Variants of CARD15, TNFA and PTPN22 and susceptibility to Crohn's disease in the Czech population: high frequency of the CARD15 1007fs

The PTPN22 C1858T (R620W) functional polymorphism in inflammatory bowel disease

Objective

In view of the discrepant data regarding the association between the protein tyrosine phosphatase non-receptor 22 (PTPN22) rs2476601 (R620W, 1858C→T) polymorphism and susceptibility to autoimmune diseases including inflammatory bowel diseases (IBD), we investigated whether this functional single-nucleotide polymorphism influences IBD risk in a group of Moroccan patients.

Results

This is the first report on the prevalence of PTPN22 (R620W) variant in a Moroccan cohort. No evidence of statistically significant differences was observed when the PTPN22 (R620W) allele and genotype distribution among IBD, Crohn’s disease (CD), ulcerative colitis (UC) patients and healthy controls were compared. The frequency of the variant allele in healthy subjects was 1.77% compared to 2.56% in the IBD patients and 1.85% in CD patients. Furthermore, the frequency of this allele was increased in UC patients compared to controls (4.17% vs. 1.77%, OR = 2.42, 95% CI 0.82–7.08; P = 0.09), but the difference was not statistically significant. Our data suggest a lack of association between PTPN22 R620W variant and IBD susceptibility in Moroccan patients.

Crohn's disease - genetic factors and progress of the disease

BACKGROUND AND OBJECTIVES

Crohn's disease is a multifactorial inflammatory disease affecting mainly the gastrointestinal tract. The genetic factors that are involved in the disease include mainly three mutations of the gene NOD2/CARD15 (R702W, G908R, 3020insC). The aim of this study was to determine the relationship between the presence of these variants and disease phenotype.

MATERIAL AND METHODS

70 patients with Crohn's disease were examined for the presence of the above-mentioned mutations. The researchers used the medical records to retrospectively obtain clinical data and together with the information obtained prospectively according to the protocol they analysed the connection between gene mutations and disease phenotype.

RESULTS

At least one mutation was found in 22 patients with Crohn's disease (32%), four patients were found to have two different mutations (composed heterozygotes - 6%) and six patients (9%) were homozygotes for the 3020insC gene. No significant differences were found between the groups with wild-type form and the mutated form of the NOD2 / CARD15 gene with respect to age at the time of diagnosis, form of the disease or localization according to the Montreal classification.

CONCLUSION

Mutations of the NOD2 / CARD15 gene did not significantly affect the frequency of reoperations, homozygotes with 3020insC gene mutations, however, represented a high risk group. The phenotype was not related significantly to the presence of the examined mutations.

rs2476601 polymorphism in PTPN22 is associated with Crohn's disease but not with ulcerative colitis: a meta-analysis of 16,838 cases and 13,356 controls

Background

Although the rs2476601 polymorphism of PTPN22 has been reported to be a susceptibility gene for Crohn’s disease (CD), results from different studies vary and remain inconclusive. Also, no association has been found between rs2476601 and the risk of ulcerative colitis (UC). The aim of this meta-analysis was to investigate the association between this PTPN22 polymorphism (rs2476601) and the risk of inflammatory bowel disease, UC and CD.

Methods

We performed a meta-analysis by identifying relevant candidate gene-based studies from EMBASE and MEDLINE. Odds ratios (OR) and 95% confidence intervals (CI) were calculated to estimate the strength of associations between rs2476601 and inflammatory bowel diseases, using a fixed effect or random effect model. Publication bias was also assessed.

Results

By pooling 14 different studies, 13,356 controls, 8182 patients with CD, and 8656 with UC were included. We found that the T allele of PTPN22 was not significantly associated with a higher risk of developing UC (OR 1.06, 95%CI 0.98-1.14) but was associated with a decreased risk of developing CD (OR 1.28, 95%CI 1.17-1.40). The T allele in rs2476601 lowered the risk of CD by 22%.

Conclusion

This study shows that PTPN22 (rs2476601) is significantly associated with the risk of developing CD, but has no association with UC. This suggests that these diseases have different pathways involved in their pathophysiology.

