The expanding universe of inflammatory bowel disease genetics

Gene Identification in Inflammatory Bowel Disease via a Machine Learning Approach

Inflammatory bowel disease (IBD) is an illness with increasing prevalence, particularly in emerging countries, which can have a substantial impact on the quality of life of the patient. The illness is rather heterogeneous with different evolution among patients. A machine learning approach is followed in this paper to identify potential genes that are related to IBD. This is done by following a Monte Carlo simulation approach. In total, 23 different machine learning techniques were tested (in addition to a base level obtained using artificial neural networks). The best model identified 74 genes selected by the algorithm as being potentially involved in IBD. IBD seems to be a polygenic illness, in which environmental factors might play an important role. Following a machine learning approach, it was possible to obtain a classification accuracy of 84.2% differentiating between patients with IBD and control cases in a large cohort of 2490 total cases. The sensitivity and specificity of the model were 82.6% and 84.4%, respectively. It was also possible to distinguish between the two main types of IBD: (1) Crohn's disease and (2) ulcerative colitis.

Phenotype of Crohn's disease according to the Montreal classification in relation to dental health status

OBJECTIVE

The relationship between oral health and Crohn's disease is uncertain. Previous studies have yielded contradictory results, reflecting perhaps the different phenotypes of the disease. The aim of the present study was to describe and analyse the dental status of a group of patients with Crohn's disease (CD), considering the positions of the inflammatory loci and disease phenotype.

METHODS

In total, 47 patients with Crohn's disease (18 males and 30 females; mean age. 48.7 years; range, 23-61 years) were consecutively recruited to this study. Interviews and clinical examinations were performed to assess dental status, medication, smoking history, heredity of inflammatory bowel disease (IBD), duration of disease, oral mucosal manifestations of Crohn's disease. Furthermore, data on subjective health assessments and family status, along with medical histories from the patients were obtained through questionnaires. The disease phenotypes were assessed and classified according to the Montreal classification. The data on oral health status were first correlated with the Montreal classifications of IBD, and, thereafter, all the collected data were included in a multivariate generalised linear model.

RESULTS

The dental status of the patients was comparable to that of the Swedish average. No statistically significant associations were found between oral status and the different CD phenotypes. However, within the Montreal classification, there were significantly fewer teeth in those patients with perianal lesions than in those without such lesions, and there was a significant correlation between deeper pocket depth and problems with strictures and penetrations. No significant differences (p = .074) between the patients with CD (N = 47) and controls (N = 38) were found regarding the presence of oral mucosal lesions.

CONCLUSION

Dental health may be adversely affected in severe cases of CD whereas most of the remaining patients with CD appear to have a level of dental health that is comparable to that in the general population.

Demography and clinical course of ulcerative colitis in Arabs - a study based on the Montreal classification

OBJECTIVE

Ulcerative colitis (UC) is generally considered a disease of the Caucasian populations in developed countries, but its incidence is increasing rapidly in many developing countries, including the Middle East. The objective of this study was to determine the clinical epidemiology of UC in Arabs.

MATERIAL AND METHODS

This cross-sectional medical record-based descriptive study collected sociodemographic and clinical information on 182 Arab patients with UC in Kuwait. Age at diagnosis, extent and severity of disease were determined according to the Montreal classification. results: Among the 182 patients, 91 (50.0%) were males. The median age at diagnosis was 28.5 years. Family history of UC was reported by 26 (14.3%) patients. The extent of the disease was limited to the rectum in 34 (18.7%) patients, left sided in 67 (36.8%) and pan colitis in 81 (44.5%). At the time of inclusion in the study, 127 (69.8%) patients were in clinical remission, 53 (29.1%) had mild-to-moderate disease and 2 (1.1%) had severe colitis. Younger age at diagnosis and non-smoking were associated with more extensive colitis. The majority of patients were treated with mesalamine, steroids and immunomodulators, while biologic therapy and surgery were needed in 5% and 4% of the patients, respectively.

