DNA Methylation Profiling in Childhood-Onset Lupus Reveals Distinct Epigenetic Clusters and Suggests Epigenetic Drivers of Disease Activity

ObjectivesSystemic lupus erythematosus (SLE) is a chronic autoimmune disease affecting multiple organs, with childhood-onset SLE (cSLE) typically presenting a more severe course and greater genetic risk than adult-onset SLE. While DNA methylation plays a key role in lupus pathogenesis, the epigenetic landscape of cSLE remains understudied. This study aimed to investigate DNA methylation changes in cSLE. MethodsA total of 64 cSLE patients and 47 healthy control DNA samples isolated from peripheral blood mononuclear cells (PBMCs), along with an independent validation cohort of 38 patient DNA samples from whole blood, were analyzed. DNA methylation was assessed using the Infinium MethylationEPIC v2.0 array (Illumina), with quality control and statistical analyses performed using the minfi and limma R packages. Methylation differences were tested via linear regression adjusting for age, sex, medication use, and cell composition. Clinical features were compared using chi-square test or Fishers exact test, and gene ontology enrichment was conducted using Metascape and GREAT. ResultsDifferential methylation analysis revealed significant hypomethylation in interferon-regulated genes (e.g., DTX3L, PARP9, IFI44L, MX1), enriched in type I interferon-related processes. Hypomethylation in genes linked to B cell activation and senescence correlated with higher SLEDAI scores. K-means clustering identified three distinct methylation-based cSLE subgroups, each enriched for different biological processes: cell adhesion/growth factor response (Cluster One), cell differentiation/fate (Cluster Two), and oxidative stress/Rap1 signaling (Cluster Three). Sex-based analysis showed immune-related hypomethylation in male patients, with over 80% of these sites validated in the replication cohort. ConclusioncSLE displays distinct DNA methylation patterns associated with disease activity, molecular subgroups, and sex, underscoring the potential for epigenetically informed diagnostics and therapies.