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Mayer C, Riera-Ponsati L, Kauppinen S, Klitgaard H, Erler JT, Hansen SN. Targeting the NRF2 pathway for disease modification in neurodegenerative diseases: mechanisms and therapeutic implications. Front Pharmacol 2024; 15:1437939. [PMID: 39119604 PMCID: PMC11306042 DOI: 10.3389/fphar.2024.1437939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/03/2024] [Indexed: 08/10/2024] Open
Abstract
Neurodegenerative diseases constitute a global health issue and a major economic burden. They significantly impair both cognitive and motor functions, and their prevalence is expected to rise due to ageing societies and continuous population growth. Conventional therapies provide symptomatic relief, nevertheless, disease-modifying treatments that reduce or halt neuron death and malfunction are still largely unavailable. Amongst the common hallmarks of neurodegenerative diseases are protein aggregation, oxidative stress, neuroinflammation and mitochondrial dysfunction. Transcription factor nuclear factor-erythroid 2-related factor 2 (NRF2) constitutes a central regulator of cellular defense mechanisms, including the regulation of antioxidant, anti-inflammatory and mitochondrial pathways, making it a highly attractive therapeutic target for disease modification in neurodegenerative disorders. Here, we describe the role of NRF2 in the common hallmarks of neurodegeneration, review the current pharmacological interventions and their challenges in activating the NRF2 pathway, and present alternative therapeutic approaches for disease modification.
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Affiliation(s)
| | - Lluís Riera-Ponsati
- NEUmiRNA Therapeutics, Copenhagen, Denmark
- Center for RNA Medicine, Aalborg University, Copenhagen, Denmark
| | - Sakari Kauppinen
- NEUmiRNA Therapeutics, Copenhagen, Denmark
- Center for RNA Medicine, Aalborg University, Copenhagen, Denmark
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Habek M, Blazekovic A, Gotovac Jercic K, Pivac N, Outero TF, Borovecki F, Brinar V. Genome-Wide Expression Profile in People with Optic Neuritis Associated with Multiple Sclerosis. Biomedicines 2023; 11:2209. [PMID: 37626706 PMCID: PMC10452153 DOI: 10.3390/biomedicines11082209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/13/2023] [Accepted: 07/20/2023] [Indexed: 08/27/2023] Open
Abstract
The aim of this study was to perform a genome-wide expression analysis of whole-blood samples from people with optic neuritis (ON) and to determine differentially expressed mRNAs compared to healthy control subjects. The study included eight people with acute ON and six healthy control subjects. Gene expression was analyzed using DNA microarrays for whole-human-genome analysis, which contain 54,675 25-base pairs. The additional biostatistical analysis included gene ontology analysis and gene set enrichment analysis (GSEA). Quantitative RT-PCR (qPCR) was used to confirm selected differentially expressed genes. In total, 722 differently expressed genes were identified, with 377 exhibiting increased, and 345 decreased, expression. Gene ontology analysis and GSEA revealed that protein phosphorylation and intracellular compartment, apoptosis inhibition, pathways involved in cell cycles, T and B cell functions, and anti-inflammatory central nervous system (CNS) pathways are implicated in ON pathology. qPCR confirmed the differential expression of eight selected genes, with SLPI, CR3, and ITGA4 exhibiting statistically significant results. In conclusion, whole-blood gene expression analysis showed significant differences in the expression profiles of people with ON compared to healthy control subjects. Additionally, pathways involved in T cell regulation and anti-inflammatory pathways within CNS were identified as important in the early phases of MS.
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Affiliation(s)
- Mario Habek
- Department of Neurology, Referral Center for Autonomic Nervous System Disorders, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Antonela Blazekovic
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb School of Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
- Department for Anatomy and Clinical Anatomy, University of Zagreb School of Medicine, 10000 Zagreb, Croatia
| | - Kristina Gotovac Jercic
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb School of Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
- Department of Neurology, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Nela Pivac
- Division of Molecular Medicine, Rudjer Bošković Institute, 10002 Zagreb, Croatia
| | - Tiago Fleming Outero
- Department of Experimental Neurodegeneration, Centre for Biostructural Imaging of Neurodegeneration, University Medical Centre Göttingen, 37075 Göttingen, Germany
- Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE1 7RU, UK
- German Centre for Neurodegenerative Diseases (DZNE), 17475 Göttingen, Germany
| | - Fran Borovecki
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb School of Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
- Department of Neurology, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Vesna Brinar
- Department of Neurology, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
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Shavit E, Menascu S, Achiron A, Gurevich M. Age-related blood transcriptional regulators affect disease progression in pediatric multiple sclerosis. Neurobiol Dis 2023; 176:105953. [PMID: 36493973 DOI: 10.1016/j.nbd.2022.105953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Pediatric onset multiple sclerosis patients (POMS) are defined as multiple sclerosis with an onset before the age of 18 years. Compared to adult onset multiple sclerosis (AOMS), POMS has more severe disease activity at onset, but better recovery. Little is known about the molecular mechanism responsible for the differences in the clinical presentations. METHODS Peripheral Blood Mononuclear Cells samples were taken from 22 POMS patients (mean age 14.1 ± 2.4 years, 15 females, 7 male), and 16 AOMS patients, (mean age 30.8 ± 6.1 years,10 females, 6 males), and gene-expression were analyzed using Affymetrix Inc. HU-133-A2 microarrays. Differentially Expressed Genes (DEGs) that significantly distinguished between POMS and AOMS with pvalue <0.05 after false discovery rate correction were evaluated using Partek software. Twenty-one matched age and gender control was applied to clarify age-related changes. Clinical assessment was performed by analysis of expanded disability status scale (EDSS) and brain MRI lesion loads. Gene functional analysis was performed by Ingenuity Pathway Analysis software. RESULTS Compared to AOMS, POMS had higher EDSS (3.0 IQR 2.0-3.0 and 2.0 IQR 2.0-3.0, p = 0.005), volume of T1 (2.72 mm3, IQR 0.44-8.39 mm3 and 0.5 mm3 IQR 0-1.29 mm3 respectively, p = 0.04) and T2 (3.70 mm3, IQR 1.3-9.6 and 0.96 mm3, IQR 0.24-4.63 respectively, p = 0.02) brain MRI lesions. The POMS transcriptional profile was characterized by 551 DEGs, enriched by cell cycling, B lymphocyte signaling and senescent pathways (p < 0.02). Of these, 183 DEGs significantly correlated with T2 lesions volume. The POMS MRI correlated DEGs (n = 183) and their upstream regulators (n = 718) has overlapped with age related DEGs obtained from healthy subjects (n = 497). This evaluated common DEGs (n = 29) defined as POMS age-related regulators, suggesting to promote effect on disease severity. CONCLUSION Our finding of higher transcriptional levels of genes involved in cell cycle, cell migration and B cell proliferation that promoted by transcriptional level of age-associated genes and transcription factors allows better understanding of the more aggressive clinical course that defines the POMS.
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Affiliation(s)
- Eitan Shavit
- Multiple Sclerosis Center, Sheba Medical Center, Ramat-Gan, Israel; St. George's Hospital Medical School, University of London, London, United Kingdom; Arrow project for medical research education, Sheba Medical Center, Ramat-Gan, Israel.
| | - Shay Menascu
- Multiple Sclerosis Center, Sheba Medical Center, Ramat-Gan, Israel; Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel.
| | - Anat Achiron
- Multiple Sclerosis Center, Sheba Medical Center, Ramat-Gan, Israel; Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel.
| | - Michael Gurevich
- Multiple Sclerosis Center, Sheba Medical Center, Ramat-Gan, Israel; Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel.
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Cappelletti C, Eriksson A, Brorson IS, Leikfoss IS, Kråbøl O, Høgestøl EA, Vitelli V, Mjaavatten O, Harbo HF, Berven F, Bos SD, Berge T. Quantitative proteomics reveals protein dysregulation during T cell activation in multiple sclerosis patients compared to healthy controls. Clin Proteomics 2022; 19:23. [PMID: 35790914 PMCID: PMC9254507 DOI: 10.1186/s12014-022-09361-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 06/22/2022] [Indexed: 12/20/2022] Open
Abstract
Background Multiple sclerosis (MS) is an autoimmune, neurodegenerative disorder with a strong genetic component that acts in a complex interaction with environmental factors for disease development. CD4+ T cells are pivotal players in MS pathogenesis, where peripherally activated T cells migrate to the central nervous system leading to demyelination and axonal degeneration. Through a proteomic approach, we aim at identifying dysregulated pathways in activated T cells from MS patients as compared to healthy controls. Methods CD4+ T cells were purified from peripheral blood from MS patients and healthy controls by magnetic separation. Cells were left unstimulated or stimulated in vitro through the TCR and costimulatory CD28 receptor for 24 h prior to sampling. Electrospray liquid chromatography-tandem mass spectrometry was used to measure protein abundances. Results Upon T cell activation the abundance of 1801 proteins was changed. Among these proteins, we observed an enrichment of proteins expressed by MS-susceptibility genes. When comparing protein abundances in T cell samples from healthy controls and MS patients, 18 and 33 proteins were differentially expressed in unstimulated and stimulated CD4+ T cells, respectively. Moreover, 353 and 304 proteins were identified as proteins exclusively induced upon T cell activation in healthy controls and MS patients, respectively and dysregulation of the Nur77 pathway was observed only in samples from MS patients. Conclusions Our study highlights the importance of CD4+ T cell activation for MS, as proteins that change in abundance upon T cell activation are enriched for proteins encoded by MS susceptibility genes. The results provide evidence for proteomic disturbances in T cell activation in MS, and pinpoint to dysregulation of the Nur77 pathway, a biological pathway known to limit aberrant effector T cell responses.
