Introduction Single nucleotide polymorphisms (SNPs) located of the NOD2/CARD15 gene (nucleotide-binding oligomerization domain containing 2/caspase recruitment domain family, member 15) are associated with increased susceptibility to Crohn's disease (CD). These SNPs are thought to disrupt the sensing of bacterial muramyl dipeptide (MDP) at the C-terminus of the NOD2 protein. The precise contribution of each of these SNPs (SNP5, 8, 12 and 13) to NF-κB activation by means of NOD2-auto-signalling and stimulation with MDP has not been investigated at low levels of NOD2 expression. Data regarding the linkage disequilibrium (LD) between these CD-associated SNPs are scarce.

Methods NOD2 variant constructs (rs2066842 (SNP5), rs2066844 (SNP8), rs2066845 (SNP12) and rs2066847 (SNP13), SNP5+8, SNP5+12 and SNP5+13) were created by site-directed mutagenesis of a pCMV plasmid containing wild-type N-terminal FLAG-NOD2. NF-κB luciferase assays were performed on HEK293 cells following transient transfection (20 h) with wildtype (WT) and NOD2 variant constructs, titrating NOD2 from 1 to 100 ng/well. The NF-κB luciferase response of NOD2 (1 ng)-transfected HEK293 cells to MDP (10 μg/well) was measured. Two-way ANOVA and unpaired t-tests were used. By means of Haploview-analysis of sequencing data of the exons and exon-intron boundaries in 24 paediatric Caucasian Crohn's disease patients, we assessed the LD between SNP5 and SNP8, 12 and 13.

Results Two-way ANOVA demonstrated an effect of NOD2 genotype and concentration on auto-signalling at low levels of expression (p<0.0001). This was due to the significant difference of auto-activation between WT and SNP5, SNP8 and SNP12 (p<0.001). At low levels of NOD2 expression (1–2 ng), the presence of SNP5 modified the auto-activating potential of SNP12 (p<0.01). Based on these titration experiments, a low NOD2 transfection of 1 ng/well was chosen for the MDP-stimulation experiment. MDP stimulation led to a significant increase of NF-κB luciferase activity in WT and all NOD2 variant constructs, except SNP13 and SNP5+13 (p<0.0001). Haplotype analysis of 11 NOD2 SNPs, identified through direct sequencing in 24 children with CD, showed that LD between SNP5 and the other CD-associated variants is low (r²<0.1), in spite of close physical proximity (D' 1.0).

Conclusion Our combined genetic and functional analyses demonstrate that the association of SNP5 with Crohn's disease is unlikely due to LD with other SNPs. At low levels of NOD2 expression, NOD2 variant constructs differ from WT in their auto-signalling and MDP-stimulated activation of NF-κB.

Competing interests None declared.