1
|
Agliardi C, Guerini FR, Zanzottera M, Bolognesi E, Caputo D, Rovaris M, Clerici M. Increased concentrations of P2X7R in oligodendrocyte derived extracellular vesicles of Multiple sclerosis patients. Neurobiol Dis 2024; 199:106601. [PMID: 38996986 DOI: 10.1016/j.nbd.2024.106601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/25/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024] Open
Abstract
Activation of the purinergic receptor P2X7 (P2X7R) is believed to be deleterious in autoimmune diseases and it was hypothesized to play a role in the pathogenesis of MS. P2X7R is an ATP-gated non-selective cationic channel; its activation can be driven by high concentrations of ATP and leads to the generation of large, cytolytic conductance pores. P2X7R activation can also result in apoptosis as a consequence of the activation of the caspase cascade via P2X7R-dependent stimulation of the NLRP3 inflammasome. We measured P2X7R in oligodendrocyte derived extracellular vesicles (ODEVs) in MS patients and in healthy subjects. Sixty-eight MS patients (50 relapsing-remitting, RR-MS, 18 primary progressive, PP-MS) and 57 healthy controls (HC) were enrolled. ODEVs were enriched from serum by a double step immunoaffinity method using an anti OMGp (oligodendrocyte myelin glycoprotein) antibody. P2X7R concentration was measured in ODEVs lysates by ELISA. One-way Anova test showed that P2X7R in ODEVs is significantly higher in PP-MS (mean: 1742.89 pg/mL) compared both to RR-MS (mean: 1277.33 pg/mL) (p < 0.001) and HC (mean: 879.79 pg/mL) (p < 0.001). Comparison between RR-MS and HC was also statistically significant (p < 0.001). Pearson's correlations showed that P2RX7 in ODEVs was positively correlated with EDSS (p = 0.002, r = 0.38, 0.15-0.57 95% CI) and MSSS (p = 0.004, r = 0.34, 0.12-0.54 95% CI) scores, considering MS patients together (PP-MS + RR-MS) and with disease duration in PP-MS group (p = 0.02, r = 0.53, 0.09-0.80 95% CI). Results suggest that ODEVs-associated P2X7R levels could be a biomarker for MS.
Collapse
Affiliation(s)
- Cristina Agliardi
- IRCCS Fondazione Don Carlo Gnocchi ONLUS, Via Capecelatro 66, Milan, Italy
| | | | - Milena Zanzottera
- IRCCS Fondazione Don Carlo Gnocchi ONLUS, Via Capecelatro 66, Milan, Italy
| | | | - Domenico Caputo
- IRCCS Fondazione Don Carlo Gnocchi ONLUS, Via Capecelatro 66, Milan, Italy
| | - Marco Rovaris
- IRCCS Fondazione Don Carlo Gnocchi ONLUS, Via Capecelatro 66, Milan, Italy
| | - Mario Clerici
- IRCCS Fondazione Don Carlo Gnocchi ONLUS, Via Capecelatro 66, Milan, Italy; Pathophysiology and Transplantation Department, University of Milan, via Francesco Sforza 35, Milan, Italy
| |
Collapse
|
2
|
Neidhart S, Vlad B, Hilty M, Högelin KA, Ziegler M, Berenjeno-Correa E, Reichen I, Stridh P, Jelcic I, Khademi M, Kockum I, Sospedra M, Al Nimer F, Martin R, Jelcic I. HLA Associations of Intrathecal IgG Production against Specific Viruses in Multiple Sclerosis. Ann Neurol 2024; 95:1112-1126. [PMID: 38551149 DOI: 10.1002/ana.26921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/05/2024] [Accepted: 03/04/2024] [Indexed: 05/18/2024]
Abstract
OBJECTIVE Specific human leucocyte antigen (HLA) alleles are not only associated with higher risk to develop multiple sclerosis (MS) and other autoimmune diseases, but also with the severity of various viral and bacterial infections. Here, we analyzed the most specific biomarker for MS, that is, the polyspecific intrathecal IgG antibody production against measles, rubella, and varicella zoster virus (MRZ reaction), for possible HLA associations in MS. METHODS We assessed MRZ reaction from 184 Swiss patients with MS and clinically isolated syndrome (CIS) and 89 Swiss non-MS/non-CIS control patients, and performed HLA sequence-based typing, to check for associations of positive MRZ reaction with the most prevalent HLA alleles. We used a cohort of 176 Swedish MS/CIS patients to replicate significant findings. RESULTS Whereas positive MRZ reaction showed a prevalence of 38.0% in MS/CIS patients, it was highly specific (97.7%) for MS/CIS. We identified HLA-DRB1*15:01 and other tightly linked alleles of the HLA-DR15 haplotype as the strongest HLA-encoded risk factors for a positive MRZ reaction in Swiss MS/CIS (odds ratio [OR], 3.90, 95% confidence interval [CI] 2.05-7.46, padjusted = 0.0004) and replicated these findings in Swedish MS/CIS patients (OR 2.18, 95%-CI 1.16-4.02, padjusted = 0.028). In addition, female MS/CIS patients had a significantly higher probability for a positive MRZ reaction than male patients in both cohorts combined (padjusted <0.005). INTERPRETATION HLA-DRB1*15:01, the strongest genetic risk factor for MS, and female sex, 1 of the most prominent demographic risk factors for developing MS, predispose in MS/CIS patients for a positive MRZ reaction, the most specific CSF biomarker for MS. ANN NEUROL 2024;95:1112-1126.
Collapse
Affiliation(s)
- Stephan Neidhart
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Benjamin Vlad
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Marc Hilty
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Klara Asplund Högelin
- Center for Molecular Medicine, Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Mario Ziegler
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Ernesto Berenjeno-Correa
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Ina Reichen
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Pernilla Stridh
- Center for Molecular Medicine, Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ivan Jelcic
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Mohsen Khademi
- Center for Molecular Medicine, Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Kockum
- Center for Molecular Medicine, Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Mireia Sospedra
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
- Clinical Research Priority Program MS (CRPP) PrecisionMS of the University of Zurich, Zurich, Switzerland
| | - Faiez Al Nimer
- Center for Molecular Medicine, Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Roland Martin
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
- Clinical Research Priority Program MS (CRPP) PrecisionMS of the University of Zurich, Zurich, Switzerland
- Center for Molecular Medicine, Therapeutic Immune Design Unit, Department of Clinical Neuroscience, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ilijas Jelcic
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
- Clinical Research Priority Program MS (CRPP) PrecisionMS of the University of Zurich, Zurich, Switzerland
| |
Collapse
|
3
|
Pagalilauan AM, Everest E, Rachimi S, Reich D, Waldman AD, Sadovnick AD, Vilariño-Guell C, Lenardo MJ. The Canadian Collaborative Project on Genetic Susceptibility to Multiple Sclerosis cohort population structure and disease etiology. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.18.24305992. [PMID: 38712288 PMCID: PMC11071557 DOI: 10.1101/2024.04.18.24305992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Background Previous genetic and epidemiological studies have examined subpopulations from the Canadian Collaborative Project on Genetic Susceptibility to Multiple Sclerosis (CCPGSMS) patient cohort, but an encompassing analysis of the study population has not yet been carried out. Objective This study examines patterns of multiple sclerosis (MS) prevalence in 13,663 cohort members, including 4,821 patients with MS or suspected MS and 8,842 family members. Methods We grouped participants into epidemiologic subgroups based on age of MS onset, clinical stage at diagnosis, symptom type at disease onset, sex, proband status, disability as measured by the EDSS, and ancestry based on reported ethnicity. Results We observed a 2.7:1 MS prevalence ratio of women to men, though disease severity was greater for male patients. Variation in the age of disease onset between patients was only slightly associated with sex and strongly associated with disease type. Specific types of clinical symptoms at disease onset were associated with the prognosis. Regional residence did not correlate with disease onset, type, or severity. Conclusion Population trends, as presented here, are not explained by environmental factors alone, highlighting the need for a comprehensive genetic analysis to understand disease variance across families.
Collapse
|
4
|
Behr M, Kumbier K, Cordova-Palomera A, Aguirre M, Ronen O, Ye C, Ashley E, Butte AJ, Arnaout R, Brown B, Priest J, Yu B. Learning epistatic polygenic phenotypes with Boolean interactions. PLoS One 2024; 19:e0298906. [PMID: 38625909 PMCID: PMC11020961 DOI: 10.1371/journal.pone.0298906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 01/31/2024] [Indexed: 04/18/2024] Open
Abstract
Detecting epistatic drivers of human phenotypes is a considerable challenge. Traditional approaches use regression to sequentially test multiplicative interaction terms involving pairs of genetic variants. For higher-order interactions and genome-wide large-scale data, this strategy is computationally intractable. Moreover, multiplicative terms used in regression modeling may not capture the form of biological interactions. Building on the Predictability, Computability, Stability (PCS) framework, we introduce the epiTree pipeline to extract higher-order interactions from genomic data using tree-based models. The epiTree pipeline first selects a set of variants derived from tissue-specific estimates of gene expression. Next, it uses iterative random forests (iRF) to search training data for candidate Boolean interactions (pairwise and higher-order). We derive significance tests for interactions, based on a stabilized likelihood ratio test, by simulating Boolean tree-structured null (no epistasis) and alternative (epistasis) distributions on hold-out test data. Finally, our pipeline computes PCS epistasis p-values that probabilisticly quantify improvement in prediction accuracy via bootstrap sampling on the test set. We validate the epiTree pipeline in two case studies using data from the UK Biobank: predicting red hair and multiple sclerosis (MS). In the case of predicting red hair, epiTree recovers known epistatic interactions surrounding MC1R and novel interactions, representing non-linearities not captured by logistic regression models. In the case of predicting MS, a more complex phenotype than red hair, epiTree rankings prioritize novel interactions surrounding HLA-DRB1, a variant previously associated with MS in several populations. Taken together, these results highlight the potential for epiTree rankings to help reduce the design space for follow up experiments.
Collapse
Affiliation(s)
- Merle Behr
- Faculty of Informatics and Data Science, University of Regensburg, Regensburg, Germany
| | - Karl Kumbier
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America
| | | | - Matthew Aguirre
- Department of Pediatrics, Stanford Medicine, Stanford, CA, United States of America
- Department of Biomedical Data Science, Stanford Medicine, Stanford, CA, United States of America
| | - Omer Ronen
- Department of Statistics, University of California at Berkeley, Berkeley, CA, United States of America
| | - Chengzhong Ye
- Department of Statistics, University of California at Berkeley, Berkeley, CA, United States of America
| | - Euan Ashley
- Division of Cardiovascular Medicine, Stanford Medicine, Stanford, CA, United States of America
| | - Atul J. Butte
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States of America
| | - Rima Arnaout
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States of America
- Division of Cardiology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Ben Brown
- Department of Statistics, University of California at Berkeley, Berkeley, CA, United States of America
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - James Priest
- Department of Pediatrics, Stanford Medicine, Stanford, CA, United States of America
| | - Bin Yu
- Department of Statistics, University of California at Berkeley, Berkeley, CA, United States of America
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California at Berkeley, Berkeley, CA, United States of America
| |
Collapse
|
5
|
Ferar K, Hall TO, Crawford DC, Rowley R, Satterfield BA, Li R, Gragert L, Karlson EW, de Andrade M, Kullo IJ, McCarty CA, Kho A, Hayes MG, Ritchie MD, Crane PK, Mirel DB, Carlson C, Connolly JJ, Hakonarson H, Crenshaw AT, Carrell D, Luo Y, Dikilitas O, Denny JC, Jarvik GP, Crosslin DR. Genetic variation in the human leukocyte antigen region confers susceptibility to Clostridioides difficile infection. Sci Rep 2023; 13:18532. [PMID: 37898691 PMCID: PMC10613277 DOI: 10.1038/s41598-023-45649-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 10/22/2023] [Indexed: 10/30/2023] Open
Abstract
Clostridioides difficile (C. diff.) infection (CDI) is a leading cause of hospital acquired diarrhea in North America and Europe and a major cause of morbidity and mortality. Known risk factors do not fully explain CDI susceptibility, and genetic susceptibility is suggested by the fact that some patients with colons that are colonized with C. diff. do not develop any infection while others develop severe or recurrent infections. To identify common genetic variants associated with CDI, we performed a genome-wide association analysis in 19,861 participants (1349 cases; 18,512 controls) from the Electronic Medical Records and Genomics (eMERGE) Network. Using logistic regression, we found strong evidence for genetic variation in the DRB locus of the MHC (HLA) II region that predisposes individuals to CDI (P > 1.0 × 10-14; OR 1.56). Altered transcriptional regulation in the HLA region may play a role in conferring susceptibility to this opportunistic enteric pathogen.