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Morris AH, Hughes KR, Oakes RS, Cai MM, Miller SD, Irani DN, Shea LD. Engineered immunological niches to monitor disease activity and treatment efficacy in relapsing multiple sclerosis. Nat Commun 2020; 11:3871. [PMID: 32747712 PMCID: PMC7398910 DOI: 10.1038/s41467-020-17629-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 07/09/2020] [Indexed: 12/19/2022] Open
Abstract
Relapses in multiple sclerosis can result in irreversible nervous system tissue injury. If these events could be detected early, targeted immunotherapy could potentially slow disease progression. We describe the use of engineered biomaterial-based immunological niches amenable to biopsy to provide insights into the phenotype of innate immune cells that control disease activity in a mouse model of multiple sclerosis. Differential gene expression in cells from these niches allow monitoring of disease dynamics and gauging the effectiveness of treatment. A proactive treatment regimen, given in response to signal within the niche but before symptoms appeared, substantially reduced disease. This technology offers a new approach to monitor organ-specific autoimmunity, and represents a platform to analyze immune dysfunction within otherwise inaccessible target tissues.
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Affiliation(s)
- Aaron H Morris
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Kevin R Hughes
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Robert S Oakes
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Michelle M Cai
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Stephen D Miller
- Department of Microbiology-Immunology and Interdepartmental Immunobiology Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - David N Irani
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Lonnie D Shea
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
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6
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Brandes MS, Gray NE. NRF2 as a Therapeutic Target in Neurodegenerative Diseases. ASN Neuro 2020; 12:1759091419899782. [PMID: 31964153 PMCID: PMC6977098 DOI: 10.1177/1759091419899782] [Citation(s) in RCA: 159] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 11/26/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022] Open
Abstract
Increased reactive oxygen species production and oxidative stress have been implicated in the pathogenesis of numerous neurodegenerative conditions including among others Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, Friedrich’s ataxia, multiple sclerosis, and stroke. The endogenous antioxidant response pathway protects cells from oxidative stress by increasing the expression of cytoprotective enzymes and is regulated by the transcription factor nuclear factor erythroid 2-related factor 2 (NRF2). In addition to regulating the expression of antioxidant genes, NRF2 has also been shown to exert anti-inflammatory effects and modulate both mitochondrial function and biogenesis. This is because mitochondrial dysfunction and neuroinflammation are features of many neurodegenerative diseases as well NRF2 has emerged as a promising therapeutic target. Here, we review evidence for a beneficial role of NRF2 in neurodegenerative conditions and the potential of specific NRF2 activators as therapeutic agents.
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Affiliation(s)
- Mikah S. Brandes
- Department of Neurology, Oregon Health and Science University, Portland, OR, USA
| | - Nora E. Gray
- Department of Neurology, Oregon Health and Science University, Portland, OR, USA
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7
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Berge T, Eriksson A, Brorson IS, Høgestøl EA, Berg-Hansen P, Døskeland A, Mjaavatten O, Bos SD, Harbo HF, Berven F. Quantitative proteomic analyses of CD4 + and CD8 + T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls. Clin Proteomics 2019; 16:19. [PMID: 31080378 PMCID: PMC6505067 DOI: 10.1186/s12014-019-9241-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/27/2019] [Indexed: 02/07/2023] Open
Abstract
Background Multiple sclerosis (MS) is an autoimmune, neuroinflammatory disease, with an unclear etiology. However, T cells play a central role in the pathogenesis by crossing the blood–brain-barrier, leading to inflammation of the central nervous system and demyelination of the protective sheath surrounding the nerve fibers. MS has a complex inheritance pattern, and several studies indicate that gene interactions with environmental factors contribute to disease onset. Methods In the current study, we evaluated T cell dysregulation at the protein level using electrospray liquid chromatography–tandem mass spectrometry to get novel insights into immune-cell processes in MS. We have analyzed the proteomic profiles of CD4+ and CD8+ T cells purified from whole blood from 13 newly diagnosed, treatment-naive female patients with relapsing–remitting MS and 14 age- and sex-matched healthy controls. Results An overall higher protein abundance was observed in both CD4+ and CD8+ T cells from MS patients when compared to healthy controls. The differentially expressed proteins were enriched for T-cell specific activation pathways, especially CTLA4 and CD28 signaling in CD4+ T cells. When selectively analyzing proteins expressed from the genes most proximal to > 200 non-HLA MS susceptibility polymorphisms, we observed differential expression of eight proteins in T cells between MS patients and healthy controls, and there was a correlation between the genotype at three MS genetic risk loci and protein expressed from proximal genes. Conclusion Our study provides evidence for proteomic differences in T cells from relapsing–remitting MS patients compared to healthy controls and also identifies dysregulation of proteins encoded from MS susceptibility genes. Electronic supplementary material The online version of this article (10.1186/s12014-019-9241-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tone Berge
- Department of Mechanical, Electronics and Chemical Engineering, Faculty of Technology, Art and Design, Oslo Met - Oslo Metropolitan University, Postboks 4, St. Olavs Plass, 0130 Oslo, Norway.,2Neuroscience Research Unit, Oslo University Hospital, Rikshospitalet, Domus Medica 4, Nydalen, Postboks 4950, 0424 Oslo, Norway.,3Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway
| | - Anna Eriksson
- 2Neuroscience Research Unit, Oslo University Hospital, Rikshospitalet, Domus Medica 4, Nydalen, Postboks 4950, 0424 Oslo, Norway.,4Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ina Skaara Brorson
- 2Neuroscience Research Unit, Oslo University Hospital, Rikshospitalet, Domus Medica 4, Nydalen, Postboks 4950, 0424 Oslo, Norway.,4Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,5Department of Neurology, Oslo University Hospital, Ullevål, Postboks 4950, 0424 Nydalen, Oslo, Norway
| | - Einar August Høgestøl
- 2Neuroscience Research Unit, Oslo University Hospital, Rikshospitalet, Domus Medica 4, Nydalen, Postboks 4950, 0424 Oslo, Norway.,4Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Pål Berg-Hansen
- 4Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,5Department of Neurology, Oslo University Hospital, Ullevål, Postboks 4950, 0424 Nydalen, Oslo, Norway
| | - Anne Døskeland
- 6Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Postboks 7804, 5020 Bergen, Norway
| | - Olav Mjaavatten
- 6Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Postboks 7804, 5020 Bergen, Norway
| | - Steffan Daniel Bos
- 2Neuroscience Research Unit, Oslo University Hospital, Rikshospitalet, Domus Medica 4, Nydalen, Postboks 4950, 0424 Oslo, Norway.,4Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,5Department of Neurology, Oslo University Hospital, Ullevål, Postboks 4950, 0424 Nydalen, Oslo, Norway
| | - Hanne F Harbo
- 4Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,5Department of Neurology, Oslo University Hospital, Ullevål, Postboks 4950, 0424 Nydalen, Oslo, Norway
| | - Frode Berven
- 6Proteomics Unit at University of Bergen (PROBE), Department of Biomedicine, University of Bergen, Postboks 7804, 5020 Bergen, Norway
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Marchetti G, Ziliotto N, Meneghetti S, Baroni M, Lunghi B, Menegatti E, Pedriali M, Salvi F, Bartolomei I, Straudi S, Manfredini F, Voltan R, Basaglia N, Mascoli F, Zamboni P, Bernardi F. Changes in expression profiles of internal jugular vein wall and plasma protein levels in multiple sclerosis. Mol Med 2018; 24:42. [PMID: 30134823 PMCID: PMC6085618 DOI: 10.1186/s10020-018-0043-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/24/2018] [Indexed: 02/06/2023] Open
Abstract
Background Multiple sclerosis (MS) is an inflammatory, demyelinating and degenerative disorder of the central nervous system (CNS). Several observations support interactions between vascular and neurodegenerative mechanisms in multiple sclerosis (MS). To investigate the contribution of the extracranial venous compartment, we analysed expression profiles of internal jugular vein (IJV), which drains blood from CNS, and related plasma protein levels. Methods We studied a group of MS patients (n = 19), screened by echo-color Doppler and magnetic resonance venography, who underwent surgical reconstruction of IJV for chronic cerebrospinal venous insufficiency (CCSVI). Microarray-based transcriptome analysis was conducted on specimens of IJV wall from MS patients and from subjects undergoing carotid endarterectomy, as controls. Protein levels were determined by multiplex assay in: i) jugular and peripheral plasma from 17 MS/CCSVI patients; ii) peripheral plasma from 60 progressive MS patients, after repeated sampling and iii) healthy individuals. Results Of the differentially expressed genes (≥ 2 fold-change, multiple testing correction, P < 0.05), the immune-related CD86 (8.5 fold-change, P = 0.002) emerged among the up regulated genes (N = 409). Several genes encoding HOX transcription factors and histones potentially regulated by blood flow, were overexpressed. Smooth muscle contraction and cell adhesion processes emerged among down regulated genes (N = 515), including the neuronal cell adhesion L1CAM as top scorer (5 fold-change, P = 5 × 10− 4). Repeated measurements in jugular/peripheral plasma and overtime in peripheral plasma showed conserved individual plasma patterns for immune-inflammatory (CCL13, CCL18) and adhesion (NCAM1, VAP1, SELL) proteins, despite significant variations overtime (SELL P < 0.0001). Both age and MS disease phenotypes were determinants of VAP1 plasma levels. Data supported cerebral related-mechanisms regulating ANGPT1 levels, which were remarkably lower in jugular plasma and correlated in repeated assays but not between jugular/peripheral compartments. Conclusions This study provides for the first time expression patterns of the IJV wall, suggesting signatures of altered vascular mRNA profiles in MS disease also independently from CCSVI. The combined transcriptome-protein analysis provides intriguing links between IJV wall transcript alteration and plasma protein expression, thus highlighting proteins of interest for MS pathophysiology. Electronic supplementary material The online version of this article (10.1186/s10020-018-0043-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giovanna Marchetti
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, via Fossato di Mortara n 74, 44121, Ferrara, Italy.
