AJMB  Vol.1 No.2 , July 2011
Effects of genetic and environmental factors and gene-environment interaction on expression variations of genes related to stroke in rat brain
Abstract: To determine if genetic and environmental (dietary) factors and gene-environment interaction impact on the expression variation of genes related to stroke, we conducted microarray experiments using two homozygous rat strains SHRSR and SHRSP fed with high and low dietary salt levels. We obtained expression data of 8,779 genes and performed the ranking analysis of microarray data. The results show that the genetic difference for stroke in rat brain has a strong effect on expression variations of genes. At false discovery rate (FDR) ≤ 5%, 534 genes were found to be differentially expressed between the genotypes resistant and prone to stroke, among which 304 genes were up-regulated in the resistant genotype and down-regulated in the prone genotype and 230 were down-regulated in the former and up-regulated in the latter. In addition, 365 were functional genes for transcription and translation, receptors (in particular, neurotransmitter receptor), channels of ions, transportation, metabolism and enzymes, and functional and structural proteins. Some of these genes are pivotal genes that cause stroke. However, dietary salt levels and GE interaction do not strongly impact on the expression variations of these genes detected on arrays.
Cite this paper: nullTan, Y. and Fornage, M. (2011) Effects of genetic and environmental factors and gene-environment interaction on expression variations of genes related to stroke in rat brain. American Journal of Molecular Biology, 1, 87-113. doi: 10.4236/ajmb.2011.12011.

[1]   [1] Mitsios, N., Gaffney, J., Kumar, P., Krupinski, J., Kumar, S. and Slevin, M. (2006) Pathophysiology of acute ischaemic stroke: An analysis of common signalling mechanisms and identification of new molecular targets. Path-biology, 73, 159-175. doi:10.1159/000096017

[2]   Mitsios, N., Saka, M., Krupinski, J., Pennucci, R., Sanfeliu, C., Wang, Q., Rubio, F., Gaffney, J., Kumar, P., Kumar, S., Sullivan, M. and Slevin, M. (2007) A microarray study of gene and protein regulation in human and rat brain following middle cerebral artery occlusion. BMC Neurosci, 8, 93. doi:10.1186/1471-2202-8-93

[3]   Slevin, M., Krupinski, J., Kumar, P., Gaffney, J. and Kumar, S. (2005) Gene activation and protein expression following ischaemic stroke: Strategies towards neuroprotection. Journal of Cellular and Molecular Medicine, 9, 85-102. doi:10.1111/j.1582-4934.2005.tb00339.x

[4]   Zhang, L., Ding, H., Yan, J., Hui, R., Wang, W., Kissling, G.E., Zeldin, D.C. and Wang, D.W. (2008) Genetic variation in cytochrome P450 2J2 and soluble epoxide hydrolase and risk of ischemic stroke in a Chinese population. Pharmacogenet Genomics, 18, 45-51. doi:10.1097/FPC.0b013e3282f313e8

[5]   Craig, H.D., Gunel, M., Cepeda, O., Johnson, E.W., Ptacek, L., Steinberg, G.K., Ogilvy, C.S., Berg, M.J., Crawford, S.C., Scott, R.M., Steichen-Gersdorf, E., Sabroe, R., Kennedy, C.T., Mettler, G., Beis, M.J., Fryer, A., Awad, I.A. and Lifton, R.P. (1998) Multilocus linkage identifies two new loci for a mendelian form of stroke, cerebral cavernous malformation, at 7p15-13 and 3q25.2-27. Human Molecular Genetics, 7, 1851-1858. doi:10.1093/hmg/7.12.1851

[6]   Joutel, A., Corpechot, C., Ducros, A., Vahedi, K., Chabriat, H., Mouton, P., Alamowitch, S., Domenga, V., Cecillion, M., Marechal, E., Maciazek, J., Vayssiere, C., Cruaud, C., Cabanis, E.A., Ruchoux, M.M., Weissenbach, J., Bach, J.F., Bousser, M.G., Tournier-Lasserve, E. (1997) Notch3 mutations in cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), a mendelian condition causing stroke and vascular dementia. Annals of the New York Academy of Sciences, 826, 21

[7]   Kobayashi, Y., Momoi, M.Y., Tominaga, K., Shimoizumi, H., Nihei, K., Yanagisawa, M., Kagawa, Y. and Ohta, S. (1991) Respiration-deficient cells are caused by a single point mutation in the mitochondrial tRNA-Leu (UUR) gene in mitochondrial myopathy, encephalopathy, lactic acidosis, and strokelike episodes (MELAS). The American Journal of Human Genetics, 49, 590-599.