CONCLUSIONS

UC presents more commonly at younger age among Arabs in Kuwait. Extensive disease at presentation is associated with younger age at diagnosis and absence of tobacco smoking. There also appears to be less need for surgery and biologic therapy for the disease in this population.

The influence of CTGF single-nucleotide polymorphisms on outcomes in Crohn's disease

OBJECTIVE

To examine the association between single-nucleotide polymorphisms (SNPs) in CTGF (connective tissue growth factor) and patient outcomes after terminal ileal resection for Crohn's disease.

BACKGROUND

The primary indication for intestinal resection in Crohn's disease is fibrostenotic terminal ileal disease. CTGF is a cytokine overexpressed in the intestine of patients with Crohn's disease that influences outcomes in other disease processes.

METHODS

DNA was extracted from formalin-fixed, paraffin-embedded tissue from 147 patients with Crohn's disease who had undergone terminal ileal resection between 1981 and 2009. Genotyping was performed for 4 CTGF SNPs (rs9402373, rs12526196, rs6918698, and rs9399005), which modulate nuclear factor binding and CTGF production, and a smad3 SNP (rs17293632) involved in the CTGF pathway. Patients were phenotyped using the Montreal Disease Classification.

RESULTS

Sixty-seven of 147 patients (45.6%) were male; the mean age at diagnosis was 30.3 ± 12.6 years and the mean follow-up duration was 8.3 ± 7.1 years. Genotype-phenotype analysis demonstrated that the rs6918698GG genotype was associated with an older age of disease onset [>40 years; 30.6% vs 13.2%; odds ratio (OR): 2.891; 95% confidence interval (CI): 1.170-7.147). The rs9402373CC genotype was positively associated with type B1 disease (50.7% vs 26.3%; OR: 2.876; 95% CI: 1.226-6.743) and negatively associated with B2 disease (37.0% vs 65.0%; OR: 0.317; 95% CI: 0.144-0.699). None of the 5 SNPs assessed influenced clinical or surgical recurrence of Crohn's disease after intestinal resection. On multivariate analysis, male sex odds ratio (OR): 0.235; 95% CI: 0.073-0.755; P = 0.015] and never having smoked tobacco (OR: 0.249; 95% CI: 0.070-0.894; P = 0.033) reduced the risk, whereas having a prior appendectomy increased the risk (OR: 5.048; 95% CI: 1.632-15.617; P = 0.005) of surgical recurrence.

CONCLUSIONS

These data implicate the rs6918698GG genotype with an age of disease onset of greater than 40 years in Crohn's disease whereas the rs9402373CC genotype is associated with a nonstricturing, nonpenetrating disease phenotype. CTGF SNPs do not influence the rate of recurrence after terminal ileal resection for Crohn's disease.

CRHR1 genotypes, neural circuits and the diathesis for anxiety and depression

The corticotrophin-releasing hormone (CRH) system integrates the stress response and is associated with stress-related psychopathology. Previous reports have identified interactions between childhood trauma and sequence variation in the CRH receptor 1 gene (CRHR1) that increase risk for affective disorders. However, the underlying mechanisms that connect variation in CRHR1 to psychopathology are unknown. To explore potential mechanisms, we used a validated rhesus macaque model to investigate association between genetic variation in CRHR1, anxious temperament (AT) and brain metabolic activity. In young rhesus monkeys, AT is analogous to the childhood risk phenotype that predicts the development of human anxiety and depressive disorders. Regional brain metabolism was assessed with (18)F-labeled fluoro-2-deoxyglucose (FDG) positron emission tomography in 236 young, normally reared macaques that were also characterized for AT. We show that single nucleotide polymorphisms (SNPs) affecting exon 6 of CRHR1 influence both AT and metabolic activity in the anterior hippocampus and amygdala, components of the neural circuit underlying AT. We also find evidence for association between SNPs in CRHR1 and metabolism in the intraparietal sulcus and precuneus. These translational data suggest that genetic variation in CRHR1 affects the risk for affective disorders by influencing the function of the neural circuit underlying AT and that differences in gene expression or the protein sequence involving exon 6 may be important. These results suggest that variation in CRHR1 may influence brain function before any childhood adversity and may be a diathesis for the interaction between CRHR1 genotypes and childhood trauma reported to affect human psychopathology.