| | - Nicole Ziliotto
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Silvia Meneghetti
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Marcello Baroni
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Barbara Lunghi
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Erica Menegatti
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Massimo Pedriali
- Department of Experimental and Diagnostic Medicine, Sant'Anna University- Hospital, Ferrara, Italy
| | - Fabrizio Salvi
- Center for Immunological and Rare Neurological Diseases, Bellaria Hospital, IRCCS of Neurological Sciences, Bologna, Italy
| | - Ilaria Bartolomei
- Center for Immunological and Rare Neurological Diseases, Bellaria Hospital, IRCCS of Neurological Sciences, Bologna, Italy
| | - Sofia Straudi
- Department of Neurosciences and Rehabilitation, Sant'Anna University- Hospital, Ferrara, Italy
| | - Fabio Manfredini
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, via Fossato di Mortara n 74, 44121, Ferrara, Italy
| | - Rebecca Voltan
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Nino Basaglia
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, via Fossato di Mortara n 74, 44121, Ferrara, Italy
| | - Francesco Mascoli
- Unit of Vascular and Endovascular Surgery, S. Anna University-Hospital, Ferrara, Italy
| | - Paolo Zamboni
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Francesco Bernardi
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
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9
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Gafson AR, Kim K, Cencioni MT, van Hecke W, Nicholas R, Baranzini SE, Matthews PM. Mononuclear cell transcriptome changes associated with dimethyl fumarate in MS. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2018; 5:e470. [PMID: 30283812 PMCID: PMC6168332 DOI: 10.1212/nxi.0000000000000470] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 04/23/2018] [Indexed: 01/28/2023]
Abstract
Objective To identify short-term changes in gene expression in peripheral blood mononuclear cells (PBMCs) associated with treatment response to dimethyl fumarate (DMF, Tecfidera) in patients with relapsing-remitting MS (RRMS). Methods Blood samples were collected from 24 patients with RRMS (median Expanded Disability Status Scale score, 2.0; range 1–7) at baseline, 6 weeks, and 15 months after the initiation of treatment with DMF (BG-12; Tecfidera). Seven healthy controls were also recruited, and blood samples were collected over the same time intervals. PBMCs were extracted from blood samples and sequenced using next-generation RNA sequencing. Treatment responders were defined using the composite outcome measure “no evidence of disease activity” (NEDA-4). Time-course and cross-sectional differential expression analyses were performed to identify transcriptomic markers of treatment response. Results Treatment responders (NEDA-4 positive, 8/24) over the 15-month period had 478 differentially expressed genes (DEGs) 6 weeks after the start of treatment. These were enriched for nuclear factor (erythroid-derived 2)-like 2 (Nrf2) and inhibition of nuclear factor κB (NFκB) pathway transcripts. For patients who showed signs of disease activity, there were no DEGs at 6 weeks relative to their (untreated) baseline. Contrasting transcriptomes expressed at 6 weeks with those at 15 months of treatment, 0 and 1,264 DEGs were found in the responder and nonresponder groups, respectively. Transcripts in the nonresponder group (NEDA-4 negative, 18/24) were enriched for T-cell signaling genes. Conclusion Short-term PBMC transcriptome changes reflecting activation of the Nrf2 and inhibition of NFκB pathways distinguish patients who subsequently show a medium-term treatment response with DMF. Relative stabilization of gene expression patterns may accompany treatment-associated suppression of disease activity.
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Affiliation(s)
- Arie R Gafson
- Division of Brain Sciences (A.R.G., M.T.C., R.N.), Department of Medicine, Imperial College London; the Department of Neurology (K.K.), Weill Institute for Neurosciences, University of California, San Francisco; icometrix (W.v.H.), Begaultlaan, Leuven, Belgium; the Department of Neurology (S.E.B.), Weill Institute for Neurosciences, Institute for Human Genetics and Graduate Program in Bioinformatics, University of California, San Francisco; and Division of Brain Sciences (P.M.M.), Department of Medicine, the Centre for Neurotechnology and the UK Dementia Research Institute, Imperial College London
| | - Kicheol Kim
- Division of Brain Sciences (A.R.G., M.T.C., R.N.), Department of Medicine, Imperial College London; the Department of Neurology (K.K.), Weill Institute for Neurosciences, University of California, San Francisco; icometrix (W.v.H.), Begaultlaan, Leuven, Belgium; the Department of Neurology (S.E.B.), Weill Institute for Neurosciences, Institute for Human Genetics and Graduate Program in Bioinformatics, University of California, San Francisco; and Division of Brain Sciences (P.M.M.), Department of Medicine, the Centre for Neurotechnology and the UK Dementia Research Institute, Imperial College London
| | - Maria T Cencioni
- Division of Brain Sciences (A.R.G., M.T.C., R.N.), Department of Medicine, Imperial College London; the Department of Neurology (K.K.), Weill Institute for Neurosciences, University of California, San Francisco; icometrix (W.v.H.), Begaultlaan, Leuven, Belgium; the Department of Neurology (S.E.B.), Weill Institute for Neurosciences, Institute for Human Genetics and Graduate Program in Bioinformatics, University of California, San Francisco; and Division of Brain Sciences (P.M.M.), Department of Medicine, the Centre for Neurotechnology and the UK Dementia Research Institute, Imperial College London
| | - Wim van Hecke
- Division of Brain Sciences (A.R.G., M.T.C., R.N.), Department of Medicine, Imperial College London; the Department of Neurology (K.K.), Weill Institute for Neurosciences, University of California, San Francisco; icometrix (W.v.H.), Begaultlaan, Leuven, Belgium; the Department of Neurology (S.E.B.), Weill Institute for Neurosciences, Institute for Human Genetics and Graduate Program in Bioinformatics, University of California, San Francisco; and Division of Brain Sciences (P.M.M.), Department of Medicine, the Centre for Neurotechnology and the UK Dementia Research Institute, Imperial College London
| | - Richard Nicholas
- Division of Brain Sciences (A.R.G., M.T.C., R.N.), Department of Medicine, Imperial College London; the Department of Neurology (K.K.), Weill Institute for Neurosciences, University of California, San Francisco; icometrix (W.v.H.), Begaultlaan, Leuven, Belgium; the Department of Neurology (S.E.B.), Weill Institute for Neurosciences, Institute for Human Genetics and Graduate Program in Bioinformatics, University of California, San Francisco; and Division of Brain Sciences (P.M.M.), Department of Medicine, the Centre for Neurotechnology and the UK Dementia Research Institute, Imperial College London
| | - Sergio E Baranzini
- Division of Brain Sciences (A.R.G., M.T.C., R.N.), Department of Medicine, Imperial College London; the Department of Neurology (K.K.), Weill Institute for Neurosciences, University of California, San Francisco; icometrix (W.v.H.), Begaultlaan, Leuven, Belgium; the Department of Neurology (S.E.B.), Weill Institute for Neurosciences, Institute for Human Genetics and Graduate Program in Bioinformatics, University of California, San Francisco; and Division of Brain Sciences (P.M.M.), Department of Medicine, the Centre for Neurotechnology and the UK Dementia Research Institute, Imperial College London
| | - Paul M Matthews
- Division of Brain Sciences (A.R.G., M.T.C., R.N.), Department of Medicine, Imperial College London; the Department of Neurology (K.K.), Weill Institute for Neurosciences, University of California, San Francisco; icometrix (W.v.H.), Begaultlaan, Leuven, Belgium; the Department of Neurology (S.E.B.), Weill Institute for Neurosciences, Institute for Human Genetics and Graduate Program in Bioinformatics, University of California, San Francisco; and Division of Brain Sciences (P.M.M.), Department of Medicine, the Centre for Neurotechnology and the UK Dementia Research Institute, Imperial College London
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10
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Bina P, Pahlevan Kakhki M, Sahraian MA, Behmanesh M. The expression of lnc-IL-7R long non-coding RNA dramatically correlated with soluble and membrane-bound isoforms of IL-7Ra gene in multiple sclerosis patients. Neurosci Lett 2017; 642:174-178. [PMID: 28174058 DOI: 10.1016/j.neulet.2017.01.068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 01/13/2017] [Accepted: 01/28/2017] [Indexed: 11/18/2022]
Abstract
BACKGROUND AND PURPOSE Multiple sclerosis (MS) is a neurological disease of the central nervous system (CNS) that causes physical and cognitive impairments. IL-7Ra is a key non-MHC gene associated with MS. IL-7Ra is a likely functional candidate for this complex disease because it is involved in the development, maturation, and homeostasis of T and B cells. Our aim was to evaluate the expression level and controlling role of lnc-IL-7R in the expression of two variants of IL-7Ra in MS patients versus healthy controls and their correlation with certain clinical features. METHODS Using the real-time PCR method, we analyzed the expression levels of membrane-bound (IL-7RB) and soluble (IL-7RS) isoforms of IL-7R gene and lnc-IL-7R in 36 MS patients versus 30 healthy controls. RESULTS Our results revealed no significant difference between the expression levels of IL-7RB and IL-7RS isoforms of IL-7R gene and lnc-IL-7R in MS patients versus healthy controls (p=0.7, p=0.6 and p=0.8, respectively). Moreover, we found a significant correlation between the expression levels of IL-7RB with lnc-IL-7R, IL-7RS with lnc-IL-7R and IL-7RB with IL-7RS in both patient and control groups. CONCLUSIONS We have probably uncovered new evidence for the controlling role of long non-coding RNAs in the expression level of genes and their roles in MS.
