Autologous induced pluripotent stem cells (iPSC)-based therapies are considered to be promising in the transplantation field, however their immunological potential is unclear. These therapies require expansion, reprogramming and differentiation of the cells in vitro. Mitochondrial (mt) DNA mutations can arise from those procedures and they have been considered to be involved in the rejection of the cells after transplantation. We therefore hypothesized that single nucleotide polymorphisms (SNPs) in the mtDNA can contribute to autologous and allogeneic graft immunoreactivity and we assessed their immunogenicity in transplantation. We studied neoantigen formation in vitro by reprogramming PBMCs from three volunteers to iPSC and differentiating them to endothelial cells (iEC). We challenged the iECs carrying mtDNA mutations with 20-residue oligomer peptides specifically designed around the SNPs. We quantified the immunological reactions with ELISpot assays. We detected nonsynonymous SNPs in mtDNA in 15 donor-recipient pairs undergoing allogeneic liver or kidney transplantation. To test the allogenicity of the SNPs we challenged the recipients' peripheral blood mononuclear cells (PBMCs) with 20-residue oligomer peptides that we generated around the SNPs. We assessed the Th1 cell response via ELISpot assays. DNA sequencing of the iEC revealed mtDNA mutations and their associated peptides induced specific immune responses quantified by IFNγ release, which increased significantly compared to the reactions against other peptides. Our analyses using the PBMCs collected from the 15 recipients that underwent solid organ transplantation, revealed that nonsynonymous SNPs in mtDNA can cause an immune reaction observed by an increase in IFNγ production in ELISpot assays. Long-term culture and differentiation of iPSC lead to mtDNA mutations that are not naturally selected against by the immune system. A single nucleotide mutation in the mtDNA giving rise to neoantigens triggers a strong immune response and may contribute to the rejection of grafted cells and thus could be of significant relevance to transplantation approaches in regenerative medicine.
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