Characteristics of miRNA interaction with 5’UTR, CDS, 3’UTR mRNA candidate genes of breast cancer subtypes
DOI:
https://doi.org/10.26577/eb-2018-2-1326Аннотация
Different subtypes of breast cancer are distinguished by a set of candidate genes involved in the development of this disease. The expression of many genes is regulated by binding of their mRNA with miRNA, therefore it is required to identify which candidate genes of oncogenesis and in what degree they can interact with miRNA. The purpose of this work was to establish the interaction characteristics of the known 3701 miRNAs with mRNA 92 candidate genes of breast cancer subtypes. 19 genes from 25 candidate genes of the her2 subtype were targets for miRNA. The binding sites of 67 miRNAs were located in 5’UTR, CDS, 3’UTR and the average free energy (ΔG) of miRNA binding with mRNA was equal to -120,2 ± -7,6 kJ/mole, -123,6 ± -9,8 kJ/mole, -110,4 ± -9,8 kJ/mole, respectively. 31 miRNA associations with mRNA, having the free binding energy more than -120 kJ/mole are recommended for the diagnosis of the her2 subtype. 33 genes from 47 candidate genes of the triple-negative subtype were targets for miRNA. The binding sites of 90 miRNAs were located in 5’UTR, CDS, 3’UTR and the average ΔG value of miRNA binding with mRNA was equal to -123,5 ± -7,0 kJ/mole, -114,1 ± –7,9 kJ/mole,
-106,9 ± –4,9 kJ/mole, respectively. 36 miRNA associations with mRNA are recommended for the diag- nosis of the triple-negative subtype. 14 genes from 20 candidate genes of luminal A and B subtypes were miRNA targets. The binding sites of 86 miRNAs were located in 5’UTR, CDS, 3’UTR and the average ΔG value of miRNA binding with mRNA was equal to -121.2 ± -9,5 kJ/mole, 120,4 ± -7,8 kJ/mole, -118,9
± -8,1 kJ/mole, respectively. 51 miRNA associations with mRNA were recommended for diagnosis of luminal A and B subtypes. In the mRNA of many genes, sites containing two or more miRNA binding sites were identified with arranging of their nucleotide sequences, which reduces the proportion of bind- ing sites in the nucleotide composition in 5’UTR, CDS, and 3’UTR several times. Based on the obtained results, the groups of miRNA and mRNA associations of candidate genes are recommended to develop methods for diagnosis subtypes of breast cancer.
Key words: miRNA, mRNA, subtypes of breast cancer, target genes.
Библиографиялық сілтемелер
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References
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�eccia F., Del Vecchio �., Mariotti E., Di Noto R., Morel A.P., Puisieux A., Salvatore F., Ansieau S. (2014) ABCG2, a novel antigen to sort luminal progenitors of BRCA1- breast cancer cells. Mol Cancer., vol. 13, pp. 213. doi: 10.1186�1476-4598-13-213.
�eontis N.B., Stombaugh �., Westhof E. (2002) The non-Watson- Crick base pairs and their associated isostericity matrices.
Nucleic Acids Research, vol. 30, no. 16, pp. 3497–3531.
�ondin E., �ohera 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.
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Pastrello C., Polesel �., Della Puppa �., Viel A., Maestro R. (2010) Association between hsa-mir-146a genotype and tumor age- of-onset in BRCA1�BRCA2-negative familial breast and ovarian cancer patients. Carcinogenesis, vol. 31, no. 12, pp. 2124-6. doi: 10.1093�carcin�bgq184.
Peurala H., Greco D., Heikkinen T., Kaur S., Bartkova �., �amshidi M., Aittomäki K., Heikkilä P., Bartek �., Blomqvist C., Büt- zow R., Nevanlinna H. (2011) MiR-34a expression has an effect for lower risk of metastasis and associates with expression patterns predicting clinical outcome in breast cancer. P�oS �ne, vol. 6, no. 11, pp. e26122. doi:10.1371�journal.pone.0026122.
