Interaction of the major inflammatory bowel disease susceptibility alleles in Crohn’s disease patients

Intronic region polymorphisms of autophagy gene ATG16L1 predispose individuals to Hepatitis B virus infection

Intronic region polymorphisms, rs2241879 G/A, rs13005285 G/T, and rs7587633 C/T of ATG16L1 were analyzed in this case-control study in HBV-infected patients to find their role in HBV infection. The mutant alleles rs2241879A (OR = 1.57) and rs13005285T (OR = 1.39) were the risk factors for HBV infection. These alleles were associated with different stages of infection: asymptomatic rs13005285T (OR = 1.91), acute rs13005285T (OR = 1.58), chronic rs2241879A (OR = 1.62), and cirrhosis rs2241879A (OR = 3.02). Moreover, on applying various genetic models, rs2241879A predisposed individuals to HBV infection (homozygous model; AA vs. GG; OR = 2.58). Patients with CHB infection, the homozygous model showed an OR of 2.79, while the dominant model had an OR of 1.96. Among cirrhosis patients, the homozygous model resulted in an OR of 9.43, and the dominant model showed an OR of 4.92. The rs13005285 variant significantly increased the risk of acute HBV infection in the co-dominant model (OR = 1.78) and dominant model (OR = 1.84). Individuals with the rs7587633 variant at the asymptomatic stage of infection showed a reduced risk under the co-dominant model (OR = 0.41) and the dominant model (OR = 0.54). We identified GCG, GTG and GCT haplotypes corresponding to rs2241879, rs7587633, and rs13005285 SNPs, which play a protective role in HBV infection. Furthermore, we also developed a PCR-ARFLP assay for genotyping rs13005285G/T which would help to analyze this polymorphism in low-income settings where high-end instrumentation is not accessible.

An artificial-restriction fragment length polymorphism (A-RFLP) method for genotyping intronic SNP rs7587633 C/T of ATG16L1

SNPs could either cause a disorder or directly alter the efficacy of a particular treatment and act as biological markers. The SNP rs7587633 C/T present in the intronic region of the ATG16L1 gene has been studied for its role in psoriasis vulgaris and Palmoplantar pustulosis. To genotype rs7587633 C/T using PCR-RFLP no restriction site is present for any of the restriction enzymes at the SNP position. To develop an artificial-RFLP method for genotyping rs7587633 C/T, the forward primer was designed in such a way that it resulted in the creation of an EcoRI restriction site in the amplified product which could further be digested with EcoRI to find the genotype of the individual. The newly developed A-RFLP method was applied to genotype the SNP rs7587633 C/T in DNA samples of 100 healthy control individuals. The allelic and genotypic frequencies of the SNPs were 0.80(C), 0.20(T) and 65%(CC), 31%(CT) and 4%(TT), respectively. In conclusion, we developed an A-RFLP method to genotype the SNP rs7587633 C/T which is not present in any of the natural restriction sites and this method could be applied to genotype this SNP in various populations/diseases to find its role.

ATG16L1 rs2241880/T300A increases susceptibility to perianal Crohn's disease: An updated meta-analysis on inflammatory bowel disease risk and clinical outcomes

BACKGROUND

ATG16L1 plays a fundamental role in the degradative intracellular pathway known as autophagy, being a mediator of inflammation and microbial homeostasis. The variant rs2241880 can diminish these capabilities, potentially contributing to inflammatory bowel disease (IBD) pathogenesis.

OBJECTIVES

To perform an updated meta-analysis on the association between ATG16L1 rs2241880 and IBD susceptibility by exploring the impact of age, ethnicity, and geography. Moreover, to investigate the association between rs2241880 and clinical features.

METHODS

Literature searches up until September 2022 across 7 electronic public databases were performed for all case-control studies on ATG16L1 rs2241880 and IBD. Pooled odds ratios (ORP ) and 95% CI were calculated under the random effects model.

RESULTS

Our analyses included a total of 30,606 IBD patients, comprising 21,270 Crohn's disease (CD) and 9336 ulcerative colitis (UC) patients, and 33,329 controls. ATG16L1 rs2241880 was significantly associated with CD susceptibility, where the A allele was protective (ORP : 0.74, 95% CI: 0.72-0.77, p-value: <0.001), while the G allele was a risk factor (ORP : 1.23, 95% CI: 1.09-1.39, p-value: 0.001), depending on the minor allele frequencies observed in this multi-ancestry study sample. rs2241880 was predominantly relevant in Caucasians from North America and Europe, and in Latin American populations. Importantly, CD patients harbouring the G allele were significantly more predisposed to perianal disease (ORP : 1.21, 95% CI: 1.07-1.38, p-value: 0.003).

CONCLUSIONS

ATG16L1 rs2241880 (G allele) is a consistent risk factor for IBD in Caucasian cohorts and influences clinical outcomes. As its role in non-Caucasian populations remains ambiguous, further studies in under-reported populations are necessary.

Saudi consensus guidance for the management of inflammatory bowel disease during pregnancy

ABSTRACT

The management of inflammatory bowel disease (IBD) in pregnant women is challenging and must be addressed on a patient-by-patient basis. Optimal patient management requires a multidisciplinary team and clear evidence-based recommendations that cater to this subset of patients. In this article, we provide concise guidelines and clinical care pathway for the management of IBD in pregnant women. Our recommendations were developed by a multidisciplinary working group that includes experts from the Saudi Ministry of Health in collaboration with the Saudi Gastroenterology Association and the Saudi Society of Clinical Pharmacology. All recommendations are based on up-to-date information following an extensive literature review. A total of 23 evidence-based expert opinion recommendations for the management of IBD in pregnant women are herein provided.

Association between Taxonomic Composition of Gut Microbiota and Host Single Nucleotide Polymorphisms in Crohn's Disease Patients from Russia

Crohn's disease (CD) is a chronic relapsing inflammatory bowel disease of unknown etiology. Genetic predisposition and dysbiotic gut microbiota are important factors in the pathogenesis of CD. In this study, we analyzed the taxonomic composition of the gut microbiota and genotypes of 24 single nucleotide polymorphisms (SNP) associated with the risk of CD. The studied cohorts included 96 CD patients and 24 healthy volunteers from Russia. Statistically significant differences were found in the allele frequencies for 8 SNPs and taxonomic composition of the gut microbiota in CD patients compared with controls. In addition, two types of gut microbiota communities were identified in CD patients. The main distinguishing driver of bacterial families for the first community type are Bacteroidaceae and unclassified members of the Clostridiales order, and the second type is characterized by increased abundance of Streptococcaceae and Enterobacteriaceae. Differences in the allele frequencies of the rs9858542 (BSN), rs3816769 (STAT3), and rs1793004 (NELL1) were also found between groups of CD patients with different types of microbiota communities. These findings confirm the complex multifactorial nature of CD.

