Orso, Stefania Del

Abstract Objectives Granulomatous myositis (GM) is defined by focal collections of activated macrophages that fuse to form multinucleated cells that aggregate into granulomas within skeletal muscle. This study aimed to elucidate the pathophysiology of GM by defining its specific transcriptomic profile. Methods Bulk RNA sequencing was performed on 722 muscle biopsies, including 38 from patients with GM, other myopathies and healthy comparators. Spatial transcriptomics and immunohistochemistry assays were used to identify the location of specific transcripts and proteins within the tissue. Results We conducted a systematic analysis of the inflammatory pathways implicated in GM. This analysis revealed that GM muscle biopsies are characterized by elevated levels of IFNγ, IFNγ-inducible genes and proinflammatory cytokine genes including IL1B, TNF and TGFB1. Additionally, we identified a specific gene signature in GM, comprising 1293 genes that were significantly upregulated and 256 significantly downregulated. These genes were strongly correlated with transcriptomic markers of disease activity. Using this gene signature, support vector machine models accurately identified GM, achieving an area under the curve of 99.6% (99.0–99.9%) and an accuracy of 98.6% (98.2–98.9%). Among the identified genes, CHIT1 emerged as the most significantly upregulated gene, with its expression strongly correlating with disease severity. Furthermore, CHIT1 was detected at both the RNA and protein levels in granulomas and giant cells. Conclusion GM is transcriptomically characterized by a strong IFNγ signature and overexpression of proinflammatory cytokines, including IL1B, TNF and TGFB1. Additionally, it exhibits a unique transcriptomic profile, including CHIT1, which correlates with disease activity.

Abstract Objective Myositis is a heterogeneous family of inflammatory myopathies. We sought to define the differential expression of cytokines, cytokine receptors and immune checkpoint genes in muscle biopsies from patients with different forms of myositis in order to characterize patterns of inflammation in each. Methods Bulk RNA-sequencing was performed on muscle biopsy samples from 669 patients, including 105 with DM, 80 with immune-mediated necrotizing myopathy (IMNM), 65 with anti-synthetase syndrome, 53 with IBM, 19 with anti-PM/Scl myositis, 310 with other inflammatory or genetic myopathies and 37 controls with normal tissue (NT). Myositis clinical groups and autoantibody subgroups were analysed separately. Expression data were analysed for 338 genes encoding cytokines, cytokine receptors and immune checkpoints. Myositis group-specific genes were identified from this list by finding genes that were specifically differentially expressed in one group compared with all samples and compared with NT (α < 0.001). Results IBM patients had the most differentially overexpressed genes (71) among all clinical groups, including 37 that were IBM-specific. Among the top genes were several involved in type 1 inflammation, including CCL5, CXCR3, CCR5, CXCL9 and IFNG. Anti-Jo1 and anti-PM/Scl patients exhibited differential overexpression of a similar set of genes, while DM patients exhibited differential overexpression of a different set of genes involved in type 1 inflammation. IMNM patients had the least number of differentially overexpressed genes with no predominant inflammatory pattern. Conclusion Each myositis clinical group and autoantibody subgroup had differentially overexpressed inflammatory mediators, including a strong type 1 inflammatory gene signature in IBM.