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Zettl UK, Rommer PS, Aktas O, Wagner T, Richter J, Oschmann P, Cepek L, Elias-Hamp B, Gehring K, Chan A, Hecker M. Interferon beta-1a sc at 25 years: a mainstay in the treatment of multiple sclerosis over the period of one generation. Expert Rev Clin Immunol 2023; 19:1343-1359. [PMID: 37694381 DOI: 10.1080/1744666x.2023.2248391] [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: 06/07/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023]
Abstract
INTRODUCTION Interferon beta (IFN beta) preparations are an established group of drugs used for immunomodulation in patients with multiple sclerosis (MS). Subcutaneously (sc) applied interferon beta-1a (IFN beta-1a sc) has been in continuous clinical use for 25 years as a disease-modifying treatment. AREAS COVERED Based on data published since 2018, we discuss recent insights from analyses of the pivotal trial PRISMS and its long-term extension as well as from newer randomized studies with IFN beta-1a sc as the reference treatment, the use of IFN beta-1a sc across the patient life span and as a bridging therapy, recent data regarding the mechanisms of action, and potential benefits of IFN beta-1a sc regarding vaccine responses. EXPERT OPINION IFN beta-1a sc paved the way to effective immunomodulatory treatment of MS, enabled meaningful insights into the disease process, and remains a valid therapeutic option in selected vulnerable MS patient groups.
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Affiliation(s)
- Uwe Klaus Zettl
- Department of Neurology, Rostock University Medical Center, Rostock, Germany
| | - Paulus Stefan Rommer
- Department of Neurology, Rostock University Medical Center, Rostock, Germany
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Orhan Aktas
- Department of Neurology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | | | | | | | | | | | - Andrew Chan
- Department of Neurology, Inselspital Bern, University Hospital Bern, Bern, Switzerland
| | - Michael Hecker
- Department of Neurology, Rostock University Medical Center, Rostock, Germany
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Jazireian P, Sasani ST, Assarzadegan F, Azimian M. TRAILR1 (rs20576) and GRIA3 (rs12557782) are not associated with interferon-β response in multiple sclerosis patients. Mol Biol Rep 2020; 47:9659-9665. [PMID: 33269432 DOI: 10.1007/s11033-020-06026-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/19/2020] [Indexed: 12/15/2022]
Abstract
Multiple sclerosis (MS) is an autoimmune-type inflammatory disorder in human central nervous system. Recombinant interferon beta (IFN-β) decreases the number of relapses and postpones disability progression in MS. However, up to 50% of patients treated with interferon beta continue experiencing relapses and/or worsening disability. Single nucleotide polymorphisms in different genes have been known to show significant associations with response to IFN-β in MS patients. In the present work, we examined the potential role of TRAILR1 and GRIA3 genes polymorphisms on response to IFN-β therapy in Iranian MS patients. The DNA was extracted from blood samples by standard procedures from 73 patients diagnosed with Multiple Sclerosis that were either responded to IFN-β or did not. We carried out RFLP -PCR and tetra-primer ARMS-PCR methods to study of rs20576 and rs12557782, respectively. All results were analyzed using the SPSS software. TRAILR1 rs20576 genotype frequencies in responders and non-responders were similar (χ2 = 0.26, P = 0.87, Fisher, s Exact test). Our results showed that response to IFN-β has not association with sex (p = 0.73). Also, genotypic frequencies of GRIA3 rs12557782 had no significant differences between two groups of female population (χ2 = 3.75, p = 0.15). Furthermore, it had not been any statistical differences between responder and non-responder males (χ2 = 0.7, p = 0.4) related to the SNP. Our results analysis revealed no significant association between the studied SNPs (TRAILR1 rs20576 and GRIA3rs 12,557,782) and response to IFN-β in Iranian MS patients.
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Affiliation(s)
- Parham Jazireian
- Department of Biology, University Campus 2, University of Guilan, Rasht, Iran
| | | | - Farhad Assarzadegan
- Department of Neurology, Imam Hossein Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mojtaba Azimian
- Rofeydeh Rehabilitation Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Abstract
Multiple sclerosis (MS) affects approximately 1 million persons in the United States, and is the leading cause of neurological disability in young adults. The concept of precision medicine is now being applied to MS and has the promise of improved care. MS patients experience a variety of neurological symptoms, and disease severity ranges from mild to severe, and the biological underpinnings of these phenotypes are now starting to be elucidated. Precision medicine involves the classification of disease subtypes based on the underlying biology, rather than clinical phenotypes alone, and may govern disease course and treatment response. Over 18 disease-modifying drugs have been approved for the treatment of MS, and several biomarkers of treatment response are emerging. This article provides an overview of the concepts of precision medicine and emerging biological markers and their evolving role in decision-making in MS management.
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Affiliation(s)
- Tanuja Chitnis
- Tanuja Chitnis Partners Multiple Sclerosis Center, Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA/Harvard Medical School, Boston, MA, USA/Ann Romney Center for Neurologic Diseases, Brigham and Women’s Hospital, Boston, MA, USA
| | - Alexandre Prat
- Alexandre Prat Department of Neurology, Université de Montréal, Montréal, QC, Canada
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Ayatollahi SA, Ghafouri-Fard S, Taheri M, Noroozi R. The efficacy of interferon-beta therapy in multiple sclerosis patients: investigation of the RORA gene as a predictive biomarker. THE PHARMACOGENOMICS JOURNAL 2019; 20:271-276. [DOI: 10.1038/s41397-019-0114-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 09/09/2019] [Accepted: 10/14/2019] [Indexed: 01/10/2023]
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Jakimovski D, Kolb C, Ramanathan M, Zivadinov R, Weinstock-Guttman B. Interferon β for Multiple Sclerosis. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a032003. [PMID: 29311124 DOI: 10.1101/cshperspect.a032003] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite that the availability of new therapeutic options has expanded the multiple sclerosis (MS) disease-modifying therapy arsenal, interferon β (IFN-β) remains an important therapy option in the current decision-making process. This review will summarize the present knowledge of IFN-β mechanism of action, the overall safety, and the short- and long-term efficacy of its use in relapsing remitting MS and clinically isolated syndromes. Data on secondary progressive MS is also provided, although no clear benefit was identified.
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Affiliation(s)
- Dejan Jakimovski
- Buffalo Neuroimaging Analysis Center, Department of Neurology, University at Buffalo, State University of New York, Buffalo, New York 14203
| | - Channa Kolb
- Jacobs MS Center, Department of Neurology, University at Buffalo, State University of New York, Buffalo, New York 14202
| | - Murali Ramanathan
- Jacobs MS Center, Department of Neurology, University at Buffalo, State University of New York, Buffalo, New York 14202.,Department of Pharmaceutical Sciences, School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York 14214
| | - Robert Zivadinov
- Buffalo Neuroimaging Analysis Center, Department of Neurology, University at Buffalo, State University of New York, Buffalo, New York 14203.,MR Imaging Clinical Translational Research Center, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14203
| | - Bianca Weinstock-Guttman
- Jacobs MS Center, Department of Neurology, University at Buffalo, State University of New York, Buffalo, New York 14202
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Down-regulation of TYK2, CBLB and LMP7 genes expression in relapsing-remitting multiple sclerosis patients treated with interferon-beta. J Neuroimmunol 2018; 314:24-29. [PMID: 29157944 DOI: 10.1016/j.jneuroim.2017.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/05/2017] [Accepted: 11/06/2017] [Indexed: 11/21/2022]
Abstract
This study aimed to examine the expression of TYK2, CBLB and LMP7 genes at both mRNA and protein levels in relapsing-remitting MS (RRMS) patients in compare with healthy controls. Seventy-eight RRMS patients treated with IFNβ-1a and 79 age- and ethnic-matched healthy subjects were studied. The mRNA expression levels of TYK2, CBLB and LMP7 in PBMCs were quantified by real-time PCR and plasma concentrations of three molecules were measured by ELISA. Results were compared between patients and controls, IFNβ-responders and non-responders. Forty-nine of 78 patients were classified as IFNβ-responders and 29 cases were non-responders. Significantly down-regulated expression of TYK2, CBLB and LMP7 genes was found in the patients group versus controls (P<0.001). Decreased plasma levels of three molecules were observed in patients compared to controls (P<0.001). IFNβ-responders had significantly higher expressions for CBLB (P=0.001) and LMP7 (P=0.02) than non-responders. Also, we observed increased expressions of LMP7 (P=0.39) and CBLB (P=0.02) genes in patients under 30y and increased expression of TYK2 in patients >40years (P=0.002). Our results suggest that expression analysis of TYK2, CBLB and LMP7 genes could be useful for evaluation of T cells immunity and clinical response to IFNβ-therapy in RRMS patients.
