Escalating protein supersaturation underlies inclusion formation in muscle proteinopathies

Abundant, aggregation prone or \"supersaturated\" proteins are a feature of neurodegeneration. Whether the principle of supersaturation can similarly explain the widespread aggregation that occurs in non-neuronal protein conformational disorders and underlies pathogenic protein aggregate formation is not established. To test this prediction we analyzed proteomic datasets of biopsies from genetic and acquired protein aggregate myopathy (PAM) patients by quantifying the changes in composition, concentration and aggregation propensity of proteins in the fibers containing inclusions and those surrounding them. We found that similar to neurodegeneration, a supersaturated subproteome of aggregate prone proteins is present in skeletal muscle from healthy patients. This subproteome escalates in degree of supersaturation as proteomic samples are taken more proximal to the pathologic inclusion, eventually exceeding its solubility limits and aggregating. While most supersaturated proteins decrease or maintain steady abundance across healthy fibers and inclusion containing fibers, supersaturated proteins within the aggregate subproteome rise in abundance, suggesting they escape normal regulation. We show in the context of a human conformational disorder that the level of supersaturation of a metastable subproteome helps to explain widespread aggregation and correlates with the histopathological state of the tissue.\n\nSignificanceIncreasing evidence implicates the phenomenon of protein supersaturation with the selective vulnerability of specific cells to protein misfolding disorders. Quantitative studies of this phenomenon, however, have only been possible post mortem in the case of neurodegenerative diseases. To overcome this limitation, we study here protein aggregate myopathies (PAMs), for which we were able to carry out systematic single fiber proteomic studies on patient-derived samples. We found not only that proteins associated with PAM inclusions are highly supersaturated in muscle but also that their supersaturation levels increases further in affected fibers. These results provide a clear illustration of how an escalation in supersaturation leads protein inclusions in vulnerable cells.