From genetic associations to functional studies in multiple sclerosis
Corresponding Author
S. D. Bos
Institute of Clinical Medicine, University of Oslo, Oslo
Department of Neurology, Oslo University Hospital, Oslo
Correspondence: S. D. Bos, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway (tel.: +47 9601 6326; fax: +47 2302 7455; e-mail: [email protected]).Search for more papers by this authorT. Berge
Institute of Clinical Medicine, University of Oslo, Oslo
Department of Neurology, Oslo University Hospital, Oslo
Search for more papers by this authorE. G. Celius
Department of Neurology, Oslo University Hospital, Oslo
Institute of Health and Society, University of Oslo, Oslo, Norway
Search for more papers by this authorH. F. Harbo
Institute of Clinical Medicine, University of Oslo, Oslo
Department of Neurology, Oslo University Hospital, Oslo
Search for more papers by this authorCorresponding Author
S. D. Bos
Institute of Clinical Medicine, University of Oslo, Oslo
Department of Neurology, Oslo University Hospital, Oslo
Correspondence: S. D. Bos, Institute of Clinical Medicine, University of Oslo, 0316 Oslo, Norway (tel.: +47 9601 6326; fax: +47 2302 7455; e-mail: [email protected]).Search for more papers by this authorT. Berge
Institute of Clinical Medicine, University of Oslo, Oslo
Department of Neurology, Oslo University Hospital, Oslo
Search for more papers by this authorE. G. Celius
Department of Neurology, Oslo University Hospital, Oslo
Institute of Health and Society, University of Oslo, Oslo, Norway
Search for more papers by this authorH. F. Harbo
Institute of Clinical Medicine, University of Oslo, Oslo
Department of Neurology, Oslo University Hospital, Oslo
Search for more papers by this authorAbstract
Genetic screens steadily reveal more loci that show robust associations to complex human diseases, including multiple sclerosis (MS). Although some of the identified genetic variants are easily interpreted into a biological function, most of the genetic associations are frequently challenging to interpret. Underlying these difficulties is the fact that chip-based assays typically detect single nucleotide polymorphisms (SNPs) representative of a stretch of DNA containing many genomic variants in linkage disequilibrium. Furthermore, a large proportion of the SNPs with strongest association to MS are located in regions of the DNA that do not directly code for proteins. Here we discuss challenges faced by MS researchers to follow up the large-scale genetic screens that have been published over the past years in search of functional consequences of the identified MS-associated SNPs. We discuss experimental design, tools and methods that may provide the much-needed biological insights in both disease etiology and disease manifestations.
References
- 1Compston A, Coles A. Multiple sclerosis. Lancet 2008; 372: 1502–1517.
- 2Gourraud PA, Harbo HF, Hauser SL, Baranzini SE. The genetics of multiple sclerosis: an up-to-date review. Immunol Rev 2012; 248: 87–103.
- 3Naito S, Namerow N, Mickey MR, Terasaki PI. Multiple sclerosis: association with HL-A3. Tissue Antigens 1972; 2: 1–4.
- 4 International Multiple Sclerosis Genetics Consortium, International IBD Genetics Consortium. Class II HLA interactions modulate genetic risk for multiple sclerosis. Nat Genet. 2015; 47: 1107–1113.
- 5 International Multiple Sclerosis Genetics Consortium, Hafler DA, Compston A, et al. Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med. 2007; 357: 851–862.
- 6 International Multiple Sclerosis Genetics Consortium, Wellcome Trust Case Control Consortium, Sawcer S, et al. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature 2011; 476: 214–219.
- 7 International Multiple Sclerosis Genetics Consortium, Beecham AH, Patsopoulos NA, et al. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Genet 2013; 45: 1353–1360.
- 8Linker RA, Kieseier BC, Gold R. Identification and development of new therapeutics for multiple sclerosis. Trends Pharmacol Sci 2008; 29: 558–565.
- 9Chitnis T. The role of CD4 T cells in the pathogenesis of multiple sclerosis. Int Rev Neurobiol 2007; 79: 43–72.
