Spatial protein expression patterns across pathologically-associated fibers revealed molecular specialization in inclusion body myositis

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Abstract

Abstract Objectives In Inclusion Body Myositis (IBM), myofibers undergo structural and functional changes, including increased regeneration, atrophy, and fibrosis. The molecular mechanisms driving pathologically -associated fibers (PAF) remain poorly understood. Methods We developed a myofiber-level proteomic workflow to identify protein signatures of three PAF subtypes. Laser-capture microdissection mass spectrometry of immunolabeled cryosections was performed, complemented by immunofluorescence and electron microscopy validation. Results Regenerating fibers expressing embryonic myosin heavy chain showed greater molecular similarity to centrally nucleated fibers than to fibers adjacent to inflammation, which were enriched in aggregation-prone proteins. These distinct proteomic profiles revealed disruptions in protein homeostasis and proteasome composition, implicating impaired proteostasis in defective regeneration. In addition, alterations in HNRNPA1 subcellular localization across PAF subtypes suggest a potential role in driving protein aggregation and inflammation in IBM. Conclusions This study underscores the value of spatial proteomics for dissecting localized pathological processes in muscle disease. It highlights the molecular heterogeneity of IBM myofibers and suggests that PAF subtype-specific mechanisms underlie impaired regeneration while pointing to potential drivers of IBM pathology.

Authors 10

1. T. I. Nijssen Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center

2. Simon A. Davis

   University of Oxford

   Affiliation as printed

   University of Oxford

3. R. A. O’Shaughnessy Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center

4. E. Bos Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center

5. A. J. van der Kooi

   Amsterdam Neuroscience

   Affiliation as printed

   Amsterdam Neuroscience

6. Joost Raaphorst

   Amsterdam Neuroscience

   Affiliation as printed

   Amsterdam Neuroscience

7. E. Aronica

   Amsterdam Neuroscience

   Affiliation as printed

   Amsterdam Neuroscience

8. Roman Fischer

   University of Oxford

   Affiliation as printed

   University of Oxford

9. B. M. Kessler

   University of Oxford

   Affiliation as printed

   University of Oxford

10. Vered Raz Aachen

    Leiden University Medical Center

    Affiliation as printed

    Leiden University Medical Center