Two missense variants in UHRF1BP1 are independently associated with systemic lupus erythematosus in Hong Kong Chinese

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Abstract

UHRF1BP1 encodes a highly conserved protein with unknown function. Previously, a coding variant in this gene was found to be associated with systemic lupus erythematosus (SLE) in populations of European ancestry (rs11755393, R454Q, P=2.22 × 10−8, odds ratio=1.17). In this study, by a combination of genome-wide study and replication involving a total of 1230 patients and 3144 controls, we confirmed the association of this coding variant to SLE in Hong Kong Chinese. We also identified another coding variant in this gene that independently contributes to SLE susceptibility (rs13205210, M1098T, P=4.44 × 10−9, odds ratio=1.49). Cross-population confirmation establishes the involvement of this locus in SLE and indicates that distinct alleles are contributing to disease susceptibility.

Main

Systemic lupus erythematosus (SLE) is a complex and potentially fatal disease characterised by production of a wide-spectrum of autoantibodies and multi-system damage. Genetic factors are highly involved in this disease, as evidenced by a sibling recurrence risk ratio at around 20–40, and much higher concordance rate for monozygotic twins compared with dizygotic twins.1, 2, 3 There is also marked differences in genetic susceptibility and disease epidemiology across different populations. African Americans, Hispanics and Asians, all have higher disease prevalence than Caucasians, and lupus nephritis is also more prevalent in Chinese than in European populations.4, 5

Genome-wide association studies (GWAS) have unveiled a number of novel susceptibility variants associated with SLE.6, 7, 8, 9, 10 So far, the majority of these genetic variants identified have been confirmed in multiple populations. For example, the associations of STAT4, TNFSF4, BANK1, TNFAIP3, IRF5 and BLK with SLE were all confirmed in Hong Kong and Thai populations.11, 12, 13, 14 Meanwhile, population differences were also observed. For instance, although Asian populations share the same risk alleles of the ITGAM gene, these alleles are rare (<2%) compared with those in Caucasians.13 PXK is a susceptibility gene reported in Caucasians,9 but did not show association with SLE in Asian populations.12, 15

Gateva et al.7 recently reported that a non-synonymous allele (R454Q) in the UHRF1BP1 gene confers SLE risk in populations of European ancestry. In the current study, by a combination of genome-wide study and subsequent replication, we provide evidence on the involvement of rs11755393 (R454Q) in disease association in an Asian population, and also report an independently contributing allele from single-nucleotide polymorphism (SNP) rs13205210, another non-synonymous polymorphism in this gene (M1098T), to SLE susceptibility.

A total of 1230 Hong Kong SLE patients were recruited from four hospitals in Hong Kong: Queen Mary Hospital, Tuen Mun Hospital, Queen Elizabeth Hospital and Pamela Youde Nethersole Eastern Hospital. The patients were all self-reported Chinese living in Hong Kong. All the patients were diagnosed according to the criteria of the American College of Rheumatology. Of all the SLE patients, 620 were selected for genotyping in the GWAS stage, carried out by Illumina (San Diego, CA, USA) Human 610-Quad Beadchip. For the 2193 controls in the GWAS stage, the data were obtained from other studies in the same institution, which were genotyped on the same platform as the SLE cases. This study was approved by the Institutional Review Board of the University of Hong Kong and Hospital Authority, Hong Kong West Cluster, New Territory West Cluster and Hong Kong East Cluster. All patients gave informed written consent for this study.

Quality control of the GWAS data was performed using PLINK.16 Briefly, individuals with low call rate and hidden first-degree relationship were removed from further analysis. Overall, 104 395 SNPs were also excluded from further analysis because of low call rate, low minor allele frequency or violation of Hardy–Weinberg equilibrium in controls. A genome-wide inflation factor of 1.03 was observed, indicating good matching between the cases and controls, in terms of population substructure. Population stratification was also examined by Eigenstrat, which showed a good match between the Hong Kong cases and controls.10, 17 After quality control, 612 cases, 2193 controls and 516 071 SNPs remained, and were analysed by PLINK.16

We extracted the SNPs in and around (±100 kb) UHRF1BP1 gene from our genome-wide association study. Eight SNPs showed promising P-values, and the results on allelic association and association by the dominant model are shown in Table 1.