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Affiliation(s)
- Parinaz Bina
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Majid Pahlevan Kakhki
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Ali Sahraian
- Iranian Center of Neurological Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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11
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Cordiglieri C, Baggi F, Bernasconi P, Kapetis D, Faggiani E, Consonni A, Andreetta F, Frangiamore R, Confalonieri P, Antozzi C, Mantegazza R. Identification of a gene expression signature in peripheral blood of multiple sclerosis patients treated with disease-modifying therapies. Clin Immunol 2016; 173:133-146. [PMID: 27720845 DOI: 10.1016/j.clim.2016.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/30/2016] [Accepted: 10/04/2016] [Indexed: 01/17/2023]
Abstract
Multiple Sclerosis (MS) is an inflammatory disease with neurodegenerative alterations, ultimately progressing to neurological handicap. Therapies are effective in counteracting inflammation but not neurodegeneration. Biomarkers predicting disease course or treatment response are lacking. We investigated whether altered gene and protein expression profiles were detectable in the peripheral blood of 78 relapsing remitting MS (RR-MS) patients treated by disease-modifying therapies. A discovery/validation study on RR-MS responsive to glatiramer acetate identified 8 differentially expressed genes: ITGA2B, ITGB3, CD177, IGJ, IL5RA, MMP8, P2RY12, and S100β. A longitudinal study on glatiramer acetate, Interferon-β, or Fingolimod treated RR-MS patients confirmed that 7 out of 8 genes were downregulated with reference to the different therapies, whereas S100β was always upregulated. Thus, we identified a peripheral gene signature associated with positive response in RR-MS which may also explain drug immunomodulatory effects. The usefulness of this signature as a biomarker needs confirmation on larger series of patients.
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Affiliation(s)
- Chiara Cordiglieri
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta", Milan, Italy
| | - Fulvio Baggi
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta", Milan, Italy
| | - Pia Bernasconi
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta", Milan, Italy
| | - Dimos Kapetis
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta", Milan, Italy
| | - Elisa Faggiani
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta", Milan, Italy
| | - Alessandra Consonni
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta", Milan, Italy
| | - Francesca Andreetta
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta", Milan, Italy
| | - Rita Frangiamore
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta", Milan, Italy
| | - Paolo Confalonieri
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta", Milan, Italy
| | - Carlo Antozzi
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta", Milan, Italy
| | - Renato Mantegazza
- Neurology IV - Neuroimmunology and Neuromuscular Diseases Unit, Neurological Institute "Carlo Besta", Milan, Italy.
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12
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Mathur D, Urena-Peralta JR, Lopez-Rodas G, Casanova B, Coret-Ferrer F, Burgal-Marti M. Bypassing hazard of housekeeping genes: their evaluation in rat granule neurons treated with cerebrospinal fluid of multiple sclerosis subjects. Front Cell Neurosci 2015; 9:375. [PMID: 26441545 PMCID: PMC4585208 DOI: 10.3389/fncel.2015.00375] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/07/2015] [Indexed: 01/09/2023] Open
Abstract
Gene expression studies employing real-time PCR has become an intrinsic part of biomedical research. Appropriate normalization of target gene transcript(s) based on stably expressed housekeeping genes is crucial in individual experimental conditions to obtain accurate results. In multiple sclerosis (MS), several gene expression studies have been undertaken, however, the suitability of housekeeping genes to express stably in this disease is not yet explored. Recent research suggests that their expression level may vary under different experimental conditions. Hence it is indispensible to evaluate their expression stability to accurately normalize target gene transcripts. The present study aims to evaluate the expression stability of seven housekeeping genes in rat granule neurons treated with cerebrospinal fluid of MS patients. The selected reference genes were quantified by real time PCR and their expression stability was assessed using GeNorm and NormFinder algorithms. GeNorm identified transferrin receptor (Tfrc) and microglobulin beta-2 (B2m) the most stable genes followed by ribosomal protein L19 (Rpl19) whereas β-actin (ActB) and glyceraldehyde-3-phosphate-dehydrogenase (Gapdh) the most fluctuated ones in these neurons. NormFinder identified Tfrc as the best invariable gene followed by B2m and Rpl19. ActB and Gapdh were the least stable genes as analyzed by NormFinder algorithm. Both methods reported Tfrc and B2m the most stably expressed genes and Gapdh the least stable one. Altogether our data demonstrate the significance of pre-validation of housekeeping genes for accurate normalization and indicates Tfrc and B2m as best endogenous controls in MS. ActB and Gapdh are not recommended in gene expression studies related to current one.
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Affiliation(s)
- Deepali Mathur
- Department of Functional Biology, University of Valencia Valencia, Spain ; Multiple Sclerosis Laboratory, Department of Biomedicine, Prince Felipe Research Center Valencia, Spain
| | - Juan R Urena-Peralta
- Multiple Sclerosis Laboratory, Department of Biomedicine, Prince Felipe Research Center Valencia, Spain
| | - Gerardo Lopez-Rodas
- Department of Biochemistry and Molecular Biology, University of Valencia and INCLIVA Biomedical Research Institute Valencia, Spain
| | - Bonaventura Casanova
- CSUR-Esclerosi Múltiple, Hospital Universitari i Politècnic La Fe, Unitat Mixta d'Esclerosi Múltiple i Neurorregeneració de l'IIS-La Fe València, Spain
| | | | - Maria Burgal-Marti
- Multiple Sclerosis Laboratory, Department of Biomedicine, Prince Felipe Research Center Valencia, Spain
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13
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Genetic variants in interleukin 7 receptor α chain (IL-7Ra) are associated with multiple sclerosis risk and disability progression in Central European Slovak population. J Neuroimmunol 2015; 282:80-4. [DOI: 10.1016/j.jneuroim.2015.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Revised: 02/09/2015] [Accepted: 03/09/2015] [Indexed: 01/14/2023]
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14
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Lassmann H. Multiple sclerosis: Lessons from molecular neuropathology. Exp Neurol 2014; 262 Pt A:2-7. [DOI: 10.1016/j.expneurol.2013.12.003] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 11/27/2013] [Accepted: 12/04/2013] [Indexed: 12/17/2022]
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15
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Byström S, Ayoglu B, Häggmark A, Mitsios N, Hong MG, Drobin K, Forsström B, Fredolini C, Khademi M, Amor S, Uhlén M, Olsson T, Mulder J, Nilsson P, Schwenk JM. Affinity proteomic profiling of plasma, cerebrospinal fluid, and brain tissue within multiple sclerosis. J Proteome Res 2014; 13:4607-19. [PMID: 25231264 DOI: 10.1021/pr500609e] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The brain is a vital organ and because it is well shielded from the outside environment, possibilities for noninvasive analysis are often limited. Instead, fluids taken from the spinal cord or circulatory system are preferred sources for the discovery of candidate markers within neurological diseases. In the context of multiple sclerosis (MS), we applied an affinity proteomic strategy and screened 22 plasma samples with 4595 antibodies (3450 genes) on bead arrays, then defined 375 antibodies (334 genes) for targeted analysis in a set of 172 samples and finally used 101 antibodies (43 genes) on 443 plasma as well as 573 cerebrospinal spinal fluid (CSF) samples. This revealed alteration of protein profiles in relation to MS subtypes for IRF8, IL7, METTL14, SLC30A7, and GAP43. Respective antibodies were subsequently used for immunofluorescence on human post-mortem brain tissue with MS pathology for expression and association analysis. There, antibodies for IRF8, IL7, and METTL14 stained neurons in proximity of lesions, which highlighted these candidate protein targets for further studies within MS and brain tissue. The affinity proteomic translation of profiles discovered by profiling human body fluids and tissue provides a powerful strategy to suggest additional candidates to studies of neurological disorders.
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Affiliation(s)
- Sanna Byström
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology , Stockholm 171 21, Sweden
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16
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Affiliation(s)
- Sergio E Baranzini
- Department of Neurology, University of California San Francisco (UCSF), San Francisco, USA
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17
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Unraveling natalizumab effects on deregulated miR-17 expression in CD4+ T cells of patients with relapsing-remitting multiple sclerosis. J Immunol Res 2014; 2014:897249. [PMID: 24901013 PMCID: PMC4036714 DOI: 10.1155/2014/897249] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/28/2014] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs (miRNAs) are a family of noncoding RNAs that play critical roles in the posttranscriptional regulation of gene expression. Accumulating evidence supports their involvement in the pathogenesis of multiple sclerosis (MS). Here, we compare miR-17 expressions in CD4+ T cells from relapsing-remitting (RR) MS patients treated with natalizumab versus untreated patients. miR-17 was downregulated under natalizumab treatment and upregulated during relapse, therefore supporting a possible role of miR-17 in MS immunopathogenesis. Downregulation of miR-17 was associated with upregulation of PTEN, BIM, E2F1, and p21 target genes. In vitro miR-17 inhibition was associated with upregulation of the same targets and resulted in impaired CD4+ T cell activation and proliferation. We further describe deregulated TGFBR2 expression in untreated patients versus healthy volunteers (HVs) and confirm in vitro the link between miR-17 and TGFBR2 expressions. These findings support an effect of natalizumab on expression of specific miRNA and subsequent expression of genes involved in proliferation and control of the cell cycle.