Ray A., Ray B.K. (2015) Induction of Ras by SAF-1�MAZ through a feed-forward loop promotes angiogenesis in breast cancer.
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Banin Hirata B.K., �da �.M., �osi Guembarovski R., Ariza C.B., de �liveira C.E., Watanabe M.A. Molecular markers for breast cancer: prediction on tumor behavior �� Dis Markers. – 2014. – Vol. 2014. – P. 513158. doi: 10.1155�2014�513158.
Barba M., Vici P., Pizzuti �., Di �auro �., Sergi D., Di Benedetto A., Ercolani C., Sperati F., Terrenato I., Botti C., Mentuccia �., Iezzi �., Gamucci T., Natoli C., Vitale I., Mottolese M., De Maria R., Maugeri-Saccà M. Body mass index modifies the relationship between γ-H2AX, a DNA damage biomarker, and pathological complete response in triple-negative breast cancer �� BMC Cancer. – 2017. – Vol. 17, No. 1. – P. 101. doi: 10.1186�s12885-016-3045-z.
Burstein M.D., Tsimelzon A., Poage G.M., Covington K.R., Contreras A., Fuqua S.A., Savage M.I., �sborne C.K., Hilsenbeck S.G., Chang �.C., Mills G.B., �au C.C., Brown P.H. Comprehensive genomic analysis identifies novel subtypes and targets of triple- negative breast cancer �� Clin Cancer Res. – 2015. – Vol. 21, No. 7. – P. 1688-98. doi: 10.1158�1078-0432.CCR-14-0432.
Chakraborty C., Chin K.�., Das S. miRNA-regulated cancer stem cells: understanding the property and the role of miRNA in carcinogenesis �� Tumour Biol. – 2016. – Vol. 37, No. 10. – P. 13039-13048. PMID: 27468722
Chaudhary S., Krishna B.M., Mishra S.K. A novel F�XA1�ESR1 interacting pathway: A study of �ncomine breast cancer mi- croarrays �� �ncol �ett. – 2017. – Vol. 14, No. 2. – P. 1247-1264. doi: 10.3892�ol.2017.6329.
Chistiakov D.A., �rekhov A.N., Bobryshev �.V. MicroRNA regulation of macrophages in human pathologies �� � Mol Cell Cardiol. – 2016. – Vol. 94. – P. 107-121. doi: 10.1016�j.yjmcc.2016.03.015
Cicatiello �., Mutarelli M., Grober �.M., Paris �., Ferraro �., Ravo M., Tarallo R., �uo S., Schroth G.P., Seifert M., Zinser C., Chiusano M.�., Traini A., De Bortoli M., Weisz A. Estrogen receptor alpha controls a gene network in luminal-like breast cancer cells comprising multiple transcription factors and microRNAs �� Am � Pathol. – 2010. – Vol. 176, No. 5. – P. 2113-30. doi: 10.2353� ajpath.2010.090837.
Donepudi M.S., Kondapalli K., Amos S.�., Venkanteshan P. Breast cancer statistics and markers �� � Cancer Res Ther. – 2014. – Vol. 10, No. 3. – P. 506-11. doi: 10.4103�0973-1482.137927.
Fasching P.A., �oibl S., Hu C., Hart S.N., Shimelis H., Moore R., Schem C., Tesch H., Untch M., Hilfrich �., Rezai M., Gerber B., Costa S.D., Blohmer �.U., Fehm T., Huober �., �iedtke C., Weinshilboum R.M., Wang �., Ingle �.N., Müller V., Nekljudova V., Weber K.E., Rack B., Rübner M., von Minckwitz G., Couch F.�. BRCA1�2 Mutations and Bevacizumab in the Neoadjuvant Treat- ment of Breast Cancer: Response and Prognosis Results in Patients With Triple-Negative Breast Cancer From the GeparQuinto Study �� � Clin �ncol. – 2018. – P. �C�2017772285. doi: 10.1200��C�.2017.77.2285.
