2022
A multiple sclerosis–protective coding variant reveals an essential role for HDAC7 in regulatory T cells
Axisa P, Yoshida T, Lucca L, Kasler H, Lincoln M, Pham G, Del Priore D, Carpier J, Lucas C, Verdin E, Sumida T, Hafler D. A multiple sclerosis–protective coding variant reveals an essential role for HDAC7 in regulatory T cells. Science Translational Medicine 2022, 14: eabl3651. PMID: 36516268, DOI: 10.1126/scitranslmed.abl3651.Peer-Reviewed Original ResearchConceptsExperimental autoimmune encephalitisRegulatory T cellsHistone deacetylase 7Multiple sclerosisT cellsMouse modelFunction of Foxp3CD4 T cellsHigher suppressive capacityVivo modelingAutoimmune encephalitisEAE severityImmunosuppressive subsetAutoimmune diseasesImmunomodulatory roleSuppressive capacityImmune cellsDisease onsetDistinct molecular classesSusceptibility lociGenetic susceptibility lociSingle-cell RNA sequencingDisease riskPatient samplesProtective variants
2020
Epigenetic fine-mapping: identification of causal mechanisms for autoimmunity
Lincoln MR, Axisa PP, Hafler DA. Epigenetic fine-mapping: identification of causal mechanisms for autoimmunity. Current Opinion In Immunology 2020, 67: 50-56. PMID: 32977183, DOI: 10.1016/j.coi.2020.09.002.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesMolecular mechanismsSusceptibility lociIndividual susceptibility lociFundamental genetic basisCausal molecular mechanismsPathogenic cell typesSpecific molecular mechanismsGenetic susceptibility lociEpigenetic techniquesGenetic basisGenetic lociAssociation studiesCell typesLociRecent advancesMechanismGeneticsAutoimmune diseasesSpectrum of autoimmunityCausal mechanismsEtiological mechanismsInflammatory diseasesTranslationAutoimmunity
2013
Network-Based Multiple Sclerosis Pathway Analysis with GWAS Data from 15,000 Cases and 30,000 Controls
Consortium I, Baranzini S, Khankhanian P, Patsopoulos N, Li M, Stankovich J, Cotsapas C, Søndergaard H, Ban M, Barizzone N, Bergamaschi L, Booth D, Buck D, Cavalla P, Celius E, Comabella M, Comi G, Compston A, Cournu-Rebeix I, D’alfonso S, Damotte V, Din L, Dubois B, Elovaara I, Esposito F, Fontaine B, Franke A, Goris A, Gourraud P, Graetz C, Guerini F, Guillot-Noel L, Hafler D, Hakonarson H, Hall P, Hamsten A, Harbo H, Hemmer B, Hillert J, Kemppinen A, Kockum I, Koivisto K, Larsson M, Lathrop M, Leone M, Lill C, Macciardi F, Martin R, Martinelli V, Martinelli-Boneschi F, McCauley J, Myhr K, Naldi P, Olsson T, Oturai A, Pericak-Vance M, Perla F, Reunanen M, Saarela J, Saker-Delye S, Salvetti M, Sellebjerg F, Sørensen P, Spurkland A, Stewart G, Taylor B, Tienari P, Winkelmann J, Consortium W, Zipp F, Ivinson A, Haines J, Sawcer S, DeJager P, Hauser S, Oksenberg J. Network-Based Multiple Sclerosis Pathway Analysis with GWAS Data from 15,000 Cases and 30,000 Controls. American Journal Of Human Genetics 2013, 92: 854-865. PMID: 23731539, PMCID: PMC3958952, DOI: 10.1016/j.ajhg.2013.04.019.Peer-Reviewed Original ResearchConceptsPathway analysisNetwork-based pathway analysisGenome-wide association studiesSubnetworks of genesExtended linkage disequilibriumNon-HLA susceptibility lociHigh-confidence candidatesSubsequent genetic studiesComplex traitsSubstantial genetic componentSignificant lociGWAS dataAssociation studiesGene levelGenetic studiesNominal statistical evidenceSusceptibility lociGenesLinkage disequilibriumSusceptibility variantsGenetic componentRelated pathwaysLociHuman leukocyte antigen (HLA) regionPowerful approach
2011
Genome‐wide meta‐analysis identifies novel multiple sclerosis susceptibility loci