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18
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Lindberg RLP, Kappos L. Transcriptional profiling of multiple sclerosis: towards improved diagnosis and treatment. Expert Rev Mol Diagn 2014; 6:843-55. [PMID: 17140371 DOI: 10.1586/14737159.6.6.843] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The development of high-throughput techniques, for example cDNA and oligonucleotide microarrays, for simultaneous analysis of the transcriptional expression of thousands of genes, even the entire genome, has provided new possibilities to get better insights into the pathogenesis of various diseases. This technology has also been applied to define biomarkers and, most importantly, possible new candidate targets for novel treatments. In multiple sclerosis, microarray studies have been performed on brain autopsy and biopsy specimens and peripheral blood. The effects of current treatments for multiple sclerosis, especially interferon-beta and glatiramer acetate, on transcriptional profiles, have also been investigated. We review the main findings revealed from these studies. The emerging potential of microarray technology to define gene signatures, diagnostic and prognostic markers for disease course, and treatment response in multiple sclerosis will be discussed.
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Affiliation(s)
- Raija L P Lindberg
- Outpatient Clinic Neurology-Neurosurgery and Department of Research, Pharmazentrum University Hospital Basel, Petersgraben 4, 4031 Basel, Switzerland.
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19
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Ratzer R, Søndergaard HB, Christensen JR, Börnsen L, Borup R, Sørensen PS, Sellebjerg F. Gene expression analysis of relapsing-remitting, primary progressive and secondary progressive multiple sclerosis. Mult Scler 2013; 19:1841-8. [PMID: 24085340 DOI: 10.1177/1352458513500553] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Previous studies of multiple sclerosis (MS) have indicated differences in the pathogenesis in relapsing-remitting (RRMS), secondary progressive (SPMS) and primary progressive (PPMS) disease. OBJECTIVE We hypothesized that different MS subtypes would show differences in gene expression that could be traced to specific subsets of peripheral blood mononuclear cells (PBMCs). METHODS Gene expression in RRMS, SPMS, PPMS and healthy control (HC) PBMCs was analyzed on Affymetrix arrays. In addition, we studied gene expression in pools of purified PBMC subsets. RESULTS We found 380 genes that were differentially expressed in RRMS, PPMS, SPMS and HCs (false discovery rate < 5%). There were no major differences between the subtypes of MS. The genes showing most prominent expression changes in RRMS were associated with adaptive immune pathways, while genes in PPMS were associated with innate immune system pathways. SPMS patients shared pathways with RRMS and PPMS patients. Gene expression changes were most prominent in B cells, CD8+ T cells and monocytes. CONCLUSION Differences in gene expression, which could be traced to B cells, CD8+ T cells and monocytes, were found between MS patients and HCs but only minor differences were observed between MS subgroups.
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Affiliation(s)
- R Ratzer
- Danish Multiple Sclerosis Center, Denmark
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20
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Nickles D, Chen HP, Li MM, Khankhanian P, Madireddy L, Caillier SJ, Santaniello A, Cree BAC, Pelletier D, Hauser SL, Oksenberg JR, Baranzini SE. Blood RNA profiling in a large cohort of multiple sclerosis patients and healthy controls. Hum Mol Genet 2013; 22:4194-205. [PMID: 23748426 DOI: 10.1093/hmg/ddt267] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Multiple sclerosis (MS) is the most common autoimmune disease of the central nervous system (CNS). It is characterized by the infiltration of autoreactive immune cells into the CNS, which target the myelin sheath, leading to the loss of neuronal function. Although it is accepted that MS is a multifactorial disorder with both genetic and environmental factors influencing its development and course, the molecular pathogenesis of MS has not yet been fully elucidated. Here, we studied the longitudinal gene expression profiles of whole-blood RNA from a cohort of 195 MS patients and 66 healthy controls. We analyzed these transcriptomes at both the individual transcript and the biological pathway level. We found 62 transcripts to be significantly up-regulated in MS patients; the expression of 11 of these genes was counter-regulated by interferon treatment, suggesting partial restoration of a 'healthy' gene expression profile. Global pathway analyses linked the proteasome and Wnt signaling to MS disease processes. Since genotypes from a subset of individuals were available, we were able to identify expression quantitative trait loci (eQTL), a number of which involved two genes of the MS gene signature. However, all these eQTL were also present in healthy controls. This study highlights the challenge posed by analyzing transcripts from whole blood and how these can be mitigated by using large, well-characterized cohorts of patients with longitudinal follow-up and multi-modality measurements.
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21
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Ashbaugh JJ, Brambilla R, Karmally SA, Cabello C, Malek TR, Bethea JR. IL7Rα contributes to experimental autoimmune encephalomyelitis through altered T cell responses and nonhematopoietic cell lineages. THE JOURNAL OF IMMUNOLOGY 2013; 190:4525-34. [PMID: 23530149 DOI: 10.4049/jimmunol.1203214] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A mutation in the IL7Rα locus has been identified as a risk factor for multiple sclerosis (MS), a neurodegenerative autoimmune disease characterized by inflammation, demyelination, and axonal damage. IL7Rα has well documented roles in lymphocyte development and homeostasis, but its involvement in disease is largely understudied. In this study, we use the experimental autoimmune encephalomyelitis (EAE) model of MS to show that a less severe form of the disease results when IL7Rα expression is largely restricted to thymic tissue in IL7RTg(IL7R-/-) mice. Compared with wild-type (WT) mice, IL7RTg(IL7R-/-) mice exhibited reduced paralysis and myelin damage that correlated with dampened effector responses, namely decreased TNF production. Furthermore, treatment of diseased WT mice with neutralizing anti-IL7Rα Ab also resulted in significant improvement of EAE. In addition, chimeric mice were generated by bone marrow transplant to limit expression of IL7Rα to cells of either hematopoietic or nonhematopoietic origin. Mice lacking IL7Rα only on hematopoietic cells develop severe EAE, suggesting that IL7Rα expression in the nonhematopoietic compartment contributes to disease. Moreover, novel IL7Rα expression was identified on astrocytes and oligodendrocytes endogenous to the CNS. Chimeric mice that lack IL7Rα only on nonhematopoietic cells also develop severe EAE, which further supports the role of IL7Rα in T cell effector function. Conversely, mice that lack IL7Rα throughout both compartments are dramatically protected from disease. Taken together, these data indicate that multiple cell types use IL7Rα signaling in the development of EAE, and inhibition of this pathway should be considered as a new therapeutic avenue for MS.
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Affiliation(s)
- Jessica J Ashbaugh
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
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22
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Sánchez-Pla A, Reverter F, Ruíz de Villa MC, Comabella M. Transcriptomics: mRNA and alternative splicing. J Neuroimmunol 2012; 248:23-31. [PMID: 22626445 DOI: 10.1016/j.jneuroim.2012.04.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 04/14/2012] [Accepted: 04/18/2012] [Indexed: 11/27/2022]
Abstract
Transcriptomics has emerged as a powerful approach for biomarker discovery. In the present review, the two main types of high throughput transcriptomic technologies - microarrays and next generation sequencing - that can be used to identify candidate biomarkers are briefly described. Microarrays, the mainstream technology of the last decade, have provided hundreds of valuable datasets in a wide variety of diseases including multiple sclerosis (MS), in which this approach has been used to disentangle different aspects of its complex pathogenesis. RNA-seq, the current next generation sequencing approach, is expected to provide similar power as microarrays but extending their capabilities to aspects up to now more difficult to analyse such as alternative splicing and discovery of novel transcripts.
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23
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Menon R, Di Dario M, Cordiglieri C, Musio S, La Mantia L, Milanese C, Di Stefano AL, Crabbio M, Franciotta D, Bergamaschi R, Pedotti R, Medico E, Farina C. Gender-based blood transcriptomes and interactomes in multiple sclerosis: Involvement of SP1 dependent gene transcription. J Autoimmun 2012; 38:J144-55. [DOI: 10.1016/j.jaut.2011.11.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/11/2011] [Accepted: 11/12/2011] [Indexed: 12/22/2022]
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24
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Dutta R, Trapp BD. Gene expression profiling in multiple sclerosis brain. Neurobiol Dis 2012; 45:108-14. [PMID: 21147224 PMCID: PMC3066282 DOI: 10.1016/j.nbd.2010.12.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 11/29/2010] [Accepted: 12/02/2010] [Indexed: 12/20/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system and the leading cause of non-traumatic neurological disability in young adults in the United States and Europe. The clinical disease course is variable and starts with reversible episodes of neurological disability in the third or fourth decade of life. Microarray-based comparative gene profiling provides a snapshot of genes underlying a particular condition. Several large scale microarray studies have been conducted using brain tissue from MS patients. In this review, we summarize existing data from different gene expression profiling studies and how they relate to understand the pathogenesis of MS.
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Affiliation(s)
- Ranjan Dutta
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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25
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Møller HJ. Soluble CD163. Scandinavian Journal of Clinical and Laboratory Investigation 2011; 72:1-13. [DOI: 10.3109/00365513.2011.626868] [Citation(s) in RCA: 258] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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26
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MicroRNA and mRNA expression profile screening in multiple sclerosis patients to unravel novel pathogenic steps and identify potential biomarkers. Neurosci Lett 2011; 508:4-8. [PMID: 22108567 DOI: 10.1016/j.neulet.2011.11.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 10/18/2011] [Accepted: 11/02/2011] [Indexed: 12/17/2022]
Abstract
Identification of novel targets and biomarkers, such as microRNAs, is extremely helpful to understand the pathogenetic mechanisms in a disease like multiple sclerosis (MS). We tested the expression profile of 1145 microRNAs in peripheral blood mononuclear cells (PBMCs) of 19 MS patients and 14 controls, and we further explored their function by performing a whole-genome mRNA profiling in same subjects and using bioinformatic prediction tool. A total of 104 miRNAs have been identified as deregulated in MS patients; 2/10 which ranked highest (let-7g and miR-150) have been validated in a replication sample, leading to the identification of putative target genes.
