(A) Applied gating strategy (one representative patient, NCH645) for the expression analysis of tumor-associated antigens in IDHmut lower-grade glioma and secondary glioblastoma GSCs, analyzed by flow cytometry in regard to an adequate isotype control. (B) Fluorescence intensity measurements for the isotype control and the antigen expressing (positive) GSC population, showing counts in percentage [%] over the mean PE-intensity.(C) Gating strategy, including the markers pacific orange (PO), CD3, and CD8, used for quantification of antigen-specific peripheral cytotoxic CD3+CD8+ T-cells by flow cytometry and (D) antigen-loaded pMHC I-tetramers (PE-conjugated) and the respective positive (Influenza M1) as well as negative control HLA-A*02-tetramers. GSCs: glioma stem-like cells, HIV: human immunodeficiency virus, HLA: human leukocyte antigen, MHC: major histocompatibility complex, PE: Phycoerythrin, pos: positive, US: unstained.
ARTICLE ABSTRACTPurpose: Successful immunotherapies for IDHmut 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.Experimental Design: Protein fractionations of tissue lysates from IDHmut gliomas (n = 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 in silico-predicted synthetic long peptides in patients of origin, additional IDHmut glioma patients (n = 16), and healthy donors (n = 13). mRNA and protein expression of immunogenic antigens was analyzed in tumor tissues and IDHmut 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.Results: 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 IDHmut glioma patients. Most immunogenic tumor-associated antigens (TAA) were expressed in IDHmut 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 IDHmut glioma patients.Conclusions: By analyzing the repertoire of T-cell target antigens in IDHmut glioma patients, we identified five novel immunogenic TAAs and confirmed their expression on IDHmut tumors and GSCs. Clin Cancer Res; 24(12); 2951–62. ©2018 AACR.