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. 2023 Jun;82(6):829-836.
doi: 10.1136/ard-2022-223792. Epub 2023 Feb 17.

Transcriptomic profiling reveals distinct subsets of immune checkpoint inhibitor induced myositis

Iago Pinal-Fernandez #  1   2 , Angela Quintana #  3   4 , Jose Cesar Milisenda #  3   5   6 , Maria Casal-Dominguez #  3   2 , Sandra Muñoz-Braceras  3 , Assia Derfoul  3 , Jiram Torres-Ruiz  3   7 , Katherine Pak  3 , Stefania Dell'Orso  3 , Faiza Naz  3 , Gustavo Gutierrez-Cruz  3 , Margherita Milone  8 , Shahar Shelly  9 , Yaiza Duque-Jaimez  5 , Ester Tobias-Baraja  5 , Ana Matas-Garcia  5   6 , Gloria Garrabou  5   6 , Joan Padrosa  6 , Javier Ros  10 , Ernesto Trallero-Araguás  11 , Brian Walitt  12 , Lisa Christopher-Stine  2   13 , Thomas E Lloyd  2 , Chen Zhao  14 , Shannon Swift  14 , Arun Rajan  14 , Josep Maria Grau-Junyent  5   6 , Albert Selva-O'Callaghan  4   15 , Teerin Liewluck #  8 , Andrew Lee Mammen #  1   2   13
Affiliations

Transcriptomic profiling reveals distinct subsets of immune checkpoint inhibitor induced myositis

Iago Pinal-Fernandez et al. Ann Rheum Dis. 2023 Jun.

Abstract

Objectives: Inflammatory myopathy or myositis is a heterogeneous family of immune-mediated diseases including dermatomyositis (DM), antisynthetase syndrome (AS), immune-mediated necrotising myopathy (IMNM) and inclusion body myositis (IBM). Immune checkpoint inhibitors (ICIs) can also cause myositis (ICI-myositis). This study was designed to define gene expression patterns in muscle biopsies from patients with ICI-myositis.

Methods: Bulk RNA sequencing was performed on 200 muscle biopsies (35 ICI-myositis, 44 DM, 18 AS, 54 IMNM, 16 IBM and 33 normal muscle biopsies) and single nuclei RNA sequencing was performed on 22 muscle biopsies (seven ICI-myositis, four DM, three AS, six IMNM and two IBM).

Results: Unsupervised clustering defined three distinct transcriptomic subsets of ICI-myositis: ICI-DM, ICI-MYO1 and ICI-MYO2. ICI-DM included patients with DM and anti-TIF1γ autoantibodies who, like DM patients, overexpressed type 1 interferon-inducible genes. ICI-MYO1 patients had highly inflammatory muscle biopsies and included all patients that developed coexisting myocarditis. ICI-MYO2 was composed of patients with predominant necrotising pathology and low levels of muscle inflammation. The type 2 interferon pathway was activated both in ICI-DM and ICI-MYO1. Unlike the other types of myositis, all three subsets of ICI-myositis patients overexpressed genes involved in the IL6 pathway.

Conclusions: We identified three distinct types of ICI-myositis based on transcriptomic analyses. The IL6 pathway was overexpressed in all groups, the type I interferon pathway activation was specific for ICI-DM, the type 2 IFN pathway was overexpressed in both ICI-DM and ICI-MYO1 and only ICI-MYO1 patients developed myocarditis.

Keywords: autoimmune diseases; dermatomyositis; polymyositis.

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Conflict of interest statement

Competing interests: None declared.

Figures

Figure 1.
Figure 1.
Groups of patients (ICI-MYO1, ICI-MYO2, ICI-DM) resulting from applying unsupervised clustering to the bulk RNA sequencing data of patients with immune checkpoint-induced (ICI) myopathy. Uniform manifold approximation and projection (UMAP) was used to perform the clustering, the number of clusters was determined using the gap statistic and the clusters were defined using the K-means algorithm.
Figure 2.
Figure 2.
Histological appearance of patients with immune-checkpoint induced myopathy from clusters ICI-DM (A-D), ICI-MYO1 (F-I), and ICI-MYO2 (J-M). ICI-DM biopsies showed perifascicular atrophy, and intense vascular damage (star marks an area of muscle infarction). ICI-MYO1 showed intense inflammatory infiltrates with abundant macrophages and T-cells. Finall, ICI-MYO2 had predominant necrosis (white arrow indicates an area of myophagocytosis) with few inflammatory cells. The first column shows H&E (A, F, J), the second MHC-1 (B, G, K), the third MHC-2 (C, H, L). The fourth column shows CD68 in I and MX1 in D and M.
Figure 3.
Figure 3.
Expression (average z-score of log2[TMM+1]) of IFNB1, IFNG, and IL6 related genes in the three clusters of patients with ICI-induced myopathy (ICI-MYO1, ICI-MYO2, and ICI-DM) and in the comparator muscles biopsies
Figure 4.
Figure 4.
Top pathways in gene set enrichment analysis using the Reactome database in the three clusters of patients with ICI-induced myopathy (ICI-DM [left], ICI-MYO1 [middle], and ICI-MYO2 [right]).
Figure 5.
Figure 5.
Percent of cells expressing genes related to the type 1 (IFIT1, MX2, ISG15, MX1) and type 2 (IFNG, IFI30, GBP2, GBP1, PSMB8) interferon pathway in muscle biopsies from clusters ICI-DM, and ICI-MYO1 of immune checkpoint-induced myopathy compared with a representative selection of patients with other types of inflammatory myopathy (4 dermatomyositis, 3 antisynthetase syndrome, 6 immune-mediated necrotizing myositis, and 2 inclusion body myositis).
Figure 6.
Figure 6.
Percent of cells expressing genes related to the IL6 pathway in muscle biopsies from immune checkpoint-induced myopathy from clusters ICI-DM, and ICI-MYO1 compared with a representative selection of patients with other types of inflammatory myopathy (4 dermatomyositis, 3 antisynthetase syndrome, 6 immune-mediated necrotizing myositis, and 2 inclusion body myositis).
Figure 7.
Figure 7.
Expression levels (log2[TMM + 1]) of IFNG, IFNG-inducible genes, ICAM1, CD8A, and CD14 in patients according to the presence of myocarditis.
See this image and copyright information in PMC

References

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