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Adamski MG, Li Y, Wagner E, Yu H, Seales-Bailey C, Soper SA, Murphy M, Baird AE. Next-generation qPCR for the high-throughput measurement of gene expression in multiple leukocyte subsets. ACTA ACUST UNITED AC 2013; 18:1008-17. [PMID: 23690294 DOI: 10.1177/1087057113489882] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Clinical studies of gene expression are increasingly using the whole blood, peripheral blood mononuclear cells, and leukocyte subsets involved in the innate and adaptive immune responses. However, the small amount of RNA available in the clinical setting is a limitation for commonly used methods such as quantitative polymerase chain reactions (qPCR) and microarrays. Our aim was to design 96 gene assays to simultaneously measure gene expression in the whole blood and seven leukocyte subsets using a new-generation qPCR method--high-throughput nanofluidic reverse transcription qPCR (HT RT-qPCR). The leukocyte subset purity was 94% to 98% for seven subsets and was less for the γδ T-cell receptor subset (80%). The HT RT-qPCR replicate sample measurements were highly reproducible (r = 0.997, p < 2.2 × 10(-16)), and the ΔΔCt values from HT RT-qPCR correlated significantly with those from qPCR. The control genes were differentially expressed across the eight leukocyte subsets in the control subjects (p = 1.3 × 10(-5), analysis of variance). Two analytical methods, absolute and relative, gave concordant results and were significantly correlated (p = 1.9 × 10(-9)). HT RT-qPCR permits the rapid, reproducible, and quantitative measurement of multiple transcripts using minimal sample amounts. The protocol described yielded leukocyte subsets of high purity and identified two analytic methods for use.
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Affiliation(s)
- Mateusz G Adamski
- 1Department of Neurology, SUNY Downstate Medical Center, Brooklyn, NY, USA
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152
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Bahou WF. Genetic dissection of platelet function in health and disease using systems biology. Hematol Oncol Clin North Am 2013; 27:443-63. [PMID: 23714307 DOI: 10.1016/j.hoc.2013.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Technological advances in protein and genetic analysis have altered the means by which platelet disorders can be characterized and studied in health and disease. When integrated into a single analytical framework, these collective technologies are referred to as systems biology, a unified approach that links platelet function with genomic/proteomic studies to provide insight into the role of platelets in broad human disorders such as cardiovascular and cerebrovascular disease. This article reviews the historical progression of these applied technologies to analyze platelet function, and demonstrates how these approaches can be systematically developed to provide new insights into platelet biomarker discovery.
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Affiliation(s)
- Wadie F Bahou
- Department of Medicine, Health Sciences Center, Stony Brook University, Stony Brook, NY 11794-8151, USA.
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153
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Fernandez-Cadenas I, del Rio-Espinola A, Domingues-Montanari S, Mendioroz M, Fernandez-Morales J, Penalba A, Rubiera M, Hernandez-Guillamon M, Rosell A, Delgado P, Chacon P, Ribo M, Alvarez-Sabin J, Molina CA, García-Arumi E, Montaner J. Genes involved in hemorrhagic transformations that follow recombinant t-PA treatment in stroke patients. Pharmacogenomics 2013; 14:495-504. [DOI: 10.2217/pgs.13.19] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Despite the benefits of recombinant t-PA (rt-PA) for stroke patients some of them suffer from adverse hemorrhagic transformations (HTs) following treatment. Our objective is to study the transcriptomics of HTs patients. Methods: We studied by microarrays 11 blood samples from patients with stroke that had received rt-PA of whom six of them had suffered a HT. For replication step RNA was collected from 14 new subjects (seven with HT, seven without) and then analyzed by real-time PCR. Four proteins were measured by ELISA in 72 new subjects to analyze their role as potential protein biomarkers. Results: The microarray analysis revealed that 14 genes were altered among the HT patients. The replication study confirmed these results for six genes. Two of them (BCL2 and OLFM4) are associated with apoptosis, whereas the other four (LTF, LCN2 [also known as NGAL], CEACAM8 and CRISP3) are involved in the regulation of neutrophil processes. Conclusion: Our data revealed that genes related to apoptosis and neutrophil regulation pathways could be associated with HTs after rt-PA. Original submitted 7 September 2012; Revision submitted 23 January 2013
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Affiliation(s)
- Israel Fernandez-Cadenas
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain and Fundació Docència i Recerca MútuaTerrassa, Sant Antoni street, 08221, Terrassa, Barcelona, Spain
| | - Alberto del Rio-Espinola
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Sophie Domingues-Montanari
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Maite Mendioroz
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Jessica Fernandez-Morales
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Anna Penalba
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Marta Rubiera
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Mar Hernandez-Guillamon
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Anna Rosell
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Pilar Delgado
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Pilar Chacon
- Lipids Unit, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Marc Ribo
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Jose Alvarez-Sabin
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Carlos A Molina
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
| | - Elena García-Arumi
- Departament de Patologia Mitocondrial i Neuromuscular, Hospital Universitari Vall d’Hebron, Institut de Recerca (VHIR), Universitat Autonoma de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades raras (CIBERER) ISCIII, Barcelona, Spain
| | - Joan Montaner
- Neurovascular Research Laboratory & Neurovascular Unit, Department of Neurology, Vall d’Hebron University Hospital, Departamento de Medicina, Universitat Autonoma de Barcelona, Vall d’Hebron Research Institute, 119–129, 08035 Barcelona, Spain
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154
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Brambilla R, Couch Y, Lambertsen KL. The effect of stroke on immune function. Mol Cell Neurosci 2013; 53:26-33. [DOI: 10.1016/j.mcn.2012.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 06/27/2012] [Accepted: 08/22/2012] [Indexed: 02/09/2023] Open
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155
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Pernow J, Jung C. Arginase as a potential target in the treatment of cardiovascular disease: reversal of arginine steal? Cardiovasc Res 2013; 98:334-43. [DOI: 10.1093/cvr/cvt036] [Citation(s) in RCA: 204] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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156
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Quirié A, Demougeot C, Bertrand N, Mossiat C, Garnier P, Marie C, Prigent-Tessier A. Effect of stroke on arginase expression and localization in the rat brain. Eur J Neurosci 2013; 37:1193-202. [PMID: 23311438 DOI: 10.1111/ejn.12111] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 10/30/2012] [Accepted: 11/28/2012] [Indexed: 11/27/2022]
Abstract
Because arginase and nitric oxide (NO) synthases (NOS) compete to degrade l-arginine, arginase plays a crucial role in the modulation of NO production. Moreover, the arginase 1 isoform is a marker of M2 phenotype macrophages that play a key role in tissue remodeling and resolution of inflammation. While NO has been extensively investigated in ischemic stroke, the effect of stroke on the arginase pathway is unknown. The present study focuses on arginase expression/activity and localization before and after (1, 8, 15 and 30 days) the photothrombotic ischemic stroke model. This model results in a cortical lesion that reaches maximal volume at day 1 post-stroke and then decreases as a result of astrocytic scar formation. Before stroke, arginase 1 and 2 expressions were restricted to neurons. Stroke resulted in up-regulation of arginase 1 and increased arginase activity in the region centered on the lesion where inflammatory cells are present. These changes were associated with an early and long-lasting arginase 1 up-regulation in activated macrophages and astrocytes and a delayed arginase 1 down-regulation in neurons at the vicinity of the lesion. A linear positive correlation was observed between expressions of arginase 1 and glial fibrillary acidic protein as a marker of activated astrocytes. Moreover, the pattern of arginase 1 and brain-derived neurotrophic factor (BDNF) expressions in activated astrocytes was similar. Unlike arginase 1, arginase 2 expression was not changed by stroke. In conclusion, increased arginase 1 expression is not restricted to macrophages in inflammation elicited by stroke but also occurs in activated astrocytes where it may contribute to neuroplasticity through the control of BDNF production.
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Affiliation(s)
- Aurore Quirié
- Faculté de Pharmacie, Unité INSERM U1093 Cognition, Action et Plasticité Sensorimotrice, Dijon, France
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157
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Baumann A, Devaux Y, Audibert G, Zhang L, Bracard S, Colnat-Coulbois S, Klein O, Zannad F, Charpentier C, Longrois D, Mertes PM. Gene Expression Profile of Blood Cells for the Prediction of Delayed Cerebral Ischemia after Intracranial Aneurysm Rupture: A Pilot Study in Humans. Cerebrovasc Dis 2013; 36:236-42. [DOI: 10.1159/000354161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 07/01/2013] [Indexed: 11/19/2022] Open
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158
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Seo JH, Guo S, Lok J, Navaratna D, Whalen MJ, Kim KW, Lo EH. Neurovascular matrix metalloproteinases and the blood-brain barrier. Curr Pharm Des 2012; 18:3645-8. [PMID: 22574977 DOI: 10.2174/138161212802002742] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 01/24/2012] [Indexed: 12/13/2022]
Abstract
Blood-brain barrier (BBB) leakage and brain edema is a critical part of stroke pathophysiology. In this mini-review, we briefly survey the potential role of matrix metalloproteinases (MMPs) in BBB dysfunction. A large body of data in both experimental models as well as clinical patient populations suggests that MMPs may disrupt BBB permeability and interfere with cell-cell signaling in the neurovascular unit. Hence, ongoing efforts are underway to validate MMPs as potential biomarkers in stroke as well as pursue MMP blockers as therapeutic opportunities. Because BBB perturbations may also occur in neurodegeneration, MMPs and associated neurovascular unit mechanisms may also be potential targets in a broader range of CNS disorders.