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Libertinova J, Meluzinova E, Tomek A, Horakova D, Kovarova I, Matoska V, Kumstyrova S, Zajac M, Hyncicova E, Liskova P, Houzvickova E, Martinkovic L, Bojar M, Havrdova E, Marusic P. Myxovirus Resistance Protein A mRNA Expression Kinetics in Multiple Sclerosis Patients Treated with IFNβ. PLoS One 2017; 12:e0169957. [PMID: 28081207 PMCID: PMC5231341 DOI: 10.1371/journal.pone.0169957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/27/2016] [Indexed: 11/28/2022] Open
Abstract
Introduction Interferon-β (IFNß) is the first-line treatment for relapsing-remitting multiple sclerosis. Myxovirus resistance protein A (MxA) is a marker of IFNß bioactivity, which may be reduced by neutralizing antibodies (NAbs) against IFNß. The aim of the study was to analyze the kinetics of MxA mRNA expression during long-term IFNβ treatment and assess its predictive value. Methods A prospective, observational, open-label, non-randomized study was designed in multiple sclerosis patients starting IFNß treatment. MxA mRNA was assessed prior to initiation of IFNß therapy and every three months subsequently. NAbs were assessed every six months. Assessment of relapses was scheduled every three months during 24 months of follow up. The disease activity was correlated to the pretreatment baseline MxA mRNA value. In NAb negative patients, clinical status was correlated to MxA mRNA values. Results 119 patients were consecutively enrolled and 107 were included in the final analysis. There was no correlation of MxA mRNA expression levels between baseline and month three. Using survival analysis, none of the selected baseline MxA mRNA cut off points allowed prediction of time to first relapse on the treatment. In NAb negative patients, mean MxA mRNA levels did not significantly differ in patients irrespective of relapse status. Conclusion Baseline MxA mRNA does not predict the response to IFNß treatment or the clinical status of the disease and the level of MxA mRNA does not correlate with disease activity in NAb negative patients.
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Affiliation(s)
- Jana Libertinova
- Department of Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Eva Meluzinova
- Department of Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Ales Tomek
- Department of Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Dana Horakova
- Department of Neurology and Center of Clinical Neuroscience, Charles University, First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Ivana Kovarova
- Department of Neurology and Center of Clinical Neuroscience, Charles University, First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Vaclav Matoska
- Laboratory of Molecular Diagnostics, Na Homolce Hospital, Prague, Czech Republic
| | - Simona Kumstyrova
- Laboratory of Molecular Diagnostics, Na Homolce Hospital, Prague, Czech Republic
| | - Miroslav Zajac
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Eva Hyncicova
- Department of Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Petra Liskova
- Department of Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Eva Houzvickova
- Department of Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Lukas Martinkovic
- Department of Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Martin Bojar
- Department of Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Eva Havrdova
- Department of Neurology and Center of Clinical Neuroscience, Charles University, First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Petr Marusic
- Department of Neurology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
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Comparative Neuroregenerative Effects of C-Phycocyanin and IFN-Beta in a Model of Multiple Sclerosis in Mice. J Neuroimmune Pharmacol 2015; 11:153-67. [PMID: 26556034 DOI: 10.1007/s11481-015-9642-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 11/05/2015] [Indexed: 10/22/2022]
Abstract
Multiple Sclerosis (MS) therapies approved so far are unable to effectively reverse the chronic phase of the disease or improve the remyelination process. Here our aim is to evaluate the effects of C-Phycocyanin (C-Pc), a biliprotein from Spirulina platensis with anti-oxidant, anti-inflammatory and cytoprotective properties, in a chronic model of experimental autoimmune encephalomyelitis (EAE) in mice. C-Pc (2, 4 or 8 mg/kg i.p.) or IFN-beta (2000 IU, s.c.) was administered daily once a day or every other day, respectively, starting at disease onset, which differ among EAE mice between 11 and 15 days postinduction. Histological and immunohistochemistry (anti-Mac-3, anti-CD3 and anti-APP) assessments were performed in spinal cord in the postinduction time. Global gene expression in the brain was analyzed with the Illumina Mouse WG-6_V2 BeadChip microarray and the expression of particular genes, assessed by qPCR using the Fast SYBR Green RT-PCR Master Mix. Oxidative stress parameters (malondialdehyde, peroxidation potential, CAT/SOD ratio and GSH) were determined spectrophoto-metrically. Results showed that C-Pc ameliorates the clinical deterioration of animals, an effect that expresses the reduction of the inflammatory infiltrates invading the spinal cord tissue, the axonal preservation and the down-regulation of IL-17 expression in brain tissue and serum. C-Pc and IFN-beta improved the redox status in mice subjected to EAE, while microarray analysis showed that both treatments shared a common subset of differentially expressed genes, although they also differentially modulated another subset of genes. Specifically, C-Pc mainly modulated the expression of genes related to remyelination, gliogenesis and axon-glia processes. Taken together, our results indicate that C-Pc has significant therapeutic effects against EAE, mediated by the dynamic regulation of multiple biological processes.
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9
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Biomarkers in multiple sclerosis. Clin Immunol 2015; 161:51-8. [DOI: 10.1016/j.clim.2015.06.015] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 11/20/2022]
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Interferon-β1a modulates glutamate neurotransmission in the CNS through CaMKII and GluN2A-containing NMDA receptors. Neuropharmacology 2015; 100:98-105. [PMID: 26116817 DOI: 10.1016/j.neuropharm.2015.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/28/2015] [Accepted: 06/17/2015] [Indexed: 12/16/2022]
Abstract
Interferons (IFNs) are widely expressed cytokines with antiviral and immune-modulating effects and have been utilised for the treatment of several human pathological conditions. In particular, the immune-modulatory drug IFN-β is utilized in the treatment of multiple sclerosis (MS), a chronic autoimmune and neurodegenerative disorder of the central nervous system (CNS). Although the effects of IFN-β on immune cells functions have been widely investigated, information about the ability of the drug to modulate neuronal transmission in the CNS is still largely lacking. The aim of this study was to investigate the ability of IFN-β1a to modulate excitatory synaptic transmission in the CNS. Whole cell patch-clamp electrophysiological recordings were performed in the nucleus striatum, one of the CNS grey matter structures that is prone to degenerate during the course of MS. We demonstrate that the drug IFN-β1a, independently from its known peripheral immune-modulating action, is able to directly modulate synaptic transmission. In particular, we demonstrated that IFN-β1a reduces the amplitude of striatal excitatory post-synaptic currents, indicating an inhibitory effect on glutamate neurotransmission, and in particular on its NMDA component. The inhibitory effect of IFN-β1a on striatal glutamate neurotransmission was found to be mediated by a novel post-synaptic mechanism requiring Ca(2+), CaMKII and the GluN2A subunit of the NMDA receptor, without the involvement of the classic STAT1 pathway. The evidence of a novel neuro-modulating effect of IFN-β shed light on the mechanisms of action of the drug and on the complex bidirectional interaction occurring between the immune and the nervous system. This article is part of the Special Issue entitled 'Synaptopathy--from Biology to Therapy'.
