Identification of Two Independent Risk Factors for Lupus within the MHC in United Kingdom Families

Abstract

The association of the major histocompatibility complex (MHC) with SLE is well established yet the causal variants arising from this region remain to be identified, largely due to inadequate study design and the strong linkage disequilibrium demonstrated by genes across this locus. The majority of studies thus far have identified strong association with classical class II alleles, in particular HLA-DRB1*0301 and HLA-DRB1*1501. Additional associations have been reported with class III alleles; specifically, complement C4 null alleles and a tumor necrosis factor promoter SNP (TNF-308G/A). However, the relative effects of these class II and class III variants have not been determined. We have thus used a family-based approach to map association signals across the MHC class II and class III regions in a cohort of 314 complete United Kingdom Caucasian SLE trios by typing tagging SNPs together with classical typing of the HLA-DRB1 locus. Using TDT and conditional regression analyses, we have demonstrated the presence of two distinct and independent association signals in SLE: HLA-DRB1*0301 (nominal p = 4.9 × 10−8, permuted p < 0.0001, OR = 2.3) and the T allele of SNP rs419788 (nominal p = 4.3 × 10−8, permuted p < 0.0001, OR = 2.0) in intron 6 of the class III region gene SKIV2L. Assessment of genotypic risk demonstrates a likely dominant model of inheritance for HLA-DRB1*0301, while rs419788-T confers susceptibility in an additive manner. Furthermore, by comparing transmitted and untransmitted parental chromosomes, we have delimited our class II signal to a 180 kb region encompassing the alleles HLA-DRB1*0301-HLA-DQA1*0501-HLA-DQB1*0201 alone. Our class III signal importantly excludes independent association at the TNF promoter polymorphism, TNF-308G/A, in our SLE cohort and provides a potentially novel locus for future genetic and functional studies.

The HLA-DRβ1 amino acid positions 11–13–26 explain the majority of SLE–MHC associations

“…We observed some suggestive associations near HLA-B and -C and non-HLA genes (PZ1.37 Â 10 À 6 ) after conditioning on all HLA-DRB1 signals. This observation could be consistent with other fine-mapping studies that showed evidence of multiple independent associations in the MHC region [6][7][8][9] . Therefore, in the future, it is important to expand the same finemapping study on HLA alleles, HLA amino acids and SNPs with a larger sample size and multiple ancestral samples.…”

“…Several studies have attempted to dissect the SLE association within the extended MHC locus characterized by a high degree of linkage disequilibrium (LD) and genetic diversity [6][7][8][9][10] . Multiple HLA alleles and non-HLA variants in MHC locus have been suggested to have independent SLE-risk effects, as demonstrated by stepwise conditional analysis or HLA allele-allele haplotype analysis to control for the LD effect [6][7][8][9] .…”

“…Multiple HLA alleles and non-HLA variants in MHC locus have been suggested to have independent SLE-risk effects, as demonstrated by stepwise conditional analysis or HLA allele-allele haplotype analysis to control for the LD effect [6][7][8][9] . However, there were inconsistent observations among the studies in terms of the number and position of independent SLE-risk loci.…”

Mapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases

“…The particularly strong LD across these haplotypes has confounded attempts to identify clearly additional independent signals, such as those previously reported for complement C4-null alleles, as well as TNF and SKIV2L variants, all encoded within the class III region (19,32,33). The influence of copy number variation at the complement C4/RCCX locus in relation to the association signals demonstrated in this study remains to be established.…”

“…1 and Table S4). The analysis detected further associations in class III; hence there seem to be at least 3 separate signals in this region tagged by the SKIV2L gene, rs1269852, and NOTCH4 (19). Together, these data indicate the presence of multiple SLE risk alleles located across the class I, class II, and class III regions.…”