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Capturing SNP Association across the NK Receptor and HLA Gene Regions in Multiple Sclerosis by Targeted Penalised Regression Models. Genes (Basel) 2021; 13:genes13010087. [PMID: 35052430 PMCID: PMC8774935 DOI: 10.3390/genes13010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022] Open
Abstract
Conventional genome-wide association studies (GWASs) of complex traits, such as Multiple Sclerosis (MS), are reliant on per-SNP p-values and are therefore heavily burdened by multiple testing correction. Thus, in order to detect more subtle alterations, ever increasing sample sizes are required, while ignoring potentially valuable information that is readily available in existing datasets. To overcome this, we used penalised regression incorporating elastic net with a stability selection method by iterative subsampling to detect the potential interaction of loci with MS risk. Through re-analysis of the ANZgene dataset (1617 cases and 1988 controls) and an IMSGC dataset as a replication cohort (1313 cases and 1458 controls), we identified new association signals for MS predisposition, including SNPs above and below conventional significance thresholds while targeting two natural killer receptor loci and the well-established HLA loci. For example, rs2844482 (98.1% iterations), otherwise ignored by conventional statistics (p = 0.673) in the same dataset, was independently strongly associated with MS in another GWAS that required more than 40 times the number of cases (~45 K). Further comparison of our hits to those present in a large-scale meta-analysis, confirmed that the majority of SNPs identified by the elastic net model reached conventional statistical GWAS thresholds (p < 5 × 10−8) in this much larger dataset. Moreover, we found that gene variants involved in oxidative stress, in addition to innate immunity, were associated with MS. Overall, this study highlights the benefit of using more advanced statistical methods to (re-)analyse subtle genetic variation among loci that have a biological basis for their contribution to disease risk.
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Yu X, Zizzo Z, Kennedy PG. An appraisal of antigen identification and IgG effector functions driving host immune responses in multiple sclerosis. Mult Scler Relat Disord 2021; 56:103328. [PMID: 34666240 DOI: 10.1016/j.msard.2021.103328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 10/05/2021] [Accepted: 10/10/2021] [Indexed: 12/16/2022]
Abstract
Increased immunoglobulin G (IgG) antibodies and oligoclonal bands (OCB) are the most characteristic features of multiple sclerosis (MS), a neuroinflammatory demyelinating disease with neurodegeneration at chronic stages. OCB are shown to be associated with disease activity and brain atrophy. Despite intensive research over the last several decades, the antigen specificities of the IgG in MS have remained elusive. We present evidence which supports that intrathecal IgG is not driven by antigen-stimulation, therefore provide reasoning for failed MS antigen identification. Further, the presence of co-deposition of IgG and activated complement products in MS lesions suggest that the IgG effector functions may play a critical role in disease pathogenesis.
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Affiliation(s)
- Xiaoli Yu
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America.
| | - Zoe Zizzo
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, CO, United States of America
| | - Peter Ge Kennedy
- Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, Scotland, United Kingdom
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Mack SJ, Udell J, Cohen F, Osoegawa K, Hawbecker SK, Noonan DA, Ladner MB, Goodridge D, Trachtenberg EA, Oksenberg JR, Erlich HA. High resolution HLA analysis reveals independent class I haplotypes and amino-acid motifs protective for multiple sclerosis. Genes Immun 2018; 20:308-326. [PMID: 29307888 PMCID: PMC6035897 DOI: 10.1038/s41435-017-0006-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/31/2017] [Accepted: 08/11/2017] [Indexed: 11/24/2022]
