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[Preprint]. 2025 Feb 21:2025.02.17.25321047.

doi: 10.1101/2025.02.17.25321047.

Distinct Cytokine and Cytokine Receptor Expression Patterns Characterize Different Forms of Myositis

Raphael A Kirou^{1

2}, Iago Pinal-Fernandez^{1

3}, Maria Casal-Dominguez^{1

3}, Katherine Pak¹, Corinna Preusse^{4

5}, Dilbe Dari⁴, Stefania Del Orso⁶, Faiza Naz⁶, Shamima Islam⁶, Gustavo Gutierrez-Cruz⁶, Elie Naddaf⁷, Teerin Liewluck⁷, Werner Stenzel⁴, Albert Selva-O'Callaghan^{8

9}, Jose C Milisenda^{10

11

12}, Andrew L Mammen^{1

3

13}

Affiliations

¹ Muscle Disease Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
² College of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA.
³ Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
⁴ Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.
⁵ Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.
⁶ Genomic Technology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
⁷ Division of Neuromuscular Medicine, Department of Neurology, Mayo Clinic, Rochester, MN, USA.
⁸ Systemic Autoimmune Disease Unit, Vall d'Hebron Institute of Research, Barcelona, Spain.
⁹ Autonomous University of Barcelona, Barcelona, Spain.
¹⁰ Muscle Research Unit, Internal Medicine Department, Hospital Clinic, Barcelona, Spain.
¹¹ Barcelona University, Barcelona, Spain.
¹² CIBERER, Barcelona, Spain.
¹³ Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

PMID: 40034760
PMCID: PMC11875321
DOI: 10.1101/2025.02.17.25321047

Distinct Cytokine and Cytokine Receptor Expression Patterns Characterize Different Forms of Myositis

Raphael A Kirou et al. medRxiv. 2025.

[Preprint]. 2025 Feb 21:2025.02.17.25321047.

doi: 10.1101/2025.02.17.25321047.

Authors

Affiliations

¹ Muscle Disease Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
² College of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA.
³ Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
⁴ Department of Neurology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.
⁵ Department of Neuropathology, Charité-Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.
⁶ Genomic Technology Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
⁷ Division of Neuromuscular Medicine, Department of Neurology, Mayo Clinic, Rochester, MN, USA.
⁸ Systemic Autoimmune Disease Unit, Vall d'Hebron Institute of Research, Barcelona, Spain.
⁹ Autonomous University of Barcelona, Barcelona, Spain.
¹⁰ Muscle Research Unit, Internal Medicine Department, Hospital Clinic, Barcelona, Spain.
¹¹ Barcelona University, Barcelona, Spain.
¹² CIBERER, Barcelona, Spain.
¹³ Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

PMID: 40034760
PMCID: PMC11875321
DOI: 10.1101/2025.02.17.25321047

Update in

Distinct cytokine and cytokine receptor expression patterns characterize different forms of myositis.
Kirou RA, Pinal-Fernandez I, Casal-Dominguez M, Pak K, Preusse C, Dari D, Del Orso S, Naz F, Islam S, Gutierrez-Cruz G, Naddaf E, Liewluck T, Stenzel W, Selva-O'Callaghan A, Milisenda JC, Mammen AL. Kirou RA, et al. Rheumatology (Oxford). 2025 Nov 1;64(11):5751-5760. doi: 10.1093/rheumatology/keaf346. Rheumatology (Oxford). 2025. PMID: 40579223 Free PMC article.

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 dermatomyositis, 80 with immune-mediated necrotizing myopathy (IMNM), 65 with anti-synthetase syndrome, 53 with inclusion body myositis (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 analyzed separately. Expression data was analyzed 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 to all samples and compared to 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 dermatomyositis 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.

Keywords: Myositis; RNA-sequencing; cytokines; dermatomyositis; inclusion body myositis.

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Conflict of interest statement

Conflict of interest statement: The authors report no conflicts of interest.

