Background: Juvenile dermatomyositis (JDM) is a rare paediatric autoimmune disease, characterised by chronic inflammation of muscle and skin tissues, with prominent interferon (IFN) pathway activation. While several studies have identified key inflammatory signatures in JDM, the spatial organisation of immune and muscle cell states within affected tissue remains poorly understood. Spatial transcriptomic approaches enable investigation of cellular interactions and gene expression while preserving tissue architecture, offering new insights into disease mechanisms.

Objectives: To define the spatially resolved transcriptional landscape of muscle tissue in JDM and to characterise inflammatory and metabolic signatures across muscle and immune cell compartments.

Methods: Skeletal muscle biopsies from three children with JDM (from the UK JDM Cohort and Biomarker Study) and three age-matched controls (from Brain UK) were analysed. Spatial single-cell transcriptomic profiling was performed using a high-plex, image-based spatial molecular imaging platform, with a 1000-plex RNA panel targeting canonical cell-type markers. A total of 43 fields of view from JDM samples and 23 from controls were analysed, comprising approximately 40,000 cells. Quality control filtering excluded cells with low transcript counts or elevated negative probe signal. Data were normalised, clustered, and annotated using Seurat v5 and InSituType, informed by canonical marker expression. Pseudobulk differential gene expression analyses were conducted across annotated cell types using DESeq2.

Results: Distinct muscle-resident and infiltrating immune cell populations were identified, including muscle fibres, fibroblasts, endothelial cells, macrophages, T lymphocytes, and B/plasma cells. Comparative pseudobulk analysis demonstrated a conserved transcriptional response in JDM muscle fibres and macrophage-lineage cells, marked by increased expression of interferon-stimulated genes (including IFIT3 , IFITM1 and ISG15 ) alongside reduced expression of genes involved in oxidative phosphorylation and antioxidant pathways (including NDUFA4L2 and COX4I2 ). These alterations indicate the presence of parallel inflammatory and metabolic stress signatures across both immune and muscle cell compartments.

Conclusions: Spatial transcriptomic profiling allowed characterization of both muscle and immune cell populations in JDM and control muscle tissue. Findings indicate shared upregulation of interferon-related transcripts and reduced metabolic gene expression and highlight the utility of spatial approaches for dissecting tissue-level disease mechanisms in paediatric inflammatory myopathies. Ongoing analyses aim to refine cell-state definitions, assess spatial patterns, and validate findings in larger cohorts.

REFERENCES: NIL.

Acknowledgments: NIL.

Disclosure of Interests: Aris Eleftherios Syntakas: None declared, Yara Elena Sanchez-Corrales: None declared, Theodoros Xenakis: None declared, Huong D Nguyen: None declared, Charalampia Papadopoulou: None declared, Muthana Al-Obaidi: None declared, Clarissa Pilkington: None declared, Olumide Ogunbiyi: None declared, Ashirwad Merve: None declared, Lucy Wedderburn Speaker fees from Pfizer paid to UCL, Consultancy with Pfizer and Cabaletta paid to UCL, Research Grant from Pfizer, Meredyth Wilkinson: None declared.