Hotspot DNA Methyltransferase 3A ( DNMT3A ) and Isocitrate Dehydrogenase 1 and 2 ( IDH1/2 ) Mutations in Acute Myeloid Leukemia and Their Relevance as Targets for Immunotherapy.

DNA methyltransferase 3A ( DNMT3A ) and isocitrate dehydrogenase 1 and 2 ( IDH1/2 ) are genes involved in epigenetic regulation, each mutated in 7-23% of patients with acute myeloid leukemia. Here, we investigated whether hotspot mutations in these genes encode neoantigens that can be targeted by immunotherapy. Five human B-lymphoblastoid cell lines expressing common HLA class I alleles were transduced with a minigene construct containing mutations that often occur in DNMT3A or IDH1/2 . From these minigene-transduced cell lines, peptides were eluted from HLA class I alleles and analyzed using tandem mass spectrometry. The resulting data are available via ProteomeXchange under the identifier PXD050560. Mass spectrometry revealed an HLA-A*01:01-binding DNMT3A R882H peptide and an HLA-B*07:02-binding IDH2 R140Q peptide as potential neoantigens. For these neopeptides, peptide-HLA tetramers were produced to search for specific T-cells in healthy individuals. Various T-cell clones were isolated showing specific reactivity against cell lines transduced with full-length DNMT3A R882H or IDH2 R140Q genes, while cell lines transduced with wildtype genes were not recognized. One T-cell clone for DNMT3A R882H also reacted against patient-derived acute myeloid leukemia cells with the mutation, while patient samples without the mutation were not recognized, thereby validating the surface presentation of a DNMT3A R882H neoantigen that can potentially be targeted in acute myeloid leukemia via immunotherapy.