NOD2 Single Nucleotide Polymorphisms Research Articles

NOD1/CARD4(G796A) and NOD2/CARD15(R702W, G908R and L1007fsinC) polymorphisms associated with Crohn's disease in Iraqi patients

Inflammatory bowel disease (IBD) applies to two main forms of chronic relapsing inflammatory intestinal disorders: Crohn's disease (CD), Ulcerative colitis (UC). CD requires an irregular immune reaction that induces intense inflammation. The cause of CD disease is not yet fully known; previous research, however, indicated inflammation of the intestines elevated or continues due to inappropriate immune responses due to associations between genetic factors, intestinal microbiota, and environmental factors contributing to the production of IBD. This study aimed to investigate predisposing genes, single nucleotide Polymorphisms (SNPs) NOD1/CARD4 and NOD2/CARD15) with CD in Iraqi patients. The common NOD1 (G796A) SNP and NOD2 SNPs R702W, G908R and L1007fsinC for NOD2 SNPs were selected. Thirty Iraqi citizens with a recognized diagnosis of CD and twenty apparently healthy controls were included in the study from November 2019 to December 2020; the common NOD1 and NOD2 polymorphisms have been screened by the polymerase chain reaction/restriction analysis length polymorphism (PCR/RFLP). The results of the current investigation for NOD1 polymorphism in studied patients and controls, the allelic and genotypic data show a highly significant association of G796A SNPs in the NOD1 with Crohn's disease, GA percentage was 56.67% in patients as compared to controls genotype was (0.00%). Furthermore, the G allele was more common in Crohn's patients than the A allele 0.72 vs. 0.28. Also, the allelic and genotypic frequency distribution of the studied NOD2 SNPs in the current study were (R702W, G908R, and L1007fs) in Iraqi patients, and controls revealed a highly significant connection between the G908R SNP with Crohn's disease susceptibility. The proportion of the genotype GC was 30% in patients while 0% in the control group, the frequency of the G allele was 0.85 vs 0.15 respectively, which was more than the frequency of the A allele. There were no significant changes in genotypic and allelic frequencies of the R702W and L1007fs SNPs in Iraqi Crohn's disease patients. The present study concluded that the NOD1 SNP of allelic and genotypic data show a highly significant association of G796A with a predisposition to Crohn's disease in Iraqi patients. And the NOD2 SNPs of G908R were also revealed to be highly effective. While the other studied SNPs were R702W and L1007fsinsC of NOD2, which showed no significant changes in the allelic and genotypic frequencies of the SNPs with Crohn's disease Iraqi patients. Keywords: Inflammatory bowel disease, Crohn's disease, NOD1/CARD4, NOD2/CARD15, polymorphisms.

The influence of single nucleotide polymorphisms of NOD2 or CD14 on the risk of Mycobacterium tuberculosis diseases: a systematic review

BackgroundTuberculosis (TB) is still one of the leading causes of death worldwide. Genetic studies have pointed to the relevance of the NOD2 and CD14 polymorphic alleles in association with the risk of diseases caused by Mycobacterium tuberculosis (Mtb) infection.MethodsA systematic review was performed on PubMed, EMBASE, Scientific Electronic Library Online (SciELO), and Literatura Latino-Americana e do Caribe em Ciências da Saúde (Lilacs) to examine the association between single nucleotide polymorphisms (SNP) and risk of Mtb diseases. Study quality was evaluated using the Newcastle-Ottawa Quality Scale (NOQS), and the linkage disequilibrium was calculated for all SNPs using a webtool (Package LDpop).ResultsThirteen studies matched the selection criteria. Of those, 9 investigated CD14 SNPs, and 6 reported a significant association between the T allele and TT genotypes of the rs2569190 SNP and increased risk of Mtb diseases. The genotype CC was found to be protective against TB disease. Furthermore, in two studies, the CD14 rs2569191 SNP with the G allele was significantly associated with increased risk of Mtb diseases. Four studies reported data uncovering the relationship between NOD2 SNPs and risk of Mtb diseases, with two reporting significant associations of rs1861759 and rs7194886 and higher risk of Mtb diseases in a Chinese Han population. Paradoxically, minor allele carriers (CG or GG) of rs2066842 and rs2066844 NOD2 SNPs were associated with lower risk of Mtb diseases in African Americans.ConclusionsThe CD14 rs2569190 and rs2569191 polymorphisms may influence risk of Mtb diseases depending on the allele. Furthermore, there is significant association between NOD2 SNPs rs1861759 and rs7194886 and augmented risk of Mtb diseases, especially in persons of Chinese ethnicity. The referred polymorphisms of CD14 and NOD2 genes likely play an important role in risk of Mtb diseases and pathology and may be affected by ethnicity.Systematic review registrationCRD42020186523

Genetic Polymorphisms in Autophagy-Associated Genes in Korean Children With Early-Onset Crohn Disease.

