. 3497–3531.
References
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12. 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, pp. 1106-1115.
13. Mizuno K., Mataki H., Arai T., Okato A., Kamikawaji K., Kumamoto T., Hiraki T., Hatanaka K., Inoue H., Seki N. (2017) The microRNA expression signature of small cell lung cancer: tumor suppressors of miR-27a-5p and miR-34b-3p and their targeted oncogenes. J Hum Genet., vol. 62, no. 7, pp. 671-678. doi: 10.1038/jhg.2017.27.
14. Niyazova R.Y., Аtambayeva S.А., Pyrkova А.Y., Ivashchenko A.T. (2015) Assotsiatsii miRNA i mRNA genov, uchastvuyushchih v razvitii nemelkokletochnogo raka legkih [Associations of miRNA and mRNA genes involved in the development of non-small cell lung cancer]. KazNU Bulletin. Biology series, vol. 65, no 3, pp. 143-148.
15. Pao W., Girard N. (2011) New driver mutations in non-small-cell lung cancer. Lancet Oncol., vol. 12, pp. 175–180. doi: 10.1016/S1470-2045(10)70087-5.
16. Shi Y.X., Yin J.Y., Shen Y., Zhang W., Zhou H.H., Liu Z.Q. (2017) Genome-scale analysis identifies NEK2, DLGAP5 and ECT2 as promising diagnostic and prognostic biomarkers in human lung cancer. Sci Rep., vol. 7, no. 1, pp. 8072. doi: 10.1038/s41598-017-08615-5.
17. Tabbò F., Nottegar A., Guerrera F., Migliore E., Luchini C., Maletta F., Veronese N., Montagna L., Gaudiano M., Di Giacomo F., Filosso P.L., Delsedime L., Ciccone G., Scarpa A., Sapino A., Oliaro A., Ruffini E., Inghirami G., Chilosi M. (2018) Cell of origin markers identify different prognostic subgroups of lung adenocarcinoma. Hum Pathol., vol. 75, pp. 167-178. doi: 10.1016/j.humpath.2018.01.017.
18. Taguchi Y.H., Iwadate M., Umeyama H. (2016) SFRP1 is a possible candidate for epigenetic therapy in non-small cell lung cancer. BMC Med Genomics, Suppl 1, pp. 28. doi: 10.1186/s12920-016-0196-3.
19. Wang J., Song J., Gao Z., Huo X., Zhang Y., Wang W., Qi J., Zheng S. (2017) Analysis of gene expression profiles of non-small cell lung cancer at different stages reveals significantly altered biological functions and candidate genes. Oncol Rep., vol. 37, no. 3, pp. 1736-1746. doi: 10.3892/or.2017.5380.
20. Wang K., Li H., Chen R., Zhang Y., Sun X.X., Huang W., Bian H., Chen Z.N. (2017) Combination of CALR and PDIA3 is a potential prognostic biomarker for non-small cell lung cancer. Oncotarget, vol. 8, no. 57, pp. 96945-96957. doi: 10.18632/oncotarget.18547.
21. Zhang F., Zhang X., Meng J., Zhao Y., Liu X., Liu Y., Wang Y., Li Y., Sun Y., Wang Z., Mei Q., Zhang T. (2015) ING5 inhibits cancer aggressiveness via preventing EMT and is a potential prognostic biomarker for lung cancer. Oncotarget, vol. 6, no. 18, pp. 16239-52.
22. Zhang W., Cui Q., Qu W., Ding X., Jiang D., Liu H. (2018) TRIM58/cg26157385 methylation is associated with eight prognostic genes in lung squamous cell carcinoma. Oncol Rep., doi: 10.3892/or.2018.6426. [Epub ahead of print]
2. Houston K.A., Henley S.J., Li J., White M.C., Richards T.B. Patterns in lung cancer incidence rates and trends by histologic type in the United States, 2004–2009 // Lung Cancer. - 2014. - Vol. 86. - P. 22–28.
3. Han S.S., Kim W.J., Hong Y., Hong S.H., Lee S.J., Ryu D.R., Lee W., Cho Y.H., Lee S., Ryu Y.J., Won J.Y., Rhee H., Park J.H., Jang S.J., Lee J.S., Choi C.M., Lee J.C., Lee S.D., Oh Y.M. RNA sequencing identifies novel markers of non-small cell lung cancer // Lung Cancer. - 2014. - Vol. 84, No. 3. - P. 229-35.
4. Ko H.L., Wang Y.S., Fong W.L., Chi M.S., Chi K.H., Kao S.J. Apolipoprotein C1 (APOC1) as a novel diagnostic and prognostic biomarker for lung cancer: A marker phase I trial // Thorac Cancer. - 2014. - Vol. 5, no. 6. - P. 500-8.
5. Liu M., Zhou K., Huang Y., Cao Y. The candidate oncogene (MCRS1) promotes the growth of human lung cancer cells via the miR-155-Rb1 pathway // J Exp Clin Cancer Res. - 2015. - Vol. 34. - P. 121.
