Elsevier

Journal of Hepatology

Volume 57, Issue 2, August 2012, Pages 366-375
Journal of Hepatology

Research Article
Extended analysis of a genome-wide association study in primary sclerosing cholangitis detects multiple novel risk loci

https://doi.org/10.1016/j.jhep.2012.03.031Get rights and content

Background & Aims

A limited number of genetic risk factors have been reported in primary sclerosing cholangitis (PSC). To discover further genetic susceptibility factors for PSC, we followed up on a second tier of single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS).

Methods

We analyzed 45 SNPs in 1221 PSC cases and 3508 controls. The association results from the replication analysis and the original GWAS (715 PSC cases and 2962 controls) were combined in a meta-analysis comprising 1936 PSC cases and 6470 controls. We performed an analysis of bile microbial community composition in 39 PSC patients by 16S rRNA sequencing.

Results

Seventeen SNPs representing 12 distinct genetic loci achieved nominal significance (preplication <0.05) in the replication. The most robust novel association was detected at chromosome 1p36 (rs3748816; pcombined = 2.1 × 10−8) where the MMEL1 and TNFRSF14 genes represent potential disease genes. Eight additional novel loci showed suggestive evidence of association (prepl <0.05). FUT2 at chromosome 19q13 (rs602662; pcomb = 1.9 × 10−6, rs281377; pcomb = 2.1 × 10−6 and rs601338; pcomb = 2.7 ×  10−6) is notable due to its implication in altered susceptibility to infectious agents. We found that FUT2 secretor status and genotype defined by rs601338 significantly influence biliary microbial community composition in PSC patients.

Conclusions

We identify multiple new PSC risk loci by extended analysis of a PSC GWAS. FUT2 genotype needs to be taken into account when assessing the influence of microbiota on biliary pathology in PSC.

Introduction

Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease of unknown etiology, characterized by progressive inflammation and fibrosis of the bile ducts, leading to liver cirrhosis in many cases [1]. An important clinical feature of PSC is the frequent autoimmune manifestations in other organ systems, most commonly inflammatory bowel disease (IBD), which is reported in 62–83% of PSC patients of Northern European descent [1]. In addition, approximately 25% of PSC patients are affected with at least one autoimmune disease outside the liver and colon [2], most commonly, type 1 diabetes, thyroid disease, rheumatoid arthritis and psoriasis. Shared genetic susceptibility could potentially explain the frequent occurrence of these immune-related co-morbidities in PSC.

The importance of genetic risk factors in PSC is demonstrated by heritability studies estimating siblings of PSC patients to be 9–39 times more likely to develop PSC than the general population [1]. The contribution of genetic variants in the HLA complex on chromosome 6p21 to the risk of PSC is well established [1]. Previously, strong evidence for associated risk factors outside the HLA region has been reported at chromosome 3p21 in MST1 and chromosome 2q13 near BCL2L11 [3]. In addition, suggestive PSC associations have been reported at six additional loci harboring the likely susceptibility genes GPBAR1, IL2RA, GPC5/GPC6, IL2/IL21, CARD9, and REL [3], [4], [5], [6]. In the most recent PSC GWAS [3], only the top 23 associated regions were selected for replication genotyping.

Replication attempts of promising, but lower ranked markers from GWAS have yielded valuable findings in several other diseases, and have been particularly fruitful when combined with a semi-hypothesis-driven approach taking into consideration gene content and potential biological relevance [7]. In an attempt to identify novel susceptibility loci in PSC, we selected a second tier of promising associated markers from an available PSC GWAS [3] for replication in an independent cohort.

Section snippets

Study subjects

The discovery panel included a total of 715 PSC cases and 2962 healthy controls, with 332 PSC cases and 262 controls from Scandinavia, and 383 PSC cases and 2700 controls from Germany [3]. The replication panel consisted of a total of 1221 PSC cases and 3508 controls, with 289 PSC cases and 820 controls from Scandinavia, 561 PSC patients and 2063 controls from Central Europe, and 371 PSC cases and 625 controls from the United States (US).

The recruitment of study subjects is described in detail

SNP selection and genotyping results

Seven hundred and fifteen PSC patients and 2962 controls were successfully genotyped and analyzed in the GWAS (Table 1). Among the 2,466,182 genotyped and imputed SNPs analyzed, a subset of 59 SNPs were selected for follow-up; 37 SNPs based on SNP selection strategy I and 22 SNPs based on SNP selection strategy II. Following quality pruning of the replication dataset, a total of 45 SNPs were included in the association analysis.

Association results

A total of 17 SNPs achieved nominal significance in the replication

Discussion

In the largest PSC cohort presented, we performed replication genotyping and a combined analysis of 45 SNPs not followed up in a previous GWAS in PSC [3]. We identified one novel PSC risk locus with association results below the threshold for genome-wide significance along with suggestive evidence for replication of 8 novel additional loci. The PSC-associated FUT2 variant was shown to significantly influence the bile microbial community composition in PSC patients.

The replicated SNP at 1p36 (

Financial support

The study was supported by The Norwegian PSC Research Center (http://ous-research.no/nopsc/) and the German Ministry of Education and Research (BMBF) through the National Genome Research Network (NGFN) and the Integrated Research and Treatment Center – Transplantation (reference number: 01EO0802) and the PopGen biobank (http://www.popgen.de). The US part of the study was supported by the NIH (DK 84960). The project received infrastructure support through the Norwegian Functional Genomics

Conflict of interest

The authors who have taken part in this study declared that they do not have anything to disclose regarding funding or conflict of interest with respect to this manuscript.

Acknowledgements

The authors are indebted to all PSC patients and healthy controls for their participation. We thank Katja Cloppenborg-Schmidt, Ilona Urbach, Irene Pauselis, Tanja Wesse, Tanja Henke, Rainer Vogler, Hege Dahlen Sollid, Bente Woldseth, and Liv Wenche Torbjørnsen for expert technical help. Paul R. Berg and Silje Karoliussen are specially thanked for providing expert assistance in the genotyping process. We are grateful to Arthur Kaser and Michael Nothnagel for helpful discussions. Benedicte A. Lie

References (36)

  • D.P. Faith

    Conservation evaluation and phylogenetic diversity

    Biol Conserv

    (1992)
  • E. Melum et al.

    Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci

    Nat Genet

    (2011)
  • M. Janse et al.

    Three ulcerative colitis susceptibility loci are associated with primary sclerosing cholangitis and indicate a role for IL2, REL, and CARD9

    Hepatology

    (2011)
  • J. Stallhofer et al.

    Analysis of IL2/IL21 Gene Variants in Cholestatic Liver Diseases Reveals an Association with Primary Sclerosing Cholangitis

    Digestion

    (2011)
  • G. Trynka et al.

    Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling

    Gut

    (2009)
  • A.L. Price et al.

    Principal components analysis corrects for stratification in genome-wide association studies

    Nat Genet

    (2006)
  • R.J. Pruim et al.

    LocusZoom: regional visualization of genome-wide association scan results

    Bioinformatics

    (2010)
  • P. Rausch et al.

    Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype

    Proc Natl Acad Sci U S A

    (2011)
  • Cited by (188)

    • Bile Duct Diseases

      2023, MacSween's Pathology of the Liver, Eighth Edition
    • Challenges for diagnosis and treatment of primary biliary cholangitis

      2022, Translational Autoimmunity: Challenges for Autoimmune Diseases: Volume 5
    View all citing articles on Scopus

    These authors contributed equally to this work.

    View full text