51
|
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.
Collapse
Affiliation(s)
- Jane E Freedman
- Whitaker Cardiovascular Institute and Evans Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA.
| | | | | |
Collapse
|
52
|
Tseveleki V, Rubio R, Vamvakas SS, White J, Taoufik E, Petit E, Quackenbush J, Probert L. Comparative gene expression analysis in mouse models for multiple sclerosis, Alzheimer's disease and stroke for identifying commonly regulated and disease-specific gene changes. Genomics 2010; 96:82-91. [PMID: 20435134 DOI: 10.1016/j.ygeno.2010.04.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 04/22/2010] [Accepted: 04/22/2010] [Indexed: 12/17/2022]
Abstract
The brain responds to injury and infection by activating innate defense and tissue repair mechanisms. Working upon the hypothesis that the brain defense response involves common genes and pathways across diverse pathologies, we analysed global gene expression in brain from mouse models representing three major central nervous system disorders, cerebral stroke, multiple sclerosis and Alzheimer's disease compared to normal brain using DNA microarray expression profiling. A comparison of dysregulated genes across disease models revealed common genes and pathways including key components of estrogen and TGF-beta signaling pathways that have been associated with neuroprotection as well as a neurodegeneration mediator, TRPM7. Further, for each disease model, we discovered collections of differentially expressed genes that provide novel insight into the individual pathology and its associated mechanisms. Our data provide a resource for exploring the complex molecular mechanisms that underlie brain neurodegeneration and a new approach for identifying generic and disease-specific targets for therapy.
Collapse
|
53
|
Jonchère V, Réhault-Godbert S, Hennequet-Antier C, Cabau C, Sibut V, Cogburn LA, Nys Y, Gautron J. Gene expression profiling to identify eggshell proteins involved in physical defense of the chicken egg. BMC Genomics 2010; 11:57. [PMID: 20092629 PMCID: PMC2827412 DOI: 10.1186/1471-2164-11-57] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 01/21/2010] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND As uricoletic animals, chickens produce cleidoic eggs, which are self-contained bacteria-resistant biological packages for extra-uterine development of the chick embryo. The eggshell constitutes a natural physical barrier against bacterial penetration if it forms correctly and remains intact. The eggshell's remarkable mechanical properties are due to interactions among mineral components and the organic matrix proteins. The purpose of our study was to identify novel eggshell proteins by examining the transcriptome of the uterus during calcification of the eggshell. An extensive bioinformatic analysis on genes over-expressed in the uterus allowed us to identify novel eggshell proteins that contribute to the egg's natural defenses. RESULTS Our 14 K Del-Mar Chicken Integrated Systems microarray was used for transcriptional profiling in the hen's uterus during eggshell deposition. A total of 605 transcripts were over-expressed in the uterus compared with the magnum or white isthmus across a wide range of abundance (1.1- to 79.4-fold difference). The 605 highly-expressed uterine transcripts correspond to 469 unique genes, which encode 437 different proteins. Gene Ontology (GO) analysis was used for interpretation of protein function. The most over-represented GO terms are related to genes encoding ion transport proteins, which provide eggshell mineral precursors. Signal peptide sequence was found for 54 putative proteins secreted by the uterus during eggshell formation. Many functional proteins are involved in calcium binding or biomineralization--prerequisites for interacting with the mineral phase during eggshell fabrication. While another large group of proteins could be involved in proper folding of the eggshell matrix. Many secreted uterine proteins possess antibacterial properties, which would protect the egg against microbial invasion. A final group includes proteases and protease inhibitors that regulate protein activity in the acellular uterine fluid where eggshell formation takes place. CONCLUSIONS Our original study provides the first detailed description of the chicken uterus transcriptome during formation of the eggshell. We have discovered a cache of about 600 functional genes and identified a large number of encoded proteins secreted into uterine fluid for fabrication of the eggshell and chemical protection of the egg. Some of these uterine genes could prove useful as biological markers for genetic improvement of phenotypic traits (i.e., egg and eggshell quality).
