INTRODUCTION: The aim of the study was to analyse genetic architecture of RA by utilizing multiparametric statistical methods such as linear discriminant analysis (LDA) and redundancy analysis (RDA). METHODS: A total of 1393 volunteers, 499 patients with RA and 894 healthy controls were included in the study. The presence of shared epitope (SE) in HLA-DRB1 and 11 SNPs (PTPN22 C/T (rs2476601), STAT4 G/T (rs7574865), CTLA4 A/G (rs3087243), TRAF1/C5 A/G (rs3761847), IRF5 T/C (rs10488631), TNFAIP3 C/T (rs5029937), AFF3 A/T (rs11676922), PADI4 C/T (rs2240340), CD28 T/C (rs1980422), CSK G/A (rs34933034) and FCGR3A A/C (rs396991), rheumatoid factor (RF), anti-citrullinated protein antibodies (ACPA) and clinical status was analysed using the LDA and RDA. RESULTS: HLA-DRB1, PTPN22, STAT4, IRF5 and PADI4 significantly discriminated between RA patients and healthy controls in LDA. The correlation between RA diagnosis and the explanatory variables in the model was 0.328 (Trace = 0.107; F = 13.715; P = 0.0002). The risk variants of IRF5 and CD28 genes were found to be common determinants for seropositivity in RDA, while positivity of RF alone was associated with the CTLA4 risk variant in heterozygous form. The correlation between serologic status and genetic determinants on the 1st ordinal axis was 0.468, and 0.145 on the 2nd one (Trace = 0.179; F = 6.135; P = 0.001). The risk alleles in AFF3 gene together with the presence of ACPA were associated with higher clinical severity of RA. CONCLUSIONS: The association among multiple risk variants related to T cell receptor signalling with seropositivity may play an important role in distinct clinical phenotypes of RA. Our study demonstrates that multiparametric analyses represent a powerful tool for investigation of mutual relationships of potential risk factors in complex diseases such as RA.

1st Department of Internal Medicine Faculty of Medicine Pavol Jozef Šafárik University in Košice Košice Slovakia

5th Department of Internal Medicine Medical Faculty of Comenius University Bratislava Slovakia

Department of Internal Medicine 3 Division of Rheumatology Medical University of Vienna Vienna Austria

Institute of Clinical and Translational Research Biomedical Centre Slovak Academy of Sciences Bratislava Slovakia

Institute of Experimental Medicine Czech Academy of Sciences Prague Czech Republic

Institute of Molecular Genetics Czech Academy of Sciences Prague Czech Republic

National Institute of Rheumatic Diseases Piešťany Slovakia

Slovak Medical University Bratislava Slovakia

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van der Helm-van Mil AH, Toes RE, Huizinga TW. Genetic variants in the prediction of rheumatoid arthritis. Ann Rheum Dis. 2010;69(9]:1694–6. 10.1136/ard.2009.123828 PubMed DOI

Stastny P. Mixed lymphocyte cultures in rheumatoid arthritis. J Clin Invest. 1976;57(5]:1148–57. PubMed PMC

Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, et al. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature. 2014;506(7488]:376–81. 10.1038/nature12873 PubMed DOI PMC

Raychaudhuri S, Sandor C, Stahl EA, Freudenberg J, Lee HS, Jia X, et al. Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis. Nat Genet. 2012;44(3]:291–6. 10.1038/ng.1076 PubMed DOI PMC

Ding B, Padyukov L, Lundstrom E, Seielstad M, Plenge RM, Oksenberg JR, et al. Different patterns of associations with anti-citrullinated protein antibody-positive and anti-citrullinated protein antibody-negative rheumatoid arthritis in the extended major histocompatibility complex region. Arthritis Rheum. 2009;60(1]:30–8. 10.1002/art.24135 PubMed DOI PMC

Huizinga TW, Amos CI, van der Helm-van Mil AH, Chen W, van Gaalen FA, Jawaheer D, et al. Refining the complex rheumatoid arthritis phenotype based on specificity of the HLA-DRB1 shared epitope for antibodies to citrullinated proteins. Arthritis Rheum. 2005;52(11]:3433–8. PubMed

Viatte S, Massey J, Bowes J, Duffus K, arc OC, Eyre S, et al. Replication of genetic loci outside the HLA conferring susceptibility to anti-CCP negative rheumatoid arthritis. Arthritis & rheumatology. 2016. PubMed PMC