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Huber AK, Duncker PC, Irani DN. The conundrum of interferon-β non-responsiveness in relapsing-remitting multiple sclerosis. Cytokine 2015; 74:228-36. [PMID: 25691330 DOI: 10.1016/j.cyto.2015.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/10/2015] [Indexed: 01/01/2023]
Abstract
A series of controlled clinical trials have shown that exogenous interferon-beta (IFN-β) benefits patients with relapsing-remitting multiple sclerosis (RRMS) by reducing relapse rate, disability progression, and the formation of new brain and spinal cord lesions on magnetic resonance imaging (MRI) scans. Unfortunately, however, the effectiveness of IFN-β is limited in this setting by the occurrence of treatment non-responsiveness in nearly 25% of patients. Furthermore, clinicians who care for RRMS patients remain unable to accurately identify IFN-β non-responders prior to the initiation of therapy, causing delays in the use of alternative treatments and sometimes requiring that patients turn to medications with more significant side effects to control their disease. Progress has been made toward understanding how both endogenous and exogenous IFN-β act to slow RRMS as well as the related mouse model, experimental autoimmune encephalomyelitis (EAE). Most studies point to its inhibitory actions on circulating immune cells as being important for suppressing both disorders, but multiple potential target cells and inflammatory pathways have been implicated and those essential to confer its benefits remain undefined. This review focuses on the role of both endogenous and exogenous IFN-β in RRMS, paying particular attention to the issue of why certain individuals appear refractory to its disease-modifying effects. A continued goal in this field remains the identification of a convenient biomarker that accurately predicts IFN-β treatment non-responsiveness in individual RRMS patients. Development of such an assay will allow clinicians to customize therapy for patients with this complex disorder.
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Affiliation(s)
- Amanda K Huber
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Patrick C Duncker
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - David N Irani
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI, USA.
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Raphael I, Webb J, Stuve O, Haskins W, Forsthuber T. Body fluid biomarkers in multiple sclerosis: how far we have come and how they could affect the clinic now and in the future. Expert Rev Clin Immunol 2014; 11:69-91. [PMID: 25523168 DOI: 10.1586/1744666x.2015.991315] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Multiple sclerosis (MS) is an autoimmune inflammatory disease of the central nervous system, which affects over 2.5 million people worldwide. Although MS has been extensively studied, many challenges still remain in regards to treatment, diagnosis and prognosis. Typically, prognosis and individual responses to treatment are evaluated by clinical tests such as the expanded disability status scale, MRI and presence of oligoclonal bands in the cerebrospinal fluid. However, none of these measures correlates strongly with treatment efficacy or disease progression across heterogeneous patient populations and subtypes of MS. Numerous studies over the past decades have attempted to identify sensitive and specific biomarkers for diagnosis, prognosis and treatment efficacy of MS. The objective of this article is to review and discuss the current literature on body fluid biomarkers in MS, including research on potential biomarker candidates in the areas of miRNA, mRNA, lipids and proteins.
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Affiliation(s)
- Itay Raphael
- University of Texas San Antonio - Biology, San Antonio, TX, USA
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Haghikia A, Faissner S, Pappas D, Pula B, Akkad DA, Arning L, Ruhrmann S, Duscha A, Gold R, Baranzini SE, Malhotra S, Montalban X, Comabella M, Chan A. Interferon-beta affects mitochondrial activity in CD4+ lymphocytes: Implications for mechanism of action in multiple sclerosis. Mult Scler 2014; 21:1262-70. [DOI: 10.1177/1352458514561909] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/06/2014] [Indexed: 12/12/2022]
Abstract
Background: Whereas cellular immune function depends on energy supply and mitochondrial function, little is known on the impact of immunotherapies on cellular energy metabolism. Objective: The objective of this paper is to assess the effects of interferon-beta (IFN-β) on mitochondrial function of CD4+ T cells. Methods: Intracellular adenosine triphosphate (iATP) in phytohemagglutinin (PHA)-stimulated CD4+ cells of multiple sclerosis (MS) patients treated with IFN-β and controls were analyzed in a luciferase-based assay. Mitochondrial-transmembrane potential (ΔΨm) in IFN-β-treated peripheral blood mononuclear cells (PBMCs) was investigated by flow cytometry. Expression of genes involved in mitochondrial oxidative phosphorylation (OXPHOS) in CD4+ cells of IFN-β-treated individuals and correlations between genetic variants in the key metabolism regulator PGC-1α and IFN-β response in MS were analyzed. Results: IFN-β-treated MS patients exhibited a dose-dependent reduction of iATP levels in CD4+ T cells compared to controls ( p < 0.001). Mitochondrial effects were reflected by depolarization of ΔΨm. Expression data revealed changes in the transcription of OXPHOS-genes. iATP levels in IFN-β-responders were reduced compared to non-responders ( p < 0.05), and the major T allele of the SNP rs7665116 of PGC-1α correlated with iATP-levels. Conclusion: Reduced iATP-synthesis ex vivo and differential expression of OXPHOS-genes in CD4+ T cells point to unknown IFN-β effects on mitochondrial energy metabolism, adding to potential pleiotropic mechanisms of action.
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Affiliation(s)
- Aiden Haghikia
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Simon Faissner
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Derek Pappas
- Department of Neurology at the University of California, San Francisco, USA
| | - Bartosz Pula
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Denis A Akkad
- Department of Human Genetics, Ruhr-University Bochum, Germany
| | - Larissa Arning
- Department of Human Genetics, Ruhr-University Bochum, Germany
| | - Sabrina Ruhrmann
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Alexander Duscha
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Ralf Gold
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Germany
| | - Sergio E Baranzini
- Department of Neurology at the University of California, San Francisco, USA
| | - Sunny Malhotra
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Institut de Receca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Spain
| | - Xavier Montalban
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Institut de Receca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Spain
| | - Manuel Comabella
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Institut de Receca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Spain
| | - Andrew Chan
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, Germany
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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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Polanski K, Rhodes J, Hill C, Zhang P, Jenkins DJ, Kiddle SJ, Jironkin A, Beynon J, Buchanan-Wollaston V, Ott S, Denby KJ. Wigwams: identifying gene modules co-regulated across multiple biological conditions. ACTA ACUST UNITED AC 2013; 30:962-70. [PMID: 24351708 PMCID: PMC3967106 DOI: 10.1093/bioinformatics/btt728] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Motivation: Identification of modules of co-regulated genes is a crucial first step towards dissecting the regulatory circuitry underlying biological processes. Co-regulated genes are likely to reveal themselves by showing tight co-expression, e.g. high correlation of expression profiles across multiple time series datasets. However, numbers of up- or downregulated genes are often large, making it difficult to discriminate between dependent co-expression resulting from co-regulation and independent co-expression. Furthermore, modules of co-regulated genes may only show tight co-expression across a subset of the time series, i.e. show condition-dependent regulation. Results: Wigwams is a simple and efficient method to identify gene modules showing evidence for co-regulation in multiple time series of gene expression data. Wigwams analyzes similarities of gene expression patterns within each time series (condition) and directly tests the dependence or independence of these across different conditions. The expression pattern of each gene in each subset of conditions is tested statistically as a potential signature of a condition-dependent regulatory mechanism regulating multiple genes. Wigwams does not require particular time points and can process datasets that are on different time scales. Differential expression relative to control conditions can be taken into account. The output is succinct and non-redundant, enabling gene network reconstruction to be focused on those gene modules and combinations of conditions that show evidence for shared regulatory mechanisms. Wigwams was run using six Arabidopsis time series expression datasets, producing a set of biologically significant modules spanning different combinations of conditions. Availability and implementation: A Matlab implementation of Wigwams, complete with graphical user interfaces and documentation, is available at: warwick.ac.uk/wigwams. Contact:k.j.denby@warwick.ac.uk Supplementary Data:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Krzysztof Polanski
- Warwick Systems Biology Centre and School of Life Sciences, University of Warwick, CV4 7AL, UK
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Interferon-β1a protects neurons against mitochondrial toxicity via modulation of STAT1 signaling: electrophysiological evidence. Neurobiol Dis 2013; 62:387-93. [PMID: 24135008 DOI: 10.1016/j.nbd.2013.09.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/09/2013] [Accepted: 09/24/2013] [Indexed: 11/22/2022] Open
Abstract
Multiple sclerosis, one of the main causes of non-traumatic neurological disability in young adults, is an inflammatory and neurodegenerative disorder of the central nervous system. Although the pathogenesis of neuroaxonal damage occurring during the course of the disease is still largely unknown, there is accumulating evidence highlighting the potential role of mitochondria in multiple sclerosis-associated neuronal degeneration. The aim of the present study was to investigate, by utilizing electrophysiological techniques in brain striatal slices, the potential protective effects of interferon-β1a, one of the most widely used medication for multiple sclerosis, against acute neuronal dysfunction induced by mitochondrial toxins. Interferon-β1a was found to exert a dose-dependent protective effect against the progressive loss of striatal field potential amplitude induced by the mitochondrial complex I inhibitor rotenone. Interferon-β1a also reduced the generation of the rotenone-induced inward current in striatal spiny neurons. Conversely, interferon-β1a did not influence the electrophysiological effects of the mitochondrial complex II inhibitor 3-nitropropionic acid. The protective effect of interferon-β1a against mitochondrial complex I inhibition was found to be dependent on the activation of STAT1 signaling. Conversely, endogenous dopamine depletion and the modulation of the p38 MAPK and mTOR pathways did not influence the effects of interferon-β1a. During experimental autoimmune encephalomyelitis (EAE) striatal rotenone toxicity was enhanced but the protective effect of interferon-β1a was still evident. These results support future studies investigating the role played by specific intracellular signaling pathways in mediating the potential link among inflammation, mitochondrial impairment and neuroaxonal degeneration in multiple sclerosis.
