44PHigh-resolution spatial transcriptomics reveals myofiber-immune cell interactions in inclusion body myositis

Inclusion Body Myositis (IBM) is the most common inflammatory muscle disease in older adults with no effective treatment available. Unlike other inflammatory myopathies, IBM follows a slowly progressing, chronic disease course characterized by intracellular inflammation, including T-cell infiltration, and degenerative myofiber pathology including protein aggregates, centralized nuclei and rimmed vacuoles - together resulting in muscle damage. To understand the interplay between immune cells and myofiber pathology in IBM, we performed high-resolution Spatial Transcriptomics on human IBM and healthy control muscle biopsies (n=3). This approach allows for in situ, subcellular molecular analyses of myofibers, fiber-immune cell interactions, and the discovery of antigens presented on myofibers involved in immune cell infiltration. Our dataset includes 5000 pre-configured genes encoding signaling components, and 480 in-house selected genes specific to muscle tissue and neuromuscular diseases. To define individual myofibers, image-based fiber segmentation was performed by developing a customized muscle-specific segmentation pipeline using Cellpose within the SPArrOW spatial library, resulting in the recovery of over 8,000 and 2,000 IBM and healthy control myofibers, respectively. Preliminary data analysis indicates an increase in number and diversity of mononuclear inflammatory cells, including an expansion of T-cells and a distinct B-cell population in IBM. Unsupervised myofiber clustering indicates a population of damaged myofibers and a reduction in Type 2 myofibers in IBM. Additionally, IBM biopsies show a specific myofiber population surrounded by immune infiltrates enriched for transcripts encoding known protein aggregates, HLA-proteins, and genes potentially involved in protein aggregation and/or antigen presentation. Our data presents a valuable resource to investigate molecular changes in IBM, enhancing our understanding of immune-myofiber crosstalk, antigen presentation, and disease progression of IBM.