Background/Purpose:  SLE is a disease where epigenetic mechanisms play a role. Methylation of DNA at CpG loci is known to influence the suppression or activation of genes that may be associated with disease pathogenesis. Methylation associated with SLE may define unique biomarkers that may serve as novel drug targets and diagnostic tools. Studies to date have focused on candidate genes or small subsets of functional genes. We present the first >480,000 CpG differentiatal methylation analysis, covering >20,000 gene promoters, in PBMCs from SLE patients.

Methods: Genome-wide methylation analysis of 6 SLE, 6 Rheumatoid Arthritis (RA), and 4 Osteoarthritis (OA) whole PBMC preparations from females was performed on Illumina HumanMethyl450 BeadChips.  DNA was purified from Ficoll prepared whole PBMCs from clinically diagnosed patients. The Kolmogorov-Smirnov (KS) test determined differentially methylated loci (DML). Only loci with an average methylation difference > 0.10 between phenotypes were tested. KS p-values were converted to multiple hypothesis corrected q-values and loci with q-values < 0.15 were labeled as DM. Differentially methylated genes (DMG) contained at least one SLE/RA or SLE/OA DML in their promoter regions (-2.5 kb to 500 bp from transcription start site [TSS]). Pathway enrichment analysis of DMG was determined using Kyoto Encyclopedia of Genes and Genomes (KEGG) data and empirical p-values, based on 500,000 randomly generated background gene sets, which were converted to q-values.

Results: Genome-wide methylation analysis of >480,000 CpG loci identified 864 and 1,537 DML in SLE/RA and SLE/OA comparisons. Associating CpGs with TSS promoter regions narrowed these loci to 274 and 422 DMG. 71% and 65% of SLE/RA and SLE/OA CpGs were hypermethylated, respectively. Hypermethylation was found in IL-23A, TNFRSF25, and PRIC285 (peroxisomal proliferator-activated receptor A interacting complex 285), genes known to regulate immune responses and inflammation. Hypomethylated CpG loci from SLE patients were identified in promoter regions associated with genes relevant to SLE, such as IFI44L (interferon-induced protein 44-like), IFITM1 (Interferon-induced transmembrane protein 1) and IL-10. Combining SLE/RA and SLE/OA genes into a single group, we found: cytokine-cytokine receptor interaction (q-value = 0.004), rheumatoid arthritis (0.004), hematopoietic cell lineage (0.004), and cell adhesion molecules (0.010) were significantly enriched KEGG pathways where differential methylation was observed. These data suggest that epigenetic mechanisms may play an important role in SLE where aberrant regulation of key immune and inflammatory genes or pathways may contribute to SLE pathogenesis and progression.

Conclusion: This study demonstrates that the first genome-wide DNA methylation analysis of whole PBMC samples is informative. The differential methylation pattern for SLE has the potential for identification of novel biomarkers for diagnostic applications. Associated genes and pathways provide a greater understanding of the pathogenic mechanisms of SLE and potential novel therapeutic targets. These findings justify further exploration, including subsets of immune cells and healthy controls.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/the-dna-methylome-of-systemic-lupus-erythematosus-sle-from-whole-peripheral-blood-mononuclear-cells-pbmcs/