Identifying radiation exposure biomarkers from mouse blood transcriptome

International Journal of Bioinformatics Research and Applications

Volumn 9, Issue 4, 2013, Pages 365-385

  Hyduke, Daniel R ^a,b,c   Laiakis, Evagelia C ^a   Li, Heng Hong ^a,b   Fornace, Albert J ^a,b,d  

^a GEORGETOWN UNIVERSITY   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

Author keywords

Inter laboratory omics variation; Ionising radiation exposure; Murine blood transcriptome; Radiation response biomarkers; Random forests; Reporter metabolites

Indexed keywords

EID: 84879617476     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2013.054701     Document Type: Article

References (60)

1. Amundson, S.A., Grace, M.B., McLeland, C.B., Epperly, M.W., Yeager, A., Zhan, Q., Greenberger, J.S. and Fornace Jr., A.J. (2004) 'Human in vivo radiation-induced biomarkers: gene expression changes in radiotherapy patients', Cancer Res., Vol. 64, pp.6368-6371.
2. Amundson, S.A., Do, K.T., Vinikoor, L., Koch-Paiz, C.A., Bittner, M.L., Trent, J.M., Meltzer, P. and Fornace Jr., A.J. (2005) 'Stress-specific signatures: expression profiling of p53 wild-type and -null human cells', Oncogene, Vol. 24, pp.4572-4579.
3. Amundson, S.A., Do, K.T., Vinikoor, L.C., Lee, R.A., Koch-Paiz, C.A., Ahn, J., Reimers, M., Chen, Y., Scudiero, D.A., Weinstein, J.N., Trent, J.M., Bittner, M.L., Meltzer, P.S. and Fornace Jr., A.J. (2008) 'Integrating global gene expression and radiation survival parameters across the 60 cell lines of the national cancer institute anticancer drug screen', Cancer Res., Vol. 68, pp.415-424.
4. Amundson, S.A., Bittner, M. and Fornace Jr., A.J. (2003) 'Functional genomics as a window on radiation stress signaling', Oncogene, Vol. 22, pp.5828-5833.
5. Ballman, K.V., Grill, D.E., Oberg, A.L. and Therneau, T.M. (2004) 'Faster cyclic loess: normalizing RNA arrays via linear models'. Bioinformatics, Vol. 20, pp.2778-2786.
6. Benjamini, Y. and Hochberg, Y. (1995) 'Controlling the false discovery rate: a practical and powerful approach to multiple testing', Journal of the Royal Statistical Society. Series B (Methodological), Vol. 57, pp.289-300.
7. Brieman, L. (2001) 'Random forests', Machine Learning, Vol. 45, pp.5-32.
8. Brown, L., Boswell, S., Raj, L. and Lee, S.W. (2007) 'Transcriptional targets of p53 that regulate cellular proliferation', Crit. Rev. Eukaryot. Gene. Expr., Vol. 17, pp.73-85.
9. Burns, T.F. and El-Deiry, W.S. (2003) 'Microarray analysis of p53 target gene expression patterns in the spleen and thymus in response to ionizing radiation', Cancer Biol. Ther., Vol. 2, pp.431-443.
10. Cakir, T., Patil, K.R., Onsan, Z., Ulgen, K.O., Kirdar, B. and Nielsen, J. (2006) 'Integration of metabolome data with metabolic networks reveals reporter reactions', Mol. Syst. Biol., Vol. 2, p.50.
11. Chipuk, J.E., Kuwana, T., Bouchier-Hayes, L., Droin, N.M., Newmeyer, D.D., Schuler, M. and Green, D.R. (2004) 'Direct activation of Bax by p53 mediates mitochondrial membrane permeabilization and apoptosis', Science, Vol. 303, pp.1010-1014.
12. Cook, J.A., Chuang, E.Y., Tsai, M.H., Coffin, D., Degraff, W., Sowers, A.L. and Mitchell, J.B. (2006) 'Radiation-induced changes in gene-expression profiles for the SCC VII tumor cells grown in vitro and in vivo', Antioxid Redox Signal., Vol. 8, pp.1263-1272.
13. Dale, W.M., Davies, J.V. and Gilbert, C.W. (1949) 'The kinetics and specificities of deamination of nitrogenous compounds by X-radiation', Biochem. J., Vol. 45, pp.93-99.
14. Dettling, M. and Buhlmann, P. (2003) 'Boosting for tumor classification with gene expression data', Bioinformatics, Vol. 19, pp.1061-1069.
