A metastable subproteome underlies inclusion formation in muscle proteinopathies

Abstract

Protein aggregation is a pathological feature of neurodegenerative disorders. We previously demonstrated that protein inclusions in the brain are composed of supersaturated proteins, which are abundant and aggregation-prone, and form a metastable subproteome. It is not yet clear, however, whether this phenomenon is also associated with non-neuronal protein conformational disorders. To respond to this question, we analyzed proteomic datasets from biopsies of patients with genetic and acquired protein aggregate myopathy (PAM) by quantifying the changes in composition, concentration and aggregation propensity of proteins in the fibers containing inclusions and those surrounding them. We found that a metastable subproteome is present in skeletal muscle from healthy patients. The expression of this subproteome escalate 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, proteins within the metastable subproteome rise in abundance, suggesting that they escape regulation. Taken together, our results show in the context of a human conformational disorder that the supersaturation of a metastable subproteome underlies widespread aggregation and correlates with the histopathological state of the tissue.

Cryptic amyloidogenic regions in intrinsically disordered proteins: Function and disease association

“…This observation led to the “living on the edge” hypothesis that suggests that protein abundance is tightly regulated to an optimal level, sufficient for proteins to develop their biological function but low enough to maintain their solubility [84] . Proteins exceeding their critical concentration are considered supersaturated and constitute a metastable subproteome, often associated with diseases [85] , [86] , [87] , [88] .…”

Heterotypic interactions in amyloid function and disease

“…A breakdown of the protein content of ALS‐related inclusion bodies indicated that co‐aggregating proteins are either interaction partners of the major protein constituents (TDP43, SOD1, FUS), or display supersaturated expression levels and increased metastability towards aggregation, suggesting that progressive impairment of the proteostatic mechanisms can trigger their co‐deposition in motor neurons [102]. Recently, it was shown that protein supersaturation levels are not only linked to neurodegenerative disorders, as a similar metastable subproteomic population was shown to dictate the formation of inclusions in muscular proteinopathies [103].…”

Targeting DNA topoisomerases or checkpoint kinases results in an overload of chaperone systems, triggering aggregation of a metastable subproteome

“…Protein supersaturation refers to proteins that are expressed at high levels relative to their intrinsic propensity to aggregate, which makes them vulnerable to aggregation. Supersaturation has been shown to underlie the widespread protein aggregation observed in age-related neurodegenerative diseases, and in general aging ( Ciryam et al, 2015 ; Ciryam et al, 2019 ; Freer et al, 2019 ; Kundra et al, 2017 ; Noji et al, 2021 ). The relevance of supersaturation is underlined by the notion that evolutionary pressures appear to have shaped proteomes along its lines, so that at a global level protein abundance is inversely correlated with aggregation propensity ( Tartaglia et al, 2007 ).…”