Is the Identification of SNP-miRNA Interactions Supporting the Prediction of Human Lymphocyte Transcriptional Radiation Responses?

Marzena Dolbniak, Joanna Zyla, Sylwia Kabacik, Grainne Manning, Christophe Badie, Ghazi Alsbeih, Joanna Polanska

2015

Abstract

Genome-Wide Association Studies (GWAS) are of great importance in identifying the genetic variants associated with traits/diseases. Due to the high number of candidate SNPs some filtering techniques are necessary to be applied. The aim of the study was to develop the comprehensive approach allowing for detailed analysis of both SNP-gene and SNP-miRNA-gene relations. We elaborated and optimized the novel signal analysis pipeline improving significantly the results of the analysis on genotype-phenotype interplay. Direct links between genotype results and gene expression levels were enriched by detailed analysis of SNP-miRNA-gene interactions at both mature miRNA structure/seed region and target binding site level. The proposed technique was applied to the data on lymphocyte radiation response and increased by almost 100% number of potential functional SNPs.

References

  1. Aureli, M., Murdica, V., Loberto, N., Samarani, M., Prinetti, A., Bassi, R., and Sonnino, S. (2014). Exploring the link between ceramide and ionizing radiation. Glycoconj J., 31(6-7):449-459.
  2. Bansal, N., Mims, J., Kuremsky, J., Olex, A., Zhao, W., Yin, L., Wani, R., Qian, J., Center, B., Marrs, G., Porosnicu, M., Fetrow, J., Tsang, A., and Furdui, C. (2014). Broad phenotypic changes associated with gain of radiation resistance in head and neck squamous cell cancer. Antioxid Redox Signal., 21(2):221-236.
  3. Beissbarth, T. and Speed, T. (2004). GOstat: find statistically overrepresented gene ontologies within a group of genes. Bioinformatics., 197(1):1464-1465.
  4. Bendl, J., Stourac, J., Salanda, O., Pavelka, A., Wieben, E., Zendulka, J., Brezovsky, J., and Dombrsky, J. (2014). PredictSNP: Robust and accurate consensus classifier for prediction of disease-related mutations. PLoS Comput Biol., 10(1):e1003440.
  5. Bhattacharya, A., Ziebarth, J., and Cui, Y. (2014). PolymiRTS database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. Nucleic Acids Res., 42(D1):D86-D91.
  6. Budworth, H., Snijders, A., Marchetti, F., Mannion, B., Bhatnagar, S., Kwoh, E., Tan, Y., Wang, S., Blakely, W., Coleman, M., Peterson, L., and Wyrobek, A. (2012). Dna repair and cell cycle biomarkers of radiation exposure and inflammation stress in human blood. PLoS One, 7(11):e48619.
  7. Bush, W. and Moore, J. (2012). Chapter 11: Genome-wide association studies. PLOS Comput Biol., 8(12).
  8. Chen, F., Zhou, C., Lu, Y., Yuan, L., Peng, F., Zheng, L., and Li, X. (2013). Expression of hsa-mir-186 and its role in human colon carcinoma cells. Nan Fang Yi Ke Da Xue Xue Bao, 33(5):654-60.
  9. Chen, F., Zhu, H., Zhou, L., Wu, S., Wang, J., and Chen, Z. (2010). Inhibition of c-flip expression by mir-512-3p contributes to taxol-induced apoptosis in hepatocellular carcinoma cells. Oncology Reports, 23(5):1457- 1462.
  10. Davis, F., Azimi, I., Faville, R., Peters, A., Jalink, K., Putney, J., Goodhill, G., Thompson, E., RobertsThomson, S., and Monteith, G. (2014). Induction of epithelialmesenchymal transition (EMT) in breast cancer cells is calcium signal dependent. Oncogene., 33:2307-2316.
  11. Deveci, M., Catalyrek, U., Svoboda, M., and Toland, A. (2014). mrSNP: Software to detect SNP effects on microRNA binding. BMC Bioinformatics., 15):doi:10.1186/1471-2105-15-73.
  12. Dhillon, A., Hagan, S., Rath, O., and Kolc, W. (2007). MAP kinase signalling pathways in cancer. Oncogene., 26:3279-3290.
  13. Dong, H., Lei, J., Ding, L., Wen, Y., Ju, H., and Zhang, X. (2013). MicroRNA: Function, detection, and bioanalysis. Chem. Rev., 113(8):6207-6233.
  14. Dweep, H., Sticht, C., Pandey, P., and Gretz, N. (2014). miRWalk - database: prediction of possible mirna binding sites by 'walking' the genes of 3 genomes. Nucleic Acids Research, 42:D'D85.
  15. Edlund, K., Lindskog, C., Saito, A., Berglund, A., Pontn, F., Gransson-Kultima, H., Isaksson, A., Jirstrm, K., Planck, M., Johansson, L., Lambe, M., Holmberg, L., Nyberg, F., Ekman, S., Bergqvist, M., Landelius, P., Lamberg, K., Botling, J., Ostman, A., and Micke, P. (2012). CD99 is a novel prognostic stromal marker in non-small cell lung cancer. Int J Cancer, 131(10):2264-2273.
