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

The majority of JAK2 ^V617F -negative myeloproliferative neoplasms (MPNs) have disease-initiating frameshift mutations in calreticulin ( CALR ), resulting in a common carboxyl-terminal mutant fragment (CALR ^MUT ), representing an attractive source of neoantigens for cancer vaccines. However, studies have shown that CALR ^MUT -specific T cells are rare in patients with CALR ^MUT MPN for unknown reasons. We examined class I major histocompatibility complex (MHC-I) allele frequencies in patients with CALR ^MUT MPN from two independent cohorts. We observed that MHC-I alleles that present CALR ^MUT neoepitopes with high affinity are underrepresented in patients with CALR ^MUT 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 ^MUT MPN would not efficiently respond to a CALR ^MUT fragment cancer vaccine but would when immunized with a modified CALR ^MUT heteroclitic peptide vaccine approach. We found that heteroclitic CALR ^MUT peptides specifically designed for the MHC-I alleles of patients with CALR ^MUT MPN efficiently elicited a CALR ^MUT cross-reactive CD8 ⁺ T cell response in human peripheral blood samples but not to the matched weakly immunogenic CALR ^MUT 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 ^MUT fragment upon immunization with a CALR ^MUT heteroclitic, but not native, peptide. Together, our data emphasize the therapeutic potential of heteroclitic peptide-based cancer vaccines in patients with CALR ^MUT MPN.