Rheumatoid arthritis: alterations in DNA methylation patterns in CD4+T-cells: Understanding pathogenesis and developing a qMSP biomarker for classification

Alterations in DNA methylation patterns have been related to several diseases, including Rheumatoid Arthritis (RA). CD4+T-cells are critical players for the early pathogenesis of RA. I hypothesise that modification of DNA methylation in CD4+T-cells happen early in RA and contribute to the disease progression by altering important physiological pathways. The aims of my thesis are
1) to gain more understanding of early events/pathways in RA pathology by studying genome-wide DNA methylation
2) to select potential CpG candidates for the development of a biomarker for the prediction of clinical outcomes.
For the first aim, Illumina methylation genome-wide array data were analysed in naïve and memory CD4+T-cell and monocytes from 6 healthy control (HC) and 10 early, drug naïve RA patients. DNA methylation pattern in naïve CD4+T-cell confirmed the involvement of several pathways (mainly IL6/STAT3 linked to TNF-α, and IFN signalling genes) in the early disease pathogenesis and importantly discovered novel pathways such as dysregulation of the commitment of Th17 polarisation in naïve cells. My findings suggested a novel disease mechanism model in which IL6 induces atypical differentiation in a small subset of naïve CD4+T-cells, potentially associated with a subset of cells previously observed in vivo in RA patients by my supervisor.
For the second aim, I used several publicly available methylation datasets to develop selection strategies to identify CpGs candidate to develop as a biomarker assay for RA classification using a quantitative Methylation-Specific PCR (qMSP) technique. A TNF qMSP assay was successfully developed. It detected difference in methylation levels between RA and other arthritis with a good classification performance (n= 284, AUROC = 0.171 (95%CI: 0.115 - 0.227). This assay also showed potential to predict response to Methotrexate (pilot study). Further validation with a larger cohort will be necessary to included such assay in the management of early RA.