Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren’s syndrome

Abstract

ObjectiveStandard assessment of interferon (IFN) system activity in systemic rheumatic diseases depends on the availability of RNA samples. In this study, we describe and evaluate alternative methods using plasma, serum and DNA samples, exemplified in the IFN-driven disease primary Sjögren’s syndrome (pSS).MethodsPatients with pSS seropositive or negative for anti-SSA/SSB and controls were included. Protein-based IFN (pIFN) scores were calculated from levels of PD-1, CXCL9 and CXCL10. DNA methylation-based (DNAm) IFN scores were calculated from DNAm levels at RSAD2, IFIT1 and IFI44L. Scores were compared with mRNA-based IFN scores measured by quantitative PCR (qPCR), Nanostring or RNA sequencing (RNAseq).ResultsmRNA-based IFN scores displayed strong correlations between B cells and monocytes (r=0.93 and 0.95, p<0.0001) and between qPCR and Nanostring measurements (r=0.92 and 0.92, p<0.0001). The pIFN score in plasma and serum was higher in patients compared with controls (p<0.0001) and correlated well with mRNA-based IFN scores (r=0.62–0.79, p<0.0001), as well as with each other (r=0.94, p<0.0001). Concordance of classification as ‘high’ or ‘low’ IFN signature between the pIFN score and mRNA-based IFN scores ranged from 79.5% to 88.6%, and the pIFN score was effective at classifying patients and controls (area under the curve, AUC=0.89–0.93, p<0.0001). The DNAm IFN score showed strong correlation to the RNAseq IFN score (r=0.84, p<0.0001) and performed well in classifying patients and controls (AUC=0.96, p<0.0001).ConclusionsWe describe novel methods of assessing IFN system activity in plasma, serum or DNA samples, which may prove particularly valuable in studies where RNA samples are not available.

Lysosome-associated membrane protein 3 misexpression in salivary glands induces a Sjögren’s syndrome-like phenotype in mice

“…[2][3][4][5] Transcriptome studies of minor salivary gland biopsies and peripheral blood mononuclear cells identified additional IFN signature genes that were increased in patients with SS. [6][7][8][9] Many cellular proteins are reported to be regulated by IFN expression include those associated with lysosomal function. Lysosome-associated membrane protein 3 (LAMP3) is a membrane glycoprotein predominantly localised in lysosomes that is reported to be induced by IFN.…”

DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren’s Syndrome

“…Therefore, IFN scores based on mRNA expression of ISGs are commonly used as a proxy. Recently, we have developed alternative tools using DNAm or protein expression that allow the assessment of IFN activation under circumstances where RNA material is missing (13). We found in general a high correlation with the IFN score derived from mRNA expression in monocytes and B cells.…”

“…DNA is more commonly collected and is more stable over time under most conditions. Recently, we have developed a method for assessing type I IFN system activation using DNA methylation (DNAm) data, which strongly correlates with mRNA-based IFN scores in multiple blood cell types (13). The aim of the current study was to determine potential associations between a DNAm-based IFN score and clinical and serological manifestations in patients with pSS.…”

Epigenetic alterations in Sjögren's syndrome patient saliva

“…Hypomethylation of IFN-regulated genes in SS patients was associated with their increased mRNA expression in B cells [12]. The same group investigated the DNA methylation levels in certain genes associated with the IFN signature (RSAD2, IFIT1 and IFI44L) and found that they possessed a strong correlation to the RNAseq IFN score (r = 0•84, P < 0•0001), also correctly classifying patients and controls [area under the curve (AUC) = 0•96, P < 0•0001] [13]. Besides the involvement of epigenetic alterations in the effector mechanisms of the immune response, there is also strong evidence that epigenetic changes may affect the autoantigen expression.…”