Mass-spectrometry based proteomics reveals tissue specific metabolic perturbations in a mitochondrial disease mouse model

Background: Mutations in the gene encoding NDUFS4, an accessory subunit of the complex I of the mitochondrial oxidative phosphorylation (OXPHOS) system, is a common cause of Leigh Syndrome (LS), an infantile heterogenous neurodegenerative disorder with variable clinical phenotypes. Understanding how different tissues/organs respond to complex I deficiency might help unravel the mechanisms involved in the heterogenous manifestation of mitochondrial disease.

Methods: To investigate tissue-specific proteomic in LS, we performed quantitative mass-spectrometry based proteomics on a LS mouse model (Ndufs4 KO) using the SWATH-MS data acquisition mode. Six distinct tissues (brainstem, cerebellum, olfactory bulb, heart, kidney, and liver) were collected from Ndufs4 KO mice (n =9) and compared to age/sex matched controls (n =9). Proteins were extracted from whole tissue lysate, digested into peptides using trypsin and analysed on the Evosep One LC system coupled to a Sciex 5600 TripleTOF mass spectrometer.

Results: Our SWATH-MS data acquisition mode resulted in the identification of more than 1, 000 proteins in each tissue based on 1% FDR. Differential expression analysis revealed significant downregulation of the NDUFS4 across the tissues. Functional enrichment analysis using gene ontology and pathway analysis on differentially expressed proteins (DEPs) unique to each tissue revealed varied cellular responses. Moreover, pathway enrichment analysis pointed towards enrichment of DEPs related to translation, neurotransmitter release cycle, fatty acid metabolism, biological oxidations, and phase II conjugations.

Conclusion: This study reveals tissue-specific cellular responses to NDUFS4 mutations in LS, providing valuable insights into the molecular mechanisms underlying LS and other mitochondrial related disorders. Understanding these tissue-specific responses can inform the development of rational therapeutic strategies for LS.