- 10Huseby ES, Huseby PG, Shah S, Smith R, Stadinski BD. Pathogenic CD8 T cells in multiple sclerosis and its experimental models. Front Immunol 2012; 3: 64.
- 11Broux B, Stinissen P, Hellings N. Which immune cells matter? The immunopathogenesis of multiple sclerosis. Crit Rev Immunol 2013; 33: 283–306.
- 12Kleinewietfeld M, Hafler DA. Regulatory T cells in autoimmune neuroinflammation. Immunol Rev 2014; 259: 231–244.
- 13Ragoussis J. Genotyping technologies for genetic research. Annu Rev Genomics Hum Genet 2009; 10: 117–133.
- 14Slatkin M. Linkage disequilibrium − understanding the evolutionary past and mapping the medical future. Nat Rev Genet 2008; 9: 477–485.
- 15Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet 2012; 44: 955.
- 16Gu B, Field J, Kilpatrick T, et al. A rare P2X7 variant ARG307GLN with absent pore formation function protects against neuroinflammation in multiple sclerosis. J Neurochem 2015; 134: 360.
- 17Farh KKH, Marson A, Zhu J, et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 2015; 518: 337–343.
- 18Scalfari A, Neuhaus A, Daumer M, Ebers G, Muraro P. The relationship between age and long-term evolution in multiple sclerosis. Eur J Neurol 2012; 19: 345.
- 19Smestad C, Sandvik L, Landro NI, Celius EG. Cognitive impairment after three decades of multiple sclerosis. Eur J Neurol 2010; 17: 499–505.
- 20Mero IL, Gustavsen MW, Saether H, et al. Genetic differences relating to oligoclonal band status in multiple sclerosis. Mult Scler J 2012; 18: 17–18.
- 21Goris A, Pauwels I, Gustavsen MW, et al. Genetic variants are major determinants of CSF antibody levels in multiple sclerosis. Brain. 2015; 138: 632–643.
- 22Matsushita T, Madireddy L, Sprenger T, et al. Genetic associations with brain cortical thickness in multiple sclerosis. Genes Brain Behav 2015; 14: 217–227.
- 23Berg-Hansen P, Moen S, Harbo H, Celius E. High prevalence and no latitude gradient of multiple sclerosis in Norway. Mult Scler 2014; 20: 1780–1782.
- 24Zhang T, Shirani A, Zhao Y, et al. Beta-interferon exposure and onset of secondary progressive multiple sclerosis. Eur J Neurol 2015; 22: 990–1000.
- 25Maher B. Personal genomes: the case of the missing heritability. Nature 2008; 456: 18–21.
- 26Buil A, Brown AA, Lappalainen T, et al. Gene−gene and gene−environment interactions detected by transcriptome sequence analysis in twins. Nat Genet 2015; 47: 88.
- 27Cortijo S, Wardenaar R, Colome-Tatche M, Gilly A, Etcheverry M, Labadie K, et al. Mapping the epigenetic basis of complex traits. Science 2014; 343: 1145–1148.
- 28Dang MN, Buzzetti R, Pozzilli P. Epigenetics in autoimmune diseases with focus on type 1 diabetes. Diabetes Metab Res Rev 2013; 29: 8–18.
- 29Baranzini SE, Mudge J, van Velkinburgh JC, et al. Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature 2010; 464: 1351–1356.
- 30Graves M, Benton M, Lea R, et al. Methylation differences at the HLA-DRB1 locus in CD4+ T-cells are associated with multiple sclerosis. Mult Scler 2013; 20: 1033–1041.
- 31Bos SD, Page CM, Andreassen BK, et al. Genome-wide DNA methylation profiles indicate CD8+ T cell hypermethylation in multiple sclerosis. PLoS One 2015; 10: e0117403.
- 32Kemppinen AK, Kaprio J, Palotie A, Saarela J. Systematic review of genome-wide expression studies in multiple sclerosis. BMJ Open 2011; 1: e000053.
- 33Baranzini SE. Gene expression profiling in MS: a fulfilled promise? Mult Scler 2013; 19: 1813–1814.
- 34Parnell GP, Gatt PN, Krupa M, et al. The autoimmune disease-associated transcription factors EOMES and TBX21 are dysregulated in multiple sclerosis and define a molecular subtype of disease. Clin Immunol 2014; 151: 16–24.