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Abstract
BACKGROUND Identifying modules from time series biological data helps us understand biological functionalities of a group of proteins/genes interacting together and how responses of these proteins/genes dynamically change with respect to time. With rapid acquisition of time series biological data from different laboratories or databases, new challenges are posed for the identification task and powerful methods which are able to detect modules with integrative analysis are urgently called for. To accomplish such integrative analysis, we assemble multiple time series biological data into a higher-order form, e.g., a gene × condition × time tensor. It is interesting and useful to develop methods to identify modules from this tensor. RESULTS In this paper, we present MultiFacTV, a new method to find modules from higher-order time series biological data. This method employs a tensor factorization objective function where a time-related total variation regularization term is incorporated. According to factorization results, MultiFacTV extracts modules that are composed of some genes, conditions and time-points. We have performed MultiFacTV on synthetic datasets and the results have shown that MultiFacTV outperforms existing methods EDISA and Metafac. Moreover, we have applied MultiFacTV to Arabidopsis thaliana root(shoot) tissue dataset represented as a gene × condition × time tensor of size 2395 × 9 × 6(3454 × 8 × 6), to Yeast dataset and Homo sapiens dataset represented as tensors of sizes 4425 × 6 × 6 and 2920 × 14 × 9 respectively. The results have shown that MultiFacTV indeed identifies some interesting modules in these datasets, which have been validated and explained by Gene Ontology analysis with DAVID or other analysis. CONCLUSION Experimental results on both synthetic datasets and real datasets show that the proposed MultiFacTV is effective in identifying modules for higher-order time series biological data. It provides, compared to traditional non-integrative analysis methods, a more comprehensive and better view on biological process since modules composed of more than two types of biological variables could be identified and analyzed.
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Affiliation(s)
- Xutao Li
- Department of Computer Science, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Internet Information Collaboration, Shenzhen, 518055, China
| | - Yunming Ye
- Department of Computer Science, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Internet Information Collaboration, Shenzhen, 518055, China
| | - Michael Ng
- Department of Mathematics, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Qingyao Wu
- Department of Computer Science, Shenzhen Graduate School, Harbin Institute of Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Internet Information Collaboration, Shenzhen, 518055, China
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Verweij CL. Research highlights: Clinical relevance of the type I interferon signature in multiple sclerosis. Pharmacogenomics 2012; 13:1883-5. [PMID: 23215880 DOI: 10.2217/pgs.12.166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Cornelis L Verweij
- VU University medical center, Department of Pathology, Section of Inflammatory Disease Profiling, CCA2.60 Amsterdam, The Netherlands.
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Pharmacogenomic update on multiple sclerosis: a focus on actual and new therapeutic strategies. THE PHARMACOGENOMICS JOURNAL 2012; 12:453-61. [PMID: 23044601 DOI: 10.1038/tpj.2012.41] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Multiple sclerosis (MS) is an inflammatory and demyelinating disease of central nervous system comprising several subtypes. Pharmacological treatment involves only few drugs. Among these, interferon beta (IFN-β) and glatiramer acetate were the most used. Although evidence supports the efficacy of these agents in treating MS symptoms, actual studies allowed to introduce new innovative drugs in clinical practice. Applying pharmacogenetic approach to MS, IFN-β and several other immune pathways were abundantly investigated. Numerous reports identified some promising therapy markers but only few markers have emerged as clinically useful. This may be partially due to differences in clinical and methodological criteria in the studies. Indeed, responder and non-responder definitions lack standardized clinical definition. The goal of this review is to treat advances in research on the pharmacogenetic markers of MS drugs and to highlight possible correlations between type of responses and genetic profile, with regard to clinical and methodological discrepancies in the studies.
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Sellebjerg F, Krakauer M, Limborg S, Hesse D, Lund H, Langkilde A, Søndergaard HB, Sørensen PS. Endogenous and recombinant type I interferons and disease activity in multiple sclerosis. PLoS One 2012; 7:e35927. [PMID: 22701554 PMCID: PMC3368920 DOI: 10.1371/journal.pone.0035927] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 03/24/2012] [Indexed: 11/18/2022] Open
Abstract
Although treatment of multiple sclerosis (MS) with the type I interferon (IFN) IFN-β lowers disease activity, the role of endogenous type I IFN in MS remains controversial. We studied CD4+ T cells and CD4+ T cell subsets, monocytes and dendritic cells by flow cytometry and analysed the relationship with endogenous type I IFN-like activity, the effect of IFN-β therapy, and clinical and magnetic resonance imaging (MRI) disease activity in MS patients. Endogenous type I IFN activity was associated with decreased expression of the integrin subunit CD49d (VLA-4) on CD4+CD26(high) T cells (Th1 helper cells), and this effect was associated with less MRI disease activity. IFN-β therapy reduced CD49d expression on CD4+CD26(high) T cells, and the percentage of CD4+CD26(high) T cells that were CD49d(high) correlated with clinical and MRI disease activity in patients treated with IFN-β. Treatment with IFN-β also increased the percentage of CD4+ T cells expressing CD71 and HLA-DR (activated T cells), and this was associated with an increased risk of clinical disease activity. In contrast, induction of CD71 and HLA-DR was not observed in untreated MS patients with evidence of endogenous type IFN I activity. In conclusion, the effects of IFN-β treatment and endogenous type I IFN activity on VLA-4 expression are similar and associated with control of disease activity. However, immune-activating effects of treatment with IFN-β may counteract the beneficial effects of treatment and cause an insufficient response to therapy.
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Affiliation(s)
- Finn Sellebjerg
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.
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21
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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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Abstract
The development of neutralizing antibodies (NAbs) is a major problem in multiple sclerosis (MS) patients treated with interferon-beta (IFN-ß). Whereas binding antibodies (BAbs) can be demonstrated in the vast majority of patients, only a smaller proportion of patients develop NAbs. The principle in NAb in vitro assays is the utilization of cultured cell lines that are responsive to IFN-ß. The cytopathic effect (CPE) assay measures the capacity of NAbs to neutralize IFN- ß's protective effect on cells challenged with virus and the MxA induction assay measures the ability of NAbs to reduce the IFN-ß-induced expression of MxA, either at the mRNA or the protein level. A titer of >20 neutralizing units/ml traditionally defines NAb posi-tivity. NAbs in high titers completely abrogate the in vivo response to IFN-ß, whereas the effect of low and intermediate titers is unpredictable. As clinically important NAbs appear only after 9-18 months IFN- ß0 therapy, short-term studies of two years or less are unsuitable for evaluation of clinical NAb effects. All long-term trials of three years or more concordantly show evidence of a detrimental effect of NAbs on relapses, disease activity on MRI, or on disease progression. Persistent high titers of NAbs indicate an abrogation of the biological response and, hence, absence of therapeutic efficacy, and this observation should lead to a change of therapy. As low and medium titers are ambiguous treatment decisions in patients with low NAb titres should be guided by determination of in vivo mRNA MxA induction and clinical disease activity.
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Affiliation(s)
- Per Soelberg Sorensen
- Danish Multiple Sclerosis Research Center Department of Neurology 2082, Copenhagen University Hospital Rigshospitalet, DK-2100 Copenhagen, Denmark.
