Comparative gene expression analysis in mouse models for multiple sclerosis, Alzheimer's disease and stroke for identifying commonly regulated and disease-specific gene changes

Genomics

Volumn 96, Issue 2, 2010, Pages 82-91

  Tseveleki, Vivian ^a   Rubio, Renee ^b   Vamvakas, Sotiris Spyros ^a   White, Joseph ^b   Taoufik, Era ^a   Petit, Edwige ^c   Quackenbush, John ^b   Probert, Lesley ^a  

^a HELLENIC PASTEUR INSTITUTE   (Greece)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c UNIVERSITÉ DE CAEN   (France)

Author keywords

Alzheimer's disease; Brain inflammation; CDNA microarrays; Cerebral stroke; Gene expression profiling; Systems biology

Indexed keywords

COMPLEMENTARY DNA; ESTROGEN; TRANSCRIPTOME; TRANSFORMING GROWTH FACTOR BETA; TRANSIENT RECEPTOR POTENTIAL CHANNEL M7; TRANSIENT RECEPTOR POTENTIAL CHANNEL M; TRPM7 PROTEIN, MOUSE;

ALZHEIMER DISEASE; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DEGENERATIVE DISEASE; DNA HYBRIDIZATION; DNA MICROARRAY; FEMALE; GENE CONTROL; GENE EXPRESSION PROFILING; MALE; MOLECULAR MECHANICS; MOUSE; MULTIPLE SCLEROSIS; NEUROPROTECTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SIGNAL TRANSDUCTION; STROKE; WILD TYPE; ANIMAL; BRAIN; CEREBROVASCULAR ACCIDENT; COMPARATIVE STUDY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; PROCEDURES; SYSTEMS BIOLOGY; TRANSGENIC MOUSE;

ALZHEIMER DISEASE; ANIMALS; BRAIN; GENE EXPRESSION REGULATION; MICE; MICE, TRANSGENIC; MULTIPLE SCLEROSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION; STROKE; SYSTEMS BIOLOGY; TRPM CATION CHANNELS;

EID: 77955323238     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2010.04.004     Document Type: Article

References (50)