15. DiCarlo, A.L., Ramakrishnan, N. and Hatchett, R.J. (2010) 'Radiation combined injury: overview of NIAID research', Health Phys., Vol. 98, pp.863-867.
16. Dinnis, D.M., Stansfield, S.H., Schlatter, S., Smales, C.M., Alete, D., Birch, J.R., Racher, A.J., Marshall, C.T., Nielsen, L.K. and James, D.C. (2006) 'Functional proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate', Biotechnol. Bioeng., Vol. 94, pp.830-841.
17. Dressman, H.K., Muramoto, G.G., Chao, N.J., Meadows, S., Marshall, D., Ginsburg, G.S., Nevins, J.R. and Chute, J.P. (2007) 'Gene expression signatures that predict radiation exposure in mice and humans', PLoS Med., Vol. 4, p.e106.
18. Duarte, N.C., Becker, S.A., Jamshidi, N., Thiele, I., Mo, M.L., Vo, T.D., Srivas, R. and Palsson, B.O. (2007) 'Global reconstruction of the human metabolic network based on genomic and bibliomic data', Proc. Natl. Acad. Sci. USA, Vol. 104, pp.1777-1782.
19. Eby, K.G., Rosenbluth, J.M., Mays, D.J., Marshall, C.B., Barton, C.E., Sinha, S., Johnson, K.N., Tang, L. and Pietenpol, J.A. (2010) 'ISG20L1 is a p53 family target gene that modulates genotoxic stress-induced autophagy', Mol. Cancer, Vol. 9, p.95.
20. Evans, S.E., Tuvim, M.J., Zhang, J., Larson, D.T., Garcia, C.D., Pro, S.M., Coombes, K.R. and Dickey, B.F. (2010) 'Host lung gene expression patterns predict infectious etiology in a mouse model of pneumonia', Respir. Res., Vol. 11, p.101.
21. Ghandhi, S.A., Yaghoubian, B. and Amundson, S.A. (2008) 'Global gene expression analyses of bystander and alpha particle irradiated normal human lung fibroblasts: synchronous and differential responses', BMC Med. Genomics., Vol. 1, p.63.
22. Green, E.L. (1966) Biology of the Laboratory Mouse, Blakiston Division, McGraw-Hill, New York.
23. Hall, E.J. and Giaccia, A.J. (2006) Radiobiology for the Radiologist, Lippincott Williams and Wilkins, Philadelphia.
24. Hall, J. and Angele, S. (1999) 'Radiation, DNA damage and cancer', Mol. Med. Today, Vol. 5, pp.157-164.
25. Hei, T.K., Zhou, H., Ivanov, V.N., Hong, M., Lieberman, H.B., Brenner, D.J., Amundson, S.A. and Geard, C.R. (2008) 'Mechanism of radiation-induced bystander effects: a unifying model', J. Pharm. Pharmacol., Vol. 60, pp.943-950.
26. Heitner, S.B., Hollenberg, S.M. and Colilla, S.A. (2010) 'Heat maps, random forests, and nearest neighbors: a peek into the new molecular diagnostic world', Crit. Care Med., Vol. 38, pp.296-298.
27. Hyduke, D.R., Amundson, S.A. and Fornace Jr., A.J. (2009) 'Complexity of stress signaling and responses', Handbook of Cell Signaling, Vol. 3, pp.2107-2125.
28. Kandasamy, S.B. and Hunt, W.A. (1990) 'Involvement of prostaglandins and histamine in radiation-induced temperature responses in rats', Radiat. Res., Vol. 121, pp.84-90.
29. Kandasamy, S.B., Hunt, W.A. and Mickley, G.A. (1988) 'Implication of prostaglandins and histamine H1 and H2 receptors in radiation-induced temperature responses of rats', Radiat. Res., Vol. 114, pp.42-53.
30. Kim, S., Dougherty, E.R., Barrera, J., Chen, Y., Bittner, M.L. and Trent, J.M. (2002) 'Strong feature sets from small samples', J. Comput. Biol., Vol. 9, pp.127-146.
31. Koenig, K.L., Goans, R.E., Hatchett, R.J., Mettler, F.A.J., Schumacher, T.A., Noji, E.K. and Jarrett, D.G. (2005) 'Medical treatment of radiological casualties: current concepts', Ann. Emerg. Med., Vol. 45, pp.643-652.
32. Laiakis, E.C. and Morgan, W.F. (2005) 'Communicating the non-targeted effects of radiation from irradiated to non-irradiated cells', Acta. Medica. Nagasakiensia, Vol. 50, pp.79-84.