Padyukov L, Seielstad M, Ong RT, Ding B, Ronnelid J, Seddighzadeh M, et al. A genome-wide association study suggests contrasting associations in ACPA-positive versus ACPA-negative rheumatoid arthritis. Ann Rheum Dis. 2011;70(2]:259–65. 10.1136/ard.2009.126821 PubMed DOI PMC

Eyre S, Bowes J, Diogo D, Lee A, Barton A, Martin P, et al. High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nat Genet. 2012;44(12]:1336–40. 10.1038/ng.2462 PubMed DOI PMC

Liu C, Ackerman HH, Carulli JP. A genome-wide screen of gene-gene interactions for rheumatoid arthritis susceptibility. Human genetics. 2011;129(5]:473–85. 10.1007/s00439-010-0943-z PubMed DOI

McClure A, Lunt M, Eyre S, Ke X, Thomson W, Hinks A, et al. Investigating the viability of genetic screening/testing for RA susceptibility using combinations of five confirmed risk loci. Rheumatology (Oxford]. 2009;48(11]:1369–74. PubMed PMC

Karlson EW, Chibnik LB, Kraft P, Cui J, Keenan BT, Ding B, et al. Cumulative association of 22 genetic variants with seropositive rheumatoid arthritis risk. Ann Rheum Dis. 2010;69(6]:1077–85. 10.1136/ard.2009.120170 PubMed DOI PMC

Chibnik LB, Keenan BT, Cui J, Liao KP, Costenbader KH, Plenge RM, et al. Genetic risk score predicting risk of rheumatoid arthritis phenotypes and age of symptom onset. PLoS One. 2011;6(9]:e24380 10.1371/journal.pone.0024380 PubMed DOI PMC

Karlson EW, Ding B, Keenan BT, Liao K, Costenbader KH, Klareskog L, et al. Association of environmental and genetic factors and gene-environment interactions with risk of developing rheumatoid arthritis. Arthritis care & research. 2013;65(7]:1147–56. PubMed PMC

Scott IC, Seegobin SD, Steer S, Tan R, Forabosco P, Hinks A, et al. Predicting the risk of rheumatoid arthritis and its age of onset through modelling genetic risk variants with smoking. PLoS Genet. 2013;9(9]:e1003808 10.1371/journal.pgen.1003808 PubMed DOI PMC

Janssens AC, Pardo MC, Steyerberg EW, van Duijn CM. Revisiting the clinical validity of multiplex genetic testing in complex diseases. Am J Hum Genet. 2004;74(3]:585–8; author reply 8–9. PubMed PMC

Meigs JB, Shrader P, Sullivan LM, McAteer JB, Fox CS, Dupuis J, et al. Genotype score in addition to common risk factors for prediction of type 2 diabetes. N Engl J Med. 2008;359(21]:2208–19. 10.1056/NEJMoa0804742 PubMed DOI PMC

Lu Q, Song Y, Wang X, Won S, Cui Y, Elston RC. The effect of multiple genetic variants in predicting the risk of type 2 diabetes. BMC proceedings. 2009;3 Suppl 7:S49 PubMed PMC

Patterson N, Price AL, Reich D. Population structure and eigenanalysis. PLoS Genet. 2006;2(12]:e190 PubMed PMC

Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006;38(8]:904–9. PubMed

Aletaha D, Neogi T, Silman AJ, Funovits J, Felson DT, Bingham CO 3rd, et al. 2010 Rheumatoid arthritis classification criteria: an American College of Rheumatology/European League Against Rheumatism collaborative initiative. Arthritis Rheum. 2010;62(9]:2569–81. 10.1002/art.27584 PubMed DOI

Fransen J, van Riel PL. The Disease Activity Score and the EULAR response criteria. Clin Exp Rheumatol. 2005;23(5 Suppl 39]:S93–9. PubMed

Fries JF, Spitz P, Kraines RG, Holman HR. Measurement of patient outcome in arthritis. Arthritis Rheum. 1980;23(2]:137–45. PubMed

Holoshitz J. The rheumatoid arthritis HLA-DRB1 shared epitope. Curr Opin Rheumatol. 2010;22(3]:293–8. 10.1097/BOR.0b013e328336ba63 PubMed DOI PMC

Iwamoto T, Ikari K, Nakamura T, Kuwahara M, Toyama Y, Tomatsu T, et al. Association between PADI4 and rheumatoid arthritis: a meta-analysis. Rheumatology (Oxford]. 2006;45(7]:804–7. PubMed

