Background NOD2 single nucleotide polymorphisms have been associated with increased risk of ileal Crohn’s disease. This exploratory study was conducted to compare ileal mucosal gene expression in Crohn’s disease (CD) patients with and without NOD2 risk alleles. Methods Ileal samples were prospectively collected from eighteen non-smoking CD patients not treated with anti-TNFα biologics and nine non-smoking control patients without inflammatory bowel disease undergoing initial resection, and genotyped for the three major NOD2 risk alleles (Arg702Trp, Gly908Arg, Leu1007fs). Microarray analysis was performed in samples from four NOD2R (at least one risk allele) CD patients, four NOD2NR (no risk alleles) CD patients and four NOD2NR controls. Candidate genes selected by significance analysis of microarrays (SAM) were confirmed by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assays of all the samples. Results SAM detected upregulation of 18 genes in affected ileum in NOD2R compared to NOD2NR CD patients, including genes related to lymphocyte activation. SAM also detected altered ileal gene expression in unaffected NOD2NR ileal mucosal CD samples compared to NOD2NR control samples. QRT-PCR conducted on all the samples confirmed that increased CD3D expression in affected samples was associated with NOD2R status, and that increased MUC1, DUOX2, DMBT1 and decreased C4orf7 expression in unaffected samples was associated with CD, independent of NOD2 status. Conclusions The results support the concept that NOD2 risk alleles contribute to impaired regulation of inflammation in the ileum. Furthermore, altered ileal gene expression, independent of NOD2 status, is detected in the unaffected proximal margin of resected ileum from CD patients.

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Genome wide association studies have identified more than 30 distinct loci linked with susceptibility to Crohn’s disease (CD), a common idiopathic inflammatory bowel disease (IBD). Among these candidate genes, NOD2/CARD15 encodes a cytosolic protein that recognizes bacterial cell wall components and results in downstream activation of innate pathways of host defense. NOD2/CARD15 Variants are associated with increased susceptibility to CD. IRGM (immunity-related GTPase family, M) is involved in autophagy and intracellular pathogen clearance. Variations in or near the IRGM locus have been associated with increased susceptibility to CD. IL23R (interleukin 23 receptor) variants appear to have a protective role in the development of IBD although the mechanism for this is unknown. Initial studies in European cohorts described an association in which NOD2/CARD15 donor or recipient variants increased severe acute GvHD/transplant-related mortality and reduced survival in HLA-matched sibling transplants. In T cell depleted unrelated donor transplants for acute leukemia, an increased risk of relapse and death was observed in pairs with recipient NOD2/CARD15 variants. However, this association was not confirmed in a recent independent study in 101 unrelated Swedish subjects. No studies have yet evaluated IRGM or IL23R variants in GvHD or other transplant outcomes. Methods: Pre-transplant samples from 390 patients and their 10/10 HLA-A, B, C, DRB1 and DQB1-matched unrelated donors were provided by the National Marrow Donor Program Research Repository. Patients received T-replete transplants for early stage AML, ALL, CML, MDS using myeloablative conditioning and accrued between 1995–2004. Gut decontamination was not routinely used. Patients and donors were of predominately European American descent 92.2% and 94.5%, respectively with 6.7% racial/ethnic minorities. DNA was genotyped for three NOD2/CARD15 SNPs (rs2066844, rs2066845 and rs2066847), two IL23R SNPs (rs11209026 and rs11465804), and two IRGM SNPs (rs4958847 and rs13361189) using Sequenom and/or Taqman assays. Multivariate analyses were performed for overall (OS) and disease free survival (DFS), transplant-related mortality (TRM), relapse, and acute and chronic GvHD, adjusting for clinical variables. Results: Out of 390 donor recipient pairs, NOD2/CARD15 variant SNPs were found in 56 donors (14%) and 67 recipients (17%), with an overall frequency of 16% in this cohort. In 12 pairs (3%), both donor and recipient had a mutant SNP. These frequencies are lower than reported in the earlier European cohorts but our study population included 6.7% racial/ethnic minorities. For IL23R, 13% of donors and 16% of recipients had variant SNPs (n=353 pairs analyzed), with 11 pairs (3%) having both donor and recipient variants. For IRGM, variant SNPs were seen in 23% of both donors and recipients (n=353 pairs analyzed). The overall incidence of 100 day acute grade III–IV (21%) and 1-year chronic (53%) GvHD as well as OS and DFS at 100 days (85 and 84%), 6 months (77 and 74%) and 1 year (67 and 63%) were similar to published outcomes. For IRGM, there was a trend (0.01<p<0.05) for recipient mutations to be associated with higher OS, LFS, and lower TRM. However, none of the 3 IBD-associated alleles showed evidence of a statistically significant association with any of the aforementioned outcomes at p <0.01. In particular there was no association between the three NOD2/CARD15 SNPs (rs2066844, rs2066845 and rs2066847) and the incidence of acute or chronic GvHD. Conclusions: Our study finds insufficient evidence to support an association between the 3 examined IBD-associated SNPs and adverse outcomes following matched unrelated donor HCTs in a (predominately Caucasian) cohort of US patients. Several factors may contribute to this discrepancy from prior studies, including our larger cohort size, differences in patient characteristics, exclusion of sibling matched donor HCTs and T cell depletion procedures. Nevertheless, our findings do not support the use of IBD-associated allele mutation status in the donor/recipient selection process.