The aim of the present study was to investigate the genetic polymorphisms of the autophagy-associated genes autophagy-related 16-like 1 (ATG16L1), immunity-related GTPase M (IRGM), Unc-51-like kinase 1 (ULK1), and NOD2 with respect to early-onset Crohn disease (CD) among Korean children. A total of 65 patients with CD from the Seoul National University Children's Hospital, from January 2000 to May 2012, and 72 unaffected controls were selected. Twelve different single nucleotide polymorphisms (SNPs) were analyzed (TaqMan assay: ATG16L1 rs2241880, IRGM SNPs [rs13361189, rs4958847, rs1000113, rs10065172, and rs72553867], ULK1 SNPs [rs12303764, rs10902469, and rs7488085], NOD2 SNPs [Arg702Trp and Gly908Arg]; direct sequencing: NOD2 leu1007fsinsC). The onset age of patients was 8.6 ± 4.7 years. Twelve patients (18.5%) had an onset age of <1 year. Two of the 12 SNPs showed significant results. IRGM rs1000113 exhibited an association with CD with respect to its minor allele frequency (odds ratio [OR] 1.71, 95% confidence interval [CI] 1.05-2.79, P = 0.03) and genotype distribution (dominant model: OR 2.17, 95% CI 1.07-4.39, P = 0.03). IRGM rs72553867 exhibited association with CD with respect to its minor allele frequency (OR 0.50, 95% CI 0.27-0.91, P = 0.02) and genotype distribution (dominant model: OR 0.50, 95% CI 0.23-0.94, P = 0.03). The 3 SNPs of NOD2 existed only as wild types for both groups. In the genotype-phenotype analysis, the onset age, disease location, and disease behavior exhibited no association. IRGM rs1000113 and IRGM rs72553867 exhibited associations with early-onset CD as risk loci and defense loci, respectively. This suggests that the autophagy pathway plays an important role in early-onset CD.

Association between genetic variants in NOD2, C13orf31, and CCDC122 genes and leprosy among the Chinese Yi population.

A significant association between single nucleotide polymorphisms in NOD2, C13orf31, and CCDC122 genes and leprosy has been reported in a previous genome-wide association study of leprosy in the Chinese Han population. However, it remains unknown whether this association exists among the Chinese Yi population. The aim of this study was to investigate whether single nucleotide polymorphisms in NOD2, C13orf31, and CCDC122 genes are associated with leprosy among the Chinese Yi population in China. We genotyped rs9302752, rs7194886, rs8057341, and rs3135499 in the NOD2 gene; rs3764147 and rs10507522 in the C13orf31 gene; and rs3088362 and rs9533634 in the CCDC122 gene in a Chinese Yi cohort comprised of 319 patients with leprosy and 355 ethnic-matched controls. The differences between the patients and healthy controls were analyzed using chi-squared analysis. Significant differences of rs3135499 in NOD2, rs3764147 and rs10507522 in C13orf31, and rs3088362 and rs9533634 in CCDC122 were observed between the patients and the healthy control groups in the cohort. The allelic P values and odd ratios were as follows: rs3135499, 1.0×10(-8) and 2.55; rs3764147, 1.7×10(-7) and 1.88; rs10507522, 1.16×10(-5) and 1.95; rs3088362, 8.2×10(-4) and 1.51; rs9533634, 5.34×10(-5) and 1.73. No significant differences were found in the distributions of rs9302752, rs7194886, and rs8057341 between the patients and healthy controls. We demonstrated that genetic variants in the NOD2, C13orf31, and CCDC122 genes are closely associated with leprosy among the Chinese Yi population, which implicates the pathogenic role of NOD2, C13orf31, and CCDC122 genes in a different ethnicity.

The NOD2 Single Nucleotide Polymorphism rs72796353 (IVS4+10 A&gt;C) Is a Predictor for Perianal Fistulas in Patients with Crohn's Disease in the Absence of Other NOD2 Mutations