Patsopoulos NA, Esposito F, Reischl J, Lehr S, Bauer D, Heubach J, Sandbrink R, Pohl C, Edan G, Kappos L, Miller D, Montalbán J, Polman C, Freedman M, Hartung H, Arnason B, Comi G, Cook S, Filippi M, Goodin D, Jeffery D, O'Connor P, Ebers G, Langdon D, Reder A, Traboulsee A, Zipp F, Schimrigk S, Hillert J, Bahlo M, Booth D, Broadley S, Brown M, Browning B, Browning S, Butzkueven H, Carroll W, Chapman C, Foote S, Griffiths L, Kermode A, Kilpatrick T, Lechner-Scott J, Marriott M, Mason D, Moscato P, Heard R, Pender M, Perreau V, Perera D, Rubio J, Scott R, Slee M, Stankovich J, Stewart G, Taylor B, Tubridy N, Willoughby E, Wiley J, Matthews P, Boneschi F, Compston A, Haines J, Hauser S, McCauley J, Ivinson A, Oksenberg J, Pericak-Vance M, Sawcer S, De Jager P, Hafler D, de Bakker P. Genome‐wide meta‐analysis identifies novel multiple sclerosis susceptibility loci. Annals Of Neurology 2011, 70: 897-912. PMID: 22190364, PMCID: PMC3247076, DOI: 10.1002/ana.22609.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle nucleotide polymorphismsSusceptibility lociHapMap Phase IIUnique single nucleotide polymorphismsGene discovery effortsNew susceptibility lociStrongest cis effectsMS genome-wide association studiesQuantitative trait analysisFlanking genesGenetic architectureRNA expression dataMultiple sclerosis susceptibility lociIntergenic regionSecond intronNew lociNovel susceptibility allelesAdditional lociTrait analysisAssociation studiesExpression dataChromosome 2p21LociFunctional consequencesThe CD6 Multiple Sclerosis Susceptibility Allele Is Associated with Alterations in CD4+ T Cell Proliferation
Kofler DM, Severson CA, Mousissian N, De Jager PL, Hafler DA. The CD6 Multiple Sclerosis Susceptibility Allele Is Associated with Alterations in CD4+ T Cell Proliferation. The Journal Of Immunology 2011, 187: 3286-3291. PMID: 21849685, DOI: 10.4049/jimmunol.1100626.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAntigens, CDAntigens, Differentiation, T-LymphocyteCD4-Positive T-LymphocytesCD8-Positive T-LymphocytesCell ProliferationCell SeparationCells, CulturedFemaleFlow CytometryGenetic Predisposition to DiseaseGenotypeHumansMaleMultiple SclerosisPhenotypeReverse Transcriptase Polymerase Chain ReactionRisk FactorsRNA, Small InterferingConceptsGenome-wide association studiesAssociation studiesAllelic variantsNew susceptibility lociSusceptibility allelesRisk allelesProliferation defectExon 5Risk-associated allelesSingle nucleotide polymorphismsExtracellular binding sitesCD6 geneSusceptibility lociLinkage disequilibriumMS risk alleleSelective knockdownT cell activationNucleotide polymorphismsAltered proliferationCell proliferationGenetic associationAllelesLong-term activationBinding sitesMS susceptibility allelesA knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility
Bush WS, McCauley JL, DeJager PL, Dudek SM, Hafler DA, Gibson RA, Matthews PM, Kappos L, Naegelin Y, Polman CH, Hauser SL, Oksenberg J, Haines JL, Ritchie MD. A knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility. Genes & Immunity 2011, 12: 335-340. PMID: 21346779, PMCID: PMC3136581, DOI: 10.1038/gene.2011.3.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesGene-gene interactionsCytoskeleton regulatory proteinsCytoskeletal regulationGenetic architectureGene clusterInteraction analysisSingle-locus analysisGWAS dataRegulatory proteinsBiological contextRelated genesAssociation studiesSusceptibility lociWeak main effectsPhospholipase CGenetic effectsΒ isoformsComplex diseasesBiological mechanismsNeurodegenerative mechanismsNew genetic effectsEpistasisACTN1Genes
2010
Chapter 3 Uncovering the Genetic Architecture of Multiple Sclerosis
De Jager P, Hafler D. Chapter 3 Uncovering the Genetic Architecture of Multiple Sclerosis. Blue Books Of Neurology 2010, 35: 43-56. DOI: 10.1016/b978-1-4160-6068-0.00003-6.Peer-Reviewed Original ResearchGenetic architectureSusceptibility lociWhole-genome association scansCommon human diseasesMajor histocompatibility complexMultiple sclerosis geneticsCommon genetic variationAssociation scanHuman genomeGenetic variationSingle locusHuman diseasesLociFirst glimpseCurrent discoveriesHistocompatibility complexGenotyped subjectsGenetic susceptibilityGenomeRapid progressHuman leukocyte antigenGeneticsHapMapConvergence of resourcesMultiple sclerosis
2009
Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci
, , McCauley J, Zuvich R, Beecham A, De Jager P, Konidari I, Whitehead P, Aubin C, Ban M, Pobywajlo S, Briskin R, Romano S, Aggarwal N, Piccio L, McArdle W, Strachan D, Evans D, Cross A, Cree B, Rioux J, Barcellos L, Ivinson A, Compston A, Hafler D, Hauser S, Oksenberg J, Sawcer S, Pericak-Vance M, Haines J. Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci. Human Molecular Genetics 2009, 19: 953-962. PMID: 20007504, PMCID: PMC2816610, DOI: 10.1093/hmg/ddp542.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle nucleotide polymorphismsAssociation studiesFirst genome-wide association studyGenome-wide association screenNumerous complex diseasesSusceptibility lociInitial genome-wide association studyGenome-wide significanceNovel susceptibility lociComplex genetic diseasesHundreds of associationsSNP hitsGWAS studiesGenetic diseasesLociComplex diseasesOriginal screenTMEM39AInitial associationIndependent data setsReplicationKIF21BInitial replicationScreenMapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases
Rioux J, Goyette P, Vyse T, Hammarström L, Fernando M, Green T, De Jager P, Foisy S, Wang J, de Bakker P, Leslie S, McVean G, Padyukov L, Alfredsson L, Annese V, Hafler D, Pan-Hammarström Q, Matell R, Sawcer S, Compston A, Cree B, Mirel D, Daly M, Behrens T, Klareskog L, Gregersen P, Oksenberg J, Hauser S. Mapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 18680-18685. PMID: 19846760, PMCID: PMC2773992, DOI: 10.1073/pnas.0909307106.Peer-Reviewed Original ResearchConceptsAutoimmune diseasesSystemic lupus erythematosusSelective IgA deficiencyStrong susceptibility locusNon-HLA genesMHC regionLupus erythematosusMyasthenia gravisUlcerative colitisCrohn's diseaseRheumatoid arthritisIgA deficiencyMultiple sclerosisMultiple susceptibility variantsMHC associationsDiseaseAppropriate control samplesPrimary association signalStrong linkage disequilibriumIndependent association signalsHuman MHCSusceptibility variantsSusceptibility lociAssociation signalsMost studiesIntegration of genetic risk factors into a clinical algorithm for multiple sclerosis susceptibility: a weighted genetic risk score
De Jager PL, Chibnik LB, Cui J, Reischl J, Lehr S, Simon KC, Aubin C, Bauer D, Heubach JF, Sandbrink R, Tyblova M, Lelkova P, the steering committees of the BENEFIT B, Havrdova E, Pohl C, Horakova D, Ascherio A, Hafler D, Karlson E. Integration of genetic risk factors into a clinical algorithm for multiple sclerosis susceptibility: a weighted genetic risk score. The Lancet Neurology 2009, 8: 1111-1119. PMID: 19879194, PMCID: PMC3099419, DOI: 10.1016/s1474-4422(09)70275-3.Peer-Reviewed Original ResearchConceptsWeighted genetic risk scoreEpstein-Barr virusHealth Study IMultiple sclerosisC-statisticRisk factorsGenetic risk scoreImmune responseRisk scoreNurses' Health Study IDiagnosis of MSNon-genetic risk factorsHigh-risk individualsMultiple sclerosis susceptibilityEnvironmental risk factorsGenetic risk factorsNHS cohortDerivation cohortTherapeutic trialsMS riskProspective studyClinical algorithmImportant clinical applicationsHigher oddsSusceptibility lociMeta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci
De Jager PL, Jia X, Wang J, de Bakker PI, Ottoboni L, Aggarwal NT, Piccio L, Raychaudhuri S, Tran D, Aubin C, Briskin R, Romano S, Baranzini S, McCauley J, Pericak-Vance M, Haines J, Gibson R, Naeglin Y, Uitdehaag B, Matthews P, Kappos L, Polman C, McArdle W, Strachan D, Evans D, Cross A, Daly M, Compston A, Sawcer S, Weiner H, Hauser S, Hafler D, Oksenberg J. Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci. Nature Genetics 2009, 41: 776-782. PMID: 19525953, PMCID: PMC2757648, DOI: 10.1038/ng.401.Peer-Reviewed Original ResearchF.27. Meta-analysis of Genome Scans and Replication Identify CD6, ICSBP1, and TNFRSF1A as Novel Multiple Sclerosis Susceptibility Loci