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Affiliation(s)
- Ji Hae Seo
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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159
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Massaro M, Scoditti E, Carluccio MA, Pellegrino M, Calabriso N, Storelli C, Martines G, De Caterina R. Dipyridamole decreases inflammatory metalloproteinase-9 expression and release by human monocytes. Thromb Haemost 2012; 109:280-9. [PMID: 23238437 DOI: 10.1160/th12-05-0326] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 10/30/2012] [Indexed: 11/05/2022]
Abstract
Matrix metalloproteinase (MMP)-9 plays an important role in stroke by accelerating matrix degradation, disrupting the blood-brain barrier and increasing infarct size. Dipyridamole is an antiplatelet agent with recognised benefits in ischaemic stroke prevention. In addition to its antiplatelet properties, recent studies have reported that dipyridamole also features anti-inflammatory and anti-oxidant properties. We therefore investigated whether dipyridamole can ameliorate the proinflammatory profile of human monocytes, a source of MMP-9 in stroke, in terms of regulation of MMP-9 activity and expression, and explored underlying mechanisms. Human peripheral blood mononuclear cells (PBMC) and U937 cells were treated with increasing concentrations of dipyridamole (up to 10 µg/ml) for 60 minutes before stimulation with tumour necrosis factor (TNF)-α or phorbol myristate acetate (PMA). Exposure of PBMC and U937 to dipyridamole reduced TNF-α- and PMA-induced MMP-9 activity and protein release as well as MMP-9 mRNA, without significantly affecting the release of TIMP-1. This inhibitory effect was independent of dipyridamole-induced cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP) increase. Correspondingly, dipyridamole also significantly inhibited TNF-α-induced nuclear factor (NF)-κB activation and nuclear translocation of the p65 NF-κB subunit through a mechanism involving the inhibition of IkBα degradation and p38 MAPK activation. In conclusion, dipyridamole, at therapeutically achievable concentrations, reduces the expression and release of MMP-9 through a mechanism involving p38 MAPK and NF-κB inhibition. These results indicate that dipyridamole exerts anti-inflammatory properties in human monocytes that may favourably contribute to its actions in the secondary prevention of stroke, independent of its antiplatelet properties.
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Affiliation(s)
- Marika Massaro
- C.N.R. Institute of Clinical Physiology, Pisa and Lecce, Italy
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160
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Bahou WF. Platelet systems biology using integrated genetic and proteomic platforms. Thromb Res 2012; 129 Suppl 1:S38-45. [PMID: 22682131 DOI: 10.1016/s0049-3848(12)70014-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Platelets retain megakaryocyte-derived mRNA, an abundant and diverse array of miRNAs, and have evolved unique adaptive signals for maintenance of genetic and protein diversity. Quiescent platelets generally display minimal translational activity, although maximally-activated platelets retain the capacity for protein synthesis. Progressive data using multiple platelet activation models clearly demonstrate that platelet responses to the majority (if not all) agonists are highly variable within the population, demonstrating considerable heritability in siblings, twins, and families with premature coronary artery disease. Research from our laboratory has adapted global profiling strategies to close the knowledge gap currently existing between genetic variability and platelet phenotypic responsiveness. We have applied iterative algorithms for genetic biomarker discovery and class prediction models of platelet phenotypes, with the goal of systematically analyzing integrated mRNA/miRNA/proteomic datasets for identification of regulatory networks that define phenotypic variability in platelet responses. This approach has the potential to define platelet genetic biomarkers predictive of thrombohemorrhagic outcomes in both normal and widely disparate clinical conditions.
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Affiliation(s)
- Wadie F Bahou
- Department of Medicine, Stony Brook University, Stony Brook, NY 11794-8151, USA.
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161
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Chan CPY, Jiang HL, Leung LY, Wan WM, Cheng NM, Ip WS, Cheung KY, Chan RWY, Wong LKS, Graham CA, Renneberg R, Rainer TH. Multiple atherosclerosis-related biomarkers associated with short- and long-term mortality after stroke. Clin Biochem 2012; 45:1308-15. [DOI: 10.1016/j.clinbiochem.2012.06.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/24/2012] [Accepted: 06/10/2012] [Indexed: 10/28/2022]
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162
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TTC7B emerges as a novel risk factor for ischemic stroke through the convergence of several genome-wide approaches. J Cereb Blood Flow Metab 2012; 32:1061-72. [PMID: 22453632 PMCID: PMC3367223 DOI: 10.1038/jcbfm.2012.24] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We hereby propose a novel approach to the identification of ischemic stroke (IS) susceptibility genes that involves converging data from several unbiased genetic and genomic tools. We tested the association between IS and genes differentially expressed between cases and controls, then determined which data mapped to previously reported linkage peaks and were nominally associated with stroke in published genome-wide association studies. We first performed gene expression profiling in peripheral blood mononuclear cells of 20 IS cases and 20 controls. Sixteen differentially expressed genes mapped to reported whole-genome linkage peaks, including the TTC7B gene, which has been associated with major cardiovascular disease. At the TTC7B locus, 46 tagging polymorphisms were tested for association in 565 Portuguese IS cases and 520 controls. Markers nominally associated in at least one test and defining associated haplotypes were then examined in 570 IS Spanish cases and 390 controls. Several polymorphisms and haplotypes in the intron 5-intron 6 region of TTC7B were also associated with IS risk in the Spanish and combined data sets. Multiple independent lines of evidence therefore support the role of TTC7B in stroke susceptibility, but further work is warranted to identify the exact risk variant and its pathogenic potential.
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163
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Alterio V, Di Fiore A, D'Ambrosio K, Supuran CT, De Simone G. Multiple binding modes of inhibitors to carbonic anhydrases: how to design specific drugs targeting 15 different isoforms? Chem Rev 2012; 112:4421-68. [PMID: 22607219 DOI: 10.1021/cr200176r] [Citation(s) in RCA: 933] [Impact Index Per Article: 77.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Vincenzo Alterio
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli, Italy
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164
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Oh SH, Kim OJ, Shin DA, Song J, Yoo H, Kim YK, Kim JK. Alteration of immunologic responses on peripheral blood in the acute phase of ischemic stroke: blood genomic profiling study. J Neuroimmunol 2012; 249:60-5. [PMID: 22591946 DOI: 10.1016/j.jneuroim.2012.04.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/30/2012] [Accepted: 04/15/2012] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Peripheral blood cells and inflammatory mediators have a detrimental effect on brain during cerebral ischemia. We investigated the immunologic changes on peripheral blood in the acute phase of ischemic stroke using RNA microarray. METHODS mRNA microarray and real time-polymerase chain reaction (RT-PCR) for genes of interest in microarray data were analyzed in 12 stroke patients and 12 controls. Plasma matrix metalloproteinase-9 (MMP-9) concentrations were measured in 120 stroke patients and 82 controls. RESULTS In microarray analysis, a total of 11 genes of interest showed different expression in patients with ischemic stroke. The three most highly expressed genes were C19orf59 (chromosome 19 open reading frame 59), MMP9 and IL18RAP (interleukin-18 receptor accessory protein), whereas gene with the lowest expression was GNLY (granulysin). The expression patterns of three selected genes (MMP9, IL18RAP and GNLY) were validated by RT-PCR. The plasma concentration of MMP-9 was significantly elevated in the stroke patients, and showed a weakly positive correlation with infarct volume. Gene set enrichment analysis (GSEA) showed that gene sets related to immunity and defense, signal transduction, transport and cell adhesion were significant in acute ischemic stroke. CONCLUSIONS In the peripheral blood, numerous genes of inflammatory mediators, including MMP9, IL18RAP and GNLY, are altered in the acute phase of ischemic stroke. This stroke-specific gene expression profiling provides valuable information about the role of peripheral inflammation to the pathophysiological mechanism of ischemic stroke.
