Shared graft-versus-leukemia minor histocompatibility antigens in DISCOVeRY-BMT

Abstract

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 alloHCT efficacy, but are limited by concurrent increases in 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 the discovery of a large set of novel GvL mHAs based on predicted immunogenicity, tissue expression, and degree of sharing among donor-recipient pairs (DRPs) in the DISCOVeRY-BMT dataset of 3231 alloHCT DRPs. Total number of predicted mHAs varied by HLA allele, and total number and number of each class of mHA significantly differed by recipient genomic ancestry group. 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 used mass spectrometry to search for high population frequency mHAs for three common HLA alleles. We validated 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 confirmed immunogenicity of an example novel mHA via T cell coculture with peptide-pulsed dendritic cells. This work demonstrates that identification of shared mHAs is a feasible and promising technique for expanding mHA-targeting immunotherapeutics.

Expanding the repertoire reveals recurrent, cryptic, and hematopoietic HLA class I minor histocompatibility antigens

“…Typically, only nonsynonymous variants leading to AA changes in normal reading frames are included. 69 , 70 , 71 , 72 , 73 To enable identification of cryptic antigens, reference databases need to be enlarged by alternative and long noncoding transcripts and translation of transcripts in all ORFs, 65 , 74 , 75 , 76 , 77 , 78 , 79 which may generate false positives in immunopeptidomics. 80 Despite this limitation, reverse strategies estimated that up to 7.5% of HLA-I–associated peptides are noncanonical peptides.…”

“…Reverse proteogenomic approaches were also used to search for hematopoietic-restricted MiHAs. 71 , 81 Polymorphic HLA-binding peptides were identified by immunopeptidomics and hematopoietic candidates characterized by bulk RNA sequencing analysis. Granados et al 81 excluded genes with ubiquitous expression >10 fragments per kilobase million (FPKM) in 27 tissues in the HPA and identified 39 hematopoietic candidates in HLA-A∗02:01 and B∗44:03 with more than or equal to twofold higher expression in bone marrow relative to skin and >1 reads per kilobase million (RPKM) in acute myeloid leukemia in the Cancer Genome Atlas.…”

“…Granados et al 81 excluded genes with ubiquitous expression >10 fragments per kilobase million (FPKM) in 27 tissues in the HPA and identified 39 hematopoietic candidates in HLA-A∗02:01 and B∗44:03 with more than or equal to twofold higher expression in bone marrow relative to skin and >1 reads per kilobase million (RPKM) in acute myeloid leukemia in the Cancer Genome Atlas. Olsen et al 71 proposed 24 candidates in HLA-A∗02:01, B∗35:01 and C∗07:02 encoded by genes with expression >50 transcripts per million in acute myeloid leukemia in the Cancer Genome Atlas and <50 transcripts per million in nonhematopoietic tissues in the Genotype-Tissue Expression Project. All MiHAs identified by our forward approach were evaluated in a stringent analysis of more than or equal to fivefold higher expression in hematopoietic vs nonhematopoietic cells in 2 independent data sets of single-cell RNA sequencing (HPA) and lab-own microarray data.…”