Collapse
Affiliation(s)
- Kathleen Ferar
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA.
| | - Taryn O Hall
- Optum Genomics, UnitedHealth Group, Minnetonka, MN, USA
| | - Dana C Crawford
- Department of Population and Quantitative Health Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Robb Rowley
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Rongling Li
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Loren Gragert
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA
| | | | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Iftikhar J Kullo
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Catherine A McCarty
- University of Minnesota Medical School, Duluth, MN, USA
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, WI, USA
| | - Abel Kho
- Divisions of General Internal Medicine and Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marylyn D Ritchie
- Department of Biochemistry and Molecular Biology, Center for Systems Genomics, Pennsylvania State University, University Park, PA, USA
| | - Paul K Crane
- Division of General Internal Medicine, University of Washington, Seattle, WA, USA
| | | | - Christopher Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - John J Connolly
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - David Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Yuan Luo
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ozan Dikilitas
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington Medical Center, Seattle, WA, USA
| | - David R Crosslin
- Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA, USA.
| |
Collapse
|
6
|
Houtman M, Dzebisashvili A, Dubnovitsky A, Kozhukh G, Rönnblom L, Klareskog L, Malmström V, Padyukov L. Five commercially-available antibodies react differentially with allelic forms of human HLA-DR beta chain. Mol Immunol 2022; 152:106-110. [DOI: 10.1016/j.molimm.2022.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/05/2022] [Accepted: 10/16/2022] [Indexed: 11/06/2022]
|
7
|
González-Madrid E, Rangel-Ramírez MA, Mendoza-León MJ, Álvarez-Mardones O, González PA, Kalergis AM, Opazo MC, Riedel CA. Risk Factors from Pregnancy to Adulthood in Multiple Sclerosis Outcome. Int J Mol Sci 2022; 23:ijms23137080. [PMID: 35806081 PMCID: PMC9266360 DOI: 10.3390/ijms23137080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
Multiple sclerosis (MS) is an autoimmune disease characterized by a robust inflammatory response against myelin sheath antigens, which causes astrocyte and microglial activation and demyelination of the central nervous system (CNS). Multiple genetic predispositions and environmental factors are known to influence the immune response in autoimmune diseases, such as MS, and in the experimental autoimmune encephalomyelitis (EAE) model. Although the predisposition to suffer from MS seems to be a multifactorial process, a highly sensitive period is pregnancy due to factors that alter the development and differentiation of the CNS and the immune system, which increases the offspring’s susceptibility to develop MS. In this regard, there is evidence that thyroid hormone deficiency during gestation, such as hypothyroidism or hypothyroxinemia, may increase susceptibility to autoimmune diseases such as MS. In this review, we discuss the relevance of the gestational period for the development of MS in adulthood.
Collapse
Affiliation(s)
- Enrique González-Madrid
- Laboratorio Endocrinología-Inmunología, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8320000, Chile; (E.G.-M.); (M.A.R.-R.); (M.J.M.-L.); (O.Á.-M.)
- Millennium Institute on Immunology and Immunotherapy, Santiago 8320000, Chile; (P.A.G.); (A.M.K.); (M.C.O.)
| | - Ma. Andreina Rangel-Ramírez
- Laboratorio Endocrinología-Inmunología, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8320000, Chile; (E.G.-M.); (M.A.R.-R.); (M.J.M.-L.); (O.Á.-M.)
- Millennium Institute on Immunology and Immunotherapy, Santiago 8320000, Chile; (P.A.G.); (A.M.K.); (M.C.O.)
| | - María José Mendoza-León
- Laboratorio Endocrinología-Inmunología, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8320000, Chile; (E.G.-M.); (M.A.R.-R.); (M.J.M.-L.); (O.Á.-M.)
- Millennium Institute on Immunology and Immunotherapy, Santiago 8320000, Chile; (P.A.G.); (A.M.K.); (M.C.O.)
| | - Oscar Álvarez-Mardones
- Laboratorio Endocrinología-Inmunología, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8320000, Chile; (E.G.-M.); (M.A.R.-R.); (M.J.M.-L.); (O.Á.-M.)
- Millennium Institute on Immunology and Immunotherapy, Santiago 8320000, Chile; (P.A.G.); (A.M.K.); (M.C.O.)
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy, Santiago 8320000, Chile; (P.A.G.); (A.M.K.); (M.C.O.)
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy, Santiago 8320000, Chile; (P.A.G.); (A.M.K.); (M.C.O.)
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile
- Departamento de Endocrinología, Escuela de Medicina, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 8320000, Chile
| | - Ma. Cecilia Opazo
- Millennium Institute on Immunology and Immunotherapy, Santiago 8320000, Chile; (P.A.G.); (A.M.K.); (M.C.O.)
- Instituto de Ciencias Naturales, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Manuel Montt 948, Providencia 7500000, Chile
| | - Claudia A. Riedel
- Laboratorio Endocrinología-Inmunología, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8320000, Chile; (E.G.-M.); (M.A.R.-R.); (M.J.M.-L.); (O.Á.-M.)
- Millennium Institute on Immunology and Immunotherapy, Santiago 8320000, Chile; (P.A.G.); (A.M.K.); (M.C.O.)
- Correspondence:
| |
Collapse
|
8
|
Houtman M, Hesselberg E, Rönnblom L, Klareskog L, Malmström V, Padyukov L. Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients. Front Immunol 2021; 12:707217. [PMID: 34484204 PMCID: PMC8416041 DOI: 10.3389/fimmu.2021.707217] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 08/02/2021] [Indexed: 01/03/2023] Open
Abstract
HLA-DRB1 alleles have been associated with several autoimmune diseases. For anti-citrullinated protein antibody positive rheumatoid arthritis (RA), HLA-DRB1 shared epitope (SE) alleles are the major genetic risk factors. In order to study the genetic regulation of major histocompatibility complex (MHC) Class II gene expression in immune cells, we investigated transcriptomic profiles of a variety of immune cells from healthy individuals carrying different HLA-DRB1 alleles. Sequencing libraries from peripheral blood mononuclear cells, CD4+ T cells, CD8+ T cells, and CD14+ monocytes of 32 genetically pre-selected healthy female individuals were generated, sequenced and reads were aligned to the standard reference. For the MHC region, reads were mapped to available MHC reference haplotypes and AltHapAlignR was used to estimate gene expression. Using this method, HLA-DRB and HLA-DQ were found to be differentially expressed in different immune cells of healthy individuals as well as in whole blood samples of RA patients carrying HLA-DRB1 SE-positive versus SE-negative alleles. In contrast, no genes outside the MHC region were differentially expressed between individuals carrying HLA-DRB1 SE-positive and SE-negative alleles, thus HLA-DRB1 SE alleles have a strong cis effect on gene expression. Altogether, our findings suggest that immune effects associated with different allelic forms of HLA-DR and HLA-DQ may be associated not only with differences in the structure of these proteins, but also with differences in their expression levels.
Collapse
Affiliation(s)
- Miranda Houtman
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Espen Hesselberg
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Klareskog
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Vivianne Malmström
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
9
|
Martin R, Sospedra M, Eiermann T, Olsson T. Multiple sclerosis: doubling down on MHC. Trends Genet 2021; 37:784-797. [PMID: 34006391 DOI: 10.1016/j.tig.2021.04.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 01/12/2023]
Abstract
Human leukocyte antigen (HLA)-encoded surface molecules present antigenic peptides to T lymphocytes and play a key role in adaptive immune responses. Besides their physiological role of defending the host against infectious pathogens, specific alleles serve as genetic risk factors for autoimmune diseases. For multiple sclerosis (MS), an autoimmune disease that affects the brain and spinal cord, an association with the HLA-DR15 haplotype was described in the early 1970s. This short opinion piece discusses the difficulties of disentangling the details of this association and recent observations about the functional involvement of not only one, but also the second gene of the HLA-DR15 haplotype. This information is not only important for understanding the pathomechanism of MS, but also for antigen-specific therapies.
Collapse
Affiliation(s)
- Roland Martin
- Neuroimmunology and Multiple Sclerosis Research, Neurology Clinic, Frauenklinikstrasse 26, 8091 Zurich, University Hospital Zurich, University Zurich, Switzerland.
| | - Mireia Sospedra
- Neuroimmunology and Multiple Sclerosis Research, Neurology Clinic, Frauenklinikstrasse 26, 8091 Zurich, University Hospital Zurich, University Zurich, Switzerland
| | - Thomas Eiermann
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
| |
Collapse
|
10
|
Wang J, Jelcic I, Mühlenbruch L, Haunerdinger V, Toussaint NC, Zhao Y, Cruciani C, Faigle W, Naghavian R, Foege M, Binder TMC, Eiermann T, Opitz L, Fuentes-Font L, Reynolds R, Kwok WW, Nguyen JT, Lee JH, Lutterotti A, Münz C, Rammensee HG, Hauri-Hohl M, Sospedra M, Stevanovic S, Martin R. HLA-DR15 Molecules Jointly Shape an Autoreactive T Cell Repertoire in Multiple Sclerosis. Cell 2020; 183:1264-1281.e20. [PMID: 33091337 PMCID: PMC7707104 DOI: 10.1016/j.cell.2020.09.054] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 08/04/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022]
Abstract
The HLA-DR15 haplotype is the strongest genetic risk factor for multiple sclerosis (MS), but our understanding of how it contributes to MS is limited. Because autoreactive CD4+ T cells and B cells as antigen-presenting cells are involved in MS pathogenesis, we characterized the immunopeptidomes of the two HLA-DR15 allomorphs DR2a and DR2b of human primary B cells and monocytes, thymus, and MS brain tissue. Self-peptides from HLA-DR molecules, particularly from DR2a and DR2b themselves, are abundant on B cells and thymic antigen-presenting cells. Furthermore, we identified autoreactive CD4+ T cell clones that can cross-react with HLA-DR-derived self-peptides (HLA-DR-SPs), peptides from MS-associated foreign agents (Epstein-Barr virus and Akkermansia muciniphila), and autoantigens presented by DR2a and DR2b. Thus, both HLA-DR15 allomorphs jointly shape an autoreactive T cell repertoire by serving as antigen-presenting structures and epitope sources and by presenting the same foreign peptides and autoantigens to autoreactive CD4+ T cells in MS. HLA-DR15 present abundant HLA-DR-derived self-peptides on B cells Autoreactive T cells in MS recognize HLA-DR-derived self-peptides/DR15 complexes Foreign peptides/DR15 complexes trigger potential autoreactive T cells in MS HLA-DR15 shape an autoreactive T cell repertoire by cross-reactivity/restriction
Collapse
Affiliation(s)
- Jian Wang
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Ivan Jelcic
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Lena Mühlenbruch
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Veronika Haunerdinger
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich 8093, Switzerland; Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, MD 20850, USA
| | - Carolina Cruciani
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Wolfgang Faigle
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Reza Naghavian
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Magdalena Foege
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Thomas M C Binder
- HLA Laboratory of the Stefan Morsch Foundation (SMS), Birkenfeld 55765, Germany
| | - Thomas Eiermann
- Department of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Lennart Opitz
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology and University of Zurich, Zurich 8057, Switzerland
| | - Laura Fuentes-Font
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - Richard Reynolds
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Julie T Nguyen
- One Lambda, Inc., a part of Transplant Diagnostics Thermo Fisher Scientific, 22801 Roscoe Blvd., West Hills, CA 91304, USA
| | - Jar-How Lee
- One Lambda, Inc., a part of Transplant Diagnostics Thermo Fisher Scientific, 22801 Roscoe Blvd., West Hills, CA 91304, USA
| | - Andreas Lutterotti
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Hans-Georg Rammensee
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Mathias Hauri-Hohl
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Mireia Sospedra
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Stefan Stevanovic
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland.
