Genomics and proteomics: Applications in autoimmune diseases

References

• HirschhornJGenomewide association studies–illuminating biologic pathwaysN Engl J Med20093601699170119369661
   PubMed Web of Science ®Google Scholar
• FeldmannMTranslating molecular insights in autoimmunity into effective therapyAnnu Rev Immunol20092712719007330
   PubMed Web of Science ®Google Scholar
• TaylorCFPatonNWLilleyKSThe minimum information about a proteomics experiment (MIAPE)Nat Biotechnol200725888789317687369
   PubMed Web of Science ®Google Scholar
• PanSAebersoldRChenRMass spectrometry based targeted protein quantification: methods and applicationsJ Proteome Res2009878779719105742
   PubMed Web of Science ®Google Scholar
• KimSMisraASNP genotyping: technologies and biomedical applicationsAnnu Rev Biomed Engin20079289320
   PubMed Web of Science ®Google Scholar
• FathmanCGLuis SoaresLChanSMUtzPJAn array of possibilities for the study of autoimmunityNature200543560561115931213
   PubMed Web of Science ®Google Scholar
• CallesenAMadsenJVachWKruseTMogensenOJensenOSerum protein profiling by solid phase extraction and mass spectrometry: A future diagnostics tool?Proteomics200991428144119235169
   PubMed Web of Science ®Google Scholar
• BalboniIChanSMKattahMTenenbaumJDButteAJUtzPJMultiplexed protein array platforms for analysis of autoimmune diseasesAnnu Rev Immunol20062439141816551254
   PubMed Web of Science ®Google Scholar
• LettreGRiouxJDAutoimmune diseases: insights from genome-wide association studiesHum Mol Genet200817R2R116R12118852199
   PubMed Web of Science ®Google Scholar
• GregersenPKOlssonLMRecent advances in the genetics of autoimmune diseaseAnnu Rev Immunol20092736339119302045
   PubMed Web of Science ®Google Scholar
• SchenaMShalonDDavisRWBrownPOQuantitative monitoring of gene expression patterns with a complementary DNA microarrayScience199527052354674707569999
   PubMed Web of Science ®Google Scholar
• MarcotteEMPellegriniMThompsonMJYeatesTOEisenbergDA combined algorithm for genome-wide prediction of protein functionNature19994026757838610573421
   PubMed Web of Science ®Google Scholar
• MacBeathGSchreiberSPrinting proteins as microarrays for high-throughput function determinationScience20002891760176310976071
   PubMed Web of Science ®Google Scholar
• ArnottDShabanowitzJHuntDFMass spectrometry of proteins and peptides: sensitive and accurate mass measurement and sequence analysisClin Chem199339200520108375091
   PubMed Web of Science ®Google Scholar
• van BaarsenLVosslamberSTijssenMPharmacogenomics of interferon-beta therapy in multiple sclerosis: baseline IFN signature determines pharmacological differences between patientsPLoS One200834e192718382694
   PubMed Web of Science ®Google Scholar
• BosCvan BaarsenLTimmerTMolecular subtypes of systemic sclerosis in association with anti-centromere antibodies and digital ulcersGenes Immun200910321021819129850
   PubMed Web of Science ®Google Scholar
• ChabasDBaranziniSEMitchellDThe influence of the pro-inflammatory cytokine, osteopontin, on autoimmune demyelinating diseaseScience20012941731173511721059
   PubMed Web of Science ®Google Scholar
• OusmanSTomookaBvan NoortJProtective and therapeutic role for alphaB-crystallin in autoimmune demyelinationNature2007448715247447917568699
   PubMed Web of Science ®Google Scholar
• HurEYoussefSHawsMZhangSSobelRSteinmanLOsteopontin-induced relapse and progression of autoimmune brain disease through enhanced survival of activated T cellsNat Immunol200781748317143274
   PubMed Web of Science ®Google Scholar
• HanMHwangSRoyDProteomic analysis of active multiple sclerosis lesions reveals therapeutic targetsNature200845171821076108118278032
   PubMed Web of Science ®Google Scholar
