Molecular markers and mechanisms of stroke: RNA studies of blood in animals and humans

Journal of Cerebral Blood Flow and Metabolism

Volumn 31, Issue 7, 2011, Pages 1513-1531

  Sharp, Frank R ^a   Jickling, Glen C ^a   Stamova, Boryana ^a   Tian, Yingfang ^a   Zhan, Xinhua ^a   Liu, Dazhi ^a   Kuczynski, Beth ^a   Cox, Christopher D ^a   Ander, Bradley P ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

brain; gene expression profiling; ischemia; microarrays

Indexed keywords

RNA;

BLOOD CLOTTING; BRAIN ATHEROSCLEROSIS; BRAIN HEMORRHAGE; BRAIN ISCHEMIA; EPILEPTIC STATE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION; HUMAN; HUMAN GENOME; HYPOGLYCEMIA; HYPOXIA; INFECTION; INFLAMMATION; MICROARRAY ANALYSIS; MONOCYTE; NERVE CELL NECROSIS; NEUTROPHIL; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; RNA SEQUENCE; RNA SPLICING; SEIZURE; SENSITIVITY AND SPECIFICITY; THROMBOCYTE; TRANSIENT ISCHEMIC ATTACK; WHITE MATTER;

EID: 85027927887     PISSN: 0271678X     EISSN: 15597016     Source Type: Journal    
DOI: 10.1038/jcbfm.2011.45     Document Type: Review

References (115)

1. Akopov S, Sercombe R, Seylaz J (1996) Cerebrovascular reactivity: role of endothelium/platelet/leukocyte interactions. Cerebrovasc Brain Metab Rev 8:11-94
2. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson Jr J, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403:503-11 (Pubitemid 30082188)
3. Allan SM, Rothwell NJ (2003) Inflammation in central nervous system injury. Philos Trans R Soc Lond B Biol Sci 358:1669-77 (Pubitemid 37298635)
4. Amarenco P, Bogousslavsky J, Caplan LR, Donnan GA, Hennerici MG (2009) Classification of stroke subtypes. Cerebrovasc Dis 27:493-501
5. Babarro EG, Rego AR, Gonzalez-Juanatey JR (2009) Cardioembolic stroke: call for a multidisciplinary approach. Cerebrovasc Dis 27(Suppl 1):82-7
6. Baird AE (2006) Blood genomic profiling: novel diagnostic and therapeutic strategies for stroke? Biochem Soc Trans 34:1313-7 (Pubitemid 46769046)
7. Baird AE (2007) Blood genomics in human stroke. Stroke 38:694-8 (Pubitemid 46184244)
8. Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P, Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, Malek RL, Milton S, Nagalla SR, O'malley JP, Palmer VS, Pattee P, Paules RS, Perou CM, Phillips K, Qin LX, Qiu Y, Quigley SD, Rodland M, Rusyn I, Samson LD, Schwartz DA, Shi Y, Shin JL, Sieber SO, Slifer S, Speer MC, Spencer PS, Sproles DI, Swenberg JA, Suk WA, Sullivan RC, Tian R, Tennant RW, Todd SA, Tucker CJ, Van Houten B, Weis BK, Xuan S, Zarbl H (2005) Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2:351-6 (Pubitemid 41130980)
9. Barr TL, Conley Y, Ding J, Dillman A, Warach S, Singleton A, Matarin M (2010) Genomic biomarkers and cellular pathways of ischemic stroke by RNA gene expression profiling. Neurology 75:1009-14
10. Beck J, Stummer W, Lehmberg J, Baethmann A, Uhl E (1997) Leukocyte-endothelium interactions in global cerebral ischemia. Acta Neurochir Suppl 70:53-5 (Pubitemid 127502049)
11. Becker KJ (2010) Modulation of the postischemic immune response to improve stroke outcome. Stroke 41:S75-8
12. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I (2001) Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125:279-84 (Pubitemid 33000466)
13. Caplan LR, Fisher M (2007) The endothelium, platelets, and brain ischemia. Rev Neurol Dis 4:113-21 (Pubitemid 47536159)
14. Carmichael ST (2003) Gene expression changes after focal stroke, traumatic brain and spinal cord injuries. Curr Opin Neurol 16:699-704 (Pubitemid 38429244)
