Apparent Lack of Derived HLA Class I Presented Neoantigens Hampers Neoplastic Cell Targeting by CD8 T Cells in Langerhans Cell Histiocytosis.

Langerhans Cell Histiocytosis (LCH) is a neoplastic disorder of hematopoietic origin characterized by inflammatory lesions containing clonal histiocytes (LCH-cells) intermixed with various immune cells, including T cells. In 50-60% of LCH-patients, the somatic driver mutation, which is common in many cancers, is detected in these LCH-cells in an otherwise quiet genomic landscape. Non-synonymous mutations like can be a source of neoantigens capable of eliciting effective antitumor CD8 T cell responses. This requires neopeptides to be stably presented by Human Leukocyte Antigen (HLA) class I molecules and sufficient numbers of CD8 T cells at tumor sites. Here, we demonstrate substantial heterogeneity in CD8 T cell density in = 101 LCH-lesions, with mutated lesions displaying significantly lower CD8 T cell:CD1a LCH-cell ratios ( = 0.01) than wildtype lesions. Because LCH-lesional CD8 T cell density had no significant impact on event-free survival, we investigated whether the intracellularly expressed protein is degraded into neopeptides that are naturally processed and presented by cell surface HLA class I molecules. Epitope prediction tools revealed a single HLA class I binding derived neopeptide (KIGDFGLATK), which indeed displayed strong to intermediate binding capacity to HLA-A03:01 and HLA-A11:01 in an peptide-HLA binding assay. Mass spectrometry-based targeted peptidomics was used to investigate the presence of this neopeptide in HLA class I presented peptides isolated from several expressing cell lines with various HLA genotypes. While the HLA-A02:01 binding wildtype peptide KIGDFGLATV was traced in peptides isolated from all five cell lines expressing this HLA subtype, KIGDFGLATK was not detected in the HLA class I peptidomes of two distinct transduced cell lines with confirmed expression of HLA-A03:01 or HLA-A11:01. These data indicate that the predicted HLA class I binding and proteasome-generated neopeptides derived from the protein are not presented by HLA class I molecules. Given that the mutation is highly prevalent in chemotherapy refractory LCH-patients who may qualify for immunotherapy, this study therefore questions the efficacy of immune checkpoint inhibitor therapy in LCH.