Abstract 1991: Characterization of the exome, transcriptome, and immunopeptidome to map alterations in primary and recurrent glioblastoma
Authors: Dubbelaar Marissa L. , Freudenmann Lena K. , Scheid Jonas , Velz Julia , Medici Gioele , Kapolou Konstantina , Mohme Malte , Bichmann Leon , Gauder Marie , Czemmel Stefan , Mohr Christopher , Kowalewski Daniel J. , Westphal Manfred , Lamszus Katrin , Regli Luca , Weller Michael , Rammensee Hans-Georg , Salih Helmut , Neidert Marian C. , Walz Juliane S. 
Published: June 2022

Glioblastoma is known as the most aggressive and most common malignant primary tumor in the central nervous system. Current treatment options comprise maximal surgical resection followed by radiation and/or chemotherapy with temozolomide. However, these therapies are not able to eliminate all tumor cells, which in turn inevitably leads to disease recurrence and an alteration of identified targets in the context of clonal evolution and potential hypermutation. T cell-based immunotherapy holds great promise to target malignant cells with CAR T cell and vaccination strategies, showing first promising results in glioblastoma. These therapies rely on the rejection of cancer cells through recognition of tumor antigens and T cell-mediated cytotoxicity. In previous work, we have characterized such tumor antigens in primary glioblastoma (Neidert et al., Acta Neuropathol, 2018), nonetheless, alterations in relapsed disease have not been addressed thus far. This study investigated the whole exome, transcriptome, and mass-spectrometry-based immunopeptidome of 38 primary and 24 recurrent tumors, including 22 autologous glioblastoma pairs, to determine alterations that occur during glioblastoma progression on multiple comics levels. In concordance with Neftel et al., Cell, 2019, we identified mutations that can be allocated to astrocyte- and mesenchymal-like classified genes. In addition, an increase in the mutation rate in recurrent glioblastoma was observed which is attributed to radiation and chemotherapy pretreatment of tumors. These newly arising tumor-specific mutations give rise to HLA-presented neoepitopes in the primary cohort. Moreover, we identified transcripts that are differentially expressed between the two cohorts, showing a higher expression of transcripts related to immune system responses in the recurrent cohort. Immunopeptidome analysis of the two cohorts revealed high frequent glioblastoma-exclusive HLA class I and class II ligands presented in both the primary and recurrent cohort, serving as universally applicable tumor antigens. Class I and II HLA ligands of each sample were analyzed and revealed 2,146 HLA class I- and 2,753 HLA class II presented antigens that were uniquely identified on primary glioblastoma. A total of 610 and 1,886 source proteins represent recurrence-exclusive antigens presented on HLA class I or II molecules, respectively. Together this work addressed differences in tumor antigen expression and presentation between primary and recurrent glioblastoma using these omics layers to create an overview of the alterations that occur during disease progression. Besides providing a deep insight into the glioblastoma (immuno-)biology during progression, this study yields targets for innovative immunotherapeutic approaches to eliminate residual cells and improve survival in glioblastoma patients.

Citation Format: Marissa L. Dubbelaar, Lena K. Freudenmann, Jonas Scheid, Julia Velz, Gioele Medici, Konstantina Kapolou, Malte Mohme, Leon Bichmann, Marie Gauder, Stefan Czemmel, Christopher Mohr, Daniel J. Kowalewski, Manfred Westphal, Katrin Lamszus, Luca Regli, Michael Weller, Hans-Georg Rammensee, Helmut Salih, Marian C. Neidert, Juliane S. Walz. Characterization of the exome, transcriptome, and immunopeptidome to map alterations in primary and recurrent glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1991.