Type I interferon pathway assays in studies of rheumatic and musculoskeletal diseases: a systematic literature review informing EULAR points to consider

Abstract

Objectives: To systematically review the literature for assay methods that aim to evaluate type I interferon (IFN-I) pathway activation and to harmonise-related terminology.

Methods: Three databases were searched for reports of IFN-I and rheumatic musculoskeletal diseases. Information about the performance metrics of assays measuring IFN-I and measures of truth were extracted and summarised. A EULAR task force panel assessed feasibility and developed consensus terminology.

Results: Of 10 037 abstracts, 276 fulfilled eligibility criteria for data extraction. Some reported more than one technique to measure IFN-I pathway activation. Hence, 276 papers generated data on 412 methods. IFN-I pathway activation was measured using: qPCR (n=121), immunoassays (n=101), microarray (n=69), reporter cell assay (n=38), DNA methylation (n=14), flow cytometry (n=14), cytopathic effect assay (n=11), RNA sequencing (n=9), plaque reduction assay (n=8), Nanostring (n=5), bisulphite sequencing (n=3). Principles of each assay are summarised for content validity. Concurrent validity (correlation with other IFN assays) was presented for n=150/412 assays. Reliability data were variable and provided for 13 assays. Gene expression and immunoassays were considered most feasible. Consensus terminology to define different aspects of IFN-I research and practice was produced.

Conclusions: Diverse methods have been reported as IFN-I assays and these differ in what elements or aspects of IFN-I pathway activation they measure and how. No 'gold standard' represents the entirety of the IFN pathway, some may not be specific for IFN-I. Data on reliability or comparing assays were limited, and feasibility is a challenge for many assays. Consensus terminology should improve consistency of reporting.

Keywords: Arthritis, Rheumatoid; Cytokines; Inflammation; Lupus Erythematosus, Systemic.

Figure 1

PRISMA chart. Search and selection strategy of publications. PRISMA, Preferred Reporting Items for Systematic Reviews and Meta-Analyses.

Figure 2

Aspects of the IFN-I pathway evaluated by each assay. The IFN pathway is a complex system with multiple subtypes of IFNs and diverse downstream effects on gene and protein expression. Existing assays measure different aspects of the IFN pathway; they do not reflect the entirety of the pathway and some are not specific for IFN-I. See text for full description of these assays.

Figure 3

Summary of RMDs evaluated using each type of IFN-I assay. Pie charts indicate the number of reports of assays for each methodology and each rheumatic musculoskeletal disease. Some publications include more than one assay, so number of papers may differ from the numbers on this figure. RMDs, rheumatic musculoskeletal diseases.

Figure 4

UpSet plot for constituents of immunoassays. Dots and bars indicate what combinations of proteins were measured in reports of IFN immunoassays. The left-hand chart shows the number of reports for each protein. The upper chart shows the number of reports for each combination.

Figure 5

UpSet plot for constituents of gene expression assays. Dots and bars indicate what combinations of genes were measured in reports of IFN gene expression assays. The left-hand chart shows the number of reports for each gene. The upper chart shows the number of reports for each combination.

Figure 6

Overlap between types of IFNs. Although there are distinct receptors for type 1, 2 and 3 IFNs, there is substantial overlap in signalling and response elements. Assays measuring segments of the pathway downstream from the IFN receptor may not be specific for one subtype of IFN and some may preferentially reflect type II or III IFNs.