Shared Graft Versus Leukemia Minor Histocompatibility Antigens in DISCOVeRY-BMT

T cell responses to minor histocompatibility antigens (mHAs) mediate graft versus leukemia (GvL) effects and graft versus host disease (GvHD) in allogeneic hematopoietic cell transplant (alloHCT). Therapies that boost T cell responses improve the efficacy of alloHCT; however, these have been limited by concurrent increases in the incidence and severity of GvHD. mHAs with expression restricted to hematopoietic tissue (GvL mHAs) are attractive targets for driving GvL without causing GvHD. Prior work to identify mHAs has focused on a small set of mHAs or population-level SNP association studies. We report here the discovery of a large set of novel GvL mHAs based on predicted peptide immunogenicity, restriction of expression to hematopoietic tissue or GvHD target organs, and degree of sharing among donor-recipient pairs (DRPs) in the DISCOVeRY-BMT dataset of 3231 alloHCT DRPs. The total number of predicted mHAs and count within each class of predicted mHAs significantly differed by recipient genomic ancestry group, with European American>Hispanic>African American for each. The number of mHAs also differed markedly by HLA allele, even among alleles of the same gene. From the pool of predicted mHAs, we identified the smallest sets of GvL mHAs needed to cover 100% of DRPs with a given HLA allele. We then used mass spectrometry to search for high population frequency mHAs for three common HLA alleles. We validated a total of 24 novel predicted GvL mHAs that cumulatively are found within 98.8%, 60.7%, and 78.9% of DRPs within DISCOVeRY-BMT that express HLA-A*02:01, HLA-B*35:01, and HLA-C*07:02 respectively. We also confirmed in vivo immunogenicity of one example novel mHA via coculture of healthy human CD8 T cells with mHA-pulsed dendritic cells. This work demonstrates that identification of shared mHAs is a feasible and promising technique for expanding mHA-targeting immunotherapeutics to larger numbers of patients.