| |
Collapse
|
11
|
Stürner KH, Siembab I, Schön G, Stellmann JP, Heidari N, Fehse B, Heesen C, Eiermann TH, Martin R, Binder TM. Is multiple sclerosis progression associated with the HLA-DR15 haplotype? Mult Scler J Exp Transl Clin 2019; 5:2055217319894615. [PMID: 31839982 PMCID: PMC6902395 DOI: 10.1177/2055217319894615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/04/2019] [Accepted: 11/09/2019] [Indexed: 11/17/2022] Open
Abstract
Background The prevalence of multiple sclerosis is associated with the major histocompatibility complex class II DR15 haplotype HLA-DRB1*15:01∼HLA-DRB5*01:01. Objective To assess whether multiple sclerosis progression is associated with the main susceptibility haplotype HLA-DRB1*15:01∼HLA-DRB5*01:01. Methods Patients (n = 1230) and healthy controls (n = 2110) were genotyped for HLA-DRB1 and HLA-DRB5. The baseline Expanded Disability Status Scale (EDSS) score was determined and patients were followed for at least 3 years. Results After follow-up of the consecutive cohort 349 patients were classified as having clinical isolated syndrome and 881 patients as having multiple sclerosis. The susceptibility allele HLA-DRB1*15:01 was more frequent in clinical isolated syndrome (odds ratio 1.56) and multiple sclerosis (odds ratio 3.17) compared to controls. HLA- DRB1*15:01 was the only enriched HLA-DRB1 allele in multiple sclerosis patients. Comparison of clinical characteristics between HLA-DRB1*15:01∼HLA-DRB5*01:01 negative and positive patients with multiple sclerosis showed that baseline EDSS score, disease duration and frequency of the category secondary progressive multiple sclerosis with relapse were increased in the HLA-DRB1*15:01∼HLA-DRB5*01:01 positive group. Conclusion The study confirmed HLA-DRB1*15:01 and HLA-DRB5*01:01 as the main susceptibility alleles and showed weak indirect evidence for a role in progression of the disease.
Collapse
Affiliation(s)
- Klarissa Hanja Stürner
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Inessa Siembab
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Gerhard Schön
- Department of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Germany
| | - Jan-Patrick Stellmann
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Nika Heidari
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, University Medical Center Hamburg-Eppendorf, Germany
| | - Christoph Heesen
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Thomas H Eiermann
- HLA Laboratory, University Medical Center Hamburg-Eppendorf, Germany
| | - Roland Martin
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Thomas Mc Binder
- HLA Laboratory, University Medical Center Hamburg-Eppendorf, Germany
| |
Collapse
|
12
|
Zakharova MY, Belyanina TA, Sokolov AV, Kiselev IS, Mamedov AE. The Contribution of Major Histocompatibility Complex Class II Genes to an Association with Autoimmune Diseases. Acta Naturae 2019; 11:4-12. [PMID: 31993230 PMCID: PMC6977962 DOI: 10.32607/20758251-2019-11-4-4-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Genetic studies of patients with autoimmune diseases have shown that one of the most important roles in the developing of these diseases is played by a cluster of genes of the major histocompatibility complex (MHC), as compared with other genome areas. Information on the specific contribution of MHC alleles, mostly MHC class II ones, to the genetic predisposition to autoimmune diseases is crucial for understanding their pathogenesis. This review dwells on the most relevant aspects of this problem: namely, the correlation between carriage of certain MHC II alleles and an increased (positively associated allele) or reduced (negatively associated allele) probability of developing the most common autoimmune diseases, such as type 1 diabetes, rheumatoid arthritis, multiple sclerosis, systemic lupus erythematosus, autoimmune thyroiditis, etc. The most universal haplotypes, DR3-DQ2 and DR4-DQ8, are positively associated with many of these diseases, while the universal allele HLA-DRB1*0701 is protective.
Collapse
Affiliation(s)
- M. Yu. Zakharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - T. A. Belyanina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| | - A. V. Sokolov
- I.M. Sechenov First Moscow State Medical University, Moscow, 119991 Russia
| | - I. S. Kiselev
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - A. E. Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997 Russia
| |
Collapse
|
13
|
Degoot AM, Chirove F, Ndifon W. Trans-Allelic Model for Prediction of Peptide:MHC-II Interactions. Front Immunol 2018; 9:1410. [PMID: 29988560 PMCID: PMC6026802 DOI: 10.3389/fimmu.2018.01410] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/06/2018] [Indexed: 12/30/2022] Open
Abstract
Major histocompatibility complex class two (MHC-II) molecules are trans-membrane proteins and key components of the cellular immune system. Upon recognition of foreign peptides expressed on the MHC-II binding groove, CD4+ T cells mount an immune response against invading pathogens. Therefore, mechanistic identification and knowledge of physicochemical features that govern interactions between peptides and MHC-II molecules is useful for the design of effective epitope-based vaccines, as well as for understanding of immune responses. In this article, we present a comprehensive trans-allelic prediction model, a generalized version of our previous biophysical model, that can predict peptide interactions for all three human MHC-II loci (HLA-DR, HLA-DP, and HLA-DQ), using both peptide sequence data and structural information of MHC-II molecules. The advantage of this approach over other machine learning models is that it offers a simple and plausible physical explanation for peptide–MHC-II interactions. We train the model using a benchmark experimental dataset and measure its predictive performance using novel data. Despite its relative simplicity, we find that the model has comparable performance to the state-of-the-art method, the NetMHCIIpan method. Focusing on the physical basis of peptide–MHC binding, we find support for previous theoretical predictions about the contributions of certain binding pockets to the binding energy. In addition, we find that binding pocket P5 of HLA-DP, which was not previously considered as a primary anchor, does make strong contribution to the binding energy. Together, the results indicate that our model can serve as a useful complement to alternative approaches to predicting peptide–MHC interactions.
Collapse
Affiliation(s)
- Abdoelnaser M Degoot
- African Institute of Mathematical Sciences (AIMS), Muizenberg, South Africa.,School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa.,DST-NRF Centre of Excellence in Mathematical and Statistical Sciences (CoE-MaSS), Gauteng, South Africa
| | - Faraimunashe Chirove
- School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Wilfred Ndifon
- African Institute of Mathematical Sciences (AIMS), Muizenberg, South Africa
| |
Collapse
|
14
|
DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis. Nat Commun 2018; 9:2397. [PMID: 29921915 PMCID: PMC6008330 DOI: 10.1038/s41467-018-04732-5] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/17/2018] [Indexed: 01/28/2023] Open
Abstract
The human leukocyte antigen (HLA) haplotype DRB1*15:01 is the major risk factor for multiple sclerosis (MS). Here, we find that DRB1*15:01 is hypomethylated and predominantly expressed in monocytes among carriers of DRB1*15:01. A differentially methylated region (DMR) encompassing HLA-DRB1 exon 2 is particularly affected and displays methylation-sensitive regulatory properties in vitro. Causal inference and Mendelian randomization provide evidence that HLA variants mediate risk for MS via changes in the HLA-DRB1 DMR that modify HLA-DRB1 expression. Meta-analysis of 14,259 cases and 171,347 controls confirms that these variants confer risk from DRB1*15:01 and also identifies a protective variant (rs9267649, p < 3.32 × 10-8, odds ratio = 0.86) after conditioning for all MS-associated variants in the region. rs9267649 is associated with increased DNA methylation at the HLA-DRB1 DMR and reduced expression of HLA-DRB1, suggesting a modulation of the DRB1*15:01 effect. Our integrative approach provides insights into the molecular mechanisms of MS susceptibility and suggests putative therapeutic strategies targeting a methylation-mediated regulation of the major risk gene.
Collapse
|
15
|
Meister D, Taimoory SM, Trant JF. Unnatural amino acids improve affinity and modulate immunogenicity: Developing peptides to treat MHC type II autoimmune disorders. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24058] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Daniel Meister
- Department of Chemistry and Biochemistry; University of Windsor, 401 Sunset Ave; Windsor Ontario N9B 3P4 Canada
| | - S. Maryamdokht Taimoory
- Department of Chemistry and Biochemistry; University of Windsor, 401 Sunset Ave; Windsor Ontario N9B 3P4 Canada
| | - John F. Trant
- Department of Chemistry and Biochemistry; University of Windsor, 401 Sunset Ave; Windsor Ontario N9B 3P4 Canada
| |
Collapse
|
16
|
The emergence of neuroepidemiology, neurovirology and neuroimmunology: the legacies of John F. Kurtzke and Richard ‘Dick’ T. Johnson. J Neurol 2016; 264:817-828. [DOI: 10.1007/s00415-016-8293-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 12/11/2022]
|
17
|
DNA Methylation: a New Player in Multiple Sclerosis. Mol Neurobiol 2016; 54:4049-4059. [PMID: 27314687 DOI: 10.1007/s12035-016-9966-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 06/08/2016] [Indexed: 12/11/2022]
Abstract
Multiple sclerosis (MS) is a neurological and chronic inflammatory disease that is mediated by demyelination and axonal degeneration in the central nervous system (CNS). Studies have shown that immune system components such as CD4+, CD8+, CD44+ T cells, B lymphatic cells, and inflammatory cytokines play a critical role in inflammatory processes and myelin damage associated with MS. Nevertheless, the pathogenesis of MS remains poorly defined. DNA methylation, a significant epigenetic modification, is reported to be extensively involved in MS pathogenesis through the regulation of gene expression. This review focuses on DNA methylation involved in MS pathogenesis. Evidence showed the hypermethylation of human leukocyte antigen-DRB1 (HLA-DRB1) in CD4+ T cells, the genome-wide DNA methylation in CD8+ T cells, the hypermethylation of interleukin-4 (IL-4)/forkhead winged helix transcription factor 3 (Foxp3), and the demethylation of interferon-γ (IFN-γ)/IL-17a in CD44+ encephalitogenic T cells. Studies also showed the hypermethylation of SH2-containing protein tyrosine phosphatase-1 (SHP-1) in peripheral blood mononuclear cells (PBMCs) and methylated changes of genes regulating oligodendrocyte and neuronal function in normal-appearing white matter. Clarifying the mechanism of aberrant methylation on MS may explain part of the pathology and will lead to the development of a new therapeutic target for the treatment of MS in the future.
