Genetics of inflammatory bowel disease: implications for the future

Application of genome-wide gene expression profiling by high-density DNA arrays to the treatment and study of inflammatory bowel disease

Identification of factors involved in the initiation, amplification, and perpetuation of the chronic immune response and the identification of markers for the characterization of patient subgroups remain critical objectives for ongoing research in inflammatory bowel disease (IBD). The Human Genome Project and the development of the expressed sequence tag (EST) clone collection and database have made possible a new revolution in gene expression analysis. Instead of measuring one or a few genes, parallel DNA microarrays are capable of simultaneously measuring expression of thousands of genes, providing a glimpse into the logic and functional grouping of gene programs encoded by our genome. Applied to clinical specimens from affected and normal individuals, this methodology has the potential to provide a new level of information about disease pathogenesis not previously possible. Two dominant platforms for the construction of high-density microarrays have emerged: cDNA arrays and GeneChips. The first involves robotic spotting of DNA molecules, often derived from EST clone collections, onto a suitable solid phase matrix such as a glass slide. The second involves direct in situ synthesis of sets of gene-specific oligonucleotides on a silicon wafer by an eloquent derivative of the photolithography process. Both cDNA and oligonucleotide arrays are interrogated by hybridization with a fluorescent-labeled cDNA or cRNA representation of the original tissue mRNA. This enables measurement of the expression levels for thousands of mucosal genes in a single experiment. These technologies have recently become less expensive and more widely accessible to all researchers. This review details the principles and methods behind DNA array technology, data analysis and mining, and potential application to research and treatment of IBD.

Crohn's disease and Mycobacterium avium subsp. paratuberculosis: current issues

Crohn's disease is a chronic debilitating inflammatory bowel disease of unknown etiology. Proposed causes include bacterial or viral infection, diet or exposure to tobacco smoke, genetic abnormality, and immune dysfunction. The bacterium Mycobacterium avium subsp. paratuberculosis (Map) has received much research attention as a potential cause of the disease. Map causes Johne's disease in ruminants. The pathology of Johne's disease superficially resembles that of Crohn's disease in humans. Some researchers have shown evidence of Map in intestinal tissues of Crohn's disease patients. Studies are in progress to investigate the possibility that Map exists in milk from infected cows and survives pasteurization. This is a controversial subject with the potential for media attention and public outcry. We examined the current literature and concluded that insufficient evidence exists at this time to implicate any one factor, including Map in milk, as the definitive cause of Crohn's disease. The high degree of uncertainty in this issue requires regulators to recognize the need for effective risk communication as ongoing research provides additional information about the disease.

The interleukin 1 receptor antagonist gene allele 2 as a predictor of pouchitis following colectomy and IPAA in ulcerative colitis

BACKGROUND & AIMS

The interleukin 1 receptor antagonist gene allele 2 has been suggested as a determinant of both disease susceptibility and extent in ulcerative colitis. The aim of this study was to assess the allele as a predictor of both the indication for colectomy and the occurrence of pouchitis after ileal pouch-anal anastomosis formation.

METHODS

Genotyping for the +2018 single nucleotide polymorphism in the interleukin 1 receptor antagonist gene was performed in 109 patients who had undergone colectomy, including 82 patients who had been followed prospectively after ileal pouch-anal anastomosis formation.

RESULTS

Patients with pouchitis had a higher allele 2 carriage rate compared with those without pouchitis (72% vs. 45%) and Kaplan-Meier survival analysis showed that allele 2 carriers had a significantly increased incidence of pouchitis compared with noncarriers (log-rank test, 6.5). After adjustment for confounding covariates in a Cox proportional hazards model, the relative hazard was 3.1 (95% confidence interval [CI], 1.2-7.8; P = 0.02). Although there was a higher allele 2 carriage rate in patients with chronic refractory compared with acute severe ulcerative colitis (63% vs. 48%), this difference was not significant (odds ratio, 1.9; 95% CI, 0.9-4.1; P = 0.1).

CONCLUSIONS

The interleukin 1 receptor antagonist gene allele 2 predicts pouchitis after ileal pouch-anal anastomosis in ulcerative colitis.

A critical review of epidemiological studies in inflammatory bowel disease

This review addresses the difficulty in interpreting the results of epidemiological studies in IBD and in making meaningful comparisons between studies. Both ulcerative colitis and Crohn disease appear to be more common in some industrialized countries such as Scandinavia, United Kingdom, North America and less common in Central and Southern Europe, Asia and Africa. Given data showing an increased incidence of ulcerative colitis in the United Kingdom, it is crucial that more studies be conducted in developing countries. While the incidence of Crohn disease has increased strikingly in many areas, the incidence of ulcerative colitis has remained fairly stable in most. This could be due to the rising number of community-based studies, as well as the improved accuracy in diagnosing Crohn disease. Although, the incidence of IBD among Blacks in Africa is low, infection rates are high, life expectancy is lower than in developed countries. Data from the USA suggest that rates are similar in Afro-American and Caucasian populations. Rates for Jewish populations may be slightly higher than in non-Jewish populations but this also varies geographically. Careful attention to genetic, environmental, and socioeconomic factors must be accounted for in these studies. There is no strong evidence to support that IBD is more common in urban than in rural settings and migration towards more accessible health care has not been adequately addressed. Recent epidemiological studies suggest that mortality rates for IBD are similar to that of the general population for the majority of patients. However, older patients with IBD and newly diagnosed cases with severe diseases are at increased risk of dying. Epidemiological studies remain important in assisting with health policy planning and in hypothesis testing of etiological factors. As better diagnostic techniques become widely available and public health registries are increasingly used, it is possible that geographic differences will diminish. International collaborative studies will be better equipped to answer research questions addressing risk factors and disease natural history. We have summarized in Table V the essential criteria to conduct a sound epidemiological study, which would permit future testing of hypotheses among different populations.

Analysis of mucosal gene expression in inflammatory bowel disease by parallel oligonucleotide arrays

DNA arrays capable of simultaneously measuring expression of thousands of genes in clinical specimens from affected and normal individuals have the potential to provide information about disease pathogenesis not previously possible. Few studies have applied mRNA profiling to diseases involving complex tissues like the intestinal mucosa, reflecting the unique challenges inherent to this type of analysis. We report the analysis of mucosal gene expression in ulcerative colitis (UC) patients and inflamed and noninflamed control specimens. Genes can be used as markers for cell recruitment, activation, and mucosal synthesis of immunoregulatory molecules. Self-organizing maps were applied to cluster and analyze gene expression patterns and were paired with histopathological scores to identify genes associated with increased disease activity. Clustering was achieved on the basis of differences in expression levels across individual specimens. Several inflammatory mediators were identified as likely determinants of characteristic histological features of active UC. These results provide proof of principle for application of functional genomics to larger inflammatory bowel disease populations for gene discovery, to facilitate identification of disease subgroups on the basis of gene expression signatures, and for prediction of disease behavior or optimal therapeutic intervention.

Current management of pediatric inflammatory bowel disease

Inflammatory bowel disease (IBD) is a relatively rare condition of childhood, although the wide range of presenting complaints, scope of complications, and choices of therapy for this condition make it particularly difficult to treat in children. Novel approaches to the management of Crohn's disease and ulcerative colitis have gained recent favor. This report summarizes the current medical and surgical management of IBD, recent advancements in clinical therapies, and particular aspects of IBD care for children.