De novo mutations in mitochondrial DNA of iPSCs produce immunogenic neoepitopes in mice and humans

Nat Biotechnol. 2019 Oct;37(10):1137-1144. doi: 10.1038/s41587-019-0227-7. Epub 2019 Aug 19.


The utility of autologous induced pluripotent stem cell (iPSC) therapies for tissue regeneration depends on reliable production of immunologically silent functional iPSC derivatives. However, rejection of autologous iPSC-derived cells has been reported, although the mechanism underlying rejection is largely unknown. We hypothesized that de novo mutations in mitochondrial DNA (mtDNA), which has far less reliable repair mechanisms than chromosomal DNA, might produce neoantigens capable of eliciting immune recognition and rejection. Here we present evidence in mice and humans that nonsynonymous mtDNA mutations can arise and become enriched during reprogramming to the iPSC stage, long-term culture and differentiation into target cells. These mtDNA mutations encode neoantigens that provoke an immune response that is highly specific and dependent on the host major histocompatibility complex genotype. Our results reveal that autologous iPSCs and their derivatives are not inherently immunologically inert for autologous transplantation and suggest that iPSC-derived products should be screened for mtDNA mutations.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Antigens
  • Cell Transplantation / methods
  • DNA, Mitochondrial / genetics*
  • Embryonic Stem Cells
  • Epitopes / genetics*
  • Epitopes / immunology*
  • Graft Rejection / immunology
  • Graft vs Host Disease / immunology*
  • Humans
  • Induced Pluripotent Stem Cells*
  • Kidney Transplantation / adverse effects
  • Liver Transplantation / adverse effects
  • Mice
  • Mice, Inbred BALB C
  • Mice, Inbred C57BL
  • Mutation
  • Transplantation, Autologous


  • Antigens
  • DNA, Mitochondrial
  • Epitopes