Skip to main content
Top

25-05-2018 | Rheumatoid arthritis | Article

Genome-wide association study of response to methotrexate in early rheumatoid arthritis patients

Journal: The Pharmacogenomics Journal

Authors: John C. Taylor, Tim Bongartz, Jonathan Massey, Borbala Mifsud, Athina Spiliopoulou, Ian C. Scott, Jianmei Wang, Michael Morgan, Darren Plant, Marco Colombo, Peter Orchard, Sarah Twigg, Iain B. McInnes, Duncan Porter, Jane E. Freeston, Jackie L. Nam, Heather J. Cordell, John D. Isaacs, Jenna L. Strathdee, Donna Arnett, Maria J. H. de Hair, Paul P. Tak, Stella Aslibekyan, Ronald F. van Vollenhoven, Leonid Padyukov, S. Louis Bridges, Costantino Pitzalis, Andrew P. Cope, Suzanne M. M. Verstappen, Paul Emery, Michael R. Barnes, Felix Agakov, Paul McKeigue, Taisei Mushiroda, Michiaki Kubo, Richard Weinshilboum, Anne Barton, Ann W. Morgan, Jennifer H. Barrett, on behalf of the MATURA,  and PAMERA,  Consortia

Publisher: Nature Publishing Group UK

Abstract

Methotrexate (MTX) monotherapy is a common first treatment for rheumatoid arthritis (RA), but many patients do not respond adequately. In order to identify genetic predictors of response, we have combined data from two consortia to carry out a genome-wide study of response to MTX in 1424 early RA patients of European ancestry. Clinical endpoints were change from baseline to 6 months after starting treatment in swollen 28-joint count, tender 28-joint count, C-reactive protein and the overall 3-component disease activity score (DAS28). No single nucleotide polymorphism (SNP) reached genome-wide statistical significance for any outcome measure. The strongest evidence for association was with rs168201 in NRG3 (p = 10−7 for change in DAS28). Some support was also seen for association with ZMIZ1, previously highlighted in a study of response to MTX in juvenile idiopathic arthritis. Follow-up in two smaller cohorts of 429 and 177 RA patients did not support these findings, although these cohorts were more heterogeneous.
Literature
1.
Singh JA, Saag KG, Bridges SL Jr, Akl EA, Bannuru RR, Sullivan MC, et al. 2015 American College of Rheumatology Guideline for the Treatment of Rheumatoid Arthritis. Arthritis Rheumatol. 2016;68:1–26.PubMed
2.
van Vollenhoven RF. Treatment of rheumatoid arthritis: state of the art 2009. Nat Rev Rheumatol. 2009;5:531–41.CrossRefPubMed
3.
Smolen JS, Aletaha D, Bijlsma JW, Breedveld FC, Boumpas D, Burmester G, et al. Treating rheumatoid arthritis to target: recommendations of an international task force. Ann Rheum Dis. 2010;69:631–7.CrossRefPubMedPubMedCentral
4.
Schoels M, Knevel R, Aletaha D, Bijlsma JW, Breedveld FC, Boumpas DT, et al. Evidence for treating rheumatoid arthritis to target: results of a systematic literature search. Ann Rheum Dis. 2010;69:638–43.CrossRefPubMedPubMedCentral
5.
Stoffer MA, Schoels MM, Smolen JS, Aletaha D, Breedveld FC, Burmester G, et al. Evidence for treating rheumatoid arthritis to target: results of a systematic literature search update. Ann Rheum Dis. 2016;75:16–22.CrossRefPubMed
6.
Hyrich KL, Watson KD, Silman AJ, Symmons DP, British Society for Rheumatology Biologics R. Predictors of response to anti-TNF-alpha therapy among patients with rheumatoid arthritis: Results from the British Society for Rheumatology Biologics Register. Rheumatology (Oxford). 2006;45:1558–65.CrossRef
7.
Dervieux T, Greenstein N, Kremer J. Pharmacogenomic and metabolic biomarkers in the folate pathway and their association with methotrexate effects during dosage escalation in rheumatoid arthritis. Arthritis Rheum. 2006;54:3095–103.CrossRefPubMed
8.
