Microarray analysis of miRNA expression profiles following whole body irradiation in a mouse model

References

• Acharya, S.S., et al., 2015. Serum microRNAs are early indicators of survival after radiation-induced hematopoietic injury. Science translational medicine, 7 (287), 287ra69.
   PubMed Web of Science ®Google Scholar
• Arora, H., et al., 2011. miR-9 and let-7g enhance the sensitivity to ionizing radiation by suppression of NF κB1. Experimental and molecular medicine, 43 (5), 298–304.
   PubMed Web of Science ®Google Scholar
• Aryankalayil, M.J., et al., 2018. Radiation-induced long noncoding RNAs in a mouse model after whole-body irradiation. Radiation Research, 189 (3), 251–263.
   PubMed Web of Science ®Google Scholar
• Beer, L., 2014. High dose ionizing radiation regulates micro RNA and gene expression changes in human peripheral blood mononuclear cells. BMC genomics, 15 (1), 814–821.
   PubMedGoogle Scholar
• Chaudhry, M.A., et al., 2013. Identification of radiation-induced microRNA transcriptome by next-generation massively parallel sequencing. Journal of radiation research, 54 (5), 808–822.
   PubMed Web of Science ®Google Scholar
• Coleman, C.N. and Koerner, J.F., 2016. Biodosimetry: medicine, science, and systems to support the medical decision-maker following a large scale nuclear or radiation incident. Radiation protection dosimetry, 172 (1–3), 38–46.
   PubMed Web of Science ®Google Scholar
• Correia, C.N., et al., 2017. Circulating microRNAs as potential biomarkers of infectious disease. Frontiers in immunology, 8, 1–17.
   PubMed Web of Science ®Google Scholar
• Cortes, C. and Vapnik, V., 1995. Support-vector networks. Machine learning, 20 (3), 273–297.
   Web of Science ®Google Scholar
• Cui, W., et al., 2011. Plasma miRNA as biomarkers for assessment of total-body radiation exposure dosimetry. PLoS One, 6 (8), e22988.
   PubMed Web of Science ®Google Scholar
• D’Amato, N.C., Howe, E.N., and Richer, J.K., 2013. MicroRNA regulation of epithelial plasticity in cancer. Cancer letters, 341 (1), 46–55.
   PubMed Web of Science ®Google Scholar
• De Lemos Pinto, M.M.P., Santos, N.F.G., and Amaral, A., 2010. Current status of biodosimetry based on standard cytogenetic methods. Radiation and environmental biophysics, 49 (4), 567–581.
   PubMed Web of Science ®Google Scholar
• Ding, N., et al., 2011. Detection of novel human MiRNAs responding to X-ray irradiation. Journal of radiation research, 52 (4), 425–432.
   PubMed Web of Science ®Google Scholar
• Griffiths-Jones, S., 2010. MiRBase: microRNA sequences and annotation. Current protocols in bioinformatics, 34, 1291–12910.
   Google Scholar
• Griffiths-Jones, S., et al., 2006. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic acids research, 34 (Database issue), D140–D144.
   PubMed Web of Science ®Google Scholar
• Griffiths-Jones, S., et al., 2007. miRBase: tools for microRNA genomics. Nucleic acids research, 36 (Database issue), D154–D158.
   PubMedGoogle Scholar
• Ha, M. and Kim, V.N., 2014. Regulation of microRNA biogenesis. Nature reviews. Molecular cell biology, 15 (8), 509–524.
   PubMed Web of Science ®Google Scholar
• Hastie, T., Tibshirani, R., and Friedman, J., 2009. Springer series in statistics: the elements of statistical learning. New York, NY: Springer-Verlag..
   Google Scholar
• Hu, H., and Gatti, R.A., 2011. MicroRNAs: new players in the DNA damage response. Journal of molecular cell biology, 3 (3), 151–158.
   PubMed Web of Science ®Google Scholar
• Huang, B. and Zhang, R., 2014. Regulatory non-coding RNAs: revolutionizing the RNA world. Molecular biology reports, 41 (6), 3915–3923.