Diagnosis and Classification of Fistula from Inflammatory Bowel Disease and Inflammatory Bowel Disease-Related Surgery

Fistula in inflammatory bowel disease (IBD) is a well-known yet poorly understood phenotype. Pathophysiology is largely based on the activation of the epithelial-mesenchymal transition (EMT); however, interactions with the microbiome, genetics, mechanical stress and the presence of stricturing disease, and surgical complications play a role. Perianal penetrating disease represents a more severe phenotype in IBD. Pouch-associated fistula can arise as a result of an anastomotic leak, surgical complications, or Crohn's disease (CD) of the pouch. Classification is site-dependent, includes a range of severity, and informs management. It is important to determine associated symptoms and recognize the complex interplay of underlying etiologies to form the basis of appropriate care.

Twin Brothers and a Sister With CD: A Case Report

Crohn’s disease (CD) has an unknown etiology, but it has a genetic component. Many cases of familial CD have been reported. We describe a Kosovar Albanian family with 6 children, of whom 3 have CD: monozygotic twins and their sister. As far as we know, this is the first such report of CD within a Kosovar family.

The emerging role of neutrophils in autoimmune-associated disorders: effector, predictor, and therapeutic targets

Neutrophils are essential components of the immune system and have vital roles in the pathogenesis of autoimmune disorders. As effector cells, neutrophils promote autoimmune disease by releasing cytokines and chemokines cascades that accompany inflammation, neutrophil extracellular traps (NETs) regulating immune responses through cell-cell interactions. More recent evidence has extended functions of neutrophils. Accumulating evidence implicated neutrophils contribute to tissue damage during a broad range of disorders, involving rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), primary sjögren's syndrome (pSS), multiple sclerosis (MS), crohn's disease (CD), and gout. A variety of studies have reported on the functional role of neutrophils as therapeutic targets in autoimmune diseases. However, challenges and controversies in the field remain. Enhancing our understanding of neutrophils' role in autoimmune disorders may further advance the development of new therapeutic approaches.

TH17/IL23 cytokine gene polymorphisms in bullous pemphigoid

Background

TH17/IL‐23 immune axis is considered to be involved in the pathogenesis of autoimmune and chronic inflammatory diseases. Bullous pemphigoid (BP) is the most frequent autoimmune blistering disease, characterized by the presence of autoantibodies against the components of the dermal‐epidermal junction. Animal studies and characterization of patient samples point toward a contribution of TH17 cells in BP pathogenesis. However, genetic polymorphisms in the genes of TH17/IL‐23 cytokines have not yet been well investigated in BP.

Methods

Detection of polymorphisms in IL‐17A (rs2275913 and rs3819025), IL‐17F (rs2397084 and rs763780), IL‐17RA (rs2229151), and IL‐23R (rs2201841, rs7530511, rs11209026, and rs10889677) genes were performed following the collection of blood samples and DNA extraction from BP patients and controls. Gene expression of IL‐23R was determined by quantitative RT‐PCR analysis.

Results

The prevalence of IL‐23R rs7530511 genotypes and alleles, as well as IL‐23R rs2201841 alleles, is significantly different between the BP patients and controls. While the minor C‐allele of IL‐23R rs7530511 is highly present in the patients, the G‐allele distribution of IL‐23R rs2201841 is significantly more prevalent in the control individuals compared to the BP patients. Genotypes and alleles of other SNPs in IL‐17A, IL‐17F, and IL‐17RA were similarly distributed in patients and controls.

Conclusions

No alteration was found in the gene expression between wild and polymorphic genotypes of IL‐23R (rs2201841 and rs7530511) variations, indicating they do not contribute to altering the levels of gene expression in blood. In summary, our data show that the alleles of two SNPs in IL‐23R rs2201841 and rs7530511 are associated with BP.

The autophagy gene ATG16L1 (T300A) variant is associated with the risk and progression of HBV infection

Autophagy pathway genes variants that play crucial roles in immune responses are involved in many diseases but their role in viral diseases is ill-defined. ATG16L1 gene plays a crucial role in the autophagy process. In this study, we have investigated the role of ATG16L1 variant T300A in the risk of HBV infection. rs2241880 (T300A) variant in 551 HBV infected patients (at various stages of infection) and 247 healthy controls were genotyped applying PCR-RFLP. Data analysis revealed that mutant allele G contributes to the risk of hepatitis B infection. Mutant alleles were significantly associated the HBV risk in allelic (OR = 1.31; 95%CI = 1.06-1.63, p = .01) and homozygous (OR = 1.87; 95%CI = 1.17-2.99, p = .009) models. On stratifying HBV infected individuals according to the stage of infection, a significant association was observed in asymptomatic (allelic; OR = 1.52; 95%CI = 1.10-2.09, p = .01 and homozygous; OR = 2.30; 95%CI = 1.22-4.36, p = .01) and chronic (allelic; OR = 1.36; 95%CI = 1.07-1.73, p = .01 and homozygous; OR = 2.07; 95%CI = 1.22-3.53, p = .008) stages of infection. High HBV DNA levels were associated with mutant genotype GG in asymptomatic and chronic carriers. Significantly higher ALT levels were observed in the liver cirrhosis patients with mutant genotypes. In conclusion, our data suggest that rs2241880 mutant allele carriers (allelic and homozygous models) were associated with increased risk of hepatitis B virus infection in North Indian population.

Genetic polymorphisms of ATG16L1 and IRGM genes in Malaysian patients with Crohn's disease

OBJECTIVE

To investigate the association between genetic polymorphisms in ATG16L1 and IRGM genes and the development of Crohn's disease (CD) in Malaysian patients.

METHODS

Altogether 335 participants were recruited, including 85 patients with CD and 250 unrelated healthy controls, and their informed consent was obtained. Genomic DNA was extracted via a conventional phenol-chloroform extraction method. Six single nucleotide polymorphisms (SNPs) in ATG16L1 and IRGM genes were genotyped using TaqMan SNP genotyping assays. Associations between SNP and CD were determined using Fisher's exact test, odds ratio, and 95% confidence interval. Statistical power and the Hardy-Weinberg equilibrium were also calculated.

RESULTS

Two SNPs (rs2241880 and rs6754677) in the ATG16L1 gene were significantly associated with the onset of CD in the Malaysian population. The A allele and homozygous A/A genotype of the rs2241880 A/G polymorphism were protective against CD in the overall Malaysian and Malay population. The G allele and homozygous G/G genotype of the rs6754677 G/A polymorphism were protective in the Indian population, whereas the homozygous A/A genotype showed a risk of developing CD. The homozygous G/G genotype of IRGM rs11747270 was significantly present in the controls. However, this significance was not observed in a race-stratified analysis. All three ATG16L1 SNPs were associated with inflamed terminal ileum. IRGM rs4958847 and rs11747270 increased the risk of developing arthritis in patients with CD.

CONCLUSION

We found a significant association between SNP, which are located in autophagy-related genes, and CD in a Malaysian population.