Lee YC, Cui J, Costenbader KH, Shadick NA, Weinblatt ME, Karlson EW. Investigation of candidate polymorphisms and disease activity in rheumatoid arthritis patients on methotrexate. Rheumatology (Oxford). 2009;48:613–7.CrossRef
9.
Jekic B, Lukovic L, Bunjevacki V, Milic V, Novakovic I, Damnjanovic T, et al. Association of the TYMS 3G/3G genotype with poor response and GGH 354GG genotype with the bone marrow toxicity of the methotrexate in RA patients. Eur J Clin Pharmacol. 2013;69:377–83.CrossRefPubMed
10.
Lima A, Monteiro J, Bernardes M, Sousa H, Azevedo R, Seabra V, et al. Prediction of methotrexate clinical response in Portuguese rheumatoid arthritis patients: implication of MTHFR rs1801133 and ATIC rs4673993 polymorphisms. Biomed Res Int. 2014;2014:368681.PubMedPubMedCentral
11.
Plant D, Wilson AG, Barton A. Genetic and epigenetic predictors of responsiveness to treatment in RA. Nat Rev Rheumatol. 2014;10:329–37.CrossRefPubMed
12.
Kung TN, Dennis J, Ma Y, Xie G, Bykerk V, Pope J, et al. RFC1 80G A is a genetic determinant of methotrexate efficacy in rheumatoid arthritis: a human genome epidemiologic review and meta-analysis of observational studies. Arthritis Rheumatol. 2014;66:1111–20.CrossRefPubMed
13.
Senapati S, Singh S, Das M, Kumar A, Gupta R, Kumar U, et al. Genome-wide analysis of methotrexate pharmacogenomics in rheumatoid arthritis shows multiple novel risk variants and leads for TYMS regulation. Pharmacogenet Genomics. 2014;24:211–9.CrossRefPubMed
14.
Cobb J, Cule E, Moncrieffe H, Hinks A, Ursu S, Patrick F, et al. Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases. Pharmacogenomics J. 2014;14:356–64.CrossRefPubMedPubMedCentral
15.
Barton A, Pitzalis C. Stratified medicine in rheumatoid arthritis-the MATURA programme. Rheumatology (Oxford). 2016;56:1247–50.CrossRef
16.
Conaghan PG, Hensor EM, Keenan AM, Morgan AW, Emery P, Consortium Y. Persistently moderate DAS-28 is not benign: loss of function occurs in early RA despite step-up DMARD therapy. Rheumatology (Oxford). 2010;49:1894–9.CrossRef
17.
Sergeant JC, Hyrich KL, Anderson J, Kopec-Harding K, Hope HF, Barton A, et al. OP0013 prediction of non-response to methotrexate therapy in the Rheumatoid Arthritis Medication Study (RAMS). Ann Rheum Dis. 2016;75:57–58.CrossRef
18.
Dumitru RB, Horton S, Hodgson R, Wakefield RJ, Hensor EM, Emery P, et al. A prospective, single-centre, randomised study evaluating the clinical, imaging and immunological depth of remission achieved by very early versus delayed Etanercept in patients with Rheumatoid Arthritis (VEDERA). BMC Musculoskelet Disord. 2016;17:61.CrossRefPubMedPubMedCentral
19.
Nam JL, Villeneuve E, Hensor EM, Conaghan PG, Keen HI, Buch MH, et al. Remission induction comparing infliximab and high-dose intravenous steroid, followed by treat-to-target: a double-blind, randomised, controlled trial in new-onset, treatment-naive, rheumatoid arthritis (the IDEA study). Ann Rheum Dis. 2014;73:75–85.CrossRefPubMed
20.
Nam JL, Villeneuve E, Hensor EM, Wakefield RJ, Conaghan PG, Green MJ, et al. A randomised controlled trial of etanercept and methotrexate to induce remission in early inflammatory arthritis: the EMPIRE trial. Ann Rheum Dis. 2014;73:1027–36.CrossRefPubMed
21.
Choy EH, Smith CM, Farewell V, Walker D, Hassell A, Chau L, et al. Factorial randomised controlled trial of glucocorticoids and combination disease modifying drugs in early rheumatoid arthritis. Ann Rheum Dis. 2008;67:656–63.CrossRefPubMed
22.
Scott IC, Ibrahim F, Simpson G, Kowalczyk A, White-Alao B, Hassell A, et al. A randomised trial evaluating anakinra in early active rheumatoid arthritis. Clin Exp Rheumatol. 2016;34:88–93.PubMed