Genetic and functional profiling of Crohn's disease: autophagy mechanism and susceptibility to infectious diseases

Crohn's disease is a complex disease in which genome, microbiome, and environment interact to produce the immunological background of the disease. Disease in childhood is more extensive and characterized by a rapid progression, leading to severe repercussions in the course of the disorder. Several genetic variations have been associated with an increased risk of developing the disease and most of these are also implicated in other autoimmune disorders. The gut has many tiers of defense against incursion by luminal microbes, including the epithelial barrier and the innate and adaptive immune responses. Moreover, recent evidence shows that bacterial and viral infections, as well as inflammasome genes and genes involved in the autophagy process, are implicated in Crohn's disease pathogenesis. The aim of this review is to establish how much the diagnostic system can improve, thus increasing the success of Crohn's disease diagnosis. The major expectation for the near future is to be able to anticipate the possible consequences of the disease already in childhood, thus preventing associated complications, and to choose the best treatment for each patient.

The effect of NOD2 polymorphism on postsurgical recurrence in Crohn's disease: a systematic review and meta-analysis of available literature

BACKGROUND

Up to 70% of patients requiring surgery for Crohn's disease (CD) develop recurrence within 10 years. Unequivocal markers predicting recurrence are needed to tailor postoperative therapy appropriately. NOD2 (nucleotide-binding oligomerization domain 2) polymorphisms increase the risk of developing CD; however, their ability to predict recurrence is uncertain. This study aims to determine the association between NOD2 variants and surgical recurrence after initial disease-modifying surgery.

METHODS

A comprehensive search for published series comparing the effect of NOD2 polymorphisms on postoperative surgical recurrence in patients with CD was performed. Random-effects methods were used to combine data.

RESULTS

Six cohort studies comprising 1003 patients with CD were included. A total of 340 patients (33.9%) expressed at least 1 of the 3 common NOD2 polymorphisms. The 1003 patients underwent surgical resection with 335 (33%) developing surgical recurrence. Of 340 NOD2-expressing patients, 130 (39%) required further resection, whereas 202 of 663 patients (30.5%) without the variant underwent repeat resection. NOD2 was not significantly associated with surgical recurrence (odds ratio: 1.58, 95% confidence interval: 0.97-2.57, P = 0.064), most likely because of study heterogeneity (Cochran Q: 12.36, P = 0.030, I: 59.6%). The sensitivity of any mutation in predicting disease recurrence was 39.7% and specificity was 69%, with the area under the receiver operating characteristic curve being 0.64.

CONCLUSIONS

Patients with CD with a NOD2 polymorphism do not have an increased risk of surgical recurrence compared with patients without the variant. These data provide insufficient evidence to support postoperative medical prophylaxis based solely on the presence of NOD2 polymorphism.

Clinical epidemiology of Crohn's disease in Arabs based on the Montreal Classification

BACKGROUND

There has been a remarkable increase in the incidence of Crohn's disease (CD) among Arabs in recent years. We conducted this study to determine the clinical epidemiology of CD in Kuwait.

METHODS

Sociodemographic and clinical information was collected for a continuous series of 206 Arab patients with CD and age at diagnosis and location and behavior of disease was determined according to the Montreal Classification.

RESULTS

Among the 206 patients, 100 (48.5%) were males and 106 (51.5%) females. The mean age at diagnosis (±SD) was 21.9 ± 10 years. Family history of CD was reported by 39 (18.9%) patients. The disease was limited to the ileum in 115 (55.8%) patients, whereas in 28 (13.6%) it involved the colon and in 63 (30.6%) it involved both the ileum and colon. The behavior of the disease was nonstricturing, nonpenetrating in 146 (70.9%) patients, whereas 49 (23.8%) had stricturing and 11 (5.3%) penetrating disease. Perianal disease was present in 41 (19.9%) patients. In the multivariate analysis, the use of biologic therapy and duration of the disease for ≥6 years were significantly associated with the presence of perianal disease, and the need for surgery was significantly associated with stricturing and penetrating disease behavior.