Table 1 SNPs in and around UHRF1BP1 that showed significant association in GWAS

Overall, 618 remaining cases from the Hong Kong SLE cohort not used in GWAS were used in the replication stage. The controls in the replication stage were recruited from blood donors from Hong Kong Red Cross. The 610-Quad Beadchip used in GWAS does not cover SNP rs11755393, the SNP reported in the study of Gateva et al. To compare the effect of this SNP with the ones we identified in our GWAS, we included this SNP in our replication stage and genotyped all the cases (N=1230) using TaqMan assay. Owing to the high-linkage disequilibrium (LD) among the SNPs listed in Table 1 (r2=1 in HapMap-CHB, r2>0.8 in GWAS data, Figure 1), we only chose rs13205210 for further replication, mainly because of its coding changing nature. Both SNPs, rs13205210 and rs11755393, were genotyped by TaqMan SNP Genotyping Assay (Applied Biosystems, Foster City, CA, USA). Analysis of disease association was again performed using PLINK.16 In Table 2, we present results on the joint analysis of GWAS data and data from the replication stage, or data from only the replication stage in the case of rs11755393. Interestingly, the G allele of rs11755393 is also the risk allele in our population but is the major allele instead. SNP rs13205210 demonstrated relatively high effect size (odds ratio=1.49, 95% confidence interval: 1.30–1.70) among the susceptibility alleles identified so far for SLE. We note that a better P-value was achieved under a dominant model than when allelic test was applied for this SNP, suggesting potentially a gain of function for this coding variant. For rs13205210, 43 samples were genotyped by both GWAS and TaqMan assay, and 100% concordance was recorded between these two platforms.

Figure 1
figure1

Linkage disequlibrium among significant SNPs in GWAS and sequence conservation of the two nonsynonymous variants among different species: (a) Linkage disequlibrium among SNPs showed significant disease association in GWAS stage and their relative position to UHRF1BP1; (b) Protein sequence conservation among different species for the region around Q454R coded by rs11755393; (c) Protein sequence conservation among different species for the region around M1098T coded by SNP rs13205210.

Table 2 Joint analyses on disease association of GWAS and replication data

To better define the relative contributions of both SNPs in UHRF1BP1, conditional logistic regression and haplotype-based association tests were performed. In the conditional logistic regression test, the effects from both rs13205210 and rs11755393 were shown to be independent (for rs13205210, P =0.021 when controlling for the effect from rs11755393; and for rs11755393, P=0.0082 when controlling for the effect from rs13205210). This is consistent with the fact that the two variants have very moderate LD, with r2=0.17 according to TaqMan data, through which both SNPs were genotyped on the same samples. Haplotype analysis supports the independent contribution from both SNPs. It shows that the GC haplotype, formed by the two SNPs (rs11755393–rs13205210), is the major risk haplotype, whereas AT is the major protective haplotype (Supplementary Table 1). Analysis was also performed for these two SNPs between patients who are positive on a certain manifestation and those we are negative, and no statistically significant difference was detected.

The function of UHRF1BP1 is unknown, except that it is a putative binding protein of UHRF1, a RING-finger type E3 ubiquitin ligase that is known to be involved in histone deacetylaion and gene expression regulation.18 Despite its unknown function, the sequence of this protein is highly conserved through evolution; the human protein has a 91% sequence identity to that of horse, and 82 and 83% similarity to those in rat and mouse, respectively, and 75 and 61% to those in opossum and chicken, respectively. For Q454R encoded by rs11755393, the position is not well conserved through evolution and neither are its surrounding amino acid residues. On the other hand, for M1098T coded by rs13205210, the position is well conserved among most species from birds to mammals (Figure 1). Although two frame-shift mutations were recorded in dbSNP (rs35753569 and rs34150205), their validity is highly questionable. The protein is widely expressed in a variety of tissues according to expressed sequence tag data from the National Center for Biotechnology Information.

It should be cautioned that, although both the previous report and our own data support the role of the two coding variants in disease association, we cannot rule out the possibility of functional roles from other genetic variants that are in LD with these two SNPs. According to HapMap CHB data, the haplotype block, in which rs11755393 and rs13205210 locate, extends more than 300 kb. This large LD block contains several genes, including C6orf106, SNRPC, UHRFBP1, TAF11, ANKS1A and SNRPC. This is also consistent with what we observe from GWAS data for SNPs in this LD block (Supplementary Figure 1). The high LD among SNPs in this region imposes tremendous difficulty to any effort trying to distinguish functional variants from genetic markers in high LD with them. However, the association of SNPs in this region to SLE is unlikely to come from LD to SNPs in the major histocompatibility complex locus, as can be seen from the LD patterns shown in Supplementary Figure 2 and conditional logistic regression results shown in Supplementary Table 2. Association of genetic variants in this locus to SLE in distinct populations establishes the role of this region in disease susceptibility, although much more work is needed to identify the functional variants and to characterise the function of the genes involved.

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Acknowledgements

This study was partially supported by the generous donation from Shun Tak District Min Yuen Tong of Hong Kong (to YLL). WY thanks support from Research Grant Council of the Hong Kong Government (GRF HKU781709M). YZ is supported by Edward the Sai Kim Hotung Paediatric Education and Research Fund and University Postgraduate Studentship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Correspondence to W Yang or Y L Lau.

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Supplementary Information accompanies the paper on Genes and Immunity website

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Zhang, Y., Yang, W., Mok, C. et al. Two missense variants in UHRF1BP1 are independently associated with systemic lupus erythematosus in Hong Kong Chinese. Genes Immun 12, 231–234 (2011) doi:10.1038/gene.2010.66

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Keywords

  • SLE
  • UHRF1BP1
  • association
  • Asian

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