15. Chai V, Vassilakos A, Lee Y, Wright JA, Young AH (2005) Optimization of the PAXgene blood RNA extraction system for gene expression analysis of clinical samples. J Clin Lab Anal 19:182-8 (Pubitemid 41407589)
16. Chalela JA (2009) Evaluating the carotid plaque: going beyond stenosis. Cerebrovasc Dis 27(Suppl 1):19-24
17. Chamorro A, Hallenbeck J (2006) The harms and benefits of inflammatory and immune responses in vascular disease. Stroke 37:291-3 (Pubitemid 43731945)
18. Chavez JC, Hurko O, Barone FC, Feuerstein GZ (2009) Pharmacologic interventions for stroke: looking beyond the thrombolysis time window into the penumbra with biomarkers, not a stopwatch. Stroke 40:e558-63
19. Clark WM, Coull BM, Briley DP, Mainolfi E, Rothlein R (1993) Circulating intercellular adhesion molecule-1 levels and neutrophil adhesion in stroke. J Neuroimmu-nol 44:123-5 (Pubitemid 23137077)
20. Courtney E, Kornfeld S, Janitz K, Janitz M (2010) Transcriptome profiling in neurodegenerative disease. J Neurosci Methods 193:189-202
21. Dassan P, Keir G, Brown MM (2009) Criteria for a clinically informative serum biomarker in acute ischaemic stroke: a review of S100B. Cerebrovasc Dis 27:295-302
22. del Zoppo GJ (2010) Acute anti-inflammatory approaches to ischemic stroke. Ann N YAcad Sci 1207:143-8
23. Dharap A, Bowen K, Place R, Li LC, Vemuganti R (2009) Transient focal ischemia induces extensive temporal changes in rat cerebral microRNAome. J Cereb Blood Flow Metab 29:675-87
24. Downes CE, Crack PJ (2010) Neural injury following stroke: are Toll-like receptors the link between the immune system and the CNS? Br J Pharmacol 160:1872-88
25. Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA (2003) Global functional profiling of gene expression. Genomics 81:98-104 (Pubitemid 36298600)
26. Du X, Tang Y, Xu H, Lit L, Walker W, Ashwood P, Gregg JP, Sharp FR (2006) Genomic profiles for human peripheral blood T cells, B cells, natural killer cells, monocytes, and polymorphonuclear cells: comparisons to ischemic stroke, migraine, and Tourette syndrome. Genomics 87:693-703 (Pubitemid 43776871)
27. El Husseini N, Laskowitz DT (2010) Clinical application of blood biomarkers in cerebrovascular disease. Expert Rev Neurother 10:189-203
28. Elkind MS (2009) Inflammatory markers and stroke. Curr Cardiol Rep 11:12-20
29. Elkind MS (2010) Inflammatory mechanisms of stroke. Stroke 41:S3-8
30. Elneihoum AM, Falke P, Axelsson L, Lundberg E, Lind-garde F, Ohlsson K (1996) Leukocyte activation detected by increased plasma levels of inflammatory mediators in patients with ischemic cerebrovascular diseases. Stroke 27:1734-8 (Pubitemid 26332495)
31. Enlimomab Acute Stroke Trial Investigators (2001) Use of anti-ICAM-1 therapy in ischemic stroke: results of the Enlimomab Acute Stroke Trial. Neurology 57:1428-34
32. Faber BC, Heeneman S, Daemen MJ, Cleutjens KB (2002) Genes potentially involved in plaque rupture. Curr Opin Lipidol 13:545-52 (Pubitemid 35231935)
33. Foerch C, Montaner J, Furie KL, Ning MM, Lo EH (2009) Invited article: searching for oracles? Blood biomarkers in acute stroke. Neurology 73:393-9
34. Franks ZG, Campbell RA, Weyrich AS, Rondina MT (2010) Platelet-leukocyte interactions link inflammatory and thromboembolic events in ischemic stroke. Ann N Y Acad Sci 1207:11-7
35. Freedman JE, Vitseva O, Tanriverdi K (2010) The role of the blood transcriptome in innate inflammation and stroke. Ann N YAcad Sci 1207:41-5
