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

The utility of autologous induced pluripotent stem cell (iPSC) strategies for tissue regeneration depends on the reliability to generate high numbers of immunologically silent functional tissue cells. Despite their autologous nature, rejection of iPSC-derived cells has been reported, although mechanistic details remain largely unknown. We hypothesized that new mutations in the mitochondrial DNA (mtDNA), which has far less reliable repair mechanisms than the chromosomal DNA, can give rise to neoantigens capable of eliciting an allogeneic immune response and causing rejection. Here we show that in both mice and humans that neoantigens from nonsynonymous mtDNA single nucleotide polymorphisms (SNPs) can appear and be enriched during the process of reprograming to the iPSC stage, long-term culture expansion, and differentiation into target cells. The immune response against mtDNA neoantigens is highly specific and dependent on the host major histocompatibility complex antigen repertoire. , mutagenic nonsynonymous mtDNA single nucleotide polymorphisms (SNPs) generate relevant neoantigens, which initiate a highly specific immune response. Furthermore, even the enrichment of rare SNPs that showed very low heteroplasmies in the parental somatic cells can generate a relevant neoantigen burden capable of inducing rejection. This neo-antigenicity of SNPs can diminish the survival of iPSC grafts and their derivatives in autologous recipients. Our results demonstrate that autologous iPSCs and their derivatives are not inherently immunologically inert for autologous transplantation and that techniques need to be developed to monitor screen for mtDNA mutations and neoantigenic SNP enrichments during the manufacturing of autologous iPSC products.