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

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.NOD2was the first and is the most replicated locus associated with adult IBD, to date. To determine the role ofNOD2and other genes in pediatric IBD, 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 who were homozygous or compound heterozygous for rare and low frequencyNOD2variants accounting for approximately 8% of our cohort, suggesting a Mendelian recessive inheritance pattern of disease. Additionally, we investigated the contribution of recessive inheritance ofNOD2alleles in adult IBD patients from the Regeneron Genetics Center (RGC)-Geisinger Health System DiscovEHR study, which links whole exome sequences to longitudinal electronic health records (EHRs) from 51,289 participants. We found that ~7% of cases in this adult IBD cohort, including ~10% of CD cases, can be attributed to recessive inheritance ofNOD2variants, confirming the observations from our pediatric IBD cohort. Exploration of EHR data showed that 14% of these adult IBD patients obtained their initial IBD diagnosis before 18 years of age, consistent with early onset disease. Collectively, our findings show that recessive inheritance of rare and low frequency deleteriousNOD2variants account for 7-10% of CD cases and implicateNOD2as a Mendelian disease gene for early onset Crohn’s Disease.Author SummaryPediatric onset inflammatory bowel disease (IBD) represents ≥25% of IBD diagnoses; yet the genetic architecture of early onset IBD remains largely uncharacterized. To investigate this, we performed whole-exome sequencing and rare variant analysis on a cohort of 1,183 pediatric onset IBD patients. We found that 8% of patients in our cohort were homozygous or compound heterozygous for rare or low frequency deleterious variants in the nucleotide binding and oligomerization domain containing 2(NOD2)gene. Further investigation of whole-exome sequencing of a large clinical cohort of adult IBD patients uncovered recessive inheritance of rare and low frequencyNOD2variants in 7% of cases and that the relative risk forNOD2variant homozygosity has likely been underestimated. While it has been reported that having >1NOD2risk alleles is associated with increased susceptibility to Crohn’s Disease (CD), our data formally demonstrate what has long been suspected: recessive inheritance ofNOD2alleles is a mechanistic driver of early onset IBD, specifically CD, likely due to loss of NOD2 protein function. Our data suggest that a subset of IBD-CD patients with early disease onset is characterized by recessive inheritance ofNOD2alleles, which has important implications for the screening, diagnosis, and treatment of IBD.