36. Furuya K, Takeda H, Azhar S, McCarron RM, Chen Y, Ruetzler CA, Wolcott KM, DeGraba TJ, Rothlein R, Hugli TE, del Zoppo GJ, Hallenbeck JM (2001) Examination of several potential mechanisms for the negative outcome in a clinical stroke trial of enlimomab, a murine anti-human intercellular adhesion molecule-1 antibody: a bedside-to-bench study. Stroke 32:2665-74 (Pubitemid 33055322)
37. Gagarin D, Yang Z, Butler J, Wimmer M, Du B, Cahan P, McCaffrey TA (2005) Genomic profiling of acquired resistance to apoptosis in cells derived from human atherosclerotic lesions: potential role of STATs, cyclinD1, BAD, and Bcl-XL. J Mol Cell Cardiol 39: 453-65 (Pubitemid 41133731)
38. Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C (2010) Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 16:991-1006
39. Grond-Ginsbach C, Hummel M, Wiest T, Horstmann S, Pfleger K, Hergenhahn M, Hollstein M, Mansmann U, Grau AJ, Wagner S (2008) Gene expression in human peripheral blood mononuclear cells upon acute is-chemic stroke. J Neurol 255:723-31
40. Grond-Ginsbach C, Horstmann S, Hummel M, Wiest T, Honold C, Pfleger K, Hergenhahn M, Hollstein M, Weninger A, Knyazev Y, Mansmann U, Wagner S, Grau AJ (2009) Increased expression of cell-cell signaling genes by stimulated mononuclear leukocytes in patients with previous atherothrombotic stroke. Awhole genome expression profile study. Eur Neurol 62:30-9
41. Guo Y, Hastie T, Tibshirani R (2007) Regularized linear discriminant analysis and its application in microar-rays. Biostatistics 8:86-100 (Pubitemid 44906104)
42. Hallenbeck J (2010) How inflammation modulates central nervous system vessel activation and provides targets for intervention-a personal perspective. Ann N Y Acad Sci 1207:1-7
43. Hansson GK (2009) Inflammatory mechanisms in atherosclerosis. J Thromb Haemost 7(Suppl 1):328-31
44. Hawkins RD, Hon GC, Ren B (2010) Next-generation geno-mics: an integrative approach. Nat Rev Genet 11:476-86
45. Hedegaard J, Arce C, Bicciato S, Bonnet A, Buitenhuis B, Collado-Romero M, Conley LN, Sancristobal M, Ferrari F, Garrido JJ, Groenen MA, Hornshoj H, Hulsegge I, Jiang L, Jimenez-Marin A, Kommadath A, Lagarrigue S, Leunissen JA, Liaubet L, Neerincx PB, Nie H, Van der Poel J, Prickett D, Ramirez-Boo M, Rebel JM, Robert-Granie C, Skarman A, Smits MA, Sorensen P, Tosser-Klopp G, Watson M (2009) Methods for interpreting lists of affected genes obtained in a DNA microarray experiment. BMC Proc 3(Suppl 4):S5
46. Holmes D, Pettigrew D, Reccius CH, Gwyer JD, Van Berkel C, Holloway J, Davies DE, Morgan H (2009) Leukocyte analysis and differentiation using high speed microfluidic single cell impedance cytometry. Lab Chip 9:2881-9
47. Hsueh HM, Chen JJ, Kodell RL (2003) Comparison of methods for estimating the number of true null hypotheses in multiplicity testing. J Biopharm Stat 13:675-89 (Pubitemid 37259710)
48. Htun P, Fateh-Moghadam S, Tomandl B, Handschu R, Klinger K, Stellos K, Garlichs C, Daniel W, Gawaz M (2006) Course of platelet activation and platelet-leukocyte interaction in cerebrovascular ischemia. Stroke 37:2283-7 (Pubitemid 44337170)
49. Jensen MB, Chacon MR, Sattin JA, Levine RL, Vemuganti R (2009) Potential biomarkers for the diagnosis of stroke. Expert Rev Cardiovasc Ther 7:389-93
50. Jeyaseelan K, Lim KY, Armugam A (2008) MicroRNA expression in the blood and brain of rats subjected to transient focal ischemia by middle cerebral artery occlusion. Stroke 39:959-66 (Pubitemid 351619577)