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Affiliation(s)
- Seung-Hun Oh
- Department of Neurology, CHA Bundang Medical Center, CHA University, Seongnam, Republic of Korea
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165
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Tian Y, Stamova B, Jickling GC, Liu D, Ander BP, Bushnell C, Zhan X, Davis RR, Verro P, Pevec WC, Hedayati N, Dawson DL, Khoury J, Jauch EC, Pancioli A, Broderick JP, Sharp FR. Effects of gender on gene expression in the blood of ischemic stroke patients. J Cereb Blood Flow Metab 2012; 32:780-91. [PMID: 22167233 PMCID: PMC3345909 DOI: 10.1038/jcbfm.2011.179] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
This study examined the effects of gender on RNA expression after ischemic stroke (IS). RNA obtained from blood of IS patients (n=51; 153 samples at < or =3, 5, and 24 hours) and from matched controls (n=52) were processed on Affymetrix microarrays. Analyses of covariance for stroke versus control samples were performed separately for both genders and the regulated genes for females compared with males. In all, 242, 227, and 338 male-specific genes were regulated at < or =3, 5, and 24 hours after IS, respectively, of which 59 were regulated at all time points. Overall, 774, 3,437, and 571 female-specific stroke genes were regulated at < or =3, 5, and 24 hours, respectively, of which 152 were regulated at all time points. Male-specific stroke genes were associated with integrin, integrin-liked kinase, actin, tight junction, Wnt/β-catenin, RhoA, fibroblast growth factors (FGF), granzyme, and tumor necrosis factor receptor (TNFR)2 signaling. Female-specific stroke genes were associated with p53, high-mobility group box-1, hypoxia inducible factor (HIF)1α, interleukin (IL)1, IL6, IL12, IL18, acute-phase response, T-helper, macrophage, and estrogen signaling. Cell death signaling was overrepresented in both genders, although the molecules and pathways differed. Gender affects gene expression in the blood of IS patients, which likely implies gender differences in immune, inflammatory, and cell death responses to stroke.
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Affiliation(s)
- Yingfang Tian
- Department of Neurology, the MIND Institute, University of California at Davis, Sacramento, CA, USA.
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166
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Abstract
Blood biomarkers may have applications in stroke diagnosis, outcome prediction, or treatment. In this article, we provide a focused review on some of the methodological challenges and potential developments of biomarkers in stroke. We review the approaches to the development of a diagnostic blood marker: a candidate marker approach, marker panels, and –omics. Then we examined the role of blood markers to predict recurrent stroke and treatment response in stroke.
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Affiliation(s)
- William Whiteley
- Division of Clinical Neurosciences, Western General Hospital, University of Edinburgh, Edinburgh, UK
| | - Yingfang Tian
- Department of Neurology and MIND institute, University of California, Sacramento, CA, USA
| | - Glen C. Jickling
- Department of Neurology and MIND institute, University of California, Sacramento, CA, USA
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167
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Graham CA, Chan RW, Chan DY, Chan CP, Wong LK, Rainer TH. Matrix metalloproteinase 9 mRNA: An early prognostic marker for patients with acute stroke. Clin Biochem 2012; 45:352-5. [DOI: 10.1016/j.clinbiochem.2011.12.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 12/05/2011] [Accepted: 12/06/2011] [Indexed: 10/14/2022]
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168
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Tian Y, Stamova B, Jickling GC, Xu H, Liu D, Ander BP, Bushnell C, Zhan X, Turner RJ, Davis RR, Verro P, Pevec WC, Hedayati N, Dawson DL, Khoury J, Jauch EC, Pancioli A, Broderick JP, Sharp FR. Y chromosome gene expression in the blood of male patients with ischemic stroke compared with male controls. ACTA ACUST UNITED AC 2012; 9:68-75.e3. [PMID: 22365286 DOI: 10.1016/j.genm.2012.01.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 01/04/2012] [Accepted: 01/09/2012] [Indexed: 10/28/2022]
Abstract
BACKGROUND Sex is suggested to be an important determinant of ischemic stroke risk factors, etiology, and outcome. However, the basis for this remains unclear. The Y chromosome is unique in males. Genes expressed in males on the Y chromosome that are associated with stroke may be important genetic contributors to the unique features of males with ischemic stroke, which would be helpful for explaining sex differences observed between men and women. OBJECTIVE We compared Y chromosome gene expression in males with ischemic stroke and male controls. METHODS Blood samples were obtained from 40 male patients ≤3, 5, and 24 hours after ischemic stroke and from 41 male controls (July 2003-April 2007). RNA was isolated from blood and was processed using Affymetrix Human U133 Plus 2.0 expression arrays (Affymetrix Inc., Santa Clara, California). Y chromosome genes differentially expressed between male patients with stroke and male control subjects were identified using an ANCOVA adjusted for age and batch. A P < 0.05 and a fold change >1.2 were considered significant. RESULTS Seven genes on the Y chromosome were differentially expressed in males with ischemic stroke compared with controls. Five of these genes (VAMP7, CSF2RA, SPRY3, DHRSX, and PLCXD1) are located on pseudoautosomal regions of the human Y chromosome. The other 2 genes (EIF1AY and DDX3Y) are located on the nonrecombining region of the human Y chromosome. The identified genes were associated with immunology, RNA metabolism, vesicle fusion, and angiogenesis. CONCLUSIONS Specific genes on the Y chromosome are differentially expressed in blood after ischemic stroke. These genes provide insight into potential molecular contributors to sex differences in ischemic stroke.
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Affiliation(s)
- Yingfang Tian
- Department of Neurology and the MIND Institute, University of California at Davis, Sacramento, California 95817, USA.
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169
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The transcriptome of cerebral ischemia. Brain Res Bull 2012; 88:313-9. [PMID: 22381515 DOI: 10.1016/j.brainresbull.2012.02.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 07/20/2011] [Accepted: 02/13/2012] [Indexed: 01/26/2023]
Abstract
The molecular causality and response to stroke is complex. Yet, much of the literature examining the molecular response to stroke has focused on targeted pathways that have been well-characterized. Consequently, our understanding of stroke pathophysiology has made little progress by way of clinical therapeutics since tissue plasminogen activator was approved for treatment nearly a decade ago. The lack of clinical translation is in part due to neuron-focused studies, preclinical models of cerebral ischemia and the paradoxical nature of neuro-inflammation. With the evolution of the Stroke Therapy Academic Industry Roundtable criteria streamlining research efforts and broad availability of genomic technologies, the ability to decipher the molecular fingerprint of ischemic stroke is on the horizon. This review highlights preclinical microarray findings of the ischemic brain, discusses the transcriptome of cerebral preconditioning and emphasizes the importance of further characterizing the role of the neurovascular unit and peripheral white blood cells in mediating stroke damage and repair within the penumbra.
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170
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Anticoagulants affect matrix metalloproteinase 9 levels in blood samples of stroke patients and healthy controls. Clin Biochem 2012; 45:483-9. [PMID: 22342361 DOI: 10.1016/j.clinbiochem.2012.01.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Revised: 01/28/2012] [Accepted: 01/31/2012] [Indexed: 11/20/2022]
Abstract
OBJECTIVES Matrix metalloproteinase-9 (MMP-9) represents a promising marker for acute stroke management. In clinical studies MMP-9 has been quantified by ELISA using differing protocols. We aimed to establish a valid protocol by evaluation of preanalytics. DESIGN AND METHODS Blood from stroke patients (n=28) and healthy controls (n=28) was drawn into tubes containing different anticoagulants (EDTA, citrate, lithium-heparin (heparin) and heparin with proteinase inhibitors) and processed after 0, 60 and 240 min. MMP-9 plasma protein and mRNA from mononuclear leukocytes were determined. RESULTS In regard to anticoagulants used, samples showed different MMP-9 protein baseline values and kinetics. Stable MMP-9 protein concentrations were only measured from EDTA samples. Particularly in samples with proteinase inhibitors protein and mRNA concentrations increased over time. Kinetics did not differ between patients and controls. CONCLUSIONS Preanalytics plays a key role for determination of MMP-9. EDTA seems to be a valid anticoagulant for MMP-9 protein measurement.
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171
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Hershey A, Horn P, Kabbouche M, O'Brien H, Powers S. Genomic expression patterns in menstrual-related migraine in adolescents. Headache 2012; 52:68-79. [PMID: 22220971 PMCID: PMC3265619 DOI: 10.1111/j.1526-4610.2011.02049.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND Exacerbation of migraine with menses is common in adolescent girls and women with migraine, occurring in up to 60% of females with migraine. These migraines are oftentimes longer and more disabling and may be related to estrogen levels and hormonal fluctuations. OBJECTIVE This study identifies the unique genomic expression pattern of menstrual-related migraine (MRM) in comparison to migraine occurring outside the menstrual period and headache-free controls. METHODS Whole blood samples were obtained from female subjects having an acute migraine during their menstrual period (MRM) or outside of their menstrual period (non-MRM) and controls (C)--females having a menstrual period without any history of headache. The messenger RNA was isolated from these samples, and genomic profile was assessed. Affymetrix Human Exon ST 1.0 (Affymetrix, Santa Clara, CA, USA) arrays were used to examine the genomic expression pattern differences between these 3 groups. RESULTS Blood genomic expression patterns were obtained on 56 subjects (MRM = 18, non-MRM = 18, and controls = 20). Unique genomic expression patterns were observed for both MRM and non-MRM. For MRM, 77 genes were identified that were unique to MRM, while 61 genes were commonly expressed for MRM and non-MRM, and 127 genes appeared to have a unique expression pattern for non-MRM. In addition, there were 279 genes that differentially expressed for MRM compared to non-MRM that were not differentially expressed for non-MRM. Gene ontology of these samples indicated many of these groups of genes were functionally related and included categories of immunomodulation/inflammation, mitochondrial function, and DNA homeostasis. CONCLUSIONS Blood genomic patterns can accurately differentiate MRM from non-MRM. These results indicate that MRM involves a unique molecular biology pathway that can be identified with a specific biomarker and suggest that individuals with MRM have a different underlying genetic etiology.