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Goertsches RH, Zettl UK, Hecker M. Sieving treatment biomarkers from blood gene-expression profiles: a pharmacogenomic update on two types of multiple sclerosis therapy. Pharmacogenomics 2011; 12:423-32. [PMID: 21449680 DOI: 10.2217/pgs.10.190] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Interferon-β (IFN-β) and glatiramer acetate are routinely used to inhibit disease activity in multiple sclerosis, but their mechanisms of action are incompletely understood. Individual treatment responses vary and candidate molecular markers that predict them have yet to be established. Why some patients respond poorly to a certain treatment while others respond well is addressed by the pharmacogenomic approach, which postulates that the molecular response to treatment correlates with the clinical effects, and thus seeks biological markers to estimate prognosis, guide therapy, comprehend the drugs' mechanisms of action and offer insights into disease pathogenesis. A poor clinical response can be owing to genetic variants in drug receptors or signaling components, or the appearance of neutralizing antibodies that interfere with the drug's binding efficacy. Independently, such mechanisms could lead to inadequate, that is to say unchanged, molecular responses, or exceedingly increased or decreased changes. By means of DNA microarray studies, various research groups endeavour to establish a clinically relevant relationship between the biological response to these drugs and treatment effects. Molecular profiles obtained in this way differ in the pattern and number of modulated genes, suggesting the existence of an individual 'drug-response fingerprint'. To further unravel the underlying regulatory interaction structure of the genes responsive to these immunotherapies represents a daunting but inevitable task. In this article, we focus on longitudinal ex vivo transcriptomic studies in multiple sclerosis and its therapy. We will discuss recurrently reported biomarker candidates, emphasizing those of immunologically meaning, and review studies with network module outputs.
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Affiliation(s)
- Robert H Goertsches
- University of Rostock, Department of Neurology, Gehlsheimer Strasse 20, 18147 Rostock, Germany.
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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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Gossner A, Roupaka S, Foster J, Hunter N, Hopkins J. Transcriptional profiling of peripheral lymphoid tissue reveals genes and networks linked to SSBP/1 scrapie pathology in sheep. Vet Microbiol 2011; 153:218-28. [PMID: 21684093 DOI: 10.1016/j.vetmic.2011.05.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 05/10/2011] [Accepted: 05/16/2011] [Indexed: 12/30/2022]
Abstract
Transmissible spongiform encephalopathies (TSEs) are slow and progressive neurodegenerative diseases of humans and animals. The major target organ for all TSEs is the brain but some TSE agents are associated with prior accumulation within the peripheral lymphoid system. Many studies have examined the effects of scrapie infection on the expression of central nervous system (CNS) genes, but this study examines the progression of scrapie pathology in the peripheral lymphoid system and how scrapie infection affects the transcriptome of the lymph nodes and spleen. Infection of sheep with SSBP/1 scrapie resulted in PrP(Sc) deposition in the draining prescapular lymph node (PSLN) by 25 days post infection (dpi) in VRQ/VRQ genotype sheep and 75 dpi in tonsils and spleen. Progression of PrP(Sc) deposition in VRQ/ARR animals was 25 dpi later in the PSLN and 250 dpi later in spleen. Microarray analysis of 75 dpi tissues from VRQ/VRQ sheep identified 52 genes in PSLN and 37 genes in spleen cells that showed significant difference (P ≤ 0.05) between scrapie-infected and mock-infected animals. Transcriptional pathway analysis highlighted immunological disease, cell death and neurological disease as the biological pathways associated with scrapie pathogenesis in the peripheral lymphoid system. PrP(Sc) accumulation of lymphoid tissue resulted in the repression of genes linked to inflammation and oxidative stress, and the up-regulation of genes related to apoptosis.
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Affiliation(s)
- Anton Gossner
- The Roslin Institute & R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
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26
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Beta-interferon for multiple sclerosis. Exp Cell Res 2011; 317:1301-11. [DOI: 10.1016/j.yexcr.2011.03.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Revised: 03/01/2011] [Accepted: 03/02/2011] [Indexed: 01/17/2023]
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Croze E. Differential gene expression and translational approaches to identify biomarkers of interferon beta activity in multiple sclerosis. J Interferon Cytokine Res 2011; 30:743-9. [PMID: 20874251 DOI: 10.1089/jir.2010.0022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
More than 16 years ago human interferon-β-1b (IFN-β-1β) was shown to be effective in the treatment of the relapsing-remitting form of multiple sclerosis (MS). Over time, IFN-β has been demonstrated to be both a safe and effective treatment. However, the mechanism of action of IFN-β in MS remains unknown. To better understand the mechanism of action of IFN-β, considerable effort has been made in transcriptional profiling of peripheral blood mononuclear cells collected from MS patients. IFN-β is known to induce a large number of genes that play an important role in regulating responses to viral infection, immune modulation, and cell proliferation. Identifying differentially induced genes that are linked to the beneficial effects observed during treatment is under active investigation. IFN biomarkers in MS patients have been proposed but have not been clearly confirmed in independent studies or consistently correlated with clinical measures of disease progression. Organizing single genes or gene signatures grouped according to molecular mechanisms meaningful in MS may help to link IFN activity measurements to clinical outcomes. In this review, IFN activity measurements will be discussed with a specific emphasis on what is known about differential gene expression and treatment effects in MS.
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Affiliation(s)
- Ed Croze
- Translational Research, Global Medical Affairs, Neurology, Specialty Medicine, Bayer HealthCare Pharmaceuticals, Inc., Richmond, California 94804, USA.
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28
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Menge T, Hartung HP, Kieseier BC. Neutralizing antibodies in interferon beta treated patients with multiple sclerosis: knowing what to do now : Commentary to: 10.1007/s00415-010-5844-5 "One-year evaluation of factors affecting the biological activity of interferon beta in multiple sclerosis patients" by S. Malucchi et al. J Neurol 2011; 258:904-7. [PMID: 21340521 DOI: 10.1007/s00415-011-5941-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Til Menge
- Department of Neurology, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
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Li Y, Ngom A. Classification of Clinical Gene-Sample-Time Microarray Expression Data via Tensor Decomposition Methods. COMPUTATIONAL INTELLIGENCE METHODS FOR BIOINFORMATICS AND BIOSTATISTICS 2011. [DOI: 10.1007/978-3-642-21946-7_22] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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Calcagno G, Staiano A, Fortunato G, Brescia-Morra V, Salvatore E, Liguori R, Capone S, Filla A, Longo G, Sacchetti L. A multilayer perceptron neural network-based approach for the identification of responsiveness to interferon therapy in multiple sclerosis patients. Inf Sci (N Y) 2010. [DOI: 10.1016/j.ins.2010.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Hecker M, Goertsches RH, Fatum C, Koczan D, Thiesen HJ, Guthke R, Zettl UK. Network analysis of transcriptional regulation in response to intramuscular interferon-β-1a multiple sclerosis treatment. THE PHARMACOGENOMICS JOURNAL 2010; 12:134-46. [PMID: 20956993 DOI: 10.1038/tpj.2010.77] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Interferon-β (IFN-β) is one of the major drugs for multiple sclerosis (MS) treatment. The purpose of this study was to characterize the transcriptional effects induced by intramuscular IFN-β-1a therapy in patients with relapsing-remitting form of MS. By using Affymetrix DNA microarrays, we obtained genome-wide expression profiles of peripheral blood mononuclear cells of 24 MS patients within the first 4 weeks of IFN-β administration. We identified 121 genes that were significantly up- or downregulated compared with baseline, with stronger changed expression at 1 week after start of therapy. Eleven transcription factor-binding sites (TFBS) are overrepresented in the regulatory regions of these genes, including those of IFN regulatory factors and NF-κB. We then applied TFBS-integrating least angle regression, a novel integrative algorithm for deriving gene regulatory networks from gene expression data and TFBS information, to reconstruct the underlying network of molecular interactions. An NF-κB-centered sub-network of genes was highly expressed in patients with IFN-β-related side effects. Expression alterations were confirmed by real-time PCR and literature mining was applied to evaluate network inference accuracy.
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Affiliation(s)
- M Hecker
- Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knoell-Institute, Jena, Germany.