51. Jickling G, Salam A, Mohammad A, Hussain MS, Scozzafava J, Nasser AM, Jeerakathil T, Shuaib A, Camicioli R (2009) Circulating endothelial progenitor cells and age-related white matter changes. Stroke 40:3191-6
52. Jickling GC, Xu H, Stamova B, Ander BP, Zhan X, Tian Y, Liu D, Turner RJ, Mesias M, Verro P, Khoury J, Jauch EC, Pancioli A, Broderick JP, Sharp FR (2010) Signatures of cardioembolic and large-vessel ischemic stroke. Ann Neurol 68:681-92
53. Kassner SS, Kollmar R, Bonaterra GA, Hildebrandt W, Schwab S, Kinscherf R (2009) The early immunological response to acute ischemic stroke: differential gene expression in subpopulations of mononuclear cells. Neuroscience 160:394-401
54. King MD, Laird MD, Ramesh SS, Youssef P, Shakir B, Vender JR, Alleyne CH, Dhandapani KM (2010) Elucidating novel mechanisms of brain injury following subarachnoid hemorrhage: an emerging role for neuroproteomics. Neurosurg Focus 28:E10
55. Kobayashi SD, Sturdevant DE, DeLeo FR (2007) Genome-scale transcript analyses in human neutrophils. Methods Mol Biol 412:441-53
56. Kotz KT, Xiao W, Miller-Graziano C, Qian WJ, Russom A, Warner EA, Moldawer LL, De A, Bankey PE, Petritis BO, Camp II DG, Rosenbach AE, Goverman J, Fagan SP, Brownstein BH, Irimia D, Xu W, Wilhelmy J, Mindrinos MN, Smith RD, Davis RW, Tompkins RG, Toner M (2010) Clinical microfluidics for neutrophil genomics and proteomics. Nat Med 16:1042-7
57. Lee D, Chen PJ, Lee GB (2010) The evolution of real-time PCR machines to real-time PCR chips. Biosens Bioelec-tron 25:1820-4
58. Li S, Overman JJ, Katsman D, Kozlov SV, Donnelly CJ, Twiss JL, Giger RJ, Coppola G, Geschwind DH, Carmi-chael ST (2010) An age-related sprouting transcriptome provides molecular control of axonal sprouting after stroke. Nat Neurosci 13:1496-504
59. Liu DZ, Tian Y, Ander BP, Xu H, Stamova BS, Zhan X, Turner RJ, Jickling G, Sharp FR (2010) Brain and blood microRNA expression profiling of ischemic stroke, intracerebral hemorrhage, and kainate seizures. J Cereb Blood Flow Metab 30:92-101
60. Marsh BJ, Stevens SL, Hunter B, Stenzel-Poore MP (2009) Inflammation and the emerging role of the toll like receptor system in acute brain ischemia. Stroke 40:S34-7
61. Maurer MH, Haux D, Sakowitz OW, Unterberg AW, Kuschinsky W (2007) Identification of early markers for symptomatic vasospasm in human cerebral micro-dialysate after subarachnoid hemorrhage: preliminary results of a proteome-wide screening. J Cereb Blood Flow Metab 27:1675-83 (Pubitemid 47476094)
62. Maurer MH, Haux D, Unterberg AW, Sakowitz OW (2008) Proteomics of human cerebral microdialysate: from detection of biomarkers to clinical application. Proteo-mics Clin Appl 2:437-43 (Pubitemid 351425371)
63. Mieczkowski J, Tyburczy ME, Dabrowski M, Pokarowski P (2010) Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measure ments. BMC Bioinformatics 11:104
64. Millenaar FF, Okyere J, May ST, Van Zanten M, Voesenek LA, Peeters AJ (2006) How to decide? Different methods of calculating gene expression from short oligonucleo-tide array data will give different results. BMC Bioinfor-matics 7:137
65. Montaner J (2009) Blood biomarkers to guide stroke thrombolysis. Front Biosci (Elite Ed) 1:200-8
66. Moore DF, Li H, Jeffries N, Wright V, Cooper Jr RA, Elkahloun A, Gelderman MP, Zudaire E, Blevins G, Yu H, Goldin E, Baird AE (2005) Using peripheral blood mononuclear cells to determine a gene expression profile of acute ischemic stroke: a pilot investigation. Circulation 111:212-21 (Pubitemid 40139734)