[8]   Levy, E., Carman, M.D., Fernandez-Madrid, I.J., Power, M.D., Lieberburg, I., van Duinen, S.G., Bots, G.T., Luyendijk, W. and Frangione, B. (1990) Mutation of the Alzheimer's disease amyloid gene in hereditary cerebral hemorrhage, Dutch type. Science, 248, 1124-1126. doi:10.1126/science.2111584

[9]   Palsdottir, A., Abrahamson, M., Thorsteinsson, L., Arnason, A., Olafsson, I., Grubb, A. and Jensson, O. (1988) Mutation in cystatin C gene causes hereditary brain haemorrhage. Lancet, 2, 603-604. doi:10.1016/S0140-6736(88)90641-1

[10]   Ikeda, H., Sasaki, T., Yoshimoto, T., Fukui, M. and Arinami, T. (1999) Mapping of a familial moyamoya disease gene to chromosome 3p24.2-p26. American Journal of Human Genetics, 64, 533-537. doi:10.1086/302243

[11]   Ikeda, K., Nara, Y., Matumoto, C., Mashimo, T., Tamada, T., Sawamura, M., Nabika, T. and Yamori, Y. (1996) The region responsible for stroke on chromosome 4 in the strokeprone spontaneously hypertensive rat. Biochemical and Biophysical Research Communications, 229, 658-662. doi:10.1006/bbrc.1996.1860

[12]   Rubattu, S., Volpe, M., Kreutz, R., Ganten, U., Ganten, D.and Lindpaintner, K. (1996) Chromosomal mapping of quantitative trait loci contributing to stroke in a rat model of complex human disease. Nature Genetics, 13, 429-434. doi:10.1038/ng0 896-429

[13]   Fornage, M., Chiang, Y.A., O'Meara, E.S., Psaty, B.M., Reiner, A.P., Siscovick, D.S., Tracy, R.P. and Longstreth, W.T. Jr. (2008) Biomarkers of inflammation and MRI-Defined small vessel disease of the brain: The cardiovascular health. study. Stroke, 39, 1952-1959. doi:10.1161/STROKEAHA.107.508135

[14]   Jin, K., Mao, X.O., Eshoo, M.W., Nagayama, T., Minami, M., Simon, R.P. and Greenberg, D.A. (2001) Microarray analysis of hippocampal gene expression in global cerebral ischemia. Annals of Neurology, 50, 93-103. doi:10.1002/ana.1073

[15]   Kim, Y.D., Sohn, N.W., Kang, C. and Soh, Y. (2002) DNA array reveals altered gene expression in response to focal cerebral ischemia. Brain Research Bulletin, 58, 491-498.doi:10.1016/S0361-9230(02)00823-7

[16]   Raghavendra Rao, V.L., Bowen, K.K., Dhodda, V.K., Song, G., Franklin, J.L., Gavva, N.R. and Dempsey, R.J. (2002) Gene expression analysis of spontaneously hyper-tensive rat cerebral cortex following transient focal cerebral ischemia. Journal of Neurochemistry, 83, 1072-1086. doi:10.1046/j.1471-4159.2002.01208.x

[17]   Roth, A., Gill, R. and Certa, U. (2003) Temporal and spatial gene expression patterns after experimental stroke in a rat model and characterization of PC4, a potential regulator of transcription. Molecular and Cellular Neuro-science. 22, 353-364. doi:10.1016/S1044-7431(02)00039-8

[18]   Ford, G., Xu, Z., Gates, A., Jiang, J. and Ford, B.D. (2006) Expression Analysis Systematic Explorer (EASE) analysis reveals differential gene expression in permanent and transient focal stroke rat models. Brain Research, 1071, 226-236. doi:10.1016/j.brainres.2005.11.090

[19]   Lu, X.C., Williams, A.J., Yao, C., Berti, R., Hartings, J.A., Whipple, R., Vahey, M.T., Polavarapu, R.G., Woller, K.L., Tortella, F.C. and Dave, J.R. (2004) Micro-array analysis of acute and delayed gene expression profile in rats after focal ischemic brain injury and reperfusion. Journal of Neuroscience Research, 77, 843-857. doi:10.1002/jnr.20218

[20]   Schmidt-Kastner, R., Zhang, B., Belayev, L., Khoutorova, L., Amin, R., Busto, and R. Ginsberg, M.D. (2002) DNA microarray analysis of cortical gene expression during early recirculation after focal brain ischemia in rat. Molecular Brain Research, 108, 81-93. doi:10.1016/S0169-328X(02)00516-8