CONCLUSIONS

CD among Arabs is equally common in males and females, presents at a relatively younger age, and in about half of the patients is limited to the small bowel. These features may indicate an underlying genetic predisposition for the disease in this population, which needs further investigation.

Role of genetics in the diagnosis and prognosis of Crohn's disease

Considering epidemiological, genetic and immunological data, we can conclude that the inflammatory bowel diseases are heterogeneous disorders of multifactorial etiology in which hereditability and environment interact to produce the disease. It is probable that patients have a genetic predisposition for the development of the disease coupled with disturbances in immunoregulation. Several genes have been so far related to the diagnosis of Crohn's disease. Those genes are related to innate pattern recognition receptors, to epithelial barrier homeostasis and maintenance of epithelial barrier integrity, to autophagy and to lymphocyte differentiation. So far, the most strong and replicated associations with Crohn's disease have been done with NOD2, IL23R and ATG16L1 genes. Many genes have so far been implicated in prognosis of Crohn's disease and many attempts have been made to classify genetic profiles in Crohn's disease. CARD15 seems not only a susceptibility gene, but also a disease-modifier gene for Crohn's disease. Enriching our understanding on Crohn's disease genetics is important but when combining genetic data with functional data the outcome could be of major importance to clinicians.

Role of genetics in the diagnosis and prognosis of Crohn's disease

Considering the epidemiological, genetic and immunological data, we can conclude that the inflammatory bowel diseases are heterogeneous disorders of multifactorial etiology in which hereditability and environment interact to produce the disease. It is probable that patients have a genetic predisposition for the development of the disease coupled with disturbances in immunoregulation. Several genes have so far been related to the diagnosis of Crohn's disease. These genes are related to innate pattern recognition receptors, to epithelial barrier homeostasis and maintenance of epithelial barrier integrity, to autophagy and to lymphocyte differentiation. So far, the strongest and most replicated associations with Crohn's disease have been demonstrated with NOD2, IL23R and ATG16L1 genes. Many genes have so far been implicated in the prognosis of Crohn's disease and many attempts have been made for classification of genetic profiles in Crohn's disease. CARD15 seems to be not only a susceptibility gene, but also a disease-modifier gene for Crohn's disease. Enriching our understanding of Crohn's disease genetics is of value, but when combining genetic data with functional data the outcome could be of major importance to clinicians.

The intestinal microbiota and chronic disorders of the gut

Mucosal surfaces of the gut are colonized by large numbers of heterogeneous bacteria that contribute to intestinal health and disease. In genetically susceptible individuals, a 'pathogenic community' may arise, whereby abnormal gut flora contributes to alterations in the mucosa and local immune system leading to gastrointestinal disease. These diseases include enteric infections, such as Clostridium difficile infection, small intestinal bacterial overgrowth, functional gastrointestinal disorders (including IBS), IBD and colorectal cancer. Prebiotics, probiotics and synbiotics (a combination of prebiotics and probiotics) have the capacity to reverse pathologic changes in gut flora and local immunity. Intestinal health and disease need to be thoroughly characterized to understand the interplay between the indigenous microbiota, the immune system and genetic host factors. This Review provides a broad overview of the importance of the intestinal microbiota in chronic disorders of the gut.

Inflammatory bowel disease

This article reviews the etiology, clinical characteristics, and treatment of inflammatory bowel disease (IBD) and associated psychological sequelae in children and adolescents with this lifelong disease. Pediatric-onset IBD, consisting of Crohn's disease and ulcerative colitis, has significant medical morbidity and in many young persons is also associated with psychological and psychosocial challenges. Depression and anxiety are particularly prevalent and have a multifaceted etiology, including IBD-related factors such as cytokines and steroids used to treat IBD and psychosocial stress. A growing number of empirically supported interventions, such as cognitive behavioral therapy, hypnosis, and educational resources, help youth and their parents cope with IBD as well as the psychological and psychosocial sequelae. While there is convincing evidence that such interventions can help improve anxiety, depression, and health-related quality of life, their effects on IBD severity and course await further study.