67. Nah HW, Kang DW, Kwon SU, Kim JS (2010) Diversity of single small subcortical infarctions according to infarct location and parent artery disease: analysis of indicators for small vessel disease and atherosclerosis. Stroke 41:2822-7
68. Pries AR, Kuebler WM (2006) Normal endothelium. Handb Exp Pharmacol 176:1-40
69. Reid G, Kirschner MB, Van Zandwijk N (2010) Circulating microRNAs: association with disease and potential use as biomarkers. Crit Rev Oncol Hematol 7:7
70. Reiner A, Yekutieli D, Benjamini Y (2003) Identifying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics 19:368-75 (Pubitemid 36284936)
71. Ridder DA, Bulashevska S, Chaitanya GV, Babu PP, Brors B, Eils R, Schneider A, Schwaninger M (2009) Discovery of transcriptional programs in cerebral ischemia by in silico promoter analysis. Brain Res 1272:3-13
72. Robbins SH, Walzer T, Dembele D, Thibault C, Defays A, Bessou G, Xu H, Vivier E, Sellars M, Pierre P, Sharp FR, Chan S, Kastner P, Dalod M (2008) Novel insights into the relationships between dendritic cell subsets in human and mouse revealed by genome-wide expression profiling. Genome Biol 9:R17
73. Rothwell NJ, Luheshi GN (2000) Interleukin 1 in the brain: biology, pathology and therapeutic target [in process citation]. Trends Neurosci 23:618-25 (Pubitemid 32007888)
74. Saenger AK, Christenson RH (2010) Stroke biomarkers: progress and challenges for diagnosis, prognosis, differentiation, and treatment. Clin Chem 56:21-33
75. Sharp FR, Xu H, Lit L, Walker W, Apperson M, Gilbert DL, Glauser TA, Wong B, Hershey A, Liu DZ, Pinter J, Zhan X, Liu X, Ran R (2006) The future of genomic profiling of neurological diseases using blood. Arch Neurol 63:1529-36 (Pubitemid 44748794)
76. Shedden K, Chen W, Kuick R, Ghosh D, Macdonald J, Cho KR, Giordano TJ, Gruber SB, Fearon ER, Taylor JM, Hanash S (2005) Comparison of seven methods for producing Affymetrix expression scores based on false discovery rates in disease profiling data. BMC Bioinfor-matics 6:26
77. Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy Jr JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukher-jee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, Von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD (2010) The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol 28:827-38
78. Shim JS, Browne AW, Ahn CH (2010) An on-chip whole blood/plasma separator with bead-packed microchannel on COC polymer. Biomed Microdevices 12:949-957
79. Stamova B, Xu H, Jickling G, Bushnell C, Tian Y, Ander BP, Zhan X, Liu D, Turner R, Adamczyk P, Khoury JC, Pancioli A, Jauch E, Broderick JP, Sharp FR (2010) Gene expression profiling of blood for the prediction of ischemic stroke. Stroke 41:2171-7
80. Stamova BS, Apperson M, Walker WL, Tian Y, Xu H, Adamczy P, Zhan X, Liu DZ, Ander BP, Liao IH, Gregg JP, Turner RJ, Jickling G, Lit L, Sharp FR (2009) Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood. BMC Med Genomics 2:49
81. Stevenson SF, Doubal FN, Shuler K, Wardlaw JM (2010) A systematic review of dynamic cerebral and peripheral endothelial function in lacunar stroke versus controls. Stroke 41:e434-42
82. Tan KS, Armugam A, Sepramaniam S, Lim KY, Setyowati KD, Wang CW, Jeyaseelan K (2009) Expression profile of MicroRNAs in young stroke patients. PLoS One 4:e7689
83. Tan YD, Fornage M, Fu YX (2006) Ranking analysis of microarray data: a powerful method for identifying differentially expressed genes. Genomics 88:846-54 (Pubitemid 44739206)