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27
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Kemppinen AK, Kaprio J, Palotie A, Saarela J. Systematic review of genome-wide expression studies in multiple sclerosis. BMJ Open 2011; 1:e000053. [PMID: 22021740 PMCID: PMC3191406 DOI: 10.1136/bmjopen-2011-000053] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Although recent genome-wide association studies have identified several genetic variants contributing to the complex aetiology of multiple sclerosis (MS), expression and functional studies are required to further understand its molecular basis. Objectives To identify genes and pathways with differential expression in MS. Design The authors conducted a systematic review of seven microarray studies, in which expression in immune cells was compared between MS patients and controls. These studies include a previously unpublished study, which is described here in detail. Results and conclusion Although in general the overlap between studies was poor, 229 genes were found to be differentially expressed in MS in at least two studies, of which 11 were in three studies and HSPA1A in four studies. After excluding the authors' unpublished experiment which may have been affected by certain confounding factors and inclusion of treated subjects, 135 genes were identified in at least two studies. The differentially expressed genes were significantly associated with several immunological pathways, including interleukin (IL)-4, IL-6, IL-17 and glucocorticoid receptor signalling pathways. 15 of the 229 loci have shown some association with MS in published genome-wide association studies (p<0.0001), including three loci with confirmed MS risk variants.
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Affiliation(s)
- A K Kemppinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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28
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Tajouri L, Fernandez F, Griffiths LR. Gene expression studies in multiple sclerosis. Curr Genomics 2011; 8:181-9. [PMID: 18645602 DOI: 10.2174/138920207780833829] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 02/14/2007] [Accepted: 03/14/2007] [Indexed: 11/22/2022] Open
Abstract
Multiple sclerosis (MS) is a serious neurological disorder affecting young Caucasian individuals, usually with an age of onset at 18 to 40 years old. Females account for approximately 60x of MS cases and the manifestation and course of the disease is highly variable from patient to patient. The disorder is characterised by the development of plaques within the central nervous system (CNS). Many gene expression studies have been undertaken to look at the specific patterns of gene transcript levels in MS. Human tissues and experimental mice were used in these gene-profiling studies and a very valuable and interesting set of data has resulted from these various expression studies. In general, genes showing variable expression include mainly immunological and inflammatory genes, stress and antioxidant genes, as well as metabolic and central nervous system markers. Of particular interest are a number of genes localised to susceptible loci previously shown to be in linkage with MS. However due to the clinical complexity of the disease, the heterogeneity of the tissues used in expression studies, as well as the variable DNA chips/membranes used for the gene profiling, it is difficult to interpret the available information. Although this information is essential for the understanding of the pathogenesis of MS, it is difficult to decipher and define the gene pathways involved in the disorder. Experiments in gene expression profiling in MS have been numerous and lists of candidates are now available for analysis. Researchers have investigated gene expression in peripheral mononuclear white blood cells (PBMCs), in MS animal models Experimental Allergic Encephalomyelitis (EAE) and post mortem MS brain tissues. This review will focus on the results of these studies.
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Affiliation(s)
- Lotti Tajouri
- Genomics Research Centre, School of Medical Science, Griffith University Gold Coast, Southport, Queensland, 4215 Australia
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Luo Y, Robinson S, Fujita J, Siconolfi L, Magidson J, Edwards CK, Wassmann K, Storm K, Norris DA, Bankaitis-Davis D, Robinson WA, Fujita M. Transcriptome profiling of whole blood cells identifies PLEK2 and C1QB in human melanoma. PLoS One 2011; 6:e20971. [PMID: 21698244 PMCID: PMC3115966 DOI: 10.1371/journal.pone.0020971] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 05/16/2011] [Indexed: 02/07/2023] Open
Abstract
Background Developing analytical methodologies to identify biomarkers in easily accessible body fluids is highly valuable for the early diagnosis and management of cancer patients. Peripheral whole blood is a “nucleic acid-rich” and “inflammatory cell-rich” information reservoir and represents systemic processes altered by the presence of cancer cells. Methodology/Principal Findings We conducted transcriptome profiling of whole blood cells from melanoma patients. To overcome challenges associated with blood-based transcriptome analysis, we used a PAXgene™ tube and NuGEN Ovation™ globin reduction system. The combined use of these systems in microarray resulted in the identification of 78 unique genes differentially expressed in the blood of melanoma patients. Of these, 68 genes were further analyzed by quantitative reverse transcriptase PCR using blood samples from 45 newly diagnosed melanoma patients (stage I to IV) and 50 healthy control individuals. Thirty-nine genes were verified to be differentially expressed in blood samples from melanoma patients. A stepwise logit analysis selected eighteen 2-gene signatures that distinguish melanoma from healthy controls. Of these, a 2-gene signature consisting of PLEK2 and C1QB led to the best result that correctly classified 93.3% melanoma patients and 90% healthy controls. Both genes were upregulated in blood samples of melanoma patients from all stages. Further analysis using blood fractionation showed that CD45− and CD45+ populations were responsible for the altered expression levels of PLEK2 and C1QB, respectively. Conclusions/Significance The current study provides the first analysis of whole blood-based transcriptome biomarkers for malignant melanoma. The expression of PLEK2, the strongest gene to classify melanoma patients, in CD45− subsets illustrates the importance of analyzing whole blood cells for biomarker studies. The study suggests that transcriptome profiling of blood cells could be used for both early detection of melanoma and monitoring of patients for residual disease.
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Affiliation(s)
- Yuchun Luo
- Department of Dermatology, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Steven Robinson
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Junichi Fujita
- Department of Dermatology, University of Colorado Denver, Aurora, Colorado, United States of America
| | | | - Jay Magidson
- Statistical Innovations, Belmont, Massachusetts, United States of America
| | - Carl K. Edwards
- Department of Dermatology, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Karl Wassmann
- Source MDx, Boulder, Colorado, United States of America
| | | | - David A. Norris
- Department of Dermatology, University of Colorado Denver, Aurora, Colorado, United States of America
| | | | - William A. Robinson
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Mayumi Fujita
- Department of Dermatology, University of Colorado Denver, Aurora, Colorado, United States of America
- * E-mail:
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Chamberlain CS, Brounts SH, Sterken DG, Rolnick KI, Baer GS, Vanderby R. Gene profiling of the rat medial collateral ligament during early healing using microarray analysis. J Appl Physiol (1985) 2011; 111:552-65. [PMID: 21596919 DOI: 10.1152/japplphysiol.00073.2011] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Ligament heals in a synchronized and complex series of events. The remodeling process may last months or years. Experimental evidence suggests the damaged ligament does not recover its normal functional properties. Specific mechanisms to prevent scar formation and to regenerate the original mechanical function remain elusive but likely involve regulation of creeping substitution. Creeping substitution creates a larger hypercellular, hypervascular, and disorganized granulation tissue mass that results in an inefficient and nonregenerative wound healing process for the ligament. Control of creeping substitution may limit the extent of this tissue compromise and reduce the time necessary for healing. The objective of this study is to better understand the mechanism behind scar formation by identifying the extracellular matrix factors and other unique genes of interest differentially expressed during rat ligament healing via microarray. For this study, rat medial collateral ligaments were either surgically transected or left intact. Ligaments were collected at day 3 or 7 postinjury and used for microarray, quantitative PCR, and/or immunohistochemistry. Results were compared with the normal intact ligament. We demonstrate that early ligament healing is characterized by the modulation of several inflammatory and extracellular matrix factors during the first week of injury. Specifically, a number of matrix metalloproteinases and collagens are differentially and significantly expressed during early ligament healing. Additionally, we demonstrate the modulation of three novel genes, periostin, collagen-triple helix repeat containing-1, and serine protease 35 in our ligament healing model. Together, control of granulation tissue creeping substitution and subsequent downstream scar formation is likely to involve these factors.
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Affiliation(s)
- Connie S Chamberlain
- Department of Orthopedics and Rehabilitation, University of Wisconsin, Madison, WI 53705, USA
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The experimental autoimmune encephalomyelitis model for proteomic biomarker studies: from rat to human. Clin Chim Acta 2011; 412:812-22. [PMID: 21333641 DOI: 10.1016/j.cca.2011.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 02/01/2011] [Accepted: 02/01/2011] [Indexed: 01/13/2023]
Abstract
Multiple sclerosis (MScl) is defined by central nervous system (CNS) inflammation, demyelination and axonal damage. Some of the disease mechanisms are known but the cause of this complex disorder stays an enigma. Experimental autoimmune encephalomyelitis (EAE) is an animal model mimicking many aspects of MScl. This review aims to provide an overview over proteomic biomarker studies in the EAE model emphasizing the translational aspects with respect to MScl in humans.
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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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Lindsey JW, Agarwal SK, Tan FK. Gene expression changes in multiple sclerosis relapse suggest activation of T and non-T cells. Mol Med 2010; 17:95-102. [PMID: 20882258 DOI: 10.2119/molmed.2010.00071] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 09/16/2010] [Indexed: 11/06/2022] Open
Abstract
A defining feature of multiple sclerosis (MS) is the occurrence of clinical relapses separated by periods of clinical stability. Better understanding of the events underlying clinical relapse might suggest new approaches to treatment. The objective of this study was to measure changes in the expression of RNA in the blood during relapse. We used microarrays to measure mRNA expression in paired samples from 14 MS patients during clinical relapse and while stable. Seventy-one transcripts changed expression at the P < 0.001 significance level. The most notable finding was decreased expression of transcripts with regulatory function, expressed primarily in non-T cells. These decreased transcripts included the interleukin-1 receptor antagonist, which had a corresponding decrease in the protein concentration in serum. Transcripts with increased expression were expressed primarily in T cells. Pathways analysis suggested involvement of the cytokine network, coagulation and complement cascades, IL-10 signaling and NF-κB signaling. We conclude that there are alterations of mRNA expression in both T cells and non-T cells during MS relapse.