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Affiliation(s)
- Andrew Hershey
- Children's Hospital Medical Center, Department of Neurology, Cincinnati, OH 45229-3039, USA.
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172
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Easter RN, Barry CG, Pyne-Geithman G, Caruso JA. Significant proteins affecting cerebral vasospasm using complementary ICPMS and MALDI-MS. Metallomics 2012; 4:48-55. [DOI: 10.1039/c1mt00079a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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173
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Shinozuka K, Dailey T, Tajiri N, Ishikawa H, Kim DW, Pabon M, Acosta S, Kaneko Y, Borlongan CV. Stem Cells for Neurovascular Repair in Stroke. ACTA ACUST UNITED AC 2012; 4:12912. [PMID: 24077523 DOI: 10.4172/2157-7633.s4-004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Stem cells exert therapeutic effects against ischemic stroke via transplantation of exogenous stem cells or stimulation of endogenous stem cells within the neurogenic niches of subventricular zone and subgranular zone, or recruited from the bone marrow through peripheral circulation. In this paper, we review the different sources of stem cells that have been tested in animal models of stroke. In addition, we discuss specific mechanisms of action, in particular neurovascular repair by endothelial progenitor cells, as key translational research for advancing the clinical applications of stem cells for ischemic stroke.
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Affiliation(s)
- Kazutaka Shinozuka
- Department of Neurosurgery and Brain Repair, University of South Florida College of Medicine, 12901 Bruce B. Downs Blvd. MDC78, Tampa, Florida 33612, USA
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Vartanian KB, Stevens SL, Marsh BJ, Williams-Karnesky R, Lessov NS, Stenzel-Poore MP. LPS preconditioning redirects TLR signaling following stroke: TRIF-IRF3 plays a seminal role in mediating tolerance to ischemic injury. J Neuroinflammation 2011; 8:140. [PMID: 21999375 PMCID: PMC3217906 DOI: 10.1186/1742-2094-8-140] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 10/14/2011] [Indexed: 12/14/2022] Open
Abstract
Background Toll-like receptor 4 (TLR4) is activated in response to cerebral ischemia leading to substantial brain damage. In contrast, mild activation of TLR4 by preconditioning with low dose exposure to lipopolysaccharide (LPS) prior to cerebral ischemia dramatically improves outcome by reprogramming the signaling response to injury. This suggests that TLR4 signaling can be altered to induce an endogenously neuroprotective phenotype. However, the TLR4 signaling events involved in this neuroprotective response are poorly understood. Here we define several molecular mediators of the primary signaling cascades induced by LPS preconditioning that give rise to the reprogrammed response to cerebral ischemia and confer the neuroprotective phenotype. Methods C57BL6 mice were preconditioned with low dose LPS prior to transient middle cerebral artery occlusion (MCAO). Cortical tissue and blood were collected following MCAO. Microarray and qtPCR were performed to analyze gene expression associated with TLR4 signaling. EMSA and DNA binding ELISA were used to evaluate NFκB and IRF3 activity. Protein expression was determined using Western blot or ELISA. MyD88-/- and TRIF-/- mice were utilized to evaluate signaling in LPS preconditioning-induced neuroprotection. Results Gene expression analyses revealed that LPS preconditioning resulted in a marked upregulation of anti-inflammatory/type I IFN-associated genes following ischemia while pro-inflammatory genes induced following ischemia were present but not differentially modulated by LPS. Interestingly, although expression of pro-inflammatory genes was observed, there was decreased activity of NFκB p65 and increased presence of NFκB inhibitors, including Ship1, Tollip, and p105, in LPS-preconditioned mice following stroke. In contrast, IRF3 activity was enhanced in LPS-preconditioned mice following stroke. TRIF and MyD88 deficient mice revealed that neuroprotection induced by LPS depends on TLR4 signaling via TRIF, which activates IRF3, but does not depend on MyD88 signaling. Conclusion Our results characterize several critical mediators of the TLR4 signaling events associated with neuroprotection. LPS preconditioning redirects TLR4 signaling in response to stroke through suppression of NFκB activity, enhanced IRF3 activity, and increased anti-inflammatory/type I IFN gene expression. Interestingly, this protective phenotype does not require the suppression of pro-inflammatory mediators. Furthermore, our results highlight a critical role for TRIF-IRF3 signaling as the governing mechanism in the neuroprotective response to stroke.
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Affiliation(s)
- Keri B Vartanian
- Department of Molecular Microbiology & Immunology, Oregon Health & Science University, Portland, 97239, USA
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175
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Zhan X, Jickling GC, Tian Y, Stamova B, Xu H, Ander BP, Turner RJ, Mesias M, Verro P, Bushnell C, Johnston SC, Sharp FR. Transient ischemic attacks characterized by RNA profiles in blood. Neurology 2011; 77:1718-24. [PMID: 21998319 DOI: 10.1212/wnl.0b013e318236eee6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Transient ischemic attacks (TIA) are common. Though systemic inflammation and thrombosis are associated with TIA, further study may provide insight into TIA pathophysiology and possibly lead to the development of treatments specifically targeted to TIA. We sought to determine whether gene expression profiles in blood could better characterize the proinflammatory and procoagulant states in TIA patients. METHODS RNA expression in blood of TIA patients (n = 26) was compared to vascular risk factor control subjects without symptomatic cardiovascular disease (n = 26) using Affymetrix U133 Plus 2.0 microarrays. Differentially expressed genes in TIA were identified by analysis of covariance and evaluated with cross-validation and functional analyses. RESULTS Patients with TIA had different patterns of gene expression compared to controls. There were 480 probe sets, corresponding to 449 genes, differentially expressed between TIA and controls (false discovery rate correction for multiple comparisons, p ≤ 0.05, absolute fold change ≥1.2). These genes were associated with systemic inflammation, platelet activation, and prothrombin activation. Hierarchical cluster analysis of the identified genes suggested the presence of 2 patterns of RNA expression in patients with TIA. Prediction analysis identified a set of 34 genes that discriminated TIA from controls with 100% sensitivity and 100% specificity. CONCLUSION Patients with recent TIA have differences of gene expression in blood compared to controls. The 2 gene expression profiles associated with TIA suggests heterogeneous responses between subjects with TIA that may provide insight into cause, risk of stroke, and other TIA pathophysiology.
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Affiliation(s)
- X Zhan
- Department of Neurology, MIND Institute Research Wet Labs-Room 2415, University of California at Davis, 2805 50 Street, Sacramento, CA 95817, USA.
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Sharp FR, Jickling GC, Stamova B, Tian Y, Zhan X, Ander BP, Cox C, Kuczynski B, Liu D. RNA expression profiles from blood for the diagnosis of stroke and its causes. J Child Neurol 2011; 26:1131-6. [PMID: 21636778 PMCID: PMC3674558 DOI: 10.1177/0883073811408093] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A blood test to detect stroke and its causes would be particularly useful in babies, young children, and patients in intensive care units and for emergencies when imaging is difficult to obtain or is unavailable. Whole genome microarrays were used to show specific gene expression profiles in rats 24 hours after ischemic and hemorrhagic stroke, hypoxia, and hypoglycemia. These proof-of-principle studies revealed that groups of genes (called gene profiles) can distinguish ischemic stroke patients from controls within 3 to 24 hours after the strokes. In addition, gene expression profiles have been developed that distinguish stroke due to large-vessel atherosclerosis from cardioembolic stroke. These profiles will be useful for predicting the causes of cryptogenic stroke. The results in adults suggest that similar diagnostic tools could be developed for children.
