Calreticulin mutant myeloproliferative neoplasms induce MHC-I skewing, which can be overcome by an optimized peptide cancer vaccine.

The majority of JAK2-negative myeloproliferative neoplasms (MPNs) have disease-initiating frameshift mutations in calreticulin (), resulting in a common carboxyl-terminal mutant fragment (CALR), representing an attractive source of neoantigens for cancer vaccines. However, studies have shown that CALR-specific T cells are rare in patients with CALR MPN for unknown reasons. We examined class I major histocompatibility complex (MHC-I) allele frequencies in patients with CALR MPN from two independent cohorts. We observed that MHC-I alleles that present CALR neoepitopes with high affinity are underrepresented in patients with CALR MPN. We speculated that this was due to an increased chance of immune-mediated tumor rejection by individuals expressing one of these MHC-I alleles such that the disease never clinically manifested. As a consequence of this MHC-I allele restriction, we reasoned that patients with CALR MPN would not efficiently respond to a CALR fragment cancer vaccine but would when immunized with a modified CALR heteroclitic peptide vaccine approach. We found that heteroclitic CALR peptides specifically designed for the MHC-I alleles of patients with CALR MPN efficiently elicited a CALR cross-reactive CD8 T cell response in human peripheral blood samples but not to the matched weakly immunogenic CALR native peptides. We corroborated this effect in vivo in mice and observed that C57BL/6J mice can mount a CD8 T cell response to the CALR fragment upon immunization with a CALR heteroclitic, but not native, peptide. Together, our data emphasize the therapeutic potential of heteroclitic peptide-based cancer vaccines in patients with CALR MPN.