• O’ConnorKCMcLaughlinKADe JagerPLSelf-antigen tetramers discriminate between myelin autoantibodies to native or denatured proteinNat Med200713221121717237795
   PubMed Web of Science ®Google Scholar
• ObermeierBMenteleRMalotkaJMatching of oligoclonal immunoglobulin transcriptomes and proteomes of cerebrospinal fluid in multiple sclerosisNat Med200814668869318488038
   PubMed Web of Science ®Google Scholar
• van MühlenCATanEMAutoantibodies in the diagnosis of systemic rheumatic diseasesArthritis Rheum199524323358
   Web of Science ®Google Scholar
• ScofieldRHAutoantibodies as predictors of diseaseLancet200436394201544154615135604
   PubMed Web of Science ®Google Scholar
• LaGasseJMBrantleyMSLeechNJSuccessful prospective prediction of type 1 diabetes in schoolchildren through multiple defined autoantibodies: an 8-year follow-up of the Washington State Diabetes Prediction StudyDiabetes Care200225350551111874938
   PubMed Web of Science ®Google Scholar
• SmolenJAletahaDGrisarJRedlichKSteinerGWagnerOThe need for prognosticators in rheumatoid arthritis. Biological and clinical markers: where are we now?Arthritis Res Ther200810320818557991
   PubMed Web of Science ®Google Scholar
• FurlanRDefinition of non-responders: biological markersNeurol Sci200829S214S21518690495
   PubMed Web of Science ®Google Scholar
• ZetheliusBBerglundLSundstromJUse of multiple biomarkers to improve the prediction of death from cardiovascular causesN Engl J Med2008358202107211618480203
   PubMed Web of Science ®Google Scholar
• SchellekensGAde JongBAvan den HoogenFHvan de PutteLBvan VenrooijWJCitrulline is an essential constituent of antigenic determinants recognized by rheumatoid arthritis-specific autoantibodiesJ Clin Invest19981012732819421490
   PubMed Web of Science ®Google Scholar
• KlareskogLRonnelidJLundbergKPadyukovLAlfredssonLImmunity to citrullinated proteins in rheumatoid arthritisAnnu Rev Immunol20082665167518173373
   PubMed Web of Science ®Google Scholar
• NishimuraKSugiyamaDKogataYMeta-analysis: diagnostic accuracy of anti-cyclic citrullinated peptide antibody and rheumatoid factor for theumatoid arthritisAnn Intern Med20071461179780817548411
   PubMed Web of Science ®Google Scholar
• FritzlerMWiikATanEA critical evaluation of enzyme immunoassay kits for detection of antinuclear autoantibodies of defined specificities. III. Comparative performance characteristics of academic and manufacturers’ laboratoriesJ Rheumatol200330112374238114677180
   PubMed Web of Science ®Google Scholar
• RobinsonWDiGennaroCHueberWAutoantigen microarrays for multiplex characterization of autoantibody responsesNat Med20028329530111875502
   PubMed Web of Science ®Google Scholar
• HueberWTomookaBHZhaoXProteomic analysis of secreted proteins in early rheumatoid arthritis: anti-citrulline autoreactivity is associated with up regulation of proinflammatory cytokinesAnn Rheum Dis200766671271916901957
   PubMed Web of Science ®Google Scholar
• RobinsonWFontouraPLeeBProtein microarrays guide tolerizing DNA vaccine treatment of autoimmune encephalomyelitisNat Biotechnol2003211033103912910246
   PubMed Web of Science ®Google Scholar
• KiddBHoPSharpeOEpitope spreading to citrullinated antigens in mouse models of autoimmune arthritis and demyelinationArthritis Res Ther200810R11918826638
   PubMed Web of Science ®Google Scholar
• HillJBellDBrintnellWArthritis induced by posttranslationally modified (citrullinated) fibrinogen in DR4-IE transgenic miceJ Exp Med2008205496797918391064
   PubMed Web of Science ®Google Scholar
• HueberWKiddBATomookaBHAntigen microarray profiling of autoantibodies in rheumatoid arthritisArthritis Rheum20055292645265516142722
   PubMed Web of Science ®Google Scholar
• KanterJNarayanaSHoPLipid microarrays identify key mediators of autoimmune brain inflammationNat Med20061213814216341241
   PubMed Web of Science ®Google Scholar
