Proteomics of cytochrome c oxidase-negative versus -positive muscle fiber sections in mitochondrial myopathy

The mosaic distribution of cytochrome c oxidase-positive (COX+) and COX-negative (COX-) muscle fibers in mitochondrial disorders allows the sampling of fibers with compensated and decompensated mitochondrial function from the same individual. We apply laser capture microdissection to excise individual COX+ and COX- fibers from biopsies of mitochondrial myopathy patients. Using mass spectrometry-based proteomics, we quantify more than 4000 proteins per patient. While COX+ fibers show higher expression of respiratory chain components, COX- fibers display protean adaptive responses, including upregulation of mitochondrial ribosomes, translation proteins and chaperones. Upregulated proteins include C1QBP, required for mitoribosome formation and protein synthesis, and STOML2, which organizes cardiolipin-enriched microdomains and the assembly of respiratory supercomplexes. Factoring in fast/slow fiber type, COX- slow fibers show a compensatory upregulation of beta-oxidation, the AAA+ protease AFG3L1, and the OPA1-dependent cristae remodeling program. These findings reveal compensatory mechanisms in muscle fibers struggling with energy shortage and metabolic stress.