Transancestral mapping of the MHC region in systemic lupus erythematosus identifies new independent and interacting loci at MSH5, HLA-DPB1 and HLA-G

Abstract

Objectives: Systemic lupus erythematosus (SLE) is a chronic multisystem genetically complex autoimmune disease characterised by the production of autoantibodies to nuclear and cellular antigens, tissue inflammation and organ damage. Genome-wide association studies have shown that variants within the major histocompatibility complex (MHC) region on chromosome 6 confer the greatest genetic risk for SLE in European and Chinese populations. However, the causal variants remain elusive due to tight linkage disequilibrium across disease-associated MHC haplotypes, the highly polymorphic nature of many MHC genes and the heterogeneity of the SLE phenotype.

Methods: A high-density case-control single nucleotide polymorphism (SNP) study of the MHC region was undertaken in SLE cohorts of Spanish and Filipino ancestry using a custom Illumina chip in order to fine-map association signals in these haplotypically diverse populations. In addition, comparative analyses were performed between these two datasets and a northern European UK SLE cohort. A total of 1433 cases and 1458 matched controls were examined.

Results: Using this transancestral SNP mapping approach, novel independent loci were identified within the MHC region in UK, Spanish and Filipino patients with SLE with some evidence of interaction. These loci include HLA-DPB1, HLA-G and MSH5 which are independent of each other and HLA-DRB1 alleles. Furthermore, the established SLE-associated HLA-DRB1*15 signal was refined to an interval encompassing HLA-DRB1 and HLA-DQA1. Increased frequencies of MHC region risk alleles and haplotypes were found in the Filipino population compared with Europeans, suggesting that the greater disease burden in non-European SLE may be due in part to this phenomenon.

Conclusion: These data highlight the usefulness of mapping disease susceptibility loci using a transancestral approach, particularly in a region as complex as the MHC, and offer a springboard for further fine-mapping, resequencing and transcriptomic analysis.

Figure 1

High-density transancestral single nucleotide polymorphism (SNP) mapping of the major histocompatibility complex (MHC) region in UK, Spanish and Filipino systemic lupus erythematosus (SLE). The panels show MHC region association plots for (A) UK, (B) Spanish and (C) Filipino SLE cohorts where genomic position (Mb) is shown on the horizontal axis with –log₁₀ p values on the vertical axis. The black squares represent genotyped SNPs and the blue squares indicate imputed SNPs in the UK cohort. The red squares represent classically typed HLA alleles in the UK (HLA-DRB1 only) and Spanish (HLA-B, HLA-DRB1 and HLA-DQB1) cohorts. The panels beneath each association plot demonstrate the recombination rate for each cohort calculated using control haplotypes only generated with the program rhomap. A scaled map of the MHC region with relevant genes is shown in the bottom panel. RCCX represents the copy variable RCCX module containing the complement C4 gene (R=RP1/STK19, C=C4A/C4B, C=CYP21A2/CYP21A1P, X=TNXA/TNXB).

Figure 2

Primary and secondary major histocompatibility complex (MHC) region association signals in UK, Spanish and Filipino systemic lupus erythematosus (SLE). This figure shows the primary and secondary association signals in UK, Spanish and Filipino SLE denoted in blue, red and green, respectively. The primary signals are labelled 1 and the secondary signals obtained by stepwise logistic regression are labelled 2–5 and correspond to the single nucleotide polymorphism (SNPs) shown in table 1. An indication of linkage disequilibrium (LD) surrounding each marker (calculated in the control population of each cohort using r² cut-off >0.8) is shown by the bars flanking each marker. LD is <30 kb where flanking bars are absent. The genomic position is shown above the plot together with the positions of the relevant MHC region genes.

Figure 3

Transancestral fine-mapping of the HLA-DRB1*15 signal in UK, Spanish and Filipino systemic lupus erythematosus (SLE). The frequencies of HLA-DRB1*15 alleles show geographical variability. For example, in Europeans the common allele is HLA-DRB1*15:01, in Pacific and South East Asians it is HLA-DRB1*15:02, while in African populations it is HLA-DRB1*15:03 (http://allelefrequencies.net/). It is well established that haplotypes harbouring HLA-DRB1*15 alleles show primary or secondary association with SLE and data from this study support this view. However, the identity of causal variation has remained elusive due to the strong linkage disequilibrium present on the common disease-associated HLA-DRB1*15:01 haplotype in northern Europeans. Using the single nucleotide polymorphism (SNP) rs9271366 as a surrogate marker for the common HLA-DRB1*15 allele in each population studied, we have refined the disease-associated region from 375 kb in northern Europeans to 87 kb in the Filipino population. The latter region encompasses the HLA-DRB1 gene itself as well as part of the intergenic interval between HLA-DRB1 and HLA-DQA1.