PT - JOURNAL ARTICLE AU - Vidyanand Anaparti AU - Prasoon Agarwal AU - Irene Smolik AU - Neeloffer Mookherjee AU - Hani Elgabalawy TI - Whole Blood Targeted Bisulfite Sequencing Validates Differential Methylation in <em>C6ORF10</em> gene of Patients with Rheumatoid Arthritis AID - 10.3899/jrheum.190376 DP - 2019 Nov 01 TA - The Journal of Rheumatology PG - jrheum.190376 4099 - http://www.jrheum.org/content/early/2019/10/28/jrheum.190376.short 4100 - http://www.jrheum.org/content/early/2019/10/28/jrheum.190376.full AB - Objective Polymorphisms in human major histocompatibility complex (MHC) are the strongest genetic associations with rheumatoid arthritis (RA). Epigenome-wide methylation studies suggest DNA methylation changes within MHC may contribute to disease susceptibility. In this study, we profiled MHC-specific methylated CpGs in autoantibody-positive RA patients and matched unaffected autoantibody-negative first-degree relatives (ACPA-/FDR) from an Indigenous North American (INA) population that is known to have prevalent RA. Methods DNA was isolated from whole blood and targeted bisulfite sequencing (TBSeq) was used to profile methylated CpGs in RA patients and ACPA-/FDR. Differentially methylated CpG loci (DMLs) were mapped and gene annotated. Ingenuity pathway analysis was used for curating biomolecular networks of mapped genes. Transcript abundance was determined by qPCR. Results We identified 74 uniquely methylated CpG sites within the MHC region that were differentially methylated in RA patients (q &lt; 0.05), compared to ACPA-/FDR. Of these, 36 DMLs were located on 19 genes. IPA network analyses showed these genes are involved in regulating the NF-kB complex and processes involved in antigen presentation, and immune cell crosstalk in autoimmunity. Pearson correlation analysis demonstrated a negative association between differentially methylated CpGs in C6ORF10 gene and risk factors associated with RA. qPCR analysis confirmed differential abundance of C6ORF10, TNXB and HCG18 mRNAs in RA patients compared to ACPA-/FDRs. Conclusion Our results confirm the presence of differential methylation at specific gene loci within the MHC region of INA RA patients. These epigenetic signatures may precede disease onset, or alternatively, may be a result of developing RA.