Mutation spectrum of NOD2 reveals recessive inheritance as a main driver of Early Onset Crohn's Disease

Abstract

Inflammatory bowel disease (IBD), clinically defined as Crohn's disease (CD), ulcerative colitis (UC), or IBD-unclassified, results in chronic inflammation of the gastrointestinal tract in genetically susceptible hosts. Pediatric onset IBD represents ≥ 25% of all IBD diagnoses and often presents with intestinal stricturing, perianal disease, and failed response to conventional treatments. NOD2 was the first and is the most replicated locus associated with adult IBD, to date. However, its role in pediatric onset IBD is not well understood. We performed whole-exome sequencing on a cohort of 1,183 patients with pediatric onset IBD (ages 0-18.5 years). We identified 92 probands with biallelic rare and low frequency NOD2 variants accounting for approximately 8% of our cohort, suggesting a Mendelian inheritance pattern of disease. Additionally, we investigated the contribution of recessive inheritance of NOD2 alleles in adult IBD patients from a large clinical population cohort. We found that recessive inheritance of NOD2 variants explains ~ 7% of cases in this adult IBD cohort, including ~ 10% of CD cases, confirming the observations from our pediatric IBD cohort. Exploration of EHR data showed that several of these adult IBD patients obtained their initial IBD diagnosis before 18 years of age, consistent with early onset disease. While it has been previously reported that carriers of more than one NOD2 risk alleles have increased susceptibility to Crohn's Disease (CD), our data formally demonstrate that recessive inheritance of NOD2 alleles is a mechanistic driver of early onset IBD, specifically CD, likely due to loss of NOD2 protein function. Collectively, our findings show that recessive inheritance of rare and low frequency deleterious NOD2 variants account for 7-10% of CD cases and implicate NOD2 as a Mendelian disease gene for early onset Crohn's Disease.

Figure 1

Mutation spectrum of NOD2 in inflammatory bowel disease (IBD) patients. NOD2 variation identified in patients with pediatric early onset IBD (upper) and adult IBD cohort from the RGC-GHS DiscovEHR collaboration (lower). Variants in blue were observed in both cohorts; variants in red are predicted loss-of-function that result in nonsense mediated decay. The three “common” low-frequency Crohn’s Disease risk variants are highlighted: R702W (purple), G908R (brown), and L1007fs (green). Also depicted are the NOD2 protein structural domains: two caspase activation and recruitment domains (CARD), a nucleotide binding and oligomerization (NOD) domain, and leucine rich repeat domains in yellow.

Figure 2

Phenome wide association analysis (PheWAS) of ICD diagnostic codes with biallelic recessive genotypes of NOD2. Analysis shows that NOD2 recessive status significantly associates with Crohn’s disease and related diagnoses.

Figure 3

Graphical representation of Odds Ratio (OR) point estimates and 95% confidence intervals (CI) for the three main CD risk alleles (p.R702W, p.G908R, p.L1007fs) under additive, genotypic, and recessive genetic models (corresponding to values in Table 3). The dotted line in the Composite panel depicts the calculated CI with corresponding calculated OR for 2 alleles under an additive genetic model; of note the point estimate (2xOR) is outside of the 95% CI for the Composite genotypic homozygous and recessive models. Diamonds correspond to estimated OR values for these same variants in the IBD Exomes Browser; no confidence intervals are provided.