   PubMed Web of Science ®Google Scholar
• Jacob, N.K., et al., 2013. Identification of sensitive serum microRNA biomarkers for radiation biodosimetry. PLoS One, 8 (2), e57603.
   PubMed Web of Science ®Google Scholar
• Javidi, M.A. et al., 2014. Cell-free microRNAs as cancer biomarkers: the odyssey of miRNAs through body fluids. Medical oncology, 31 (12), 295.
   PubMed Web of Science ®Google Scholar
• John-Aryankalayil, M., et al., 2010. Fractionated radiation therapy can induce a molecular profile for therapeutic targeting. Radiation research, 174 (4), 446–458.
   PubMed Web of Science ®Google Scholar
• Joly-Tonetti, N., et al., 2013. Differential miRNA expression profiles in proliferating or differentiated keratinocytes in response to gamma irradiation. BMC genomics, 14 (1), 184.
   PubMedGoogle Scholar
• Karimian, A., Ahmadi, Y., and Yousefi, B., 2016. Multiple functions of p21 in cell cycle, apoptosis and transcriptional regulation after DNA damage. DNA repair, 42, 63–71.
   PubMed Web of Science ®Google Scholar
• Kozomara, A. and Griffiths-Jones, S., 2011. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic acids research, 39 (Database issue), D152–D157.
   PubMed Web of Science ®Google Scholar
• Kozomara, A. and Griffiths-Jones, S., 2014. MiRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic acids research, 42 (D1), D68–D73.
   PubMed Web of Science ®Google Scholar
• Kuhn, M. and contributions from Jed Wing, S. W. caret: Classification and Regression Training. (R package version 6.0-78). Available from https://cran.r-project.org/package=caret.
   Google Scholar
• Lee, Y., et al., 2014. MicroRNA142-3p promotes tumor-initiating and radioresistant properties in malignant pediatric brain tumors. Cell transplantation, 23 (4–5), 669–690.
   PubMed Web of Science ®Google Scholar
• Leung, C., et al., 2014. Comprehensive microRNA profiling of prostate cancer cells after ionizing radiation treatment. Oncology reports, 31 (3), 1067–1078.
   PubMed Web of Science ®Google Scholar
• Liu, C., et al., 2011. MiR-34a in age and tissue related radio-sensitivity and serum miR-34a as a novel indicator of radiation injury. International journal of biological sciences, 7 (2), 221–233.
   PubMed Web of Science ®Google Scholar
• Mendell, J.T., Olson, E.N., and Review, 2012. MicroRNAs in stress signaling and human disease. Cell, 148 (6), 1172–1187.
   PubMed Web of Science ®Google Scholar
• Mogilyansky, E. and Rigoutsos, I., 2013. The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease. Cell death and differentiation, 20 (12), 1603.
   PubMed Web of Science ®Google Scholar
• Monticelli, S., 2013. MicroRNAs in T helper cell differentiation and plasticity. Seminars in immunology, 25 (4), 291–298.
   PubMed Web of Science ®Google Scholar
• Nouraee, N. and Mowla, S.J., 2015. miRNA therapeutics in cardiovascular diseases: promises and problems. Frontiers in genetics, 6, 232.
   PubMed Web of Science ®Google Scholar
• Olive, V., Li, Q., and He, L., 2013. miR-17-92: a polycistronic oncomir with pleiotropic functions. Immunological reviews, 253 (1), 158–166.
   PubMedGoogle Scholar
• Palayoor, S.T., et al., 2014. Differential expression of stress and immune response pathway transcripts and miRNAs in normal human endothelial cells subjected to fractionated or single-dose radiation. Molecular cancer research, 12 (7), 1002–1016.
   PubMed Web of Science ®Google Scholar
• Rnas, A., Daugaard, I., and Hansen, T.B., 2017. Biogenesis and Function of Ago-Associated RNAs. Trends in genetics, 33 (3), 208–219.
   PubMed Web of Science ®Google Scholar
• Rottiers, V. and Naar, A., 2012. MicroRNAs in metabolism and metabolic disorders. Nature reviews molecular cell biology, 13 (4), 239.