Using metabolomic analysis to understand inflammatory bowel diseases

Crohn's disease (CD) and ulcerative colitis (UC) are inflammatory bowel diseases (IBD) attributed to a dysregulated immune response towards intestinal microbiota. Although various susceptibility genes have been identified for CD and UC, the exact disease etiology is unclear and complicated by the influence of environmental factors. Metabolomic analysis enables high sample throughput measurements of multiple metabolites in biological samples. The use of metabolomic analysis in medical sciences has revealed metabolite perturbations associated with diseases. This article provides a summary of the current understanding of IBD, and describes potential applications and previous metabolomic analysis in IBD research to understand IBD pathogenesis and improve IBD therapy.

Association of Mycobacterium avium subspecies paratuberculosis with Crohn Disease in pediatric patients

OBJECTIVES

The aim of the present study was to determine the prevalence of Mycobacterium avium subsp paratuberculosis (MAP) DNA in intestinal biopsies from pediatric patients with granulomatous Crohn disease (CD) or ulcerative colitis (UC), and matched control subjects without inflammatory bowel disease (IBD).

PATIENTS AND METHODS

DNA was extracted from formalin-fixed paraffin-embedded colonic and ileal biopsies from patients with CD (n = 22) or UC (n = 20), and from controls without IBD (n = 21). IS900 nested polymerase chain reaction was performed in triplicate to determine the presence of MAP-specific DNA.

RESULTS

In mucosal biopsies from terminal ileum, IS900 amplicons were detected in 1 of 19 (5.2%) control subjects, 1 of 20 (5%) patients with UC, and 7 of 20 (35%) patients with CD (P < 0.05 vs controls, odds ratio 9.6). In colonic biopsies, IS900 amplicons were detected in 0 of 19 control subjects, 1 of 19 (5.2%) patients with UC, and 5 of 19 (26.3%) patients with CD (P < 0.05 vs controls, odds ratio 14.8). In patients with CD, there was no correlation between disease activity and the presence of IS900.

CONCLUSIONS

Our technique enabled sensitive and specific detection of MAP DNA in archival endoscopic biopsy specimens. Although MAP-specific DNA can be detected in about 5% of intestinal biopsies from children with UC or controls without IBD, its presence was significantly associated with pediatric granulomatous CD, being particularly prevalent in ileal tissue. This easily defined clinical subset of patients may be useful for additional studies to determine the role of MAP in CD.

Granulomas in Crohn's disease: are newly discovered genetic variants involved?

BACKGROUND

Non-caseating granulomas exist in a substantial portion of patients with Crohn's disease (CD). Several single nucleotide polymorphisms (SNPs) have been identified as a having strong association with CD, including SNPs within the autophagy related 4 homolog A (ATG4A) gene and the neutrophil cytosolic factor 4 (NCF4) gene. We hypothesized a possible association between the presence of granulomas in CD patients and variants in the ATG4A and NCF4 genes.

AIMS

To investigate whether variants in the NCF4 and ATG4A genes are associated with granuloma formation in a cohort of Israeli patients with CD, exploring demographic and clinical characteristics that differ between granuloma positive and granuloma negative patients.

METHODS

307 Israeli patients with CD were studied. Patients with CD who underwent biopsy or resection of the intestine were classified according to presence or absence of granulomas. Using PCR-RFLP we determined the allele frequency in SNP rs4821544 (NCF4 gene) and SNP rs807185 (ATG4A gene) for all patients.

RESULTS

Granulomas were found in 85 out of 307 CD patients (27%). There were no significant differences between patients with or without granulomas in allele frequency in SNPs rs4821544 and rs807185. CD Patients with granuloma were younger at diagnosis than patients without granuloma (mean age 19 vs. 27, respectively, P<0.0001) and were more likely to undergo surgery (55.3% vs. 34.8%, respectively, P=0.002).

