Proton radiation-induced miRNA signatures in mouse blood: Characterization and comparison with ⁵⁶Fe-ion and gamma radiation

References

• Aypar U, Morgan WF, Baulch JE. 2011. Radiation-induced epigenetic alterations after low and high LET irradiations. Mutation Research 707:24–33.
   PubMed Web of Science ®Google Scholar
• Bartel DP. 2009. MicroRNAs: Target recognition and regulatory functions. Cell 136:215–233.
   PubMed Web of Science ®Google Scholar
• Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society B 57:289–300.
   Web of Science ®Google Scholar
• Cha HJ, Seong KM, Bae S, Jung JH, Kim CS, Yang KH, Jin YW, An S. 2009a. Identification of specific microRNAs responding to low and high dose gamma-irradiation in the human lymphoblast line IM9. Oncology Reports 22:863–868.
   PubMed Web of Science ®Google Scholar
• Cha HJ, Shin S, Yoo H, Lee EM, Bae S, Yang KH, Lee SJ, Park IC, Jin YW, An S. 2009b. Identification of ionizing radiation-responsive microRNAs in the IM9 human B lymphoblastic cell line. International Journal of Oncology 34:1661–1668.
   PubMed Web of Science ®Google Scholar
• Chaudhry MA. 2009. Real-time PCR analysis of micro-RNA expression in ionizing radiation-treated cells. Cancer Biotherapy & Radiopharmaceuticals 24:49–56.
   Google Scholar
• Croce CM. 2009. Causes and consequences of microRNA dysregulation in cancer. Nature Reviews Genetics 10:704–714.
   PubMed Web of Science ®Google Scholar
• Dickey JS, Zemp FJ, Martin OA, Kovalchuk O. 2011. The role of miRNA in the direct and indirect effects of ionizing radiation. Nature Reviews Genetics 50:491–499.
   Google Scholar
• Ding LH, Shingyoji M, Chen F, Chatterjee A, Kasai KE, Chen DJ. 2005. Gene expression changes in normal human skin fibroblasts induced by HZE-particle radiation. Radiation Research 164: 523–526.
   PubMed Web of Science ®Google Scholar
• Ferracin M, Veronese A, Negrini M. 2010. Micromarkers: miRNAs in cancer diagnosis and prognosis. Expert Review of Molecular Diagnostics 10:297–308.
   PubMed Web of Science ®Google Scholar
• Friedman RC, Farh KK, Burge CB, Bartel DP. 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Research 19:92–105.
   PubMed Web of Science ®Google Scholar
• Grimson A, Farh KK, Johnston WK, Garrett-Engele P, Lim LP, Bartel DP. 2007. MicroRNA targeting specificity in mammals: Determinants beyond seed pairing. Molecular Cell 27:91–105.
   PubMed Web of Science ®Google Scholar
• Hebert SS, De Strooper B. 2009. Alterations of the microRNA network cause neurodegenerative disease. Trends in Neuroscience 32:199–206.
   PubMed Web of Science ®Google Scholar
• Ishii H, Saito T. 2006. Radiation-induced response of micro RNA expression in murine embryonic stem cells. Medicinal Chemistry 2:555–563.
   PubMedGoogle Scholar
• Josson S, Sung SY, Lao K, Chung LW, Johnstone PA. 2008. Radiation modulation of microRNA in prostate cancer cell lines. Prostate 68:1599–1606.
   PubMedGoogle Scholar
• Kerr TA, Davidson NO. 2010. Therapeutic RNA manipulation in liver disease. Hepatology 51:1055–1061.
   PubMed Web of Science ®Google Scholar
• Kraemer A, Anastasov N, Angermeier M, Winkler K, Atkinson MJ, Moertl S. 2011. MicroRNA-mediated processes are essential for the cellular radiation response. Radiation Research 176:575–586.
   PubMed Web of Science ®Google Scholar
• Latronico MV, Condorelli G. 2009. MicroRNAs and cardiac pathology. Nature Reviews Cardiology 6:419–429.
   PubMed Web of Science ®Google Scholar
• Lee ML. 2004. Power and sample size considerations. Analysis of microarray gene expression data. Norwell, MA, USA: Kluwer Academic Publishers. pp 193–234.
   Google Scholar
• Lee ML, Whitmore GA. 2002. Power and sample size for DNA microarray studies. Statistics in Medicine 21:3543–3570.
   PubMed Web of Science ®Google Scholar
• Lewis BP, Burge CB, Bartel DP. 2005. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20.
   PubMed Web of Science ®Google Scholar
• Maes OC, An J, Sarojini H, Wu H, Wang E. 2008. Changes in MicroRNA expression patterns in human fibroblasts after low-LET radiation. Journal of Cell Biochemistry 105:824–834.
   PubMed Web of Science ®Google Scholar
• Marsit CJ, Eddy K, Kelsey KT. 2006. MicroRNA responses to cellular stress. Cancer Research 66:10843–10848.
   PubMed Web of Science ®Google Scholar
• Matsumoto Y, Iwakawa M, Furusawa Y, Ishikawa K, Aoki M, Imadome K, Matsumoto I, Tsujii H, Ando K, Imai T. 2008. Gene expression analysis in human malignant melanoma cell lines exposed to carbon beams. International Journal of Radiation Biology 84:299–314.