  16. Eke, I. and Cordes, N. (2014). Focal adhesion signaling and therapy resistance in cancer. Semin Cancer Biol., pii: S1044-579X(14)00098-4.
  17. Evangelou, E. and Ioannidis, J. (2013). Meta-analysis methods for genome-wide association studies and beyond. Nat. Rev. Genet., 14:379389.
  18. Finnon, P., Robertson, N., Dziwura, D., Raffy, C., Zhang, W., Ainsbury, L., Kaprio, J., Badie, C., and Bouffler, S. (2008). Evidence for significant heritability of apoptotic and cell cycle responses to ionising radiation. Hum Genet., 123(5):485-493.
  19. Griffiths-Jones, S., Saini, H., van Dongen, S., and Enright, A. (2008). mirbase tools for microrna genomics. Nucleic Acids, 36:154-158.
  20. Han, X., Xue, L., Zhou, L., Gong, L., Zhu, S., Yao, L., Wang, S., Lan, M., Li, Y., and Zhang, W. (2013). The role of ptpn13 in invasion and metastasis of lung squamous cell carcinoma. Exp Mol Pathol., 95(3):270-58.
  21. Hatakeyamai, S. (2011). TRIM proteins and cancer. Nat Rev Cancer, 11(11):792-804.
  22. Hirshoren, N., Bulvik, R., Neuman, T., Rubinstein, A., Meirovitz, A., and Elkin, M. (2014). Induction of heparanase by HPV E6 oncogene in head and neck squamous cell carcinoma. J Cell Mol Med., 18(1):181- 186.
  23. Hsu, S., Tseng, Y., Shrestha, S., Lin, Y., Khaleel, A., Chou, C., Chu, C., Huang, H., Lin, C., Ho, S., Jian, T., Lin, F., Chang, T., Weng, S., Liao, K., Liao, I., Liu, C., and Huang, H. (2014). MiRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Research, 42:D'D85.
  24. Jianq, N., Zhu, S., Chen, J., Niu, Y., and Zhou, L. (2013). A-methylacyl-CoA racemase (AMACR) and prostatecancer risk: a meta-analysis of 4,385 participants. PLoS One., 8(10):e74386.
  25. Kabacik, S., Mackay, A., Tamber, N., Manning, G., Finnon, P., Paillier, F., Ashworth, A., Bouffler, S., and Badie, C. (2011a). Gene expression following ionising radiation: identification of biomarkers for dose estimation and prediction of individual response. Int J Radiat Biol., 87(2):115-129.
  26. Kabacik, S., Ortega-Molina, A., Efayan, A., Finnon, P., Bouffler, S., Serrano, M., and Badie, C. (2011b). A minimally invasive assay for individual assessment of the atm/chek2/p53 pathway activity. Cell Cycle., 10(7):1152-1161.
  27. Kapoor, S. (2014). Maspin and its evolving role in tumor progression in systemic malignancies. Breast Cancer., 21(2):249.
  28. Lahtz, C. and Pfeifer, G. (2011). Epigenetic changes of dna repair genes in cancer. J Mol Cell Biol., 3(1):51-55.
  29. Lewis, B., Burge, C., and Bartel, D. (2005). Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microrna targets.
  30. Cell, 120:15-20.
  31. Li, X., Pan, Y., Seigel, G., Hu, Z., Huang, M., and Yu, A. (2011). Breast cancer resistance protein BCRP/ABCG2 regulatory microRNAs (hsa-mir-328, -519c and -520h) and their differential expression in stem-like ABCG2+ cancer cells. Biochemical Pharmacology, 81(6):783 - 792.
  32. Liu, C., Zhang, F., Li, T., Lu, M., Wang, L., Yue, W., and Zhang, D. (2012). MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPSs and eQTLs. BMC Genomics., 13:661.
  33. Ma, S., Liu, X., Jiao, B., Yang, Y., and Liu, X. (2010). Lowdose radiation-induced responses: focusing on epigenetic regulation. Int J Radiat Biol., 86(7):517-528.
  34. Mangoni, M., Bisanzi, S., Carozzi, F., Sani, C., Biti, G., Livi, L., Barletta, E., Costantini, A., and Gorini, G. (2011). Association between genetic polymorphisms in the xrcc1, xrcc3, xpd, gstm1, gstt1, msh2, mlh1, msh3, and mgmt genes and radiosensitivity in breast cancer patients. Int J Radiat Oncol Biol Phys., 81(1):52-58.
  35. Manning, G., Kabacik, S., Finnon, P., Bouffler, S., and Badie, C. (2013). High and low dose responses of transcriptional biomarkers in ex vivo x-irradiated human blood. Int J Radiat Biol., 89(7):511-522.
  36. Miedema, K., Tissing, W., Poele, E. T., Kamps, W., Alizadeh, B., Kerkhof, M., de Jongste, J., Smit, H., de Pagter, A., Bierings, M., Boezen, H., Postma, D., de Bont, E., and Koppelman, G. (2012). Polymorphisms in the TLR6 gene associated with the inverse association between childhood acute lymphoblastic leukemia and atopic disease. Leukemia., 26(6):1203- 1210.