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Affiliation(s)
- J William Lindsey
- Department of Neurology, University of Texas Health Science Center, Houston, TX, USA.
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Mechelli R, Annibali V, Ristori G, Vittori D, Coarelli G, Salvetti M. Multiple sclerosis etiology: beyond genes and environment. Expert Rev Clin Immunol 2010; 6:481-90. [PMID: 20441432 DOI: 10.1586/eci.10.11] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Multiple sclerosis (MS) is a disorder of the CNS with inflammatory and neurodegenerative components. The etiology is unknown, but there is evidence for a role of both genetic and environmental factors. Among the heritable factors, MHC class II genes are strongly involved, as well as genes coding for others molecules of immunological relevance, genes controlling neurobiological pathways and genes of unknown function. Among nonheritable factors, many infectious agents (mainly viruses) and environmental factors (e.g., smoke, sun exposition and diet) seem to be of etiologic importance. Here, we report and discuss recent findings in MS on largely unexplored fields: the alternative splicing of mRNAs and regulatory noncoding RNAs, the major sources of transcriptome diversity; and epigenetic changes with special attention paid to DNA methylation and histone acetylation, the main regulators of gene expression.
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Affiliation(s)
- Rosella Mechelli
- Neurology and Center for Experimental Neurological Therapies, S. Andrea Hospital, Sapienza University of Rome, Via di Grottarossa 1035, 00189 Rome, Italy
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Genomics in multiple sclerosis. Clin Neurol Neurosurg 2010; 112:621-4. [PMID: 20471158 DOI: 10.1016/j.clineuro.2010.03.028] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 03/23/2010] [Accepted: 03/29/2010] [Indexed: 11/22/2022]
Abstract
Multiple sclerosis (MS) is chronic, inflammatory disease of the central nervous system that mainly affects young adults and is characterized with dissemination of demyelinating lesions in time and space. It is well known that MS is very heterogeneous disease, so biomarkers that would reliably determine disease course, outcome or treatment response in early stages of the disease (preferentially clinically isolated syndrome) are desperately needed. Genome-wide expression analysis represents the profile of all genes in a certain tissue or cell population in a certain time point. Therefore, as the sequence of the human genome is entirely known, it is possible to analyze any given human gene in any given context. This review will discuss results and possible applications of genome-wide expression studies in brain tissue and blood samples of MS patients.
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Otaegui D, Baranzini SE, Armañanzas R, Calvo B, Muñoz-Culla M, Khankhanian P, Inza I, Lozano JA, Castillo-Triviño T, Asensio A, Olaskoaga J, López de Munain A. Differential micro RNA expression in PBMC from multiple sclerosis patients. PLoS One 2009; 4:e6309. [PMID: 19617918 PMCID: PMC2708922 DOI: 10.1371/journal.pone.0006309] [Citation(s) in RCA: 182] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 06/19/2009] [Indexed: 12/15/2022] Open
Abstract
Differences in gene expression patterns have been documented not only in Multiple Sclerosis patients versus healthy controls but also in the relapse of the disease. Recently a new gene expression modulator has been identified: the microRNA or miRNA. The aim of this work is to analyze the possible role of miRNAs in multiple sclerosis, focusing on the relapse stage. We have analyzed the expression patterns of 364 miRNAs in PBMC obtained from multiple sclerosis patients in relapse status, in remission status and healthy controls. The expression patterns of the miRNAs with significantly different expression were validated in an independent set of samples. In order to determine the effect of the miRNAs, the expression of some predicted target genes of these were studied by qPCR. Gene interaction networks were constructed in order to obtain a co-expression and multivariate view of the experimental data. The data analysis and later validation reveal that two miRNAs (hsa-miR-18b and hsa-miR-599) may be relevant at the time of relapse and that another miRNA (hsa-miR-96) may be involved in remission. The genes targeted by hsa-miR-96 are involved in immunological pathways as Interleukin signaling and in other pathways as wnt signaling. This work highlights the importance of miRNA expression in the molecular mechanisms implicated in the disease. Moreover, the proposed involvement of these small molecules in multiple sclerosis opens up a new therapeutic approach to explore and highlight some candidate biomarker targets in MS.
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Affiliation(s)
- David Otaegui
- Multiple Sclerosis Unit, Biodonostia Institute, San Sebastián, Spain.
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Bernal F, Elias B, Hartung HP, Kieseier BC. Regulation of matrix metalloproteinases and their inhibitors by interferon-beta: a longitudinal study in multiple sclerosis patients. Mult Scler 2009; 15:721-7. [PMID: 19383643 DOI: 10.1177/1352458509102920] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Matrix metalloproteinases (MMPs) represent a large family of proteolytic enzymes, with some members being implicated in the immunopathogenesis of multiple sclerosis (MS). Interferon (IFN)-beta is one of the current mainstays in MS therapy and known to downregulate the expression of MMP-9. However, only sparse information is available on the effects of IFN-beta on the other 20 members of the MMP family. METHODS This is a longitudinal analysis on the RNA expression pattern of all known MMPs and their endogenous inhibitors before and after 1 and 6 months of IFN-beta therapy. RNA expression levels were assessed in peripheral venous blood cells from 14 MS patients and 8 matched controls by real time-PCR. RESULTS RNA expression levels before treatment differed in part in MS patients compared to healthy controls (MMP-9, MMP-14, MMP-19, TIMP-1, TIMP-2). Some of the MMPs responded to therapy specifically (MMP-8, MMP-9, MMP-19), whereas others remained unchanged over time. CONCLUSIONS These data suggest that MMPs may differ in their expression levels in MS patients and that this group of enzymes is differentially regulated during the treatment with IFN-beta in MS for at least 6 months.
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Affiliation(s)
- F Bernal
- Department of Neurology, Research Group for Clinical and Experimental Neuroimmunology, Heinrich-Heine-University, Düsseldorf, Germany
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40
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Thessen Hedreul M, Gillett A, Olsson T, Jagodic M, Harris RA. Characterization of Multiple Sclerosis candidate gene expression kinetics in rat experimental autoimmune encephalomyelitis. J Neuroimmunol 2009; 210:30-9. [PMID: 19269041 DOI: 10.1016/j.jneuroim.2009.02.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2009] [Revised: 02/20/2009] [Accepted: 02/20/2009] [Indexed: 01/05/2023]
Abstract
The immunological mechanisms underlying autoimmunity are being elucidated through genetic and functional analyses in both humans and rodent models. However, acceptance of models as valid equivalents of human disease is variable, and the validation of defined human candidate molecules in experimental models is hitherto limited. We thus aimed to determine the kinetic expression of several Multiple Sclerosis (MS) candidate genes in the myelin oligodendrocyte glycoprotein (MOG)-induced rat experimental autoimmune encephalomyelitis (EAE) model using susceptible DA and resistant PVG inbred strains. Increased expression of MS candidate genes IL2RA and IL7RA associated with disease susceptibility. Higher expression of these candidate genes and IL18R1 in susceptible rats may lead to enhancement of the disease-driving T(H)1 and T(H)17 pathways. Susceptible DA rats had augmented marker molecules of these pathways and upon restimulation with autoantigen produced increased effector molecules including IFN-gamma, IL-17F and IL-22. The altered T helper cell differentiation pathways led to differences in a MOG-specific proliferative and autoantibody response, which ultimately results in infiltration in the central nervous system and EAE induction. Our results validate the MOG-induced EAE model as having similar mechanisms to human MS and determined the kinetics of several disease mechanisms in relevant tissues.
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Affiliation(s)
- Melanie Thessen Hedreul
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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Noorbakhsh F, Overall CM, Power C. Deciphering complex mechanisms in neurodegenerative diseases: the advent of systems biology. Trends Neurosci 2009; 32:88-100. [DOI: 10.1016/j.tins.2008.10.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 10/08/2008] [Accepted: 10/08/2008] [Indexed: 11/28/2022]
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Vergara D, Chiriacò F, Acierno R, Maffia M. Proteomic map of peripheral blood mononuclear cells. Proteomics 2008; 8:2045-51. [PMID: 18491318 DOI: 10.1002/pmic.200700726] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the field of proteomics extensive efforts have been focused on the knowledge of proteins expressed by different cell types. In particular, enormous progress has been done in the characterization of blood cellular components. In this work, we have established a public 2-DE database for human peripheral blood mononuclear cells (PBMCs) proteins. Two hundred and forty-six spots corresponding to 174 different proteins have been identified on 2-DE gels from PBMCs isolated from six healthy individuals. All the identified proteins have been classified in thirteen categories on the basis of their differential functions or cellular localization and annotated at the http://physiology.unile.it/proteomics. The role of several proteins has been discussed in relation to their biological function. We intend to show the potentiality of PBMCs to investigate the proteomics changes possibly associated with a large number of pathologies such as autoimmune, neurodegenerative and cancer diseases.
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Affiliation(s)
- Daniele Vergara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
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Oksenberg JR, Baranzini SE, Sawcer S, Hauser SL. The genetics of multiple sclerosis: SNPs to pathways to pathogenesis. Nat Rev Genet 2008; 9:516-26. [PMID: 18542080 DOI: 10.1038/nrg2395] [Citation(s) in RCA: 257] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Multiple sclerosis (MS) is an autoimmune demyelinating disease and a common cause of neurological disability in young adults. The modest heritability of MS reflects complex genetic effects and multifaceted gene-environment interactions. The human leukocyte antigen (HLA) region is the strongest susceptibility locus for MS, but a genome-wide association study recently identified new susceptibility genes. Progress in high-throughput genotyping and sequencing technologies and a better understanding of the structural organization of the human genome, together with powerful brain-imaging techniques that refine the phenotype, suggest that the tools could finally exist to identify the full set of genes influencing the pathogenesis of MS.
