Chromosome Y-encoded antigens associate with acute graft-versus-host disease in sex-mismatched stem cell transplant

Abstract

Allogeneic hematopoietic stem cell transplantation (allo-HCT) is a curative option for blood cancers, but the coupled effects of graft-versus-tumor and graft-versus-host disease (GVHD) limit its broader application. Outcomes improve with matching at HLAs, but other factors are required to explain residual risk of GVHD. In an effort to identify genetic associations outside the major histocompatibility complex, we conducted a genome-wide clinical outcomes study on 205 acute myeloid leukemia patients and their fully HLA-A-, HLA-B-, HLA-C-, HLA-DRB1-, and HLA-DQB1-matched (10/10) unrelated donors. HLA-DPB1 T-cell epitope permissibility mismatches were observed in less than half (45%) of acute GVHD cases, motivating a broader search for genetic factors affecting clinical outcomes. A novel bioinformatics workflow adapted from neoantigen discovery found no associations between acute GVHD and known, HLA-restricted minor histocompatibility antigens (MiHAs). These results were confirmed with microarray data from an additional 988 samples. On the other hand, Y-chromosome-encoded single-nucleotide polymorphisms in 4 genes (PCDH11Y, USP9Y, UTY, and NLGN4Y) did associate with acute GVHD in male patients with female donors. Males in this category with acute GVHD had more Y-encoded variant peptides per patient with higher predicted HLA-binding affinity than males without GVHD who matched X-paralogous alleles in their female donors. Methods and results described here have an immediate impact for allo-HCT, warranting further development and larger genomic studies where MiHAs are clinically relevant, including cancer immunotherapy, solid organ transplant, and pregnancy.

Graphical abstract

Figure 1.

Measurement of genetic similarity. Frequency distributions of IBD segments normalized by the total lengths of regions of interest for the following: (A) MHC, including HLA-A, HLA-B, HLA-C, HLA-DR, and HLA-DQ; (B) chromosome 6; (C) and the whole genome. Horizontal black bars represent median values. Outliers (green dots) are shown only for panel A (see text for details).

Figure 2.

Autosomal variants do not associate with GVHD. The number of patient-specific missense variants (A) as well as known unrestricted (B) and HLA-restricted (C) MiHAs is comparable in the acute GVHD and non-GVHD groups. (D) Known, HLA-restricted MiHAs ordered by log-odds ratio (acute GVHD to non-GVHD). SNP, single-nucleotide polymorphism.

Figure 3.

Y-chromosome variants associate with acute GVHD. (A) Acute GVHD in sex-matched and sex-mismatched donor–recipient pairs, including a statistically significant association (star) in female-to-male (F>M) allogeneic stem cell transplant. Variants were identified in 4 genes (PCDH11Y, USP9Y, UTY, and NLGN4Y), which are displayed with approximate locations on the Y chromosome (B). Precise genomic coordinates and nucleotide and amino acid positions are tabulated, with variant residues shown in red. In some cases, alternative proteasomal cleavage prediction resulted in multiple peptides. (C-E) HLA-restricted affinity prediction for each color-coded peptide is shown for acute GVHD and non-GVHD patients (C) and summarized (D), with application of the recommended threshold for strong binders per male recipient (E). WT, wild-type.

Figure 4.

Paralogous X-Y mismatching explains acute GVHD risk in male recipients with female donors. (A) Six missense variants on the Y chromosome are exclusive to sex-mismatched male patients with acute GVHD. These variants correspond to 9 variant peptides, which are restricted to 4 genes. Genomic positions for PCDH11Y, USP9Y, UTY, and NLGN4Y are shown with dotted lines to paralogous genes on the X chromosome. Protein coding sequence alignments indicating identity matches (bars) and mismatches (dots) are shown for regions that contain individual variant residues (red) and peptides with high-affinity prediction (bold). Ending amino acid coordinates are given to the right of each sequence alignment. Two male-specific variants are named biallelic polymorphisms rs2524543 and rs2563389 with minor allele frequencies 46% and 45%, respectively (red). Note the predicted cleavage sites (black triangles) created by coding variants in PCDH11Y and USP9Y. *For clarity, other alternative cleavage sites are not shown (see Figure 4 for details), and chromosome X is shown in reverse (3′) orientation. (B) The number of predicted high-affinity binding peptides per patient in male-to-male allogeneic HCT recipients with and without acute GVHD.

Figure 5.

MiHAs contribute to the therapeutic benefits and adverse effects of allo-HCT. In the donor-to-recipient direction, germline-encoded variant peptides (some of which may be presented by recipient HLA molecules) are expressed on both normal and tumor tissue and thus may contribute to GVT or graft-versus-host (GvH) effects. Tumor-specific somatic mutations that encode immunoreactive neoantigens contribute to GVT. In the recipient-to-donor direction, MiHAs may have host-versus-graft (HvG) effects in various clinical contexts leading to rejection in HCT and solid organ transplant (SOT) or miscarriage in pregnancy. Matching of HLAs reduces alloreactive responses from donor or host immune systems in transplantation settings. With cord blood HCT, HLA matching is usually performed at fewer (6) loci. This model does not fully illustrate the genomic and immunological complexities of graft predominance with multiple unit infusion. With haploidentical pairs, GvH effects in the recipient are controlled nongenetically with prophylaxis. Predictable patterns of germline inheritance determine match rates at HLA (4/8) and MiHAs (50%) with consequent effects on GVT. The presence and therapeutic benefit of neoantigens (because they are not heritable) are predicted to be independent of graft source.