  37. Nass, D., Rosenwald, S., ans S. Gilad, E. M., TabibianKeissar, H., Schlosberg, A., Kuker, H., Sion-Vardy, N., Tobar, A., Kharenko, O., Sitbon, E., Yanai, G. L., Elyakim, E., Cholakh, H., Gibori, H., Spector, Y., Bentwich, Z., Barshack, I., and Rosenfeld, N. (2009). Mir-92b and mir-9/9* are specifically expressed in brain primary tumors and can be used to differentiate primary from metastatic brain tumors. Brain Pathology, 19:375-383.
  38. Nenoi, M., Wang, B., and Vares, G. (2014). In vivo radioadaptive response: A review of studies relevant to radiation-induced cancer risk. Hum Exp Toxicol., pii: 0960327114537537.
  39. Ochi, K., Mori, T., Toyama, Y., Nakamura, Y., and Arakawa, H. (2002). Identification of semaphorin3B as a direct target of p53. Neoplasia., 4(1):82-87.
  40. O'Donovan, M., Freemantle, M., Hull, G., Bell, D., Arlett, C., and Cole, J. (1995). Extended-term cultures of human t-lymphocytes: a practical alternative to primary human lymphocytes for use in genotoxicity testing. Mutagenesis., 10(3):189-201.
  41. Patel, J., Appaiah, H., Burnett, R., Bhat-Nakshatri, P., Wang, G., Mehta, R., Badve, S., Thomson, M., Hammond, S., Steeg, P., Liu, Y., and Nakshatri, H. (2011). Control of EVI-1 oncogene expression in metastatic breast cancer cells through microRNA mir-22. Oncogene, 30(11):1290-1301.
  42. Patnala, R., Clements, J., and Batra, J. (2013). Candidate gene association studies: a comprehensive guide to useful in silico tools. BMC Genet., 14:39:doi: 10.1186/1471-2156-14-39.
  43. Rocchi, A., Manara, M., Sciandra, M., Zambelli, D., Nardi, F., Nicoletti, G., Garofalo, C., Meschini, S., Astolfi, A., Colombo, M., Lessnick, S., Picci, P., and Scotlandi, K. (2010). CD99 inhibits neural differentiation of human ewing sarcoma cells and thereby contributes to oncogenesis. J Clin Invest, 120(3):668-680.
  44. Slaby, O., Bienertova-Vasku, J., Svoboda, M., and Vyzula, R. (2012). Genetic polymorphisms and microRNAs: new direction in molecular epidemiology of solid cancer. J Cell Mol Med., 16(1):8-21.
  45. Szkiba, D., Kapun, M., von Haeseler, A., and Gallach, M. (2014). SNP2GO: functional analysis of genomewide association studies. Genetics., 197(1):285-289.
  46. Vergoulis, T., Vlachos, T., Alexiou, P., Georgakilas, G., Maragkakis, M., Reczko, M., Gerangelos, S., Koziris, N., Dalamagas, T., and Hatzigeorgiou, A. (2012). Tarbase 6.0: Capturing the exponential growth of mirna targets with experimental support. Nucleic Acids Resources, 40(D1):222-229.
  47. Vitale, A., Tan, H., and Jin, P. (2011). MicroRNAs, SNPSs and cancer. Nucleic Acids Invest., 2(6):32-38.
  48. Wang, K., Li, M., and Hakonarson, H. (2010). Analysing biological pathways in genome-wide association studies. Nat. Rev. Genet., 11:843-854.
  49. Xu, Z. and Taylor, J. (2009). SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies. Nucl. Acids Res., (Web Server issue):W600-5.
  50. Yamada, A., Ishikawa, T., Ota, I., Kimura, M., Shimizu, D., Tanabe, M., Chishima, T., Sasaki, T., Ichikawa, Y., Morita, S., Yoshiura, K., Takabe, K., and Endo, I. (2013). High expression of ATP-binding cassette transporter ABCC11 in breast tumors is associated with aggressive subtypes and low disease-free survival. Breast Cancer Res Treat., 137(3):773-782.
  51. Yu, F., Yao, H., Zhu, P., Zhang, X., Pan, Q., Gong, C., Huang, Y., Hu, X., Su, F., Lieberman, J., and Song, E. (2007). let-7 regulates self renewal and tumorigenicity of breast cancer cells. Cell, 131(6):1109 - 1123.
  52. Yu, J. and Zhang, L. (2005). The transcriptional targets of p53 in apoptosis control. Biochem Biophys Res Commun., 3(331):851-858.
  53. Zhao, L., Bode, A., Cao, Y., and Dong, Z. (2012). Regulatory mechanisms and clinical perspectives of miRNA in tumor radiosensitivity. Carcinogenesis., 33(11):2220-2227.
  54. Zyla, J., Badie, C., Alsbeih, G., and Polanska, J. (2014). Modelling of genetic interactions in GWAS reveals more complex relations between genotype and phenotype. In Proceeding of: Bioinformatics 2014: 5th International Conference on Bioinformatics Models, Methods and Algorithms. SCITEPRESS.
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Paper Citation