BackgroundA previous study suggested an association of the single nucleotide polymorphism (SNP) rs72796353 (IVS4+10 A>C) in the NOD2 gene with susceptibility to Crohn’s disease (CD). However, this finding has not been confirmed. Given that NOD2 variants still represent the most important predictors for CD susceptibility and phenotype, we evaluated the association of rs72796353 with inflammatory bowel disease (IBD) susceptibility and the IBD phenotype.MethodologyGenomic DNA from 2256 Caucasians, including 1073 CD patients, 464 patients with ulcerative colitis (UC), and 719 healthy controls, was genotyped for the NOD2 SNP rs72796353 and the three main CD-associated NOD2 mutations rs2066844, rs2066845, and rs2066847. Subsequently, IBD association and genotype-phenotype analyses were conducted.ResultsIn contrast to the strong associations of the NOD2 SNPs rs2066844 (p=3.51 x 10-3), rs2066845 (p=1.54 x 10-2), and rs2066847 (p=1.61 x 10-20) with CD susceptibility, no significant association of rs72796353 with CD or UC susceptibility was found. However, in CD patients without the three main CD-associated NOD2 mutations, rs72796353 was significantly associated with the development of perianal fistulas (p=2.78 x 10-7, OR 5.27, [95% CI 2.75-10.12] vs. NOD2 wild-type carriers).Conclusion/SignificanceCurrently, this study represents the largest genotype-phenotype analysis of the impact of the NOD2 variant rs72796353 on the disease phenotype in IBD. Our data demonstrate that in CD patients the IVS4+10 A>C variant is strongly associated with the development of perianal fistulas. This association is particularly pronounced in patients who are not carriers of the three main CD-associated NOD2 mutations, suggesting rs72796353 as additional genetic marker for the CD disease behaviour.

Su1286 Incidence of Clostridium difficile in Hispanics With Inflammatory Bowel Disease and Association With ATG16L1 and NOD2 Single Nucleotide Polymorphisms

Su1286 Incidence of Clostridium difficile in Hispanics With Inflammatory Bowel Disease and Association With ATG16L1 and NOD2 Single Nucleotide Polymorphisms

Genetic determinants associated with early age of diagnosis of IBD.

Inflammatory bowel disease (IBD) is typically diagnosed at 20 to 40 years of age. However, very young versus elderly patients with IBD may have different mechanisms of disease that may affect prognosis and care. The purpose of this work was to identify single nucleotide polymorphisms associated with age of onset of Crohn's disease and ulcerative colitis. Patients were genotyped using a custom microarray chip containing 332 IBD-associated single nucleotide polymorphisms. Age at diagnosis as a continuous variable was assessed using linear regression. Patients were then subgrouped by age at diagnosis and compared by the Fisher exact test. Bonferroni correction was used in all of the analyses. This study was conducted at a tertiary academic hospital. Sixty patients with Crohn's disease and 26 with ulcerative colitis were ≤ 16 years old, 259 patients with Crohn's disease and 248 with ulcerative colitis were 17-60 years old, and 10 patients with Crohn's disease and 20 with ulcerative colitis were >60 years old at diagnosis and included in this study. Age at diagnosis and single nucleotide polymorphism correlations were measured in this study. The NOD2 single nucleotide polymorphism rs2076756 was associated with younger age at Crohn's disease diagnosis (p = 0.0002). Patients with the AA/wild-type genotype were diagnosed at 31.9 ± 1.23 years, AG heterozygotes at 25.6 ± 0.99 years, and GG/at-risk allele homozygotes at 22.6 ± 1.32 years. Depending on age categories compared, single nucleotide polymorphisms in POU5F1, TNFSF15, and HLA DRB1*501 were associated with age of Crohn's disease diagnosis. No genetic associations were seen between ulcerative colitis and linear age at diagnosis; however, the G allele of the LAMB1 single nucleotide polymorphism rs886774 was found to be associated with ulcerative colitis diagnosed at ≤ 16 versus >17 years old (p = 0.008). This study was limited to known IBD single nucleotide polymorphisms. This analysis reaffirms the association between NOD2, a molecule of innate immunity, and early Crohn's disease onset. This is the first report of a possible association between early Crohn's disease and the POU5F1, TNFSF15, and HLA DRB1*501 genes. The LAMB1 gene, associated with mucosal basement membrane integrity, was associated with early onset ulcerative colitis and, thus, suggests a fundamentally different mechanism of early disease pathogenesis in ulcerative colitis versus Crohn's disease.

Polymorphisms in TICAM2 and IL1B are associated with TB.

BackgroundHuman genetic susceptibility for tuberculosis (TB) has been demonstrated by several studies, but few have examined multiple innate and adaptive immunity genes comprehensively, age-specific effects, and/or resistance to Mycobacterium tuberculosis (Mtb) infection (RSTR). We hypothesized that RSTR, defined by a persistently negative tuberculin skin test, may have different genetic influences than Mtb disease.MethodsWe examined 29 candidate genes in pathways that mediate immune responses to Mtb in subjects in a household contact study in Kampala, Uganda. We genotyped 546 haplotype-tagging single nucleotide polymorphisms (SNPs) in 835 individuals from 481 families; 28.7% had TB, 10.5% were RSTR, and the remaining 60.8% had latent Mtb infection.ResultsAmong our most significant findings were SNPs in TICAM2 (p=3.6×10−6) and IL1B (p=4.3×10−5) associated with TB. Multiple SNPs in IL4 and TOLLIP were associated with TB (p<0.05). Age-genotype interaction analysis revealed SNPs in IL18 and TLR6 that were suggestively associated with TB in children ≤ 10 years old (p=2.9×10−3). By contrast, RSTR was associated with SNPs in NOD2, SLC6A3 and TLR4 (nominal p < 0.05); these genes were not associated with TB, suggesting distinct genetic influences.ConclusionsWe report the first association between TICAM2 polymorphisms and TB, and between IL18 and pediatric TB.