Collapse
|
18
|
Martinez-Orozco FJ, Vicario JL, De Andres C, Fernandez-Arquero M, Peraita-Adrados R. Comorbidity of Narcolepsy Type 1 With Autoimmune Diseases and Other Immunopathological Disorders: A Case-Control Study. J Clin Med Res 2016; 8:495-505. [PMID: 27298657 PMCID: PMC4894018 DOI: 10.14740/jocmr2569w] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2016] [Indexed: 01/12/2023] Open
Abstract
Background Several evidences suggest that autoimmune diseases (ADs) tend to co-occur in an individual and within the same family. Narcolepsy type 1 (NT1) is a chronic sleep disorder caused by a selective loss of hypocretin-producing neurons due to a mechanism of neural destruction that indicates an autoimmune pathogenesis, although no evidence is available. We report on the comorbidity of ADs and other immunopathological diseases (including allergy diseases) in narcolepsy. Methods We studied 158 Caucasian NT1 patients (60.7% male; mean age 49.4 ± 19.7 years), in whom the diagnosis was confirmed by polysomnography followed by a multiple sleep latency test, or by hypocretin-1 levels measurements. Results Thirty out of 158 patients (18.99%; 53.3% female; 29 sporadic and one familial cases) had one or more immunopathological diseases associated. A control group of 151 subjects were matched by gender and age with the narcolepsy patients. Results demonstrated that there was a higher frequency of ADs in our series of narcolepsy patients compared to the sample of general population (odds ratio: 3.17; 95% confidence interval: 1.01 - 10.07; P = 0.040). A temporal relationship with the age at onset of the diseases was found. Conclusions Cataplexy was significantly more severe in NT1 patients with immunopathological diseases, and immunopathological diseases are a risk factor for severe forms of cataplexy in our series (odds ratio: 23.6; 95% confidence interval: 5.5 - 100.1).
Collapse
Affiliation(s)
| | - Jose Luis Vicario
- Histocompatibility, Blood Center of the Community of Madrid, Madrid, Spain
| | - Clara De Andres
- Neurology Service, Gregorio Maranon University Hospital, Madrid, Spain
| | | | - Rosa Peraita-Adrados
- Sleep and Epilepsy Unit, Clinical Neurophysiology Service, Gregorio Maranon University Hospital, Madrid, Spain
| |
Collapse
|
19
|
Ruhrmann S, Stridh P, Kular L, Jagodic M. Genomic imprinting: A missing piece of the Multiple Sclerosis puzzle? Int J Biochem Cell Biol 2015; 67:49-57. [PMID: 26002250 DOI: 10.1016/j.biocel.2015.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 05/10/2015] [Accepted: 05/11/2015] [Indexed: 12/14/2022]
Abstract
Evidence for parent-of-origin effects in complex diseases such as Multiple Sclerosis (MS) strongly suggests a role for epigenetic mechanisms in their pathogenesis. In this review, we describe the importance of accounting for parent-of-origin when identifying new risk variants for complex diseases and discuss how genomic imprinting, one of the best-characterized epigenetic mechanisms causing parent-of-origin effects, may impact etiology of complex diseases. While the role of imprinted genes in growth and development is well established, the contribution and molecular mechanisms underlying the impact of genomic imprinting in immune functions and inflammatory diseases are still largely unknown. Here we discuss emerging roles of imprinted genes in the regulation of inflammatory responses with a particular focus on the Dlk1 cluster that has been implicated in etiology of experimental MS-like disease and Type 1 Diabetes. Moreover, we speculate on the potential wider impact of imprinting via the action of imprinted microRNAs, which are abundantly present in the Dlk1 locus and predicted to fine-tune important immune functions. Finally, we reflect on how unrelated imprinted genes or imprinted genes together with non-imprinted genes can interact in so-called imprinted gene networks (IGN) and suggest that IGNs could partly explain observed parent-of-origin effects in complex diseases. Unveiling the mechanisms of parent-of-origin effects is therefore likely to teach us not only about the etiology of complex diseases but also about the unknown roles of this fascinating phenomenon underlying uneven genetic contribution from our parents. This article is part of a Directed Issue entitled: Epigenetics dynamics in development and disease.
Collapse
Affiliation(s)
- Sabrina Ruhrmann
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Pernilla Stridh
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
20
|
Kaushansky N, Eisenstein M, Boura-Halfon S, Hansen BE, Nielsen CH, Milo R, Zeilig G, Lassmann H, Altmann DM, Ben-Nun A. Role of a Novel Human Leukocyte Antigen-DQA1*01:02;DRB1*15:01 Mixed Isotype Heterodimer in the Pathogenesis of "Humanized" Multiple Sclerosis-like Disease. J Biol Chem 2015; 290:15260-78. [PMID: 25911099 DOI: 10.1074/jbc.m115.641209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Indexed: 11/06/2022] Open
Abstract
Gene-wide association and candidate gene studies indicate that the greatest effect on multiple sclerosis (MS) risk is driven by the HLA-DRB1*15:01 allele within the HLA-DR15 haplotype (HLA-DRB1*15:01-DQA1*01:02-DQB1*0602-DRB5*01:01). Nevertheless, linkage disequilibrium makes it difficult to define, without functional studies, whether the functionally relevant effect derives from DRB1*15:01 only, from its neighboring DQA1*01:02-DQB1*06:02 or DRB5*01:01 genes of HLA-DR15 haplotype, or from their combinations or epistatic interactions. Here, we analyzed the impact of the different HLA-DR15 haplotype alleles on disease susceptibility in a new "humanized" model of MS induced in HLA-transgenic (Tg) mice by human oligodendrocyte-specific protein (OSP)/claudin-11 (hOSP), one of the bona fide potential primary target antigens in MS. We show that the hOSP-associated MS-like disease is dominated by the DRB1*15:01 allele not only as the DRA1*01:01;DRB1*15:01 isotypic heterodimer but also, unexpectedly, as a functional DQA1*01:02;DRB1*15:01 mixed isotype heterodimer. The contribution of HLA-DQA1/DRB1 mixed isotype heterodimer to OSP pathogenesis was revealed in (DRB1*1501xDQB1*0602)F1 double-Tg mice immunized with hOSP(142-161) peptide, where the encephalitogenic potential of prevalent DRB1*1501/hOSP(142-161)-reactive Th1/Th17 cells is hindered due to a single amino acid difference in the OSP(142-161) region between humans and mice; this impedes binding of DRB1*1501 to the mouse OSP(142-161) epitope in the mouse CNS while exposing functional binding of mouse OSP(142-161) to DQA1*01:02;DRB1*15:01 mixed isotype heterodimer. This study, which shows for the first time a functional HLA-DQA1/DRB1 mixed isotype heterodimer and its potential association with disease susceptibility, provides a rationale for a potential effect on MS risk from DQA1*01:02 through functional DQA1*01:02;DRB1*15:01 antigen presentation. Furthermore, it highlights a potential contribution to MS risk also from interisotypic combination between products of neighboring HLA-DR15 haplotype alleles, in this case the DQA1/DRB1 combination.
Collapse
Affiliation(s)
| | - Miriam Eisenstein
- Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Bjarke Endel Hansen
- the Institute for Inflammation Research, Department of Infectious Diseases and Rheumatology, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Claus Henrik Nielsen
- the Institute for Inflammation Research, Department of Infectious Diseases and Rheumatology, Rigshospitalet, Copenhagen University Hospital, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - Ron Milo
- the Department of Neurology, Barzilai Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Ashkelon 78278, Israel
| | - Gabriel Zeilig
- the Department of Neurological Rehabilitation, Chaim Sheba Medical Center, Tel Hashomer 52621, Israel, the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Hans Lassmann
- the Center for Brain Research, Department of Neuroimmunology, Medical University of Vienna, 1090 Vienna, Austria, and
| | - Daniel M Altmann
- the Department of Medicine, Imperial College, Hammersmith Hospital, London W12 0HS, United Kingdom
| | | |
Collapse
|
21
|
Pravica V, Markovic M, Cupic M, Savic E, Popadic D, Drulovic J, Mostarica-Stojkovic M. Multiple sclerosis: individualized disease susceptibility and therapy response. Biomark Med 2013; 7:59-71. [PMID: 23387485 DOI: 10.2217/bmm.12.113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Multiple sclerosis (MS) is a heterogeneous disease in which diverse genetic, pathological and clinical backgrounds lead to variable therapy response. Accordingly, MS care should be tailored to address disease traits unique to each person. At the core of personalized management is the emergence of new knowledge, enabling optimized treatment and disease-modifying therapies. This overview analyzes the promise of genetic and nongenetic biomarkers in advancing decision-making algorithms to assist diagnosis or in predicting the disease course and therapy response in any given MS patient.
Collapse
Affiliation(s)
- Vera Pravica
- Institute of Microbiology & Immunology, School of Medicine, University of Belgrade, Belgrade, Serbia.
| | | | | | | | | | | | | |
Collapse
|
22
|
Bordner AJ. Structure-based prediction of Major Histocompatibility Complex (MHC) epitopes. Methods Mol Biol 2013; 1061:323-43. [PMID: 23963947 DOI: 10.1007/978-1-62703-589-7_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Because of the enormous diversity of both MHC proteins and peptide epitopes, computational epitope prediction methods are needed in order to supplement limited experimental data. These prediction methods are useful for guiding experiments and have many potential biomedical applications. Unlike popular sequence-based methods, structure-based epitope prediction methods can predict epitopes for multiple MHC types with highly distinct peptide binding propensities. In this chapter, we describe in detail our previously developed structure-based epitope prediction methods for both class I and class II MHC proteins. We also discuss the relative advantages and disadvantages of sequence-based versus structure-based methods and how to evaluate prediction performance.
Collapse
|
23
|
Vidaurre OG, Liu J, Haines J, Sandoval J, Nowakowski R, Casaccia P. An integrated approach to design novel therapeutic interventions for demyelinating disorders. Eur J Neurosci 2012; 35:1879-86. [PMID: 22708599 DOI: 10.1111/j.1460-9568.2012.08118.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Therapeutic strategies are often based on two general principles: interference with the pathogenic process and repair of the damaged tissues. Recent studies, however, have suggested that several pathological conditions may result from the interplay between genetic susceptibility traits and environmental influences that, by modulating the epigenome, also affect disease onset and progression. Based on lessons from neural development, it is conceivable that new lines of preventive and possibly therapeutic intervention might be developed to modulate disease onset or decrease the severity of the symptoms. This review will discuss these concepts within the context of multiple sclerosis, the most common demyelinating disease of the central nervous system, and the leading cause of progressive neurological disability in young adults.
Collapse
Affiliation(s)
- Oscar G Vidaurre
- Department of Neuroscience and Genetics and Genomics, Mount Sinai School of Medicine, One Gustave Levy Place, Box 1065, New York, NY 10029, USA
| | | | | | | | | | | |
Collapse
|
24
|
|
25
|
Quandt JA, Huh J, Baig M, Yao K, Ito N, Bryant M, Kawamura K, Pinilla C, McFarland HF, Martin R, Ito K. Myelin basic protein-specific TCR/HLA-DRB5*01:01 transgenic mice support the etiologic role of DRB5*01:01 in multiple sclerosis. THE JOURNAL OF IMMUNOLOGY 2012; 189:2897-908. [PMID: 22888134 DOI: 10.4049/jimmunol.1103087] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genetic susceptibility to multiple sclerosis (MS) has been linked to the HLA-DR15 haplotype consisting of DRB1*15:01(DR2b) and DRB5*01:01(DR2a) alleles. Given almost complete linkage disequilibrium of the two alleles, recent studies suggested differential roles in susceptibility (DR2b) or protection from MS (DR2a). Our objective was to assess the potential contribution of DR2a to disease etiology in MS using a humanized model of autoimmunity. To assess the potential contribution of DR2a to disease etiology, we created DR2a humanized transgenic (Tg) mice and subsequently crossed them to Tg mice expressing TL3A6, an MS patient-derived myelin basic protein 83-99-specific TCR. In TL3A6/DR2a Tg mice, CD4 Tg T cells escape thymic and peripheral deletion and initiate spontaneous experimental autoimmune encephalomyelitis (EAE) at low rates, depending on the level of DR2a expression. The ability to induce active EAE was also increased in animals expressing higher levels of DR2a. Inflammatory infiltrates and neuronal damage were present throughout the spinal cord, consistent with a classical ascending EAE phenotype with minor involvement of the cerebellum, brainstem, and peripheral nerve roots in spontaneous, as well as actively induced, disease. These studies emphasize the pathologic contribution of the DR2a allele to the development of autoimmunity when expressed as the sole MHC class II molecule, as well as strongly argue for DR2a as a contributor to the CNS autoimmunity in MS.
