The Immunopeptidomic Landscape of Ependymomas Provides Actionable Antigens for T Cell-Based Immunotherapy

Ependymoma are primary tumors of the nervous system. Due to their growth pattern, many ependymomas can be managed with neurosurgical resection alone. A substantial proportion of these tumors recurs or displays infiltrative growth patterns. Further established therapeutic options include radiation therapy. Systemic treatment options include platinum-based therapeutic regimes or a combination of lapatinib and temozolomide. Peptide-based immunotherapy represents a promising therapeutic strategy relying on the induction of tumor-specific T cells targeting human leukocyte antigens (HLA)-presented peptides. Our work aimed to analyze the landscape of naturally presented HLA class I and II ligands of primary ependymomas (EPN) to delineate EPN-associated antigens.

We investigated 22 EPN tissue samples using a comparative mass spectrometry-based immunopeptidomic approach. Additionally, EPN-specific antigens were functionally characterized in T cell-based immunogenicity assays.

We discovered a subset of EPN-exclusive peptides including HLA-A*02 and HLA-A*25/HLA-A*26–restricted HLA ligands and identified a small panel of cancer/testis antigens (CTAs)-derived HLA ligands. Furthermore, we outlined immunopeptidomic alterations in different ependymoma subgroups and progressive ependymoma. Subsequently, we performed functional characterization of the previously identified HLA-A*02:01 restricted peptide FLDS to demonstrate immunogenicity in vitro.

The immunopeptidome landscape of EPNs provides actionable targets that could further be explored as a T-cell-based immunotherapeutic strategy in this tumor entity.