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Affiliation(s)
- Frank R. Sharp
- Department of Neurology, University of California at Davis, Sacramento, CA, USA
| | - Glen C. Jickling
- Department of Neurology, University of California at Davis, Sacramento, CA, USA
| | - Boryana Stamova
- Department of Neurology, University of California at Davis, Sacramento, CA, USA
| | - Yingfang Tian
- Department of Neurology, University of California at Davis, Sacramento, CA, USA
| | - Xinhua Zhan
- Department of Neurology, University of California at Davis, Sacramento, CA, USA
| | - Bradley P. Ander
- Department of Neurology, University of California at Davis, Sacramento, CA, USA
| | - Christopher Cox
- Department of Neurology, University of California at Davis, Sacramento, CA, USA
| | - Beth Kuczynski
- Department of Neurology, University of California at Davis, Sacramento, CA, USA
| | - DaZhi Liu
- Department of Neurology, University of California at Davis, Sacramento, CA, USA
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177
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Katan M, Elkind MSV. Inflammatory and neuroendocrine biomarkers of prognosis after ischemic stroke. Expert Rev Neurother 2011; 11:225-39. [PMID: 21306210 DOI: 10.1586/ern.10.200] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Stroke is the third leading cause of mortality in the USA and one of the leading causes of severe morbidity. It is important to provide stroke patients and physicians with the most accurate prognostic information to optimize care and allocation of healthcare resources. Reliable prognostic markers available during the initial phase after acute stroke may aid clinical decision-making. Several interesting candidate biomarkers have been studied to address prognostic questions; this article will focus on selected inflammatory and neuroendocrine markers. The utility of a biomarker is defined by its ability to improve clinical decision-making and add timely information beyond that readily available from clinical examination and routine imaging. This aim has not been completely achieved yet for any biomarkers, but promising data are available and further studies are ongoing.
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Affiliation(s)
- Mira Katan
- Stroke Division, Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA.
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178
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Abstract
Whole genome expression microarrays can be used to study gene expression in blood, which comes in part from leukocytes, immature platelets, and red blood cells. Since these cells are important in the pathogenesis of stroke, RNA provides an index of these cellular responses to stroke. Our studies in rats have shown specific gene expression changes 24 hours after ischemic stroke, hemorrhage, status epilepticus, hypoxia, hypoglycemia, global ischemia, and following brief focal ischemia that simulated transient ischemic attacks in humans. Human studies show gene expression changes following ischemic stroke. These gene profiles predict a second cohort with >90% sensitivity and specificity. Gene profiles for ischemic stroke caused by large-vessel atherosclerosis and cardioembolism have been described that predict a second cohort with >85% sensitivity and specificity. Atherosclerotic genes were associated with clotting, platelets, and monocytes, and cardioembolic genes were associated with inflammation, infection, and neutrophils. These gene profiles predicted the cause of stroke in 58% of cryptogenic patients. These studies will provide diagnostic, prognostic, and therapeutic markers, and will advance our understanding of stroke in humans. New techniques to measure all coding and noncoding RNAs along with alternatively spliced transcripts will markedly advance molecular studies of human stroke.
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Abstract
This review provides a summary of the protein and RNA biomarkers that have been studied for the diagnosis and assessment of ischemic stroke. Many of the biomarkers identified relate to the pathophysiology of ischemic stroke, including ischemia of CNS tissue, acute thrombosis and inflammatory response. These biomarkers are summarized by their intended clinical application in ischemic stroke including diagnosis, prediction of stroke severity and outcome, and stratification of patients for stroke therapy. Among the biomarkers discussed are recent whole genome studies using RNA expression profiles to diagnose ischemic stroke and stroke etiology. Though many candidate blood based biomarkers for ischemic stroke have been identified, none are currently used in clinical practice. With further well designed study and careful validation, the development of blood biomarkers to improve the care of patients with ischemic stroke may be achieved.
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Affiliation(s)
- Glen C Jickling
- Department of Neurology and MIND Institute, University of California at Davis, Sacramento, CA 95817, USA.
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180
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Transcriptomic and nuclear architecture of immune cells after LPS activation. Chromosoma 2011; 120:501-20. [DOI: 10.1007/s00412-011-0328-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 06/01/2011] [Accepted: 06/01/2011] [Indexed: 01/06/2023]
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181
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Mendrick DL. Transcriptional profiling to identify biomarkers of disease and drug response. Pharmacogenomics 2011; 12:235-49. [PMID: 21332316 DOI: 10.2217/pgs.10.184] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The discovery, biological qualification and analytical validation of genomic biomarkers requires extensive collaborations between individuals with expertise in biology, statistics, bioinformatics, chemistry, clinical medicine, regulatory science and so on. For clinical utility, blood-borne biomarkers (e.g., mRNA and miRNA) of organ damage, drug toxicity and/or response would be preferred to those that are tissue based. Currently used biomarkers such as serum creatinine (indicating renal dysfunction) denote organ damage whether caused by disease, physical injury or drugs. Therefore, it is anticipated that studies of disease will discover biomarkers that can also be used to identify drug-induced injury and vice versa. This article describes transcriptomic blood-borne biomarkers that have been reported to be connected with disease and drug toxicity. Much more qualification and validation needs to be carried out before many of these biomarkers can prove useful. Discussed here are some of the lessons learned and roadblocks to success.
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Affiliation(s)
- Donna L Mendrick
- Division of Systems Biology, HFT-230, National Center for Toxicological Research, US FDA, 3900 NCTR Rd, Jefferson, AR 72079-4502, USA.
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Turner RJ, Jickling GC, Sharp FR. Are Underlying Assumptions of Current Animal Models of Human Stroke Correct: from STAIRs to High Hurdles? Transl Stroke Res 2011; 2:138-43. [PMID: 21654913 PMCID: PMC3085747 DOI: 10.1007/s12975-011-0067-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 01/18/2011] [Accepted: 01/20/2011] [Indexed: 10/29/2022]
Abstract
Animal models of acute ischemic stroke have been criticized for failing to translate to human stroke. Nevertheless, animal models are necessary to improve our understanding of stroke pathophysiology and to guide the development of new stroke therapies. The rabbit embolic clot model is one animal model that has led to an effective therapy in human acute ischemic stroke, namely tissue plasminogen activator (tPA). We propose that potential compounds that demonstrate efficacy in non-rabbit animal models of acute ischemic stroke should also be tested in the rabbit embolic blood clot model and, where appropriate, compared to tPA prior to investigation in humans. Furthermore, the use of anesthesia needs to be considered as a major confounder in animal models of acute ischemic stroke, and death should be included as an outcome measure in animal stroke studies. These steps, along with the current STAIRs recommendations, may improve the successful translation of experimental therapies to clinical stroke treatments.
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Affiliation(s)
- Renée J. Turner
- Department of Neurology, University of California at Davis, Sacramento, CA 95817 USA
- M.I.N.D. Institute, University of California at Davis, Sacramento, CA 95817 USA
- Discipline of Pathology, The University of Adelaide, North Terrace, Adelaide, 5005 SA Australia
| | - Glen C. Jickling
- Department of Neurology, University of California at Davis, Sacramento, CA 95817 USA
- M.I.N.D. Institute, University of California at Davis, Sacramento, CA 95817 USA
| | - Frank R. Sharp
- Department of Neurology, University of California at Davis, Sacramento, CA 95817 USA
- M.I.N.D. Institute, University of California at Davis, Sacramento, CA 95817 USA
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Time course proteomic profiling of human myocardial infarction plasma samples: An approach to new biomarker discovery. Clin Chim Acta 2011; 412:1086-93. [DOI: 10.1016/j.cca.2011.02.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 01/30/2011] [Accepted: 02/19/2011] [Indexed: 01/22/2023]
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Lin S, Rhodes PG, Cai Z. Whole body hypothermia broadens the therapeutic window of intranasally administered IGF-1 in a neonatal rat model of cerebral hypoxia-ischemia. Brain Res 2011; 1385:246-56. [PMID: 21316352 DOI: 10.1016/j.brainres.2011.02.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Revised: 02/02/2011] [Accepted: 02/03/2011] [Indexed: 11/17/2022]
Abstract
To investigate whether whole body hypothermia after neonatal cerebral hypoxia-ischemia (HI) could broaden the therapeutic window of intranasal treatment of IGF-1 (iN-IGF-1), postnatal day 7 rat pups were subjected to right common carotid artery ligation, followed by 8% oxygen inhalation for 2h. After HI, one group of pups were returned to their dams and kept at room temperature (24.5±0.2°C). A second group of pups were subjected to whole body hypothermia in a cool environment (21.5±0.3°C) for 2 or 4h before being returned to their dams. Two doses of 50 μg recombinant human IGF-1 were administered intranasally at a 1h interval starting at 0, 2 or 4h after hypothermia. Hypothermia decreased the rectal temperature of pups by 4.5°C as compared to those kept at room temperature. While hypothermia or iN-IGF-1 administered 2h after HI alone did not provide neuroprotection, the combined treatment of hypothermia with iN-IGF-1 significantly protected the neonatal rat brain from HI injury. Hypothermia treatment extended the therapeutic window of IGF-1 to 6h after HI. The extended IGF-1 therapeutic window by hypothermia was associated with decreases in infiltration of polymorphonuclear leukocytes and activation of microglia/macrophages and with attenuation of NF-κB activation in the ipsilateral hemisphere following HI.