Collapse
Affiliation(s)
| | | | | | - Cédric Cabau
- INRA, UR83 Recherches Avicoles, F-37380 Nouzilly, France
| | - Vonick Sibut
- INRA, UR83 Recherches Avicoles, F-37380 Nouzilly, France
- Institut Technique Avicole, F-37380 Nouzilly, France
| | - Larry A Cogburn
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19717 USA
| | - Yves Nys
- INRA, UR83 Recherches Avicoles, F-37380 Nouzilly, France
| | - Joel Gautron
- INRA, UR83 Recherches Avicoles, F-37380 Nouzilly, France
| |
Collapse
|
54
|
Lee HM, Mima T, Sugino H, Aoki C, Adachi Y, Yoshio-Hoshino N, Matsubara K, Nishimoto N. Interactions among type I and type II interferon, tumor necrosis factor, and beta-estradiol in the regulation of immune response-related gene expressions in systemic lupus erythematosus. Arthritis Res Ther 2009; 11:R1. [PMID: 19121222 PMCID: PMC2688231 DOI: 10.1186/ar2584] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Revised: 11/14/2008] [Accepted: 01/03/2009] [Indexed: 01/28/2023] Open
Abstract
INTRODUCTION Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease characterized by various clinical manifestations. Several cytokines interact and play pathological roles in SLE, although the etiopathology is still obscure. In the present study we investigated the network of immune response-related molecules expressed in the peripheral blood of SLE patients, and the effects of cytokine interactions on the regulation of these molecules. METHODS Gene expression profiles of peripheral blood from SLE patients and from healthy women were analyzed using DNA microarray analysis. Differentially expressed genes classified into the immune response category were selected and analyzed using bioinformatics tools. Since interactions among TNF, IFNgamma, beta-estradiol (E2), and IFNalpha may regulate the expression of interferon-inducible (IFI) genes, stimulating and co-stimulating experiments were carried out on peripheral blood mononuclear cells followed by analysis using quantitative RT-PCR. RESULTS Thirty-eight downregulated genes and 68 upregulated genes were identified in the functional category of immune response. Overexpressed IFI genes were confirmed in SLE patient peripheral bloods. Using network-based analysis on these genes, several networks including cytokines--such as TNF and IFNgamma--and E2 were constructed. TNF-regulated genes were dominant in these networks, but in vitro TNF stimulation on peripheral blood mononuclear cells showed no differences in the above gene expressions between SLE and healthy individuals. Co-stimulating with IFNalpha and one of TNF, IFNgamma, or E2 revealed that TNF has repressive effects while IFNgamma essentially has synergistic effects on IFI gene expressions in vitro. E2 showed variable effects on IFI gene expressions among three individuals. CONCLUSIONS TNF may repress the abnormal regulation by IFNalpha in SLE while IFNgamma may have a synergistic effect. Interactions between IFNalpha and one of TNF, IFNgamma, or E2 appear to be involved in the pathogenesis of SLE.
Collapse
Affiliation(s)
- Hooi-Ming Lee
- Laboratory of Immune Regulation, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-Oka, Suita City, Osaka 565-0871, Japan
| | - Toru Mima
- Laboratory of Immune Regulation, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-Oka, Suita City, Osaka 565-0871, Japan
| | - Hidehiko Sugino
- Laboratory of Immune Regulation, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-Oka, Suita City, Osaka 565-0871, Japan
| | - Chieko Aoki
- Laboratory of Immune Regulation, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-Oka, Suita City, Osaka 565-0871, Japan
| | - Yasuo Adachi
- Laboratory of Immune Regulation, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-Oka, Suita City, Osaka 565-0871, Japan
| | - Naoko Yoshio-Hoshino
- Laboratory of Immune Regulation, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-Oka, Suita City, Osaka 565-0871, Japan
| | - Kenichi Matsubara
- DNA Chip Research Incorporated, 1-1-43 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Norihiro Nishimoto
- Laboratory of Immune Regulation, Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamada-Oka, Suita City, Osaka 565-0871, Japan
| |
Collapse
|
55
|
