Human Induced Pluripotent Stem Cells Harbor Homoplasmic and Heteroplasmic Mitochondrial DNA Mutations While Maintaining Human Embryonic Stem Cell–like Metabolic Reprogramming

Abstract

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 contribute to the pathology of a number of human disorders. Furthermore, the lack of mtDNA integrity may alter cellular bioenergetics and limit efficient differentiation. We demonstrated previously that the derivation of iPSCs is associated with mitochondrial remodeling and a metabolic switch towards glycolysis. Here, we have discovered that alterations of mtDNA can occur upon the induction of pluripotency. 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), not present in the parental cells. mtDNA modifications were mostly common variants and not disease related. Moreover, iPSC lines bearing different mtDNA mutational loads maintained a consistent human embryonic stem cell-like reprogramming of energy metabolism. This involved the upregulation of glycolytic enzymes, increased glucose-6-phosphate levels, and the over-expression of pyruvate dehydrogenase kinase 1 protein, which reroutes the bioenergetic flux toward glycolysis. Hence, mtDNA mutations within iPSCs may not necessarily impair the correct establishment of pluripotency and the associated metabolic reprogramming. Nonetheless, the occurrence of pathogenic mtDNA modifications might be an important aspect to monitor when characterizing iPSC lines. Finally, we speculate that this random rearrangement of mtDNA molecules might prove beneficial for the derivation of mutation-free iPSCs from patients with mtDNA disorders.

Tissue- and cell-type–specific manifestations of heteroplasmic mtDNA 3243A>G mutation in human induced pluripotent stem cell-derived disease model

“…We found that a rapid bimodal shift toward wild-type or mutant homoplasmy occurred upon reprogramming in MELAS iPSCs, replicating findings of recent reports (40,41). Rapid shifts in mitochondrial heteroplasmy have been observed to occur in germ line (i.e., stem cells) in cows (42,43), in human patients (44,45), in mice with heteroplasmic neutral or potentially pathogenic mtDNA variants (18,25,34), and in primates (46).…”

Metabolic control of cancer cell stemness: Lessons from iPS cells

“…[33][34][35][36][37][38][39][40][41][42][43][44][45][46][47] Similar to well-recognized genetic and epigenetic factors, OXPHOS-to-glycolysis bioenergetic resetting appears to operate as a crucial enabling regulator of nuclear reprogramming because the self-renewal and pluripotency attributes cannot be efficiently acquired in the presence of an inadequate bioenergetic metabotype. Thus, efficiency of reprogramming is greater the closer the glycolytic/OXPHOS energy metabolism profiles of the starting somatic cells are to those of embryonic stem cells (ESC).…”

Cell Metabolomics

“…Several other excellent examples of the application of quantitative metabolomics in cell culture analysis were presented for the analysis of neuroendocrine cancers and in the analysis of cancer cell metabolic phenotype (Costello et al, 2011). Examples of such analysis include profiling of central metabolism in human cancer cells, identification of metabolic fluxes in hepatic cells (Westra et al, 2011), and several other examples that have been reviewed previously (Prigione et al, 2011).…”