Collapse
Affiliation(s)
- Jacqueline A Quandt
- Neuroimmunology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Cocco E, Sardu C, Pieroni E, Valentini M, Murru R, Costa G, Tranquilli S, Frau J, Coghe G, Carboni N, Floris M, Contu P, Marrosu MG. HLA-DRB1-DQB1 haplotypes confer susceptibility and resistance to multiple sclerosis in Sardinia. PLoS One 2012; 7:e33972. [PMID: 22509268 PMCID: PMC3324467 DOI: 10.1371/journal.pone.0033972] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 02/24/2012] [Indexed: 01/28/2023] Open
Abstract
Introduction Genetic predisposition to multiple sclerosis (MS) in Sardinia (Italy) has been associated with five DRB1*-DQB1* haplotypes of the human leukocyte antigen (HLA). Given the complexity of these associations, an in-depth re-analysis was performed with the specific aims of confirming the haplotype associations; establishing the independence of the associated haplotypes; and assessing patients' genotypic risk of developing MS. Methods and Results A transmission disequilibrium test (TDT) of the DRB1*-DQB1* haplotypes in 943 trio families, confirmed a higher than expected transmission rate (over-transmission) of the *13:03-*03:01 (OR = 2.9, P = 7.6×10−3), *04:05-*03:01 (OR = 2.4, P = 4.4×10−6) and *03:01-*02:01 (OR = 2.1, P = 1.0×10−15) haplotype. In contrast, the *16:01-*05:02 (OR = 0.5, P = 5.4×10−11) and the *15:02-*06:01 (OR = 0.3, P = 1.5×10−3) haplotypes exhibited a lower than expected transmission rate (under-transmission). The independence of the transmission of each positively and negatively associated haplotype was confirmed relative to all positively associated haplotypes, and to the negatively associated *16:01-*05:02 haplotype. In patients, carriage of two predisposing haplotypes, or of protective haplotypes, respectively increased or decreased the patient's risk of developing MS. The risk of MS followed a multiplicative model of genotypes, which was, in order of decreasing ORs: *04:05-*0301/*03:01-*02:01 (OR = 4.5); *03:01-*02:01/*03:01-*02:01 (OR = 4.1); and the *16:01-*05:02/*16:01-*0502 (OR = 0.2) genotypes. Analysis of DRB1 and DQB1 protein chain residues showed that the Val/Gly residue at position 86 of the DRB1 chain was the only difference between the protective *16:01- *15:02 alleles and the predisposing *15:01 one. Similarly, the Ala/Val residue at position 38 of the DQB1 chain differentiated the positively associated *06:02 allele and the negatively associated *05:02, *06:01 alleles. Conclusions These findings show that the association of specific, independent DRB1*-DQB1* haplotypes confers susceptibility or resistance to MS in the MS-prone Sardinian population. The data also supports a functional role for specific residues of the DRB1 and DQB1 proteins in predisposing patients to MS.
Collapse
Affiliation(s)
- Eleonora Cocco
- Department Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Claudia Sardu
- Department Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Enrico Pieroni
- CRS4 (Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna), Science and Technology Park Polaris - Piscina Manna, Pula (Cagliari), Italy
| | - Maria Valentini
- CRS4 (Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna), Science and Technology Park Polaris - Piscina Manna, Pula (Cagliari), Italy
| | - Raffaele Murru
- Department Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Gianna Costa
- Department Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Stefania Tranquilli
- Department Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Jessica Frau
- Department Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Giancarlo Coghe
- Department Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Nicola Carboni
- Department Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Matteo Floris
- CRS4 (Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna), Science and Technology Park Polaris - Piscina Manna, Pula (Cagliari), Italy
| | - Paolo Contu
- Department Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Maria Giovanna Marrosu
- Department Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
- * E-mail:
| |
Collapse
|
27
|
Martinelli-Boneschi F, Esposito F, Brambilla P, Lindström E, Lavorgna G, Stankovich J, Rodegher M, Capra R, Ghezzi A, Coniglio G, Colombo B, Sorosina M, Martinelli V, Booth D, Oturai AB, Stewart G, Harbo HF, Kilpatrick TJ, Hillert J, Rubio JP, Abderrahim H, Wojcik J, Comi G. A genome-wide association study in progressive multiple sclerosis. Mult Scler 2012; 18:1384-94. [DOI: 10.1177/1352458512439118] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: The role played by genetic factors in influencing the clinical course of multiple sclerosis (MS) is not yet well established. Objective: We aimed to identify genetic variants associated with progressive MS (PrMS). Methods: We conducted a genome-wide association study (GWAS) in 197 patients with PrMS and 234 controls of Italian origin. We tested the top 20 single nucleotide polymorphisms (SNPs) with suggestive evidence of association ( p-value<10−4) in two independent sets of primary progressive MS cases and controls. Results: We identified a risk-associated SNP in the HLA region in linkage disequilibrium (LD) with DRB1*1501 and DQB*0602 loci, with genome-wide significance (rs3129934T, pcombined=6.7×10-16, OR=2.34, 95% CI=1.90–2.87), and a novel locus on chromosome 7q35 with suggestive evidence of association (rs996343G, pcombined=2.4×10-5, OR=0.70, 95% CI=0.59–0.83) which maps within a human endogenous retroviral (HERV) element. The new locus did not have a ‘ cis’ effect on RNA expression in lymphoblastic cell lines, but pathway analyses of ‘ trans’ effects point to an expression regulation of genes involved in neurodegeneration, including glutamate metabolism ( p<0.01) and axonal guidance signalling ( p<0.02). Conclusions: We have confirmed the established association with the HLA region and, despite the low statistical power of the study, we found suggestive evidence for association with a novel locus on chromosome 7, with a putative regulatory role.
Collapse
Affiliation(s)
- Filippo Martinelli-Boneschi
- Institute of Experimental Neurology (INSPE) and Department of Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
- These two authors contributed equally to the work
| | - Federica Esposito
- Institute of Experimental Neurology (INSPE) and Department of Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
- These two authors contributed equally to the work
| | - Paola Brambilla
- Institute of Experimental Neurology (INSPE) and Department of Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Eva Lindström
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | - Jim Stankovich
- Menzies Research Institute, University of Tasmania, Australia
| | - Mariaemma Rodegher
- Institute of Experimental Neurology (INSPE) and Department of Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Ruggero Capra
- Multiple Sclerosis Centre, Department of Neurology, Spedali Civili di Brescia, Italy
| | - Angelo Ghezzi
- Centro Studi Sclerosi Multipla, Ospedale di Gallarate (VA), Italy
| | | | - Bruno Colombo
- Institute of Experimental Neurology (INSPE) and Department of Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Melissa Sorosina
- Institute of Experimental Neurology (INSPE) and Department of Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Vittorio Martinelli
- Institute of Experimental Neurology (INSPE) and Department of Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - David Booth
- Westmead Millennium Institute, University of Sydney, Australia
| | - Annette Bang Oturai
- The Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital Rigshospitalet, Denmark
| | - Graeme Stewart
- Westmead Millennium Institute, University of Sydney, Australia
| | - Hanne F. Harbo
- Department of Neurology, Oslo University, Hospital and University of Oslo, Norway
| | | | - Jan Hillert
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Justin P Rubio
- Florey Neuroscience Institutes, University of Melbourne, Australia
| | | | - Jerome Wojcik
- Merck-Serono Genetics Research Center, Geneva, Switzerland
| | - Giancarlo Comi
- Institute of Experimental Neurology (INSPE) and Department of Neurology, Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| |
Collapse
|
28
|
Kollaee A, Ghaffarpor M, Ghlichnia HA, Ghaffari SH, Zamani M. The influence of the HLA-DRB1 and HLA-DQB1 allele heterogeneity on disease risk and severity in Iranian patients with multiple sclerosis. Int J Immunogenet 2012; 39:414-22. [PMID: 22404765 DOI: 10.1111/j.1744-313x.2012.01104.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Multiple sclerosis (MS) is a common autoimmune disorder of the central nervous system. Recent studies have shown that the HLA-DRB1 and DQB1 alleles are associated with MS susceptibility and severity. However, this is controversial in different population studies. In the present study, the roles of HLA-DRB1 and DQB1 alleles and the amino acids were investigated on disease risk and severity in 120 Iranian patients with MS and 120 controls. Our findings indicate that the DRB1*1501 allele (OR = 3.203 P = 0.001), the DRB1*1501-DQB1*0602 haplotype (OR = 7.792 P = 0.003) and the DRB1*1501/0701- genotype (OR = 3.320 P = 0.006) and amino acid Leu26 (OR = 1.645 P = 0.005) and Phe9 (OR = 1.893 P = 0.009) on the DQβ1 chain are significantly associated with MS susceptibility. DRB1*1001 was the only allele that had a protective effect against MS (P = 0.0004). We also found that the DQB1*0303 allele was significantly associated with disease severity (mean Multiple Sclerosis Severity Score difference = 1.979, P = 0.002). However, protective effect of the DRB1*1001 against MS and also association of DQB1*0303 allele with MS severity need to be confirmed by larger sample size.
Collapse
Affiliation(s)
- A Kollaee
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | | | | |
Collapse
|
29
|
Lopez de Lapuente A, Alloza I, Goertsches R, Zettl UK, Urcelay E, Arroyo R, Comabella M, Montalban X, Antigüedad A, Vandenbroeck K. Analysis of the IL28RA locus as genetic risk factor for multiple sclerosis. J Neuroimmunol 2012; 245:98-101. [PMID: 22386267 DOI: 10.1016/j.jneuroim.2012.02.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 01/24/2012] [Accepted: 02/06/2012] [Indexed: 01/07/2023]
Abstract
Recently, we reported an association between a SNP in IL28RA and MS. Here, we performed a fine-mapping of the IL28RA locus by genotyping 10 haplotype-tagging SNPs in a Basque-Spanish population. In addition, based on shared genetic risk loci between autoimmune diseases, a psoriasis-associated SNP located at this locus, rs4649203, was genotyped in four independent populations, comprising a total of 2582 cases and 2614 controls. We did not find any consistent association between IL28RA and MS in these populations, suggesting that, although it may play a role in other autoimmune diseases, this gene is unlikely of general relevance to MS pathogenesis.
Collapse
|
30
|
Alcina A, Abad-Grau MDM, Fedetz M, Izquierdo G, Lucas M, Fernández Ó, Ndagire D, Catalá-Rabasa A, Ruiz A, Gayán J, Delgado C, Arnal C, Matesanz F. Multiple sclerosis risk variant HLA-DRB1*1501 associates with high expression of DRB1 gene in different human populations. PLoS One 2012; 7:e29819. [PMID: 22253788 PMCID: PMC3258250 DOI: 10.1371/journal.pone.0029819] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/06/2011] [Indexed: 01/19/2023] Open
Abstract
The human leukocyte antigen (HLA) DRB1*1501 has been consistently associated with multiple sclerosis (MS) in nearly all populations tested. This points to a specific antigen presentation as the pathogenic mechanism though this does not fully explain the disease association. The identification of expression quantitative trait loci (eQTL) for genes in the HLA locus poses the question of the role of gene expression in MS susceptibility. We analyzed the eQTLs in the HLA region with respect to MS-associated HLA-variants obtained from genome-wide association studies (GWAS). We found that the Tag of DRB1*1501, rs3135388 A allele, correlated with high expression of DRB1, DRB5 and DQB1 genes in a Caucasian population. In quantitative terms, the MS-risk AA genotype carriers of rs3135388 were associated with 15.7-, 5.2- and 8.3-fold higher expression of DQB1, DRB5 and DRB1, respectively, than the non-risk GG carriers. The haplotype analysis of expression-associated variants in a Spanish MS cohort revealed that high expression of DRB1 and DQB1 alone did not contribute to the disease. However, in Caucasian, Asian and African American populations, the DRB1*1501 allele was always highly expressed. In other immune related diseases such as type 1 diabetes, inflammatory bowel disease, ulcerative colitis, asthma and IgA deficiency, the best GWAS-associated HLA SNPs were also eQTLs for different HLA Class II genes. Our data suggest that the DR/DQ expression levels, together with specific structural properties of alleles, seem to be the causal effect in MS and in other immunopathologies rather than specific antigen presentation alone.