- 35Lossius A, Johansen JN, Vartdal F, et al. High-throughput sequencing of TCR repertoires in multiple sclerosis reveals intrathecal enrichment of EBV-reactive CD8(+) T cells. Eur J Immunol 2014; 44: 3439–3452.
- 36Maurano MT, Humbert R, Rynes E, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 2012; 337: 1190–1195.
- 37Disanto G, Kjetil Sandve G, Ricigliano VA, et al. DNase hypersensitive sites and association with multiple sclerosis. Hum Mol Genet 2014; 23: 942–948.
- 38Kent WJ, Sugnet CW, Furey TS, et al. The Human Genome Browser at UCSC. Genome Res 2002; 12: 996–1006.
- 39Robinson JT, Thorvaldsdottir H, Winckler W, et al. Integrative Genomics Viewer. Nat Biotechnol 2011; 29: 24–26.
- 40Couturier N, Bucciarelli F, Nurtdinov RN, et al. Tyrosine kinase 2 variant influences T lymphocyte polarization and multiple sclerosis susceptibility. Brain 2011; 134: 693–703.
- 41van Luijn MM, Kreft KL, Jongsma ML, et al. Multiple sclerosis-associated CLEC16A controls HLA class II expression via late endosome biogenesis. Brain 2015; 6: 1531–1547.
- 42Constantinescu CS, Farooqi N, O'Brien K, Gran B. Experimental autoimmune encephalomyelitis (EAE) as a model for multiple sclerosis (MS). Br J Pharmacol 2011; 164: 1079–1106.
- 43Madsen LS, Andersson EC, Jansson L, et al. A humanized model for multiple sclerosis using HLA-DR2 and a human T-cell receptor. Nat Genet 1999; 23: 343–347.
- 44t Hart BA, vanKooyk Y, Geurts JJ, Gran B. The primate autoimmune encephalomyelitis model; a bridge between mouse and man. Ann Clin Transl Neurol 2015; 2: 581–593.
- 45Su LF, Han A, McGuire HM, Furman D, Newell EW, Davis MM. The promised land of human immunology. Cold Spring Harb Symp Quant Biol 2013; 78: 203–213.
- 46Guerau-de-Arellano M, et al. Micro-RNA dysregulation in multiple sclerosis favours pro-inflammatory T-cell-mediated autoimmunity. Brain 2011; 134: 3575–3586.
- 47Charpentier E, Doudna JA. Biotechnology: rewriting a genome. Nature 2013; 495: 50–51.
- 48Goris A, Pauwels I, Dubois B. Progress in multiple sclerosis genetics. Curr Genomics 2012; 13: 646–663.
- 49Gregory AP, Dendrou CA, Attfield KE, et al. TNF receptor 1 genetic risk mirrors outcome of anti-TNF therapy in multiple sclerosis. Nature 2012; 488: 508.
- 50Stahl EA, Raychaudhuri S, Remmers EF, et al. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet 2010; 42: 508–514.
- 51Franke A, McGovern DPB, Barrett JC, et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat Genet 2010; 42: 1118.
- 52Mero IL, Ban M, Lorentzen AR, et al. Exploring the CLEC16A gene reveals a MS-associated variant with correlation to the relative expression of CLEC16A isoforms in thymus. Genes Immun 2011; 12: 191–198.
- 53Leikfoss IS, Mero IL, Dahle MK, et al. Multiple sclerosis-associated single-nucleotide polymorphisms in CLEC16A correlate with reduced SOCS1 and DEXI expression in the thymus. Genes Immun 2013; 14: 62–66.
- 54Zuvich RL, Bush WS, McCauley JL, et al. Interrogating the complex role of chromosome 16p13.13 in multiple sclerosis susceptibility: independent genetic signals in the CIITA-CLEC16A-SOCS1 gene complex. Hum Mol Genet 2011; 20: 3517–3524.
- 55Soleimanpour SA, Gupta A, Bakay M, et al. The diabetes susceptibility gene clec16a regulates mitophagy. Cell 2014; 157: 1577–1590.