84. Tang Y, Gilbert DL, Glauser TA, Hershey AD, Sharp FR (2005) Blood gene expression profiling of neurologic diseases: a pilot microarray study. Arch Neurol 62:210-5 (Pubitemid 40204742)
85. Tang Y, Hershey AD, Powers SW, Gilbert DL, Glauser TA, Sharp FR (2004a) Genomic abnormalities in patients with migraine and chronic migraine: blood gene expression evidence of platelet abnomalities. Headache 44:994-1004 (Pubitemid 39532341)
86. Tang Y, Lu A, Aronow BJ, Sharp FR (2001) Blood genomic responses differ after stroke, seizures, hypoglycemia, and hypoxia: blood genomic fingerprints of disease. Ann Neurol 50:699-707 (Pubitemid 33116129)
87. Tang Y, Lu A, Aronow BJ, Wagner KR, Sharp FR (2002) Genomic responses of the brain to ischemic stroke, intracerebral haemorrhage, kainate seizures, hypoglyce-mia, and hypoxia. Eur J Neurosci 15:1937-52 (Pubitemid 35471884)
88. Tang Y, Lu A, Ran R, Aronow BJ, Schorry EK, Hopkin RJ, Gilbert DL, Glauser TA, Hershey AD, Richtand NW, Privitera M, Dalvi A, Sahay A, Szaflarski JP, Ficker DM, Ratner N, Sharp FR (2004b) Human blood genomics: distinct profiles for gender, age and neurofibromatosis type 1. Brain Res Mol Brain Res 132:155-67 (Pubitemid 39586758)
89. Tang Y, Nee AC, Lu A, Ran R, Sharp FR (2003) Blood genomic expression profile for neuronal injury. J Cereb Blood Flow Metab 23:310-9 (Pubitemid 36307575)
90. Tang Y, Schapiro MB, Franz DN, Patterson BJ, Hickey FJ, Schorry EK, Hopkin RJ, Wylie M, Narayan T, Glauser TA, Gilbert DL, Hershey AD, Sharp FR (2004c) Blood expression profiles for tuberous sclerosis complex 2, neurofibromatosis type 1, and Down's syndrome. Ann Neurol 56:808-14 (Pubitemid 39578444)
91. Tang Y, Xu H, Du X, Lit L, Walker W, Lu A, Ran R, Gregg JP, Reilly M, Pancioli A, Khoury JC, Sauerbeck LR, Carrozzella JA, Spilker J, Clark J, Wagner KR, Jauch EC, Chang DJ, Verro P, Broderick JP, Sharp FR (2006) Gene expression in blood changes rapidly in neutrophils and monocytes after ischemic stroke in humans: a microarray study. J Cereb Blood Flow Metab 26:1089-102 (Pubitemid 44134079)
92. Taub MA, Corrada Bravo H, Irizarry RA (2010) Overcoming bias and systematic errors in next generation sequencing data. Genome Med 2:87
93. Thach DC, Lin B, Walter E, Kruzelock R, Rowley RK, Tibbetts C, Stenger DA (2003) Assessment of two methods for handling blood in collection tubes with RNA stabilizing agent for surveillance of gene expression profiles with high density microarrays. J Immunol Methods 283:269-79 (Pubitemid 37505016)
94. Tian Y, Apperson ML, Ander BP, Liu D, Stomova BS, Jickling GC, Enriquez R, Agius MA, Sharp FR (2010) Differences in exon expression and alternatively spliced genes in blood of multiple sclerosis compared to healthy control subjects. J Neuroimmunol 2:2
95. Tian Y, Liao IH, Zhan X, Gunther JR, Ander BP, Liu D, Lit L, Jickling GC, Corbett BA, Bos-Veneman NG, Hoekstra PJ, Sharp FR (2011) Exon expression and alternatively spliced genes in Tourette syndrome. Am J Med Genet B Neuropsychiatr Genet 156:72-8
96. Tibshirani R, Hastie T, Narasimhan B, Chu G (2002) Diagnosis of multiple cancer types by shrunken cen-troids of gene expression. Proc Natl Acad Sci USA 99:6567-72 (Pubitemid 34526173)
97. Turner R, Jickling GC, Sharp FR (2011a) Are underlying assumptions of current animal models of human stroke correct: from STAIRs to high hurdles? Trans Stroke Res; advance online publication, 12 February 2011.
