Genome-wide DNA methylation analysis of Chinese patients with paediatric-onset systemic lupus erythematosus

Abstract

About 10% of Systemic Lupus Erythematosus (SLE) is diagnosed in patients less than 18 years of age, representing a rare group of patients in SLE. Patients with paediatric-onset SLE often present with more severe clinical courses than the adult-onset patients. Whole blood is comprised of different immune cell populations, and different cell types have different roles in the pathogenesis of SLE. In this study, the cell type-specific DNA methylation changes of CD4+ T cells, CD8+ T cells, B cells, neutrophils and whole blood were characterized in SLE patients whose disease onset before 18 years of age. The DNAm profiles of four purified immune cell lineages were compared in 16 Chinese SLE patients and 13 healthy controls using the Illumina HumanMethylationEPIC BeadChip. The DNA methylation dataset consisted of 145 samples, including data from CD4+ T cells, CD8+ T cells, B cells, neutrophils and whole blood. For each specific region in each immune cell populations, Wilcoxon rank-sum test was used for group comparisons, and false discovery rate control 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. There were four important findings in this study. First, principal component analysis of the DNA methylation data set after quality controls showed that the 145 samples clustered according to cell types rather than disease manifestation, suggesting DNA methylation is confounded by cell composition. Second, a SLE-specific DNA methylation signature can be identified in all cell lineages, which constituted of 21 hypomethylated CpG sites representing 15 genes. Gene ontology analysis showed that these genes were enriched in type I interferon signaling pathway. Third, the SLE-specific DNA methylation signature identified in paediatric-onset SLE had significant overlap with that of the adult-onset patients, suggesting that hypomethylation of genes in the type I interferon signaling pathway is a common phenomenon in SLE regardless of the age of disease onset. Finally, there were some differentially methylated genes which can only be identified in specific immune cell population. These cell lineage-specific differentially methylated genes indicated specific epigenetic dysregulation in each cell type. Remarkably, hypermethylated genes in CD4+ T cells were enriched in T cell receptor signaling pathway, suggesting dysregulations of T cell signaling pathway in helper T cells. In conclusion, the SLE-specific DNA methylation signature had a great potential to be used as a biomarker for diagnosis of SLE, which is important for paediatric-onset patients because the diagnosis of SLE in children can be challenging. This study also highlighted the importance of studying DNA methylation changes in different immune cell lineages, instead of using whole blood only. The cell type-specific DNA methylation changes facilitated the elucidation of cell-type specific molecular pathophysiology of SLE.