Background: Psoriasis is an immune-mediated skin disorder that is inherited as a multifactorial trait. Linkage analyses have clearly mapped a primary disease susceptibility locus to the major histocompatibility complex (MHC) region on chromosome 6p21. More recently, whole-genome association studies have identified two non-MHC disease genes (IL12B and IL23R), both of which also confer susceptibility to Crohn disease (CD).
Objective and methods: To ascertain the genetic overlap between these two inflammatory conditions further, we investigated 15 CD-associated loci in a psoriasis case–control dataset.
Results: The analysis of 1256 patients and 2938 unrelated controls found significant associations for loci mapping to chromosomes 1q24 (rs12035082, p = 0.009), 6p22 (rs6908425, p = 0.00015) and 21q22 (rs2836754, p = 0.0003). Notably, the marker showing the strongest phenotypic effect (rs6908425) maps to CDKAL1, a gene also associated with type 2 diabetes.
Conclusions: These results substantiate emerging evidence for a pleiotropic role for s genes that contribute to the pathogenesis of immune-mediated disorders.
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Psoriasis is a chronic, immune-mediated skin disorder that affects up to 4% of the population.1
Familial recurrence of the disease is well documented, and psoriasis has long been regarded as a multifactorial trait. Linkage studies have repeatedly identified a primary disease susceptibility locus (PSORS1), lying within the major histocompatibility complex (MHC) on chromosome 6p21.2 Several putative non-MHC loci with smaller effects (PSORS2–10) have also been described.3 These regions tend to overlap with genomic intervals conferring susceptibility to other inflammatory conditions, notably Crohn disease (CD).4 5 The observation of an increased incidence of psoriasis among patients with CD6 is consistent with these findings and suggests the existence of genetic determinants predisposing to both inflammatory conditions. We and others have previously shown that CD-associated sequence variants in the IL23R and IL12B genes confer a significant increase in psoriasis risk.7 8 In this study, we investigated the contribution of CD genetic determinants to psoriasis susceptibility. We assessed 15 CD susceptibility loci recently identified by genome-wide association analysis, and identified three novel and significant disease associations with psoriasis.
In total, 1256 patients (645 male and 611 female patients) were recruited within the UK through St John’s Institute of Dermatology, London (n = 638), Glasgow Western Infirmary (n = 211) and the Dermatology Centre, University of Manchester (n = 407). All patients were of north European descent and had early-onset (occurring before 40 years of age) psoriasis vulgaris. Less than 1% of the patients (n = 8) also had CD. These patients were matched with 2938 controls (1488 male, 1450 female patients), previously analysed by the Wellcome Trust Case–Control Consortium (WTCCC).9 All patients and controls gave informed consent for the use of their DNA in genetic epidemiology analyses. The study was approved by the Guy’s and St Thomas’ Hospitals Ethics Committee of Kings College London, the Salford and Trafford Local Research Ethics Committee and North Glasgow University Hospitals NHS Trust Local Research Ethics Committee.
Genotyping and statistical analyses
Patients were typed using TaqMan assays (Applied Biosystems, Foster City, California, USA). Control genotypes were obtained from publicly released data (available at www.wtccc.org.uk/info/summary_stats.shtml). The allele frequencies of cases and controls were compared using a χ2 test with one degree of freedom, after confirming that the genotype distributions did not deviate from Hardy–Weinberg equilibrium (p>0.05). Regression analysis was carried out using PLINK software.10
We examined 15 SNPs that had been associated with CD susceptibility in the WTCCC scan9 and its follow-up study,11 based on the observation of p values <10−5. We did not analyse any single-nucleotide polymorphism (SNP) from the CARD15/NOD2 locus, as we had previously shown that psoriasis is not associated with sequence variants in this gene.12 We also excluded chromosome 6p21 markers from our study, as linkage disequilibrium with PSORS1 alleles would have confounded the interpretation of association signals.
We performed association analyses by comparing the allele frequencies of our patients with those of the WTCCC controls. We applied an assumption that cases could be matched with controls that had been typed on a different platform (the Affymetrix 500 K array set), having shown a 99.7% concordance rate between the WTCCC genotypes and those generated by Taqman assays.11
Following χ2 analysis, we observed significant disease associations for three independent markers rs12035082 (p = 0.009; OR = 1.14; 95% CI 1.03 to 1.25), rs6908425 (p = 0.00015; OR = 1.26; 95% CI 1.12 to 1.42) and rs2836754 (p = 0.0003; OR = 1.17; 95% CI 1.06 to 1.30). We also found an association of marginal significance for SNP rs1000113 (p = 0.045; OR = 1.20; 95% CI 1.00 to 1.45). In order to address the issue of multiple testing, we calculated false discovery rates (FDR)13 for the analysis of 15 SNPs. We found that all three significant associations surpassed the 5% FDR threshold (p⩽0.01), with two (rs6908425 and rs2836754) exceeding 1% FDR (p<0.001).
We next carried out logistic regression analysis, using age and sex as specific covariates. This confirmed that the significance of our association results was not affected by either of these variables.
In order to assess the presence of epistasis between the various disease-associated alleles, we implemented a case-only test for the detection of gene–gene interaction.14 Under the null hypothesis of no interaction, the genotype frequencies of unlinked markers are expected to be independent from each other. We therefore analysed the distribution of patient genotypes by carrying out χ2 tests on standard contingency tables. We observed non-significant χ2 values for all pair-wise comparisons between disease-associated SNPs (rs12035082 v rs6908425; rs12035082 v rs2836754; rs6908425 v rs2836754). We used the same approach to test for interactions with HLA-Cw*0602, the strongest determinant of disease risk from the PSORS1 locus. The p values for the HLA-C v rs6908425 and HLA-C v rs2836754 comparisons were non-significant, but the HLA-C v rs12035082 analysis generated suggestive evidence for an interaction between the two loci (p = 0.02).