98. Turner RJ, Bushnell CD, Register TJ, Sharp FR (2011b) Gender dependent correlations of carotid intima media thickness with gene expression in blood. Trans Stroke Res (in press)
99. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98:5116-21 (Pubitemid 32397092)
100. Vartanian K, Slottke R, Johnstone T, Casale A, Planck SR, Choi D, Smith JR, Rosenbaum JT, Harrington CA (2009) Gene expression profiling of whole blood: comparison of target preparation methods for accurate and reproducible microarray analysis. BMC Genomics 10:2
101. Vemuganti R, Dempsey RJ (2005) Carotid atherosclerotic plaques from symptomatic stroke patients share the molecular fingerprints to develop in a neoplastic fashion: a microarray analysis study. Neuroscience 131:359-74 (Pubitemid 40222445)
102. Walker WL, Liao IH, Gilbert DL, Wong B, Pollard KS, McCulloch CE, Lit L, Sharp FR (2008) Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients. BMC Genomics 9:494
103. Werner T (2010) Next generation sequencing in functional genomics. Brief Bioinform 2010:25
104. Whiteley W, Chong WL, Sengupta A, Sandercock P (2009a) Blood markers for the prognosis of ischemic stroke: a systematic review. Stroke 40:e380-9
105. Whiteley W, Jackson C, Lewis S, Lowe G, Rumley A, Sandercock P, Wardlaw J, Dennis M, Sudlow C (2009b) Inflammatory markers and poor outcome after stroke: a prospective cohort study and systematic review of interleukin-6. PLoS Med 6:e1000145
106. Wong HR, Freishtat RJ, Monaco M, Odoms K, Shanley TP (2010) Leukocyte subset-derived genomewide expres sion profiles in pediatric septic shock. Pediatr Crit Care Med 11:349-55
107. Wu TC, Grotta JC (2010) Stroke treatment and prevention: five new things. Neurology 75:S16-21
108. Xu H, Stamova B, Jickling G, Tian Y, Zhan X, Ander BP, Liu D, Turner R, Rosand J, Goldstein LB, Furie KL, Verro P, Johnston SC, Sharp FR, Decarli CS (2010) Distinctive RNA expression profiles in blood associated with white matter hyperintensities in brain. Stroke 41:2744-9
109. Xu H, Tang Y, Liu DZ, Ran R, Ander BP, Apperson M, Liu XS, Khoury JC, Gregg JP, Pancioli A, Jauch EC, Wagner KR, Verro P, Broderick JP, Sharp FR (2008) Gene expression in peripheral blood differs after cardioem-bolic compared with large-vessel atherosclerotic stroke: biomarkers for the etiology of ischemic stroke. J Cereb Blood Flow Metab 28:1320-8 (Pubitemid 351896646)
110. Yamamoto T, Sekiyama A, Sekiguchi H, Yoshida T, Miyagi Y (2006) Examination of stability of bone marrow blood RNA in the PAXgene tube. Lab Hematol 12:143-7 (Pubitemid 44377595)
111. Yao H, Nakahara T, Nakagawa N, Hashimoto K, Kuroki T (2009) Regional and temporal changes in proteomic profile after middle cerebral artery occlusion with or without reperfusion in rats. Neurochem Res 34:1999-2007
112. Zakharkin SO, Kim K, Mehta T, Chen L, Barnes S, Scheirer KE, Parrish RS, Allison DB, Page GP (2005) Sources of variation in Affymetrix microarray experiments. BMC Bioinformatics 6:214
113. Zhan X, Ander BP, Jickling G, Turner R, Stamova B, Xu H, Liu D, Davis RR, Sharp FR (2010) Brief focal cerebral ischemia that simulates transient ischemic attacks in humans regulates gene expression in rat peripheral blood. J Cereb Blood Flow Metab 30:110-8
114. Zhan X, Kim C, Sharp FR (2008) Very brief focal ischemia simulating transient ischemic attacks (TIAs) can injure brain and induce Hsp70 protein. Brain Res 1234:183-97
115. Zhang X, Guo T, Wang H, He W, Mei H, Hong M, Yu J, Hu Y, Song S (2008) Potential biomarkers of acute cerebral infarction detected by SELDI-TOF-MS. Am J Clin Pathol 130:299-304