The NOD2 p.Leu1007fsX1008 mutation (rs2066847) is a stronger predictor of the clinical course of Crohn's disease than the FOXO3A intron variant rs12212067.

BackgroundVery recently, a sub-analysis of genome-wide association scans revealed that the non-coding single nucleotide polymorphism (SNP) rs12212067 in the FOXO3A gene is associated with a milder course of Crohn's disease (CD) (Cell 2013;155:57–69). The aim of our study was to evaluate the clinical value of the SNP rs12212067 in predicting the severity of CD by correlating CD patient genotype status with the most relevant complications of CD such as stenoses, fistulas, and CD-related surgery.Methodology/Principal FindingsWe genotyped 550 CD patients for rs12212067 (FOXO3A) and the three common CD-associated NOD2 mutations rs2066844, rs2066847, and rs2066847 and performed genotype-phenotype analyses.ResultsNo significant phenotypic differences were found between the wild-type genotype TT of the FOXO3A SNP rs12212067 and the minor genotypes TG and GG independently from NOD2 variants. The allele frequency of the minor G allele was 12.7%. Age at diagnosis, disease duration, body mass index, surgery rate, stenoses, fistula, need for immunosuppressive therapy, and disease course were not significantly different. In contrast, the NOD2 mutant p.Leu1007fsX1008 (rs2066847) was highly associated with penetrating CD (p = 0.01), the development of fistulas (p = 0.01) and stenoses (p = 0.01), and ileal disease localization (p = 0.03). Importantly, the NOD2 SNP rs2066847 was a strong separator between an aggressive and a mild course of CD (p = 2.99×10−5), while the FOXO3A SNP rs12212067 did not separate between mild and aggressive CD behavior in our cohort (p = 0.35). 96.2% of the homozygous NOD2 p.Leu1007fsX1008 carriers had an aggressive disease behavior compared to 69.3% of the patients with the NOD2 wild-type genotype (p = 0.007).Conclusion/SignificanceIn clinical practice, the NOD2 variant p.Leu1007fsX1008 (rs2066847), in particular in homozygous form, is a much stronger marker for a severe clinical phenotype than the FOXO3A rs12212067 SNP for a mild disease course on an individual patient level despite its important impact on the inflammatory response of monocytes.

Association between NOD2 single nucleotide polymorphisms and Grade III–IV acute graft-versus-host disease: A meta-analysis

ObjectivesThe effects of NOD2 single nucleotide polymorphisms (SNPs) on Grade III–IV acute graft-versus-host disease (aGVHD) risk are somewhat contradictory in different studies. The aim of the meta-analysis was to clarify the effects of NOD2 SNPs on the incidence of Grade III–IV aGVHD.MethodsWe searched PubMed, EMBASE, Web of SCIENCE, WanFang and Chinese National Knowledge Infrastructure (CNKI) databases to collect eligible publications. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the association between NOD2 polymorphisms and Grade III–IV aGVHD risk.ResultsA total of nine studies from eight publications met the inclusion criteria and were included in this meta-analysis. Patient NOD2 SNPs were not associated with aGVHD risk. A tendency of higher risk to develop Grade III–IV aGVHD was found in patients with pairs NOD2 SNPs. Subgroup analyses showed that pairs NOD2 SNPs were associated with Grade III–IV aGVHD in the Caucasian population and in identical sibling donors (IS), but not in matched unrelated donors (MUD). In patients who received hematopoietic stem cell transplantation (HSCT) with T-cell depletion and gut decontamination, there was still an association between pairs NOD2 SNPs and Grade III–IV aGVHD risk.ConclusionsOur meta-analysis suggests that pairs NOD2 SNPs, not patient NOD2 SNPs, may be associated with Grade III–IV aGVHD risk, especially in the Caucasian population. It is also indicated that in pairs NOD2 polymorphisms group, patients who receive HSCT from IS may experience higher risk of Grade III–IV aGVHD.