• HueberWTomookaBBatliwallaFBlood autoantibody and cytokine profiles predict response to anti-tumor necrosis factor therapy in rheumatoid arthritisArthritis Res Ther2009113R7919476613
   PubMed Web of Science ®Google Scholar
• SilvermanGSrikrishnanRGermarKGenetic imprinting of autoantibody repertoires in systemic lupus erythematosus patientsClin Exp Immunol200815310211618510544
   PubMed Web of Science ®Google Scholar
• ZhenQLXieCWuTIdentification of autoantibody clusters that best predict lupus disease activity using glomerular proteome arraysJ Clin Invest2005115123428343916322790
   PubMed Web of Science ®Google Scholar
• CambridgeGIsenbergDEdwardsJB cell depletion therapy in systemic lupus erythematosus: relationships among serum B lymphocyte stimulator levels, autoantibody profile and clinical responseAnn Rheum Dis2008671011101617962238
   PubMed Web of Science ®Google Scholar
• ArbuckleMMcClainMRubertoneMDevelopment of autoantibodies before the clinical onset of systemic lupus erythematosusN Engl J Med2003349161526153314561795
   PubMed Web of Science ®Google Scholar
• FeserMDerberLDeaneKPlasma 25,OH vitamin D concentrations are not associated with rheumatoid arthritis (RA)-related autoantibodies in individuals at elevated risk for RAJ Rheumatol200936594394619286844
   PubMed Web of Science ®Google Scholar
• NielenMvan SchaardenburgDReesinkHSpecific autoantibodies precede the symptoms of rheumatoid arthritis: a study of serial measurements in blood donorsArthritis Rheum200450238038614872479
   PubMed Web of Science ®Google Scholar
• Rantapää-DahlqvistSde JongBBerglinEAntibodies against cyclic citrullinated peptide and IgA rheumatoid factor predict the development of rheumatoid arthritisArthritis Rheum200348102701270514558071
   PubMed Web of Science ®Google Scholar
• DwivediRDhindsaNKrokhinOCortensJWilkinsJEl-GabalawyHThe effects of infliximab therapy on the serum proteome of rheumatoid arthritis patientsArthritis Res Ther2009112R3219265537
   PubMed Web of Science ®Google Scholar
• AndersonNLAndersonNGThe human plasma proteome: history, character, and diagnostic prospectsMol Cell Proteomics2002184586712488461
   PubMed Web of Science ®Google Scholar
• JacksonDHerathASwintonJConsiderations for powering a clinical proteomics study: Normal variability in the human plasma proteomeProteomics Clin Appl20093394407
   PubMed Web of Science ®Google Scholar
• AndersonNEsquer-BlascoRHofmannJAndersonNA two-dimensional gel database of rat liver proteins useful in gene regulation and drug effects studiesElectrophoresis1991129079301724422
   PubMed Web of Science ®Google Scholar
• RaiAStemmerPZhangZAnalysis of Human Proteome Organization Plasma Proteome Project (HUPO PPP) reference specimens using surface enhanced laser desorption/ionization-time of flight (SELDI-TOF) mass spectrometry: multi-institution correlation of spectra and identification of biomarkersProteomics200553467347416052624
   PubMed Web of Science ®Google Scholar
• TabushiYNakanishiTTakeuchiTDetection of citrullinated proteins in synovial fluids derived from patients with rheumatoid arthritis by proteomics-based analysisAnn Clin Biochem200845441341718583628
   PubMed Web of Science ®Google Scholar
• KinlochALundbergKWaitRSynovial fluid is a site of citrullination of autoantigens in inflammatory arthritisArthritis Rheum20085882287229518668562
   PubMed Web of Science ®Google Scholar
• RodriguezAEspinaBEspinaVLiottaLAutomated laser capture micro-dissection for tissue proteomicsMethods Mol Biol2008441719018370312
   PubMedGoogle Scholar
• ChaussabelDQuinnCShenJA modular analysis framework for blood genomics studies: application to systemic lupus erythematosusImmunity20082991118631452
   PubMed Web of Science ®Google Scholar
