Multi-proteomics unveils multi-level dysregulations in methylmalonic acidemia

Methylmalonic acidemia (MMA) is a rare metabolic disorder due to deficiency of the methylmalonyl-CoA mutase (MUT) enzyme. MMA patients show aberrant degradation of odd-chain fatty acids, cholesterol, and branched-chain amino acids due to the block in the conversion of the methylmalonyl-CoA into succinyl-CoA catalyzed by MUT, with subsequent accumulation of toxic metabolites into body fluids, such as methylmalonic acid and methylcitric acid. Despite the prompt diagnosis of MMA is feasible owing to the mass spectrometry-based newborn screening, actually the damage and stress mechanisms in MMA are not fully clarified and the current therapies are ineffective.

To shed light on MMA pathogenesis, diverse MMA cell models were employed, including an engineered MUT-knockout HEK-293 cell line and dermal fibroblasts derived from patients.

Multi-proteomic analyses were performed on the MMA models to characterize the whole cell proteomes and their sub-proteomes. Global proteome analysis mainly showed alterations in autophagy- and lysosomal-related pathways, demonstrating the compromission of the lysosomal/autophagic machinery in MUT-deficient cells, which are not able to fully degrade accumulated matter. Both the cell models also showed profound dysregulations in the mitochondrial routes. In fact, the analysis of the mitochondrial proteome enriched specific pathways related to fatty acid and carbohydrate metabolism, revealing unbalances in energetic metabolism. The profiling of the nuclear proteome highlighted epigenetic and structural modifications affecting the MMA cells. Finally, an XL-MS-based approach was applied to study the interactions of the membranome of MUT-deficient cells, indicating novel actors important for cell-cell connections and structural architecture.

These data suggest that multi-level dysregulations occurring in MMA patients trigger the cellular and organ damage, providing hints towards novel potential pathways to be targeted to develop efficient therapeutic intervention in MMA.