6. Zhang F., Zhang X., Meng J., Zhao Y., Liu X., Liu Y., Wang Y., Li Y., Sun Y., Wang Z., Mei Q., Zhang T. ING5 inhibits cancer aggressiveness via preventing EMT and is a potential prognostic biomarker for lung cancer // Oncotarget. - 2015. - Vol. 6, No. 18. - P. 16239-52.
7. Choi Y.Y., Lee S.Y., Lee W.K., Jeon H.S., Lee E.B., Lee H.C., Choi J.E., Kang H.G., Lee E.J., Bae E.Y., Yoo S.S., Lee J., Cha S.I., Kim C.H., Kim I.S., Lee M.H., Kim Y.T., Jheon S., Park J.Y. RACK1 is a candidate gene associated with the prognosis of patients with early stage non-small cell lung cancer // Oncotarget. - 2015. - Vol. 6, No. 6. - P. 4451-66.
8. Huang T., Yang J., Cai Y.D. Novel candidate key drivers in the integrative network of genes, microRNAs, methylations, and copy number variations in squamous cell lung carcinoma // Biomed Res Int. - 2015. - Vol. 2015. - P. 358125.
9. Taguchi Y.H., Iwadate M., Umeyama H. SFRP1 is a possible candidate for epigenetic therapy in non-small cell lung cancer // BMC Med Genomics. - 2016. - Suppl 1. - P. 28.
10. Shi Y.X., Yin J.Y., Shen Y., Zhang W., Zhou H.H., Liu Z.Q. Genome-scale analysis identifies NEK2, DLGAP5 and ECT2 as promising diagnostic and prognostic biomarkers in human lung cancer // Sci Rep. - 2017. - Vol. 7, No. 1. - P. 8072.
11. Kim E.K., Kim K.A., Lee C.Y., Shim H.S. The frequency and clinical impact of HER2 alterations in lung adenocarcinoma // PLoS One. - 2017. - Vol. 12, No. 2. - e0171280.
12. Wang K., Li H., Chen R., Zhang Y., Sun X.X., Huang W., Bian H., Chen Z.N. Combination of CALR and PDIA3 is a potential prognostic biomarker for non-small cell lung cancer // Oncotarget. - 2017. - Vol. 8, No. 57. - P. 96945-96957.
13. Mizuno K., Mataki H., Arai T., Okato A., Kamikawaji K., Kumamoto T., Hiraki T., Hatanaka K., Inoue H., Seki N. The microRNA expression signature of small cell lung cancer: tumor suppressors of miR-27a-5p and miR-34b-3p and their targeted oncogenes // J Hum Genet. - 2017. - Vol. 62, No. 7. - P. 671-678.
14. Wang J., Song J., Gao Z., Huo X., Zhang Y., Wang W., Qi J., Zheng S. Analysis of gene expression profiles of non-small cell lung cancer at different stages reveals significantly altered biological functions and candidate genes // Oncol Rep. - 2017. - Vol. 37, No. 3. - P. 1736-1746.
15. Zhang W., Cui Q., Qu W., Ding X., Jiang D., Liu H. TRIM58/cg26157385 methylation is associated with eight prognostic genes in lung squamous cell carcinoma // Oncol Rep. - 2018. doi: 10.3892/or.2018.6426. [Epub ahead of print]
16. Ding X., Zhang S., Li X., Feng C., Huang Q., Wang S., Wang S., Xia W., Yang F., Yin R., Xu L., Qiu M., Li M., Wang J. Profiling expression of coding genes, long noncoding RNA, and circular RNA in lung adenocarcinoma by ribosomal RNA-depleted RNA sequencing // FEBS Open Bio. - 2018. - Vol. 8, No. 4. - P. 544-555.
17. Tabbò F., Nottegar A., Guerrera F., Migliore E., Luchini C., Maletta F., Veronese N., Montagna L., Gaudiano M., Di Giacomo F., Filosso P.L., Delsedime L., Ciccone G., Scarpa A., Sapino A., Oliaro A., Ruffini E., Inghirami G., Chilosi M. Cell of origin markers identify different prognostic subgroups of lung adenocarcinoma // Hum Pathol. - 2018. - Vol. 75. - P. 167-178.
18. Ниязова Р.Е., Атамбаева Ш.А., Пыркова А.Ю., Иващенко А.Т. Ассоциации miRNA и mRNA генов, участвующих в развитии немелкоклеточного рака легких // Вестник КазНУ. Серия биологическая. - 2015. - №3. - C. 143 – 148.
19. Londin E., Lohera P., Telonisa A.G., Quanna K., et al. Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs // PNAS USA. - 2015. - Vol. 112, No. 10. - P. 1106-1115.
20. Ivashchenko A.T., Pyrkova A.Y., Niyazova R.Y., Alybayeva A., Baskakov K. Prediction of miRNA binding sites in mRNA // Bioinformation. - 2016. - Vol. 12, No. 4. - P. 237-240.
21. Kool E.T. Hydrogen bonding, base stacking, and steric effects in DNA replication // Annual Review of Biophysics and Biomolecular Structure. - 2001. - Vol. 30. - P. 1–22.
22. Leontis N.B., Stombaugh J., Westhof E. The non-Watson- Crick base pairs and their associated isostericity matrices // Nucleic Acids Research. - 2002. - Vol. 30, No. 16. - P. 3497–3531.