CONCLUSIONS

No association was found between SNPs rs4821544 and rs807185 and the presence of granulomas in CD patients. Granuloma positive patients were more likely to be younger and to undergo surgery.

Inflammatory bowel disease

This article reviews the etiology, clinical characteristics, and treatment of inflammatory bowel disease (IBD) and associated psychological sequelae in children and adolescents with this lifelong disease. Pediatric-onset IBD, consisting of Crohn's disease and ulcerative colitis, has significant medical morbidity and in many young persons is also associated with psychological and psychosocial challenges. Depression and anxiety are particularly prevalent and have a multifaceted etiology, including IBD-related factors such as cytokines and steroids used to treat IBD and psychosocial stress. A growing number of empirically supported interventions, such as cognitive behavioral therapy, hypnosis, and educational resources, help youth and their parents cope with IBD as well as the psychological and psychosocial sequelae. While there is convincing evidence that such interventions can help improve anxiety, depression, and health-related quality of life, their effects on IBD severity and course await further study.

[Multifactorial etiology and pathogenic factors in inflammatory bowel disease]

All the currently available evidence suggests that the two types of inflammatory bowel disease (IBD), Crohn's disease (CD) and ulcerative colitis (UC), involve a conflict between the immune system of the intestinal mucosa and intraluminal antigens, mainly the intestinal microflora, which are normally tolerated by the immune system. This conflict is modulated by numerous environmental factors and a clear polygenetic predisposition. The present article reviews the behavior of all the etiologic circumstances (microbial, genetic and environmental) and subsequently analyzes the possible pathogenic factors in which the etiologies can be found, namely: dysfunction of the intestinal epithelium, innate immune system alterations, and distortion of the cellular and humoral arms of the acquired immune system. The role of tissue ischemia in CD and expression of "extraintestinal inflammatory metastases", both in CD and UC, are briefly discussed. Finally, the view that IBD may be a spectrum of pathological processes provoked by distinct etiopathogenic factors and the possible biological significance of the growing incidence of this disease in the western world, coinciding with the decline in infectious diseases in this geographical area, are discussed.

Genomewide association studies: history, rationale, and prospects for psychiatric disorders

OBJECTIVE

The authors conducted a review of the history and empirical basis of genomewide association studies (GWAS), the rationale for GWAS of psychiatric disorders, results to date, limitations, and plans for GWAS meta-analyses.

METHOD

A literature review was carried out, power and other issues discussed, and planned studies assessed.

RESULTS

Most of the genomic DNA sequence differences between any two people are common (frequency >5%) single nucleotide polymorphisms (SNPs). Because of localized patterns of correlation (linkage disequilibrium), 500,000 to 1,000,000 of these SNPs can test the hypothesis that one or more common variants explain part of the genetic risk for a disease. GWAS technologies can also detect some of the copy number variants (deletions and duplications) in the genome. Systematic study of rare variants will require large-scale resequencing analyses. GWAS methods have detected a remarkable number of robust genetic associations for dozens of common diseases and traits, leading to new pathophysiological hypotheses, although only small proportions of genetic variance have been explained thus far and therapeutic applications will require substantial further effort. Study design issues, power, and limitations are discussed. For psychiatric disorders, there are initial significant findings for common SNPs and for rare copy number variants, and many other studies are in progress.

CONCLUSIONS

GWAS of large samples have detected associations of common SNPs and of rare copy number variants with psychiatric disorders. More findings are likely, since larger GWAS samples detect larger numbers of common susceptibility variants, with smaller effects. The Psychiatric GWAS Consortium is conducting GWAS meta-analyses for schizophrenia, bipolar disorder, major depressive disorder, autism, and attention deficit hyperactivity disorder. Based on results for other diseases, larger samples will be required. The contribution of GWAS will depend on the true genetic architecture of each disorder.