Association of tumor necrosis factor-α and -β gene polymorphisms in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a complex, multifactorial, chronic inflammatory disorder of the gastrointestinal tract in which immune dysregulation caused by genetic and/or environmental factors plays an important role. The aim of this case–control study was to evaluate the association of tumor necrosis factor-alpha (TNF-α) (308) and -β (+252) polymorphisms with susceptibility of IBD. A total of 379 Saudi subjects including 179 IBD patients (ulcerative colitis (UC) =84 and Crohn’s disease (CD) =95) and 200 age- and sex-matched healthy controls were recruited. TNF-α and TNF-β genes were amplified using an amplification refractory mutation systems polymerase chain reaction methodology to detect TNF-α (−308) and -β (+252) polymorphisms. The frequency of the GA genotype of TNF-α (−308G/A) was higher, and the frequencies of the GG and AA genotypes were significantly lower in IBD patients compared with those in controls, indicating that genotype GA-positive individuals are susceptible to IBD and that the GG and AA genotypes exert a protective effect. The frequency of allele A of TNF-α (−308G/A) was significantly higher and that of allele G was lower in IBD patients compared with those in controls, indicating an association of allele A with IBD risk in Saudi patients. On stratification of IBD patients into UC and CD, an almost similar pattern was noticed in both the groups. The results of TNF-β (+252A/G) polymorphisms showed a significant increase in the frequency of the GG genotype in IBD patients, suggesting a positive association of GG genotype with IBD risk. On stratification of IBD patients into UC and CD, the genotype GG of TNF-β was associated with susceptibility risk to UC but not CD. The frequencies of alleles and genotypes of both TNF-α and-β polymorphisms are not affected by sex or type of IBD (familial or sporadic). TNF-α (−308G/A) and TNF-β (+252A/G) polymorphisms are associated with risk of developing IBD in Saudi population.

NOD2/CARD15 mutations in Polish and Bosnian populations with and without Crohn's disease: prevalence and genotype-phenotype analysis

Data on prevalence and phenotypic consequences of nucleotide-binding oligomerisation domain 2/caspase recruitment domains 15 (NOD2/CARD15) variants in Crohn's disease (CD) population in Poland and Bosnia and Herzegovina (B&H) are nonexistent. We aimed to determine the prevalence of NOD2/CARD15 mutations and their association with disease phenotype in Polish and Bosnian patients with CD and in healthy controls. We prospectively recruited 86 CD patients and 83 controls in Poland and 30 CD patients and 30 controls in B&H, 229 in total. We determined the prevalence of NOD2/CARD15 mutations and their association with the disease phenotype according to Montreal classification. Participants were genotyped for Leu1007fsinsC and Gly908Arg mutations. At least one CD-associated allele was found in 29/86 (33.7%) of Polish CD patients and in 9/83 (10.8%) of healthy controls (p<0.001). In both CD patients and controls in Bosnian sample, at least one NOD2 mutation was found in equal number of patients (3/30; 10%) with all of the NOD2 mutation positive CD patients being homozygous, while controls being heterozygous. In Polish sample, perianal disease was less frequent in CD patients with any NOD2 mutation (1/21; 4.8%) compared to those without (11/41; 26.8%; p=0.046). Higher percentage of patients with NOD2 mutations had history of CD related surgery when compared with those without mutations (66.7% vs. 43.3%; p=0.05). The risk for CD is increased in patients with NOD2 mutations (Poland) and especially in the presence of homozygous NOD2 mutations (Poland and Bosnia). The presence of variant NOD2 alleles is associated with increased need for surgery and reduced occurrence of perianal disease.

The relationship between serum bilirubin and Crohn's disease

BACKGROUND

The oxidative stress is thought to play an important role in Crohn's disease (CD). As serum bilirubin represents the major endogenous antioxidant, this article aimed to evaluate in a clinical study, whether serum bilirubin levels and genes affecting its systemic concentrations are associated with CD.

METHODS

This exploratory case-control study was based on pediatric (n = 119) and adult (n = 504) patients with CD and 370 appropriate healthy control subjects. The (GT)n and (TA)n dinucleotide variations in heme oxygenase 1 (HMOX1) and bilirubin UDP-glucuronosyl transferase (UGT1A1) gene promoters were determined by fragment analysis. Serum bilirubin levels were compared in a subset of 90 cases and 229 controls, for whom biochemical data were available.

RESULTS

Substantially lower serum bilirubin levels were detected in patients with CD compared with controls (7.4 versus 12.1 μmol/L, P < 10). Serum bilirubin levels were significantly lower in patients with CD within all UGT1A1*28 genotypes (P < 0.05). UGT1A1*28 homozygotes with wild-type NOD2 gene variant exhibited significant delay in CD manifestation (P = 0.004), while the protective effect of UGT1A1*28 homozygosity was lost in those patients with mutated NOD2 gene. No associations between CD risk and individual HMOX1 gene variants were observed.

CONCLUSIONS

CD is associated with significantly low serum bilirubin levels, most likely as a result of increased oxidative stress accompanying this inflammatory disease. UGT1A1*28 allele homozygosity, responsible for higher bilirubin levels, seems to be an important modifier of CD manifestation.

Differential association of two PTPN22 coding variants with Crohn's disease and ulcerative colitis

BACKGROUND

The PTPN22 gene is an important risk factor for human autoimmunity. The aim of this study was to evaluate for the first time the role of the R263Q PTPN22 polymorphism in ulcerative colitis (UC) and Crohn's disease (CD), and to reevaluate the association of the R620W PTPN22 polymorphism with both diseases.

