Genome-wide Association Study Identifies HLA-DPB1 as a Significant Risk Factor for Severe Aplastic Anemia

Abstract

Severe aplastic anemia (SAA) is a rare disorder characterized by hypoplastic bone marrow and progressive pancytopenia. The etiology of acquired SAA is not understood but is likely related to abnormal immune responses and environmental exposures. We conducted a genome-wide association study of individuals with SAA genetically matched to healthy controls in discovery (359 cases, 1,396 controls) and validation sets (175 cases, 1,059 controls). Combined analyses identified linked SNPs in distinct blocks within the major histocompatibility complex on 6p21. The top SNP encodes p.Met76Val in the P4 binding pocket of the HLA class II gene HLA-DPB1 (rs1042151A>G, odds ratio [OR] 1.75, 95% confidence interval [CI] 1.50-2.03, p = 1.94 × 10^-13) and was associated with HLA-DP cell surface expression in healthy individuals (p = 2.04 × 10^-6). Phylogenetic analyses indicate that Val76 is not monophyletic and likely occurs in conjunction with different HLA-DP binding groove conformations. Imputation of HLA-DPB1 alleles revealed increased risk of SAA associated with Val76-encoding alleles DPB1^∗03:01, (OR 1.66, p = 1.52 × 10^-7), DPB1^∗10:01 (OR 2.12, p = 0.0003), and DPB1^∗01:01 (OR 1.60, p = 0.0008). A second SNP near HLA-B, rs28367832G>A, reached genome-wide significance (OR 1.49, 95% CI 1.22-1.78, p = 7.27 × 10^-9) in combined analyses; the association remained significant after excluding cases with clonal copy-neutral loss-of-heterozygosity affecting class I HLA genes (8.6% of cases and 0% of controls). SNPs in the HLA class II gene HLA-DPB1 and possibly class I (HLA-B) are associated with SAA. The replacement of Met76 to Val76 in certain HLA-DPB1 alleles might influence risk of SAA through mechanisms involving DP peptide binding specificity, expression, and/or other factors affecting DP function.

Keywords: GWAS; HLA; HLA-DP; aplastic anemia; bone marrow failure; etiology; genome-wide association study; hematpoietic cell transplantation.

Figure 1

Genomic Locations of Single-Nucleotide Polymorphims Associated with Severe Aplastic Anemia (A) Manhattan plot of genome-wide association result for combined discovery and validation sets of European ancestry severe aplastic anemia cases and genomically matched controls. (B) A portion of the Manhattan plot of the major histocompatibility complex (MHC) genomic region showing locations of SNPs in human leukocyte antigen (HLA) genes by HLA class. (C) Schematic of HLA-DPB1 with SNPs of interest noted.

Figure 2

Cell Surface Expression of HLA-DP is Associated with rs1042151 Genotype The cell surface expression levels of specific HLA alleles were determined in healthy individuals and plotted based on their rs1042151 genotype (see Online Methods).

Figure 3

Phylogenic Tree of Coding Regions of HLA-DPB1 The HLA-DBP1 alleles are color coded according to the amino acid at residue 76 as follows: red, methionine, M; black, isoleucine, I; green, valine, V. The neighbor-joining tree is based on Kimura’s 2-parameter distances for the entire 777 base pair coding region.