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Affiliation(s)
- Shuying Lin
- Department of Pediatrics, Division of Newborn Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
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185
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Rosell A, Vilalta A, García-Berrocoso T, Fernández-Cadenas I, Domingues-Montanari S, Cuadrado E, Delgado P, Ribó M, Martínez-Sáez E, Ortega-Aznar A, Montaner J. Brain perihematoma genomic profile following spontaneous human intracerebral hemorrhage. PLoS One 2011; 6:e16750. [PMID: 21311749 PMCID: PMC3032742 DOI: 10.1371/journal.pone.0016750] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 01/10/2011] [Indexed: 01/09/2023] Open
Abstract
Background Spontaneous intracerebral hemorrhage (ICH) represents about 15% of all strokes and is associated with high mortality rates. Our aim was to identify the gene expression changes and biological pathways altered in the brain following ICH. Methodology/Principal Findings Twelve brain samples were obtained from four deceased patients who suffered an ICH including perihematomal tissue (PH) and the corresponding contralateral white (CW) and grey (CG) matter. Affymetrix GeneChip platform for analysis of over 47,000 transcripts was conducted. Microarray Analysis Suite 5.0 was used to process array images and the Ingenuity Pathway Analysis System was used to analyze biological mechanisms and functions of the genes. We identified 468 genes in the PH areas displaying a different expression pattern with a fold change between −3.74 and +5.16 when compared to the contralateral areas (291 overexpressed and 177 underexpressed). The top genes which appeared most significantly overexpressed in the PH areas codify for cytokines, chemokines, coagulation factors, cell growth and proliferation factors while the underexpressed codify for proteins involved in cell cycle or neurotrophins. Validation and replication studies at gene and protein level in brain samples confirmed microarray results. Conclusions The genomic responses identified in this study provide valuable information about potential biomarkers and target molecules altered in the perihematomal regions.
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Affiliation(s)
- Anna Rosell
- Neurovascular Research Laboratory and Department of Neurology, Universitat Autònoma de Barcelona, Institut de Recerca, Hospital Vall d'Hebron, Barcelona, Spain
| | - Anna Vilalta
- Neurovascular Research Laboratory and Department of Neurology, Universitat Autònoma de Barcelona, Institut de Recerca, Hospital Vall d'Hebron, Barcelona, Spain
| | - Teresa García-Berrocoso
- Neurovascular Research Laboratory and Department of Neurology, Universitat Autònoma de Barcelona, Institut de Recerca, Hospital Vall d'Hebron, Barcelona, Spain
| | - Israel Fernández-Cadenas
- Neurovascular Research Laboratory and Department of Neurology, Universitat Autònoma de Barcelona, Institut de Recerca, Hospital Vall d'Hebron, Barcelona, Spain
| | - Sophie Domingues-Montanari
- Neurovascular Research Laboratory and Department of Neurology, Universitat Autònoma de Barcelona, Institut de Recerca, Hospital Vall d'Hebron, Barcelona, Spain
| | - Eloy Cuadrado
- Neurovascular Research Laboratory and Department of Neurology, Universitat Autònoma de Barcelona, Institut de Recerca, Hospital Vall d'Hebron, Barcelona, Spain
| | - Pilar Delgado
- Neurovascular Research Laboratory and Department of Neurology, Universitat Autònoma de Barcelona, Institut de Recerca, Hospital Vall d'Hebron, Barcelona, Spain
| | - Marc Ribó
- Stroke Unit and Department of Neurology, Universitat Autònoma de Barcelona, Hospital Vall d'Hebron, Barcelona, Spain
| | - Elena Martínez-Sáez
- Neuropathology Unit, Department of Pathology, Universitat Autònoma de Barcelona, Hospital Vall d'Hebron, Barcelona, Spain
| | - Arantxa Ortega-Aznar
- Neuropathology Unit, Department of Pathology, Universitat Autònoma de Barcelona, Hospital Vall d'Hebron, Barcelona, Spain
| | - Joan Montaner
- Neurovascular Research Laboratory and Department of Neurology, Universitat Autònoma de Barcelona, Institut de Recerca, Hospital Vall d'Hebron, Barcelona, Spain
- Stroke Unit and Department of Neurology, Universitat Autònoma de Barcelona, Hospital Vall d'Hebron, Barcelona, Spain
- * E-mail:
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Ferronato S, Lira MG, Olivato S, Scuro A, Veraldi GF, Romanelli MG, Patuzzo C, Malerba G, Pignatti PF, Mazzucco S. Upregulated expression of Toll-like receptor 4 in peripheral blood of ischaemic stroke patients correlates with cyclooxygenase 2 expression. Eur J Vasc Endovasc Surg 2011; 41:358-63. [PMID: 21236709 DOI: 10.1016/j.ejvs.2010.11.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 11/17/2010] [Indexed: 10/18/2022]
Abstract
OBJECTIVES An inflammatory process following stroke in human brains and systemic inflammatory responses after stroke in humans have been reported by numerous investigators. The aim of the study was to investigate if genes involved in the cyclooxygenase 2 (COX-2) pathway are upregulated at peripheral level in patients after transient ischaemic attack (TIA) and stroke. DESIGN OF STUDY Blood samples were obtained from two groups of patients undergoing carotid endarterectomy. The first group included 25 patients who presented TIA or ischaemic stroke. The second group included 35 patients who had an asymptomatic internal carotid artery stenosis. Total RNA was isolated and the expression of Toll-like Receptor 4 (TLR4), COX-2, membrane-associated Prostaglandin E synthase (mPGES-1), Prostaglandin E₂ receptors (EP3 and EP4) was analysed by real time RT-PCR. RESULTS Expression of COX-2 and TLR4 were significantly increased in symptomatic patients (p < 0.001). Correlation analysis showed that TLR4 expression significantly correlated with COX-2 expression (R = 0.65; p < 0.01) in ischaemic stroke patients. This correlation was not observed in TIA and asymptomatic patients. CONCLUSIONS Our results suggest that the peripheral mechanism of inflammatory injury after stroke may be mediated by TLR4 through a COX-2-dependent pathway.
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Affiliation(s)
- S Ferronato
- Department of Life and Reproduction Sciences, Section of Biology and Genetics, University of Verona, Verona, Italy
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Tian Y, Liao IH, Zhan X, Gunther JR, Ander BP, Liu D, Lit L, Jickling GC, Corbett BA, Bos-Veneman NGP, Hoekstra PJ, Sharp FR. Exon expression and alternatively spliced genes in Tourette Syndrome. Am J Med Genet B Neuropsychiatr Genet 2011; 156B:72-8. [PMID: 21184586 PMCID: PMC3070201 DOI: 10.1002/ajmg.b.31140] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 10/07/2010] [Indexed: 11/08/2022]
Abstract
Tourette Syndrome (TS) is diagnosed based upon clinical criteria including motor and vocal tics. We hypothesized that differences in exon expression and splicing might be useful for pathophysiology and diagnosis. To demonstrate exon expression and alternatively spliced gene differences in blood of individuals with TS compared to healthy controls (HC), RNA was isolated from the blood of 26 un-medicated TS subjects and 23 HC. Each sample was run on Affymetrix Human Exon 1.0 ST (HuExon) arrays and on 3' biased U133 Plus 2.0 (HuU133) arrays. To investigate the differentially expressed exons and transcripts, analyses of covariance (ANCOVA) were performed, controlling for age, gender, and batch. Differential alternative splicing patterns between TS and HC were identified using analyses of variance (ANOVA) models in Partek. Three hundred and seventy-six exon probe sets were differentially expressed between TS and HC (raw P < 0.005, fold change >|1.2|) that separated TS and HC subjects using hierarchical clustering and Principal Components Analysis. The probe sets predicted TS compared to HC with a >90% sensitivity and specificity using a 10-fold cross-validation. Ninety genes (transcripts) had differential expression of a single exon (raw P < 0.005) and were predicted to be alternatively spliced (raw P < 0.05) in TS compared to HC. These preliminary findings might provide insight into the pathophysiology of TS and potentially provide prognostic and diagnostic biomarkers. However, the findings are tempered by the small sample size and multiple comparisons and require confirmation using PCR or deep RNA sequencing and a much larger patient population.