Collapse
Affiliation(s)
- Antonio Alcina
- Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
- * E-mail: (FM); (AA)
| | - María del Mar Abad-Grau
- Departamento de Lenguajes y Sistemas Informáticos, CITIC, Universidad de Granada, Granada, Spain
| | - María Fedetz
- Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | | | - Miguel Lucas
- Servicio de Biología Molecular, Hospital Virgen Macarena, Sevilla, Spain
| | - Óscar Fernández
- Servicio de Neurología, Instituto de Neurociencias Clínicas, Hospital Carlos Haya, Málaga, Spain
| | - Dorothy Ndagire
- Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Antonio Catalá-Rabasa
- Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Agustín Ruiz
- Departamento de Genómica Estructural, Neocodex, Sevilla, Spain
| | - Javier Gayán
- Departamento de Genómica Estructural, Neocodex, Sevilla, Spain
| | | | - Carmen Arnal
- Servicio de Neurología, Hospital Virgen de las Nieves, Granada, Spain
| | - Fuencisla Matesanz
- Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
- Unidad de Esclerosis Múltiple, Hospital Virgen Macarena, Sevilla, Spain
- * E-mail: (FM); (AA)
| |
Collapse
|
31
|
Guerini FR, Cagliani R, Forni D, Agliardi C, Caputo D, Cassinotti A, Galimberti D, Fenoglio C, Biasin M, Asselta R, Scarpini E, Comi GP, Bresolin N, Clerici M, Sironi M. A functional variant in ERAP1 predisposes to multiple sclerosis. PLoS One 2012; 7:e29931. [PMID: 22253828 PMCID: PMC3257233 DOI: 10.1371/journal.pone.0029931] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 12/07/2011] [Indexed: 01/22/2023] Open
Abstract
The ERAP1 gene encodes an aminopeptidase involved in antigen processing. A functional polymorphism in the gene (rs30187, Arg528Lys) associates with susceptibility to ankylosying spondylitis (AS), whereas a SNP in the interacting ERAP2 gene increases susceptibility to another inflammatory autoimmune disorder, Crohn's disease (CD). We analysed rs30187 in 572 Italian patients with CD and in 517 subjects suffering from multiple sclerosis (MS); for each cohort, an independent sex- and age-matched control group was genotyped. The frequency of the 528Arg allele was significantly higher in both disease cohorts compared to the respective control population (for CD, OR = 1.20 95%CI: 1.01–1.43, p = 0.036; for RRMS, OR = 1.26; 95%CI: 1.04–1.51, p = 0.01). Meta-analysis with the Wellcome Trust Cases Control Consortium GWAS data confirmed the association with MS (pmeta = 0.005), but not with CD. In AS, the rs30187 variant has a predisposing effect only in an HLA-B27 allelic background. It remains to be evaluated whether interaction between ERAP1 and distinct HLA class I alleles also affects the predisposition to MS, and explains the failure to provide definitive evidence for a role of rs30187 in CD. Results herein support the emerging concept that a subset of master-regulatory genes underlay the pathogenesis of autoimmunity.
Collapse
|
32
|
Kollaee A, Ghaffarpor M, Pourmahmoudian H, Shahbazi M, Zamani M. Investigation of CD24 and its expression in Iranian relapsing-remitting multiple sclerosis. Int J Neurosci 2011; 121:684-90. [PMID: 21815873 DOI: 10.3109/00207454.2011.610529] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
CD24 is a glycosylphosphatidylinositol (GPI)-linked cell surface glycoprotein expressed in central nervous system cells. Recent investigations have suggested that CD24 participates in the pathogenesis of experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS). However, a limited number of studies have been published regarding the contribution of CD24 to the risk and severity of MS in humans. We investigated the contribution of a CD24 single nucleotide polymorphism (SNP) to MS disease risk and severity. We also studied mRNA expression of the CD24 gene in Iranian MS patients using quantitative real-time polymerase chain reaction (PCR). Our findings showed that the CD24(v/v) genotype was significantly more frequent in MS patients compared with controls (p(c) = .004). Moreover, a statistically significant difference in the Multiple Sclerosis Severity Score (MSSS) was found between MS patients carrying CD24(a/a) and CD24(v/v) genotypes (p = .008). The results also indicated that the expression of CD24 mRNA was 1.7 times more in MS patients compared with controls. In conclusion, our results suggest that the CD24(v/v) genotype influences both MS disease risk and severity in Iranian MS patients, and the high disease severity in CD24(v/v) patients may indicate that they require more aggressive treatment than do patients carrying CD24(a/a).
Collapse
Affiliation(s)
- Abolghasem Kollaee
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | | | | |
Collapse
|
33
|
Abstract
Multiple sclerosis (MS) is a one of the group of diseases labeled as "common complex". Virtually all common complex traits, genetic and environmental components have important roles, both independently and interactively, in disease susceptibility and stochastic and epigenetic effects cannot be overlooked. Data presented are largely part of the Canada-wide prospective, population-based longitudinal Canadian Collaborative Project on Genetic Susceptibility to MS (CCPGSMS) which includes over 30,000 unique families having at least 1 member with MS. Findings do not support a general propensity to autoimmune disease in MS families, but clearly highlight the importance of controlling for gender (patient, informant) when conducting such studies. The MHC class II association has been fine-mapped to the HLA-DRB5*0101-HLA-DRB1*1501-HLA-DQA1*0102-HLA-DQB1*0602 extended haplotype. This HLA haplotype confers a relative risk of approximately 3 and homozygosity for this haplotype increases the risk by over 6 fold. However, the HLA haplotype loci interactions are complex and include, epistasis, trans and cis effects, and parent-of-origin effects. As well, there may be interactions of EBV and vitamin D with the HLA, In conclusion, using MS as an example, susceptibility for common complex disease most likely results from interactions of genes, environmental interactions and gene/environment interactions.
Collapse
Affiliation(s)
- A Dessa Sadovnick
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.
| |
Collapse
|
34
|
Relationship between HLA-DRB1 polymorphism and susceptibility or resistance to multiple sclerosis in Caucasians: a meta-analysis of non-family-based studies. Autoimmun Rev 2011; 10:474-81. [PMID: 21440682 DOI: 10.1016/j.autrev.2011.03.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Accepted: 03/16/2011] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To identify the contribution of HLA-DRB1 alleles to susceptibility or resistance to multiple sclerosis (MS) in Caucasians through a meta-analysis of non-family-based studies. METHODS A systematic review of case-control studies in Caucasians was performed. Studies examining allele or phenotype frequencies were analyzed separately. Odds ratio (OR) and 95% confidence intervals (CIs) were used. We also used the relatively predispositional effect (RPE) method to analyze several allele frequency studies to avoid skewed results due to some strongly associated alleles. RESULTS A total of 5464 cases and 7809 controls from 14 allele frequency studies and a total of 5401 cases and 7538 controls from 23 phenotype frequency studies were analyzed. DRB1*15 was definitely the strongest risk factor for MS (allele group, Pc<0.00013, OR 2.59, 95%CI 2.34-2.87; phenotype group, Pc<0.00013, OR 3.35, 95%CI 2.95-3.80). DRB1*03 frequencies were significantly increased among MS cases in the phenotype group (Pc= 0.0013, OR 1.21, 95%CI 1.09-1.33) but not in the allele group. DRB1*14 and DRB1*07 showed protective effects against MS in both groups (DRB1*14, allele group, Pc<0.00013, OR 0.53, 95%CI 0.42-0.66; phenotype group, Pc<0.00013, OR 0.57, 95%CI 0.45-0.71; DRB1*07, allele group, Pc<0.0026, OR 0.75, 95%CI 0.64-0.87; phenotype group, Pc<0.00013, OR 0.67, 95%CI 0.61-0.73). By RPE method, DRB1*14, and DRB1*07 showed protective effects after excluding DRB1*15 from the analysis. DRB1*03 was significantly higher in MS cases than controls after removing both DRB1*15 and DRB1*14. CONCLUSIONS In Caucasians, we highlighted the definite protective role of HLA-DRB1*14 and DRB1*07 for MS. DRB1*03 is probably the only risk factor for MS besides DRB1*15 and a common genetic foundation for autoimmune disease. Targeting to these alleles may have potential values in prevention or therapy for MS in the specific population.
Collapse
|
35
|
Ramagopalan SV, Dyment DA. What is Next for the Genetics of Multiple Sclerosis? Autoimmune Dis 2011; 2011:519450. [PMID: 21541245 PMCID: PMC3085300 DOI: 10.4061/2011/519450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 01/26/2011] [Indexed: 11/20/2022] Open
Abstract
We review here our current understanding of the genetic aetiology of the common complex neurological disease multiple sclerosis (MS). The strongest genetic risk factor for MS is the major histocompatibility complex which was identified in the 1970s. In 2011, after a number of genome-wide association studies have been completed and have identified approximately 20 new genes for MS, we ask the question—what is next for the genetics of MS?
Collapse
|
36
|
Disanto G, Magalhaes S, Handel AE, Morrison KM, Sadovnick AD, Ebers GC, Banwell B, Bar-Or A. HLA-DRB1 confers increased risk of pediatric-onset MS in children with acquired demyelination. Neurology 2011; 76:781-6. [PMID: 21288988 DOI: 10.1212/wnl.0b013e31820ee1cd] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Multiple sclerosis (MS) in the pediatric age group is being increasingly recognized. In adults, complex interactions between genetic and environmental factors contribute to risk and the major genetic component of MS susceptibility localizes to the major histocompatibility complex (human leukocyte antigen [HLA]). Whether HLA alleles predict MS in at-risk children presenting with acquired demyelinating syndromes (ADS) of the CNS is unknown. METHODS HLA-DRB1 alleles were typed using an allele-specific PCR amplification method on samples from 266 children presenting with ADS enrolled in the prospective Canadian Pediatric Demyelinating Disease Study and from 196 healthy controls. RESULTS Sixty-four of 266 children with ADS met established criteria for a diagnosis of MS during a mean follow-up of 3.2 ± 1.5 years. Children harboring DRB1*15 alleles were more likely to be diagnosed with MS (χ(2) = 12.2, p < 0.001; OR = 2.7), an observation strengthened by children of European ancestry (χ(2) = 10.5, p = 0.001; OR = 3.3). DRB1*15 allele frequencies in children with ADS of European ancestry subsequently diagnosed with MS were greater than in children with monophasic ADS (χ(2) = 10.7, p = 0.001) or healthy controls (χ(2) = 12.5, p < 0.001). The proportion of children with non-European ancestry diagnosed with MS was not influenced by DRB1*15 status. CONCLUSION DRB1*15 alleles confer increased susceptibility to pediatric-onset MS, supporting a fundamental similarity in genetic contribution to MS risk in both pediatric- and adult-onset disease. The specificity of the DRB1*15 risk allele for children with subsequent MS diagnosis, but not for all children with ADS, indicates that the risk conveyed by DRB1*15 relates to chronic CNS disease (MS), rather than acquired demyelination in general.