Intestinal Microbiota: From Inflammatory Bowel Disease to Bone Marrow Transplantation

AbstractAbstract SCI-50A dysregulated interaction of the intestinal microbiome with the patient’s innate and adaptive immune response seems to contribute to both inflammatory bowel disease (IBD) and intestinal graft-versus-host disease (GVHD). In IBD, polymorphisms within genes involved in antibacterial defense have been identified as genetic risk factors, such as in NOD2, a gene coding for an intracytoplasmatic receptor for muramyldipeptide, a bacterial cell wall compound, or in ATG16L1, a gene involved in autophagy of bacteria. Disruption of these genes results in dysfunction of Paneth cells, which are the major producers of antimicrobial peptides such as defensins. They thereby protect epithelial stem cells from invasion and destruction by intestinal bacteria and contribute to homeostasis of the intestinal microbiota. Based on van Bekkum’s finding of the absence of intestinal GVHD in germ-free mice and the central role of TNF-α release in intestinal GVHD, our group focused on the microbiome/host interactions in GVHD. In prospective studies on genetic risk factors of GVHD, single-nucleotide polymorphisms (SNPs) of NOD2 and also ATG16L1 turned out to be predictive for severe intestinal GVHD and IBD. In addition, however, pulmonary complications revealed an altered production of antibacterial peptides in the presence of NOD2 SNPs. We therefore speculated that human intestinal GVHD similar to IBD might be associated with disruption of the bacterial diversity. We applied metabolomic analyses of metabolites processed in the presence of intestinal bacteria as well as 16s rRNA sequencing to serial urine and stool samples from patients receiving allogeneic stem cell transplantation. Urinary indoxylsulfate (IS) levels dropped during the period of decontamination and use of antibiotics during the neutropenic period but recovered to pretransplant levels in patients with uneventful courses. In contrast, patients developing intestinal GVHD had significantly lower IS levels, suggesting suppression of bacterial diversity in intestinal GVHD. Analysis of 16s rRNA confirmed a major shift from an almost normal distribution pretransplant toward a loss of Firmicutes and an increase in enterococci in the neutropenic period. Although this shift may be partially explained by antibiotic decontamination or treatment during this period that was given to all patients, those patients with subsequent development of intestinal GVHD showed a significantly stronger shift toward enterococci in this period (p=0.002). Whereas patients without intestinal GVHD returned to pretransplant diversity thereafter, predominance of enteroccal flora persisted in patients with intestinal GVHD. These data indicate early microbiome changes in patients with intestinal GVHD. We are currently addressing potential Paneth cell damage and loss of antimicrobial peptides as an underlying mechanism. In summary, our data confirm the relevance of the close interaction of microbiome and host defense in GVHD patients, similar to what has been described in IBD, and raise new options for immune system modulation by restoration of intestinal tolerance. Disclosures:No relevant conflicts of interest to declare.

Patients with Inflammatory Bowel Disease Exhibit Dysregulated Responses to Microbial DNA

BackgroundA critical role for the gut epithelium lies in its ability to discriminate between pathogens and commensals and respond appropriately. Dysfunctional interactions between microbes and epithelia are believed to have a role in inflammatory bowel disease (IBD). In this study, we analyzed microbiota and gene expression in IBD patients and examined responses of mucosal biopsies to bacterial DNA.MethodsBiopsies were taken from non-inflamed areas of the colon in healthy controls (HC) and Crohn's disease (CD) and ulcerative colitis (UC) patients in remission. Biopsies were snap-frozen or cultured with DNA from Lactobacillus plantarum (LP) or Salmonella dublin (SD). Gene expression was analyzed under basal conditions and in response to DNA. Gene networks were analyzed using Ingenuity Pathways software. Mucosal-associated microbiota was analyzed using terminal restriction fragment length polymorphism. Frequency of single nucleotide polymorphisms in NOD2 and TLR9 was assessed.ResultsPatients with IBD had altered microbiota, enhanced expression of inflammatory genes, and increased correlations between specific gene expression and microbes. Principle component analysis showed CD and UC patients to cluster independently from healthy controls in both gene expression and microbial analysis. DNA from LP stimulated anti-inflammatory pathways in controls and UC patients, but induced an upregulation of IL17A in CD patients. There were no differences in SNP frequencies of TLR9 or NOD2 in the groups.ConclusionsPatients with Crohn's disease exhibit altered responses to bacterial DNA. These findings suggest that the gut response to bacterial DNA may depend not only on the specific type of bacterial DNA, but also on the host.

