Clinical Dilemmas in Inflammatory Bowel Disease

New Challenges

Peter Irving, Corey A. Siegel, David Rampton, Fergus Shanahan, Peter Irving, MD, MRCP, Corey A. Siegel, David Rampton, Fergus Shanahan

• Publisher: Wiley-Blackwell
• Year: 2011
• Print ISBN: 9781444334548
• eBook ISBN: 9781444342550
• Edition: 2
• Topic: Medicine
• Subtopic: Gastroenterology & Hepatology

The second edition of Clinical Dilemmas in Inflammatory Bowel Disease: New Challenges, is a practical, up-to-date handbook providing expert guidance on specific clinical dilemmas and areas of difficulty that the gastroenterologist regularly faces in day-to-day practice.

In this new edition, 75% of the "dilemmas" are brand new dilemmas facing the IBD specialist concerning emerging treatment therapies, such as the use of cannabinoids and Viagra for Crohn's disease. The remaining 25% of the dilemmas are fully updated from the previous edition, incorporating the latest clinical thinking.

Each of the 57 evidence-based chapters contains clear learning points, addresses different topics, and provides sound guidance on subjects ranging from optimizing current management through to special management problems and novel treatments.

This book is suitable for all medical professionals involved in the care of patients with IBD: established and trainee gastroenterologists, colorectal surgeons, pathologists, radiologists, specialist nurses, pharmacists, dieticians and counselors.

Part I

Genes and Phenotype in IBD

1

Which will take us further in IBD—study of coding variation or epigenetics?

Miles Parkes

Department of Gastroenterology, Addenbrooke's Hospital and University of Cambridge, Cambridge, UK

LEARNING POINTS

• Genome-wide association scans have revealed many genetic risk factors for Crohn's disease and ulcerative colitis.
• As with environmental risk factors, some of the genetic risk is shared and some is specific to either Crohn's disease or ulcerative colitis.
• Only about 20% of the variance in heritability has been accounted for by known genetic loci.
• The study of genetic variants is valuable because it reveals insights into disease pathogenesis.
• Increasing evidence suggests that much of the host susceptibility to IBD may be epigenetic, lying at the level of the regulation of gene expression.
• Epigenetic risk is heritable through mitosis and possibly meiosis, and many of the known environmental or lifestyle risk factors may operate at an epigenetic level by influencing gene transcription.

Genetic susceptibility to inflammatory bowel disease (IBD) is complex. While genome-wide association scans (GWAS) have pushed Crohn's disease (CD) to the front of the field of complex disease genetics, the recognition that only 20% of the variance in heritability has so far been accounted for provides a salutary reminder of the challenges ahead [1]. The main achievement of GWAS has been to highlight a number of previously unsuspected pathogenic pathways for IBD and to provide a stable base-camp from which to explore the genetic higher ground—defining causal variants at each of the loci identified, accounting for the remaining 80% of heritability and exploring functional implications.

This chapter discusses what is understood regarding causal mechanisms in IBD genetics, particularly the relative contributions of simple variation in DNA coding sequence and epigenetic regulation of gene transcription. For some readers, epigenetic regulation of gene transcription may be an unfamiliar concept: it involves changes in gene expression resulting from mechanisms such as chromatin packaging, histone acetylation (affecting electrostatic charge and hence DNA binding), and DNA methylation.

Gene expression: sequence variation versus epigenetic factors

The human genome is thought to encode some 23,000 protein-coding genes, comprising just 1.5% of the total of 3 billion base pairs. Sequence variation can take many forms from single nucleotide polymorphisms (SNPs) to indels (insertion–deletion polymorphisms) to copy number variants, where segments up to thousands of base pairs long can be deleted or duplicated. SNPs are the commonest variant. They occur approximately every 200 base pairs, but less frequently in coding sequence because of potential for adversely affecting protein function and hence incurring negative selection pressure.

Genes comprise exons (the coding sequence) and introns, which are removed prior to mRNA being translated to protein. Gene density varies considerably, with lengthy tracts of noncoding sequence, formerly and erroneously referred to as “junk DNA,” being interposed. Increasingly, it is recognized that much of the complexity of human biology derives not from the coding sequence, but from the complex, networked regulation of gene transcription by a host of epigenetic mechanisms. These include alternative exon splicing and control of mRNA stability by microRNAs, as well as DNA methylation and histone binding. These mechanisms (reviewed in [2]) allow dynamic activation or silencing of genes, and are heritable in being transmissible at mitosis, for example, to maintain tissue-specificity of gene expression, but they are not related to changes in DNA sequence.

