Identification of CRKII, CFL1, CNTN1, NME2, and TKT as Novel and Frequent T-Cell Targets in Human IDH-Mutant Glioma

• Published in: Clinical cancer research 2018-06, Vol.24 (12), p.2951-2962
• Main Authors: Dettling, Steffen, Stamova, Slava, Warta, Rolf, Schnölzer, Martina, Rapp, Carmen, Rathinasamy, Anchana, Reuss, David, Pocha, Kolja, Roesch, Saskia, Jungk, Christine, Warnken, Uwe, Eckstein, Volker, Grabe, Niels, Schramm, Christoph, Weigand, Markus A, von Deimling, Andreas, Unterberg, Andreas, Beckhove, Philipp, Herold-Mende, Christel
• Format: Article
• Language: English
• Subjects: Antigen (tumor-associated); Antigens; Brain; Brain tumors; Cytotoxicity; Enzyme-linked immunosorbent assay; Epitopes; Experimental design; Fractions; Gene expression; Glioma cells; Histocompatibility antigen HLA; Immunogenicity; Immunotherapy; Lymphocytes; Lymphocytes T; Lysates; Mass spectrometry; Mass spectroscopy; mRNA; Patients; Peptides; Proteins; T cell receptors; Tissues; Tumors; γ-Interferon
• ISSN: 1078-0432; 1557-3265
• DOI: 10.1158/1078-0432.CCR-17-1839

Successful immunotherapies for IDH gliomas require better knowledge of T-cell target antigens. Here, we elucidated their antigen repertoire recognized by spontaneous T-cell responses using an unbiased proteomic approach. Protein fractionations of tissue lysates from IDH gliomas ( = 4) were performed. Fractions were tested by IFNγ ELISpot assay for recognition through patients' T cells. Proteins of immunogenic fractions were identified by mass spectrometry and validated by -predicted synthetic long peptides in patients of origin, additional IDH glioma patients ( = 16), and healthy donors ( = 13). mRNA and protein expression of immunogenic antigens was analyzed in tumor tissues and IDH glioma stem-like cells (GSC). HLA-A*02-restricted T-cell epitopes were functionally determined by short peptides and numbers of antigen-specific T cells by HLA-peptide tetramer analysis. A total of 2,897 proteins were identified in immunogenic tumor fractions. Based on a thorough filter process, 79 proteins were selected as potential T-cell antigens. Twenty-six of these were recognized by the patients' T cells, and five of them (CRKII, CFL1, CNTN1, NME2, and TKT) in up to 56% unrelated IDH glioma patients. Most immunogenic tumor-associated antigens (TAA) were expressed in IDH gliomas and GSCs, while being almost absent in normal brain tissues. Finally, we identified HLA-A*02-restricted epitopes for CRKII, NME2, and TKT that were recognized by up to 2.82% of antigen-specific peripheral cytotoxic T cells in IDH glioma patients. By analyzing the repertoire of T-cell target antigens in IDH glioma patients, we identified five novel immunogenic TAAs and confirmed their expression on IDH tumors and GSCs. .