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Satoh JI. Bioinformatics approach to identifying molecular biomarkers and networks in multiple sclerosis. ACTA ACUST UNITED AC 2010. [DOI: 10.1111/j.1759-1961.2010.00013.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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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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Hesse D, Krakauer M, Lund H, Søndergaard H, Langkilde A, Ryder L, Sorensen P, Sellebjerg F. Breakthrough disease during interferon-β therapy in MS. Neurology 2010; 74:1455-62. [DOI: 10.1212/wnl.0b013e3181dc1a94] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background: Disease activity is highly variable in patients with multiple sclerosis (MS), both untreated and during interferon (IFN)-β therapy. Breakthrough disease is often regarded as treatment failure; however, apart from neutralizing antibodies (NAbs), no blood biomarkers have been established as reliable indicators of treatment response, despite substantial, biologically measurable effects. We studied the biologic response to treatment in a cohort of NAb-negative patients to test whether difference in responsiveness could segregate patients with and without breakthrough disease during therapy.Methods: Gene expression in blood cells from 23 patients with relapsing-remitting MS was analyzed by microarray and PCR. Samples were collected pretreatment and 9–12 hours after IFNβ injection at 3 and 6 months' treatment. Definition of breakthrough disease was based on the occurrence of relapses, disability progression, or subclinical activity on 3T MRI at 3 and 6 months.Results: Sixteen patients had breakthrough disease and 7 patients were stable. Microarray and PCR showed marked effects of IFNβ on gene expression profiles, but biologic responses did not differ between patients with breakthrough disease and stable patients. However, pretreatment variables did differ: patients with breakthrough disease had lower baseline IL10 expression, more gadolinium-enhancing lesions, and a higher number and volume of T2 lesions.Conclusions: Breakthrough disease during interferon (IFN)-β treatment is not paralleled by differences in biologic responsiveness to treatment in NAb-negative patients; most likely, the spontaneously occurring variation in underlying disease activity between patients causes the varying level of breakthrough disease observed in IFNβ-treated patients with multiple sclerosis.
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O'Doherty C, Favorov A, Heggarty S, Graham C, Favorova O, Ochs M, Hawkins S, Hutchinson M, O'Rourke K, Vandenbroeck K. Genetic polymorphisms, their allele combinations and IFN-beta treatment response in Irish multiple sclerosis patients. Pharmacogenomics 2010; 10:1177-86. [PMID: 19604093 DOI: 10.2217/pgs.09.41] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION IFN-beta is widely used as first-line immunomodulatory treatment for multiple sclerosis. Response to treatment is variable (30-50% of patients are nonresponders) and requires a long treatment duration for accurate assessment to be possible. Information about genetic variations that predict responsiveness would allow appropriate treatment selection early after diagnosis, improve patient care, with time saving consequences and more efficient use of resources. MATERIALS & METHODS We analyzed 61 SNPs in 34 candidate genes as possible determinants of IFN-beta response in Irish multiple sclerosis patients. Particular emphasis was placed on the exploration of combinations of allelic variants associated with response to therapy by means of a Markov chain Monte Carlo-based approach (APSampler). RESULTS The most significant allelic combinations, which differed in frequency between responders and nonresponders, included JAK2-IL10RB-GBP1-PIAS1 (permutation p-value was p(perm) = 0.0008), followed by JAK2-IL10-CASP3 (p(perm) = 0.001). DISCUSSION The genetic mechanism of response to IFN-beta is complex and as yet poorly understood. Data mining algorithms may help in uncovering hidden allele combinations involved in drug response versus nonresponse.
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Goertsches RH, Hecker M, Koczan D, Serrano-Fernandez P, Moeller S, Thiesen HJ, Zettl UK. Long-term genome-wide blood RNA expression profiles yield novel molecular response candidates for IFN-β-1b treatment in relapsing remitting MS. Pharmacogenomics 2010; 11:147-61. [DOI: 10.2217/pgs.09.152] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Aims: In multiple sclerosis patients, treatment with recombinant IFN-β (rIFN-β) is partially efficient in reducing clinical exacerbations. However, its molecular mechanism of action is still under scrutiny. Materials & methods: We used DNA microarrays (Affymetrix, CA, USA) and peripheral mononuclear blood cells from 25 relapsing remitting multiple sclerosis patients to analyze the longitudinal transcriptional profile within 2 years of rIFN-β administration. Sets of differentially expressed genes were attained by applying a combination of independent criteria, thereby providing efficient data curation and gene filtering that accounted for technical and biological noise. Gene ontology term-association analysis and scientific literature text mining were used to explore evidence of gene interaction. Results: Post-therapy initiation, we identified 42 (day 2), 175 (month 1), 103 (month 12) and 108 (month 24) differentially expressed genes. Increased expression of established IFN-β marker genes, as well as differential expression of circulating IFN-β-responsive candidate genes, were observed. MS4A1 (CD20), a known target of B-cell depletion therapy, was significantly downregulated after one month. CMPK2, FCER1A, and FFAR2 appeared as hitherto unrecognized multiple sclerosis treatment-related differentially expressed genes that were consistently modulated over time. Overall, 84 interactions between 54 genes were attained, of which two major gene networks were identified at an earlier stage of therapy: the first (n = 15 genes) consisted of mostly known IFN-β-activated genes, whereas the second (n = 12) mainly contained downregulated genes that to date have not been associated with IFN-β effects in multiple sclerosis array research. Conclusion: We achieved both a broadening of the knowledge of IFN-β mechanism-of-action-related constituents and the identification of time-dependent interactions between IFN-β regulated genes.
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Affiliation(s)
- Robert H Goertsches
- Department of Neurology, University of Rostock, Gehlsheimer Str. 20, 18047 Rostock, Germany
- Leibniz Institute for Natural Product Research & Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Michael Hecker
- Leibniz Institute for Natural Product Research & Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Dirk Koczan
- Institute of Immunology, University of Rostock, Schillingallee 70, 18055 Rostock, Germany
| | | | - Steffen Moeller
- Institute of Immunology, University of Rostock, Schillingallee 70, 18055 Rostock, Germany
| | - Hans-Juergen Thiesen
- Institute of Immunology, University of Rostock, Schillingallee 70, 18055 Rostock, Germany
| | - Uwe K Zettl
- Department of Neurology, University of Rostock, Gehlsheimer Str. 20, 18047 Rostock, Germany
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Rani MRS, Xu Y, Lee JC, Shrock J, Josyula A, Schlaak J, Chakraborthy S, Ja N, Ransohoff RM, Rudick RA. Heterogeneous, longitudinally stable molecular signatures in response to interferon-beta. Ann N Y Acad Sci 2010; 1182:58-68. [PMID: 20074275 DOI: 10.1111/j.1749-6632.2009.05068.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Interferons (IFNs) are widely used in therapy for viral, neoplastic, and inflammatory disorders, but clinical response varies among patients. The biological basis for variable clinical response is not known. We determined the primary molecular response to IFN-beta (IFN-beta) injections in 35 treatment-naïve multiple sclerosis (MS) patients using a customized cDNA macroarray with 186 interferon-stimulated genes (ISGs). Our results revealed striking interindividual heterogeneity, both in the magnitude as well as the nature of the primary molecular response to IFN-beta injections. Despite marked between-subject variability in the molecular response, responses within individual subjects were stable over a 6-month interval. Our data suggest that clinical response to IFN-beta therapy for MS differs among patients because of qualitative rather than quantitative variability in the primary molecular response to the drug.