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Affiliation(s)
- Jorge R Oksenberg
- Department of Neurology, School of Medicine, University of California at San Francisco, 513 Parnassus Avenue, San Francisco, California 94143-0435, USA.
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Beck IM, Rückert R, Brandt K, Mueller MS, Sadowski T, Brauer R, Schirmacher P, Mentlein R, Sedlacek R. MMP19 is essential for T cell development and T cell-mediated cutaneous immune responses. PLoS One 2008; 3:e2343. [PMID: 18523579 PMCID: PMC2386969 DOI: 10.1371/journal.pone.0002343] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Accepted: 04/23/2008] [Indexed: 12/11/2022] Open
Abstract
Matrix metalloproteinase-19 (MMP19) affects cell proliferation, adhesion, and migration in vitro but its physiological role in vivo is poorly understood. To determine the function of MMP19, we generated mice deficient for MMP19 by disrupting the catalytic domain of mmp19 gene. Although MMP19-deficient mice do not show overt developmental and morphological abnormalities they display a distinct physiological phenotype. In a model of contact hypersensitivity (CHS) MMP19-deficient mice showed impaired T cell-mediated immune reaction that was characterized by limited influx of inflammatory cells, low proliferation of keratinocytes, and reduced number of activated CD8(+) T cells in draining lymph nodes. In the inflamed tissue, the low number of CD8(+) T cells in MMP19-deficient mice correlated with low amounts of proinflammatory cytokines, especially lymphotactin and interferon-inducible T cell alpha chemoattractant (I-TAC). Further analyses showed that T cell populations in the blood of immature, unsensitized mice were diminished and that this alteration originated from an altered maturation of thymocytes. In the thymus, thymocytes exhibited low proliferation rates and the number of CD4(+)CD8(+) double-positive cells was remarkably augmented. Based on the phenotype of MMP19-deficient mice we propose that MMP19 is an important factor in cutaneous immune responses and influences the development of T cells.
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Affiliation(s)
- Inken M. Beck
- Institute of Biotechnology, Prague, Czech Republic
- Institute of Molecular Genetics, Prague, Czech Republic
| | - René Rückert
- Research Center Borstel, Department of Immunology and Cell Biology, Borstel, Germany
| | - Katja Brandt
- Research Center Borstel, Department of Immunology and Cell Biology, Borstel, Germany
| | | | | | - Rena Brauer
- Department of Biochemistry, University of Kiel, Kiel, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Rolf Mentlein
- Department of Anatomy, University of Kiel, Kiel, Germany
| | - Radislav Sedlacek
- Institute of Molecular Genetics, Prague, Czech Republic
- Department of Biochemistry, University of Kiel, Kiel, Germany
- * E-mail:
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Arthur AT, Armati PJ, Bye C, Heard RNS, Stewart GJ, Pollard JD, Booth DR. Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission. BMC MEDICAL GENETICS 2008; 9:17. [PMID: 18366677 PMCID: PMC2324081 DOI: 10.1186/1471-2350-9-17] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Accepted: 03/19/2008] [Indexed: 11/30/2022]
Abstract
Background Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system (CNS). Although the pathogenesis of MS remains unknown, it is widely regarded as an autoimmune disease mediated by T-lymphocytes directed against myelin proteins and/or other oligodendrocyte epitopes. Methods In this study we investigated the gene expression profiles of peripheral blood cells from patients with RRMS during the relapse and the remission phases utilizing gene microarray technology. Dysregulated genes encoded in regions associated with MS susceptibility from genomic screens or previous trancriptomic studies were identified. The proximal promoter region polymorphisms of two genes were tested for association with disease and expression level. Results Distinct sets of dysregulated genes during the relapse and remission phases were identified including genes involved in apoptosis and inflammation. Three of these dysregulated genes have been previously implicated with MS susceptibility in genomic screens: TGFβ1, CD58 and DBC1. TGFβ1 has one common SNP in the proximal promoter: -508 T>C (rs1800469). Genotyping two Australian trio sets (total 620 families) found a trend for over-transmission of the T allele in MS in females (p < 0.13). Upregulation of CD58 and DBC1 in remission is consistent with their putative roles in promoting regulatory T cells and reducing cell proliferation, respectively. A fourth gene, ALOX5, is consistently found over-expressed in MS. Two common genetic variants were confirmed in the ALOX5 putatve promoter: -557 T>C (rs12762303) and a 6 bp tandem repeat polymorphism (GGGCGG) between position -147 and -176; but no evidence for transmission distortion found. Conclusion The dysregulation of these genes tags their metabolic pathways for further investigation for potential therapeutic intervention.
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Affiliation(s)
- Ariel T Arthur
- Department of Medicine and the Nerve Research Foundation, the University of Sydney, Sydney, Australia.
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Abstract
Multiple sclerosis (MS) clusters with the so-called complex genetic diseases, a group of common disorders characterized by modest disease risk heritability and multifaceted gene-environment interactions. The major histocompatibility complex (MHC) is the only genomic region consistently associated with MS, and susceptible MHC haplotypes have been identified. Although the MHC does not account for all genetic contribution to MS, the other genetic contributors have been elusive. Microarray gene-expression studies, which also have not identified a major MS locus, have, however, been promising in elucidating some of the possible pathways involved in the disease. Yet, microarray studies thus far have been unable to separate the genetic causes of MS from the expression consequences of MS. The use of new methodologies and technologies to refine the phenotype, such as brain spectroscopy, PET and functional magnetic resonance imaging combined with novel computational tools and a better understanding of the human genome architecture, may help resolve the genetic causes of MS.
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Affiliation(s)
- J P McElroy
- Department of Neurology, School of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
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Domenici E, Muglia P. The search for peripheral disease markers in psychiatry by genomic and proteomic approaches. ACTA ACUST UNITED AC 2007; 1:235-51. [DOI: 10.1517/17530059.1.2.235] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Gregory SG, Schmidt S, Seth P, Oksenberg JR, Hart J, Prokop A, Caillier SJ, Ban M, Goris A, Barcellos LF, Lincoln R, McCauley JL, Sawcer SJ, Compston DAS, Dubois B, Hauser SL, Garcia-Blanco MA, Pericak-Vance MA, Haines JL. Interleukin 7 receptor alpha chain (IL7R) shows allelic and functional association with multiple sclerosis. Nat Genet 2007; 39:1083-91. [PMID: 17660817 DOI: 10.1038/ng2103] [Citation(s) in RCA: 462] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 06/18/2007] [Indexed: 01/22/2023]
Abstract
Multiple sclerosis is a demyelinating neurodegenerative disease with a strong genetic component. Previous genetic risk studies have failed to identify consistently linked regions or genes outside of the major histocompatibility complex on chromosome 6p. We describe allelic association of a polymorphism in the gene encoding the interleukin 7 receptor alpha chain (IL7R) as a significant risk factor for multiple sclerosis in four independent family-based or case-control data sets (overall P = 2.9 x 10(-7)). Further, the likely causal SNP, rs6897932, located within the alternatively spliced exon 6 of IL7R, has a functional effect on gene expression. The SNP influences the amount of soluble and membrane-bound isoforms of the protein by putatively disrupting an exonic splicing silencer.
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Affiliation(s)
- Simon G Gregory
- Center for Human Genetics, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
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Comabella M, Martin R. Genomics in multiple sclerosis—Current state and future directions. J Neuroimmunol 2007; 187:1-8. [PMID: 17400297 DOI: 10.1016/j.jneuroim.2007.02.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Revised: 02/21/2007] [Accepted: 02/22/2007] [Indexed: 10/23/2022]
Abstract
Microarray-based gene expression profiling of large numbers of genes or even the whole genome has only recently become possible. Several studies have employed this technology in multiple sclerosis (MS) and its animal model, experimental allergic encephalomyelitis (EAE), and although results are promising, microarray-based genomics research is still viewed with skepticism. It is often negatively perceived as a fishing expedition rather than a discovery-oriented effort that takes into account the immense complexity of diseases such as MS. Besides these conceptual concerns, technical reproducibility and the strategies to analyze and interpret the massive amounts of data present problems that can cause considerable variability between studies. In this review, we summarize existing data from different gene expression profiling studies that have been conducted in MS and EAE, discuss potential problems and propose future directions for the use of microarrays in MS.
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Affiliation(s)
- Manuel Comabella
- Unitat de Neuroimmunologia Clinica, Institut de Recerca, Hospital Universitari Vall d'Hebron, Barcelona, Spain.
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Liu T, Donahue KC, Hu J, Kurnellas MP, Grant JE, Li H, Elkabes S. Identification of differentially expressed proteins in experimental autoimmune encephalomyelitis (EAE) by proteomic analysis of the spinal cord. J Proteome Res 2007; 6:2565-75. [PMID: 17571869 PMCID: PMC2430926 DOI: 10.1021/pr070012k] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The present study used isobaric tags for relative and absolute quantitation (iTRAQ) to identify novel targets in experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis. The expression of 41 proteins was significantly altered in the inflamed spinal cord. Twenty of these are implicated in EAE for the first time and many have previously been shown to play a role in antigen processing, inflammation, neuroprotection, or neurodegeneration.
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Affiliation(s)
- Tong Liu
- Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School Cancer Center, Newark, New Jersey 07103, USA
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