Twin DNA Methylation Profiling Reveals Flare‐Dependent Interferon Signature and B Cell Promoter Hypermethylation in Systemic Lupus Erythematosus

Objective Systemic lupus erythematosus ( SLE ) has limited monozygotic twin concordance, implying a role for pathogenic factors other than genetic variation, such as epigenetic changes. Using the disease‐discordant twin model, we investigated genome‐wide DNA methylation changes in sorted CD 4+ T cells, monocytes, granulocytes, and B cells in twin pairs with at least 1 SLE ‐affected twin. Methods Peripheral blood obtained from 15 SLE ‐affected twin pairs (6 monozygotic and 9 dizygotic) was processed using density‐gradient centrifugation for the granulocyte fraction. CD 4+ T cells, monocytes, and B cells were further isolated using magnetic beads. Genome‐wide DNA methylation was analyzed using Infinium HumanMethylation450K BeadChips. When comparing probes from SLE‐affected twins and co‐twins, differential DNA methylation was considered statistically significant when the P value was less than 0.01 and biologically relevant when the median DNA methylation difference was >7%. Findings were validated by pyrosequencing and replicated in an independent case–control sample. Results In paired analyses of twins discordant for SLE restricted to the gene promoter and start region, we identified 55, 327, 247, and 1,628 genes with differentially methylated CpGs in CD 4+ T cells, monocytes, granulocytes, and B cells, respectively. All cell types displayed marked hypomethylation in interferon‐regulated genes, such as IFI 44L, PARP 9 , and IFITM 1 , which was more pronounced in twins who experienced a disease flare within the past 2 years. In contrast to what was observed in the other cell types, differentially methylated CpGs in B cells were predominantly hypermethylated, and the most important upstream regulators included TNF and EP 300 . Conclusion Hypomethylation of interferon‐regulated genes occurs in all major cellular compartments in SLE ‐affected twins. The observed B cell promoter hypermethylation is a novel finding with potential significance in SLE pathogenesis.