Abstract
We investigated association between HLA class I and class II alleles and haplotypes, and KIR loci and their HLA class I ligands, with multiple sclerosis (MS) in 412 European-American MS patients and 419 ethnically-matched controls, using next generation sequencing. The DRB1*15:01~DQB1*06:02 haplotype was highly predisposing (odds ratio (OR) = 3.98; 95% confidence interval (CI) = 3−5.31; p-value (p) = 2.22E−16), as was DRB1*03:01~DQB1*02:01 (OR = 1.63; CI = 1.19–2.24; p = 1.41E−03). Hardy-Weinberg (HW) analysis in MS patients revealed a significant DRB1*03:01~DQB1*02:01 homozyote excess (15 observed, 8.6 expected; p = 0.016). The OR for this genotype (5.27; CI = 1.47–28.52; p = 0.0036) suggests a recessive MS risk model. Controls displayed no HW deviations. The C*03:04~B*40:01 haplotype (OR = 0.27; CI = 0.14–0.51; p = 6.76E−06) was highly protective for MS, especially in haplotypes with A*02:01 (OR = 0.15; CI = 0.04–0.45; p = 6.51E−05). By itself, A*02:01 is moderately protective, (OR = 0.69; CI = 0.54–0.87; p = 1.46E−03), and haplotypes of A*02:01 with the HLA-B Thr80 Bw4 variant (Bw4T) more so (OR = 0.53; CI = 0.35–0.78; p = 7.55E−04). Protective associations with the Bw4 KIR ligand resulted from linkage disequilibrium (LD) with DRB1*15:01, but the Bw4T variant was protective (OR = 0.64; CI = 0.49–0.82; p = 3.37E−04) independent of LD with DRB1*15:01. The Bw4I variant was not associated with MS. Overall, we find specific class I HLA polymorphisms to be protective for MS, independent of the strong predisposition conferred by DRB1*15:01.
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Affiliation(s)
- Steven J Mack
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA.
| | - Julia Udell
- University of Minnesota Twin Cities, Minneapolis, MN, USA
| | - Franziska Cohen
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Kazutoyo Osoegawa
- Histocompatibility, Immunogenetics & Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Sharon K Hawbecker
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - David A Noonan
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Martha B Ladner
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | | | | | - Jorge R Oksenberg
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Henry A Erlich
- Center for Genetics, Children's Hospital Oakland Research Institute, Oakland, CA, USA
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Öckinger J, Hagemann-Jensen M, Kullberg S, Engvall B, Eklund A, Grunewald J, Piehl F, Olsson T, Wahlström J. T-cell activation and HLA-regulated response to smoking in the deep airways of patients with multiple sclerosis. Clin Immunol 2016; 169:114-120. [PMID: 27339331 DOI: 10.1016/j.clim.2016.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/15/2016] [Accepted: 06/18/2016] [Indexed: 12/17/2022]
Abstract
Cigarette smoking is a risk factor for multiple sclerosis (MS), and the risk is further multiplied for HLA-DRB1*15(+) smokers. To define the smoke-induced immune responses in the lung we performed bronchoscopy with bronchoalveolar lavage (BAL) on smokers and non-smokers, both MS-patients and healthy volunteers. In the BAL, non-smokers with MS showed an increased preformed CD40L expression in CD4(+) T-cells while smokers displayed an increase in proliferating (Ki-67(+)) T-cells. In addition, our results confirm that smoking induces an increase of alveolar macrophages in BAL, and further defined a significant attenuation of this response in carriers of the HLA-DRB1*15 allele, in both MS patients and healthy controls. This first systematic investigation of the immune response in the lungs of smokers and non-smokers diagnosed with MS, thus suggests an MS-associated lung T-cell phenotype, involvement of a specific T-cell response to smoke, and a genetic regulation of the macrophage response.
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Affiliation(s)
- Johan Öckinger
- Respiratory Medicine Unit, Department of Medicine and Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden.
