Type I interferon-inducible gene expression in blood is present and reflects disease activity in dermatomyositis and polymyositis

Abstract

Objective: To apply gene expression profiling to the study of peripheral blood mononuclear cells from patients with inflammatory myopathies, in order to provide insight into disease pathogenesis and identify potential biomarkers associated with disease activity.

Methods: We used Affymetrix whole-genome microarrays to measure the expression of approximately 38,500 genes in 65 blood and 15 muscle samples from 44 patients with dermatomyositis (DM), polymyositis (PM), inclusion body myositis (IBM), myasthenia gravis, or genetically determined myopathies and from 12 healthy volunteers. In 9 patients, 2 samples were obtained at different time points, when disease was either active or improving, and these paired blood samples were also compared. Bioinformatics techniques were used to identify genes with significant differential expression among diagnostic categories and in relation to disease activity. We corroborated the microarray data with quantitative real-time reverse transcriptase-polymerase chain reaction.

Results: Most patients with active DM or PM, but not patients with IBM, had significant and high up-regulation of the type I interferon-alpha/beta (IFNalpha/beta)-inducible genes in blood. Furthermore, the up-regulation of these genes correlated with disease activity in DM and PM, with down-regulation occurring when disease was controlled with treatment.

Conclusion: DM and PM are diseases characterized by the systemic overexpression of IFNalpha/beta-inducible genes. The magnitude of the overexpression of these genes is higher in DM and correlates with disease activity in both disorders. Although PM and IBM have been modeled as having similar immunologic processes occurring within muscle, there are substantial differences in the expression of IFNalpha/beta-inducible genes in blood in these diseases.

Figure 1

Blood interferon-α/β (IFNα/β)–inducible gene expression signature in inflammatory myopathies. A, Hierarchical clustering and visual representation of the magnitude of expression of the 25 most highly expressed genes in active dermatomyositis (DMA) compared with that in normal subjects (NORM) (see Table 2). At least 84% of these are known IFNα/β-inducible genes. Expression levels are higher in active dermatomyositis and active polymyositis (PMA) than in improving dermatomyositis (DMI), improving polymyositis (PMI), and active inclusion body myositis (IBM) compared with those in normal subjects. Values for individual patients are in columns. Values for genes are in rows. Red represents the highest expression levels. Blue represents the lowest expression levels. B, Comparison of the magnitude of the type I IFN signature for the 10 most up-regulated genes in active dermatomyositis with that in active polymyositis and active IBM. Values are the mean ± SEM for each gene.

Figure 2

Down-regulation of 6 IFNα/β-inducible genes in 8 patients correlates with improvement in clinical disease from time point 1 (active) to time point 2 (improving). A, Gene expression studies and analysis of paired blood samples from 2 visits between which clinical improvement occurred, in 8 patients, showed marked down-regulation of multiple IFNα/β-inducible gene transcripts. Six of these genes are shown. B, In patient BGE92, with refractory active DM, expression of most of these 6 genes increased or remained unchanged in serial samples. See Figure 1 for definitions.

Figure 3

Comparison of microarray results in muscle and blood from patients with active DM. Shown are microarray data from 5 muscle samples and 8 blood samples. Values are the mean ± SEM for each gene. Although type I IFN–inducible genes are up-regulated in both blood and muscle from patients with DM, the degree of up-regulation is generally much greater in muscle than in blood and specifically greater for certain genes that accordingly may be more associated with direct mechanisms of tissue injury. Shown are fold increases for each gene transcript in muscle or blood from patients with active DM, compared with expression in muscle or blood, respectively, from normal subjects. See Figure 1 for definitions.

Figure 4

Distinct muscle expression of IFNα/β-inducible genes and protein in DM compared with that in PM and IBM. A, Muscle microarray data for 20 individuals (5 DM patients, 5 PM patients, 5 IBM patients, and 5 normal subjects). Values are the mean ± SEM for each group. The most highly differentially regulated genes in DM muscle are expressed at orders of magnitude greater than in PM and IBM. B, Immunohistochemistry for the IFNα/β-inducible protein myxovirus resistance A (MxA or Mx1) in DM, PM, and IBM. In DM, the protein is shown to be expressed by muscle fibers themselves, in contrast to PM and IBM, in which expression of MxA is limited to that by invading inflammatory cells. (Original magnification × 40.) See Figure 1 for other definitions.