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Affiliation(s)
- Yingfang Tian
- M.I.N.D. Institute, Department of Neurology, University of California at Davis, Sacramento, 95817, USA.
| | - Isaac H. Liao
- M.I.N.D. Institute and Department of Neurology, University of California at Davis, Sacramento, California. USA
| | - Xinhua Zhan
- M.I.N.D. Institute and Department of Neurology, University of California at Davis, Sacramento, California. USA
| | - Joan R. Gunther
- M.I.N.D. Institute and Department of Neurology, University of California at Davis, Sacramento, California. USA
| | - Bradley P. Ander
- M.I.N.D. Institute and Department of Neurology, University of California at Davis, Sacramento, California. USA
| | - Dazhi Liu
- M.I.N.D. Institute and Department of Neurology, University of California at Davis, Sacramento, California. USA
| | - Lisa Lit
- M.I.N.D. Institute and Department of Neurology, University of California at Davis, Sacramento, California. USA
| | - Glen C. Jickling
- M.I.N.D. Institute and Department of Neurology, University of California at Davis, Sacramento, California. USA
| | - Blythe A. Corbett
- M.I.N.D. Institute and Department of Psychiatry, University of California at Davis, Sacramento, California. USA
| | - Netty GP. Bos-Veneman
- Department of Psychiatry, University Medical Center Groningen, University of Groningen, Netherlands
| | - Pieter J. Hoekstra
- Department of Psychiatry, University Medical Center Groningen, University of Groningen, Netherlands
| | - Frank R. Sharp
- M.I.N.D. Institute and Department of Neurology, University of California at Davis, Sacramento, California. USA
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188
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Abstract
BACKGROUND Chronic daily headache (CDH) and chronic migraine (CM) are one of the most frequent problems encountered in neurology, are often difficult to treat, and frequently complicated by medication-overuse headache (MOH). Proper recognition of MOH may alter treatment outcome and prevent long term disability. OBJECTIVE This study identifies the unique genomic expression pattern MOH that respond to cessation of the overused medication. METHODS Baseline occurrence of MOH and typical pattern of response to medication cessation were measured from a large database. Whole blood samples from patients with CM with or without MOH were obtained and their genomic profile was assessed. Affymetrix human U133 plus2 arrays were used to examine the genomic expression patterns prior to treatment and 6-12 weeks later. Headache characterisation and response to treatment based on headache frequency and disability were compared. RESULTS Of 1311 patients reporting daily or continuous headaches, 513 (39.1%) reported overusing analgesic medication. At follow-up, 44.5% had a 50% or greater reduction in headache frequency, while 41.6% had no change. Blood genomic expression patterns were obtained on 33 patients with 19 (57.6%) overusing analgesic medication with a unique genomic expression pattern in MOH that responded to cessation of analgesics. Gene ontology of these samples indicated a significant number were involved with brain and immunological tissues, including multiple signalling pathways and apoptosis. CONCLUSIONS Blood genomic patterns can accurately identify MOH patients that respond to medication cessation. These results suggest that MOH involves a unique molecular biology pathway that can be identified with a specific biomarker.
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189
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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. Signatures of cardioembolic and large-vessel ischemic stroke. Ann Neurol 2010; 68:681-92. [PMID: 21031583 DOI: 10.1002/ana.22187] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The cause of stroke remains unknown or cryptogenic in many patients. We sought to determine whether gene expression signatures in blood can distinguish between cardioembolic and large-vessel causes of stroke, and whether these profiles can predict stroke etiology in the cryptogenic group. METHODS A total of 194 samples from 76 acute ischemic stroke patients were analyzed. RNA was isolated from blood and run on Affymetrix U133 Plus2.0 microarrays. Genes that distinguish large-vessel from cardioembolic stroke were determined at 3, 5, and 24 hours following stroke onset. Predictors were evaluated using cross-validation and a separate set of patients with known stroke subtype. The cause of cryptogenic stroke was predicted based on a model developed from strokes of known cause and identified predictors. RESULTS A 40-gene profile differentiated cardioembolic stroke from large-vessel stroke with >95% sensitivity and specificity. A separate 37-gene profile differentiated cardioembolic stroke due to atrial fibrillation from nonatrial fibrillation causes with >90% sensitivity and specificity. The identified genes elucidate differences in inflammation between stroke subtypes. When applied to patients with cryptogenic stroke, 17% are predicted to be large-vessel and 41% to be cardioembolic stroke. Of the cryptogenic strokes predicted to be cardioembolic, 27% were predicted to have atrial fibrillation. INTERPRETATION Gene expression signatures distinguish cardioembolic from large-vessel causes of ischemic stroke. These gene profiles may add valuable diagnostic information in the management of patients with stroke of unknown etiology though they need to be validated in future independent, large studies.
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Affiliation(s)
- Glen C Jickling
- Department of Neurology and the MIND Institute, University of California at Davis, Sacramento, CA 95817, USA.
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190
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Barr TL, Alexander S, Conley Y. Gene expression profiling for discovery of novel targets in human traumatic brain injury. Biol Res Nurs 2010; 13:140-53. [PMID: 21112922 DOI: 10.1177/1099800410385671] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Several clinical trials have failed to demonstrate a significant effect on outcome following human traumatic brain injury (TBI) despite promising results obtained in preclinical animal studies. These failures may be due in part to a misinterpretation of the findings obtained in preclinical animal models of TBI, a misunderstanding of the complexity of the human response to TBI, limited knowledge about the biological pathways that interact to contribute to good and bad outcomes after brain injury, and the effects of genomic variability and environment on individual recovery. Recent publications suggest that data obtained from gene expression profiling studies of complex neurological diseases such as stroke, multiple sclerosis (MS), Alzheimer's and Parkinson's may contribute to a more informed understanding of what affects outcome following TBI. These data may help to bridge the gap between successful preclinical studies and negative clinical trials in humans to reveal novel targets for therapy. Gene expression profiling has the capability to identify biomarkers associated with response to TBI, elucidate complex genetic interactions that may play a role in outcome following TBI, and reveal biological pathways related to brain health. This review highlights the current state of the literature on gene expression profiling for neurological disease and discusses its ability to aid in unraveling the variable human response to TBI and the potential for it to offer treatment strategies in an area where we currently have limited therapeutic options primarily based on supportive care.
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Affiliation(s)
- Taura L Barr
- West Virginia University School of Nursing & Center for Neuroscience, Morgantown, WV, USA.
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191
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Freedman JE, Vitseva O, Tanriverdi K. The role of the blood transcriptome in innate inflammation and stroke. Ann N Y Acad Sci 2010; 1207:41-5. [PMID: 20955424 DOI: 10.1111/j.1749-6632.2010.05731.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cerebrovascular disease is a major cause of death and disability, with a poorer outcome in patients having select risk factors including diabetes and hypertension. Risk factors and the state of cerebral ischemia-reperfusion associated with cerebrovascular occlusion are known to cause inflammatory changes. These events and the inflammatory state are reflected by transcript changes in various components of the blood and can be specifically measured. By defining these changes, new insight into cerebrovascular disease and its therapeutics is being achieved.
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Affiliation(s)
- Jane E Freedman
- Whitaker Cardiovascular Institute and Evans Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA.
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192
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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. Distinctive RNA expression profiles in blood associated with white matter hyperintensities in brain. Stroke 2010; 41:2744-9. [PMID: 20966416 DOI: 10.1161/strokeaha.110.591875] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
BACKGROUND AND PURPOSE White matter hyperintensities (WMH) are areas of high signal detected by T2 and fluid-attenuated inversion recovery sequences on brain MRI. Although associated with aging, cerebrovascular risk factors, and cognitive impairment, the pathogenesis of WMH remains unclear. Thus, RNA expression was assessed in the blood of individuals with and without extensive WMH to search for evidence of oxidative stress, inflammation, and other abnormalities described in WMH lesions in brain. METHODS Subjects included 20 with extensive WMH (WMH+), 45% of whom had Alzheimer disease, and 18 with minimal WMH (WMH-), 44% of whom had Alzheimer disease. All subjects were clinically evaluated and underwent quantitative MRI. Total RNA from whole blood was processed on human whole genome Affymetrix HU133 Plus 2.0 microarrays. RNA expression was analyzed using an analysis of covariance. RESULTS Two hundred forty-one genes were differentially regulated at ± 1.2-fold difference (P < 0.005) in subjects with WMH+ as compared to WMH-, regardless of cognitive status and 50 genes were differentially regulated with ± 1.5-fold difference (P < 0.005). Cluster and principal components analyses showed that the expression profiles for these genes distinguished WMH+ from WMH- subjects. Function analyses suggested that WMH-specific genes were associated with oxidative stress, inflammation, detoxification, and hormone signaling, and included genes associated with oligodendrocyte proliferation, axon repair, long-term potentiation, and neurotransmission. CONCLUSIONS The unique RNA expression profile in blood associated with WMH is consistent with roles of systemic oxidative stress and inflammation, as well as other potential processes in the pathogenesis or consequences of WMH.
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Affiliation(s)
- Huichun Xu
- Department of Neurology and M.I.N.D. Institute, University of California at Davis, Sacramento, CA 95817, USA.
