Common variants in the NLRP3 region contribute to Crohn's disease susceptibility

Abstract

We used a candidate gene approach to identify a set of SNPs, located in a predicted regulatory region on chromosome 1q44 downstream of NLRP3 (previously known as CIAS1 and NALP3) that are associated with Crohn's disease. The associations were consistently replicated in four sample sets from individuals of European descent. In the combined analysis of all samples (710 father-mother-child trios, 239 cases and 107 controls), these SNPs were strongly associated with risk of Crohn's disease (Pcombined = 3.49 × 10−9, odds ratio = 1.78, confidence interval = 1.47–2.16 for rs10733113), reaching a level consistent with the stringent significance thresholds imposed by whole-genome association studies. In addition, we observed significant associations between SNPs in the associated regions and NLRP3 expression and IL-1β production. Mutations in NLRP3 are known to be responsible for three rare autoinflammatory disorders1,2. These results suggest that the NLRP3 region is also implicated in the susceptibility of more common inflammatory diseases such as Crohn's disease.

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Figure 1: Association results for the five Crohn's disease sample sets.
Figure 2: NLRP3 functional study results.

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References

  1. 1

    Agostini, L. et al. NALP3 forms an IL-1beta-processing inflammasome with increased activity in Muckle-Wells autoinflammatory disorder. Immunity 20, 319–325 (2004).

    CAS  Article  Google Scholar 

  2. 2

    Mariathasan, S. & Monack, D.M. Inflammasome adaptors and sensors: intracellular regulators of infection and inflammation. Nat. Rev. Immunol. 7, 31–40 (2007).

    CAS  Article  Google Scholar 

  3. 3

    Podolsky, D.K. Inflammatory bowel disease. N. Engl. J. Med. 347, 417–429 (2002).

    CAS  Article  Google Scholar 

  4. 4

    Ting, J.P., Kastner, D.L. & Hoffman, H.M. CATERPILLERs, pyrin and hereditary immunological disorders. Nat. Rev. Immunol. 6, 183–195 (2006).

    CAS  Article  Google Scholar 

  5. 5

    Pétrilli, V., Dostert, C., Muruve, D.A. & Tschopp, J. The inflammasome: a danger sensing complex triggering innate immunity. Curr. Opin. Immunol. 19, 615–622 (2007).

    Article  Google Scholar 

  6. 6

    Martinon, F. & Tschopp, J. Inflammatory caspases and inflammasomes: master switches of inflammation. Cell Death Differ. 14, 10–22 (2007).

    CAS  Article  Google Scholar 

  7. 7

    Taylor, J. et al. ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements. Genome Res. 16, 1596–1604 (2006).

    CAS  Article  Google Scholar 

  8. 8

    de Bakker, P.I. et al. Efficiency and power in genetic association studies. Nat. Genet. 37, 1217–1223 (2005).

    CAS  Article  Google Scholar 

  9. 9

    Kummer, J.A. et al. Inflammasome components NALP 1 and 3 show distinct but separate expression profiles in human tissues suggesting a site-specific role in the inflammatory response. J. Histochem. Cytochem. 55, 443–452 (2007).

    CAS  Article  Google Scholar 

  10. 10

    Martinon, F., Agostini, L., Meylan, E. & Tschopp, J. Identification of bacterial muramyl dipeptide as activator of the NALP3/cryopyrin inflammasome. Curr. Biol. 14, 1929–1934 (2004).

    CAS  Article  Google Scholar 

  11. 11

    Hawkins, P.N., Lachmann, H.J. & McDermott, M.F. Interleukin-1-receptor antagonist in the Muckle-Wells syndrome. N. Engl. J. Med. 348, 2583–2584 (2003).

    Article  Google Scholar 

  12. 12

    Hoffman, H.M. et al. Prevention of cold-associated acute inflammation in familial cold autoinflammatory syndrome by interleukin-1 receptor antagonist. Lancet 364, 1779–1785 (2004).

    CAS  Article  Google Scholar 

  13. 13

    Li, J. et al. Regulation of IL-8 and IL-1beta expression in Crohn's disease associated NOD2/CARD15 mutations. Hum. Mol. Genet. 13, 1715–1725 (2004).

    CAS  Article  Google Scholar 

  14. 14

    Van Heel, D.A. et al. Muramyl dipeptide and toll-like receptor sensitivity in NOD2-associated Crohn's disease. Lancet 365, 1794–1796 (2005).

    CAS  Article  Google Scholar 

  15. 15

    Kramer, M., Netea, M.G., de Jong, D.J., Kullberg, B.J. & Adema, G.J. Impaired dendritic cell function in Crohn's disease patients with NOD2 3020insC mutation. J. Leukoc. Biol. 79, 860–866 (2006).

    CAS  Article  Google Scholar 

  16. 16

    van Beelen, A.J. et al. Stimulation of the intracellular bacterial sensor NOD2 programs dendritic cells to promote interleukin-17 production in human memory T cells. Immunity 27, 660–669 (2007).

