HapMap scanning of novel human minor histocompatibility antigens

Abstract

Minorhistocompatibility antigens (mHags) are molecular targets of alloimmunity associated with hematopoietic stem cell transplantation (HSCT) and involved in graft-versus-host disease, but they also have beneficial antitumor activity. mHags are typically defined by host SNPs that are not shared by the donor and are immunologically recognized by cytotoxic T cells isolated from post-HSCT patients. However, the number of molecularly identified mHags is still too small to allow prospective studies of their clinical importance in transplantation medicine, mostly due to the lack of an efficient method for isolation. Here we show that when combined with conventional immunologic assays, the large data set from the International HapMap Project can be directly used for genetic mapping of novel mHags. Based on the immunologically determined mHag status in HapMap panels, a target mHag locus can be uniquely mapped through whole genome association scanning taking advantage of the unprecedented resolution and power obtained with more than 3 000 000 markers. The feasibility of our approach could be supported by extensive simulations and further confirmed by actually isolating 2 novel mHags as well as 1 previously identified example. The HapMap data set represents an invaluable resource for investigating human variation, with obvious applications in genetic mapping of clinically relevant human traits. (Blood. 2009;113:5041-5048) IntroductionThe antitumor activity of allogeneic hematopoietic stem cell transplantation (HSCT), which is a curative treatment for many patients with hematologic malignancies, is mediated in part by immune responses that are elicited as a consequence of incompatibility in genetic polymorphisms between the donor and the recipient. 1,2 Analysis of patients treated for posttransplantation relapse with donor lymphocytes has shown tumor regression to be correlated with expansion of cytotoxic T lymphocytes (CTLs) specific for hematopoiesis-restricted minor histocompatibility antigens (mHags). 3,4 mHags are peptides, presented by major histocompatibility complex (MHC) molecules, derived from intracellular proteins that differ between donor and recipient due mostly to single nucleotide polymorphisms (SNPs) or copy number variations (CNVs). 1,2,5 Identification and characterization of mHags that are specifically expressed in hematopoietic but not in other normal tissues could contribute to graft-versus-leukemia/lymphoma (GVL) effects, while minimizing unfavorable graft-versus-host disease, one of the most serious complications of allo-HSCT. 1,2 Unfortunately, however, efforts to prospectively target mHags to invoke T cell-mediated selective GVL effects have been hampered by the scarcity of eligible mHags, largely due to the lack of efficient methods for mapping the relevant genetic loci. Several methods have been developed to identify mHags, including peptide elution from MHC, 6,7 cDNA expression cloning, 8,9 and linkage analysis. 3,10 We have recently reported a novel genetic method that combines whole genome as...

Isolation of Human CD4/CD8 Double-Positive, Graft-Versus-Host Disease–Protective, Minor Histocompatibility Antigen–Specific Regulatory T Cells and of a Novel HLA-DR7–Restricted HY-Specific CD4 Clone

“…Several HLA class I-restricted minor H Ags have been identified in humans by screening of plasmid cDNA libraries, elution of HLA-bound peptides, and genetic linkage analysis (13)(14)(15)(16). Recently, a novel strategy using whole-genome association scanning reported characterization of 10 new HLA class I-restricted minor H Ags (17).…”

Minor histocompatibility Ags: identification strategies, clinical results and translational perspectives

“…The genetic polymorphism information required for these analyses was frequently derived from the HapMap project including 44 × 10 6 SNP genotypes for different ethnical populations. 21 Making use of the fact that several of the CEPH family members were included as trios (father-mother-child) in the databases of the HapMap Project, we developed a powerful and convenient genome-wide association study (GWAS). Based on the Mendelian inheritance pattern of mHags, we could determine the mHag zygosities for many individuals from their mHag phenotypes.…”

“…Using this extra information in the GWAS analyses, we could rapidly identify the mHags CD19 L , SLC19A1 R and UTA2-1 L . 6,[21][22][23] IMPLEMENTING THE 1000 GENOMES PROJECT IN mHAG IDENTIFICATION STRATEGIES Although efficient and often successful, the above-described genetic correlation strategies were still unable to identify the target Ag of a number of mHag-specific T-cell clones, probably because of the limited number of genetic variations represented in the genetic databases. Therefore, we recently further improved the genetic correlation analyses by the implementation of the 1000 Genomes Project.…”

Genomic studies of GVHD—lessons learned thus far

“…To demonstrate the applicability of GWAS for GVHD, Ogawa et al 49 measured the SNP-by-SNP donor --recipient disparity in a cohort of 1598 HLA-A, B, C, DRB1 and DQB1 matched unrelated donor --recipient pairs. A number of these pairs were unmatched at HLA-DPB1, and the study successfully associated SNPs around this locus with aGVHD.…”