A window into intracellular events in myositis through subcellular proteomics

• Published in: Inflammation research Vol. 74; no. 1; p. 31
• Main Authors: Peterson, Jennifer M., Leclair, Valérie, Oyebode, Olumide E., Herzallah, Dema M., Nestor-Kalinoski, Andrea L., Morais, Jose, Zahedi, René P., Alamr, Mazen, Di Battista, John A., Hudson, Marie
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01.12.2025; Springer Nature B.V
• Subjects: Abnormalities; Adult; Aged; Allergology; Biomedical and Life Sciences; Biomedicine; Biopsy; Cell division; Clustering; Cytoskeleton; Cytosol; Degeneration; Dermatology; Endoplasmic reticulum; Energy metabolism; Female; Gene expression; Gene regulation; Golgi apparatus; Humans; Immunology; Inclusion bodies; Inclusions; Male; Membranes; Middle Aged; Mitochondria; Muscle contraction; Muscle, Skeletal - metabolism; Muscle, Skeletal - pathology; Muscles; Musculoskeletal system; Myopathy; Myositis; Myositis - metabolism; Myositis - pathology; Neurology; Organelles; Pharmacology/Toxicology; Polymyositis; Protein folding; Protein interaction; Protein transport; Protein turnover; Proteins; Proteomics; Rheumatology; Skeletal muscle; Human; Myositis; Muscle; Biopsy; Proteomics
• ISSN: 1023-3830; 1420-908X; 1420-908X
• DOI: 10.1007/s00011-025-01996-8

Objective and design Idiopathic inflammatory myopathies (IIM) are a heterogeneous group of inflammatory muscle disorders of unknown etiology. It is postulated that mitochondrial dysfunction and protein aggregation in skeletal muscle contribute to myofiber degeneration. However, molecular pathways that lead to protein aggregation in skeletal muscle are not well defined. Subjects Here we have isolated membrane-bound organelles (e.g., nuclei, mitochondria, sarcoplasmic/endoplasmic reticulum, Golgi apparatus, and plasma membrane) from muscle biopsies of normal (n = 3) and muscle disease patients (n = 11). Of the myopathy group, 10 patients displayed mitochondrial abnormalities (IIM (n = 9); mitochondrial myopathy (n = 1)), and one IIM patient did not show mitochondrial abnormalities (polymyositis). Methods Global proteomic analysis was performed using an Orbitrap Fusion mass spectrometer. Upon unsupervised clustering, normal and mitochondrial myopathy muscle samples clustered separately from IIM samples. Results We have confirmed previously known protein alterations in IIM and identified several new ones. For example, we found differential expression of (i) nuclear proteins that control cell division, transcription, RNA regulation, and stability, (ii) ER and Golgi proteins involved in protein folding, degradation, and protein trafficking in the cytosol, and (iii) mitochondrial proteins involved in energy production/metabolism and alterations in cytoskeletal and contractile machinery of the muscle. Conclusions Our data demonstrates that molecular alterations are not limited to protein aggregations in the cytosol (inclusions) and occur in nuclear, mitochondrial, and membrane compartments of IIM skeletal muscle.