The absence of interleukin 10 affects the morphology, differentiation, granule content and the production of cryptidin-4 in Paneth cells in mice

Paneth cells (PCs) are specialized epithelial cells of the small bowel that contain multiple secretory granules filled with antimicrobial peptides and trophic factors, which are essential for the control of the microorganisms growth and maintaining intestinal integrity. Alterations in their function are associated with an imbalance of the normal microbiota, gastrointestinal infections and inflammatory processes, such as Crohn's disease (CD). One of the most common murine models for studying CD is IL-10-/- mouse. IL-10-/- mice when housed in conventional conditions and take contact with commensal microorganisms develop an acute enterocolitis mediated by a Th1 immune response. Even though, alterations in PCs function are related to CD, they had not been characterized yet in this mouse model. Here we show that in specific pathogen free conditions IL-10-/- mice have aberrant granules and a large number of immature PCs at the bottom of the crypt in the ileum of IL-10-/- mice before developing intestinal inflammation, along with a reduced expression of Indian Hedgehog. In addition, IL-10-/- Paneth cells presented a reduced expression of cryptidin-4, and a heterogeneous distribution of lysozyme+ granules. The alterations in the maturation of the PCs at the bottom of the crypt were not modified after the colonization by the conventional microbiota. On the other hand, depletion of microbiota altered the phenotype, but did not normalize PCs. Our results suggest that IL-10 could be necessary for the integrity of PCs. Moreover, our results help to explain why IL-10-/- mice develop enterocolitis in response to microorganisms.

Association of Autophagy Gene ATG16L1 Polymorphism with Human Prostate Cancer and Bladder Cancer in Turkish Population

Background: Urological cancers (prostate cancer and bladder cancers) are the most common cancers in Western population and its rate is increasing in the Eastern World. Autophagy has appeared as a fundamental repair mechanism for degrading damaged organelles and proteins. It was clear that autophagy gene polymorphisms are correlated with development of inflammatory bowel disease and it can also be related with prostate cancer (PCa) or bladder cancer (BCa). In this study, we aimed to determine if ATG16L1 (Thr300Ala) polymorphism is associated with an increased risk of developing PCa and BCa and to establish correlations between ATG16L1 genotypes and morphological parameters. Methods: This study included 269 healthy controls and 131 patients (62 PCa and 69 BCa) with PCa and BCa. The ATG16L1 (rs2241880) gene regions were amplified using polymerase chain reaction (PCR), detected by restriction fragment length polymorphism (RFLP). Results: At the end of our research, we found out that the genotype AG was prevalent on patients and controls (34% vs 42%), followed by genotypes AA (35% vs 27%) and GG (31% vs 31%) in PCa. The prevalence of genotypes of AA (wild-type), AG (heterozygous mutant) and GG (homozygous mutant) profiles for the ATG16L1 Thr300Ala polymorphism were 35%, 40% and 25% respectively in BCa patients, and 32%, 40% and 28% respectively in healthy control groups. The G allele frequency was 0.53 for in BCa patients and the control groups. Conclusion: No association was found between ATG16L1 (Thr300Ala) polymorphism and patients with PCa and BCa in Turkish population we studied.

Autophagy-related 16-like 1gene polymorphism, risk factors for cardiovascular disease and associated carotid intima-media thickness in postmenopausal women

BACKGROUND

Early identification of asymptomatic postmenopausal women (PW), who are more predisposed to developing cardiovascular disease (CVD), is an important preventive strategy. Autophagy-related 16-like 1 (ATG16L1) is an autophagy gene known to control host immune responses and is associated with a variety of diseases, including CVD.

OBJECTIVE

The aim of the study was to associate the ATG16L1 polymorphism variant with subclinical carotid atherosclerosis in asymptomatic PW.

STUDY DESIGN

This cross-sectional study included 210 Brazilian postmenopausal women (age ≥ 45 years with amenorrhea ≥12 months). Clinical, anthropometric and biochemical assessments were performed to evaluate the cardiovascular risk factors. DNA was extracted from buccal cells and the ATG16L1 (T300A) polymorphism was determined by the polymerase chain reaction (PCR). The carotid intima-media thickness and/or the presence of plaques were evaluated by carotid duplex ultrasound. For statistical analysis, the t-test, logistic regression and analysis of covariance (ANCOVA) were used.

RESULTS

The presence of the polymorphic allele forATG16L1 (T300A) was found in 77.47% (A/G = 49.87%, G/G = 27.60%). The ATG16L1 (T300A) polymorphism is significantly associated with increased carotid intima-media thickness (IMT) after adjustments of the confounding variables (P < .037). No significant associations were observed between the polymorphism with other risk factors for CVD in PW.

CONCLUSION

In postmenopausal women, the ATG16L1 (T300A) polymorphism is significantly associated with increased carotid IMT (marker of atherosclerotic disease) after adjustments of the confounding variables (P < .037). Thus, identifying the ATG16L1 polymorphism is an important strategy for screening asymptomatic PW who are more predisposed to developing CVD.

Targeted Gene Sequencing in Children with Crohn's Disease and Their Parents: Implications for Missing Heritability

Crohn’s disease is a complex genetic trait characterized by chronic relapsing intestinal inflammation. Genome wide association studies (GWAS) have identified more than 170 loci associated with the disease, accounting for ∼14% of the disease variance. We hypothesized that rare genetic variation in GWAS positional candidates also contribute to disease pathogenesis. We performed targeted, massively-parallel sequencing of 101 genes in 205 children with Crohn’s disease, including 179 parent-child trios and 200 controls, both of European ancestry. We used the gene burden test implemented in VAAST and estimated effect sizes using logistic regression and meta-analyses. We identified three genes with nominally significant p-values: NOD2, RTKN2, and MGAT3. Only NOD2 was significant after correcting for multiple comparisons. We identified eight novel rare variants in NOD2 that are likely disease-associated. Incorporation of rare variation and compound heterozygosity nominally increased the proportion of variance explained from 0.074 to 0.089. We estimated the population attributable risk and total heritability of variation in NOD2 to be 32.9% and 3.4%, respectively, with 3.7% and 0.25% accounted for by rare putatively functional variants. Sequencing probands (as opposed to genotyping) to identify rare variants and incorporating phase by sequencing parents can recover a portion of the missing heritability of Crohn’s disease.

Association of ATG16L1 gene haplotype with inflammatory bowel disease in Indians

Inflammatory bowel disease (IBD) is characterized by multigenic inheritance. Defects in autophagy related genes are considered to show genetic heterogeneity between populations. We evaluated the association of several single nucleotide polymorphisms (SNPs) in the autophagy related 16 like 1 (ATG16L1) gene with IBD in Indians. The ATG16L1 gene was genotyped for ten different SNPs using DNA extracted from peripheral blood of 234 patients with Crohn's disease (CD), 249 patients with ulcerative colitis (UC) and 393 healthy controls The SNPs rs2241880, rs4663396, rs3792106, rs10210302, rs3792109, rs2241877, rs6737398, rs11682898, rs4663402 and rs4663421 were genotyped using the Sequenom MassArray platform. PLINK was used for the association analysis and pairwise linkage disequilibrium (LD) values. Haplotype analysis was done using Haploview. All SNPs were in Hardy Weinberg equilibrium in cases and controls. The G allele at rs6737398 exhibited a protective association with both CD and UC. The T allele at rs4663402 and C allele at rs4663421 were positively associated with CD and UC. The T allele at rs2241877 exhibited protective association with UC only. The AA genotype at rs4663402 and the GG genotype at rs4663421 were protectively associated with both CD and UC. Haplotype analysis revealed that all the SNPs in tight LD (D' = 0.76-1.0) and organized in a single haplotype block. Haplotype D was positively associated with IBD (P = 5.8 x 10-6 for CD and 0.002 for UC). SNPs in ATG16L1 were associated with IBD in Indian patients. The relevance to management of individual patients requires further study.

