iPSC-derived 2D and 3D models of mitochondrial disease reveal early defects in neuronal morphogenesis and identify intervention strategies

Our understanding of the mechanisms underlying the human neuronal pathology associated with impaired oxidative phosphorylation (OXPHOS) is hampered by a lack of effective model systems. Using patient-derived induced pluripotent stem cells (iPSCs) and CRISPR/Cas9 engineering, we developed a human model of Leigh syndrome (LS) caused by mutations in the gene SURF1, which is the most frequent and severe manifestation of mitochondrial disease in children. Single-cell RNA-sequencing and multi-omics analysis revealed compromised neuronal differentiation and morphogenesis of two-dimensional (2D) neuronal cultures and of three-dimensional (3D) cerebral organoids. The phenotypes emerged at the level of neural progenitor cells (NPCs). Mutant NPCs could not shift to OXPHOS and retained a glycolytic proliferative state that failed to support neuronal morphogenesis. Improving NPC bioenergetics by increasing mitochondrial biogenesis via bezafibrate treatment restored early morphogenesis. SURF1 gene augmentation also counteracted the phenotypes, while exposure to hypoxia did not lead to amelioration. Our findings provide mechanistic insights and suggest therapeutic avenues for mitochondrial disease, a rare disease with major unmet medical need. Overall design: analysis of iPSCs, neuronal culture and brain organoids derived from Leigh Syndrome patients and controls