Sequence and haplotype analysis supports HLA-C as the psoriasis susceptibility 1 gene

Abstract

Previous studies have narrowed the interval containing PSORS1, the psoriasis-susceptibility locus in the major histocompatibility complex (MHC), to an approximately 300-kb region containing HLA-C and at least 10 other genes. In an effort to identify the PSORS1 gene, we cloned and completely sequenced this region from both chromosomes of five individuals. Two of the sequenced haplotypes were associated with psoriasis (risk), and the other eight were clearly unassociated (nonrisk). Comparison of sequence of the two risk haplotypes identified a 298-kb region of homology, extending from just telomeric of HLA-B to the HCG22 gene, which was flanked by clearly nonhomologous regions. Similar haplotypes cloned from unrelated individuals had nearly identical sequence. Combinatorial analysis of exonic variations in the known genes of the candidate interval revealed that HCG27, PSORS1C3, OTF3, TCF19, HCR, STG, and HCG22 bore no alleles unique to risk haplotypes among the 10 sequenced haplotypes. SPR1 and SEEK1 both had messenger RNA alleles specific to risk haplotypes, but only HLA-C and CDSN yielded protein alleles unique to risk. The risk alleles of HLA-C and CDSN (HLA-Cw6 and CDSN*TTC) were genotyped in 678 families with early-onset psoriasis; 620 of these families were also typed for 34 microsatellite markers spanning the PSORS1 interval. Recombinant haplotypes retaining HLA-Cw6 but lacking CDSN*TTC were significantly associated with psoriasis, whereas recombinants retaining CDSN*TTC but lacking HLA-Cw6 were not associated, despite good statistical power. By grouping recombinants with similar breakpoints, the most telomeric quarter of the 298-kb candidate interval could be excluded with high confidence. These results strongly suggest that HLA-Cw6 is the PSORS1 risk allele that confers susceptibility to early-onset psoriasis.

Figure 1

Delineation of the PSORS1 candidate interval. Known genes are shown below the coordinate axis, and key microsatellite markers are shown above. The candidate interval is depicted as originally defined (59.7-kb RH1 interval14), after its initial expansion on the basis of sequencing the regions immediately flanking RH1 (140-kb PSORS1 interval) and after incorporating results with reassessment of the association of an HLA-Cw8-B65 haplotype with psoriasis (300-kb PSORS1 interval17).

Figure 2

Divergence of sequenced haplotypes from the HLA-Cw6-B57 risk haplotype. Known genes and their direction of transcription are shown below the coordinate axis, and microsatellite markers are shown above. The 298-kb PSORS1 candidate region is also depicted. The weighted percentage difference of polymorphism alleles, when compared with the sequence of the HLA-Cw6-B57 haplotype, is plotted by 2.5-kb intervals for each of the remaining six distinct haplotype clusters that were sequenced. Only those polymorphisms observed among the 10 sequenced haplotypes were considered when computing percentage difference. A plot for the second risk haplotype is shown first, followed by plots for the five nonrisk haplotypes. The bottom panel plots the number of polymorphisms observed among the 10 sequenced haplotypes, for 2.5-kb intervals of the sequenced region. The Cw6-B57 haplotype was derived from two individuals, because the region telomeric of CDSN on the Cw6-B57 chromosome of the person originally selected for cloning is actually derived from a Cw7-B8 haplotype by ancestral recombination.

Figure 3

Locations of polymorphisms unique to risk haplotypes within the PSORS1 candidate region. Polymorphisms with alleles borne by the two sequenced risk haplotypes that differ from the alleles borne by all eight sequenced nonrisk haplotypes are plotted, with circles, to the nearest 5-kb interval. Fill color of the circle indicates whether the polymorphism occurs within a gene exon (red), gene intron (yellow), or intergenic region (green). Known genes and their direction of transcription and the PSORS1 candidate interval are shown below the coordinate axis.

Figure 4

Recombinant haplotypes and test regions used to map the PSORS1 locus. Key genes and their direction of transcription, along with microsatellite markers used in this study, are depicted immediately above the coordinate axis. All founder haplotypes bearing an ancestral recombination between the HLA-Cw6 and CDSN*TTC psoriasis risk alleles are shown above the axis, and those regions tested for exclusion of the PSORS1 locus are shown below the axis. Haplotypes and test regions of the unassociated (see table 12) HLA-Cw6⁻/CDSN*TTC⁺ recombinants are shown in red; those of the associated HLA-Cw6⁺/CDSN*TTC⁻ recombinants are shown in blue. Line segments for the recombinant haplotypes indicate that portion of the extended HLA-Cw6⁺/CDSN*TTC⁺ risk haplotype within the 298-kb PSORS1 candidate region that is retained by the recombinant; to be conservative, the largest possible portion of the extended risk haplotype carried by HLA-Cw6⁺ recombinants and the smallest possible portion of the extended haplotype not carried by HLA-Cw6⁻ recombinants are plotted. The test regions and their bounds are shown in the same order as in table 12. The numbers of founder chromosomes in the pedigree sample are shown for each recombinant haplotype, as are the numbers of qualifying recombinant founder chromosomes for each of the tests for exclusion.

Figure 5

Comparison of the reduced PSORS1 candidate region, established by this study, with two rare haplotypes that are possibly associated with psoriasis. Above the coordinate axis, the I-shaped line segment depicts the boundaries of the 224-kb reduced PSORS1 candidate interval, and unblackened rectangles depict the maximum possible regions of the “double recombinant” HLA-Cw6-B45 (cluster 40) and HLA-Cw7-B58 putative risk haplotypes that are homologous to the ancestral HLA-Cw6-B57 risk haplotype. Known genes and their direction of transcription are depicted below the axis. A summary of the psoriasis-risk status of these two haplotypes, as determined by this study and other studies, is also shown.