Association between ATG16L1 gene polymorphism and the risk of Crohn's disease

Objective

To perform a meta-analysis to evaluate studies investigating the association between ATG16L1 gene polymorphism and Crohn’s disease.

Methods

PubMed, Embase and Web of Science databases were searched for all studies focusing on the association of ATG16L1 and Crohn’s disease. Combined odds ratios with 95% confidence intervals were calculated for four genetic models (allelic model: G allele versus A allele; additive model: GG versus AA; dominant model: GA + GG versus AA; recessive model: GG versus GA + AA) using either a random effects or fixed effects model.

Results

A total of 47 case–control studies involving 18 638 cases and 30 181 controls were included in the final meta-analysis. There was a significant association between ATG16L1 and Crohn’s disease for all four genetic models. Significant associations were also shown in subgroup analyses when stratified by study design (population- or hospital-based).

Conclusion

In this meta-analysis, the ATG16L1 genotype was significantly associated with the risk of developing Crohn’s disease.

May autophagy be a novel biomarker and antitumor target in colorectal cancer?

Autophagy is a catabolic process associated with intracellular self-digestion of damaged organelles or redundant proteins enabling maintenance of cell homeostasis. It is accepted that impaired autophagy is closely linked to cancer development and has been extensively studied in a variety of malignancies including colorectal cancer (CRC) to elucidate its influence on carcinogenesis, metastasis and antitumor therapy response. CRC remains a great epidemiological problem because of poor 5-year survival and treatment resistance. Many studies concerning autophagy in CRC gave inconsistent and contradictory results, illustrating a multifaceted nature of this process. In this review, we focus on current knowledge of autophagy in CRC development to determinate its role as a potential prognostic and predictive biomarker as well as target in antitumor therapy.

Association of Interleukin-23 receptor gene polymorphisms with susceptibility to Crohn's disease: A meta-analysis

Studies investigating the association between Interleukin-23 receptor (IL-23R) gene polymorphisms and Crohn’s disease (CD) report conflicting results. Thus, a meta-analysis was carried out to assess the association between the IL-23R polymorphisms and CD. A systematic literature search was conducted to identify all relevant studies. Pooled odds ratio (ORs) with 95% confidence interval (CIs) was used to estimate the strength of association. Finally, a total of 60 case-control studies in 56 articles, involving 22,820 CD patients and 27,401 healthy controls, were included in the meta-analysis. Overall, a significant association was found between all CD and the rs7517847 polymorphism (OR = 0.699, 95% CI = 0.659 ~ 0.741, P < 0.001). Meta-analysis of the rs11209026, rs1343151, rs10489629 and rs11465804 polymorphisms indicated the same pattern as for rs7517847. Meta-analysis showed an association between the rs10889677A allele and CD (OR = 1.393, 95% CI = 1.328 ~ 1.461, P < 0.001). Similarly, meta-analysis of the rs2201840, rs1004819, rs1495965 and rs11209032 polymorphisms revealed the same pattern as that shown by meta-analysis of rs10889677. Stratification by ethnicity revealed that IL-23R gene polymorphisms were associated with CD in the Caucasian group, but not in Asians. In summary, the meta-analysis suggests a significant association between IL-23R polymorphisms and CD, especially in Caucasians.

ATG16L1 and IL23R variants and genetic susceptibility to crohn's disease: mode of inheritance based on meta-analysis of genetic association studies

BACKGROUND

Autophagy and regulation of IL-23 signaling pathways have been implicated in the pathogenesis of Crohn's disease (CD). We studied the mode of inheritance and reviewed the association of 2 polymorphic variants of ATG16L1 and IL23R with CD.

METHODS

We searched the PubMed and ISI Web of Science databases (up to May 2014) for pertinent articles. We included all studies that had a case-control design, with cases having CD and controls being healthy and reported full genotype frequencies for the ATG16L1 and/or IL23R variant of interest. We quantified the relative genetic risk using the model-free approach of the generalized odds ratio metric (ORG) and reported 95% precision estimates. Also, we explored the mode of inheritance using the degree of dominance h-index.

RESULTS

Fifty-one studies fulfilled these requirements and were included in the analysis. These studies involved 12,762 patients and 16,735 controls evaluating the association of ATG16L1 (rs2241880 p.Thr300Ala) and 8110 patients and 11,900 controls evaluating the association of IL23R (rs11209026 p.Arg381Gln) with CD. The ATG16L1 variant rs2241880 was associated with increased susceptibility to CD (combined ORG = 1.38; 95% confidence interval, 1.29-1.48) and a nondominant mode of inheritance (suggesting that the effect of heterozygosity lies exactly in the middle of extreme homozygotes, h = 0). The IL23R variant rs11209026 was associated with significant protection (ORG = 0.46; 95% confidence interval, 0.41-0.53) and a recessive mode of inheritance, indicating that the effect of a heterozygous genotype would lie close to the wild-type homozygous genotype. In subgroup analysis, the significant effects persisted across Caucasian ancestry studies and pediatric populations but were lacking across studies in Asian populations.

CONCLUSIONS

The ATG16L1 variant rs2241880 was associated with 38% increase in the risk for CD for higher mutational load, whereas IL23R variant rs11209026 decreased the risk by 54% for higher mutational load. The mode of inheritance for ATG16L1 variant demonstrated perfect additivity for genetic risk, whereas it showed recessiveness for the IL23R variant. This analysis permits risk stratification for CD based on the mutational status and highlight the need for additional studies in certain populations.

