Population‐Specific Patterns of Epigenetic Defects in the B Cell Lineage in Patients With Systemic Lupus Erythematosus

Abstract

Objective. To determine the stage of B cell development at which a systemic lupus erythematosus (SLE)associated DNA methylation signature originates in African American (AA) and European American (EA) subjects, and to assess whether epigenetic defects in B cell development patterns could be predictive of SLE status in individual and mixed immune cell populations.Methods. B cells from AA patients (n = 31) and EA patients (n = 49) with or without SLE were sorted using fluorescence-activated cell sorting into 5 B cell subsets. DNA methylation, measured at ~460,000 CpG sites, was interrogated in each subset. Enrichment analysis of transcription factor interaction at SLE-associated methylation sites was performed. A random forests algorithm was used to identify an epigenetic signature of SLE in the B cell subsets, which was then validated in an independent cohort of AA and EA patients and healthy controls.Results. Regression analysis across all B cell stages resulted in identification of 60 CpGs that reached genomewide significance for SLE-associated methylation differences (P ≤ 1.07 × 10 −7 ). Interrogation of ethnicity-specific CpGs associated with SLE revealed a hypomethylated pattern that was enriched for interferon (IFN)-regulated genes and binding of EBF1 in AA patients (each P < 0.001). AA patients with SLE could be distinguished from healthy controls when the predictive model developed with the transitional B cell subset was applied to other B cell subsets (mean receiver operating characteristic [ROC] area under the curve [AUC] 0.98), and when applied to CD19+ pan-B cells (mean ROC AUC 0.95) and CD4+ pan-T cells (mean ROC AUC 0.97) from the independent validation cohort.Conclusion. These results indicate that SLE-specific methylation patterns are ethnicity dependent. A pattern of epigenetic changes near IFN-regulated genes early in B cell development is a hallmark of SLE in AA female subjects. EBF1 binding sites are highly enriched for significant methylation changes, implying that this may be a potential regulator of SLE-associated epigenetic changes.

Cluster of highly expressed interferon-stimulated genes associate more with African ancestry than disease activity in patients with systemic lupus erythematosus. A systematic review of cross-sectional studies

“…18 Interestingly, 1 study has shown that the pattern of hypomethylation in IFN-regulated genes occurs early in B-cell development in African Americans, and could distinguish African American SLE patients from healthy controls in several B-cell subsets, whereas DNA methylation changes in European American SLE patients occurred in mature Bcell stages. 59 Altogether, evidence from epigenetic studies suggests the existence of DNA methylation differences between populations that might point to etiological differences between African American SLE patients compared to those from other populations.…”

Nucleic Acid-Sensing and Interferon-Inducible Pathways Show Differential Methylation in MZ Twins Discordant for Lupus and Overexpression in Independent Lupus Samples: Implications for Pathogenic Mechanism and Drug Targeting

“…The earliest of these genome-wide studies interrogated 27,578 CpG sites in 12 SLE patients and 12 healthy controls using the Illumina Infinium HumanMethylation27 Beadchip, and identified 336 differentially methylated genes, the majority of which were hypomethylated in the cases relative to the controls [ 11 ]. Subsequent studies have examined genome-wide methylation in larger samples of SLE patients using the HumanMethylation450 Beadchip (>485,000 CpG sites) in a number of cell types, including naïve CD4+ T cells [ 12 , 13 , 14 , 15 , 16 ], memory and regulatory T cells [ 17 ], CD19+ B cells [ 17 ], CD14+ monocytes [ 14 , 17 ], granulocytes [ 14 ], neutrophils [ 18 ], and whole blood or peripheral blood mononuclear cells (PBMC) [ 19 , 20 , 21 , 22 , 23 , 24 , 25 ]. Differential methylation has not only been observed when comparing SLE patients to healthy controls, but similar patterns have been identified in SLE patients with nephritis [ 12 , 19 , 22 ], skin involvement [ 13 ], specific antibodies [ 20 ], and pediatric SLE [ 26 ].…”

Recent Advances in Lupus B Cell Biology: PI3K, IFNγ, and Chromatin

“…Hypomethylation is observed in the vicinity of type 1 IFN-regulated genes in lupus, consistent with the characteristic IFN signature ( 96 – 99 ). A recent study ( 100 ) found that ethnicity influences these DNA methylation patterns. They were most pronounced in African American SLE patients compared to healthy women and were apparent as early as the transitional B cell stage in African American patients.…”