Prevalence of genetic variants associated with inflammatory bowel disease in a healthy First Nations cohort

Inflammatory bowel disease is the result of both genes and environment. Canadian First Nations people, despite living in a region with a high prevalence of inflammatory bowel disease, are relatively protected from this disease. We aimed to compare the carriage of genetic variants associated with inflammatory bowel disease in healthy First Nations and white people. DNA was extracted from the venous blood of healthy First Nations (n = 340) and white (n = 285) participants from Manitoba. Genotyping was performed for 69 single nucleotide polymorphisms (SNPs) with known or suspected associations with inflammatory bowel disease. We compared the genotypes between groups by logistic regression, adjusting for multiple testing. We calculated a risk score for the NOD2 gene by adding the number of risk alleles at three important NOD2 SNPs (G908R, R702W and 3020insC). We found genetic variation between white and First Nations participants at 45 of 69 SNPs. Notably, carriage of the ATG16L1 T300A mutation was lower in First Nations participants (p = 4.1 × 10(-30)). Cumulative carriage of important NOD2 variants was significantly lower among First Nations participants (3.9% v. 15.2%; p < 0.0001 for risk score) than among white participants. Risk variants in IL23R (p = 0.014) and IL12B (p = 1.2 × 10(-16)), among others, were more prevalent among First Nations participants than among white participants. The low prevalence of variants associated with bacterial processing and handling in First Nations people may explain their relative protection from inflammatory bowel disease. Increased carriage of a number of risk variants, for example in the interleukin-23/Th17 pathway, is especially intriguing given their importance in other inflammatory diseases of high incidence in First Nations populations.

Immunologic and Genetic Markers in Patients With Idiopathic Ocular Inflammation and a Family History of Inflammatory Bowel Disease

To evaluate the prevalence of immunologic and genetic markers in patients with idiopathic ocular inflammation and a family history of inflammatory bowel disease. Matched case-control study. Patients with a diagnosis of idiopathic ocular inflammation and family history of inflammatory bowel disease who did not have inflammatory bowel disease themselves were identified and matched to control patients with idiopathic ocular inflammation. Serum was evaluated for immunologic markers using Prometheus IBD Serology 7. Genomic DNA was analyzed for single nucleotide polymorphisms (SNP) of the NOD2 gene associated with Crohn disease. Fifteen patients with idiopathic ocular inflammation and family history of inflammatory bowel disease were matched to 15 control patients based on age, sex, and race. Eight of 15 patients (53%) with a family history of inflammatory bowel disease had elevated p-ANCA antibody levels compared to 3 of 15 controls (20%) (1-sided P = .04) with a matched analysis odds ratio of 6.0 (1-sided P = .06). Four of 15 patients (27%) with family history of inflammatory bowel disease tested positive for immunologic markers predicting ulcerative colitis, while no control patients tested positive (1-sided P = .06). Carrier rates of NOD2 SNPs did not differ significantly between the test and control groups. One-quarter of patients with idiopathic ocular inflammation and a family history of inflammatory bowel disease had immunologic markers predicting bowel disease, and one-half had elevated p-ANCA levels. Prometheus IBD Serology 7 may be useful in the evaluation of selected patients with unexplained uveitis.

Clinical predictors of inflammatory bowel disease in a genetically well-defined Caucasian population

BackgroundCrohn's disease (CD) and ulcerative colitis (UC), the two main types of inflammatory bowel disease (IBD), are multifactorial conditions of unknown etiology. The objective of this study is to examine the combined gene-environment interactions influencing IBD susceptibility in a well-defined Caucasian cohort in rural mid-America.MethodsPatients were diagnosed to have CD or UC using conventional radiologic, endoscopic, and/or histopathologic findings. Histological diagnosis was made by a single specialist gastrointestinal pathologist with a particular interest in IBD. Information regarding cigarette smoke exposure was obtained by administration of the Behavioral Risk Factor Surveillance System Survey (BRFSS) to all patients. Genomic DNA was extracted from peripheral blood leukocytes, and polymerase chain reaction (PCR) amplification and genotyping were performed for 11 Single Nucleotide Polymorphisms (SNP) in NOD2, IL23r, OCTN1 genes along with IGR.ResultsOur cohort consists of 1196 patients: 435 controls, 485 CD patients, and 276 UC patients. Only patients with genotype data for at least 7 of 11 SNPs were included in our data analysis. The control groups for all 11 SNPs were in Hardy-Weinberg Equilibrium. In genotype-association SNP analysis, all NOD2 SNPs (rs5743293, rs2066844, rs2066845) and the IL23r SNP (rs11465804) showed a significant association to IBD (p < 0.03). A multiple gene-interaction analysis showed an association between NOD2 and IL23r with UC (p = 0.04). There were no associations between any OCTN1 and IGR SNPs and IBD in this cohort. A multivariable logistic regression analysis showed that female gender, "current" or "former" smoking status, family history of IBD, and NOD2 SNP minor alleles were associated with CD.ConclusionIBD remains to be challenging to properly diagnose, characterize, and treat. Our study proposes a combined genetic, phenotypic, and environmental approach in an attempt to better understand IBD. Previously demonstrated associations between OCTN1 and IGR and IBD were not confirmed.

