Assessment of Type I Interferon Signaling in Pediatric Inflammatory Disease

Abstract

Purpose: Increased type I interferon is considered relevant to the pathology of a number of monogenic and complex disorders spanning pediatric rheumatology, neurology, and dermatology. However, no test exists in routine clinical practice to identify enhanced interferon signaling, thus limiting the ability to diagnose and monitor treatment of these diseases. Here, we set out to investigate the use of an assay measuring the expression of a panel of interferon-stimulated genes (ISGs) in children affected by a range of inflammatory diseases.

Design, setting, and participants: A cohort study was conducted between 2011 and 2016 at the University of Manchester, UK, and the Institut Imagine, Paris, France. RNA PAXgene blood samples and clinical data were collected from controls and symptomatic patients with a genetically confirmed or clinically well-defined inflammatory phenotype. The expression of six ISGs was measured by quantitative polymerase chain reaction, and the median fold change was used to calculate an interferon score (IS) for each subject compared to a previously derived panel of 29 controls (where +2 SD of the control data, an IS of >2.466, is considered as abnormal). Results were correlated with genetic and clinical data.

Results: Nine hundred ninety-two samples were analyzed from 630 individuals comprising symptomatic patients across 24 inflammatory genotypes/phenotypes, unaffected heterozygous carriers, and controls. A consistent upregulation of ISG expression was seen in 13 monogenic conditions (455 samples, 265 patients; median IS 10.73, interquartile range (IQR) 5.90-18.41), juvenile systemic lupus erythematosus (78 samples, 55 patients; median IS 10.60, IQR 3.99-17.27), and juvenile dermatomyositis (101 samples, 59 patients; median IS 9.02, IQR 2.51-21.73) compared to controls (78 samples, 65 subjects; median IS 0.688, IQR 0.427-1.196), heterozygous mutation carriers (89 samples, 76 subjects; median IS 0.862, IQR 0.493-1.942), and individuals with non-molecularly defined autoinflammation (89 samples, 69 patients; median IS 1.07, IQR 0.491-3.74).

Conclusions and relevance: An assessment of six ISGs can be used to define a spectrum of inflammatory diseases related to enhanced type I interferon signaling. If future studies demonstrate that the IS is a reactive biomarker, this measure may prove useful both in the diagnosis and the assessment of treatment efficacy.

Keywords: Interferon; autoinflammation; autoinflammatory disease; interferonopathy.

Fig. 1

Flow chart showing inclusion/exclusion criteria for study participation. The number of measurements (samples) is given, together with the number of individuals/number of families below/in brackets. Treatment* refers to samples excluded (n = 93) because patients were on reverse transcriptase or JAK inhibitors

Fig. 2

Interferon score plotted for each sample according to genotype/phenotype. a 455 group 1 patient samples. b 30 group 2 patient samples. c 340 group 3 patient samples. Black horizontal lines represent the median for each patient group. Interferon scores calculated from the median fold change in RQ (relative quantification) values of a panel of six interferon-stimulated genes (ISGs). Blue dots represent an interferon score of less than 2.466. Red dots represent an interferon score of greater than 2.466. Magenta dots represent patients treated with IL1 blockade. Analyzed by one-way ANOVA with Dunnett’s multiple comparison test

Fig. 3

Median fold expression of six interferon-stimulated genes according to genotype. Median relative quantification (RQ) value for each of six interferon-stimulated genes (ISGs) measured in a 74 TREX1, 11 RNASEH2A, 115 RNASEH2B, 16 RNASEH2C, 45 SAMHD1, 52 ADAR1, and 59 IFIH1 samples with a positive (>2.466) interferon score; b 14 ACP5, 14 TMEM173, four C1QA, and five ISG15 samples with a positive (>2.466) interferon score; c 101 JDM, 21 sJIA, 58 autoinflammatory, 72 molecularly undefined interferonopathy, 78 JSLE, and ten pJIA. RQ is equal to 2^−∆∆Ct, i.e., the normalized fold change relative to a control

Fig. 4

Interferon scores in patients where four or more serial samples were recorded. Data shown are interferon scores plotted against time (years) since first sampling. Interferon scores are calculated from the median fold change in relative quantification (RQ) values for a panel of six interferon-stimulated genes (ISGs). The blue dashed line represents the boundary of a positive/negative score (2.466). The number of serial samples for each patient is shown in brackets in the legend