1. Bertram L., Tanzi R.E. Thirty years of Alzheimer's disease genetics: the implications of systematic meta-analyses. Nat. Rev. Neurosci. 2008, 9:768-778.
2. Soba P., Eggert S., Wagner K., Zentgraf H., Siehl K., Kreger S., Lower A., Langer A., Merdes G., Paro R., Masters C.L., Muller U., Kins S., Beyreuther K. Homo- and heterodimerization of APP family members promotes intercellular adhesion. EMBO J. 2005, 24:3624-3634.
3. Young-Pearse T.L., Chen A.C., Chang R., Marquez C., Selkoe D.J. Secreted APP regulates the function of full-length APP in neurite outgrowth through interaction with integrin beta1. Neural Dev. 2008, 3:15.
4. Hsieh H., Boehm J., Sato C., Iwatsubo T., Tomita T., Sisodia S., Malinow R. AMPAR removal underlies Abeta-induced synaptic depression and dendritic spine loss. Neuron 2006, 52:831-843.
5. Sturchler-Pierrat C., Abramowski D., Duke M., Wiederhold K.H., Mistl C., Rothacher S., Ledermann B., Burki K., Frey P., Paganetti P.A., Waridel C., Calhoun M.E., Jucker M., Probst A., Staufenbiel M., Sommer B. Two amyloid precursor protein transgenic mouse models with Alzheimer disease-like pathology. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:13287-13292.
6. Van Dam D., D'Hooge R., Staufenbiel M., Van Ginneken C., Van Meir F., De Deyn P.P. Age-dependent cognitive decline in the APP23 model precedes amyloid deposition. Eur. J. Neurosci. 2003, 17:388-396.
7. Meyer E.P., Ulmann-Schuler A., Staufenbiel M., Krucker T. Altered morphology and 3D architecture of brain vasculature in a mouse model for Alzheimer's disease. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:3587-3592.
8. Dirnagl U., Iadecola C., Moskowitz M.A. Pathobiology of ischaemic stroke: an integrated view. Trends Neurosci. 1999, 22:391-397.
9. Aboul-Enein F., Lassmann H. Mitochondrial damage and histotoxic hypoxia: a pathway of tissue injury in inflammatory brain disease?. Acta Neuropathol. 2005, 109:49-55.
10. Peers C., Pearson H.A., Boyle J.P. Hypoxia and Alzheimer's disease. Essays Biochem. 2007, 43:153-164.
11. Welsh F.A., Sakamoto T., McKee A.E., Sims R.E. Effect of lactacidosis on pyridine nucleotide stability during ischemia in mouse brain. J. Neurochem. 1987, 49:846-851.
12. Dutta R., Trapp B.D. Pathogenesis of axonal and neuronal damage in multiple sclerosis. Neurology 2007, 68:S22-S31.
13. Akassoglou K., Bauer J., Kassiotis G., Pasparakis M., Lassmann H., Kollias G., Probert L. Oligodendrocyte apoptosis and primary demyelination induced by local TNF/p55TNF receptor signaling in the central nervous system of transgenic mice: models for multiple sclerosis with primary oligodendrogliopathy. Am. J. Pathol. 1998, 153:801-813.
14. Mastronardi F.G., Wood D.D., Mei J., Raijmakers R., Tseveleki V., Dosch H.M., Probert L., Casaccia-Bonnefil P., Moscarello M.A. Increased citrullination of histone H3 in multiple sclerosis brain and animal models of demyelination: a role for tumor necrosis factor-induced peptidylarginine deiminase 4 translocation. J. Neurosci. 2006, 26:11387-11396.
15. Akassoglou K., Adams R.A., Bauer J., Mercado P., Tseveleki V., Lassmann H., Probert L., Strickland S. Fibrin depletion decreases inflammation and delays the onset of demyelination in a tumor necrosis factor transgenic mouse model for multiple sclerosis. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:6698-6703.
16. Simon R.M., Dobbin K. Experimental design of DNA microarray experiments. Biotechniques 2003, (Suppl):16-21.
17. Dobbin K., Simon R. Comparison of microarray designs for class comparison and class discovery. Bioinformatics 2002, 18:1438-1445.
18. P. Hegde, R. Qi, K. Abernathy, C. Gay, S. Dharap, R. Gaspard, J.E. Hughes, E. Snesrud, N. Lee, J. Quackenbush. A concise guide to cDNA microarray analysis. Biotechniques 29 (2000) 548-4, 556.