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Affiliation(s)
- M R Sandhya Rani
- Neuroinflammation Research Center, Department of Neurosciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
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38
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Serrano-Fernández P, Möller S, Goertsches R, Fiedler H, Koczan D, Thiesen HJ, Zettl UK. Time course transcriptomics of IFNB1b drug therapy in multiple sclerosis. Autoimmunity 2009; 43:172-8. [DOI: 10.3109/08916930903219040] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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39
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Koning N, Uitdehaag BMJ, Huitinga I, Hoek RM. Restoring immune suppression in the multiple sclerosis brain. Prog Neurobiol 2009; 89:359-68. [PMID: 19800386 DOI: 10.1016/j.pneurobio.2009.09.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 08/26/2009] [Accepted: 09/28/2009] [Indexed: 12/30/2022]
Abstract
Multiple sclerosis is a very disabling inflammatory demyelinating disease of the brain of unknown etiology. Current therapies can reduce new lesion development and partially prevent clinical disease activity, but none can halt the progression, or cure the disease. We will review current therapeutic strategies, which are mostly discussed in literature in terms of their effective inhibition of T cells. However, we argue that many of these treatments also influence the myeloid compartment. Interestingly, recent evidence indicates that myelin phagocytosis by infiltrated macrophages and activated microglia is not just a hallmark of multiple sclerosis, but also a key determinant of lesion development and disease progression. We reason that severe side effects and/or insufficient effectiveness of current treatments necessitates the search for novel therapeutic targets, and postulate that these should aim at manipulation of the activation and phagocytic capacity of macrophages and microglia. We will discuss three candidate targets with high potential, namely the complement receptor 3, CD47-SIRPalpha interaction as well as CD200-CD200R interaction. Blocking the actions of complement receptor 3 could inhibit myelin phagocytosis, as well as migration of myeloid cells into the brain. CD47 and CD200 are known to inhibit macrophage/microglia activation through binding to their receptors SIRPalpha and CD200R, expressed on phagocytes. Triggering these receptors may thus dampen the inflammatory response. Our recent findings indicate that the CD200-CD200R interaction is the most specific and hence probably best-suited target to suppress excessive macrophage and microglia activation, and restore immune suppression in the brain of patients with multiple sclerosis.
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Affiliation(s)
- Nathalie Koning
- Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
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40
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Annibali V, Di Giovanni S, Cannoni S, Giugni E, Bomprezzi R, Mattei C, Elkahloun A, Coccia EM, Alfò M, Orzi F, Ristori G, Salvetti M. Gene expression profiles reveal homeostatic dynamics during interferon-β therapy in multiple sclerosis. Autoimmunity 2009; 40:16-22. [PMID: 17364493 DOI: 10.1080/08916930601135241] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Understanding the mechanisms that sustain the effects of disease modifying drugs in multiple sclerosis (MS) may help refine current therapies and improve our knowledge of disease pathogenesis. By using cDNA microarrays, we investigated gene expression in the peripheral blood mononuclear cells (PBMC) of 7 MS patients, at baseline (T0) as well as after 1 (T1) and 3 months (T3) of interferon beta-1a (IFN-beta-1a; Rebif 44 microg) therapy. Gene expression changes involved genes of both immunological and non-immunological significance. We validated IL-10 up-regulation, which is in accordance with previous reports, and other novel changes that underscore the capacity of IFN-beta to impair antigen presentation and migration of inflammatory elements into the central nervous system (up-regulation of filamin B and down-regulation of IL-16 and rab7). Overall, gene expression changes became less pronounced after 3 months of therapy, suggesting a homeostatic response to IFN-beta. This may be of use for the design of new treatment schedules.
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Affiliation(s)
- Viviana Annibali
- Department of Neurology and Center for Experimental Neurological Therapy, S Andrea Hospital, University of Rome La Sapienza, Rome, Italy
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41
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Sellebjerg F, Krakauer M, Hesse D, Ryder LP, Alsing I, Jensen PEH, Koch-Henriksen N, Svejgaard A, Soelberg Sørensen P. Identification of new sensitive biomarkers for thein vivoresponse to interferon-β treatment in multiple sclerosis using DNA-array evaluation. Eur J Neurol 2009; 16:1291-8. [DOI: 10.1111/j.1468-1331.2009.02716.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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42
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Zhang X, Jin J, Tang Y, Speer D, Sujkowska D, Markovic-Plese S. IFN-beta1a inhibits the secretion of Th17-polarizing cytokines in human dendritic cells via TLR7 up-regulation. THE JOURNAL OF IMMUNOLOGY 2009; 182:3928-36. [PMID: 19265172 DOI: 10.4049/jimmunol.0802226] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
IFN-beta, an effective therapy against relapsing-remitting multiple sclerosis, is naturally secreted during the innate immune response against viral pathogens. The objective of this study was to characterize the immunomodulatory mechanisms of IFN-beta targeting innate immune response and their effects on dendritic cell (DC)-mediated regulation of T cell differentiation. We found that IFN-beta1a in vitro treatment of human monocyte-derived DCs induced the expression of TLR7 and the members of its downstream signaling pathway, including MyD88, IL-1R-associated kinase 4, and TNF receptor-associated factor 6, while it inhibited the expression of IL-1R. Using small interfering RNA TLR7 gene silencing, we confirmed that IFN-beta1a-induced changes in MyD88, IL-1R-associated kinase 4, and IL-1R expression were dependent on TLR7. TLR7 expression was also necessary for the IFN-beta1a-induced inhibition of IL-1beta and IL-23 and the induction of IL-27 secretion by DCs. Supernatant transfer experiments confirmed that IFN-beta1a-induced changes in DC cytokine secretion inhibit Th17 cell differentiation as evidenced by the inhibition of retinoic acid-related orphan nuclear hormone receptor C and IL-17A gene expression and IL-17A secretion. Our study has identified a novel therapeutic mechanism of IFN-beta1a that selectively targets the autoimmune response in multiple sclerosis.
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Affiliation(s)
- Xin Zhang
- Department of Neurology, University of North Carolina, Chapel Hill, NC 27599, USA
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43
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Goertsches RH, Hecker M, Zettl UK. Monitoring of multiple sclerosis immunotherapy: from single candidates to biomarker networks. J Neurol 2009; 255 Suppl 6:48-57. [PMID: 19300960 DOI: 10.1007/s00415-008-6010-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Applying microarray technology to identify new diagnostic and prognostic markers in peripheral blood cells (PBC) after therapeutic intervention opens great perspectives regarding patient subclassification. Three recombinant products of the pleiotropic agent interferon beta (rIFN-beta) are available for disease modifying therapy of relapsing remitting multiple sclerosis (RRMS), a complex inflammatory autoimmune disease that targets the central nervous system. They differ according to formulation, route of administration and dosage regimens. The currently, only partially understood mechanism of action of injected rIFN-beta into human organisms needs provision with accessory key molecules; in addition, the significance of established clinical IFN-beta response criteria that distinguish responding from non-responding patients remain unclear.With respect to these major questions, we discuss promising candidates on the gene transcription level, attained from scientific MS literature that included a longitudinal aspect. Reviewed studies were in part carried out with distinct gene interrogating platforms (GeneArrays; RT-PCR), settings (in vitro; ex vivo), and study designs (drug formulations and regimen; inclusion criteria and clinical endpoints), hampering meaningful meta-analysis. Nevertheless, PBC from therapy-naïve MS patients, rIFN-beta treated MS patients, and healthy controls served to characterize facets of both the disease and its treatment. Hence, the field of MS transcriptomics in immunomodulatory therapy is (by far) not adequately understood and should be embedded into systems biology disciplines, yielding multi-layer analyses that deliver timely identification of MS subjects who will profit from applied rIFN-beta therapy.
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Affiliation(s)
- Robert H Goertsches
- Department of Neurology, University of Rostock, Gehlsheimer Strasse 20, 18147 Rostock, Germany.
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44
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Vosslamber S, van Baarsen LGM, Verweij CL. Pharmacogenomics of IFN-beta in multiple sclerosis: towards a personalized medicine approach. Pharmacogenomics 2009; 10:97-108. [PMID: 19102719 DOI: 10.2217/14622416.10.1.97] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Multiple sclerosis (MS) is an inflammatory disease of the CNS. The clinical presentation of MS is heterogeneous. Interferons (IFNs) were the first agents to show clinical efficacy in the treatment of MS and prolonged treatment is still the best available therapy. Although IFN treatment ameliorates immune dysfunction, the response is partial. Clinical experience indicates that there are responders and nonresponders. This distinction suggests that a subset of patients are insensitive or resistant to the action of IFN. This implies that pharmacodynamic responses may differ between patients, leading to interindividual differences in clinical response. Understanding of the factors that underlie the therapeutic response is key to the identification of predictive markers. Here, we describe novel developments in pharmacogenomics research to improve the understanding of the pharmacological effects of IFN therapy, and the identification of biomarkers that allow stratification of MS patients for their response to IFN-beta. Ultimately, this information will lead to a personalized form of medicine, whereby a specific therapy will be applied that is best suited to an individual patient.