   PubMed Web of Science ®Google Scholar
• Meadows SK, Dressman HK, Muramoto GG, Himburg H, Salter A, Wei Z, Ginsburg GS, Chao NJ, Nevins JR, Chute JP. 2008. Gene expression signatures of radiation response are specific, durable and accurate in mice and humans. PLoS One 3:e1912.
   PubMed Web of Science ®Google Scholar
• Meadows SK, Dressman HK, Daher P, Himburg H, Russell JL, Doan P, Chao NJ, Lucas J, Nevins JR, Chute JP. 2010. Diagnosis of partial body radiation exposure in mice using peripheral blood gene expression profiles. PLoS One 5:e11535.
   PubMed Web of Science ®Google Scholar
• Nana-Sinkam SP, Hunter MG, Nuovo GJ, Schmittgen TD, Gelinas R, Galas D, Marsh CB. 2009. Integrating the MicroRNome into the study of lung disease. American Journal of Respiratory and Critical Care Medicine 179:4–10.
   PubMed Web of Science ®Google Scholar
• Niemoeller OM, Niyazi M, Corradini S, Zehentmayr F, Li M, Lauber K, Belka C. 2011. MicroRNA expression profiles in human cancer cells after ionizing radiation. Radiation Oncology 6:29.
   PubMed Web of Science ®Google Scholar
• Nikiforova MN, Gandi M, Kelly L, Nikiforov YE. 2011. MicroRNA dysregulation in human thyroid cells following exposure to ionizing radiation. Thyroid 21:261–266.
   PubMed Web of Science ®Google Scholar
• Paul S, Amundson SA. 2008. Development of gene expression signatures for practical radiation biodosimetry. International Journal of Radiation, Oncology Biology Physics 71:1236–1244.
   PubMed Web of Science ®Google Scholar
• Peng Y, Brown N, Finnon R, Warner CL, Liu X, Genik PC, Callan MA, Ray FA, Borak TB, Badie C, . 2009. Radiation leukemogenesis in mice: Loss of PU.1 on chromosome 2 in CBA and C57BL/6 mice after irradiation with 1 GeV/nucleon 56Fe ions, X rays or gamma rays. Part I. Experimental observations. Radiation Research 171:474–483.
   PubMed Web of Science ®Google Scholar
• Pradervand S, Weber J, Lemoine F, Consales F, Paillusson A, Dupasquier M, Thomas J, Richter H, Kaessmann H, Beaudoing E, . 2010. Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs. Biotechniques 48:219–222.
   Google Scholar
• Shin S, Cha HJ, Lee EM, Lee SJ, Seo SK, Jin HO, Park IC, Jin YW, An S. 2009. Alteration of miRNA profiles by ionizing radiation in A549 human non-small cell lung cancer cells. International Journal of Oncology 35:81–86.
   PubMed Web of Science ®Google Scholar
• Shkumatava A, Stark A, Sive H, Bartel DP. 2009. Coherent but overlapping expression of microRNAs and their targets during vertebrate development. Genes Development 23:466–481.
   PubMed Web of Science ®Google Scholar
• Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y. 2007. Analysis of gene expression data using BRB-array tools. Cancer Information 3:11–17.
   PubMedGoogle Scholar
• Simone NL, Soule BP, Ly D, Saleh AD, Savage JE, Degraff W, Cook J, Harris CC, Gius D, Mitchell JB. 2009. Ionizing radiation-induced oxidative stress alters miRNA expression. PLoS One 4:e6377.
   PubMed Web of Science ®Google Scholar
• Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS. 2010. Non-coding RNAs: Regulators of disease. Journal of Pathology 220:126–139.
   PubMed Web of Science ®Google Scholar
• Templin T, Amundson SA, Brenner DJ, Smilenov LB. 2011a. Whole mouse blood microRNA as biomarkers for exposure to -rays and (56)Fe ion. International Journal of Radiation Biology 87:653–662.
   PubMed Web of Science ®Google Scholar
• Templin T, Paul S, Amundson SA, Young EF, Barker CA, Wolden SL, Smilenov LB. 2011b. Radiation-induced micro-RNA expression changes in peripheral blood cells of radiotherapy patients. International Journal of Radiation Oncology, Biology, Physics 80: 549–557.
   PubMed Web of Science ®Google Scholar
• Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. 2003. PANTHER: A library of protein families and subfamilies indexed by function. Genome Research 13:2129–2141.
   PubMed Web of Science ®Google Scholar
• Qiu W, Ting Lee M-L, Whitmore GA. 2012. Sample Size and Power Calculation in Microarray Studies Using the sizepower package http://www.bioconductor.org/packages/devel/bioc/html/sizepower.html
   Google Scholar
• Wright GW, Simon RM. 2003. A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics 19:2448–2455.
   PubMed Web of Science ®Google Scholar
• Yauk CL, Rowan-Carroll A, Stead JD, Williams A. 2010. Cross-platform analysis of global microRNA expression technologies. BMC Genomics 11:330.
   PubMed Web of Science ®Google Scholar
• Zhang R, Burns FJ, Chen H, Chen S, Wu F. 2006. Alterations in gene expression in rat skin exposed to 56Fe ions and dietary vitamin A acetate. Radiation Research 165:570–581.
   PubMed Web of Science ®Google Scholar