Toxoplasma gondii oral infection induces intestinal inflammation and retinochoroiditis in mice genetically selected for immune oral tolerance resistance

Toxoplasmosis is a worldwide disease with most of the infections originating through the oral route and generates various pathological manifestations, ranging from meningoencephalitis to retinochoroiditis and inflammatory bowel disease. Animal models for these pathologies are scarce and have limitations. We evaluated the outcome of Toxoplasma gondii oral infection with 50 or 100 cysts of the ME-49 strain in two lines of mice with extreme phenotypes of susceptibility (TS) or resistance (TR) to immune oral tolerance. Therefore, the aim of this study was to evaluate the behaviour of TS and TR mice, orally infected by T. gondii, and determine its value as a model for inflammatory diseases study. Mortality during the acute stage of the infection for TR was 50% for both dosages, while 10 and 40% of the TS died after infection with these respective dosages. In the chronic stage, the remaining TS succumbed while TR survived for 90 days. The TS displayed higher parasite load with lower intestinal inflammation and cellular proliferation, notwithstanding myocarditis, pneumonitis and meningoencephalitis. TR presented massive necrosis of villi and crypt, comparable to inflammatory bowel disease, with infiltration of lymphoid cells in the lamina propria of the intestines. Also, TR mice infected with 100 cysts presented intense cellular infiltrate within the photoreceptor layer of the eyes, changes in disposition and morphology of the retina cell layers and retinochoroiditis. During the infection, high levels of IL-6 were detected in the serum of TS mice and TR mice presented high amounts of IFN-γ and TNF-α. Both mice lineages developed different disease outcomes, but it is emphasized that TR and TS mice presented acute and chronic stages of the infection, demonstrating that the two lineages offer an attractive model for studying toxoplasmosis.

NOD2/CARD15 and IL23R genetic variability in 204 Algerian Crohn's disease

NOD2/CARD15 and IL23R gene variants play an important role in the susceptibility to Crohn's disease (CD). Studies of genotype-phenotype relationship suggest that these variants are associated with the development of the disease and specific phenotype. Preliminary reports analyzing the association between these variants have never been made on Algerian CD's. In a case-control design, 204 Algerian with CD diagnosed for at least 5years and 201 controls were included were genotyped for single nucleotide polymorphisms (SNP) in the NOD2/CARD15 gene R702W (SNP8, rs2066844), G908R (SNP12, rs2066845) and IL23R R381Q (rs11209026) gene variants were determined using the TaqMan SNP genotyping assays. NOD2/CARD15 908R was carried by 3% of the patients and none in control subjects (χ(2)=8.6, Pc=0.003, OR=13.20). NOD2/CARD15 702W was associated to CD outcome (χ(2)=17.2, Pc=0.00003, OR=12.5) and early onset of disease (group A1, χ(2)=19.3, Pc=1.10(-5), OR=14.05, PM-H=2.10(-6)). IL23R 381Q variants was more frequent in CD's patients than controls (χ(2)=8, Pc=0.005, OR=3.48), it was associated to earlier onset (group A1, χ(2)=7.1, Pc=0.007, OR=1.04, PM-H=0.002), extra-intestinal manifestations (EIM) outcome (χ(2)=10.6, Pc=0.001, OR=1.05, PM-H=0.002) and ileocolonic location (χ(2)=6.8, Pc=0.009, OR=1.05, PM-H=0.001). In this Algerian cohort, NOD2/CARD15 and IL23R variants were associated with CD's outcomes and linked to a particular clinical phenotype.

IL23R and ATG16L1 variants in Moroccan patients with inflammatory bowel disease

BACKGROUND

Inflammatory bowel diseases (IBD) are chronic diseases of the gastrointestinal tract. Although their pathogenesis is unclear, the combination of genetic predisposition and environmental components are believed to be the main cause of these diseases. Recently, many variants in interleukin 23 receptor (IL23R) and autophagy-related 16-like 1 (ATG16L1) genes have been associated with the disease. Our objective was to assess the frequency of ATG16L1 (T300A) and IL23R (L310P) variants in Moroccan IBD (Crohn's disease and Ulcerative Colitis) patients and to evaluate a possible effect of these variants on disease's phenotype and clinical course.

METHODS

96 Moroccan IBD patients and 114 unrelated volunteers were genotyped for ATG16L1 (T300A) and IL23R (L310P) variants by PCR-restriction fragment length polymorphism.

RESULTS

This is the first report on the prevalence of ATG16L1 (T300A) and IL23R (L310P) variants in a Moroccan group. We found that IL23R (L310P) variant conferred a protective effect for crohn's disease (CD) but not ulcerative colitis (UC) patients. The presence of ATG16L1 (T300A) mutated alleles was associated with CD type but not with disease onset. In addition, the carriage of T300A variant alleles conferred a protective effect in UC.

CONCLUSION

Our results showed that the prevalence of ATG16L1 and IL23R variants was not significantly different between patients and controls. However a possible role of ATG16L1 (T300A) on CD phenotype was suggested.

T300A GENETIC POLYMORPHISM: a susceptibility factor for Crohn’s disease?

ContextCrohn’s disease is characterized by a chronic and debilitating inflammatory disorder of the gastrointestinal tract. Several factors may contribute to its development. From extensive studies of the human genome, the polymorphism T300A of the gene ATG16L1 (autophagy-related 16-like 1) has been related to increased risk of developing this disease.ObjectivesAnalyze the role of polymorphism T300A (rs2241880) in patients with Crohn’s disease.Methods238 samples from (control group) and 106 samples from patients with Crohn’s disease recruited at five Southern Brazilian reference centers were evaluated. The genotyping consisted of the amplification via Polymerase Chain Reaction of the genomic segment encompassing T300A, followed by Restriction Fragment Length Polymorphism analysis. The amplicons and fragments were separated by agarose gel electrophoresis and confirmed under ultraviolet light.ResultsThe genotype AG was more prevalent among patients and controls (50% vs 44.8%), followed by genotypes AA (26.4% vs 35.1%) and GG (23.6% vs 20.1%). The frequency of the allele G of the polymorphism T300A was higher in the group of patients with Crohn’s disease (48.6%) than in controls (42.4%), although not reaching statistical significance.ConclusionsIt was not possible to confirm the increased susceptibility on development of Crohn’s disease conferred by polymorphism T300A.

Susceptibility to ulcerative colitis in Hungarian patients determined by gene-gene interactions

AIM: To study the inflammatory bowel disease-5 locus (IBD5) and interleukin-23 receptor (IL23R) gene variants in UC patients and test for gene-gene interaction.

METHODS: The study population (n = 625) was comprised of 320 unrelated ulcerative colitis (UC) patients with Caucasian origin and 316 age- and gender-matched, healthy controls. Five variants in the IBD5 locus (IGR2198a_1 rs11739135, IGR2096a_1 rs12521868, IGR2230a_1 rs17622208, SLC22A4 rs1050152 and SLC22A5 rs2631367) and two of the IL23R gene (rs1004819, rs2201841) were analysed. PCR and restriction fragment length polymorphism methods were used for genotyping, the SLC22A4 rs1050152 genotypes were determined by direct sequencing. Interactions and specific genotype combinations of the seven variants were tested by binary logistic regression analysis. The IL23R genotypes were stratified by IBD5 genotypes for further interaction analyses.