Genetic variation in IBD

What forms of genetic variation contribute to IBD? The answer is likely to be “all of them,” to a greater or lesser extent, perhaps including mechanisms yet to be characterized. Extrapolation from monogenic disease initially suggested that coding variation was likely to be most relevant, and its obvious impact on protein structure and function supported this intuition. Further, the three relatively common causal variants in NOD2, the first IBD gene to be identified, were all coding variants [3]. Thus, early genome-wide genotyping arrays, which could accommodate relatively few SNPs, focussed only on “nonsynonymous” SNPs. Although some interesting results were obtained, particularly in identifying the importance of ATG16L1 and autophagy in CD, the yield was unimpressive [4].

Truly hypothesis-free GWAS studies have followed, interrogating most if not all common variations (allele frequency >5%) genome-wide. Interestingly, the yield from these “proper” GWAS studies has been much greater than from nonsynonymous SNP scans and many lessons have been learned.

One remarkably consistent feature of GWAS studies has been the number of “gene deserts” showing association across a range of complex diseases. The supposition is that these loci contain elements that regulate transcription, and there is now evidence that sequence variation influences transcription for many genes. Thus, epigenetic regulation is itself a heritable trait and may be the key factor contributing to phenotypic variation in humans [5].

Several “gene desert” associations have been seen in IBD: indeed in the first meta-analysis plus replication of CD GWAS studies from the international IBD genetics consortium, 6 out of the 32 confirmed loci mapped to gene deserts. More than this, our now detailed knowledge of all common sequence variations genome-wide allowed us to identify how many of the CD susceptibility loci correlated with any known coding variation. The answer, rather startlingly, was just 9 [1]. To emphasize this point, coding variation has to date been confirmed as causal for just two loci—NOD2 and ATG16L1, with one other at IL23R strongly implicated.

Regulation of gene expression in IBD

Accepting the indirect evidence that regulatory effects are important, is there any direct evidence? The answer is emphatically yes. In the Belgian CD GWAS, the strongest association was seen with a 1.25-Mb gene desert on chromosome 5. Using publicly available expression quantitative trait loci (eQTL) data, Libioulle et al. showed that these same SNPs that showed association with CD also correlated strongly with expression of the prostaglandin receptor gene EP4 270 Kb away [6]. The international CD meta-analysis study identified a number of other such correlations [1], and in its most recent analysis identified association at a DNA methyltransferase gene, emphasizing the importance of epigenetic regulation and its interrelationship with sequence variation in CD susceptibility.

Evidence from basic research corroborates the importance and potential complexity of epigenetic effects. Thus, the toll-like receptor-induced inflammatory response in mouse macrophages is regulated at a gene-specific level by transient chromatin modification, with Th2 “bias” being conferred by a transcriptional regulator of IL-4 called Mina. Highlighting the interplay of sequence variation with epigenetics, production of Mina is itself strongly correlated with SNP haplotypes in its promoter [7].

Identifying correlation between IBD association signals and gene expression hints at functional regulatory elements, but usually does not explain the mechanism. The expectation is that genome-wide assays for DNA methylation, ChIP seq, histone binding, and DNA tertiary structure (e.g., chromatin conformation capture or 3C), will provide some answers over the next few years [8]. They should allow both a better understanding of the mechanisms underlying current GWAS signals and also permit de novo genome-wide studies.

Limitations of current studies of epigenetic mechanisms in IBD

At present, difficulties in defining which cell type to target for expression analyses are limiting. The relevance of this comes from the recognition that many gene regulatory effects are cell-type specific—as seen for the CD-associated allele of IRGM which affects expression in opposite directions in different cell types [9]. Further concerns relate to the confounding effects of inflammation and drug therapy. Nonetheless, the evidence that epigenetic mechanisms are crucial in regulating gene transcription and thereby affecting susceptibility to disease will drive development of the appropriate resources to tackle these questions.

Epigenetic regulation is also significantly influenced by environmental factors, including diet, smoking, and infection—all of which are implicated in IBD pathogenesis. For example, aryl hydrocarbon receptor (AhR) agonists, which are present in substances as varied as cigarette smoke and Brassica vegetables, can strongly influence COX-2 expression. The effect may be related to AhR acting directly as a transcriptional regulator and also by regulating histone acetylation and hence chromatin structure [10]. The AhR also plays a key role in modulating Th17 lymphocyte development through epigenetic mechanisms [11]. The suggestion that some epigenetic regulatory influences may be transmissible through meiosis to the next generation adds particular interest to this story [12].

Conclusions

At present, GWAS studies are being widely deployed not because they provide all the answers, but rather because they are technologically tractable and provide robust and reproducible data. More technologically challenging and complex studies will follow to advance our ...

Table of contents

• Cover
• Title Page
• Copyright
• Contributors
• Preface
• Part I: Genes and Phenotype in IBD
• Part II: Bugs and IBD—Good, Bad, or Indifferent?
• Part III: Investigating IBD
• Part IV: Medical Therapy
• Part V: Other Treatments
• Part VI: Surgical Dilemmas in IBD
• Part VII: Unsolved Issues in IBD
• Part VIII: Nutrition in IBD
• Part IX: Management Process
• Index