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Affiliation(s)
- Saskia Vosslamber
- VU University Medical Center, Deptartment of Pathology, Amsterdam, The Netherlands
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45
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Samarajiwa SA, Forster S, Auchettl K, Hertzog PJ. INTERFEROME: the database of interferon regulated genes. Nucleic Acids Res 2009; 37:D852-7. [PMID: 18996892 PMCID: PMC2686605 DOI: 10.1093/nar/gkn732] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 09/30/2008] [Accepted: 10/01/2008] [Indexed: 01/05/2023] Open
Abstract
INTERFEROME is an open access database of types I, II and III Interferon regulated genes (http://www.interferome.org) collected from analysing expression data sets of cells treated with IFNs. This database of interferon regulated genes integrates information from high-throughput experiments with annotation, ontology, orthologue sequences from 37 species, tissue expression patterns and gene regulatory information to enable a detailed investigation of the molecular mechanisms underlying IFN biology. INTERFEROME fulfils a need in infection, immunity, development and cancer research by providing computational tools to assist in identifying interferon signatures in gene lists generated by high-throughput expression technologies, and their potential molecular and biological consequences.
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Affiliation(s)
- Shamith A. Samarajiwa
- Center for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, and CRC for chronic inflammatory disease, North Melbourne, Victoria, Australia
| | - Sam Forster
- Center for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, and CRC for chronic inflammatory disease, North Melbourne, Victoria, Australia
| | - Katie Auchettl
- Center for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, and CRC for chronic inflammatory disease, North Melbourne, Victoria, Australia
| | - Paul J. Hertzog
- Center for Innate Immunity and Infectious Diseases, Monash Institute of Medical Research, Monash University, Clayton, and CRC for chronic inflammatory disease, North Melbourne, Victoria, Australia
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46
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Martinez-Forero I, Pelaez A, Villoslada P. Pharmacogenomics of multiple sclerosis: in search for a personalized therapy. Expert Opin Pharmacother 2008; 9:3053-67. [DOI: 10.1517/14656560802515553] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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47
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Weinstock-Guttman B, Ramanathan M, Zivadinov R. Interferon-beta treatment for relapsing multiple sclerosis. Expert Opin Biol Ther 2008; 8:1435-47. [PMID: 18694361 DOI: 10.1517/14712598.8.9.1435] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Recombinant forms of IFN-beta were the first therapeutic intervention found to be effective at interfering with the course of multiple sclerosis (MS), a chronic and debilitating disease affecting the CNS in young adults. OBJECTIVE/METHODS To examine the application of IFN-beta to MS treatment by a review of relevant literature. RESULTS The different IFN-beta products available are similar in their clinical effects. However, the response to IFN-beta therapy is only partial and the most efficient individual-specific dose, route and frequency of administration are not elucidated fully. The mechanism of action of IFN-beta in MS is also not understood fully but its immunomodulatory effects are probably more important than its anti-proliferative and antiviral activities. CONCLUSIONS Although new therapeutic approaches are being sought to better treat MS, IFN-beta remains one of the most recognized and approved worldwide therapeutic options for this disease.
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Affiliation(s)
- Bianca Weinstock-Guttman
- The Jacobs Neurological Institute, Department of Neurology, University at Buffalo, State University of New York, Buffalo, NY 14203, USA.
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48
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Weinstock-Guttman B, Bhasi K, Badgett D, Tamaño-Blanco M, Minhas M, Feichter J, Patrick K, Munschauer F, Bakshi R, Ramanathan M. Genomic effects of once-weekly, intramuscular interferon-beta1a treatment after the first dose and on chronic dosing: Relationships to 5-year clinical outcomes in multiple sclerosis patients. J Neuroimmunol 2008; 205:113-25. [PMID: 18950872 DOI: 10.1016/j.jneuroim.2008.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 08/25/2008] [Accepted: 09/02/2008] [Indexed: 01/10/2023]
Abstract
PURPOSE To characterize gene expression in multiple sclerosis (MS) patients after the first dose and chronic dosing of 30 microg, once weekly, intramuscular interferon-beta1a (IFN-beta) and to delineate the pharmacogenomic differences between Good Responders and Partial Responders to IFN-beta therapy. METHODS The treatment responses after the first IFN-beta dose and chronic IFN-beta dosing were assessed in 22 relapsing MS patients (17 females, 5 males; average age: 41.5+/-SD 10.4 years). Gene expression profiles in peripheral blood mononuclear cells were obtained prior to treatment and at 1, 2, 4, 8, 24, 48, 120, 168 h after the first IFN-beta dose and at 1, 6 and 12 months after chronic dosing with once-weekly 30 microg IFN-beta-1a intramuscularly. Repeated measures statistics with false discovery rate control were used. The functional characteristics, biological pathways and transcription factor sites were analyzed. RESULTS Of the 1000 genes modulated following the first dose and upon chronic dosing of IFN-beta in MS patients, approximately 35% were up-regulated and 65% were down- regulated; the percentage of modulated genes in common was approximately 50%. The expression of the pharmacodynamic mRNA markers of IFN-beta effect showed differences in time profiles for the Good Responder and Partial Responders to IFN-beta therapy and the Jak-STAT, TNFRSF10B, IL6, TGFbeta, retinoic acid and CDC42 pathways were differentially modulated. The patients with side effects to therapy showed differences in the TGFbeta1, IFNG/STAT3 and TNF pathways. CONCLUSIONS Gene expression is a valuable tool for understanding the molecular mechanisms of IFN-beta action in MS patients.
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49
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Translation towards personalized medicine in Multiple Sclerosis. J Neurol Sci 2008; 274:68-75. [PMID: 18789804 DOI: 10.1016/j.jns.2008.07.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Revised: 07/19/2008] [Accepted: 07/24/2008] [Indexed: 12/24/2022]
Abstract
In recent years the realization that the concept 'one drug fits all' - does not work, created the need to shift gears from 'treating the disease' to 'treating the patient', and implementation of 'Personalized Medicine' where treatment is tailored to the individual. In chronic and progressive diseases, such as Multiple Sclerosis (MS), the need for tailored therapeutics is especially imperative, as the consequences of an ineffective medication might be irreversible dysfunction. In recent years accumulating evidence indicates that MS is not a single disease and that patients with different disease subtypes respond differently to a medication. Environment and genetics are among the factors that determine disease subtype and activity, and the patient's response to medication. Additional factors include demographic characteristics such as gender and age, as well as chrono-biological indicators. During the last few years, advances and availability of new technologies have brought genome-wide gene expression profiling studies to many medical fields, including MS. Genomic technologies have also stimulated pharmacogenetics studies, that aim to identify genetic factors that affect response to treatment. However, pharmacogenetics information is still immature to allow its translation to clinical practice in MS. Notably, one of the major limitations in obtaining reproducible data across MS pharmacogenetics studies has been the lack of a consensus as to the appropriate method for determining clinical response. In light of the rapid advances in technology and progress in applying individualized treatment strategies in other diseases, 'Personalized Medicine' for MS seems feasible within the coming years.
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50
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Lin TH, Kaminski N, Bar-Joseph Z. Alignment and classification of time series gene expression in clinical studies. Bioinformatics 2008; 24:i147-55. [PMID: 18586707 PMCID: PMC2718630 DOI: 10.1093/bioinformatics/btn152] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Motivation: Classification of tissues using static gene-expression data has received considerable attention. Recently, a growing number of expression datasets are measured as a time series. Methods that are specifically designed for this temporal data can both utilize its unique features (temporal evolution of profiles) and address its unique challenges (different response rates of patients in the same class). Results: We present a method that utilizes hidden Markov models (HMMs) for the classification task. We use HMMs with less states than time points leading to an alignment of the different patient response rates. To focus on the differences between the two classes we develop a discriminative HMM classifier. Unlike the traditional generative HMM, discriminative HMM can use examples from both classes when learning the model for a specific class. We have tested our method on both simulated and real time series expression data. As we show, our method improves upon prior methods and can suggest markers for specific disease and response stages that are not found when using traditional classifiers. Availability: Matlab implementation is available from http://www.cs.cmu.edu/~thlin/tram/ Contact:zivbj@cs.cmu.edu
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Affiliation(s)
- Tien-ho Lin
- School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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