[21]   Soriano, M.A., Tessie,r M., Certa, U. and Gill, R. (2000) Parallel gene expression monitoring using oligo-nucleotide probe arrays of multiple transcripts with an animal model of focal ischemia. Journal of Cerebral Blood Flow & Metabolism, 20, 1045-1055. doi:10.1097/00004647-200007000-00004

[22]   Tang, Y., Lu, A., Aronow, B.J., Wagne, K.R. and Sharp, F.R. (2002) Genomic responses of the brain to ischemic stroke, intracerebral haemorrhage, kainate seizures, hypoglycemia, and hypoxia. European Journal of Neuro-science, 15, 1937-1952. doi:10.1046/j.1460-9568.2002.02030.x

[23]   Moore, D.F., Li, H., Jeffries, N., Wright, V., Cooper, RA, Jr., Elkahloun, A., Gelderman, M.P., Zudaire, E., Blevins, G., Yu, H., Goldin, E. and Baird, A.E. (2005) Using peripheral blood mononuclear cells to determine a gene expression profile of acute ischemic stroke: A pilot investigation. Circulation, 111, 212-221. doi:10.1161/01.CIR.0000152105.79665.C6

[24]   Tang, Y., Xu, H., Du, X., Lit, L., Walker, W., Lu., A, Ran, R., Gregg, J.P., Reilly, M., Pancioli, A., Khoury, J.C., Sauerbeck, L.R., Carrozzella, J.A., Spilker, J., Clark, J., Wagner, K.R., Jauch, E.C., Chang, D.J., Verro, P., Broderick, J.P. and Sharp, F.R. (2006) Gene expression in blood changes rapidly in neutrophils and monocytes after ischemic stroke in humans: a microarray study. Journal of Cerebral Blood Flow & Metabolism, 26, 1089-1102. doi:10.1038/sj.jcbfm.9600264

[25]   Yamori, Y., Horie, R., Tanase, H., Fujiwara, K., Nara, Y. and Lovenberg, W. (1984) Possible role of nutritional factors in the incidence of cerebral lesions in strokeprone spontaneously hypertensive rats. Hypertension, 6, 49-53.

[26]   Smeda, J.S. (1989) Hemorrhagic stroke development in spontaneously hypertensive rats fed a North American, Japanese-style diet. Stroke, 20, 1212-1218. doi:10.1161/01.STR.20.9.1212

[27]   Tobian, L., Lange, J., Ulm, K., Wold, L. and Iwai, J. (1985) Potassium reduces cerebral hemorrhage and death rate in hypertensive rats, even when blood pressure is not lowered. Hypertension, 7, I110-114.

[28]   Tobian, L., Lange, J.M., Ulm, K.M., Wold, L.J. and Iwai, J. (1984) Potassium prevents death from strokes in hypertensive rats without lowering blood pressure. Journal of Hypertension, 2 (Supplement), S363-366.

[29]   Kerr, M.K., Martin, M. and Churchill, G.A. (2000) Analysis of variance for gene expression microarray data. Journal of Computational Biology, 7, 819-837. doi:10.1089/10665270050514954

[30]   Black, M.A. and Doerge, R.W. (2002) Calculation of the minimum number of replicate spots required for detection of significant gene expression fold change in microarray experiments. Bioinformatics, 18, 1609-1616. doi:10.1093/bioinformatics/18.12.1609

[31]   Tan, Y.D., Fornage, M. and Fu, Y.X. (2006) Ranking analysis of microarray data: A powerful method for identifying differentially expressed genes. Genomics, 88, 846-854. doi:10.1016/j.ygeno.2006.08.003

[32]   Tusher, V.G., Tibshirani, R. and Chu, G. (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proceeding of the National Academy of Sciences of the United States of America, 98, 5116-5121. doi:10.1073/pnas.091062498

[33]   Tan, Y.D. (2011) Ranking analysis of correlation coefficients in gene expressions. Genomics, 97, 58-68. doi:10.1016/j.ygeno.2010.09.002

[34]   Fornage, M., Swank, M.W. and Borwinkle, E, P. A. D. (2003) Gene expression profiling and functional proteomic analysis reveal perturbed kinase-mediated signaling in genetic stroke susceptibility. Physiological Genomics, 15, 75-83.