Lai DM, Li H, Lee CC, Tzeng YS, Hsieh YH, Hsu WM, Hsieh FJ, Cheng JT, Tu YK. Angiopoietin-like protein 1 decreases blood brain barrier damage and edema following focal cerebral ischemia in mice. Neurochem Int 2008; 52:470-7. [DOI: 10.1016/j.neuint.2007.08.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 07/27/2007] [Accepted: 08/15/2007] [Indexed: 01/12/2023]
|
56
|
Delahaye NF, Coltel N, Puthier D, Barbier M, Benech P, Joly F, Iraqi FA, Grau GE, Nguyen C, Rihet P. Gene expression analysis reveals early changes in several molecular pathways in cerebral malaria-susceptible mice versus cerebral malaria-resistant mice. BMC Genomics 2007; 8:452. [PMID: 18062806 PMCID: PMC2246131 DOI: 10.1186/1471-2164-8-452] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Accepted: 12/06/2007] [Indexed: 11/10/2022] Open
Abstract
Background Microarray analyses allow the identification and assessment of molecular signatures in whole tissues undergoing pathological processes. To better understand cerebral malaria pathogenesis, we investigated intra-cerebral gene-expression profiles in well-defined genetically cerebral malaria-resistant (CM-R) and CM-susceptible (CM-S) mice, upon infection by Plasmodium berghei ANKA (PbA). We investigated mouse transcriptional responses at early and late stages of infection by use of cDNA microarrays. Results Through a rigorous statistical approach with multiple testing corrections, we showed that PbA significantly altered brain gene expression in CM-R (BALB/c), and in CM-S (CBA/J and C57BL/6) mice, and that 327 genes discriminated between early and late infection stages, between mouse strains, and between CM-R and CM-S mice. We further identified 104, 56, 84 genes with significant differential expression between CM-R and CM-S mice on days 2, 5, and 7 respectively. The analysis of their functional annotation indicates that genes involved in metabolic energy pathways, the inflammatory response, and the neuroprotection/neurotoxicity balance play a major role in cerebral malaria pathogenesis. In addition, our data suggest that cerebral malaria and Alzheimer's disease may share some common mechanisms of pathogenesis, as illustrated by the accumulation of β-amyloid proteins in brains of CM-S mice, but not of CM-R mice. Conclusion Our microarray analysis highlighted marked changes in several molecular pathways in CM-S compared to CM-R mice, particularly at early stages of infection. This study revealed some promising areas for exploration that may both provide new insight into the knowledge of CM pathogenesis and the development of novel therapeutic strategies.
Collapse
Affiliation(s)
- Nicolas F Delahaye
- Laboratoire de Pharmacogénétique des maladies parasitaires-EA864, Université de la Méditerranée, IFR48, Marseille, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
57
|
A microarray study of gene and protein regulation in human and rat brain following middle cerebral artery occlusion. BMC Neurosci 2007; 8:93. [PMID: 17997827 PMCID: PMC2194693 DOI: 10.1186/1471-2202-8-93] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Accepted: 11/12/2007] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Altered gene expression is an important feature of ischemic cerebral injury and affects proteins of many functional classes. We have used microarrays to investigate the changes in gene expression at various times after middle cerebral artery occlusion in human and rat brain. RESULTS Our results demonstrated a significant difference in the number of genes affected and the time-course of expression between the two cases. The total number of deregulated genes in the rat was 335 versus 126 in the human, while, of 393 overlapping genes between the two array sets, 184 were changed only in the rat and 36 in the human with a total of 41 genes deregulated in both cases. Interestingly, the mean fold changes were much higher in the human. The expression of novel genes, including p21-activated kinase 1 (PAK1), matrix metalloproteinase 11 (MMP11) and integrase interactor 1, was further analyzed by RT-PCR, Western blotting and immunohistochemistry. Strong neuronal staining was seen for PAK1 and MMP11. CONCLUSION Our findings confirmed previous studies reporting that gene expression screening can detect known and unknown transcriptional features of stroke and highlight the importance of research using human brain tissue in the search for novel therapeutic agents.
