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

Cell Communication and Signaling, vol. 24

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 Department of Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Department of Human Genetics, Leiden University Medical Center, Postbus 9600, Leiden, 2300 RC, The Netherlands

2. Simon J. Davis

   University of Oxford

   Affiliation as printed

   Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK

   Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK

3. R. A. O’Shaughnessy Aachen Department of Human Genetics

   Leiden University Medical Center

   Affiliation as printed

   Department of Human Genetics, Leiden University Medical Center, Postbus 9600, Leiden, 2300 RC, The Netherlands

4. Erik Bos Aachen Department of Chemical Cell Biology

   Leiden University Medical Center

   Affiliation as printed

   Department of Chemical Cell Biology, Leiden University Medical Center, Leiden, The Netherlands

5. A. J. van der Kooi

   Amsterdam Neuroscience · Amsterdam University Medical Centers · University of Amsterdam

   Affiliation as printed

   Department of Neurology, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands

6. Joost Raaphorst

   Amsterdam Neuroscience · Amsterdam University Medical Centers · University of Amsterdam

   Affiliation as printed

   Department of Neurology, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands

7. Eleonora Aronica

   Amsterdam Neuroscience · Amsterdam University Medical Centers · University of Amsterdam

   Affiliation as printed

   Department of Neuropathology, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands

8. Roman Fischer

   University of Oxford

   Affiliation as printed

   Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK

   Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK

9. Benedikt Mathias Kessler

   University of Oxford

   Affiliation as printed

   Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK

   Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, England, UK

10. Vered Raz corresponding Aachen Department of Human Genetics

    Leiden University Medical Center

    Affiliation as printed

    Department of Human Genetics, Leiden University Medical Center, Postbus 9600, Leiden, 2300 RC, The Netherlands. v.raz@lumc.nl