19. Saeed A.I., Sharov V., White J., Li J., Liang W., Bhagabati N., Braisted J., Klapa M., Currier T., Thiagarajan M., Sturn A., Snuffin M., Rezantsev A., Popov D., Ryltsov A., Kostukovich E., Borisovsky I., Liu Z., Vinsavich A., Trush V., Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34:374-378.
20. Brazma A., Parkinson H., Sarkans U., Shojatalab M., Vilo J., Abeygunawardena N., Holloway E., Kapushesky M., Kemmeren P., Lara G.G., Oezcimen A., Rocca-Serra P., Sansone S.A. ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2003, 31:68-71.
21. Rozen S., Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol. 2000, 132:365-386.
22. Bordet R., Ouk T., Petrault O., Gele P., Gautier S., Laprais M., Deplanque D., Duriez P., Staels B., Fruchart J.C., Bastide M. PPAR: a new pharmacological target for neuroprotection in stroke and neurodegenerative diseases. Biochem. Soc. Trans. 2006, 34:1341-1346.
23. Cramer S., Chopp M., M Recovery recapitulates ontogeny. Trends Neurosci. 2000, 23:265-271.
24. Ponomarev E.D., Shriver L.P., Maresz K., Pedras-Vasconcelos J., Verthelyi D., Dittel B.N. GM-CSF production by autoreactive T cells is required for the activation of microglial cells and the onset of experimental autoimmune encephalomyelitis. J. Immunol. 2007, 178:39-48.
25. Brann D.W., Dhandapani K., Wakade C., Mahesh V.B., Khan M.M. Neurotrophic and neuroprotective actions of estrogen: basic mechanisms and clinical implications. Steroids 2007, 72:381-405.
26. Au E., Richter M.W., Vincent A.J., Tetzlaff W., Aebersold R., Sage E.H., Roskams A.J. SPARC from olfactory ensheathing cells stimulates Schwann cells to promote neurite outgrowth and enhances spinal cord repair. J. Neurosci. 2007, 27:7208-7221.
27. Alexander J.S., Minagar A., Harper M., Robinson-Jackson S., Jennings M., Smith S.J. Proteomic analysis of human cerebral endothelial cells activated by multiple sclerosis serum and IFNbeta-1b. J. Mol. Neurosci. 2007, 32:169-178.
28. Krapivinsky G., Mochida S., Krapivinsky L., Cibulsky S.M., Clapham D.E. The TRPM7 ion channel functions in cholinergic synaptic vesicles and affects transmitter release. Neuron 2006, 52:485-496.
29. Aarts M., Iihara K., Wei W.L., Xiong Z.G., Arundine M., Cerwinski W., MacDonald J.F., Tymianski M. A key role for TRPM7 channels in anoxic neuronal death. Cell 2003, 115:863-877.
30. Sun H.S., Jackson M.F., Martin L.J., Jansen K., Teves L., Cui H., Kiyonaka S., Mori Y., Jones M., Forder J.P., Golde T.E., Orser B.A., Macdonald J.F., Tymianski M. Suppression of hippocampal TRPM7 protein prevents delayed neuronal death in brain ischemia. Nat. Neurosci. 2009, 12:1300-1307.
31. Landman N., Jeong S.Y., Shin S.Y., Voronov S.V., Serban G., Kang M.S., Park M.K., Di Paolo G., Chung S., Kim T.W. Presenilin mutations linked to familial Alzheimer's disease cause an imbalance in phosphatidylinositol 4, 5-bisphosphate metabolism. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:19524-19529.
32. Tsai J., Sultana R., Lee Y., Pertea G., Karamycheva S., Antonescu V., Cho J., Parvizi B., Cheung F., Quackenbush J. RESOURCERER: a database for annotating and linking microarray resources within and across species. Genome Biol. 2001, 2. (SOFTWARE0002).
33. Blalock E.M., Geddes J.W., Chen K.C., Porter N.M., Markesbery W.R., Landfield P.W. Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumor suppressor responses. Proc. Natl. Acad. Sci. U. S. A. 2004, 101:2173-2178.
34. Mitsios N., Saka M., Krupinski J., Pennucci R., Sanfeliu C., Wang Q., Rubio F., Gaffney J., Kumar P., Kumar S., Sullivan M., Slevin M. A microarray study of gene and protein regulation in human and rat brain following middle cerebral artery occlusion. BMC Neurosci. 2007, 8:93.