Collapse
|
58
|
Li Y, Xu Z, Ford GD, Croslan DR, Cairobe T, Li Z, Ford BD. Neuroprotection by neuregulin-1 in a rat model of permanent focal cerebral ischemia. Brain Res 2007; 1184:277-83. [PMID: 17961519 DOI: 10.1016/j.brainres.2007.09.037] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 09/12/2007] [Accepted: 09/15/2007] [Indexed: 12/25/2022]
Abstract
Neuregulin-1 (NRG-1) is a growth factor with potent neuroprotective capacity in ischemic stroke. We recently showed that NRG-1 reduced neuronal death following transient middle cerebral artery occlusion (tMCAO) by up to 90% with an extended therapeutic window. Here, we examined the neuroprotective potential of NRG-1 using a permanent MCAO ischemia (pMCAO) rat model. NRG-1 reduced infarction in pMCAO by 50% when administered prior to ischemia. We previously demonstrated using gene expression profiling that pMCAO was associated with an exaggerated excitotoxicity response compared to tMCAO. Therefore, we examined whether co-treatment with an inhibitor of excitotoxicity would augment the effect of NRG-1 following pMCAO. Both NRG-1 and the N-methyl-D-aspartate (NMDA) antagonist MK-801 similarly reduced infarct size following pMCAO. However, combination treatment with both NRG-1 and MK-801 resulted in greater neuroprotection than either compound alone, including a 75% reduction in cortical infarction compared to control. Consistent with these findings, NRG-1 reduced neuronal death using an in vitro ischemia model and this effect was augmented by MK-801. These results demonstrate the efficacy of NRG-1 in pMCAO rat focal ischemia model. Our findings further indicate the potential clinically relevance of NRG-1 alone or as a combination strategy for treating ischemic stroke.
Collapse
Affiliation(s)
- Yonggang Li
- Department of Anatomy and Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | | | | | | | | | | | | |
Collapse
|
59
|
Lehnert SA, Reverter A, Byrne KA, Wang Y, Nattrass GS, Hudson NJ, Greenwood PL. Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds. BMC DEVELOPMENTAL BIOLOGY 2007; 7:95. [PMID: 17697390 PMCID: PMC2031903 DOI: 10.1186/1471-213x-7-95] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 08/16/2007] [Indexed: 12/03/2022]
Abstract
BACKGROUND The muscle fiber number and fiber composition of muscle is largely determined during prenatal development. In order to discover genes that are involved in determining adult muscle phenotypes, we studied the gene expression profile of developing fetal bovine longissimus muscle from animals with two different genetic backgrounds using a bovine cDNA microarray. Fetal longissimus muscle was sampled at 4 stages of myogenesis and muscle maturation: primary myogenesis (d 60), secondary myogenesis (d 135), as well as beginning (d 195) and final stages (birth) of functional differentiation of muscle fibers. All fetuses and newborns (total n = 24) were from Hereford dams and crossed with either Wagyu (high intramuscular fat) or Piedmontese (GDF8 mutant) sires, genotypes that vary markedly in muscle and compositional characteristics later in postnatal life. RESULTS We obtained expression profiles of three individuals for each time point and genotype to allow comparisons across time and between sire breeds. Quantitative reverse transcription-PCR analysis of RNA from developing longissimus muscle was able to validate the differential expression patterns observed for a selection of differentially expressed genes, with one exception. We detected large-scale changes in temporal gene expression between the four developmental stages in genes coding for extracellular matrix and for muscle fiber structural and metabolic proteins. FSTL1 and IGFBP5 were two genes implicated in growth and differentiation that showed developmentally regulated expression levels in fetal muscle. An abundantly expressed gene with no functional annotation was found to be developmentally regulated in the same manner as muscle structural proteins. We also observed differences in gene expression profiles between the two different sire breeds. Wagyu-sired calves showed higher expression of fatty acid binding protein 5 (FABP5) RNA at birth. The developing longissimus muscle of fetuses carrying the Piedmontese mutation shows an emphasis on glycolytic muscle biochemistry and a large-scale up-regulation of the translational machinery at birth. We also document evidence for timing differences in differentiation events between the two breeds. CONCLUSION Taken together, these findings provide a detailed description of molecular events accompanying skeletal muscle differentiation in the bovine, as well as gene expression differences that may underpin the phenotype differences between the two breeds. In addition, this study has highlighted a non-coding RNA, which is abundantly expressed and developmentally regulated in bovine fetal muscle.
