A definitive diagnosis of systemic lupus erythematosus (SLE) differentiating it from other rheumatic and autoimmune diseases can be challenging, because of a lack of definitive tests with sufficient sensitivity and specificity, as well as the absence of reliable biomarkers. To address this need, Shoemaker and colleagues (ACR 2013; Abstract 2519) conducted a genome-wide DNA methylation analysis of peripheral blood mononuclear cells (PBMCs) from patients with SLE to assess whether SLE has a unique DNA methylation signature that could be used as a reliable diagnostic test. The underlying rationale for this concept is that epigenetic mechanisms, such as DNA methylation, have been shown to significantly impact autoimmune diseases, including SLE.
PBMC genomic DNA was isolated from 252 patients and was evaluated with Illumina HumanMethyl450 BeadChips. The 49-patient sample training set—which included PBMCs from15 patients with SLE, 15 patients with rheumatoid arthritis (RA), 13 patients with osteoarthritis, as well as 7 healthy controls—was analyzed first. Then, an independent, blinded PBMC sample test set was assessed from 17 patients with SLE, 9 patients with RA, 14 healthy controls, and 4 patients with non-RA/SLE rheumatologic conditions (including ankylosing spondylitis, psoriatic arthritis, reactive arthritis, and spondyloarthropathy).
The goal of this study was to find specific cytosine-phosphate-guanine (CpG) base pairs that could be used in the annotation and prediction of gene function that were preferentially methylated in SLE samples compared with non-SLE samples, and that could be used as a diagnostic assay.
Of more than 456,000 autosomal CpGs whose methylation frequencies were assessed, a 10–gene-based 25–demeter-like (DML) panel was found to be differentially expressed in the SLE training set. In the prospective, blinded PBMC samples, this panel correctly classified 14 of 17 independent SLE samples (82% sensitivity) and 86 of the 88 non-SLE samples (98% sensitivity), achieving an overall accuracy of 95%. The genes associated with the 25-DML panel were enriched for interferon-signaling and activation or interferon regulatory factors.
The data from this study suggest that SLE can be distinguished from other autoimmune diseases using DNA methylation markers from PBMCs. These biomarkers could also be used to identify the underlying molecular pathways associated with SLE that could be used to select therapies for patients with SLE or to identify novel therapeutic targets. However, it will be necessary to make this technology readily and widely available for use before it can be utilized as a routine laboratory procedure in the diagnosis and management of patients with SLE.