Untargeted 1H NMR Metabolomics and Pathway Analysis Reveals Dysregulated Proteostasis in Cyclophilin D (CypD)-deficient Mice Tissues

Cyclophilin D (CypD) is a nuclear-encoded mitochondrial protein. Although best known as a regulator of the mitochondrial permeability transition pore (MPTP), it is also implicated in the regulation of cellular bioenergetics and extramitochondrial activities. In addition, being a peptidyl prolyl cis-trans isomerase (PPIase), deletion of CypD is likely to affect protein stability in the mitochondria; however, there is little direct evidence of this. In this study, untargeted 1H NMR metabolomics, coupled with multivariate analysis, was used to describe simultaneous changes in the metabolic system of CypD-deficient mice liver, heart, and pancreas, with data from the serum to identify systematic changes. Metabolomics Pathway Analyses (MetPA) revealed commonly perturbed metabolites in the different mouse tissues lacking CypD, with significantly enriched pathways that are related to amino acid, glucose and purine metabolisms, and bioenergetics. Serum from CypD-deficient mice confirmed changes in tissue urea cycle, lipid metabolism and ketogenesis. Overall this study reveals the role of CypD in maintaining protein homeostasis, concurring with its biochemical property as a peptidyl-prolyl isomerase and also demonstrates the wider metabolic adaptations induced by the deletion of the ppif gene, resulting in a CypD-deficient mice metabolome that is different from the wild-type system.