Discovery of Novel Antigen Targets for Cancer Immunotherapy

Abstract

With the breakthrough of immune checkpoint inhibitors in cancer treatment, other T cell-based cancer immunotherapies such as adoptive T cell transfer and vaccination strategies come into focus and show promising results in patients. However, these therapies, which rely on the rejection of cancer cells through recognition of tumor antigens and T cell-mediated cytotoxicity are still only available and effective in small subsets of cancer patients and single tumor entities. In order to enhance modern T cell-based immunotherapies we require a deeper understanding of the specific human leukocyte antigen (HLA)-presented antigens that enable precise targeting of cancer cells. Therefore, this thesis aims to identify, verify, and translate novel HLA-presented antigen targets of malignant diseases by the application of state-of-the-art mass spectrometry-based immunopeptidomics. The first project covered in this thesis, focuses on the identification, characterization, and immunotherapeutic application of HLA-presented neoantigens specific for the DNAJB1-PRKACA fusion transcript in fibrolamellar hepatocellular carcinoma. We proved that DNAJB1-PRKACA-derived HLA class I and HLA class II ligands were naturally presented on HLA and induced multifunctional cytotoxic T cells. Our preclinical and clinical findings identify the DNAJB1-PRKACA protein as source for immunogenic neoepitopes and corresponding T cell receptors and provide efficacy in a single-patient study of T cell-based immunotherapy specifically targeting this oncogenic fusion. In the second chapter we investigate the de-repression of endogenous retroviral element (ERV)-encoded promoters induced by epigenetic therapies, leading to the transcription and subsequent presentation of cryptic treatment-induced neopeptides on HLA molecules. This was achieved by RNA sequencing guided immunopeptidomics from cancer cell lines treated with DNA methyltransferase inhibitor and histone deacetylase inhibitor. We further illustrated the potential of the identified treatment-induced neopeptides to elicit a T-cell response to effectively target cancer cells. Our findings highlight the potential of ERV-derived neoantigens in epigenetic and immune therapies. The third part of this thesis comprehensively studies the effect of epigenetic therapies on the immunopeptidome of primary acute myeloid leukemia (AML) to facilitate the synergistic combination of epigenetic drug treatment with targeted T cell-based immunotherapies. Treatment of AML patient samples with Decitabine alone or in combination with Vorinostat induced DNA hypomethylation, altered gene expression and the transcription of cryptic transcripts as shown by CpG methylation screening combined with deep short- and long-read RNA sequencing. Subsequent mass spectrometry-based immunopeptidomics analysis showed the translation of these treatment-induced changes into the immunopeptidome of AML patients by presentation of treatment-exclusive HLA-presented peptides originating from canonical proteins, cancer-testis antigens, and cryptic antigens. These antigens serve as promising targets for the development of combinatorial immunotherapy approaches for AML patients under epigenetic drug treatment.

Dissertation ist gesperrt bis 9. Dezember 2026 !