Feldinger K., Generali D., Kramer-Marek G., Gijsen M., Ng T.B., Wong �.H., Strina C., Cappelletti M., Andreis D., �i �.�., Bridges E., Turley H., �eek R., Roxanis I., Capala �., Murphy G., Harris A.�., Kong A. ADAM10 mediates trastuzumab resistance and is correlated with survival in HER2 positive breast cancer �� �ncotarget. – 2014. – Vol. 5, No. 16. – P. 6633-46.
Hamam R., Ali A.M., Alsaleh K.A., Kassem M., Alfayez M., Aldahmash A., Alajez N.M. microRNA expression profiling on individual breast cancer patients identifies novel panel of circulating microRNA for early detection �� Sci Rep. – 2016. – Vol. 6. – P. 25997. doi:10.1038�srep25997.
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Ivashchenko A., Berillo �., Pyrkova A., Niyazova R., Atambayeva Sh. The properties of binding sites of miR-619-5p, miR- 5095, miR-5096 and miR-5585-3p in the mRNAs of human genes �� Biomed Research International. – 2014. – Vol. 2014. – P. e8.
Ivashchenko A., Berillo �., Pyrkova A., Niyazova R. Binding Sites of miR-1273 Family on the mRNA of Target Genes �� Biomed Research International. – 2014. – Vol. 2014. – P. e11.
Ivashchenko A.T., Pyrkova A.�., Niyazova R.�., Alybayeva A., Baskakov K. Prediction of miRNA binding sites in mRNA �� Bioinformation. – 2016. – Vol. 12, No. 4. – P. 237-240.
�in �., Wessely �., Marcusson E.G., Ivan C., Calin G.A., Alahari S.K. Prooncogenic factors miR-23b and miR-27b are regu- lated by Her2�Neu, EGF, and TNF-α in breast cancer �� Cancer Res. – 2013. – Vol. 73, No. 9. – P. 2884-96. doi: 10.1158�0008-5472. CAN-12-2162.
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�ohnson �., Thijssen B., McDermott U., Garnett M., Wessels �.F., Bernards R. Targeting the RB-E2F pathway in breast cancer
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Kool E.T. Hydrogen bonding, base stacking, and steric effects in DNA replication �� Annual Review of Biophysics and Biomo- lecular Structure. – 2001. – Vol.30. – P. 1–22.
�eccia F., Del Vecchio �., Mariotti E., Di Noto R., Morel A.P., Puisieux A., Salvatore F., Ansieau S. ABCG2, a novel antigen to sort luminal progenitors of BRCA1- breast cancer cells �� Mol Cancer. – 2014. – Vol. 13. – P. 213. doi: 10.1186�1476-4598-13-213.
�eontis N.B., Stombaugh �., Westhof E. The non-Watson- Crick base pairs and their associated isostericity matrices �� Nucleic Acids Research. – 2002. – Vol. 30, No. 16. – P. 3497–3531.
�ondin E., �ohera 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.
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Pastrello C., Polesel �., Della Puppa �., Viel A., Maestro R. Association between hsa-mir-146a genotype and tumor age-of-onset in BRCA1�BRCA2-negative familial breast and ovarian cancer patients �� Carcinogenesis. – 2010. – Vol. 31, No. 12. – P. 2124-6. doi: 10.1093�carcin�bgq184.
Peurala H., Greco D., Heikkinen T., Kaur S., Bartkova �., �amshidi M., Aittomäki K., Heikkilä P., Bartek �., Blomqvist C., Bützow R., Nevanlinna H. MiR-34a expression has an effect for lower risk of metastasis and associates with expression patterns predicting clinical outcome in breast cancer �� P�oS �ne. – 2011. – Vol. 6, No. 11. – P. e26122. doi:10.1371�journal.pone.0026122. Ray A., Ray B.K. Induction of Ras by SAF-1�MAZ through a feed-forward loop promotes angiogenesis in breast cancer �� Can-
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Wang C., Zheng X., Shen C., Shi �. MicroRNA-203 suppresses cell proliferation and migration by targeting BIRC5 and �ASP1 in human triple-negative breast cancer cells �� � Exp Clin Cancer Res. – 2012. – Vol. 31. – P. 58. doi: 10.1186�1756-9966-31-58.