[35]   Markgraf, C.G., Johnson, M.P., Braun, D.L. and Bickers, M.V. (1997) Behavioral recovery patterns in rats receiving the NMDA receptor antagonist MDL 100,453 immediately post-stroke. Pharmacology Biochemistry and Behavior, 56, 391-397. doi:10.1016/S0091-3057(96)00231-6

[36]   Bederson, J.B., Pitts, L.H., Germano, S.M., Nishimura, M.C., Davis, R.L. and Bartkowski, H.M. (1986) Evaluation of 2,3,5-triphenyltetrazolium chloride as a stain for detection and quantification of experimental cerebral infarction in rats. Stroke, 17, 1304-1308. doi:10.1161/01.STR.17.6.1304

[37]   Chomczynski, P. and Sacchi, N. (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical Biochemistry, 162, 156-159. doi:10.1016/0003-2697(87)90021-2

[38]   Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittman, M., Wang, C., KobayashiI, M., Horton, H., et al., (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnology, 14, 1675-1680. doi:10.1038/nbt1296-1675

[39]   Lee, M.L., Kuo, F.C., Whitmore, G.A. and Sklar, J. (2000) Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations. Proceeding of the National Academy of Sciences of the United States of America, 97, 9834-9839. doi:10.1073/pnas.97.18.9834

[40]   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), 57, 289-300.

[41]   Xu, J., Li, C., Yin, X.H. and Zhang, G.Y. (2008) Additive neuroprotection of GABA A and GABA B receptor agonists in cerebral ischemic injury via PI-3K/ Akt pathway inhibiting the ASK1-JNK cascade. Neuro-pharmacology, 54, 1029-1040. doi:10.1016/j.neuropharm.2008.01.014

[42]   Sheldon AL, M. B. R. (2007) The role of glutamate transporters in neurodegenerative diseases and potential opportunities for intervention. Neurochemistry International, 51, 333-355. doi:10.1016/j.neuint.2007.03.012

[43]   Yamashita, A., Mmkita, K. and Kuroiwa T, K. T. (2006) Glutamate transporters GLAST and EAAT4 regulate postischemic Purkinje cell death: An in vivo study using a cardiac arrest model in mice lacking GLAST or EAAT4. Neuroscience Research, 55, 264-270. doi:10.1016/j.neures.2006.03.007

[44]   Harvey, E.J., Li, N. and Ramji, D.P. (2007) Critical role for casein kinase 2 and Phosphoinositide-3-Kinase in the Interferon-[gamma]-Induced expression of monocyte chemoattractant Protein-1 and other key genes implicated in atherosclerosis. Arteriosclerosis, Thrombosis & Vascular Biology, 27, 806-812. doi:10.1161/01.ATV.0000258867.79411.96

[45]   Han, H.S., Karabiyikoglu, M., Kelly, S., Sobel, R.A. and Yenari, M.A. (2003) Mild hypothermia inhibits nuclear factor-kappaB translocation in experimental stroke. Journal of Cerebral Blood Flow & Metabolism, 23, 589-598. doi:10.1097/01.WCB.0000059566.39780.8D

[46]   Shen, J., Channavajhala, P., Seldin, D.C. and Sonenshein, G.E. (2001) Phosphorylation by the protein kinase CK2 promotes calpain-mediated degradation of IκBα. The Journal of Immunology, 167, 4919-4925.

[47]   Barroga, C.F., Stevenson, J.K., Schwarz, E.M. and Verma, I.M. (1995) Constitutive phosphorylation of I B by casein kinase II. Proceeding of the National Academy of Sciences of the United States of America, 92, 763-767. doi:10.1073/pnas.92.17.7637

[48]   Janosch, P., Schellerer, M., Seitz, T., Reim, P., Eulitz, M., Brielmeier, M., Kolch, W., Sedivy, J.M. and Mischak, H. (1996) Characterization of IkappaB kinases. IkappaB-alpha is not phosphorylated by Raf-1 or protein kinase C isozymes, but is a casein kinase II substrate. The Journal of Biological Chemistry, 271, 13868-13874. doi:10.1074/jbc.271.23.13868

[49]   McElhinny, J.A., Trushin, S.A., Bren, G.D., Chester, N. and Paya, C.V. (1996) Casein kinase II phosphorylates I kappa B alpha at S-283, S-289, S-293, and T-291 and is required for its degradation. Molecular and Cellular Biology, 16, 899-906.

[50]   Schwarz, E.M., Van Antwerp, D. and Verma, I.M. (1996) Constitutive phosphorylation of IkappaBalpha by casein kinase II occurs preferentially at serine 293: requirement for degradation of free IkappaBalpha. Molecular and Cellular Biology, 16, 3554-3559.

[51]   Shumway, S.D., Maki, M. and Miyamoto, S. (1999) The PEST domain of IkappaBalpha is necessary and sufficient for in vitro degradation by mucalpain. The Journal of Biological Chemistry, 274, 30874-30881. doi:10.1074/jbc.274.43.30874

[52]   Sukhova, G.K., Zhang, Y., Pan, J.H., Wada, Y., Yamamoto, T., Naito, M., Kodama, T., Tsimikas, S., Witztum, J.L., Lu, M.L., Sakara, Y., Chin, M.T., Libby, P. and Shi, G.P. (2003) Deficiency of cathepsin S reduces atherosclerosis in LDL receptor-deficient mice. Journal of Clinical Investigation, 111, 897-906.