Martinez A, Valdivia A, Pascual-Salcedo D, Lamas JR, Fernandez-Arquero M, Balsa A, et al. PADI4 polymorphisms are not associated with rheumatoid arthritis in the Spanish population. Rheumatology (Oxford]. 2005;44(10]:1263–6. PubMed

Burr ML, Naseem H, Hinks A, Eyre S, Gibbons LJ, Bowes J, et al. PADI4 genotype is not associated with rheumatoid arthritis in a large UK Caucasian population. Ann Rheum Dis. 2010;69(4]:666–70. 10.1136/ard.2009.111294 PubMed DOI PMC

Dieguez-Gonzalez R, Calaza M, Perez-Pampin E, de la Serna AR, Fernandez-Gutierrez B, Castaneda S, et al. Association of interferon regulatory factor 5 haplotypes, similar to that found in systemic lupus erythematosus, in a large subgroup of patients with rheumatoid arthritis. Arthritis Rheum. 2008;58(5]:1264–74. 10.1002/art.23426 PubMed DOI

Wang C, Kokkonen H, Sandling JK, Johansson M, Seddighzadeh M, Padyukov L, et al. Preferential association of interferon regulatory factor 5 gene variants with seronegative rheumatoid arthritis in 2 Swedish case-control studies. J Rheumatol. 2011;38(10]:2130–2. 10.3899/jrheum.110322 PubMed DOI

Stahl EA, Raychaudhuri S, Remmers EF, Xie G, Eyre S, Thomson BP, et al. Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet. 2010;42(6]:508–14. 10.1038/ng.582 PubMed DOI PMC

Kurreeman F, Liao K, Chibnik L, Hickey B, Stahl E, Gainer V, et al. Genetic basis of autoantibody positive and negative rheumatoid arthritis risk in a multi-ethnic cohort derived from electronic health records. Am J Hum Genet. 2011;88(1]:57–69. 10.1016/j.ajhg.2010.12.007 PubMed DOI PMC

van der Helm-van Mil AH, Verpoort KN, Breedveld FC, Huizinga TW, Toes RE, de Vries RR. The HLA-DRB1 shared epitope alleles are primarily a risk factor for anti-cyclic citrullinated peptide antibodies and are not an independent risk factor for development of rheumatoid arthritis. Arthritis Rheum. 2006;54(4]:1117–21. PubMed

Karlson EW, Chibnik LB, Cui J, Plenge RM, Glass RJ, Maher NE, et al. Associations between human leukocyte antigen, PTPN22, CTLA4 genotypes and rheumatoid arthritis phenotypes of autoantibody status, age at diagnosis and erosions in a large cohort study. Ann Rheum Dis. 2008;67(3]:358–63. PubMed PMC

Chang Foreman HC, Van Scoy S, Cheng TF, Reich NC. Activation of interferon regulatory factor 5 by site specific phosphorylation. PLoS One. 2012;7(3]:e33098 10.1371/journal.pone.0033098 PubMed DOI PMC

Romo-Tena J, Gomez-Martin D, Alcocer-Varela J. CTLA-4 and autoimmunity: new insights into the dual regulator of tolerance. Autoimmun Rev. 2013;12(12]:1171–6. 10.1016/j.autrev.2013.07.002 PubMed DOI

Han TU, Bang SY, Kang C, Bae SC. TRAF1 polymorphisms associated with rheumatoid arthritis susceptibility in Asians and in Caucasians. Arthritis Rheum. 2009;60(9]:2577–84. 10.1002/art.24759 PubMed DOI

Gough SC, Walker LS, Sansom DM. CTLA4 gene polymorphism and autoimmunity. Immunol Rev. 2005;204:102–15. PubMed

Plenge RM, Padyukov L, Remmers EF, Purcell S, Lee AT, Karlson EW, et al. Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. Am J Hum Genet. 2005;77(6]:1044–60. PubMed PMC

Costenbader KH, Chang SC, De Vivo I, Plenge R, Karlson EW. Genetic polymorphisms in PTPN22, PADI-4, and CTLA-4 and risk for rheumatoid arthritis in two longitudinal cohort studies: evidence of gene-environment interactions with heavy cigarette smoking. Arthritis Res Ther. 2008;10(3]:R52 10.1186/ar2421 PubMed DOI PMC

Viatte S, Plant D, Bowes J, Lunt M, Eyre S, Barton A, et al. Genetic markers of rheumatoid arthritis susceptibility in anti-citrullinated peptide antibody negative patients. Ann Rheum Dis. 2012;71(12]:1984–90. 10.1136/annrheumdis-2011-201225 PubMed DOI PMC