35. Graumann U., Reynolds R., Steck A.J., Schaeren-Wiemers N. Molecular changes in normal appearing white matter in multiple sclerosis are characteristic of neuroprotective mechanisms against hypoxic insult. Brain Pathol. 2003, 13:554-573.
36. Comabella M., Martin R. Genomics in multiple sclerosis-current state and future directions. J. Neuroimmunol. 2007, 187:1-8.
37. Wekerle H. Breaking ignorance: the case of the brain. Curr. Top. Microbiol. Immunol. 2006, 305:25-50.
38. Alvarez-de-la-Rosa M., Silva I., Nilsen J., Perez M.M., Garcia-Segura L.M., Avila J., Naftolin F. Estradiol prevents neural tau hyperphosphorylation characteristic of Alzheimer's disease. Ann. N. Y. Acad. Sci. 2005, 1052:210-224.
39. Yue X., Lu M., Lancaster T., Cao P., Honda S., Staufenbiel M., Harada N., Zhong Z., Shen Y., Li R. Brain estrogen deficiency accelerates Abeta plaque formation in an Alzheimer's disease animal model. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:19198-19203.
40. Dhandapani K.M., Brann D.W. Transforming growth factor-beta: a neuroprotective factor in cerebral ischemia. Cell Biochem. Biophys. 2003, 39:13-22.
41. Tesseur I., Zou K., Esposito L., Bard F., Berber E., Can J.V., Lin A.H., Crews L., Tremblay P., Mathews P., Mucke L., Masliah E., Wyss-Coray T. Deficiency in neuronal TGF-beta signaling promotes neurodegeneration and Alzheimer's pathology. J. Clin. Invest. 2006, 116:3060-3069.
42. Zencak D., Lingbeek M., Kostic C., Tekaya M., Tanger E., Hornfeld D., Jaquet M., Munier F.L., Schorderet D.F., van Lohuizen M., Arsenijevic Y. Bmi1 loss produces an increase in astroglial cells and a decrease in neural stem cell population and proliferation. J. Neurosci. 2005, 25:5774-5783.
43. Soriano M.A., Tessier M., Certa U., Gill R. Parallel gene expression monitoring using oligonucleotide probe arrays of multiple transcripts with an animal model of focal ischemia. J. Cereb. Blood Flow Metab. 2000, 20:1045-1055.
44. Tang Y., Lu A., Aronow B.J., Wagner K.R., Sharp F.R. Genomic responses of the brain to ischemic stroke, intracerebral haemorrhage, kainate seizures, hypoglycemia, and hypoxia. Eur. J. Neurosci. 2002, 15:1937-1952.
45. Roth A., Gill R., Certa U. Temporal and spatial gene expression patterns after experimental stroke in a rat model and characterization of PC4, a potential regulator of transcription. Mol. Cell. Neurosci. 2003, 22:353-364.
46. Ford G., Xu Z., Gates A., Jiang J., Ford B.D. Expression Analysis Systematic Explorer (EASE) analysis reveals differential gene expression in permanent and transient focal stroke rat models. Brain Res. 2006, 1071:226-236.
47. Miller D.H., Leary S.M. Primary-progressive multiple sclerosis. Lancet Neurol. 2007, 6:903-912.
48. Lock C., Hermans G., Pedotti R., Brendolan A., Schadt E., Garren H., Langer-Gould A., Strober S., Cannella B., Allard J., Klonowski P., Austin A., Lad N., Kaminski N., Galli S.J., Oksenberg J.R., Raine C.S., Heller R., Steinman L. Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis. Nat. Med. 2002, 8:500-508.
49. De Jager P.L., Jia X., Wang J., de Bakker P.I., Ottoboni L., Aggarwal N.T., Piccio L., Raychaudhuri S., Tran D., Aubin C., Briskin R., Romano S., International MS Genetics Consortium, Baranzini S.E., McCauley J.L., Pericak-Vance M.A., Haines J.L., Gibson R.A., Naeglin Y., Uitdehaag B., Matthews P.M., Kappos L., Polman C., McArdle W.L., Strachan D.P., Evans D., Cross A.H., Daly M.J., Compston A., Sawcer S.J., Weiner H.L., Hauser S.L., Hafler D.A., Oksenberg J.R. Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci. Nat. Genet 2009, 41:776-782.
50. Lundmark F., Duvefelt K., Iacobaeus E., Kockum I., Wallström E., Khademi M., Oturai A., Ryder L.P., Saarela J., Harbo H.F., Celius E.G., Salter H., Olsson T., Hillert J. Variation in interleukin 7 receptor alpha chain (IL7R) influences risk of multiple sclerosis. Nat Genet. 2007, 39:1108-1113.