   PubMed Web of Science ®Google Scholar
• Sand, M., 2014. The pathways of miRNA maturation. New York, NY: Humana Press.
   Google Scholar
• Santangelo, A., et al., 2017. Circulating microRNAs as emerging non-invasive biomarkers for gliomas. Annals of translational medicine, 5 (13), 277–278.
   PubMed Web of Science ®Google Scholar
• Schwarzenbach, H., et al., 2014. Clinical relevance of circulating cell-free microRNAs in cancer. Nature reviews. Clinical oncology, 11 (3), 145–156.
   PubMed Web of Science ®Google Scholar
• Sharma, V. and Misteli, T., 2013. Non-coding RNAs in DNA damage and repair. FEBS letters, 587 (13), 1832–1839.
   PubMed Web of Science ®Google Scholar
• Shin, S., et al., 2009. MicroRNAs are significantly influenced by p53 and radiation in HCT116 human colon carcinoma cells. International journal of oncology, 34 (6), 1645–1652.
   PubMed Web of Science ®Google Scholar
• Simone, N.L., et al., 2009. Ionizing radiation-induced oxidative stress alters miRNA expression. PLoS One, 4 (7), e6377.
   PubMed Web of Science ®Google Scholar
• Smith, C.L., et al., 2018. Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse. Nucleic acids research, 46 (D1), D836–D842.
   PubMed Web of Science ®Google Scholar
• Sokolov, M.V., Panyutin, I.V., and Neumann, R.D., 2012. Unraveling the global microRNAome responses to ionizing radiation in human embryonic stem cells. PLos One, 7 (2), e31028.
   PubMed Web of Science ®Google Scholar
• Sproull, M. and Camphausen, K., 2016. State-of-the-art advances in radiation biodosimetry for mass casualty events involving radiation exposure. Radiation research, 186 (5), 423–435.
   PubMed Web of Science ®Google Scholar
• Stevens, C. and Thangue, N.B., 2003. La. E2F and cell cycle control: a double-edged sword. Archives of biochemistry and biophysics, 412 (2), 157–169.
   PubMed Web of Science ®Google Scholar
• The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature, 489 (7414), 57–74.
   PubMed Web of Science ®Google Scholar
• Tibshirani, R., et al., 2003. Class prediction by nearest shrunken centroids, with applications to DNA microarrays. Statistical science, 18 (1), 104–117.
   Web of Science ®Google Scholar
• Valentino, A., et al., 2016. Exosomal microRNAs in liquid biopsies: future biomarkers for prostate cancer. Clinical and translational oncology, 19 (6), 651–657.
   Web of Science ®Google Scholar
• Vincenti, S., et al., 2011. HUVEC respond to radiation by inducing the expression of pro-angiogenic microRNAs. Radiation research, 175 (5), 535–546.
   PubMed Web of Science ®Google Scholar
• Worby, C.A. and Dixon, J.E., 2014. PTEN. Annual review of biochemistry, 83, 641–669.
   PubMed Web of Science ®Google Scholar
• Yan, H-l., et al., 2009. Repression of the miR-17-92 cluster by p53 has an important function in hypoxia-induced apoptosis. The EMBO journal, 28 (18), 2719–2732.
   PubMed Web of Science ®Google Scholar
• Zhang, C. and Peng, G., 2015. Non-coding RNAs: an emerging player in DNA damage response. Mutation research. Reviews in mutation research, 763, 202–211.
   PubMed Web of Science ®Google Scholar
• Zhao, L., et al., 2015. The role of exosomes and ‘exosomal shuttle microRNA’ in tumorigenesis and drug resistance. Cancer letters, 356 (2 Pt B), 339–346.
   PubMed Web of Science ®Google Scholar
• Zoni, E., et al., 2015. Epithelial plasticity in cancer: unmasking a MicroRNA network for TGF-β-, notch-, and Wnt-mediated EMT. Journal of oncology, 2015, 198967.
   PubMed Web of Science ®Google Scholar