References
1. Choi Y.Y., Lee S.Y., Lee W.K., Jeon H.S., Lee E.B., Lee H.C., Choi J.E., Kang H.G., Lee E.J., Bae E.Y., Yoo S.S., Lee J., Cha S.I., Kim C.H., Kim I.S., Lee M.H., Kim Y.T., Jheon S., Park J.Y. (2015) RACK1 is a candidate gene associated with the prognosis of patients with early stage non-small cell lung cancer. Oncotarget, vol. 6, no. 6, pp. 4451-66.
2. Ding X., Zhang S., Li X., Feng C., Huang Q., Wang S., Wang S., Xia W., Yang F., Yin R., Xu L., Qiu M., Li M., Wang J. (2018) Profiling expression of coding genes, long noncoding RNA, and circular RNA in lung adenocarcinoma by ribosomal RNA-depleted RNA sequencing. FEBS Open Bio., vol. 8, no. 4, pp. 544-555. doi: 10.1002/2211-5463.12397.
3. Han S.S., Kim W.J., Hong Y., Hong S.H., Lee S.J., Ryu D.R., Lee W., Cho Y.H., Lee S., Ryu Y.J., Won J.Y., Rhee H., Park J.H., Jang S.J., Lee J.S., Choi C.M., Lee J.C., Lee S.D., Oh Y.M. (2014) RNA sequencing identifies novel markers of non-small cell lung cancer. Lung Cancer, vol. 84, no. 3, pp. 229-35. doi: 10.1016/j.lungcan.2014.03.018.
4. Houston K.A., Henley S.J., Li J., White M.C., Richards T.B. (2014) Patterns in lung cancer incidence rates and trends by histologic type in the United States, 2004–2009. Lung Cancer., vol. 86, pp. 22–28. doi: 10.1016/j.lungcan.2014.08.001.
5. Huang T., Yang J., Cai Y.D. (2015) Novel candidate key drivers in the integrative network of genes, microRNAs, methylations, and copy number variations in squamous cell lung carcinoma. Biomed Res Int., vol. 2015, pp. 358125. doi: 10.1155/2015/358125.
6. 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.
7. Kim E.K., Kim K.A., Lee C.Y., Shim H.S. (2017) The frequency and clinical impact of HER2 alterations in lung adenocarcinoma. PLoS One, vol. 12, no. 2, e0171280. doi: 10.1371/journal.pone.0171280.
8. Ko H.L., Wang Y.S., Fong W.L., Chi M.S., Chi K.H., Kao S.J. (2014) Apolipoprotein C1 (APOC1) as a novel diagnostic and prognostic biomarker for lung cancer: A marker phase I trial. Thorac Cancer, vol. 5, no. 6, pp. 500-8. doi: 10.1111/1759-7714.12117.
9. Kool E.T. (2001) Hydrogen bonding, base stacking, and steric effects in DNA replication. Annual Review of Biophysics and Biomolecular Structure, vol. 30, pp. 1–22.
10. Leontis N.B., Stombaugh J., Westhof E. (2002) The non-Watson- Crick base pairs and their associated isostericity matrices. Nucleic Acids Research, vol. 30, no. 16, pp. 3497–3531.
11. Liu M., Zhou K., Huang Y., Cao Y. (2015) The candidate oncogene (MCRS1) promotes the growth of human lung cancer cells via the miR-155-Rb1 pathway. J Exp Clin Cancer Res., vol. 34, pp. 121. doi: 10.1186/s13046-015-0235-5.
12. 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, pp. 1106-1115.
13. Mizuno K., Mataki H., Arai T., Okato A., Kamikawaji K., Kumamoto T., Hiraki T., Hatanaka K., Inoue H., Seki N. (2017) The microRNA expression signature of small cell lung cancer: tumor suppressors of miR-27a-5p and miR-34b-3p and their targeted oncogenes. J Hum Genet., vol. 62, no. 7, pp. 671-678. doi: 10.1038/jhg.2017.27.
14. Niyazova R.Y., Аtambayeva S.А., Pyrkova А.Y., Ivashchenko A.T. (2015) Assotsiatsii miRNA i mRNA genov, uchastvuyushchih v razvitii nemelkokletochnogo raka legkih [Associations of miRNA and mRNA genes involved in the development of non-small cell lung cancer]. KazNU Bulletin. Biology series, vol. 65, no 3, pp. 143-148.
15. Pao W., Girard N. (2011) New driver mutations in non-small-cell lung cancer. Lancet Oncol., vol. 12, pp. 175–180. doi: 10.1016/S1470-2045(10)70087-5.
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Как цитировать
Niyazova, R. E., Mamirova, A., Atambayeva, S. A., & Ivashchenko, A. T. (2018). Характеристики взаимодействия miRNA c mRNA кандидатных генов немелкоклеточного рака легкого. Вестник КазНУ. Серия биологическая, 76(3), 83–96. https://doi.org/10.26577/eb-2018-3-1341
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МОЛЕКУЛЯРНАЯ БИОЛОГИЯ И ГЕНЕТИКА
