Human iPSCs harbor homoplasmic and heteroplasmic mitochondrial DNA mutations while maintaining hESC-like metabolic reprogramming

摘要

Human induced pluripotent stem cells (iPSCs) have been recently found to harbor genomic alterations. However, the integrity of mitochondrial DNA (mtDNA) within reprogrammed cells has yet to be investigated. mtDNA mutations occur at a high rate and are believed to contribute to the pathology of a number of human disorders. Furthermore, lack of mtDNA integrity may alter cellular bioenergetics and limit efficient differentiation. We previously demonstrated that the derivation of iPSCs is associated with mitochondrial remodeling and a metabolic switch towards glycolysis. Here, we aimed to determine the consequences of reprogramming on mtDNA integrity. Massively parallel pyrosequencing of mtDNA revealed that human iPSCs derived from young healthy donors harbored single base mtDNA mutations (substitutions, insertions, and deletions), both homoplasmic (in all mtDNA molecules) and heteroplasmic (in a fraction of mtDNAs). Interestingly, the level of heteroplasmy varied among iPSC lines derived from the same parental fibroblasts. This phenomenon could potentially be exploited for the generation of mtDNA mutation-free iPSCs from patients with mtDNA disorders. By integrating transcriptional, metabolic, and functional bioenergetic data, we unveiled that iPSC lines bearing different mtDNA mutational loads maintained a consistent hESC-like reprogramming of energy metabolism. This included over-expression of glycolytic enzymes, increased amount of G6P, and elevated protein expression of PDK1, which re-routes the bioenergetic flux towards glycolysis. Overall, although the mtDNA mutations within our iPSCs did not affect the reprogramming-associated metabolic modulation, the occurrence of pathogenic mtDNA modifications might be an important aspect to monitor when characterizing iPSC lines.