A Novel Rare Missense Variation of the NOD2 Gene: Evidencesof Implication in Crohn's Disease

Abstract

The NOD2 gene, involved in innate immune responses to bacterial peptidoglycan, has been found to be closely associated with Crohn's Disease (CD), with an Odds Ratio ranging from 3⁻36. Families with three or more CD-affected members were related to a high frequency of NOD2 gene variations, such as R702W, G908R, and 1007fs, and were reported in the EPIMAD Registry. However, some rare CD multiplex families were described without identification of common NOD2 linked-to-disease variations. In order to identify new genetic variation(s) closely linked with CD, whole exome sequencing was performed on available subjects, comprising four patients in two generations affected with Crohn's disease without R702W and G908R variation and three unaffected related subjects. A rare and, not yet, reported missense variation of the NOD2 gene, N1010K, was detected and co-segregated across affected patients. In silico evaluation and modelling highlighted evidence for an adverse effect of the N1010K variation with regard to CD. Moreover, cumulative characterization of N1010K and 1007fs as a compound heterozygous state in two, more severe CD family members strongly suggests that N1010K could well be a new risk factor involved in Crohn's disease genetic susceptibility.

Keywords: Crohn’s disease; NOD2 gene; WES; variation.

Figure 1

(A) Pedigree of family F49M with segregation of the c.3030A>C; p.(N1010K) and c.3019dupC; p.(L1007fs) variations. (B) Chromatograms for NOD2 coding region in exon 11. The red arrows show the c.3030A>C nucleotide substitution consisting of the amino acid substitution N1010K. The black arrows show the c.3019dupC frameshift variation (rs2066847).

Figure 2

(A) Location of the p.R702W (rs2066844), p.G908R (rs2066845), p.L1007fs (rs2066847) and p.N1010K NOD2 protein-altering variations. (B) Multiple alignments for the amino acid sequence of the NOD2 proteins in 11 species in agreement with a conserved amino acid.

Figure 3

(A) Structural predictions of the human native NOD2 protein (amino-acids 219–1040) and the human R702W mutated NOD2 proteins (amino-acids 219–1040); (B) structural predictions of the human native NOD2 protein (amino-acids 219–1040) and the human G908R mutated NOD2 proteins (amino-acids 219–1040); (C) structural predictions of the human native NOD2 protein (amino-acids 219–1040) and the human N1010K mutated NOD2 proteins (amino-acids 219–1040).