Genetic Predictors of Crohnʼs Disease of the Ileal Pouch Anal Anastomosis: 2011 ACG IBD Award

Purpose: Ileal-pouch anal anastomosis (IPAA) is the surgical treatment of choice for patients with ulcerative colitis (UC) and indeterminate colitis who require surgery. A subsequent change in diagnosis to Crohn's disease (CD) involving the IPAA is an uncommon but increasingly recognized complication of this surgery and can be associated with risk of pouch loss. Based on increasing knowledge of genetic susceptibility in CD and UC, our aim was to determine if genetic factors are associated with risk of being diagnosed with CD of IPAA. Methods: A total of 837 subjects from a DNA bank met inclusion criteria: 97 subjects with CD of IPAA, 470 with “typical” CD and 270 with UC. CD of IPAA was diagnosed on the basis of one or more of the following: 1) colectomy pathology consistent with CD, 2) evidence of ulcers or strictures in the ileum proximal to the pouch in the absence of NSAID use, 3) development of perianal or abdominal fistulizing disease more than 1 year after IPAA surgery. Genotyping for single nucleotide polymorphisms (SNPs) in NOD2 (SNPs 8, 12 and 13), ATG16L1, IRGM, IL23R, and PTPN2 was performed using TaqMan assays. Results: There were baseline differences between the three groups with UC subjects having a higher proportion of male gender, a lower rate of current smoking, and a lower rate of family history of IBD (Table 1). Differences in variant allele frequency across the 3 groups were seen for IL23R, ATG16L1 and NOD2 SNPs but ATG16L1 appeared to best distinguish CD of IPAA from UC subjects. Multivariable baseline-category logit regression analysis was performed to assess associations between ATG16L1, smoking history and family history with CD of IPAA disease status versus UC and CD separately. The ATG16L1 G allele variant (OR = 1.4; P = 0.05) and current smoking (OR = 6.8; P < 0.001) were associated with increased risk of CD of IPAA compared to UC whereas no differences were seen between CD of IPAA versus CD. For each ATG16L1 G allele, subjects were 40% more likely to have CD of IPAA versus UC after adjusting for smoking and family history.Table 1: Demographic features and genotype resultsConclusion: The ATG16L1 variant is associated with increased risk of CD of IPAA. However, since this variant also occurs commonly in UC, its use in predicting subsequent diagnosis of CD at time of surgery for UC is limited. Current smoking, a modifiable risk factor, is strongly associated with CD of IPAA.Table 2: Logistic regression model: Crohn's of the Pouch vs, ulcerative colitis

Efficacy of differential non-invasive approaches in determining the clinical course in patients with Crohn's disease

Background: We tested the hypothesis that, elevated levels of C-reactive protein might serve as prognostic marker for the classification of Crohn’s disease and its clinical course. Objectives: The present study was undertaken to explore if serum C-reactive protein (sCRP) levels along with the conventional cytogenetic and molecular genetic approaches might serve as efficient prognostic markers with respect to disease classification and clinical course in Crohn’s disease (CD) patients. Methods: We enrolled 43 patients with Crohn’s disease from Tamilnadu region, south of India. The patients were mainly classified into four groups based on disease location. A further sub-classification based on activity of disease was also undertaken in the study. Classification of type of disease activity was based on colonoscopic reports and radiological findings. An equal number of healthy normal age and sex-matched controls were also taken for the study. Results: A positive correlation between sCRP levels, and disease location was observed. Employing a cut-off level of 10 mg/dL, the index CRP level was found to discriminate patients with different locations of the disease along with disease condition when compared to controls. Cytogenetic analysis showed sporadic changes in such patients. The widely reported NOD2 single nucleotide polymorphisms (SNPs) were absent in the patients studied. Conclusion: Different levels of sCRP seem to correlate well with disease location and disease activity. In some of the patients, the CRP levels appeared to reflect disease activity, while in others persistently high levels seem to suggest active disease. Altogether, a positive correlation of CDAI values with CRP levels along with an increase in frequency of chromosomal aberrations was observed in CD patients. Keywords: Chromosomal aberrations, crohn’s disease, c-reactive protein, inflammation, NOD2, SNP

Evaluation of 22 genetic variants with Crohn's Disease risk in the Ashkenazi Jewish population: a case-control study

