DNA methylation identified as potential anti-TNF response biomarker for RA

DNA methylation the next step forward in RA treatment stratification

DNA methylation has been identified as a potential biomarker of response to etanercept and adalimumab in patients with rheumatoid arthritis (RA) according to preliminary results from one of the largest methylome-wide investigations of treatment response to anti-TNF therapies. These data, presented today at the European League Against Rheumatism Annual Congress (EULAR 2014), bring clinicians a step closer to being able to personalise a patient's treatment pathway.

Anti-TNF therapies have proved a huge advance for the treatment of rheumatoid arthritis and have transformed the treatment of inflammatory arthritis for millions of people around the world. However, only 20-40% of patients achieve a good response according to EULAR criteria.

"It can take several years to identify the most effective treatment for an RA patient. This is not only costly in terms of the financial burden, but also in terms of patient outcomes and the irreversible joint damage that is being done," said Amy Webster, University of Manchester, United Kingdom. "Because of this, the identification of biomarkers that can predict a patient's response to a treatment is an important area of research which will allow the most effective treatment for each patient to be identified early in the course of the disease."

She continued, "Based on recent studies showing a role for epigenetics in RA and other autoimmune disorders, we hypothesised that epigenetic changes, such as DNA methylation, may provide potential biomarkers of response to anti-TNFs."

RA is a chronic systemic disease that affects the joints, connective tissues, muscle, tendons, and fibrous tissue. A disabling condition that often causes pain and deformity, symptoms of RA tend to appear between the ages of 20 and 40. The prevalence of RA globally varies between 0.3% and 1% and is more common in women and in developed countries. Within 10 years of onset, at least 50% of patients in developed countries are unable to maintain a full-time job.3 1In this study, patients were selected from the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate (BRAGGSS) longitudinal cohort based on having an extreme response phenotype after three months of treatment with etanercept or adalimumab. Of the patients in the study, 36 patients were good responders to etanercept and 45 to adalimumab as defined by having an endpoint of DAS28<2.6. Poor responders to etanercept (35) and adalimumab (27) were defined by having an improvement of <0.6 or between 0.6-1.2 with an endpoint DAS28 of >5.1.

DNA from each patient was sampled before therapy was initiated. Following bisulfite conversion of the DNA, an epigenome-wide association study was conducted using the HumanMethylation450 BeadChip (Illumina) to determine unmethylated versus methylated cytosines within the DNA. The results from each drug were analysed separately and together using the minfi package in R and probes with a detection-p value > 0.01 were removed. Differentially methylated positions between responders and non-responders were identified using the F-test following quantile normalisation.

In the etanercept study, four CpG sites showed differential DNA methylation that passed a false discovery rate of 0.05, while in the adalimumab study less significant results were observed. The most differentially methylated position in etanercept patients mapped to the LRPAP1 gene (p=1.46x10-8). This gene encodes a chaperone of low density lipoprotein receptor-related protein 1 (LRP1) which is known to influence TGF-β activity. Technical validation of methylation at this site by pyrosequencing showed very good correlation (Spearmans r=0.8). In the adalimumab patients, the most differentially methylated position maps to the PDZD8 gene. Joint analysis of the two drugs together identified a differentially methylated region overlapping the CRYZ and TYW3 genes, which have previously been associated with inflammation and Type 2 diabetes.