in Harvard Style

Dolbniak M., Zyla J., Kabacik S., Manning G., Badie C., Alsbeih G. and Polanska J. (2015). Is the Identification of SNP-miRNA Interactions Supporting the Prediction of Human Lymphocyte Transcriptional Radiation Responses? . In Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015) ISBN 978-989-758-070-3, pages 243-250. DOI: 10.5220/0005286102430250


in Bibtex Style

@conference{bioinformatics15,
author={Marzena Dolbniak and Joanna Zyla and Sylwia Kabacik and Grainne Manning and Christophe Badie and Ghazi Alsbeih and Joanna Polanska},
title={Is the Identification of SNP-miRNA Interactions Supporting the Prediction of Human Lymphocyte Transcriptional Radiation Responses?},
booktitle={Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)},
year={2015},
pages={243-250},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005286102430250},
isbn={978-989-758-070-3},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms - Volume 1: BIOINFORMATICS, (BIOSTEC 2015)
TI - Is the Identification of SNP-miRNA Interactions Supporting the Prediction of Human Lymphocyte Transcriptional Radiation Responses?
SN - 978-989-758-070-3
AU - Dolbniak M.
AU - Zyla J.
AU - Kabacik S.
AU - Manning G.
AU - Badie C.
AU - Alsbeih G.
AU - Polanska J.
PY - 2015
SP - 243
EP - 250
DO - 10.5220/0005286102430250