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

• Published in: Biomedicines Vol. 12; no. 5; p. 1086
• Main Authors: Struckman, Nadine E, de Jong, Rob C M, Honders, M Willy, Smith, Sophie-Anne I, van der Lee, Dyantha I, Koutsoumpli, Georgia, de Ru, Arnoud H, Mikesch, Jan-Henrik, van Veelen, Peter A, Falkenburg, J H Frederik, Griffioen, Marieke
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 14.05.2024
• Subjects: Acute myeloid leukemia; Alleles; Bone marrow; cancer immunotherapy; Cloning; CRISPR; Dehydrogenases; DNA methylation; DNA methyltransferase; DNA methyltransferase 3A; Enzymes; Epigenetics; Epstein-Barr virus; Gene regulation; Genes; Genomes; Histocompatibility antigen HLA; hotspot mutation; Immunotherapy; Isocitrate dehydrogenase; isocitrate dehydrogenase 2; Leukemia; Lymphoblastoid cell lines; Lymphocytes T; Mass spectrometry; Mass spectroscopy; Mutation; Mutation hot spots; neoantigen; Neoantigens; Patients; Peptides; Remission (Medicine); Scientific imaging; Stem cell transplantation; United States > US; Germany; DNA methyltransferase 3A; neoantigen; acute myeloid leukemia; cancer immunotherapy; hotspot mutation; isocitrate dehydrogenase 2; T-cell therapy
• ISSN: 2227-9059; 2227-9059
• DOI: 10.3390/biomedicines12051086

DNA methyltransferase 3A ( ) and isocitrate dehydrogenase 1 and 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 or . 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 peptide and an HLA-B*07:02-binding IDH2 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 or genes, while cell lines transduced with wildtype genes were not recognized. One T-cell clone for DNMT3A 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 neoantigen that can potentially be targeted in acute myeloid leukemia via immunotherapy.