Induced pluripotent stem cells display a unique set of MHC I-associated peptides shared by cancer cells

We used a proteogenomic approach combining RNA-sequencing and mass spectrometry to study the MHC I-immunopeptidome specific to human iPSC samples. iPSCs were also analyzed after a 72h treatment with IFN-g (IFN-gamma) to boost MHC I levels and increase our chance for pluripotency-associated MHC I-associated peptide (paMAP) discovery. We identified 46 paMAPs which were absent from the RNA-seq of healthy somatic tissues and adult stem cells, but 40 of them were expressed in multiple cancer types from The Cancer Genome Atlas (TCGA). The antigens shared by iPSCs and tumors represent attractive targets for immunotherapy of poorly differentiated cancers. Overall design: The RNA-Seq of hiPSCs was used to construct sample-specific databases for the mass spectrometry-based identification of MHC I-associated peptides. Data reported here are paired-end stranded RNA-sequencing (R1 map on reverse strand and R2 on forward strand for hiPSC22 and hiPSC22_IFN; R1 map on forward and R2 map on reverse strand for Fibro-iPSC.1 and Fibro-iPSC.2, with or without IFN-g), with a coverage > 170M reads per sample.