METHODS

A total of 1677 UC patients, 1903 CD patients, and 3111 healthy controls from an initial case-control set of Spanish Caucasian ancestry and two independent sample sets of European ancestry (Dutch and New Zealand) were included in the study. Genotyping was performed using TaqMan SNP assays for the R263Q (rs33996649) and R620W (rs2476601) PTPN22 polymorphisms. Meta-analysis was performed on 6977 CD patients, 5695 UC patients, and 9254 controls to test the overall effect of the minor allele of R620W and R263Q polymorphisms.

RESULTS

The PTPN22 263Q loss-of-function variant showed initial evidence of association with UC in the Spanish cohort (P = 0.026, odds ratio [OR] = 0.61, 95% confidence interval [CI]: 0.39-0.95), which was confirmed in the meta-analysis (P = 0.013 pooled, OR = 0.69, 95% CI: 0.51-0.93). In contrast, the 263Q allele showed no association with CD (P = 0.22 pooled, OR = 1.16, 95% CI: 0.91-1.47). We found in the pooled analysis that the PTPN22 620W gain-of-function variant was associated with reduced risk of CD (P = 7.4E-06 pooled OR = 0.81, 95% CI: 0.75-0.89) but not of UC (P = 0.88 pooled, OR = 0.98, 95% CI: 0.85-1.15).

CONCLUSIONS

Our data suggest that two autoimmunity-associated polymorphisms of the PTPN22 gene are differentially associated with CD and UC. The R263Q polymorphism only associated with UC, whereas the R620W was significantly associated with only CD.

Two independent genetic factors responsible for the associations of the IBD5 locus with Crohn's disease in the Czech population

BACKGROUND

The role of the IBD5 locus in development of Crohn's disease (CD) has not been clarified. In the Czech population we examined its genetic association using variants of the SLC22A4 (rs1050152), SLC22A5 (rs2631367), two single nucleotide polymorphisms (SNPs) shown to be associated with CD in genome-wide studies (rs6596075 and rs2188962), and four SNPs previously shown to tag the haplotype blocks 4, 7, 9, 10 of the IBD5 locus (IGR2063b_1, IGR2230a_1, IGR100Xa_1, IGR3236a_1).

METHODS

The genotype, phenotype, and allelic frequencies were compared between 469 unrelated patients with CD (177 pediatric-onset, 292 adult-onset) and 470 unrelated healthy controls, all Caucasians of Czech ancestry.

RESULTS

The most significant difference between patients and controls was found for the SNP rs6596075 (odds ratio [OR] = 0.70 for the G allele; 95% CI 0.52-0.94) in the dominant model and SNP IGR2063b_1 (OR = 1.38 for the G allele; 95% CI 1.14-1.67) in the log-additive model. We found a strong linkage disequilibrium across the IBD5 locus except rs6596075. The haplotype consisting of minor alleles of all tested SNPs except rs6596075 was carried by 31% patients and 23% control subjects (OR = 1.35, 95% CI 1.06-1.72). The association of variants in SLC22A4 and SLC22A5 was dependent on this risk haplotype, while the strong association of the rs6596075 was seemingly independent. In the analysis of subphenotypes we found only an association of the penetrating disease with rs6596075 (OR = 2.13; 95% CI 1.31-3.47).

CONCLUSIONS

Our study confirms the importance of IBD5 in determining CD susceptibility, and demonstrates that two independent genetic factors may be responsible for the association observed within this locus.

SNPman: a program for genotype calling using run data from TaqMan allelic discrimination

SUMMARY

The SNPman program calls the genotypes of single nucleotide polymorphisms (SNP) from TaqMan allelic discrimination assays. It utilizes the fluorescence data collected over the whole PCR run, rather than relying on the end point fluorescence measurements that is the basis of the genotype calling process in most software solutions sold with the real-time instruments. This inspection of run data facilitates genotype calls in difficult sample sets, especially in those containing various concentrations of DNA or inhibitors, as indicated by results of a reanalysis of 3738 genotyping samples. The program works with data from three different widely used PCR instruments.

AVAILABILITY

The compiled program is available online at http://sourceforge.net/projects/snpman/files/, along with its user documentation and demonstration data files. It is free of charge for non-commercial users.

CONTACT

Ondrej.Cinek@Lfmotol.cuni.cz

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Role of negative regulators of TLR/IL-1 signaling in the pathogenesis of inflammatory bowel disease

Inflammatory bowel disease (IBD) is an autoimmune-like disorder characterized by chronic, idiopathic inflammation of the intestinal mucosa. Ulcerative colitis and Crohn's disease are known as the two forms of IBD. Although the etiology of IBD is still unclear, many experimental and clinical observations suggest the involvement of environmental, hereditary and immunological factors in the pathogenesis of IBD. Recent studies have showed that IBD is associated with immunologic dysfunction. Toll-like receptors (TLR) are pathogen pattern recognition receptors expressed by immune and nonimmune cells in the intestinal mucosa that play a central role in the initiation of innate immune responses and subsequent adaptive immune responses to microbial pathogens. In recent years there has been rapid progress in our understanding of the role of positive regulation of TLR signaling in the pathogenesis of IBD. However, the role of negative regulators of TLR signaling in this process remains unclear and will therefore be summarized in this paper.

