A desperate need for novel therapies in pediatric ependymoma (EPN) exists, as chemotherapy remains ineffective and radiotherapy often fails. EPN have significant infiltration of immune cells, which correlates with outcome. Immune checkpoint inhibitors provide an avenue for new treatments. This study characterizes tumor‐infiltrating immune cells in EPN and aims at predicting candidates for clinical trials using checkpoint inhibitors targeting PD‐L1/PD‐1 (programmed death ligand 1/programmed death 1).

The transcriptomic profiles of the primary study cohort of EPN and other pediatric brain tumors were interrogated to identify PD‐L1 expression levels. Transcriptomic findings were validated using the western blotting, immunohistochemistry and flow cytometry.

We evaluated PD‐L1 mRNA expression across four intracranial subtypes of EPN in two independent cohorts and found supratentorial RELA fusion (ST‐RELA) tumors to have significantly higher levels. There was a correlation between high gene expression and protein PD‐L1 levels in ST‐RELA tumors by both the western blot and immunohistochemisty. The investigation of EPN cell populations revealed PD‐L1 was expressed on both tumor and myeloid cells in ST‐RELA. Other subtypes had little PD‐L1 in either tumor or myeloid cell compartments. Lastly, we measured PD‐1 levels on tumor‐infiltrating T cells and found ST‐RELA tumors express PD‐1 in both CD4 and CD8 T cells. A functional T‐cell exhaustion assay found ST‐RELA T cells to be exhausted and unable to secrete IFNγ on stimulation.

These findings in ST‐RELA suggest tumor evasion and immunsuppression due to PD‐L1/PD‐1‐mediated T‐cell exhaustion. Trials of checkpoint inhibitors in EPN should be enriched for ST‐RELA tumors.