RESULTS: For the IL23R rs1004819 A allele we found significantly higher allele frequency (P = 0.032) in UC patients compared to control subjects. The SNP rs1004819 showed significant association with UC risk for carriers (P = 0.004, OR = 1.606; 95%CI: 1.160-2.223) and the SNP rs2201841 for homozygotes (P = 0.030, OR = 1.983; 95%CI: 1.069-3.678). Individually none of the IBD5 markers conferred risk to UC development. There was no evidence for statistical interaction either between IBD5 loci and IL23R genes using logistic regression analysis. After genotype stratification, we could detect a positive association on the background of rs1004819 A allele for SLC22A4 T, SLC22A5 C, IGR2198a_1 C or IGR2096a_1 T allele, the highest OR was calculated in the presence of SLC22A4 T allele (P = 0.005, OR = 2.015; 95%CI: 1.230-3.300). There was no association with UC for any combinations of rs1004819 and IGR2230a_1. The IL23R rs2201841 homozygous genotype and IBD5 carrier status together did not confer susceptibility for UC.

CONCLUSION: The present study has shown that UC susceptibility genes are likely to act in a complex interactive manner similar to CD.

Association of Egr-1 and autophagy-related gene polymorphism in men with chronic obstructive pulmonary disease

BACKGROUND/PURPOSE

Autophagy is important in cellular homeostasis and control of inflammatory immune response. Increased autophagy has recently been associated with increased cell death and chronic obstructive pulmonary disease (COPD) pathogenesis. Two autophagy regulator genes have been identified: Egr-1 (early growth response), associated with different phenotype expressions in asthma; and, Atg16L1 (autophagy related 16-like 1), a candidate gene responsible for susceptibility to chronic inflammatory diseases. We will explore the role of the Egr-1 and Atg16L1 gene polymorphisms in COPD.

METHODS

The genotypes of 151 male smoking patients with COPD and 100 male smoking controls were evaluated by polymerase chain reaction followed by restriction fragment length polymorphism analysis of the Egr-1 (-4071 A → G) rs7729723 and Atg16L-1 (T300A) rs2241880 variants.

RESULTS

The G allele of the Egr-1 gene polymorphism was associated with an increased risk of developing COPD [odds ratio (OR), 2.05; 95% confidence interval (CI), 1.15-3.72], and participants with the G allele polymorphism (GG and GA genotypes) had a 2.56-fold higher risk (OR, 2.56; 95% CI, 1.31-5.16) of having COPD than those homozygous for the A allele [35.8% (54/151) vs. 24.0% (24/100); p = 0.007]. Participants with the A allele of the Atg16L1 gene polymorphism (AA and AG genotypes) had a 3.34-fold higher risk (OR, 3.34; 95% CI, 1.32-8.97) of having COPD than those homozygous for the G allele [93.4% (141/151) vs. 81.0% (81/100); p = 0.013].

CONCLUSION

The Egr-1 and Atg16L1 genes' polymorphisms were significant risk factors for susceptibility to COPD. These results demonstrate that autophagy regulator genetic mutations are associated with COPD in male smokers.

Unique variation in genetic selection among Black North American women and its potential influence on pregnancy outcome

We hypothesize that variations in the frequency of genetic polymorphisms, reflecting ancestral differences in living conditions and exposure to microorganisms, increase susceptibility to adverse pregnancy outcome among present day Black North American women. Striking differences were observed in the frequency of genetic variants between Black and White or Hispanic women in 5 genes (IL1RN, MBL2, PPARA, ATG16L1, CIAS1) associated with inflammation and anti-microbial immunity. The CIAS1 and IL1RN polymorphisms were associated with altered interleukin-1β serum levels; the MBL2 polymorphism resulted in a decreased serum mannose-binding lectin concentration. Gene polymorphisms associated with an alteration in innate immunity were most frequent in Black women. This may reflect an evolutionary selection in response to an ancient environment containing a high multitude of microorganisms, and may increase susceptibility of Black women to infection-associated preterm birth in the current North American environment.

A polymorphism in an autophagy-related gene, ATG16L1, influences time to delivery in women with an unfavorable cervix who require labor induction

Autophagy is an intracellular process that maintains homeostasis by the removal of damaged organelles and proteins. A single nucleotide polymorphism (SNP) in the autophagy-related 16-like 1 (ATG16L1) gene results in decreased autophagy. We evaluated whether the ATG16L1 polymorphism influenced the time to delivery during labor induction in pregnant women with an unfavorable cervix. DNA from 69 women with an unfavorable cervix who required labor induction due to post-term (>294 days) (n=26), oligohydramnios (n=17), hypertension or pre-eclampsia (n=10), abnormal fetal heart rate (n=8), diabetes (n=3) or other reasons (n=5) was tested by gene amplification and endonuclease digestion for a SNP in ATG16L1 (rs2241880). The mean hours (SD) from induction to delivery was 20.8 (9.7) for women who were A,A homozygotes, 19.2 (8.8) for A,G heterozygotes and 14.3 (6.6) for homozygote carriers of the G,G variant (P=0.03 A,A vs. G,G, P=0.04 A,A/A,G vs. G,G). The G,G prevalence was 24.4% and 4.2% for those who delivered in ≤24 and >24 h, respectively (P=0.04). There was no difference in genotype distribution by indication for induction. A decreased genetic capacity for autophagy may be beneficial in women with an unfavorable cervix whose labor has to be induced.

NOD2 mutations are associated with the development of intestinal failure in the absence of Crohn's disease

BACKGROUND & AIMS

Short bowel syndrome (SBS) and intestinal failure (IF) are multi-factorial conditions which in adults result from extensive intestinal resection. NOD2 is an intracellular pattern recognition receptor associated with CD. An unexpected high frequency of NOD2 mutations has been found in patients undergoing intestinal transplantation (35%). The role of NOD2 in a cohort with SBS/IF not specifically requiring intestinal transplantation has not been studied yet.

METHODS

The course of 85 patients with non-malignant SBS/IF was characterized. The major NOD2 mutations, as well as ATG16L1 and IL23R were determined. The allele frequencies were compared to the published frequencies of CD patients and controls.

RESULTS

In non-CD patients (72%) allele frequencies of NOD2 mutations were statistically more frequent than in controls (14% vs 6%, p = 0.006). In CD patients (28%) allele frequencies were not different between SBS and controls (29% vs 22%, p = 0.23). NOD2 mutations were neither associated with parameters potentially heralding the need for transplantation nor with an earlier time to the indication for intestinal transplantation.

CONCLUSIONS

NOD2 mutations are associated with the development of SBS/IF in the absence of CD, but not with specific complications. NOD2 mutations may increase the risk for more extensive intestinal resection or may impair intestinal adaptation.

Genome-wide peripheral blood leukocyte DNA methylation microarrays identified a single association with inflammatory bowel diseases

BACKGROUND

Crohn's disease (CD) and ulcerative colitis (UC) are common forms of inflammatory bowel disease (IBD). Monozygotic (MZ) twin discordance rates and epidemiologic data implicate that environmental changes and epigenetic factors may play a pathogenic role in IBD. DNA methylation (the methylation of cytosines within CpG dinucleotides) is an epigenetic modification, which can respond to environmental influences. We investigated whether DNA methylation might be connected with IBD in peripheral blood leukocyte (PBL) DNA by utilizing genome-wide microarrays.

