Single-cell profiling of peripheral blood and muscle cells reveals inflammatory features of juvenile dermatomyositis

Abstract

Introduction: Juvenile dermatomyositis (JDM) is a rare yet serious childhood systemic autoimmune condition that primarily causes skin rashes and inflammatory myopathy of the proximal muscles. Although the associated immune response involves the innate and adaptive arms, a detailed analysis of the pertinent immune cells remains to be performed. This study aims to investigate the dynamic changes of cell type, cell composition and transcriptional profiles in peripheral blood and muscle tissues, and in order to clarify the involvement of immune cells in the pathogenesis of JDM and provide a theoretical reference for JDM.Methods: Single-cell RNA sequencing combined with bioinformatic analyses were used to investigate the dynamic changes in cell composition and transcriptional profiles.Results: Analysis of 45,859 cells revealed nine and seven distinct cell subsets in the peripheral blood and muscle tissues respectively. IFITM2+ and CYP4F3+ monocytes were largely produced, and CD74+ smooth muscle cells (SMCs) and CCL19+ fibroblasts were identified as inflammatory-related cell subtypes in JDM patients, exhibiting patient-specific cell population heterogeneity.The dynamic gene expression patterns presented an enhanced type I interferon response in peripheral blood monocytes and T-cells, and SMCs and fibroblasts in muscle of untreated JDM patients. EGR1 and IRF7 may play central roles in the inflammation in both CD74+ SMCs and CCL19+ fibroblasts. Moreover, inflammatory-related monocytes could regulate T-cells, and the interaction between immune cells and SMCs or fibroblasts in muscle was enhanced under the inflammatory state.Conclusions: Immune dysregulation is one of the key pathogenic factors of JDM, and type I interferon responses are significantly enhanced in peripheral blood Monos and T cells as well as SMCs and fibroblasts. EGR1 and IRF7 may play central roles in the inflammation and are considered as potential therapeutic targets for JDM.

Coordinated immune dysregulation in Juvenile Dermatomyositis revealed by single-cell genomics

“…Broadly, we observe that the composition of PBMCs changes in JDM, with an under-representation of innate immune cells and an expansion of lymphocytes with bias toward immature naive populations over memory phenotypes in B and CD4T cells. Within the B cell compartment, the distinctive transcriptomic and proteomic signature of immature naive B cells is consistent with what we and others previously reported in treatment-naive disease (16, 24). Given that autoantibodies are thought to play a role in disease pathogenesis, this skewing of the B cell compartment would seem counterintuitive.…”

“…A common finding across all cell types was overexpression of genes enriched in Type I IFN processes, which was previously reported in bulk expression data (33, 34) and confirmed in single-cell studies (Supplemental Figure 5) (16, 24). Taking advantage of our richer dataset, we also identified that the strength of the IFN gene signature varied widely across both patients (Fig 3c) and cell types.…”

“…We identified B9, an immature naive B cell program ( CD24 , CD38 , MME )), to be significantly associated with disease activity (Figure 6B). This gene program shared several top markers ( TCL1A, SOX4, NEIL1 ) with the immature B cell population that we and others previously found to be expanded in treatment-naive JDM (16, 24). Notably, expression of this activated immature B cell program could be attributed to the B_naive1 cluster that we observed to be increased in treatment-naive JDM during our previous compositional analysis (Supplemental Figure 14).…”

“…However, while ICOS expression was higher (Benjamini-Hochberg (BH) p < 0.05), no difference was found in surface expression of CXCR5 between CD45RO hi PD-1 hi CD4 + T cells and CD45RO lo PD-1 lo CD4 + T cells, and these cells were not significantly expanded in JDM (Supplemental Figure 3C-E). Taken together, these compositional and immunophenotyping observations add to the growing body of work showing that JDM in the treatment-naive state is characterized by relative imbalances of naive and mature lymphocyte states (16, 24), reduced innate immune populations (23) and distinct CD4 + T and B cell immunophenotypes (17,18).…”

“…In the first single-cell study of peripheral blood of JDM patients, we previously described a pan-cell-type IFN gene signature over-expressed in treatment-naive JDM that was most strongly correlated with disease activity in cytotoxic cell types (16). This signature has since been independently identified in the peripheral blood of treatment-naive patients (24). However, these studies have utilized small cohorts and lack adequate controls, in part due to the rarity of JDM in the human population.…”