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

TL;DR

The study reveals how different types of muscle fibers in inclusion body myositis have unique protein patterns linked to disease mechanisms.

Contribution

A novel myofiber-level proteomic workflow was developed to uncover subtype-specific molecular signatures in pathologically-associated fibers of IBM.

Findings

Regenerating fibers with embryonic myosin show molecular similarity to centrally nucleated fibers, not inflammation-adjacent fibers.

PAF subtypes exhibit distinct proteomic profiles linked to impaired proteostasis and aggregation-prone proteins.

HNRNPA1 localization changes suggest a role in protein aggregation and inflammation in IBM.

Abstract

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.

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.

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.

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.

The online version contains supplementary material available at 10.1186/s12964-026-02720-7.

• 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 points to PAF subtype–specific mechanisms underlying impaired regeneration and potential drivers of pathology.

• Regulators of pathology-associated myofibers can be identified as potential targets for translational studies.

The online version contains supplementary material available at 10.1186/s12964-026-02720-7.

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