TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits


Diogo D, Bastarache L, Liao KP, Graham RR, Fulton RS, Greenberg JD, Eyre S, Bowes J, Cui J, Lee A, et al. TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits. PLoS OnePLoS ONEPLoS ONE. 2015;10 :e0122271.


Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3 x 10(-21)), A928V (rs35018800, OR = 0.53, P = 1.2 x 10(-9)), and I684S (rs12720356, OR = 0.86, P = 4.6 x 10(-7)). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6 x 10(-18)), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; P(omnibus) = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases.


Diogo, DorotheeBastarache, LisaLiao, Katherine PGraham, Robert RFulton, Robert SGreenberg, Jeffrey DEyre, SteveBowes, JohnCui, JingLee, AnnettePappas, Dimitrios AKremer, Joel MBarton, AnneCoenen, Marieke J HFranke, BarbaraKiemeney, Lambertus AMariette, XavierRichard-Miceli, CorrineCanhao, HelenaFonseca, Joao Ede Vries, NiekTak, Paul PCrusius, J Bart ANurmohamed, Michael TKurreeman, FinaMikuls, Ted ROkada, YukinoriStahl, Eli ALarson, David EDeluca, Tracie LO'Laughlin, MichelleFronick, Catrina CFulton, Lucinda LKosoy, RomanRansom, MichaelBhangale, Tushar ROrtmann, WardCagan, AndrewGainer, VivianKarlson, Elizabeth WKohane, IsaacMurphy, Shawn NMartin, JavierZhernakova, AlexandraKlareskog, LarsPadyukov, LeonidWorthington, JaneMardis, Elaine RSeldin, Michael FGregersen, Peter KBehrens, TimothyRaychaudhuri, SoumyaDenny, Joshua CPlenge, Robert MengR01-AR056768/AR/NIAMS NIH HHS/R01-AR057108/AR/NIAMS NIH HHS/R01-AR059648/AR/NIAMS NIH HHS/R01-AR063759/AR/NIAMS NIH HHS/U01-GM092691/GM/NIGMS NIH HHS/UH2 AR067677/AR/NIAMS NIH HHS/Research Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov't2015/04/08 06:00PLoS One. 2015 Apr 7;10(4):e0122271. doi: 10.1371/journal.pone.0122271. eCollection 2015.