    CAS  Article  Google Scholar 

  17. 17

    Duerr, R.H. et al. A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 314, 1461–1463 (2006).

    CAS  Article  Google Scholar 

  18. 18

    Rioux, J.D. et al. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat. Genet. 39, 596–604 (2007).

    CAS  Article  Google Scholar 

  19. 19

    Libioulle, C. et al. Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. PLoS Genet. 3, e58 (2007).

    Article  Google Scholar 

  20. 20

    Parkes, M. et al. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat. Genet. 39, 830–832 (2007).

    CAS  Article  Google Scholar 

  21. 21

    Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661–678 (2007).

  22. 22

    Barrett, J.C. et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat. Genet. 40, 955–962 (2008).

    CAS  Article  Google Scholar 

  23. 23

    Lennard-Jones, J.E. Classification of inflammatory bowel disease. Scand. J. Gastroenterol. Suppl. 170, 2–6 (1989).

    CAS  Article  Google Scholar 

  24. 24

    Silverberg, M.S. et al. Toward an integrated clinical, molecular and serological classification of inflammatory bowel disease: Report of a Working Party of the 2005 Montreal World Congress of Gastroenterology. Can. J. Gastroenterol. (Suppl A), 19, 5–36 (2005).

    Article  Google Scholar 

  25. 25

    Bell, P.A. et al. SNPstream UHT: ultra-high throughput SNP genotyping for pharmacogenomics and drug discovery. Biotechniques Suppl 70–72, 74, 76–77 (2002).

  26. 26

    van den Boom, D. & Ehrich, M. Discovery and identification of sequence polymorphisms and mutations with MALDI-TOF MS. Methods Mol. Biol. 366, 287–306 (2007).

    CAS  Article  Google Scholar 

  27. 27

    Barrett, J.C., Fry, B., Maller, J. & Daly, M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265 (2005).

    CAS  Article  Google Scholar 

  28. 28

    Dudbridge, F. Likelihood-based association analysis for nuclear families and unrelated subjects with missing genotype data. Hum. Hered. 66, 87–98 (2008).

    Article  Google Scholar 

  29. 29

    Spielman, R.S., McGinnis, R.E. & Ewens, W.J. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet. 52, 506–516 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30

    Holland, P.M., Abramson, R.D., Watson, R. & Gelfand, D.H. Detection of specific polymerase chain reaction product by utilizing the 5′→3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proc. Natl. Acad. Sci. USA 88, 7276–7280 (1991).

    CAS  Article  Google Scholar 

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Acknowledgements

We thank the study participants and their families for their collaboration; A. Montpetit and the genotyping and sequencing platforms of the McGill University and Genome Québec Innovation Centre for their technical assistance; T. McKenzie, G. Bonventi and C. Landolt-Maticorena for their help with acquisition and preparation of the PBCs; F. Martinon and J. Tschopp for their technical assistance in designing the functional studies; and T. Kwan for helpful discussion. This research was supported by grants to D.F. from the Canada Foundation for Innovation, the Canada Research Chair program, the Research Institute of the McGill University Health Centre and the Crohn's & Colitis Foundation of Canada (CCFC). A.-C.V. is supported by a PhD training award from the Fonds de la recherche en santé du Québec. M.S.S. is funded by the National Institute of Diabetes and Digestive and Kidney Diseases (DK624230), the CCFC and the Mount Sinai Hospital Gale and Graham Wright Research Chair in Digestive Diseases. J.D.R. is funded by grants from the National Institutes of Allergy and Infectious Diseases (AI065687 and AI067152), the National Institute of Diabetes and Digestive and Kidney Diseases (DK064869 and DK062432) and the Crohn's and Colitis Foundation of America (SRA512). E.L. is a senior research associate at the Belgium Foundation for Scientific Research (FNRS). S.V. is a clinical investigator for the Funds for Scientific Research of Flanders. T.J.H. is the recipient of an Investigator Award from the Ontario Institute for Cancer Research through funding from the Government of Ontario's Ministry of Research and Innovation. D.F. is a senior clinical scientist at the Belgium FNRS. None of the funding agencies had any role in the design and conduct of the study; in the collection, analysis and interpretation of the data; or in the preparation, review or approval of the manuscript.

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A.-C.V., G.F. and D.F. conceived and designed the experiments. A.-C.V., G.F., C.C. and N.B. did the experiments. A.-C.V. and M.L. analyzed the data. E.L., M.S.S., C.L., J.B., A.B., D.G., A.C., D.L., P.R.F., J.E.W., M.S., P.R., J.D.R., S.V., T.J.H. and D.F. provided study samples. A.-C.V., M.L. and D.F. wrote the paper, with contributions from all authors.

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Correspondence to Alexandra-Chloé Villani or Denis Franchimont.

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Supplementary Methods, Supplementary Tables 1–6 and Supplementary Figures 1 and 2 (PDF 3222 kb)

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Villani, AC., Lemire, M., Fortin, G. et al. Common variants in the NLRP3 region contribute to Crohn's disease susceptibility. Nat Genet 41, 71–76 (2009). https://doi.org/10.1038/ng.285

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