Single-cell RNA sequencing reveals clonally expanded CD4+ tissue-resident memory T cells in histidyl-tRNA synthetase–induced myositis
Decheng Li, Daniel P. Reay, Iago Pinal-Fernandez, Maria Casal-Dominguez, Andrew L. Mammen, Sarah L. Gaffen, Timothy B. Oriss, Dana P. Ascherman
Decheng Li, Daniel P. Reay, Iago Pinal-Fernandez, Maria Casal-Dominguez, Andrew L. Mammen, Sarah L. Gaffen, Timothy B. Oriss, Dana P. Ascherman
View: Text | PDF
Research Article Immunology

Single-cell RNA sequencing reveals clonally expanded CD4+ tissue-resident memory T cells in histidyl-tRNA synthetase–induced myositis

Abstract

The precise mechanisms underlying the pathogenesis of idiopathic inflammatory myopathy (IIM) remain undefined. However, there has been increasing recognition that tissue-resident memory T cells (TRMs) play an important role in the pathogenesis of systemic autoimmune disease. In IIM, TRM-associated transcriptional signatures have been reported but on a very limited basis. By using multimodal single-cell RNA-sequencing analysis in our established murine model of histidyl-tRNA synthetase–induced myositis, we identified a prominent population of CD4+ TRMs in inflamed skeletal muscle. Muscle CD4+ TRMs exhibited high expression of genes encoding Cd69, Cxcr6, Runx3, and Prdm1, alongside low expression of Klf2, Ccr7, Sell, S1pr1, and Tcf7 — a profile that is generally consistent with previous reports of TRM gene signature and that we validate through comparison with transcriptomic profiles of human muscle tissue. Detailed pathway analysis in our model indicates that muscle CD4+ TRMs contribute to innate immune regulatory pathways enriched for TNF and IFN-γ signaling. Furthermore, analysis of TCR clonotype distribution and CDR3 sequence similarity revealed pronounced clonal expansion of CD4+ TRMs relative to other T cell subsets — a pattern that remained stable from 2 to 6 weeks after immunization. Collectively, these results suggest a potential role for CD4+ TRMs in the pathogenesis of autoimmune myositis.

Authors

Decheng Li, Daniel P. Reay, Iago Pinal-Fernandez, Maria Casal-Dominguez, Andrew L. Mammen, Sarah L. Gaffen, Timothy B. Oriss, Dana P. Ascherman

×

Figure 1

Bulk RNA sequencing analysis of human myositis biopsy specimens.

Options: View larger image (or click on image) Download as PowerPoint
Bulk RNA sequencing analysis of human myositis biopsy specimens. (A) Lef...
(A) Left: Volcano plot displaying differentially expressed genes (DEGs) in anti–Jo-1 myositis patients (n = 37) compared with healthy controls (n = 37), identified by Wilcoxon’s rank-sum test, with adjusted P value < 0.05 and log2 fold change (FC) > 1 or < –1. Genes with log2 FC > 1 and adjusted P < 0.05 were designated as upregulated (Up); those with a log2 FC < –1 and adjusted P < 0.05 were classified as downregulated (Down). Right: Bar plot demonstrating Gene Ontology (GO) enrichment analysis comparing anti–Jo-1 myositis with healthy muscle, ordered by normalized enrichment scores. FDR < 0.05; minimum gene IDs in category = 20. (B) Left: Volcano plot displaying DEGs in anti–Jo-1 myositis patients (n = 37) compared with all other myositis subtypes (n = 625). Right: Bar plot demonstrating GO enrichment analysis ordered by normalized enrichment scores. FDR < 0.05; minimum gene IDs in category = 20. (C) The depicted heatmap demonstrates relative expression of key genes representative of resident memory T cells (TRMs) in different subsets of inflammatory myopathy, genetic myopathies, and healthy controls. Genes reflecting type I versus type II interferon responses are included. (D and E) Illustration of gene set enrichment for selected biological processes identified by GO comparing anti–Jo-1 myositis with non-myositis controls (D) or other subtypes of myositis (E). ASyS, anti-synthetase syndrome; DM, dermatomyositis; IBM, inclusion body myositis; PM, polymyositis; Scl, scleroderma; HMGCR, HMG-CoA reductase (3-hydroxy-3-methylglutaryl-CoA reductase); SRP, signal recognition particle.