23.
Moreland LW, O’Dell JR, Paulus HE, Curtis JR, Bathon JM, St Clair EW, et al. A randomized comparative effectiveness study of oral triple therapy versus etanercept plus methotrexate in early aggressive rheumatoid arthritis: the treatment of Early Aggressive Rheumatoid Arthritis Trial. Arthritis Rheum. 2012;64:2824–35.CrossRefPubMedPubMedCentral
24.
van Vollenhoven RF, Ernestam S, Geborek P, Petersson IF, Coster L, Waltbrand E, et al. Addition of infliximab compared with addition of sulfasalazine and hydroxychloroquine to methotrexate in patients with early rheumatoid arthritis (Swefot trial): 1-year results of a randomised trial. Lancet. 2009;374:459–66.CrossRefPubMed
25.
de Hair MJ, Lehmann KA, van de Sande MG, Maijer KI, Gerlag DM, Tak PP. The clinical picture of rheumatoid arthritis according to the 2010 American College of Rheumatology/European League Against Rheumatism criteria: Is this still the same disease? Arthritis Rheum. 2012;64:389–93.CrossRefPubMed
26.
Kronisch C, McLernon DJ, Dale J, Paterson C, Ralston SH, Reid DM, et al. Brief report: predicting functional disability: one-year results from the Scottish Early Rheumatoid Arthritis Inception Cohort. Arthritis Rheumatol. 2016;68:1596–602.CrossRefPubMed
27.
Jones G, Sebba A, Gu J, Lowenstein MB, Calvo A, Gomez-Reino JJ, et al. Comparison of tocilizumab monotherapy versus methotrexate monotherapy in patients with moderate to severe rheumatoid arthritis: the AMBITION study. Ann Rheum Dis. 2010;69:88–96.CrossRefPubMed
28.
Emery P, Deodhar A, Rigby WF, Isaacs JD, Combe B, Racewicz AJ, et al. Efficacy and safety of different doses and retreatment of rituximab: a randomised, placebo-controlled trial in patients who are biological naive with active rheumatoid arthritis and an inadequate response to methotrexate (Study Evaluating Rituximab’s Efficacy in MTX iNadequate rEsponders (SERENE)). Ann Rheum Dis. 2010;69:1629–35.CrossRefPubMedPubMedCentral
29.
Rubbert-Roth A, Tak PP, Zerbini C, Tremblay JL, Carreno L, Armstrong G, et al. Efficacy and safety of various repeat treatment dosing regimens of rituximab in patients with active rheumatoid arthritis: results of a Phase III randomized study (MIRROR). Rheumatology (Oxford). 2010;49:1683–93.CrossRef
30.
Tak PP, Rigby WF, Rubbert-Roth A, Peterfy CG, van Vollenhoven RF, Stohl W, et al. Inhibition of joint damage and improved clinical outcomes with rituximab plus methotrexate in early active rheumatoid arthritis: the IMAGE trial. Ann Rheum Dis. 2011;70:39–46.CrossRefPubMed
31.
Emery P, Rigby W, Tak PP, Dorner T, Olech E, Martin C, et al. Safety with ocrelizumab in rheumatoid arthritis: results from the ocrelizumab phase III program. PLoS ONE. 2014;9:e87379.CrossRefPubMedPubMedCentral
32.
Reich D, Price AL, Patterson N. Principal component analysis of genetic data. Nat Genet. 2008;40:491–2.CrossRefPubMed
33.
Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 2009;5:e1000529.CrossRefPubMedPubMedCentral
34.
Delaneau O, Howie B, Cox AJ, Zagury JF, Marchini J. Haplotype estimation using sequencing reads. Am J Hum Genet. 2013;93:687–96.CrossRefPubMedPubMedCentral
35.
Spiliopoulou A, Colombo M, Orchard P, Agakov F, McKeigue P. GeneImp: fast imputation to large reference panels using genotype likelihoods from ultra-low coverage sequencing. Genetics. 2017;91–104.
36.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–75.CrossRefPubMedPubMedCentral
37.
Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet. 2007;39:906–13.CrossRefPubMed
38.
Higgins JP, Thompson SG. Quantifying heterogeneity in a meta-analysis. Stat Med. 2002;21:1539–58.CrossRefPubMed
