Dissecting the genetic complexity of the association between human leukocyte antigens and rheumatoid arthritis

Abstract

Rheumatoid arthritis (RA) is an inflammatory disease with a complex genetic component. An association between RA and the human leukocyte antigen (HLA) complex has long been observed in many different populations, and most studies have focused on a direct role for the HLA-DRB1 "shared epitope" in disease susceptibility. We have performed an extensive haplotype analysis, using 54 markers distributed across the entire HLA complex, in a set of 469 multicase families with RA. The results show that, in addition to associations with the DRB1 alleles, at least two additional genetic effects are present within the major histocompatibility complex. One of these lies within a 497-kb region in the central portion of the HLA complex, an interval that excludes DRB1. This genetic risk factor is present on a segment of a highly conserved ancestral A1-B8-DRB1*03 (8.1) haplotype. Additional risk genes may also be present in the HLA class I region in a subset of DRB1*0404 haplotypes. These data emphasize the importance of defining haplotypes when trying to understand the HLA associations with disease, and they clearly demonstrate that such associations with RA are complex and cannot be completely explained by the DRB1 locus.

Figure 1

Results of the single-marker PDT analysis. The −log₁₀ of the P value obtained from the global PDT (Y-axis) is plotted against the order in which the markers are arranged across the HLA complex (X-axis). In addition to DRB1, four markers within the class III region show a significant association (P<.005) with RA. The association with marker D6S2656 (allele 8), just centromeric to DRB1, reflects strong linkage disequilibrium with DRB1*04 alleles. However, as discussed in the text, the marker associations at TNFb (allele 3), TNFa (allele 2), TNFd (allele 3), and D6S2669 (allele 9) reflect an association with a portion of the ancestral A1-B8-DRB1*03 (8.1) haplotype. See table A to correlate marker numbers with marker names and actual position (fig. A).

Figure 2

A three-marker “moving window” used to assess the similarity of transmitted (solid line; with dots in panels A and C) and untransmitted (dashed line) haplotypes to the ancestral 8.1 haplotype consensus sequence. The frequency of three-marker windows matching the “consensus” 8.1 haplotype sequence (Y-axis) is plotted against marker positions (X-axis). Marker positions and corresponding marker names are listed in table A. The sample sizes for the transmitted (T) and untransmitted (U) haplotypes are also shown. A, When all haplotypes have DRB1*0301, the transmitted haplotypes are more similar to the consensus sequence than are the untransmitted haplotypes. B, The same pattern is observed for DRB1*01, *15/*16, and *0401 but not for *0404. C, The combined data from all non-DRB1*0301 haplotypes are summarized (top panel) (details shown in figure B). It also shows that the transmitted haplotypes are significantly different (P<.05) (bottom panel) from the untransmitted ones in the interval between D6S2678 and MN6S2021.

Figure 3

Normalized entropy plots for the transmitted (solid line) and untransmitted (dashed line) haplotypes in the DRB1*01 and *0404 haplotype groups. (For marker names, see table A.) The ΔE value given for each plot reflects the difference in diversity between untransmitted and transmitted haplotypes. DRB1*01 haplotypes do not display a large difference in diversity between transmitted and untransmitted haplotypes. By contrast, for the DRB1*0404 haplotypes, ΔE is strongly positive, and this reflects the much lower diversity (lower E value) among transmitted haplotypes compared to the untransmitted haplotypes. As discussed in the text and shown in figure 3, the lower diversity among DRB1*0404 transmitted haplotypes cannot be explained by the presence of sequences derived from the 8.1 conserved haplotype. E values for other haplotype groups appear in figure C.

Figure A

Physical locations of all 53 microsatellite markers and the HLA-DRB1 locus analyzed in the present study. This physical map of the HLA complex is based on the current consensus 3,673,778-bp sequence available from the Sanger Institute. The positions of markers indicate the centromeric end of the amplimer, and the positions of genes indicate the translation start codon.

Figure B

Frequency of three-marker windows from different HLA-DRB1 groups matching the “consensus” 8.1 haplotype sequence (Y-axis) plotted against marker positions (X-axis). For most DRB1 groups, except for DRB1*0404, the transmitted haplotypes (solid line) are more similar to the consensus 8.1 haplotype sequence than are the untransmitted haplotypes (dashed line). Sample sizes for transmitted (T) and untransmitted (U) haplotypes are also shown. Plots for the DRB1*08, *09, and *10 groups were not included, because of the small sample sizes among transmitted and untransmitted haplotypes.

Figure C

Normalized entropy plots for the transmitted (solid line) and untransmitted (dashed line) DRB1 haplotype groups. The difference in entropy (ΔE) between the transmitted and untransmitted haplotypes is shown for each group. The highest ΔE is observed for DRB1*0404. Sample sizes for the DRB1*08, *09, and *10 groups were very small, and the corresponding plots were not included.