Figures

**Figure 1.. Correlation heatmaps for top differentially overexpressed genes by clinical group vs. muscle and leukocyte markers.**
For all heatmaps, the x-axis displays the top 15 differentially overexpressed genes for that clinical group, or all differentially overexpressed genes if there are less than 15, ordered from lowest q-value vs. all samples to highest. The y-axis displays mature muscle markers (*ACTA1, MYH1, MYH2*), markers of muscle regeneration (*NCAM1, MYOG, PAX7, MYH3, MYH8*), mitochondrial markers (*MT-CO1, MT-CO2*), B cell markers (*CD19, MS4A1*), T cell markers (*CD3E, CD4, CD8A*), macrophage markers (*CD14, CD68*), dendritic cell markers (*CD1C, CD1E*), type 1 markers (*TBX21, STAT1*), type 2 markers (*GATA3, STAT6*), and type 3 markers (*RORC, STAT3*). Heatmaps displayed are for DM (A), IMNM (B), ASyS (C), IBM (D), and PM/Scl (E).

**Figure 2.. Correlation heatmaps for top differentially overexpressed genes by autoantibody subgroup vs. muscle and leukocyte markers.**
For all heatmaps, the x-axis displays the top 15 differentially overexpressed genes for that autoantibody subgroup, or all differentially overexpressed genes if there are less than 15, ordered from lowest q-value vs. all samples to highest. The y-axis displays mature muscle markers (*ACTA1, MYH1, MYH2*), markers of muscle regeneration (*NCAM1, MYOG, PAX7, MYH3, MYH8*), mitochondrial markers (*MT-CO1, MT-CO2*), B cell markers (*CD19, MS4A1*), T cell markers (*CD3E, CD4, CD8A*), macrophage markers (*CD14, CD68*), dendritic cell markers (*CD1C, CD1E*), type 1 markers (*TBX21, STAT1*), type 2 markers (*GATA3, STAT6*), and type 3 markers (*RORC, STAT3*). Heatmaps displayed are for Mi2 (A), MDA5 (B), NXP2 (C), TIF1 (D), HMGCR (E), SRP (F), and Jo1 (G).

**Figure 3.. Heatmap of type 1, type 2, and type 3 gene expression by group.**
The heatmap displays median expression levels of type 1, type 2, and type 3 genes for each group. Groups included are all autoantibody subgroups (Mi2, MDA5, NXP2, TIF1, HMGCR, SRP, Jo1, PM/Scl), as well as IBM (no autoantibody subgroup) and NT (control).

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References

1. Selva-O’Callaghan A, Pinal-Fernandez I, Trallero-Araguas E, Milisenda JC, Grau-Junyent JM, Mammen AL. Classification and management of adult inflammatory myopathies. Lancet Neurol 2018;17(9):816–28. - PMC - PubMed
1. Pinal-Fernandez I, Casal-Dominguez M, Derfoul A, et al. Machine learning algorithms reveal unique gene expression profiles in muscle biopsies from patients with different types of myositis. Ann Rheum Dis 2020;79(9):1234–42. - PMC - PubMed
1. Annunziato F, Romagnani C, Romagnani S. The 3 major types of innate and adaptive cell-mediated effector immunity. J Allergy Clin Immunol 2015;135(3):626–35. - PubMed
1. Musai J, Mammen AL, Pinal-Fernandez I. Recent Updates on the Pathogenesis of Inflammatory Myopathies. Curr Rheumatol Rep 2024. - PMC - PubMed
1. Greenberg SA. Inclusion body myositis: clinical features and pathogenesis. Nat Rev Rheumatol 2019;15(5):257–72. - PubMed

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This is a preprint.

Distinct Cytokine and Cytokine Receptor Expression Patterns Characterize Different Forms of Myositis

Affiliations

Distinct Cytokine and Cytokine Receptor Expression Patterns Characterize Different Forms of Myositis

Authors

Affiliations

Update in

Abstract

Conflict of interest statement

Figures

References

Publication types

LinkOut - more resources

Full Text Sources

Research Materials

Miscellaneous