39.
Mikkelsen TS, Thorn CF, Yang JJ, Ulrich CM, French D, Zaza G, et al. PharmGKB summary: methotrexate pathway. Pharmacogenet Genomics. 2011;21:679–86.CrossRefPubMedPubMedCentral
40.
Plenge RM, Cotsapas C, Davies L, Price AL, de Bakker PI, Maller J, et al. Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. Nat Genet. 2007;39:1477–82.CrossRefPubMedPubMedCentral
41.
Julia A, Ballina J, Canete JD, Balsa A, Tornero-Molina J, Naranjo A, et al. Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility. Arthritis Rheum. 2008;58:2275–86.CrossRefPubMed
42.
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;506:376–81.CrossRefPubMed
43.
Kataoka H. EGFR ligands and their signaling scissors, ADAMs, as new molecular targets for anticancer treatments. J Dermatol Sci. 2009;56:148–53.CrossRefPubMed
44.
Rivera-Valentin RK, Hua YQ, Zhang Y, Lala N, Yang YW, Hughes DPM. Her-4 mediates anoikis resistance, chemoresistance, and metastatic potential in osteosarcoma. Cancer Res. 2014;74:(20 Suppl):Abstract nr A71.
45.
Bansard C, Lequerre T, Derambure C, Vittecoq O, Hiron M, Daragon A, et al. Gene profiling predicts rheumatoid arthritis responsiveness to IL-1Ra (anakinra). Rheumatology (Oxford). 2011;50:283–92.CrossRef
46.
Martin P, McGovern A, Orozco G, Duffus K, Yarwood A, Schoenfelder S, et al. Capture Hi-C reveals novel candidate genes and complex long-range interactions with related autoimmune risk loci. Nat Commun. 2015;6:10069.CrossRefPubMedPubMedCentral
47.
Cairns J, Freire-Pritchett P, Wingett SW, Varnai C, Dimond A, Plagnol V, et al. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol. 2016;17:127.CrossRefPubMedPubMedCentral
48.
Wang YC, Chiang EP. Low-dose methotrexate inhibits methionine S-adenosyltransferase in vitro and in vivo. Mol Med. 2012;18:423–32.PubMed
49.
Ellinghaus D, Ellinghaus E, Nair RP, Stuart PE, Esko T, Metspalu A, et al. Combined analysis of genome-wide association studies for Crohn disease and psoriasis identifies seven shared susceptibility loci. Am J Hum Genet. 2012;90:636–47.CrossRefPubMedPubMedCentral
50.
International Multiple Sclerosis Genetics C, Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, et al. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Genet. 2013;45:1353–60.CrossRef
51.
Fewings NL, Gatt PN, McKay FC, Parnell GP, Schibeci SD, Edwards J, et al. The autoimmune risk gene ZMIZ1 is a vitamin D responsive marker of a molecular phenotype of multiple sclerosis. J Autoimmun. 2017;78:57–69.CrossRefPubMed
52.
Jennewein C, Zacharowski K. Abstracts of Sepsis 2012. Paris, France. November 14-16, 2012. Crit Care. 2012;16 Suppl 3:P22.
53.
Arciuch VGA, Tedesco L, Fuertes M, Arzt E. Role of RSUME in inflammation and cancer. FEBS Lett. 2015;589:3330–5.CrossRef
54.
Sieberts SK, Zhu F, Garcia-Garcia J, Stahl E, Pratap A, Pandey G, et al. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nat Commun. 2016;7:12460.CrossRefPubMedPubMedCentral
55.
Umicevic Mirkov M, Janss L, Vermeulen SH, van de Laar MA, van Riel PL, Guchelaar HJ, et al. Estimation of heritability of different outcomes for genetic studies of TNFi response in patients with rheumatoid arthritis. Ann Rheum Dis. 2015;74:2183–7.CrossRefPubMed
56.
van Gestel AM, Prevoo ML, van ‘t Hof MA, van Rijswijk MH, van de Putte LB, van Riel PL. Development and validation of the European League Against Rheumatism response criteria for rheumatoid arthritis. Comparison with the preliminary American College of Rheumatology and the World Health Organization/International League Against Rheumatism Criteria. Arthritis Rheum. 1996;39:34–40.CrossRefPubMed