| | - Michael Hagemann-Jensen
- Respiratory Medicine Unit, Department of Medicine and Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Susanna Kullberg
- Respiratory Medicine Unit, Department of Medicine and Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden; Lung Allergy Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Benita Engvall
- Respiratory Medicine Unit, Department of Medicine and Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Anders Eklund
- Respiratory Medicine Unit, Department of Medicine and Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden; Lung Allergy Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Grunewald
- Respiratory Medicine Unit, Department of Medicine and Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden; Lung Allergy Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Piehl
- Neuroimmunology Unit, Department of Clinical Neuroscience and Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience and Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
| | - Jan Wahlström
- Respiratory Medicine Unit, Department of Medicine and Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, SE-171 76 Stockholm, Sweden
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Myhr KM, Grytten N, Torkildsen Ø, Wergeland S, Bø L, Aarseth JH. The Norwegian Multiple Sclerosis Registry and Biobank. Acta Neurol Scand 2016; 132:24-8. [PMID: 26046555 DOI: 10.1111/ane.12427] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2015] [Indexed: 02/01/2023]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system with unknown cause and various benefits from disease modifying therapies. Systematic recording of data into national MS registries is therefore needed to optimize treatment and define the pathogenesis of the disease. The Norwegian MS Registry and Biobank was established for systematic collection of clinical and epidemiological data, as well as biological samples. Data collection is based on informed consent from the individual patients and recordings by treating neurologists. All researchers have, by application, access to data and biological samples from the Norwegian Multiple Sclerosis Registry and Biobank. By this combined effort from both patients and healthcare personnel, the Registry and Biobank aims to facilitate research for improved understanding of disease mechanisms and improved health care in MS.
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Affiliation(s)
- K.-M. Myhr
- Norwegian Multiple Sclerosis Registry and Biobank; Department of Neurology; Haukeland University Hospital; Bergen Norway
- KG Jebsen MS Research Centre; Department of Clinical Medicine; University of Bergen; Bergen Norway
| | - N. Grytten
- KG Jebsen MS Research Centre; Department of Clinical Medicine; University of Bergen; Bergen Norway
- Norwegian Multiple Sclerosis Competence Centre; Department of Neurology; Haukeland University Hospital; Bergen Norway
| | - Ø. Torkildsen
- KG Jebsen MS Research Centre; Department of Clinical Medicine; University of Bergen; Bergen Norway
- Norwegian Multiple Sclerosis Competence Centre; Department of Neurology; Haukeland University Hospital; Bergen Norway
| | - S. Wergeland
- KG Jebsen MS Research Centre; Department of Clinical Medicine; University of Bergen; Bergen Norway
- Norwegian Multiple Sclerosis Competence Centre; Department of Neurology; Haukeland University Hospital; Bergen Norway
| | - L. Bø
- KG Jebsen MS Research Centre; Department of Clinical Medicine; University of Bergen; Bergen Norway
- Norwegian Multiple Sclerosis Competence Centre; Department of Neurology; Haukeland University Hospital; Bergen Norway
| | - J. H. Aarseth
- Norwegian Multiple Sclerosis Registry and Biobank; Department of Neurology; Haukeland University Hospital; Bergen Norway
- KG Jebsen MS Research Centre; Department of Clinical Medicine; University of Bergen; Bergen Norway
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Hillert J, Stawiarz L. The Swedish MS registry – clinical support tool and scientific resource. Acta Neurol Scand 2016; 132:11-9. [PMID: 26046553 PMCID: PMC4657484 DOI: 10.1111/ane.12425] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2015] [Indexed: 01/01/2023]
Abstract
The Swedish MS registry (SMSreg) is designed to assure quality health care for patients with multiple sclerosis (MS). It has been active since 2001 and web-based since 2004. It runs on government funding only and is used in all Swedish neurology departments. The SMSreg currently includes data on 14,500 of Sweden's estimated 17,500 prevalent patients with MS. One important function of SMSreg, to which participation is voluntary, is to serve as a tool for decision support and to provide an easy overview of the patient information needed at clinical visits. This is its core feature and explains why the majority of Swedish MS specialists contribute data. Another success factor for SMSreg is that entered data can be readily accessed, either through a query function into Excel format or through a set of predesigned tables and diagrams in which parameters can be selected. Recent development includes a portal allowing patients to view a summary of their registered data and to report a set of patient-reported outcomes. SMSreg data have been used in close to 100 published scientific reports. Current projects include an incidence cohort (EIMS), post-marketing cohorts of patients on novel disease-modifying drugs (IMSE), and a prevalence cohort (GEMS). As these studies combine physical sampling and questionnaire data with clinical documentation and possible linkage to other public registries, together they provide an excellent platform for integrated MS research.
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Affiliation(s)
- J. Hillert
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
- Department of Neurology Karolinska University Hospital Stockholm Sweden
| | - L. Stawiarz
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
- Department of Neurology Karolinska University Hospital Stockholm Sweden
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