33. Lanz, C., Patterson, A.D., Slavik, J., Krausz, K.W., Ledermann, M., Gonzalez, F.J. and Idle, J.R. (2009) 'Radiation metabolomics. 3. Biomarker discovery in the urine of gamma-irradiated rats using a simplified metabolomics protocol of gas chromatography-mass spectrometry combined with random forests machine learning algorithm', Radiat. Res., Vol. 172, pp.198-212.
34. Lewis, N.E., Cho, B.K., Knight, E.M. and Palsson, B.O. (2009) 'Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content', J. Bacteriol., Vol. 191, pp.3437-3444.
35. Liaw, A. and Wiener, M. (2002) 'Classification and regression by random forest', R. News, Vol. 2, pp.18-22.
36. Liu, X. and Erikson, R.L. (2003) 'Polo-like kinase 1 in the life and death of cancer cells', Cell Cycle, Vol. 2, pp.424-425.
37. Loft, S. and Poulsen, H.E. (1996) 'Cancer risk and oxidative DNA damage in man', J. Mol. Med., Vol. 74, pp.297-312.
38. Lohr, K., Moritz, C., Contente, A. and Dobbelstein, M. (2003) 'p21/CDKN1A mediates negative regulation of transcription by p53', J. Biol. Chem., Vol. 278, pp.32507-32516.
39. Lorimore, S.A. and Wright, E.G. (2003) 'Radiation-induced genomic instability and bystander effects: related inflammatory-type responses to radiation-induced stress and injury? A review', Int. J. Radiat. Biol., Vol. 79, pp.15-25.
40. Mizuno, T., Zhong, X. and Rothstein, T.L. (2003) 'Fas-induced apoptosis in B cells', Apoptosis, Vol. 8, pp.451-460.
41. Mothersill, C., Moriarty, M.J. and Seymour, C.B. (2005) 'Bystander and other delayed effects and multi-organ involvement and failure following high dose exposure to ionising radiation', BJR Suppl., Vol. 27, pp.128-131.
42. Oliveira, A.P., Patil, K.R. and Nielsen, J. (2008) 'Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks', BMC Syst. Biol., Vol. 2, p.17.
43. Patil, K.R. and Nielsen, J. (2005) 'Uncovering transcriptional regulation of metabolism by using metabolic network topology', Proc. Natl. Acad. Sci. USA, Vol. 102, pp.2685-2689.
44. Paul, S. and Amundson, S.A. (2008) 'Development of gene expression signatures for practical radiation biodosimetry', Int. J. Radiat. Oncol. Biol. Phys., Vol. 71, pp.1236-1244.
45. Ramaswamy, S., Tamayo, P., Rifkin, R., Mukherjee, S., Yeang, C.H., Angelo, M., Ladd, C., Reich, M., Latulippe, E., Mesirov, J.P., Poggio, T., Gerald, W., Loda, M., Lander, E.S. and Golub, T.R. (2001) 'Multiclass cancer diagnosis using tumor gene expression signatures', Proc. Natl. Acad. Sci. USA, Vol. 98, pp.15149-15154.
46. Reimers, M. and Carey, V.J. (2006) 'Bioconductor: an open source framework for bioinformatics and computational biology', Methods Enzymol., Vol. 411, pp.119-134.
47. Ressom, H.W., Varghese, R.S., Zhang, Z., Xuan, J. and Clarke, R. (2008) 'Classification algorithms for phenotype prediction in genomics and proteomics', Front Biosci., Vol. 13, pp.691-708.
48. Riley, P.A. (1994) 'Free radicals in biology: oxidative stress and the effects of ionizing radiation', Int. J. Radiat. Biol., Vol. 65, pp.27-33.
49. Schellenberger, J., Park, J.O., Conrad, T.M. and Palsson, B.O. (2010) 'BiGG: a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions', BMC Bioinformatics, Vol. 11, p.213.
