Patient HLA Germline Variation and Transplant Survivorship

Abstract

Purpose HLA mismatching increases mortality after unrelated donor hematopoietic cell transplantation. The role of the patient's germline variation on survival is not known. Patients and Methods We previously identified 12 single nucleotide polymorphisms within the HLA region as markers of transplantation determinants and tested these in an independent cohort of 1,555 HLA-mismatched unrelated transplants. Linkage disequilibrium mapping across class II identified candidate susceptibility features. The candidate gene was confirmed in an independent cohort of 3,061 patients. Results Patient rs429916AA/AC was associated with increased transplantation-related mortality compared with rs429916CC (hazard ratio [HR], 1.39; 95% CI, 1.12 to 1.73; P = .003); rs429916A positivity was a proxy for DOA*01:01:05. Mortality increased with one (HR, 1.17; 95% CI, 1.0 to 1.36; P = .05) and two (HR, 2.51; 95% CI, 1.41 to 4.45; P = .002) DOA*01:01:05 alleles. HLA-DOA*01:01:05 was a proxy for HLA-DRB1 alleles encoding FEY ( P < 10E^-15) and FDH ( P < 10E^-15) amino acid substitutions at residues 26/28/30 that influence HLA-DRβ peptide repertoire. FEY- and FDH-positive alleles were positively associated with rs429916A ( P < 10E^-15); FDY-positive alleles were negatively associated. Mortality was increased with FEY (HR, 1.66; 95% CI, 1.29 to 2.13; P = .00008) and FDH (HR, 1.40; 95% CI, 1.02 to 1.93; P = .04), whereas FDY was protective (HR, 0.88; 95% CI, 0.78 to 0.98; P = .02). Of the three candidate motifs, FEY was validated as the susceptibility determinant for mortality (HR, 1.29; 95% CI, 1.00 to 1.67; P = .05). Although FEY was found frequently among African and Hispanic Americans, it increased mortality independently of ancestry. Conclusion Patient germline HLA-DRB1 alleles that encode amino acid substitutions that influence the peptide repertoire of HLA-DRβ predispose to increased death after transplantation. Patient germline variation informs transplantation outcomes across US populations and may provide a means to reduce risks for high-risk patients through pretransplantation screening and evaluation.

Fig 1.

Study design. A previous survey of 1,108 single nucleotide polymorphisms (SNPs) within the major histocompatibility complex (MHC) was conducted in 2,628 patients to identify markers that correlate with clinical outcome after transplantation from unrelated donors with one HLA mismatch (cohort 1, first column). Of the 1,108 SNPs, 11 were associated with one clinical end point (acute graft-versus-host disease [grades 2 to 4 or 3 to 4], chronic graft-versus-host disease, relapse, transplantation-related mortality, disease-free survival, or mortality) in one genetic form (patient genotype, donor genotype, or patient-donor mismatch). One of the 12 SNPs was associated with mortality, disease-free survival, and transplantation-related mortality, all in the patient genotype model. In total, the discovery phase identified 14 associations or hypotheses worthy of validation. The current study was designed to identify the true susceptibility gene responsible for clinical outcome. To that end, the same 14 hypotheses were tested in an independent cohort of 1,555 patients who received a transplant from an unrelated donor with one HLA-A, -B, -C, -DRB1, or -DQB1 mismatch for a blood disorder (cohort 2; second column). Each SNP was tested for the original clinical end point and genetic form that was identified in cohort 1. Of the 14 hypotheses tested, patient genotype at rs429916 was validated for transplantation-related mortality. To identify the gene responsible for increased mortality, linkage disequilibrium mapping across 500,000 base pairs of the class II region of the MHC was performed in cohort 1 and 2 patients with residual DNA (third column). HLA-DRB1 was identified as the candidate susceptibility locus, and alleles that encode amino acid substitutions that influence the peptide-binding region of HLA-DRβ were identified as candidate alleles worthy of validation. Risks associated with HLA-DRB1 residues were evaluated in an independent cohort of 3,061 patients who received a transplant from an unrelated donor with one HLA mismatch (cohort 3; fourth column). HLA-DRB1 alleles encoding the FEY motif at residues 26/28/30 of HLA-DRβ were validated as the susceptibility alleles for mortality.

Fig 2.

Linkage disequilibrium (LD) within the HLA class II genetic region. (A) The location of HLA class II genes is shown relative to the rs429916 marker for mortality (indicated by a star). (B) Long-range positive LD exists between rs429916 and variation across the region in both white and African American populations from HapMap Phase II. Data on the left are for 267 white individuals (Utah residents with northern and western European ancestry from the Centre d’Etude du Polymorphism Humain collection [n = 165] and Toscani from Italy [n = 102]). Data on the right include 584 African American individuals (African ancestry from southwestern United States [n = 87]; Maasai from Kinyawa, Kenya [n = 184]; Yoruba from Ibadan, Nigeria [n = 203]; and Luhya from Webuye, Kenya [n = 110]). Class II genes are noted on the LD plots by green bars and represent (1) HLA-DRB1, (2) HLA-DQA1, (3) HLA-DQB1, (4) HLA-DOB, (5) HLA-DMB, (6) HLA-DMA, (7) HLA-DOA (red), (8) HLA-DPA1, and (9) HLA-DPB1. (C) LD within the HLA-DOA genetic region is illustrated for white individuals on the left and African American individuals on the right. Specific LD measurements (D′) are provided in the Data Supplement.

Fig 3.

Effect of amino acid variation at residues 26/28/30 on the HLA-DRβ peptide-binding groove. Positions 26/28/30 HLA-DRβ form the constituent residues that influence the P7 position of peptides accommodated by the HLA-DR binding groove and to a lesser extent the P5 position. (A) Illustration of the crystal structure complex between HLA-DM (dark green and dark blue) and HLA-DR1 (light green and light blue).^, The α-carbon positions of key residues evaluated in the study are represented by yellow spheres and numbered by sequence position. The side-chains of these residues all point inward toward the bound peptide in the groove and do not mediate direct interactions with HLA-DM, T-cell receptor, CD4, or any other cognate receptor/coreceptor. (B) The crystal structure of HLA-DR1 is shown in a molecular surface representation (gray) that highlights the peptide-binding groove.^, The bound peptide (residues 102 to 120 of CLIP, with a methionine-to-tryptophan mutation at residue 107) is shown in a licorice-stick representation colored by atom type. This view is the perspective from an incoming T-cell receptor. Contributions to the molecular surface from side-chains from residues at positions 26/28/30 are shown in yellow. The multivariable models that demonstrate risks of mortality associated with substitutions at residues 26/28/30 are presented in Table 2. Residues are numbered according to the IPD-IMGT/HLA Database.