• DoyleHMamulaMPosttranslational modifications of self-antigensAnn N Y Acad Sci200510501916014515
   PubMed Web of Science ®Google Scholar
• DoyleHMamulaMA failure to repair self-proteins leads to T cell hyperproliferation and autoantibody productionJ Immunol200317162840284712960305
   PubMed Web of Science ®Google Scholar
• KattahMAlemiGThibaultDBalboniIUtzPA new two-color Fab labeling method for autoantigen protein microarraysNat Methods20063974575116929321
   PubMed Web of Science ®Google Scholar
• ThalerMBuhlAWelterHBiosensor analyses of serum autoantibodies: application to antiphospholipid syndrome and systemic lupus erythematosusAnal Bioanal Chem200939351417142918759105
   PubMed Web of Science ®Google Scholar
• AllantazFChaussabelDStichwehDBlood leukocyte microarrays to diagnose systemic onset juvenile idiopathic arthritis and follow the response to IL-1 blockadeJ Exp Med200720492131214417724127
   PubMed Web of Science ®Google Scholar
• PascualVAllantazFPatelPPaluckaAChaussabelDBanchereauJHow the study of children with rheumatic diseases identified interferon-alpha and interleukin-1 as novel therapeutic targetsImmunol Rev2008223395918613829
   PubMed Web of Science ®Google Scholar
• NakouMKnowltonNFrankMGene expression in systemic lupus erythematosus: bone marrow analysis differentiates active from inactive disease and reveals apoptosis and granulopoiesis signaturesArthritis Rheum200858113541354918975309
   PubMed Web of Science ®Google Scholar
• ChaussabelDAllmanWMejiasAAnalysis of significance patterns identifies ubiquitous and disease-specific gene-expression signatures in patient peripheral blood leukocytesAnn NY Acad Sci2005106214615416461797
   PubMed Web of Science ®Google Scholar
• AdenNShiwenXAdenDProteomic analysis of scleroderma lesional skin reveals activated wound healing phenotype of epidermal cell layerRheumatology200847121754176018829709
   PubMed Web of Science ®Google Scholar
• BaechlerEBauerJSlatteryCAn interferon signature in the peripheral blood of dermatomyositis patients is associated with disease activityMol Med2007131–2596817515957
   PubMed Web of Science ®Google Scholar
• HinksABartonAShephardNIdentification of a novel susceptibility locus for juvenile idiopathic arthritis by genome-wide association analysisArthritis Rheum200960125826319116933
   PubMed Web of Science ®Google Scholar
• MaoLDongHYangPMALDI-TOF/TOF-MS reveals elevated serum haptoglobin and amyloid A in Behçet’s diseaseJ Proteome Res20087104500450718754684
   PubMed Web of Science ®Google Scholar
• RottoliPMagiBPerariMCytokine profile and proteome analysis in bronchoalveolar lavage of patients with sarcoidosis, pulmonary fibrosis associated with systemic sclerosis and idiopathic pulmonary fibrosisProteomics2005551423143015761959
   PubMed Web of Science ®Google Scholar
• AndreasKHauplTLubkeCAntirheumatic drug response signatures in human chondrocytes: potential molecular targets to stimulate cartilage regenerationArthritis Res Ther2009111R1519192274
   PubMed Web of Science ®Google Scholar
• HaiderASLowesMASuarez-FarinasMIdentification of cellular pathways of “Type 1,” Th17 T Cells, and TNF- and inducible nitric oxide synthase-producing dendritic cells in autoimmune inflammation through pharmacogenomic study of cyclosporine A in psoriasisJ Immunol200818031913192018209089
   PubMed Web of Science ®Google Scholar
• QuintanaFFarezMWeinerHSystems biology approaches for the study of multiple sclerosisJ Cell Mol Med20081241087109318505469
   PubMed Web of Science ®Google Scholar
• AltshulerDDalyMLanderEGenetic mapping in human diseaseScience200832288188818988837
   PubMed Web of Science ®Google Scholar
• RischNMerikangasKThe future of genetic studies of complex human diseasesScience1996273151615178801636
   PubMed Web of Science ®Google Scholar
