Treatment with tumor necrosis factor inhibitor (TNFi) therapy restores homeostatic blood methylation in patients with rheumatoid arthritis (RA), according to study results published in eBio Medicine.
The study analyzed the peripheral blood methylome of patients with RA across time in a longitudinal discovery cohort and a longitudinal validation cohort. Because the efficacy of TNFis in patients with RA is heterogeneous, the researchers sought to identify epigenetic variation that is associated with response to TNFi therapy. With use of a novel cell deconvolution approach, altered DNA methylation associated with response to TNFi treatment was also tested in the 6 main immune cell types in blood.
Patients from the discovery cohort and the validation cohort were recruited by the Immune-Mediated Inflammatory Diseases Consortium. The 2 longitudinal cohorts were obtained from the rheumatology departments of 12 different university hospitals in Spain.
In the discovery cohort, peripheral blood samples were obtained from 62 adult patients with RA who were initiating TNFi therapy. These patients had a disease activity score for 28 joints (DAS28) of greater than 3.2 at the start of treatment. A second blood sample was obtained for methylation analysis at 12 weeks. The validation cohort was comprised of 60 patients with RA who were chosen using the same criteria as those in the discovery cohort.
At week 12, the efficacy of TNFi therapy was assessed with use of the European Alliance of Associations for Rheumatology (EULAR) response criteria. The EULAR criteria are based on the temporal change in DAS28, categorizing patients as good, moderate, or nonresponders. Good and moderate patients were grouped into a single responder class.
Treatment with TNFi therapy was associated with significant longitudinal peripheral blood methylation changes in biologic pathways related to RA, with 144 of the 246 pathways (58.5%) shown to be differentially methylated in the discovery cohort (false-discovery rate [FDR], <0.05). When the 144 pathways were analyzed in the validation cohort, a total of 139 biological functions (96.5%) were modified with TNFi therapy. Resampling testing of the methylation direction analysis supported the same methylation changes in 84.2% (117 of 139) of these pathways.
When the researchers tested whether RA pathways were also linked to clinical response to TNFi therapy, a total of 6 RA pathways differed significantly at week 0 between responders and nonresponders (2.4%; FDR, <0.05) in the discovery cohort. The association of 4 of them with response was replicated in the validation cohort when tested in the validation cohort (FDR, <0.05).
Differences in the methylation profile of T-cell activation and differentiation, GTPase-mediated signaling, and actin filament organization pathways were all linked to clinical response to treatment.
A major limitation of the study was the fact that lack of statistical power of small cohorts may have hampered the discovery of other biologically relevant pathways that contribute to response to TNFi therapy or the investigation of clinical subgroups of patients.
The researchers concluded that additional studies are warranted to fully understand the mechanisms behind the methylation variation that was identified at baseline in order to predict patient response to TNFi therapy. This study will hopefully establish the basis for the development of epigenetic-based biomarkers for patient stratification and provide support for alternative, more efficacious therapies for TNFi nonresponders.
Disclosure: Some of the study authors have declared affiliations with biotech, pharmaceutical, and/or device companies. Please see the original reference for a full list of authors’ disclosures.
Julià A, Gómez A, López-Lasanta M, et al. Longitudinal analysis of blood DNA methylation identifies mechanisms of response to tumor necrosis factor inhibitor therapy in rheumatoid arthritis. EBioMedicine. Published online May 13, 2022. doi:10.1016/j.ebiom.2022.104053