The existence of shared genetic determinants between psoriasis and CD is clearly documented, with variants in the IL23R and IL12B genes showing highly significant associations with both diseases.7 8 With this study we have further investigated the role of CD genes in psoriasis pathogenesis, by examining a panel of CD susceptibility loci, recently identified by whole-genome association analysis. In selecting markers for genotyping, we used a conservative level of statistical significance (p<10−5), as several studies have demonstrated the merit of following association signals of this order of magnitude.11 15 16 Our results further validate this approach, as we were able to document associations with psoriasis for three of the examined SNPs.
The possibility that our findings are due to population stratification is unlikely, given that cases and controls have the same ethnic and geographical origin. Moreover, the regional variation data generated by the WTCCC (available at http://www.b58cgene.sgul.ac.uk/) show that the allele frequencies of SNPs rs12035082, rs6908425 and rs2836754 are homogeneous across the UK, ruling out the possibility that the association is due to hidden population structure.
As our study is based on the same set of controls that allowed the identification of CD susceptibility genes in the WTCCC association scan, we cannot formally exclude the possibility that the similarity of findings may reflect a control sampling effect. However, the fact that the population frequencies of SNP rs12035082 and rs2836754 have been validated in another UK sample11 argues against this hypothesis.
Given the multifactorial nature of psoriasis inheritance, we implemented a series of case-only tests to assess the presence of epistasis between disease-associated loci. We found suggestive evidence for an interaction between rs12035082 and HLA-C, a finding that should be interpreted with caution, given its marginal significance (p = 0.02) and the degree of multiple testing inherent in interaction analyses. Validation of such a modest effect will probably require analysis of a substantially larger patient cohort.
All three disease-associated SNPs map to non-coding regions. Rs6908425, which lies within intron 5 of the CDKAL1 transcripts, is the only disease-associated SNP found within a known gene. Although the function of CDKAL1 is unknown, intron 5 variants have been associated with both type 2 diabetes17 and CD,9 suggesting that the gene may play an important role in the pathogenesis of both conditions. Given the high frequency of type 2 diabetes, it is probable that a significant percentage of our psoriatic patients (5–10%) may also exhibit diabetes. Although this is undoubtedly a confounding factor, it is unlikely that the results obtained for SNP rs6908425 simply reflect an association with type 2 diabetes. In fact, our calculations indicate that a sample including up to 20% of this patient cohort would have very limited power (∼15%) to detect an association with type 2 diabetes, at the observed level of significance. An accurate assessment of rs6908425 effect size will eventually require in-depth clinical characterisation of psoriatic cohorts, including metabolic analysis. The remaining disease-associated markers identified in our study map to intergenic regions. SNP rs2836754 lies between the NP_001001692 and C21orf104 anonymous transcripts on chromosome 21q22. SNP rs12035082 lies in a “gene desert” on chromosome 1q24, within a 77-kb linkage disequilibrium (LD) block. Although the LD block does not include any known gene, it encompasses several genomic segments that are highly conserved among mammals and that may regulate the expression of the downstream TNFSF18 gene. As TNFSF18 is a mediator of nuclear factor kappa-b signalling and is a key molecule for the maintenance of immunological self-tolerance,18 it is interesting to speculate that disease-associated alleles may confer susceptibility to psoriasis and CD by altering TNFSF18 expression levels.
In conclusion, we have shown that psoriasis is associated with sequence variants predisposing to type 2 diabetes and CD. These observations provide increased support for the existence of critical, yet pleiotropic loci, conferring susceptibility to clinically distinct disorders. Further genetic and functional analyses will now be required to characterise fully the role of disease-associated variants.
Psoriasis is an inflammatory skin disorder that is inherited as a multifactorial trait. Previous studies have demonstrated that two Crohn disease (CD) susceptibility genes (IL23R and IL12B) are also associated with psoriasis.
To further investigate the overlap between psoriasis and CD susceptibility determinants, we examined 15 CD-associated single-nucleotide polymorphisms (SNPs) in a dataset of1256 psoriatic patients and 2938 controls.
We found that three of the examined SNPs are significantly associated with psoriasis. Of note, the marker showing the strongest phenotypic effect maps to a gene previously associated with type 2 diabetes. These results provide further evidence for the existence of pleiotropic genes predisposing to multiple disorders.
We wish to express our gratitude to the patients and clinicians who have contributed to this study. We also wish to thank S Fisher for her helpful comments and advice.
Funding: The work was supported by a Medical Research Council PhD studentship (NW), a Stiefel Laboratories PhD studentship (RS), a Psoriasis Association PhD studentship (MO) and grants from the Medical Research Council (grant G0601387; RCT, JNB), The Psoriasis Association (JNB, DB, CEMG) and Arthritis Research Campaign (JW). We acknowledge use of genotype data from the British 1958 Birth Cohort DNA collection, funded by the Medical Research Council (grant G0000934) and The Wellcome Trust (grant 068545/Z/02). None of the above sponsors had any involvement in study design and execution, in the writing of the report, or in the decision to submit the paper for publication.
Competing interests: None.