METHODS

Two different high-throughput microarray-based methods for genome-wide DNA methylation analysis were employed. First, DNA isolated from MZ twin pairs concordant (CD: 4; UC: 3) and discordant (CD: 4; UC: 7) for IBD was interrogated by a custom-made methylation-specific amplification microarray (MSAM). Second, the recently developed Illumina Infinium HumanMethylation450 BeadChip arrays were used on 48 samples of PBL DNA from discordant MZ twin pairs (CD: 3; UC: 3) and treatment-naive pediatric cases of IBD (CD: 14; UC: 8), as well as controls (n = 14). The microarrays were validated with bisulfite pyrosequencing.

RESULTS

The MSAMs did not yield significant IBD associations. The Methylation BeadChip approach identified a single DNA methylation association of IBD at TEPP (testis, prostate and placenta-expressed protein) when DNA isolated selectively from peripheral blood mononuclear cells was analyzed (8.6% increase in methylation between CD and control, FDR = 0.0065).

CONCLUSIONS

Microarray interrogation of IBD-dependent DNA methylation from PBLs appears to have limited ability to detect significant disease associations. More detailed and/or selective approaches may be useful for the elucidation of connections between the DNA methylome and IBD in the future.

Association between inflammatory bowel disease gene 5 (IBD5) and interleukin-23 receptor (IL23R) genetic polymorphisms in Malaysian patients with Crohn's disease

OBJECTIVE

This study was aimed to investigate the possible association of Crohn's disease (CD) with inflammatory bowel disease gene 5 (IBD5) IGR2198a_1 (rs11739135), IGR2096a_1 (rs12521868) and interleukin-23 receptor (IL23R) genetic variant (rs1004819) in the Malaysian population.

METHODS

Blood samples from 80 CD patients and 100 healthy controls were recruited. Genomic DNA was extracted and analyzed by polymerase chain reaction-restriction fragment length polymorphism.

RESULTS

The results revealed that there was an increased frequency of IGR2198a_1 C allele (8.8% in CD, 1.5% in controls, P < 0.05, OR 6.30, 95% CI 1.77-22.31) and IGR2096a_1 T allele (6.9% in CD, 1.5% in controls, P < 0.05, OR 4.85, 95% CI 1.33-17.69) in the CD patients as compared to the controls, suggesting the two variants were potential risk factors of CD. Both risk alleles (C and T) were highest in Indians. In contrast, no significant difference was observed for the IL23R gene variant (rs1004819) between these two groups (P = 0.941). All genotypes and alleles of this gene variant were present in equal ratios in the CD and control groups (OR 1.02, 95% CI 0.66-1.57 for T allele and OR 0.98, 95% CI 0.64-1.52 for C allele).

CONCLUSIONS

There is a strong association between both IBD5 locus variants but not the IL23R gene variant with CD in the Malaysian population. The IBD5 locus variants were highest in Indians, which may explain the increased susceptibility of this particular ethnic group to the disease.

Investigation of JAK2, STAT3 and CCR6 polymorphisms and their gene-gene interactions in inflammatory bowel disease

Genome-wide association studies identified many loci associated with the two forms of inflammatory bowel disease (IBD), Crohn's disease (CD) and ulcerative colitis (UC). Components of the interleukin-23 signalling pathway, such as IL23R, JAK2 and STAT3, have been implicated in both diseases. In addition, emerging evidence supports the role of IL23-driven Th17 cells in inflammation. Here, we studied the susceptibility nature of three components of IL23 signalling and Th17 cell differentiation: JAK2 rs10758669, STAT3 rs744166 and CCR6 rs2301436 initially associated with CD in Hungarian CD and UC patients. A total of 616 unrelated subjects with either form of IBD and 496 healthy controls were genotyped with PCR-RFLP methods. We also tested the genetic interactions of JAK2, STAT3 and CCR6 polymorphisms in a pairwise fashion with regard to disease risk. We could confirm the susceptibility of STAT3 rs744166 TT homozygotes for UC (OR: 1.483, 95% CI: 1.103-1.992, P = 0.009). Data on genetic interaction reveals that the above JAK2 and STAT3 risk alleles contribute to CD susceptibility in combination with each other (OR: 2.218; 95% CI: 1.097-4.487; P = 0.024), while the JAK2 variant shows a tendency to confer UC risk only on a wild-type STAT3 background (OR: 1.997, 95%CI: 0.994-4.009, P = 0.049). Our results may help in understanding how these natural variants contribute to development of IBD through their genetic association.

Role of ATG16L, NOD2 and IL23R in Crohn’s disease pathogenesis

Inflammatory bowel disease is a group of diseases that includes Crohn’s disease (CD) and ulcerative colitis. CD is characterized as a chronic inflammatory disease of the gastrointestinal tract, ranging from the mouth to the anus. Although there are gross pathological and histological similarities between CD and Johne’s disease of cattle, the cause of CD remains controversial. It is vital to understand fully the cause of this disease because it affects approximately 500 000 people in North America and Europe. It ranges from 27 to 48 cases per 100 000 people. There are many theories on the cause of CD ranging from possible association with environmental factors including microorganisms to imbalance in the intestinal normal flora of the patients. Regardless of the environmental trigger, there is strong evidence that a genetic disposition is a major key in acquiring CD. Many studies have proven the link between mutations in the ATG16L, NOD2/CARD15, IBD5, CTLA4, TNFSF15 and IL23R genes, and CD. The purpose of this review is to examine all genetic aspects and theories of CD, including up to date multiple population studies performed worldwide.

Canine breeds at high risk of developing inflammatory bowel disease in the south-eastern UK

Genetics are an important factor in the development of human inflammatory bowel disease (IBD); however, there is very little information available regarding the role of genetics in canine IBD. The purpose of this study was to gather information about which canine breeds in the south-eastern UK are at a high risk for developing IBD. Determination of such breeds may help further genetic research in this complex disease. The computer medical records at the Queen Mother Hospital for Animals, Royal Veterinary College dating from August 1, 2003 to December 31, 2009 were retrospectively searched for cases diagnosed with IBD. Five hundred and forty-six dogs with IBD were identified, representing 86 different breeds. The comparison group consisted of all dogs from these same 86 breeds without IBD admitted to the hospital during the same period that amounted to 27,463 dogs. The breeds at significantly higher risk of developing IBD compared with mixed-breed dogs consisted of weimaraner (odds ratio [OR]=3.6797, 95 per cent confidence interval [CI]=2.0167 to 6.7141, P<0.0001), rottweiler (OR=2.9697, 95 per cent CI=1.7569 to 5.0196, P<0.0001), German shepherd dog (GSD) (OR=2.4101, 95 per cent CI=1.5826 to 3.36705, P<0.0001), border collie (OR=1.9936, 95 per cent CI=1.1655 to 3.4101, P=0.0118) and boxer (OR=1.6961, 95 per cent CI=1.0441 to 2.755, P=0.0328). This study demonstrates for the first time canine breeds in the south-eastern UK that are highly susceptible to developing IBD. Identification of such breeds may allow for a more focused investigation of genetic mutations associated with canine IBD.