Collapse
Affiliation(s)
- Sigrid A Lehnert
- Cooperative Research Centre for Cattle and Beef Quality, Australia
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia 4067, Australia
| | - Antonio Reverter
- Cooperative Research Centre for Cattle and Beef Quality, Australia
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia 4067, Australia
| | - Keren A Byrne
- Cooperative Research Centre for Cattle and Beef Quality, Australia
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia 4067, Australia
| | - Yonghong Wang
- Cooperative Research Centre for Cattle and Beef Quality, Australia
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia 4067, Australia
| | - Greg S Nattrass
- Cooperative Research Centre for Cattle and Beef Quality, Australia
- South Australian Research & Development Institute (SARDI), Livestock Systems, Roseworthy 5371, Australia
| | - Nicholas J Hudson
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia 4067, Australia
- School of Integrative Biology, University of Queensland, St Lucia 4072, Australia
| | - Paul L Greenwood
- Cooperative Research Centre for Cattle and Beef Quality, Australia
- Beef Industry Centre of Excellence, NSW Department of Primary Industries, JSF Barker Building, University of New England, Armidale 2351, Australia
| |
Collapse
|
60
|
Han HS, Yenari MA. Effect on gene expression of therapeutic hypothermia in cerebral ischemia. FUTURE NEUROLOGY 2007. [DOI: 10.2217/14796708.2.4.435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Therapeutic hypothermia has gained considerable interest, given that it appears to improve neurological outcomes in patients who have suffered cardiac arrest. In spite of its remarkable beneficial effect, the mechanism of protection by brain cooling is still unclear. Hypothermia is known to alter gene expression; thus, gene profiling may help to identify relevant mechanisms of neuroprotection. Recent studies have demonstrated that brain ischemia-induced gene expression is modulated by hypothermia, but the mechanism of hypothermic gene regulation is quite diverse. Hypothermia can alter transcription factors, leading to changes in gene and protein expression. Enhanced or reduced mRNA stability can also influence gene transcription. This review will summarize reports of altered gene expression following hypothermic treatment in brain ischemia.
Collapse
Affiliation(s)
- Hyung Soo Han
- Assistant Professor Kyungpook National University School of Medicine, Department of Physiology, 101 Dongin 2 Ga, Jung Gu, Daegu, 700–422, Korea
| | - Midori A Yenari
- Associate Professor University of California, San Francisco, Department of Neurology, Neurology (127) VAMC 4150 Clement St, San Francisco, CA 94121, USA
| |
Collapse
|
61
|
Jumppanen M, Gruvberger-Saal S, Kauraniemi P, Tanner M, Bendahl PO, Lundin M, Krogh M, Kataja P, Borg Å, Fernö M, Isola J. Basal-like phenotype is not associated with patient survival in estrogen-receptor-negative breast cancers. Breast Cancer Res 2007; 9:R16. [PMID: 17263897 PMCID: PMC1851391 DOI: 10.1186/bcr1649] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Revised: 12/12/2006] [Accepted: 01/31/2007] [Indexed: 01/04/2023] Open
Abstract
INTRODUCTION Basal-phenotype or basal-like breast cancers are characterized by basal epithelium cytokeratin (CK5/14/17) expression, negative estrogen receptor (ER) status and distinct gene expression signature. We studied the clinical and biological features of the basal-phenotype tumors determined by immunohistochemistry (IHC) and cDNA microarrays especially within the ER-negative subgroup. METHODS IHC was used to evaluate the CK5/14 status of 445 stage II breast cancers. The gene expression signature of the CK5/14 immunopositive tumors was investigated within a subset (100) of the breast tumors (including 50 ER-negative tumors) with a cDNA microarray. Survival for basal-phenotype tumors as determined by CK5/14 IHC and gene expression signature was assessed. RESULTS From the 375 analyzable tumor specimens, 48 (13%) were immunohistochemically positive for CK5/14. We found adverse distant disease-free survival for the CK5/14-positive tumors during the first years (3 years hazard ratio (HR) 2.23, 95% confidence interval (CI) 1.17 to 4.24, p = 0.01; 5 years HR 1.80, 95% CI 1.02 to 3.15, p = 0.04) but the significance was lost at the end of the follow-up period (10 years HR 1.43, 95% CI 0.84 to 2.43, p = 0.19). Gene expression profiles of immunohistochemically determined CK5/14-positive tumors within the ER-negative tumor group implicated 1,713 differently expressed genes (p < 0.05). Hierarchical clustering analysis with the top 500 of these genes formed one basal-like and a non-basal-like cluster also within the ER-negative tumor entity. A highly concordant classification could be constructed with a published gene set (Sorlie's intrinsic gene set, concordance 90%). Both gene sets identified a basal-like cluster that included most of the CK5/14-positive tumors, but also immunohistochemically CK5/14-negative tumors. Within the ER-negative tumor entity there was no survival difference between the non-basal and basal-like tumors as identified by immunohistochemical or gene-expression-based classification. CONCLUSION Basal cytokeratin-positive tumors have a biologically distinct gene expression signature from other ER-negative tumors. Even if basal cytokeratin expression predicts early relapse among non-selected tumors, the clinical outcome of basal tumors is similar to non-basal ER-negative tumors. Immunohistochemically basal cytokeratin-positive tumors almost always belong to the basal-like gene expression profile, but this cluster also includes few basal cytokeratin-negative tumors.