Collapse
Affiliation(s)
- G Disanto
- McGill University, Montreal Neurological Institute, Montreal, Quebec, H3A2B4, Canada
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Bordner AJ. Towards universal structure-based prediction of class II MHC epitopes for diverse allotypes. PLoS One 2010; 5:e14383. [PMID: 21187956 PMCID: PMC3004863 DOI: 10.1371/journal.pone.0014383] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 11/30/2010] [Indexed: 01/10/2023] Open
Abstract
The binding of peptide fragments of antigens to class II MHC proteins is a crucial step in initiating a helper T cell immune response. The discovery of these peptide epitopes is important for understanding the normal immune response and its misregulation in autoimmunity and allergies and also for vaccine design. In spite of their biomedical importance, the high diversity of class II MHC proteins combined with the large number of possible peptide sequences make comprehensive experimental determination of epitopes for all MHC allotypes infeasible. Computational methods can address this need by predicting epitopes for a particular MHC allotype. We present a structure-based method for predicting class II epitopes that combines molecular mechanics docking of a fully flexible peptide into the MHC binding cleft followed by binding affinity prediction using a machine learning classifier trained on interaction energy components calculated from the docking solution. Although the primary advantage of structure-based prediction methods over the commonly employed sequence-based methods is their applicability to essentially any MHC allotype, this has not yet been convincingly demonstrated. In order to test the transferability of the prediction method to different MHC proteins, we trained the scoring method on binding data for DRB1*0101 and used it to make predictions for multiple MHC allotypes with distinct peptide binding specificities including representatives from the other human class II MHC loci, HLA-DP and HLA-DQ, as well as for two murine allotypes. The results showed that the prediction method was able to achieve significant discrimination between epitope and non-epitope peptides for all MHC allotypes examined, based on AUC values in the range 0.632-0.821. We also discuss how accounting for peptide binding in multiple registers to class II MHC largely explains the systematically worse performance of prediction methods for class II MHC compared with those for class I MHC based on quantitative prediction performance estimates for peptide binding to class II MHC in a fixed register.
Collapse
Affiliation(s)
- Andrew J Bordner
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona, United States of America.
| |
Collapse
|
38
|
Disanto G, Berlanga AJ, Handel AE, Para AE, Burrell AM, Fries A, Handunnetthi L, De Luca GC, Morahan JM. Heterogeneity in multiple sclerosis: scratching the surface of a complex disease. Autoimmune Dis 2010; 2011:932351. [PMID: 21197462 PMCID: PMC3005811 DOI: 10.4061/2011/932351] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 10/27/2010] [Indexed: 12/19/2022] Open
Abstract
Multiple Sclerosis (MS) is the most common demyelinating disease of the central nervous system. Although the etiology and the pathogenesis of MS has been extensively investigated, no single pathway, reliable biomarker, diagnostic test, or specific treatment have yet been identified for all MS patients. One of the reasons behind this failure is likely to be the wide heterogeneity observed within the MS population. The clinical course of MS is highly variable and includes several subcategories and variants. Moreover, apart from the well-established association with the HLA-class II DRB1*15:01 allele, other genetic variants have been shown to vary significantly across different populations and individuals. Finally both pathological and immunological studies suggest that different pathways may be active in different MS patients. We conclude that these "MS subtypes" should still be considered as part of the same disease but hypothesize that spatiotemporal effects of genetic and environmental agents differentially influence MS course. These considerations are extremely relevant, as outcome prediction and personalised medicine represent the central aim of modern research.
Collapse
Affiliation(s)
- Giulio Disanto
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Bordner AJ, Mittelmann HD. MultiRTA: a simple yet reliable method for predicting peptide binding affinities for multiple class II MHC allotypes. BMC Bioinformatics 2010; 11:482. [PMID: 20868497 PMCID: PMC2957400 DOI: 10.1186/1471-2105-11-482] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Accepted: 09/24/2010] [Indexed: 12/26/2022] Open
Abstract
Background The binding of peptide fragments of antigens to class II MHC is a crucial step in initiating a helper T cell immune response. The identification of such peptide epitopes has potential applications in vaccine design and in better understanding autoimmune diseases and allergies. However, comprehensive experimental determination of peptide-MHC binding affinities is infeasible due to MHC diversity and the large number of possible peptide sequences. Computational methods trained on the limited experimental binding data can address this challenge. We present the MultiRTA method, an extension of our previous single-type RTA prediction method, which allows the prediction of peptide binding affinities for multiple MHC allotypes not used to train the model. Thus predictions can be made for many MHC allotypes for which experimental binding data is unavailable. Results We fit MultiRTA models for both HLA-DR and HLA-DP using large experimental binding data sets. The performance in predicting binding affinities for novel MHC allotypes, not in the training set, was tested in two different ways. First, we performed leave-one-allele-out cross-validation, in which predictions are made for one allotype using a model fit to binding data for the remaining MHC allotypes. Comparison of the HLA-DR results with those of two other prediction methods applied to the same data sets showed that MultiRTA achieved performance comparable to NetMHCIIpan and better than the earlier TEPITOPE method. We also directly tested model transferability by making leave-one-allele-out predictions for additional experimentally characterized sets of overlapping peptide epitopes binding to multiple MHC allotypes. In addition, we determined the applicability of prediction methods like MultiRTA to other MHC allotypes by examining the degree of MHC variation accounted for in the training set. An examination of predictions for the promiscuous binding CLIP peptide revealed variations in binding affinity among alleles as well as potentially distinct binding registers for HLA-DR and HLA-DP. Finally, we analyzed the optimal MultiRTA parameters to discover the most important peptide residues for promiscuous and allele-specific binding to HLA-DR and HLA-DP allotypes. Conclusions The MultiRTA method yields competitive performance but with a significantly simpler and physically interpretable model compared with previous prediction methods. A MultiRTA prediction webserver is available at http://bordnerlab.org/MultiRTA.
Collapse
Affiliation(s)
- Andrew J Bordner
- Mayo Clinic, 13400 East Shea Boulevard, Scottsdale, AZ 85259, USA.
| | | |
Collapse
|
40
|
Nikolaou K, Kalatzis FG, Giannakeas N, Markoula S, Chatzikyriakidou A, Georgiou I, Fotiadis DI. Polymerase chain reaction (PCR) and sequence specific oligonucleotide probes (SSOP) genotyping assay for detection of genes associated with rheumatoid arthritis and multiple sclerosis. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2010; 2010:6202-6205. [PMID: 21097159 DOI: 10.1109/iembs.2010.5627739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In this paper an assay for the detection of genes associated with rheumatoid arthritis (RA) and multiple sclerosis, using polymerase chain reaction (PCR) and sequence specific oligonucleotide probes (SSOP) is presented, in order to be further applied in a portable Lab-On-Chip (LOC) device. A substantial part of these reagents were based on the literature (11th International Histocompatibility Workshop, IHW), bearing the advantage of proven successful implementation in genotyping, while others were designed for this study. More precisely, our methodology discriminates HLA-DRB1 as DRB1*01, *04 and *10, which include shared epitope (SE) alleles associated with RA and additionally DRB1*15 allele, including DRB1*1501 associated with MS (broad genotyping method). To further present the basic elements of the assay for high resolution genotyping of SE DRB1 alleles, we provide as an example the case of HLA-DRB1*10 alleles (HLADRB1* 100101, *100102, *100103, *1002 and *1003). Regarding the methodology for developing a detection assay, for SNPs associated with RA or MS the basic steps are presented. DNA sequence data are obtained from IMGT/HLA and SNP database. Online software tools are used to define hybridization specificity of primers and probes towards human DNA, leading to hybridization patterns that uniquely designate a target allele and evaluate parameters influencing PCR efficiency. Respecting current technological limitations of autonomous molecular-based LOC systems the approach of broad genotyping of HLA-DRB1*01/*04/*10/*15 genes, is intended to be initially used, leaving, high resolution genotyping of SE alleles for future implementations. This method is easy to be updated and extended to detect additional associated loci with RA or MS.
Collapse
Affiliation(s)
- Konstantina Nikolaou
- Unit of Medical Technology and Intelligent Information Systems, Dept. of Material Science & Engineering, University of Ioannina, GR-45110, Greece.
| | | | | | | | | | | | | |
Collapse
|
41
|
Abstract
Previous studies reported an association with multiple sclerosis (MS) of distinct HLA-class I markers, namely HLA-A*02, HLA-Cw*05 and MOG-142L. In this work, we tested the association with MS of A*02 and Cw*05 in 1273 Italian MS patients and 1075 matched controls, which were previously analyzed for MOG-142, and explored the relationship among these three markers in modulating MS risk. HLA-A*02 conferred a statistically robust MS protection (odds ratio, OR=0.61; 95% confidence intervals, CI=0.51–0.72, P<10−9), which was independent of DRB1*15 and of any other DRB1* allele and remained similar after accounting for the other two analyzed class I markers. Conversely, the protective effect we previously observed for MOG-142L was secondary to its linkage disequilibrium with A*02. Cw*05 was not associated considering the whole sample, but its presence significantly enhanced the protection in the HLA-A*02-positive group, independently of DRB1: the OR conferred by A*02 in Cw*05-positive individuals (0.22, 95% CI=0.13–0.38) was significantly lower than in Cw*05-negative individuals (0.69, 95% CI=0.58–0.83) with a significant (P=4.94 × 10−5) multiplicative interaction between the two markers. In the absence of A*02, Cw*05 behaved as a risk factor, particularly in combination with DRB1*03 (OR=3.89, P=0.0006), indicating that Cw*05 might be a marker of protective or risk haplotypes, respectively.
Collapse
|
42
|
Ramagopalan SV, Ebers GC. Multiple sclerosis: major histocompatibility complexity and antigen presentation. Genome Med 2009; 1:105. [PMID: 19895714 PMCID: PMC2808740 DOI: 10.1186/gm105] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Multiple sclerosis (MS), like many putative autoimmune diseases, has been known to be associated with the human leukocyte antigen (HLA) class II region for more than 3 decades. However, exactly how HLA class II alleles increase the risk of MS is not yet conclusively known. Recent work in large human cohorts has highlighted the fact that nearly all common HLA-DRB1 allelotypes are either positively or negatively associated with the disease, detracting from allele-specific antigen presentation as the sole mechanism of MHC associated disease susceptibility. Here, we put into context recent data on the HLA class II region in MS, including allelic heterogeneity, gene-environment interactions and epigenetics. It is clear that a complete understanding of the epistatic interactions and epigenetic features of this region will be crucial to comprehending disease pathogenesis.
Collapse
Affiliation(s)
- Sreeram V Ramagopalan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7BN, UK
| | | |
Collapse
|
43
|
Sadovnick AD. European Charcot Foundation Lecture: the natural history of multiple sclerosis and gender. J Neurol Sci 2009; 286:1-5. [PMID: 19782378 DOI: 10.1016/j.jns.2009.09.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 09/01/2009] [Accepted: 09/04/2009] [Indexed: 01/21/2023]
Abstract
The role of gender in the natural history of multiple sclerosis (MS) is multi-faceted. Earliest debate on this topic was about the sex ratio (female:male) among affected individuals. It was only clearly shown within the last 4 decades that females are more often affected. The sex ratio continues to intrigue researchers. An observed increase in the sex ratio among more recently born MS patients has now been taken as a clear indication that the rate of MS is truly increasing in many geographical areas. This temporal increase in females has been relatively rapid, implicating environmental rather than genetic risk factors. Gender issues in MS expand beyond the scope of sex ratio. Gender has an impact on various aspects of MS, including age of onset, "parent-of-origin" effects (seen in half-siblings, twin sibships, avuncular pairs, transmission of HLA haplotype), recurrence risks for relatives of MS patients and the topic of reproduction when one parent has MS. Gender issues can also confound data collection and analyses with respect to studies on comorbidity, risk factors and family history. In fact, it has now been clearly validated and quantified that among persons with MS, there is a sex-specificity of recall and reporting bias as well a greater female awareness of medical history.
