Identification of cell‐specific differential DNA methylation associated with methotrexate treatment response in rheumatoid arthritis

OBJECTIVE To estimate changes in cell-specific DNA methylation (DNAm) associated with methotrexate (MTX) response from whole-blood samples collected from rheumatoid arthritis (RA) patients before and after initiation of MTX treatment. METHODS Patients in this study were from the Rheumatoid Arthritis Medication Study (RAMS, n=66) and the University of California San Francisco Rheumatoid Arthritis study (UCSF-RA, n=11). All patients met the American College of Rheumatology RA classification criteria. Blood samples were collected at baseline and following treatment. DAS28-CRP was collected at baseline and after 3-6 months of treatment. Methylation profiles were generated with Illumina 450K and EPIC arrays using DNA from whole blood. MTX response was defined using the EULAR criteria (Responder: good/moderate response, Non-responder: no response). Differentially methylated positions (DMPs) were identified using limma and tensor composition analysis (TCA). TCA is a method for identifying cell-specific differential DNAm at the CpG level from bulk tissue. Differentially Methylated Regions (DMRs) were identified using Comb-p. RESULTS We found evidence for differential global methylation between treatment response groups. Further, we found patterns of cell-specific differential global methylation associated with MTX response. One DMP was associated at after correction for multiple tests with differential DNAm between responders and non-responders at baseline in CD4T, CD8T, and NK cells. Thirty-nine cell-specific DMRs associated with MTX response were identified. There were no significant findings in whole blood analyses. CONCLUSION We identified cell-specific changes in DNAm associated with MTX response in RA patients. Future studies of DNAm and MTX response should include measurements of DNAm from sorted cells.