Interaction between CTLA4 gene and IBD5 locus in Hungarian Crohn's disease patients

BACKGROUNDS AND AIMS

The IGR2198a_1 and IGR2096a_1 variants of the IBD5 region were found to be associated with Crohn's disease (CD) in the Hungarian population, while IGR2230a_1 does not seem to confer risk for the disease. In the present study, our aim was to investigate the statistical interaction of these three IBD5 polymorphisms with the +49 A/G substitution within the cytotoxic T lymphocyte antigen-4 (CTLA4) gene, detected previously as neutral gene variant in Hungarian IBD patients.

METHODS

A total of 305 unrelated subjects with CD and 310 healthy controls were genotyped with PCR-RFLP methods.

RESULTS

In contrast with single gene effects, after genotype stratification, the IGR2198a_1 C and IGR2096a_1 T variants were found to confer susceptibility only in subjects with CTLA4 +49 AA genotype (P = 0.008; OR = 1.86 and P = 0.016; OR = 1.74, respectively), for IGR2230a_1 no such effect on disease risk could be demonstrated.

CONCLUSION

Analysis of specific genotype combinations unfolded a possible association between the CTLA4 +49 A/G substitution and two of the observed IBD5 variants with respect to disease risk.

Role of NOD1/CARD4 and NOD2/CARD15 gene polymorphisms in cancer etiology

NOD1/CARD4 and NOD2/CARD15 are members of Nod-like receptor family. They are located in cytosol, bind bacterial and viral ligands and play a key role in realization of innate and adaptive immune response, apoptosis, autophagy, and reactive oxygen species generation. Polymorphisms in NOD1/CARD4 and NOD2/CARD15 genes may shift balance between pro- and anti-inflammatory cytokines, modulating the risk of infection, chronic inflammation and cancer. NOD1/CARD4 and NOD2/CARD15 gene polymorphisms may be associated with altered risk of gastric, colorectal, breast, ovarian, prostate, testicular, lung, laryngeal, liver, gallbladder, biliary tract, pancreatic, small bowel, kidney, urinary bladder cancer, skin cancer, nonthyroid endocrine tumors, lymphoma and leukemia. The short list of such polymorphisms perspective for oncogenomic investigations may include rs2006847, rs2066845, rs2066844, rs2066842, ND(1)+32656, rs2075820 whereas rs104895493, rs104895476, rs104895475, rs104895474, rs104895473, rs104895472, rs104895462, rs104895461, rs104895460, rs104895438, rs5743291, rs5743260, rs2076756, rs2066843, Pro371Thr, Ala794Pro, Gln908His, rs72551113, rs72551107, rs6958571, rs2907749, rs2907748, rs2075822, rs2075819, rs2075818 may be added to the extended list. Reasons of discrepancies between different studies include confounding host genetic, bacterial, or environmental factors modulating penetrance of variant allele and affecting risk of condition increasing cancer risk, different bacterial impact in aetiology of such conditions, differences in sample size, clinicopathological characteristics, diagnostics, stratification, genotyping methods, and chance.

Contribution of the IBD5 locus to inflammatory bowel disease: a meta-analysis

To evaluate the association of the IBD5 locus to the predisposition of inflammatory bowel diseases (IBDs), a series of meta-analyses between five IBD5 variants (OCTN1 C1672T, OCTN2 G-207C, OCTN1/2 TC haplotype, IGR2096a_1, IGR2198a_1 and IGR2230a_1) and Crohn's disease (CD) and ulcerative colitis (UC) were performed, which included a total of 26 studies. Overall, five IBD5 variants in a per-allele model of inheritance were significantly associated with elevated CD risk (for OCTN1: OR = 1.23, 95% CI = 1.16-1.30, P < 0.001; for OCTN2: OR = 1.20, 95% CI = 1.11-1.30, P < 0.001; for IGR2096a_1: OR = 1.36, 95% CI = 1.24-1.46, P < 0.001; for IGR2198a_1: OR = 1.34, 95% CI = 1.24-1.46, P < 0.001; for IGR2230a_1: OR = 1.35, 95% CI = 1.23-1.48, P < 0.001) and OCTN1/2 TC haplotype (OR = 1.32, 95% CI = 1.22-1.43, P < 0.001). In the subgroup analysis, the statistically significant associations were also observed in adult- and pediatric-onset CD and in Caucasians for five IBD5 variants and the OCTN1/2 TC haplotype. A statistically significant increase in the risk of UC was detected in a recessive model of inheritances for OCTN1 (OR = 1.23, 95% CI = 1.08-1.40, P < 0.001), OCTN2 (OR = 1.18, 95% CI = 1.05-1.33, P = 0.006), IGR2096a_1 (OR = 1.37, 95% CI = 1.15-1.62, P < 0.001) and IGR2198a_1 (OR = 1.35, 95% CI = 1.10-1.66, P = 0.004); the increased risks of UC were maintained in the adult and Caucasian subgroups, but not the pediatric subgroup. In summary, our results suggested that the IBD5 locus contributes to the susceptibility of CD in a per-allele manner in adults, children and Caucasians, and the locus contributes to the susceptibility of UC in a recessive manner in adult and Caucasian populations.

[Barrier- and autophagic functions of the intestinal epithelia: role of disturbances in the pathogenesis of Crohn's disease]

Crohn's disease is a widely known debilitating chronic inflammatory disease, mostly affecting terminal ileum and/or colon. Epidemiological, familial and twin studies suggest that genetic factors play an important role in susceptibility to the disease. Clinical observations suggest that ill-defined environmental factors also play a part. Advances in molecular genotyping technology, statistical methodologies, bioinformatics and the combined use of them in genome wide scanning and association studies resulted in the identification of more than 30 susceptibility genes and loci associated with Crohn's disease and revealed and highlighted a number of new previously unsuspected pathways playing a role in the pathogenesis of Crohn's disease. Close association of the disease with polymorphisms in the genes encoding the pattern recognition receptors particularly the NOD2 protein, the Wnt pathway transcription factor Tcf4 (also known as TCFL2) and the autophagic regulator ATG16L1 have been found. The polymorphisms involved are associated with decreased defensin production (defensin deficiency) which can lead to changes in the composition of the commensal microbial flora, defects in the intestinal barrier functions and bacterial invasion of the mucosa. Other recently recognized consequences of the polymorphisms involving the genes encoding NOD2 and ATG16L1 proteins are that the truncated NOD2 protein is unable to induce autophagy and this protein, just like the ATG16L1 T300A mutant protein, leads to failure adequately to destroy phagocytosed bacteria. The consequence is persisting low level infection, chronic intestinal inflammation, tissue injury and the clinical symptoms of the disease. Thus, Crohn's disease can be seen to be caused by defects in the innate immune defense, in particular defects in bacterial processing and clearance. The accumulated evidence suggests that Crohn's disease is associated with an exaggerated adaptive immune response to the persisting intestinal microbes in genetically susceptible hosts. Intervention in these circumstances should probably be geared to strengthening of the innate immune responses rather than simple attempts to suppress adaptive immunity.