BackgroundCrohn's disease (CD) has the highest prevalence among individuals of Ashkenazi Jewish (AJ) descent compared to non-Jewish Caucasian populations (NJ). We evaluated a set of well-established CD-susceptibility variants to determine if they can explain the increased CD risk in the AJ population.MethodsWe recruited 369 AJ CD patients and 503 AJ controls, genotyped 22 single nucleotide polymorphisms (SNPs) at or near 10 CD-associated genes, NOD2, IL23R, IRGM, ATG16L1, PTGER4, NKX2-3, IL12B, PTPN2, TNFSF15 and STAT3, and assessed their association with CD status. We generated genetic scores based on the risk allele count alone and the risk allele count weighed by the effect size, and evaluated their predictive value.ResultsThree NOD2 SNPs, two IL23R SNPs, and one SNP each at IRGM and PTGER4 were independently associated with CD risk. Carriage of 7 or more copies of these risk alleles or the weighted genetic risk score of 7 or greater correctly classified 92% (allelic count score) and 83% (weighted score) of the controls; however, only 29% and 47% of the cases were identified as having the disease, respectively. This cutoff was associated with a >4-fold increased disease risk (p < 10e-16).ConclusionsCD-associated genetic risks were similar to those reported in NJ population and are unlikely to explain the excess prevalence of the disease in AJ individuals. These results support the existence of novel, yet unidentified, genetic variants unique to this population. Understanding of ethnic and racial differences in disease susceptibility may help unravel the pathogenesis of CD leading to new personalized diagnostic and therapeutic approaches.

The NOD2 Single Nucleotide Polymorphisms rs2066843 and rs2076756 Are Novel and Common Crohn's Disease Susceptibility Gene Variants

BackgroundThe aims were to analyze two novel NOD2 variants (rs2066843 and rs2076756) in a large cohort of patients with inflammatory bowel disease and to elucidate phenotypic consequences.Methodology/Principal FindingsGenomic DNA from 2700 Caucasians including 812 patients with Crohn's disease (CD), 442 patients with ulcerative colitis (UC), and 1446 healthy controls was analyzed for the NOD2 SNPs rs2066843 and rs2076756 and the three main CD-associated NOD2 variants p.Arg702Trp (rs2066844), p.Gly908Arg (rs2066847), and p.Leu1007fsX1008 (rs2066847). Haplotype and genotype-phenotype analyses were performed. The SNPs rs2066843 (p = 3.01×10−5, OR 1.48, [95% CI 1.23-1.78]) and rs2076756 (p = 4.01×10−6; OR 1.54, [95% CI 1.28-1.86]) were significantly associated with CD but not with UC susceptibility. Haplotype analysis revealed a number of significant associations with CD susceptibility with omnibus p values <10−10. The SNPs rs2066843 and rs2076756 were in linkage disequilibrium with each other and with the three main CD-associated NOD2 mutations (D'>0.9). However, in CD, SNPs rs2066843 and rs2076756 were more frequently observed than the other three common NOD2 mutations (minor allele frequencies for rs2066843 and rs2076756: 0.390 and 0.380, respectively). In CD patients homozygous for these novel NOD2 variants, genotype-phenotype analysis revealed higher rates of a penetrating phenotype (rs2076756: p = 0.015) and fistulas (rs2076756: p = 0.015) and significant associations with CD-related surgery (rs2076756: p = 0.003; rs2066843: p = 0.015). However, in multivariate analysis only disease localization (p<2×10−16) and behaviour (p = 0.02) were significantly associated with the need for surgery.Conclusion/SignificanceThe NOD2 variants rs2066843 and rs2076756 are novel and common CD susceptibility gene variants.

Genetic Variations of Interleukin-23R (1143A>G) and BPI (A645G), but Not of NOD2, Are Associated with Acute Graft-versus-Host Disease after Allogeneic Transplantation

Single nucleotide polymorphisms (SNPs) in genes of the immune system predict for aGVHD and mortality after allo-SCT. We investigated the effect of SNPs in the NOD2, BPI, and IL-23R genes on posttransplantation outcome in a cohort of 304 patients. NOD2 patient and donor genotype and BPI recipient genotype were not associated with the occurrence of aGVHD. However, IL-23R-SNP in the donor was correlated with less aGVHD. This association could be confirmed in multivariate analysis (odds ratio [OR], 0.39; P = .039), which identified in vivo T cell depletion (OR, 0.32; P < .001) and multiagent GVHD prophylaxis (OR, 0.51; P = .031) as other independent factors predicting for less-severe aGVHD. This multivariate model also revealed a trend toward less aGVHD in patients receiving a BPI G allele transplant (OR, 0.60; P = .067) and in those receiving a transplant from an HLA-matched donor (OR, 0.57; P = .058). Incontrast, relapse was more frequent in patients with NOD2-SNPs (46.2% for SNP vs 33.2% for wild-type; P= .020). This association was found to be of borderline significance in multivariate analysis. Neither BPI nor IL-23R genotype predicted for relapse, and none of the investigated SNPs was correlated with 5-year overall survival. In our analysis, NOD2 SNPs did not predict aGVHD, but IL-23R(1142A>G) and BPI(A645G) SNPs appeared to be promising markers in this regard. The importance of these markers in prediction models for GVHD and relapse remain to be defined in large prospective clinical trials.