Integrated multi-omics reveals anaplerotic insufficiency in methylmalonyl-CoA mutase deficiency

Abstract

Multi-layered omics technologies can help define relationships between genetic factors, biochemical processes and phenotypes thus extending research of monogenic diseases beyond identifying their cause. We implemented a multi-layered omics approach for the inherited metabolic disorder methylmalonic aciduria. We performed whole genome sequencing, transcriptomic sequencing, and mass spectrometry-based proteotyping from matched primary fibroblast samples of 230 individuals (210 affected, 20 controls) and related the molecular data to 105 phenotypic features. Integrative analysis identified a molecular diagnosis for 84% (179/210) of affected individuals, the majority (150) of whom had pathogenic variants in methylmalonyl-CoA mutase (MMUT). Untargeted integration of all three omics layers revealed dysregulation of TCA cycle and surrounding metabolic pathways, a finding that was further supported by multi-organ metabolomics of a hemizygous Mmut mouse model. Stratification by phenotypic severity indicated downregulation of oxoglutarate dehydrogenase and upregulation of glutamate dehydrogenase in disease. This was supported by metabolomics and isotope tracing studies which showed increased glutamine-derived anaplerosis. We further identified MMUT to physically interact with both, oxoglutarate dehydrogenase and glutamate dehydrogenase providing a mechanistic link. This study emphasizes the utility of a multi-modal omics approach to investigate metabolic diseases and highlights glutamine anaplerosis as a potential therapeutic intervention point in methylmalonic aciduria.