[53]   Sukhova, G.K., Zhang, Y., Pan, J.H., Wada, Y., Yamamoto, T., Naito, M., Kodama, T., Tsimikas, S., Witztum, J.L., Lu, M.L., Sakara, Y., Chin, M.T., Libby, P. and Shi, G.P. (2003) Deficiency of cathepsin S reduces atherosclerosis in LDL receptor-deficient mice. Journal of Clinical Investigation, 111, 897-906.

[54]   Taleb, S., Lacasa, D., Bastard, J.P., Poitou, C., Cancello, R., Pelloux, V., Viguerie, N., Benis, A., Zucker, J.D., Bouillot, J.L., Coussieu, C., Basdevant, A., Langin, D. and Clement, K.. (2005) Cathepsin S, a novel biomarker of adiposity: Relevance to atherogenesis. The Federation of American Societies for Experimental Biology Journal, 19, 1540-1542.

[55]   Guo, R.W., Yang, L.X., Wang, H., Liu, B. and Wang, L. (2008) Angiotensin II induces matrix metalloproteinase-9 expression via a nuclear factor-kappaB-dependent pathway in vascular smooth muscle cells. Regulatory Peptides, 147, 37-44. doi:10.1016/j.regpep.2007.12.005

[56]   Bickel, C.A., Knepper, M.A., Verbalis, J.G. and Ecel- barger, C.A. (2002) Dysregulation of renal salt and water transport proteins in diabetic Zucker rats. Kidney International, 61, 2099-2110. doi:10.1046/j.1523-1755.2002.00353.x

[57]   Riazi, S., Madala-Halagappa, V.K. and Hu, X. (2006) Ecelbarger and body-type interactions in the regulation of renal sodium transporter levels, urinary excretion, and activity in lean and obese Zucker rats. Gender Medicine, 3, 309-327. doi:10.1016/S1550-8579(06)80219-6

[58]   Yang, L.E., Leong, P.K. and McDonough, A.A. (2007) Reducing blood pressure in SHR with enalapril provokes redistribution of NHE3, NaPi2, and NCC and decreases NaPi2 and ACE abundance. American journal of physiology Renal physiology, 293, F1197-1208. doi:10.1152/ajprenal.00040.2007

[59]   Letavernier, E., Perez, J., Bellocq, A., Mesnard, L., de Castro K.A., Haymann, J.P. and Baud, L. (2008) Targeting the calpain/ calpastatin system as a new strategy to prevent cardio-vascular remodeling in angiotensin II-induced hypertension. Circulation Research, 102, 720-728. doi:10.1161/CIRCRESAHA.107.160077

[60]   Rane, M.J., Gozal, D., Butt, W., Gozal, E., Pierce, W.M., Jr., Guo, S.Z., Wu, R. Goldbart, A.D. Thongboonkerd, V., McLeish, K.R. and Klein, J.B. (2005) Gamma-amino butyric acid type B receptors stimulate neutrophil chemotaxis during ischemia-reperfusion. The Journal of Immunology, 174, 7242-7249.

[61]   Arai, S., Kinouchi, H., Akabane, A., Owada, Y., Kamii, H., Kawase, M. and Yoshimoto, T. (1996) Induction of brain-derived neurotrophic factor (BDNF) and the receptor trk B mRNA following middle cerebral artery occlusion in rat. Neuroscience Letters, 211, 57-60. doi:10.1016/0304-3940(96)12720-8

[62]   Ferrer, I., Ballabriga, J., Marti, E., Perez, E., Alberch, J. and Arenas, E. (1998) BDNF up-regulates TrkB protein and prevents the death of CA1 neurons following transient forebrain ischemia. Brain Pathology, 8, 253-261.doi:10.1111/j.1750-3639.1998.tb00151.x

[63]   Tropea, D., Kreiman. G., Lyckman, A., Mukheriee, S., Yu, H., Horng, S. and Ur, M.S. (2006) Gene expression changes and molecular pathways mediating activity-dependent plasticity in visual cortex. Nature neuro-science, 9, 660- 668. doi:10.1038/nn1689

[64]   Tobian, L., Lang, J.M., Ulm, K.M., Wold, L.J. and Iwai, J. (1984) Potassium prevents death from strokes in hypertensive rats without lowering blood pressure. Journal of Hypertension, 2 (Supplement), S363-S366.