Meta-analysis: polymorphisms in TNF-alpha gene promoter and Crohn's disease

BACKGROUND

Tumour necrosis factor alpha (TNF-alpha) is involved in the pathogenesis of Crohn's disease (CD). However, results on the association between the polymorphisms in TNF-alpha promoter and the risk of CD are inconsistent.

AIM

To perform a quantitative synthesis for the genetic polymorphisms in TNF-alpha promoter and CD risk.

METHODS

Databases were searched (up to 2009) and 31 studies were included. Risks of CD associated with the polymorphisms in TNF-alpha promoter were assessed.

RESULTS

Overall, individuals with -1031 TC+CC genotype had a slightly increased risk to develop CD compared with individuals with -1031 TT genotype (OR, 1.32; 95% CI, 1.03-1.70). In the further stratified analysis, we found Asians with the -1031T>C, -863 C>A and -857 C>T variant polymorphisms have almost one and a half CD risk compared with other genotypes (OR, 1.58; 95% CI, 1.16-2.15; OR, 1.55; 95% CI, 1.18-2.02; OR, 1.54; 95% CI, 1.19-1.99 respectively). We did not find -308 G>A variant associated with CD location and disease behaviours in stratified analysis.

CONCLUSIONS

TNF-alpha polymorphisms in the promoter region might be used as a biomarker for CD risk prediction. Larger studies with mixed ethnicity subjects and stratified by clinical and sub clinical characteristics are needed to validate our findings.

The CTLA4 variants may interact with the IL23R- and NOD2-conferred risk in development of Crohn's disease

BACKGROUND

The CTLA4 (cytotoxic T-lymphocyte antigen 4) gene is associated with several immunopathologic diseases and because of its important immuno-regulatory role it may be considered also a plausible candidate for a genetic association with inflammatory bowel diseases. Previously published studies found no association of CTLA4 with Crohn's disease itself, but some indicated an association with its subphenotypes. The aim of this study was to assess the association in the Czech population, using a set of markers shown to associate with other diseases.

METHODS

Six polymorphisms within the CTLA4 region were investigated in 333 patients with Crohn's disease and 482 unrelated healthy controls, all Caucasians of Czech origin. The genotypes of the SNPs were determined using the TaqMan SNP genotyping assays. Haplotypes were reconstructed using an expectation-maximization algorithm, and their association with the condition was assessed using log-linear modeling. Then, potential interactions were tested between the CTLA4 variants and other genetic factors known to confer the disease susceptibility.

RESULTS

No crude associations with Crohn's disease were found for the tested CTLA4 variants under the log-additive or dominant models. However, when stratified for the genetic risk conferred by the variants in the NOD2 (the p.Leu1007fsX1008, rs5743293) or the IL23R (p.R381Q, rs11209026), a significant negative association emerged for the minor alleles of CTLA4 CT60 (rs3087243), JO31 (rs11571302), JO27-1 (rs11571297) polymorphisms. This negative association with CTLA4 was apparent only in the strata defined by presence minor alleles at the NOD2 rs5743293 (here the CTLA4 CT60 A coffered an OR = 0.43, 95%CI 0.19 - 0.95 for the presence of CT60 A), or IL23R rs11209026 (here the OR for presence of CT60 A was 0.23, 95%CI 0.07 - 0.71). We observed this effect also for the haplotype consisting of minor alleles of the three tightly linked CTLA4 markers. Furthermore, this haplotype was associated with the younger age at diagnosis (OR 1.52, 95%CI 1.09 - 2.11, p = 0.014).

CONCLUSIONS

A protective effect of a CTLA4 haplotype was unmasked after stratification for the risk variants in the NOD2 and IL23R genes, and may point towards the biological relevance of the molecule in the pathogenesis of the disease.

Research progress in susceptible genes of inflammatory bowel disease

The mechanism of inflammatory bowel disease (IBD) is partially understood, but it is certain that a genetic predisposition, through the inheritance of a number of contributory genetic polymorphisms, contributes to the pathogenesis of IBD. These variant forms of genes may be associated with an abnormal response to normal luminal bacteria. Those genes that have been consistently associated with IBD thus far primarily fall into one of three classes: those affecting bacterial recognition, those affecting immune response, and a third group affecting mucosal transport polarity or mucosal transporter function. This article reviews the IBD related genes mentioned above.