De Rycke L, Peene I, Hoffman IE, Kruithof E, Union A, Meheus L, et al. Rheumatoid factor and anticitrullinated protein antibodies in rheumatoid arthritis: diagnostic value, associations with radiological progression rate, and extra-articular manifestations. Ann Rheum Dis. 2004;63(12]:1587–93. PubMed PMC

Meyer O, Nicaise-Roland P, Santos MD, Labarre C, Dougados M, Goupille P, et al. Serial determination of cyclic citrullinated peptide autoantibodies predicted five-year radiological outcomes in a prospective cohort of patients with early rheumatoid arthritis. Arthritis Res Ther. 2006;8(2]:R40 PubMed PMC

van der Helm-van Mil AH, Verpoort KN, Breedveld FC, Toes RE, Huizinga TW. Antibodies to citrullinated proteins and differences in clinical progression of rheumatoid arthritis. Arthritis Res Ther. 2005;7(5]:R949–58. PubMed PMC

Knevel R, de Rooy DP, Zhernakova A, Grondal G, Krabben A, Steinsson K, et al. Association of variants in IL2RA with progression of joint destruction in rheumatoid arthritis. Arthritis Rheum. 2013;65(7]:1684–93. 10.1002/art.37938 PubMed DOI

Li C, Bazzano LA, Rao DC, Hixson JE, He J, Gu D, et al. Genome-wide linkage and positional association analyses identify associations of novel AFF3 and NTM genes with triglycerides: the GenSalt study. Journal of genetics and genomics = Yi chuan xue bao. 2015;42(3]:107–17. 10.1016/j.jgg.2015.02.003 PubMed DOI PMC

Sandholm N, Salem RM, McKnight AJ, Brennan EP, Forsblom C, Isakova T, et al. New susceptibility loci associated with kidney disease in type 1 diabetes. PLoS Genet. 2012;8(9]:e1002921 10.1371/journal.pgen.1002921 PubMed DOI PMC

Kerekes G, Nurmohamed MT, Gonzalez-Gay MA, Seres I, Paragh G, Kardos Z, et al. Rheumatoid arthritis and metabolic syndrome. Nat Rev Rheumatol. 2014;10(11]:691–6. 10.1038/nrrheum.2014.121 PubMed DOI

Steiner G, Urowitz MB. Lipid profiles in patients with rheumatoid arthritis: mechanisms and the impact of treatment. Semin Arthritis Rheum. 2009;38(5]:372–81. 10.1016/j.semarthrit.2008.01.015 PubMed DOI

Ursini F, Russo E, D'Angelo S, Arturi F, Hribal ML, D'Antona L, et al. Prevalence of Undiagnosed Diabetes in Rheumatoid Arthritis: an OGTT Study. Medicine. 2016;95(7]:e2552 10.1097/MD.0000000000002552 PubMed DOI PMC

Barton A, Eyre S, Ke X, Hinks A, Bowes J, Flynn E, et al. Identification of AF4/FMR2 family, member 3 (AFF3] as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes. Hum Mol Genet. 2009;18(13]:2518–22. 10.1093/hmg/ddp177 PubMed DOI PMC

Plant D, Flynn E, Mbarek H, Dieude P, Cornelis F, Arlestig L, et al. Investigation of potential non-HLA rheumatoid arthritis susceptibility loci in a European cohort increases the evidence for nine markers. Ann Rheum Dis. 2010;69(8]:1548–53. 10.1136/ard.2009.121020 PubMed DOI PMC

Stark K, Rovensky J, Blazickova S, Grosse-Wilde H, Ferencik S, Hengstenberg C, et al. Association of common polymorphisms in known susceptibility genes with rheumatoid arthritis in a Slovak population using osteoarthritis patients as controls. Arthritis Res Ther. 2009;11(3]:R70 10.1186/ar2699 PubMed DOI PMC

Plenge RM. Recent progress in rheumatoid arthritis genetics: one step towards improved patient care. Curr Opin Rheumatol. 2009;21(3]:262–71. 10.1097/BOR.0b013e32832a2e2d PubMed DOI

Ioannidis JP. Non-replication and inconsistency in the genome-wide association setting. Human heredity. 2007;64(4]:203–13. PubMed

Weir BS, Cardon LR, Anderson AD, Nielsen DM, Hill WG. Measures of human population structure show heterogeneity among genomic regions. Genome research. 2005;15(11]:1468–76. PubMed PMC