De Jager P, de Bakker P, Wang J, Ottoboni L, Consortium I, Hauser S, Oksenberg J, Hafler D. F.27. Meta-analysis of Genome Scans and Replication Identify CD6, ICSBP1, and TNFRSF1A as Novel Multiple Sclerosis Susceptibility Loci. Clinical Immunology 2009, 131: s101. DOI: 10.1016/j.clim.2009.03.294.Peer-Reviewed Original ResearchMultiple sclerosis susceptibility lociSusceptibility lociInfection-Triggered Familial or Recurrent Cases of Acute Necrotizing Encephalopathy Caused by Mutations in a Component of the Nuclear Pore, RANBP2
Neilson DE, Adams MD, Orr CM, Schelling DK, Eiben RM, Kerr DS, Anderson J, Bassuk AG, Bye AM, Childs AM, Clarke A, Crow YJ, Di Rocco M, Dohna-Schwake C, Dueckers G, Fasano AE, Gika AD, Gionnis D, Gorman MP, Grattan-Smith PJ, Hackenberg A, Kuster A, Lentschig MG, Lopez-Laso E, Marco EJ, Mastroyianni S, Perrier J, Schmitt-Mechelke T, Servidei S, Skardoutsou A, Uldall P, van der Knaap MS, Goglin KC, Tefft DL, Aubin C, de Jager P, Hafler D, Warman ML. Infection-Triggered Familial or Recurrent Cases of Acute Necrotizing Encephalopathy Caused by Mutations in a Component of the Nuclear Pore, RANBP2. American Journal Of Human Genetics 2009, 84: 44-51. PMID: 19118815, PMCID: PMC2668029, DOI: 10.1016/j.ajhg.2008.12.009.Peer-Reviewed Original ResearchConceptsRecurrent ANERecurrent casesAcute Necrotizing EncephalopathyMissense mutationsCommon viral infectionsSusceptibility allelesFamilial ANENecrotizing EncephalopathyHealthy childrenViral infectionBinding protein 2PatientsAdditional kindredsAutosomal dominant traitUnaffected controlsObligate carriersIdentical mutationsProtein 2Index familySusceptibility loci
2007
A second major histocompatibility complex susceptibility locus for multiple sclerosis
Yeo TW, De Jager PL, Gregory SG, Barcellos LF, Walton A, Goris A, Fenoglio C, Ban M, Taylor CJ, Goodman RS, Walsh E, Wolfish CS, Horton R, Traherne J, Beck S, Trowsdale J, Caillier SJ, Ivinson AJ, Green T, Pobywajlo S, Lander ES, Pericak-Vance MA, Haines JL, Daly MJ, Oksenberg JR, Hauser SL, Compston A, Hafler DA, Rioux JD, Sawcer S, . A second major histocompatibility complex susceptibility locus for multiple sclerosis. Annals Of Neurology 2007, 61: 228-236. PMID: 17252545, PMCID: PMC2737610, DOI: 10.1002/ana.21063.Peer-Reviewed Original ResearchConceptsMajor histocompatibility complexMultiple sclerosisHLA-C geneHLA-DRB1 geneHuman leukocyte antigen (HLA) typingResidual associationHLA-DRB1 locusComplex susceptibility lociTight linkage disequilibriumControl subjectsAntigen typingProtective effectSclerosisClass II regionHistocompatibility complexHLA lociRisk haplotypeClassical HLA lociSingle nucleotide polymorphismsIndependent effectsChromosome 6p21AssociationNucleotide polymorphismsTrio familiesSusceptibility loci
2006
The role of inflammatory bowel disease susceptibility loci in multiple sclerosis and systemic lupus erythematosus
De Jager PL, Graham R, Farwell L, Sawcer S, Richardson A, Behrens TW, Compston A, Hafler DA, Kere J, Vyse TJ, Rioux JD. The role of inflammatory bowel disease susceptibility loci in multiple sclerosis and systemic lupus erythematosus. Genes & Immunity 2006, 7: 327-334. PMID: 16642031, DOI: 10.1038/sj.gene.6364303.Peer-Reviewed Original ResearchMeSH KeywordsChromosomes, Human, Pair 5ExonsGenetic Predisposition to DiseaseHumansInflammatory Bowel DiseasesIntracellular Signaling Peptides and ProteinsLupus Erythematosus, SystemicMembrane ProteinsMultiple SclerosisNod2 Signaling Adaptor ProteinPolymorphism, Single NucleotideTumor Suppressor ProteinsConceptsSystemic lupus erythematosusInflammatory bowel diseaseMultiple sclerosisRisk allelesLupus erythematosusInflammatory diseasesCases of SLERisk of SLECARD15/NOD2 geneGeneral susceptibility locusIBD risk allelesChronic inflammatory diseaseIBD5 locusComplex inflammatory diseaseInflammatory bowel disease susceptibility lociEvidence of associationLupus nephritisBowel diseaseSLE subjectsPooled analysisCARD15 geneSusceptibility lociNOD2 geneDiseaseErythematosus