Blood cell type-specific genome-wide DNA methylation analysis of Chinese patients with early-onset systemic lupus erythematosus identifies loss of DNA methylation in genes related to the Type I Interferon pathway

Abstract

Background: About 20% of Systemic Lupus Erythematosus (SLE) is diagnosed in children under 18. These children often present with more active and severe disease than adult-onset patients. Since whole blood is comprised of different immune cells, we aimed to identify the cell type-specific DNA methylation signatures of CD4+ T cells, CD8+ T cells, B cells, neutrophils and whole blood in individuals with SLE patients who presented before 18-years of age. Method: Specific immune cells were isolated by positive selection using MACS MicroBeads (Miltenyi Biotec). We compared the DNA methylation profiles of different blood cells for 16 Chinese SLE patients to that of 13 healthy controls using the Illumina HumanMethylationEPIC BeadChip. Data pre-processing was performed to remove cross-reactive probes, probes with SNPs at the target site, and probes from sex chromosomes. For each specific region, Wilcoxon rank-sum test was used for group comparisons, and false discovery rate was used for multiple testing corrections. CpG sites with an adjusted p-value < 0.05 and a mean methylation change > 0.1 were considered to be differentially methylated. Results: After data pre-processing, 775280 probes remained and principal component analysis showed that samples clustered according to specific cell types rather than disease manifestation. Global changes of DNA methylation were not observed among different cell types. The number of differentially methylated CpG sites ranged from 46 to 160 in comparisons of different cell types, with more CpG sites showing hypomethylation than hypermethylation. Principal component analysis showed that samples could be separated according to disease manifestation. Gene ontology analysis was performed for each cell type and revealed that in all the cell types examined, hypomethylated genes identified were overrepresented in the type I interferon pathway. This suggests that the DNA methylation changes in different immune cells of SLE patients target the same biological pathway. As type I interferon has long been believed to be involved in the pathogenesis of SLE, our findings support the importance of an epigenetic mechanism in the dysregulation of type I interferon in SLE pathogenesis. Acknowledge: This work was supported by the General Research Fund (Ref: HKU 765513).