Identification of distinctive interferon gene signatures in different types of myositis

Abstract

Objective: Activation of the type 1 interferon (IFN1) pathway is a prominent feature of dermatomyositis (DM) muscle and may play a role in the pathogenesis of this disease. However, the relevance of the IFN1 pathway in patients with other types of myositis such as the antisynthetase syndrome (AS), immune-mediated necrotizing myopathy (IMNM), and inclusion body myositis (IBM) is largely unknown. Moreover, the activation of the type 2 interferon (IFN2) pathway has not been comprehensively explored in myositis. In this cross-sectional study, our objective was to determine whether IFN1 and IFN2 pathways are differentially activated in different types of myositis by performing RNA sequencing on muscle biopsy samples from 119 patients with DM, IMNM, AS, or IBM and on 20 normal muscle biopsies.

Methods: The expression of IFN1- and IFN2-inducible genes was compared between the different groups.

Results: The expression of IFN1-inducible genes was high in DM, moderate in AS, and low in IMNM and IBM. In contrast, the expression of IFN2-inducible genes was high in DM, IBM, and AS but low in IMNM. The expression of IFN-inducible genes correlated with the expression of genes associated with inflammation and muscle regeneration. Of note, ISG15 expression levels alone performed as well as composite scores relying on multiple genes to monitor activation of the IFN1 pathway in myositis muscle biopsies.

Conclusions: IFN1 and IFN2 pathways are differentially activated in different forms of myositis. This observation may have therapeutic implications because immunosuppressive medications may preferentially target each of these pathways.

Figure 1. Expression of IFN1-inducible genes in myositis muscle biopsies

(A) Relative and (B) raw (95% confidence interval) expression levels of the type 1 interferon (IFN1)–inducible genes among the different clinical and serologic groups. AS = antisynthetase syndrome; DM = dermatomyositis; FPKM = fragments per kilobase of transcript per million mapped reads; IBM = inclusion body myositis; IMNM = immune-mediated necrotizing myositis; [Jo1] = AS autoantibody group; [Mi2, NXP2, TIF1, MDA5] = DM autoantibody groups; NT = normal biopsies; [SRP, HMGCR] = IMNM autoantibody groups.

Figure 2. Expression of IFN2-inducible genes in myositis muscle biopsies

(A) Relative and (B) raw (95% confidence interval) expression levels of type 2 interferon (IFN2)–inducible genes among the different clinical and serologic groups. AS = antisynthetase syndrome; DM = dermatomyositis; FPKM = fragments per kilobase of transcript per million mapped reads; IBM = inclusion body myositis; IMNM = immune-mediated necrotizing myositis; [Jo1] = AS autoantibody group; [Mi2, NXP2, TIF1, MDA5] = DM autoantibody groups; NT = normal biopsies; [SRP, HMGCR] = IMNM autoantibody groups.

Figure 3. Correlation of IFN-inducible gene expression with expression of inflammatory cell and muscle regeneration genes

Correlation of type 1 and type 2 interferon (IFN)–inducible genes with the expression of genes related to T cells (CD3E, CD4, and CD8A), macrophages (CD14 and CD68), muscle regeneration (NCAM1, MYOG, MYOD1, PAX7), and adult muscle structural proteins (ACTA1, MYH1, MYH2).

Figure 4. Correlation of type 1 and type 2 interferon-inducible genes with the CK and strength in different types of myositis

AS = antisynthetase syndrome; CK = creatine kinase; DM = dermatomyositis; IBM = inclusion body myositis; IMNM = immune-mediated necrotizing myositis.

Figure 5. Spearman correlation of the different type 1 and type 2 interferon-inducible genes in all the biopsies included in the study

Figure 6. ISG15 or PSMB8 expression vs composite IFN1-inducible gene scores

Correlation of the expression level (log₂[FKPM+1]) of (A) ISG15 and (B) PSMB8 with the previously proposed 13-gene type 1 interferon (IFN1) score. AS = antisynthetase syndrome; DM = dermatomyositis; FPKM = fragments per kilobase of transcript per million mapped reads; IBM = inclusion body myositis; IMNM = immune-mediated necrotizing myositis; NT = normal biopsies.