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193
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Barr TL, Conley Y, Ding J, Dillman A, Warach S, Singleton A, Matarin M. Genomic biomarkers and cellular pathways of ischemic stroke by RNA gene expression profiling. Neurology 2010; 75:1009-14. [PMID: 20837969 DOI: 10.1212/wnl.0b013e3181f2b37f] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE The objective of this study was to provide insight into the molecular mechanisms of acute ischemic cerebrovascular syndrome (AICS) through gene expression profiling and pathway analysis. METHODS Peripheral whole blood samples were collected from 39 MRI-diagnosed patients with AICS and 25 nonstroke control subjects ≥ 18 years of age. Total RNA was extracted from whole blood stabilized in Paxgene RNA tubes, amplified, and hybridized to Illumina HumanRef-8v2 bead chips. Gene expression was compared in a univariate manner between stroke patients and control subjects using t test in GeneSpring. The significant genes were tested in a logistic regression model controlling for age, hypertension, and dyslipidemia. Inflation of type 1 error was corrected by Bonferroni and Ingenuity Systems Pathway analysis was performed. Validation was performed by QRT-PCR using Taqman gene expression assays. RESULTS A 9-gene profile was identified in the whole blood of ischemic stroke patients using gene expression profiling. Five of these 9 genes were identified in a previously published expression profiling study of stroke and are therefore likely biomarkers of stroke. Pathway analysis revealed toll-like receptor signaling as a highly significant canonical pathway present in the peripheral whole blood of patients with AICS. CONCLUSIONS Our study highlights the relevance of the innate immune system through toll-like receptor signaling as a mediator of response to ischemic stroke and supports the claim that gene expression profiling can be used to identify biomarkers of ischemic stroke. Further studies are needed to validate and refine these biomarkers for their diagnostic potential.
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Affiliation(s)
- T L Barr
- National Institute of Nursing Research, Tissue Injury Unit Building, Bethesda, MD 20812, USA.
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194
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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. Gene expression profiling of blood for the prediction of ischemic stroke. Stroke 2010; 41:2171-7. [PMID: 20798371 DOI: 10.1161/strokeaha.110.588335] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND AND PURPOSE A blood-based biomarker of acute ischemic stroke would be of significant value in clinical practice. This study aimed to (1) replicate in a larger cohort our previous study using gene expression profiling to predict ischemic stroke; and (2) refine prediction of ischemic stroke by including control groups relevant to ischemic stroke. METHODS Patients with ischemic stroke (n=70, 199 samples) were compared with control subjects who were healthy (n=38), had vascular risk factors (n=52), and who had myocardial infarction (n=17). Whole blood was drawn ≤3 hours, 5 hours, and 24 hours after stroke onset and from control subjects. RNA was processed on whole genome microarrays. Genes differentially expressed in ischemic stroke were identified and analyzed for predictive ability to discriminate stroke from control subjects. RESULTS The 29 probe sets previously reported predicted a new set of ischemic strokes with 93.5% sensitivity and 89.5% specificity. Sixty- and 46-probe sets differentiated control groups from 3-hour and 24-hour ischemic stroke samples, respectively. A 97-probe set correctly classified 86% of ischemic strokes (3 hour+24 hour), 84% of healthy subjects, 96% of vascular risk factor subjects, and 75% with myocardial infarction. CONCLUSIONS This study replicated our previously reported gene expression profile in a larger cohort and identified additional genes that discriminate ischemic stroke from relevant control groups. This multigene approach shows potential for a point-of-care test in acute ischemic stroke.
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Affiliation(s)
- Boryana Stamova
- Department of Neurology and the MIND Institute, University of California at Davis, Sacramento, Calif 95817, USA.
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195
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Genetics and genomics of stroke: novel approaches. J Am Coll Cardiol 2010; 56:245-53. [PMID: 20633816 DOI: 10.1016/j.jacc.2010.02.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 02/02/2010] [Accepted: 02/09/2010] [Indexed: 01/11/2023]
Abstract
Evidence for a genetic basis for stroke comes from twin and family studies and from the occurrence of a number of uncommon monogenic disorders, but the contribution of genetic factors identified for stroke so far is small. Advances in genetics and genomics may permit new insights. In recent genome-wide association studies, a number of single-nucleotide polymorphisms have been associated with specific stroke subtypes and major stroke risk factors such as diabetes and atrial fibrillation. These await replication. Studies of messenger ribonucleic acid expression have also shown promise for the development of genomic signatures for stroke classification. Stroke and coronary heart disease share some features of pathophysiology, risk, and treatment, and their genetic and genomic bases also appear to overlap.
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196
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Mendrick DL, Schnackenberg L. Genomic and metabolomic advances in the identification of disease and adverse event biomarkers. Biomark Med 2010; 3:605-15. [PMID: 20477528 DOI: 10.2217/bmm.09.43] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Incomplete knowledge of tissue pathogenesis is hampering the identification of biomarkers for the appropriate therapeutic targets to prevent or inhibit disease processes, and the prediction and diagnosis of injury due to disease and adverse events of drug therapy. The revolution in genomics and metabolomics, combined with advanced bioinformatics and computational methods for mining such large, complex data sets, are beginning to provide critical insights into tissue injury. Such results will move us closer to the promise of personalized medicine.
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Affiliation(s)
- Donna L Mendrick
- Division of Systems Toxicology, HFT-230, National Center for Toxicological Research, US FDA, 3900 NCTR Road, Jefferson, AR 72079-4502, USA.
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197
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Pascual V, Chaussabel D, Banchereau J. A genomic approach to human autoimmune diseases. Annu Rev Immunol 2010; 28:535-71. [PMID: 20192809 DOI: 10.1146/annurev-immunol-030409-101221] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The past decade has seen an explosion in the use of DNA-based microarrays. These techniques permit assessment of RNA abundance on a genome-wide scale. Medical applications emerged in the field of cancer, with studies of both solid tumors and hematological malignancies leading to the development of tests that are now used to personalize therapeutic options. Microarrays have also been used to analyze the blood transcriptome in a wide range of diseases. In human autoimmune diseases, these studies are showing potential for identifying therapeutic targets as well as biomarkers for diagnosis, assessment of disease activity, and response to treatment. More quantitative and sensitive high-throughput RNA profiling methods are starting to be available and will be necessary for transcriptome analyses to become routine tests in the clinical setting. We expect this to crystallize within the coming decade, as these methods become part of the personalized medicine armamentarium.
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Affiliation(s)
- Virginia Pascual
- Baylor Institute for Immunology Research, INSERM U, Dallas, Texas 75204, USA.
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198
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Jickling GC, Zhan X, Ander BP, Turner RJ, Stamova B, Xu H, Tian Y, Liu D, Davis RR, Lapchak PA, Sharp FR. Genome response to tissue plasminogen activator in experimental ischemic stroke. BMC Genomics 2010; 11:254. [PMID: 20406488 PMCID: PMC2875237 DOI: 10.1186/1471-2164-11-254] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 04/21/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tissue plasminogen activator (tPA) is known to have functions beyond fibrinolysis in acute ischemic stroke, such as blood brain barrier disruption. To further delineate tPA functions in the blood, we examined the gene expression profiles induced by tPA in a rat model of ischemic stroke. RESULTS tPA differentially expressed 929 genes in the blood of rats (p <or= 0.05, fold change >or= |1.2|). Genes identified had functions related to modulation of immune cells. tPA gene expression was found to be dependent on the reperfusion status of cerebral vasculature. The majority of genes regulated by tPA were different from genes regulated by ischemic stroke. CONCLUSIONS tPA modulates gene expression in the blood of rats involving immune cells in a manner that is dependent on the status of vascular reperfusion. These non-fibrinolytic activities of tPA in the blood serve to better understand tPA-related complications.
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Affiliation(s)
- Glen C Jickling
- Department of Neurology and M,I,N,D, Institute, University of California at Davis, Sacramento, California 95817, USA.
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199
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Lovrecic L, Kastrin A, Kobal J, Pirtosek Z, Krainc D, Peterlin B. Gene expression changes in blood as a putative biomarker for Huntington's disease. Mov Disord 2010; 24:2277-81. [PMID: 19844910 DOI: 10.1002/mds.22477] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Several studies demonstrated alterations of gene expression in blood in various neurological disorders including Huntington's disease (HD). Using microarray technology, a recent study identified a large number of significantly altered mRNAs in HD blood, from which a 12-gene set was selected as classifier for discriminating controls and HD patients. The aim of our study was to validate expression changes of these 12 genes in an independent cohort of HD patients and evaluate their sensitivity and specificity. Four different subject groups were included--patients with HD, Parkinson's disease (PD), acute ischemic stroke (AS) and healthy controls. Although the previous results were successfully validated, gene expression changes in HD blood partly overlapped with those observed in blood from PD and AS patients. Predictive value of the selected biomarker set for HD group was 78%, with 82% sensitivity and 53% specificity. Further gene expression analyses in longitudinal studies are needed to validate and refine possible transcriptomic blood biomarkers in HD.
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Affiliation(s)
- Luca Lovrecic
- Institute of Medical Genetics, University Medical Centre, Ljubljana, Slovenia
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200
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Abstract
In this review, we discuss the genetic factors in both the aetiology and treatment of ischaemic stroke. We discuss candidate gene association studies, family linkage studies and the more recent whole genome association studies and whole genome expression studies. We also briefly discuss genetic testing for stroke risk and genetic analysis of treatment complications.
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Affiliation(s)
- M Matarin
- Laboratory of Neurogenetics, NIA/NIH, Bethesda, MD, USA
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