• JakobsdottirJGorinMConleyYFerrellRWeeksDInterpretation of genetic association studies: markers with replicated highly significant odds ratios may be poor classifiersPLoS Genet200952e100033719197355
   PubMed Web of Science ®Google Scholar
• Wellcome Trust Case Control ConsortiumGenome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controlsNature2007447714566167817554300
   PubMed Web of Science ®Google Scholar
• DuerrRHTaylorKDBrantSRRiouxJDSilverbergMSA genome-wide association study identifies IL23R as an inflammatory bowel disease geneScience2006314146117068223
   PubMed Web of Science ®Google Scholar
• WangKZhangHKugathasanSDiverse genome-wide association studies associate the IL12/IL23 pathway with Crohn diseaseAm J Human Genet200984339940519249008
   PubMed Web of Science ®Google Scholar
• WeersmaRKStokkersPCFCleynenIConfirmation of multiple Crohn’s disease susceptibility Loci in a large Dutch-Belgian cohortAm J Gastroenterol2009104363063819174780
   PubMed Web of Science ®Google Scholar
• BarrettJCHansoulSNicolaeDLChoJHDuerrRHGenome-wide association defines more than 30 distinct susceptibility loci for Crohn’s diseaseNat Genet20084095596218587394
   PubMed Web of Science ®Google Scholar
• OguraYBonenDKInoharaNNicolaeDLChenFFA frameshift mutation in NOD2 associated with susceptibility to Crohn’s diseaseNature200141160360611385577
   PubMed Web of Science ®Google Scholar
• HugotJPLaurent-PuigPGower-RousseauCOlsonJMLeeJCMapping of a susceptibility locus for Crohn’s disease on chromosome 16Nature19963798218238587604
   PubMed Web of Science ®Google Scholar
• RiouxJDXavierRJTaylorKDSilverbergMSGoyettePGenome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesisNat Genet20073959660417435756
   PubMed Web of Science ®Google Scholar
• ParkesMBarrettJCPrescottNJTremellingMAndersonCASequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn’s disease susceptibilityNat Genet20073983083217554261
   PubMed Web of Science ®Google Scholar
• CurtinKIlesMCampNIdentifying rarer genetic variants for common complex diseases: Diseased versus neutral discovery panelsAnn Hum Genet2009731546019132978
   PubMed Web of Science ®Google Scholar
• AlexPGucekMLiXApplications of proteomics in the study of inflammatory bowel diseases: Current status and future directions with available technologiesInflamm Bowel Dis200915461662918844215
   PubMed Web of Science ®Google Scholar
• MeuwisMAFilletMGeurtsPBiomarker discovery for inflammatory bowel disease, using proteomic serum profilingBiochem Pharmacol20077391422143317258689
   PubMed Web of Science ®Google Scholar
• MeuwisMAFilletMLutteriLProteomics for prediction and characterization of response to infliximab in Crohn‘s disease: A pilot studyClin Biochem2008411296096718489908
   PubMed Web of Science ®Google Scholar
• ShkodaAWernerTDanielHGunckelMRoglerGHallerDDifferential protein expression profile in the intestinal epithelium from patients with inflammatory bowel diseaseJ Proteome Res2007631114112517330946
   PubMed Web of Science ®Google Scholar
• BowcockAMGenomics: Guilt by associationNature2007447714564564617554292
   PubMed Web of Science ®Google Scholar
• RifaiNGilletteMCarrSProtein biomarker discovery and validation: the long and uncertain path to clinical utilityNature Biotechnol20062497198316900146
   PubMed Web of Science ®Google Scholar
• MaurerMProteomics of brain extracellular fluid (ECF) and cerebrospinal fluid (CSF)Mass Spectrom Rev200810.1002/mas.20213
   Web of Science ®Google Scholar
• AvasaralaJCerebrospinal fluid proteomics - Work in progressEurop J Neurol2008159891892
   Web of Science ®Google Scholar
• CayrolRWosikKBerardJLActivated leukocyte cell adhesion molecule promotes leukocyte trafficking into the central nervous systemNat Immunol20089213714518157132
   PubMed Web of Science ®Google Scholar