50. Shi, L., Reid, L.H., Jones, W.D., Shippy, R., Warrington, J.A., Baker, S.C., Collins, P.J., de Longueville, F., Kawasaki, E.S., Lee, K.Y., Luo, Y., Sun, Y.A., Willey, J.C., Setterquist, R.A., Fischer, G.M., Tong, W., Dragan, Y.P., Dix, D.J., Frueh, F.W., Goodsaid, F.M., Herman, D., Jensen, R.V., Johnson, C.D., Lobenhofer, E.K., Puri, R.K., Schrf, U., Thierry-Mieg, J., Wang, C., Wilson, M., Wolber, P.K., Zhang, L., Amur, S., Bao, W., Barbacioru, C.C., Lucas, A.B., Bertholet, V., Boysen, C., Bromley, B., Brown, D., Brunner, A., Canales, R., Cao, X.M., Cebula, T.A., Chen, J.J., Cheng, J., Chu, T.M., Chudin, E., Corson, J., Corton, J.C., Croner, L.J., Davies, C., Davison, T.S., Delenstarr, G., Deng, X., Dorris, D., Eklund, A.C., Fan, X.H., Fang, H., Fulmer-Smentek, S., Fuscoe, J.C., Gallagher, K., Ge, W., Guo, L., Guo, X., Hager, J., Haje, P.K., Han, J., Han, T., Harbottle, H.C., Harris, S.C., Hatchwell, E., Hauser, C.A., Hester, S., Hong, H., Hurban, P., Jackson, S.A., Ji, H., Knight, C.R., Kuo, W.P., LeClerc, J.E., Levy, S., Li, Q.Z., Liu, C., Liu, Y., Lombardi, M.J., Ma, Y., Magnuson, S.R., Maqsodi, B., McDaniel, T., Mei, N., Myklebost, O., Ning, B., Novoradovskaya, N., Orr, M.S., Osborn, T.W., Papallo, A., Patterson, T.A., Perkins, R.G., Peters, E.H., Peterson, R., Philips, K.L., Pine, P.S., Pusztai, L., Qian, F., Ren, H., Rosen, M., Rosenzweig, B.A., Samaha, R.R., Schena, M., Schroth, G.P., Shchegrova, S., Smith, D.D., Staedtler, F., Su, Z., Sun, H., Szallasi, Z., Tezak, Z., Thierry-Mieg, D., Thompson, K.L., Tikhonova, I., Turpaz, Y., Vallanat, B., Van, C., Walker, S.J., Wang, S.J., Wang, Y., Wolfinger, R., Wong, A., Wu, J., Xiao, C., Xie, Q., Xu, J., Yang, W., Zhang, L., Zhong, S., Zong, Y. and Slikker, W.J. (2006) 'The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements', Nat. Biotechnol., Vol. 24, pp.1151-1161.
51. Song, M. and Rajasekaran, S. (2010) 'A greedy algorithm for gene selection based on SVM and correlation', Int. J. Bioinform Res. Appl., Vol. 6, pp.296-307.
52. Strobl, C., Boulesteix, A.L., Kneib, T., Augustin, T. and Zeileis, A. (2008) 'Conditional variable importance for random forests', BMC Bioinformatics, Vol. 9, p.307.
53. Team, R.D.C. (2010) R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna.
54. Tibshirani, R., Hastie, T., Narasimhan, B. and Chu, G. (2002) 'Diagnosis of multiple cancer types by shrunken centroids of gene expression', Proc. Natl. Acad. Sci. USA, Vol. 99, pp.6567-6572.
55. Tomasini, R., Seux, M., Nowak, J., Bontemps, C., Carrier, A., Dagorn, J.C., Pebusque, M.J., Iovanna, J.L. and Dusetti, N.J. (2005) 'TP53INP1 is a novel p73 target gene that induces cell cycle arrest and cell death by modulating p73 transcriptional activity', Oncogene, Vol. 24, pp.8093-8104.
56. Tyburski, J.B., Patterson, A.D., Krausz, K.W., Slavik, J., Fornace Jr., A.J., Gonzalez, F.J. and Idle, J.R. (2008) 'Radiation metabolomics. 1. Identification of minimally invasive urine biomarkers for gamma-radiation exposure in mice', Radiat. Res., Vol. 170, pp.1-14.
57. Tyburski, J.B., Patterson, A.D., Krausz, K.W., Slavik, J., Fornace Jr., A.J., Gonzalez, F.J. and Idle, J.R. (2009) 'Radiation metabolomics. 2. Dose-and time-dependent urinary excretion of deaminated purines and pyrimidines after sublethal gamma-radiation exposure in mice', Radiat. Res., Vol. 172, pp.42-57.
58. Wheeler, D.L., Church, D.M., Federhen, S., Lash, A.E., Madden, T.L., Pontius, J.U., Schuler, G.D., Schriml, L.M., Sequeira, E., Tatusova, T.A. and Wagner, L. (2003) 'Database resources of the national center for biotechnology', Nucleic Acids Res., Vol. 31, pp.28-33.
59. Whitlock, M.C. (2005) 'Combining probability from independent tests: the weighted Z-method is superior to Fisher's approach', J. Evol. Biol., Vol. 18, pp.1368-1373.
60. Yoo, J., Ghiassi, M., Jirmanova, L., Balliet, A.G., Hoffman, B., Fornace Jr., A.J., Liebermann, D.A., Bottinger, E.P. and Roberts, A.B. (2003) 'Transforming growth factor-beta-induced apoptosis is mediated by Smad-dependent expression of GADD45b through p38 activation', J. Biol. Chem., Vol. 278, pp.43001-43007.