Multi-modal single-cell sequencing identifies cellular immunophenotypes associated with juvenile dermatomyositis disease activity

Juvenile dermatomyositis (JDM) is a rare autoimmune condition with insufficient biomarkers and treatments, in part, due to incomplete knowledge of the cell types mediating disease. We investigated immunophenotypes and cell-specific genes associated with disease activity using multiplexed RNA and protein single-cell sequencing applied to PBMCs from 4 treatment-naive JDM (TN-JDM) subjects at baseline, 2, 4, and 6 months and 4 subjects with inactive disease. Analysis of 55,564 cells revealed separate clustering of TN-JDM cells within monocyte, NK, CD8+ effector T and naive B populations. The proportion of CD16+ monocytes was reduced in TN-JDM, and naive B cells were expanded. Cell-type differential gene expression analysis and hierarchical clustering identified a pan-cell-type IFN gene signature over-expressed in TN-JDM in all cell types and correlated with disease activity. TN-JDM monocytes displayed an inflammatory state: CD16+ monocytes expressed the highest IFN gene score and differential protein expression of adhesion molecules, CD49d and CD56, compared to CD14+ inflammatory monocytes. A transitional B cell population expressing higher CD24 and CD5 proteins and an IFN-hi naive B population were associated with TN-JDM and exhibited less CD39, an immunoregulatory protein. This data provides new insights into JDM immune dysregulation at cellular resolution and novel resource for myositis investigators.