Collapse
Affiliation(s)
- Mervi Jumppanen
- Department of Pathology, Seinäjoki Central Hospital, Hanneksenrinne 7, FIN-60220 Seinäjoki, Finland
- Institute of Medical Technology, University and University Hospital of Tampere, Biokatu 6, FIN-33520 Tampere, Finland
| | - Sofia Gruvberger-Saal
- Department of Oncology, Clinical Sciences, University of Lund, Klinikgatan 7, SE-221 85 Lund, Sweden
| | - Päivikki Kauraniemi
- Institute of Medical Technology, University and University Hospital of Tampere, Biokatu 6, FIN-33520 Tampere, Finland
| | - Minna Tanner
- Institute of Medical Technology, University and University Hospital of Tampere, Biokatu 6, FIN-33520 Tampere, Finland
- Department of Oncology, Tampere University Hospital, Teiskontie 35, FIN-33520 Tampere, Finland
| | - Pär-Ola Bendahl
- Department of Oncology, Clinical Sciences, University of Lund, Klinikgatan 7, SE-221 85 Lund, Sweden
| | - Mikael Lundin
- Biomedical Informatics group, Department of Oncology, University of Helsinki, Haartmanninkatu 8, FIN-00290 Helsinki, Finland
| | - Morten Krogh
- Department of Theoretical Physics, Lund University, Sölvegatan 14A, SE-221 85 Lund, Sweden
| | - Pasi Kataja
- Institute of Medical Technology, University and University Hospital of Tampere, Biokatu 6, FIN-33520 Tampere, Finland
| | - Åke Borg
- Department of Oncology, Clinical Sciences, University of Lund, Klinikgatan 7, SE-221 85 Lund, Sweden
| | - Mårten Fernö
- Department of Oncology, Clinical Sciences, University of Lund, Klinikgatan 7, SE-221 85 Lund, Sweden
| | - Jorma Isola
- Institute of Medical Technology, University and University Hospital of Tampere, Biokatu 6, FIN-33520 Tampere, Finland
| |
Collapse
|
62
|
Mitsios N, Gaffney J, Kumar P, Krupinski J, Kumar S, Slevin M. Pathophysiology of Acute Ischaemic Stroke: An Analysis of Common Signalling Mechanisms and Identification of New Molecular Targets. Pathobiology 2006; 73:159-75. [PMID: 17119345 DOI: 10.1159/000096017] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Accepted: 07/17/2006] [Indexed: 12/18/2022] Open
Abstract
Stroke continues to be a major cause of death and disability. The currently available therapies have proven to be highly unsatisfactory (except thrombolysis) and attempts are being made to identify and characterize signalling proteins which could be exploited to design novel therapeutic modalities. The pathophysiology of stroke is a complex process. Delaying interventions from the first hours to days or even weeks following blood vessel occlusion may lead to worsening or impairment of recovery in later stages. The objective of this review is to critically evaluate the major mechanisms underlying stroke pathophysiology, especially the role of cell signalling in excitotoxicity, inflammation, apoptosis, neuroprotection and angiogenesis, and highlight potential novel targets for drug discovery.
Collapse
Affiliation(s)
- N Mitsios
- Department of Biological Sciences, Manchester Metropolitan University, Manchester, UK
| | | | | | | | | | | |
Collapse
|