Collapse
Affiliation(s)
- A D Sadovnick
- Department of Medical Genetics and Faculty of Medicine, Division of Neurology, University of British Columbia, Vancouver, Canada
| |
Collapse
|
44
|
Vandiedonck C, Knight JC. The human Major Histocompatibility Complex as a paradigm in genomics research. BRIEFINGS IN FUNCTIONAL GENOMICS & PROTEOMICS 2009; 8:379-94. [PMID: 19468039 PMCID: PMC2987720 DOI: 10.1093/bfgp/elp010] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Since its discovery more than 50 years ago, the human Major Histocompatibility Complex (MHC) on chromosome 6p21.3 has been at the forefront of human genetic research. Here, we review from a historical perspective the major advances in our understanding of the nature and consequences of genetic variation which have involved the MHC, as well as highlighting likely future directions. As a consequence of its particular genomic structure, its remarkable polymorphism and its early implication in numerous diseases, the MHC has been considered as a model region for genomics, being the first substantial region to be sequenced and establishing fundamental concepts of linkage disequilibrium, haplotypic structure and meiotic recombination. Recently, the MHC became the first genomic region to be entirely re-sequenced for common haplotypes, while studies mapping gene expression phenotypes across the genome have strongly implicated variation in the MHC. This review shows how the MHC continues to provide new insights and remains in the vanguard of contemporary research in human genomics.
Collapse
Affiliation(s)
- Claire Vandiedonck
- Wellcome Trust Centre for Human Genetics (WTCHG), University of Oxford, Oxford, UK.
| | | |
Collapse
|
45
|
Dam-Tuxen R, Riise E. Antibodies against a class II HLA-peptide complex raised by active immunization of mice with antigen mimicking peptides. Scand J Immunol 2009; 70:93-100. [PMID: 19630914 DOI: 10.1111/j.1365-3083.2009.02275.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Multiple sclerosis (MS) is an autoimmune disease linked to the human leucocyte antigen (HLA) class II genes DRB1*1501, DRB5*0101 and DQB1*0602. T cells reactive towards the DRB1*1501 in complex with various peptides derived from myelin basic protein (MBP), which is the major component of myelin, have been found in the peripheral blood of MS patients. These autoreactive T cells are believed to play a role in the pathogenesis of MS. In this article, antibodies against the HLA complex DR2b (DRA1*0101/DRB1*1501) in complex with the MBP-derived peptide MBP(85-99) have been generated by immunization of NMRI mice with three different antigen mimicking peptides displayed on M13 bacteriophages. The peptides mimick the epitope of a monoclonal antibody specific for the DR2b-MBP(85-99) complex. The mice developed IgG antibodies not only against the peptides injected, but they also developed antibodies against the DR2b complex and specific antibodies against the DR2b-MBP(85-99) complex. These data open up the possibility of designing antigen mimicking peptides for vaccination against MS.
Collapse
Affiliation(s)
- R Dam-Tuxen
- Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, Copenhagen OE, Denmark
| | | |
Collapse
|
46
|
Variants in ST8SIA1 do not play a major role in susceptibility to multiple sclerosis in Canadian families. J Neuroimmunol 2009; 212:142-4. [PMID: 19428123 DOI: 10.1016/j.jneuroim.2009.04.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2009] [Revised: 04/27/2009] [Accepted: 04/28/2009] [Indexed: 11/20/2022]
Abstract
Multiple sclerosis (MS) is a complex trait with a significant genetic component. Recent work has implicated the ST8SIA1 gene, encoding a ganglioside synthase, in susceptibility to the disease, perhaps with a parent-of-origin effect. In this investigation of 1318 MS patients from 756 Canadian families, we analysed the transmission of the four single nucleotide polymorphisms in ST8SIA previously shown to be associated with MS. No significant association was found in the entire sample or when stratifying by transmitting parent, indicating that this gene plays little or no role in susceptibility to MS in the Canadian population.
Collapse
|
47
|
Abstract
PURPOSE OF REVIEW Multiple sclerosis (MS) is the most common neurological disease affecting young adults. The cause is unknown, but detailed epidemiological and genetic studies have shown a clear inherited component. We review here some of the recent findings of MS genetics with a particular focus on genes of the major histocompatibility complex (MHC). RECENT FINDINGS Recent studies add further complexity to the role of the MHC in MS. Reported MHC associations are complex, involving haplotypes rather than single alleles and may involve epigenetic mechanisms and other modulators of gene expression. MHC class II haplotypes display a hierarchy of risks, including protective effects and epistatic interactions, which together dwarf any non-MHC genetic effect. Genes in the MHC region have been shown to influence disease severity, display parent-of-origin effects and interact with a major environmental candidate for MS, vitamin D. SUMMARY The MHC class II association with MS is not as straightforward as previously thought. A complete understanding of the epistatic interactions and epigenetic features of this region will be important to understand disease pathogenesis and likely aid the discovery of new therapeutics.
Collapse
|
48
|
Clinical, pathological, and immunologic aspects of the multiple sclerosis model in common marmosets (Callithrix jacchus). J Neuropathol Exp Neurol 2009; 68:341-55. [PMID: 19337065 DOI: 10.1097/nen.0b013e31819f1d24] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The efficacy of many new immunomodulatory therapies for multiple sclerosis (MS) patients has often been disappointing, reflecting our incomplete understanding of this enigmatic disease. There is a growing awareness that, at least in part, there may be limited applicability to the human disease of results obtained in the widely studied MS model experimental autoimmune encephalomyelitis in rodents. This review describes the experimental autoimmune encephalomyelitis model developed in a small neotropical primate, the common marmoset (Callithrix jacchus). The model has features including clinicopathologic correlation patterns, lesion heterogeneity, immunologic mechanisms, and disease markers that more closely mimic the human disease. Several unique features of experimental autoimmune encephalomyelitis in marmosets, together with their outbred nature and close genetic and immunologic similarities to humans, create an attractive experimental model for translational research into MS, particularly for the preclinical evaluation of new biologic therapeutic molecules that cannot be investigated in rodents because of their species specificity. Moreover, this model provides new insights into possible pathogenetic mechanisms in MS.
Collapse
|
49
|
Expression of the multiple sclerosis-associated MHC class II Allele HLA-DRB1*1501 is regulated by vitamin D. PLoS Genet 2009; 5:e1000369. [PMID: 19197344 PMCID: PMC2627899 DOI: 10.1371/journal.pgen.1000369] [Citation(s) in RCA: 328] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 01/05/2009] [Indexed: 11/25/2022] Open
Abstract
Multiple sclerosis (MS) is a complex trait in which allelic variation in the MHC class II region exerts the single strongest effect on genetic risk. Epidemiological data in MS provide strong evidence that environmental factors act at a population level to influence the unusual geographical distribution of this disease. Growing evidence implicates sunlight or vitamin D as a key environmental factor in aetiology. We hypothesised that this environmental candidate might interact with inherited factors and sought responsive regulatory elements in the MHC class II region. Sequence analysis localised a single MHC vitamin D response element (VDRE) to the promoter region of HLA-DRB1. Sequencing of this promoter in greater than 1,000 chromosomes from HLA-DRB1 homozygotes showed absolute conservation of this putative VDRE on HLA-DRB1*15 haplotypes. In contrast, there was striking variation among non–MS-associated haplotypes. Electrophoretic mobility shift assays showed specific recruitment of vitamin D receptor to the VDRE in the HLA-DRB1*15 promoter, confirmed by chromatin immunoprecipitation experiments using lymphoblastoid cells homozygous for HLA-DRB1*15. Transient transfection using a luciferase reporter assay showed a functional role for this VDRE. B cells transiently transfected with the HLA-DRB1*15 gene promoter showed increased expression on stimulation with 1,25-dihydroxyvitamin D3 (P = 0.002) that was lost both on deletion of the VDRE or with the homologous “VDRE” sequence found in non–MS-associated HLA-DRB1 haplotypes. Flow cytometric analysis showed a specific increase in the cell surface expression of HLA-DRB1 upon addition of vitamin D only in HLA-DRB1*15 bearing lymphoblastoid cells. This study further implicates vitamin D as a strong environmental candidate in MS by demonstrating direct functional interaction with the major locus determining genetic susceptibility. These findings support a connection between the main epidemiological and genetic features of this disease with major practical implications for studies of disease mechanism and prevention. Multiple Sclerosis (MS) is a complex neurological disease with a strong genetic component. The Major Histocompatibility Complex (MHC) on chromosome 6 exerts the strongest genetic effect on disease risk. A region at or near the HLA-DRB1 locus in the MHC influences the risk of MS. HLA-DRB1 has over 400 different alleles. The dominant haplotype of Northern Europe, marked by the presence of DRB1*1501, increases risk of MS by 3-fold. The environment also plays a key role in MS. The most striking illustration of this is the geographical distribution of the disease in populations matched for ethnicity. This has led to the proposal that sunshine, and in particular, vitamin D, is an environmental factor influencing the risk of MS. Circumstantial evidence supporting this comes from studies showing the involvement of vitamin D in immune and nervous system function. The current investigation sought to uncover any relationship between vitamin D and HLA-DRB1. It was found that vitamin D specifically interacts with HLA-DRB1*1501 to influence its expression. This study therefore provides more direct support for the already strong epidemiological evidence implicating sunlight and vitamin D in the determination of MS risk, and implies that vitamin D supplementation at critical time periods may be key to disease prevention.
Collapse
|
50
|
Ramagopalan SV, McMahon R, Dyment DA, Sadovnick AD, Ebers GC, Wittkowski KM. An extension to a statistical approach for family based association studies provides insights into genetic risk factors for multiple sclerosis in the HLA-DRB1 gene. BMC MEDICAL GENETICS 2009; 10:10. [PMID: 19193207 PMCID: PMC2669470 DOI: 10.1186/1471-2350-10-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2008] [Accepted: 02/04/2009] [Indexed: 11/17/2022]
Abstract
Background Multiple sclerosis (MS) is a complex trait in which genes in the MHC class II region exert the single strongest effect on genetic susceptibility. The principal MHC class II haplotype that increases MS risk in individuals of Northern European descent are those that bear HLA-DRB1*15. However, several other HLA-DRB1 alleles have been positively and negatively associated with MS and each of the main allelotypes is composed of many sub-allelotypes with slightly different sequence composition. Given the role of this locus in antigen presentation it has been suggested that variations in the peptide binding site of the allele may underlie allelic variation in disease risk. Methods In an investigation of 7,333 individuals from 1,352 MS families, we assessed the nucleotide sequence of HLA-DRB1 for any effects on disease susceptibility extending a recently published method of statistical analysis for family-based association studies to the particular challenges of hyper-variable genetic regions. Results We found that amino acid 60 of the HLA-DRB1 peptide sequence, which had previously been postulated based on structural features, is unlikely to play a major role. Instead, empirical evidence based on sequence information suggests that MS susceptibility arises primarily from amino acid 13. Conclusion Identifying a single amino acid as a major risk factor provides major practical implications for risk and for the exploration of mechanisms, although the mechanism of amino acid 13 in the HLA-DRB1 sequence's involvement in MS as well as the identity of additional variants on MHC haplotypes that influence risk need to be uncovered.
Collapse
Affiliation(s)
- Sreeram V Ramagopalan
- 1Department of Clinical Neurology, University of Oxford, The West Wing, The John Radcliffe Hospital, Oxford, OX3 9DU, UK.
| | | | | | | | | | | |
Collapse
|