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Ivashchenko A., Berillo �., Pyrkova A., Niyazova R. (2014) Binding Sites of miR-1273 Family on the mRNA of Target Genes.
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Ivashchenko A.T., Pyrkova A.�., Niyazova R.�., Alybayeva A., Baskakov K. (2016) Prediction of miRNA binding sites in mRNA. Bioinformation, vol. 12, no. 4, pp. 237-240.
�in �., Wessely �., Marcusson E.G., Ivan C., Calin G.A., Alahari S.K. (2013) Prooncogenic factors miR-23b and miR-27b are regulated by Her2�Neu, EGF, and TNF-α in breast cancer. Cancer Res., vol. 73, no. 9, pp. 2884-96. doi: 10.1158�0008-5472.CAN- 12-2162.
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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.
�eccia F., Del Vecchio �., Mariotti E., Di Noto R., Morel A.P., Puisieux A., Salvatore F., Ansieau S. (2014) ABCG2, a novel antigen to sort luminal progenitors of BRCA1- breast cancer cells. Mol Cancer., vol. 13, pp. 213. doi: 10.1186�1476-4598-13-213.
�eontis N.B., Stombaugh �., Westhof E. (2002) The non-Watson- Crick base pairs and their associated isostericity matrices.
Nucleic Acids Research, vol. 30, no. 16, pp. 3497–3531.
�ondin E., �ohera 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.
Madoux F., Dreymuller D., Pettiloud �.P., Santos R., Becker-Pauly C., �udwig A., Fields G.B., Bannister T., Spicer T.P., Cudic M., Scampavia �.D., Minond D. (2016) Discovery of an enzyme and substrate selective inhibitor of ADAM10 using an exosite- binding glycosylated substrate. Sci Rep., vol. 6, no. 1, pp. 11. doi: 10.1038�s41598-016-0013-4.
Pastrello C., Polesel �., Della Puppa �., Viel A., Maestro R. (2010) Association between hsa-mir-146a genotype and tumor age- of-onset in BRCA1�BRCA2-negative familial breast and ovarian cancer patients. Carcinogenesis, vol. 31, no. 12, pp. 2124-6. doi: 10.1093�carcin�bgq184.
Peurala H., Greco D., Heikkinen T., Kaur S., Bartkova �., �amshidi M., Aittomäki K., Heikkilä P., Bartek �., Blomqvist C., Büt- zow R., Nevanlinna H. (2011) MiR-34a expression has an effect for lower risk of metastasis and associates with expression patterns predicting clinical outcome in breast cancer. P�oS �ne, vol. 6, no. 11, pp. e26122. doi:10.1371�journal.pone.0026122.
Ray A., Ray B.K. (2015) Induction of Ras by SAF-1�MAZ through a feed-forward loop promotes angiogenesis in breast cancer.
Cancer Med, vol. 4, no. 2, pp. 224-34. doi: 10.1002�cam4.362.
Wang C., Zheng X., Shen C., Shi �. (2012) MicroRNA-203 suppresses cell proliferation and migration by targeting BIRC5 and �ASP1 in human triple-negative breast cancer cells. � Exp Clin Cancer Res., vol. 31, pp. 58. doi: 10.1186�1756-9966-31-58.
Жүктелулер
Как цитировать
Aisina, D., Niyazova, R., Atambayeva, S., Imyanitov, E., & Ivashchenko, A. (2018). Characteristics of miRNA interaction with 5’UTR, CDS, 3’UTR mRNA candidate genes of breast cancer subtypes. ҚазҰУ Хабаршысы. Биология сериясы, 75(2), 30–48. https://doi.org/10.26577/eb-2018-2-1326
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МОЛЕКУЛЯРНАЯ БИОЛОГИЯ И ГЕНЕТИКА
