Muscle spatial transcriptomic reveals heterogeneous profiles in untreated juvenile dermatomyositis and the persistence of pathological signature after remission

This study aimed to investigate the spatial heterogeneity of molecular signature in the muscle of juvenile dermatomyositis (JDM) patients before and after treatment in comparison to healthy paediatric muscle tissue. Unsupervised reference-free deconvolution of spatial transcriptomics and standardized morphometry were performed in two JDM muscle biopsies with different clinical severity at disease onset and compared to healthy paediatric muscle. In a second step, identified signatures were scored in two additional JDM muscle biopsies from the same patient before and after remission. Disappearance of the normal muscle signature mostly corresponding to mitochondrial biology was observed in JDM. Three pathological transcriptomic signatures were isolated, related to "myofibrillar stress", "muscle remodeling" and "interferon signaling" signatures. The "myofibrillar stress signature" was prominent in the most severe biopsy while the "muscle remodeling" signature was mostly present in the biopsy from the patient with good outcome. These signatures unveiled genes not previously associated with JDM including ANKRD1 and FSLT1 for "myofibrillar stress" and "muscle remodeling" signatures, respectively. Post-treatment analysis of muscle after two years of remission showed a persistence of pathological signatures. This study of JDM muscle identified spatially distributed pathological signatures that persist after remission. This work paves the way for a better understanding of the pathophysiology in affected muscle and the identification of biomarkers that predict relapse.