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Crohn’s disease (CD) is a chronic inflammatory bowel disease (IBD) of the digestive tract in humans. There is evidence that Parabacteroides distasonis could contribute to IBD. Here, we present the complete genome sequence of a strain designated CavFT-hAR46, which was isolated from a gut intramural cavernous fistulous tract (CavFT) microlesion in a CD patient.

The challenges posed by complex diseases such as chronic inflammatory, autoimmune, metabolic, and neoplastic disorders are many, ranging from correct clinical diagnosis to proper classification, precise and effective therapy, long-term monitoring, and prediction of ultimate outcome. This is certainly the case for the two main forms of inflammatory bowel disease (IBD), Crohn’s disease (CD) and ulcerative colitis (UC), despite the considerable progress witnessed in the last couple of decades. Facing the above challenges, it is not surprising that physicians and patients alike yearn for objective and highly specific tests that can provide clear answers to what is the correct diagnosis, what is the best treatment, and how the patient will fare in the long run. The quest for simple answers to complicated questions is intrinsic to human nature, but in biology and medicine, expectations are seldom matched by reality. Nevertheless, the medical community is still searching for ideal biomarkers [1], traditionally defined as “cellular, biochemical or molecular alterations that are measurable in human tissues, cells, or fluids” [2] and more recently including “biological characteristics measured as indicators of normal and pathogenic processes, or pharmacological responses to a therapeutic intervention” [3]. These are broad and ambitious definitions that reflect the desire of having tests that can inform about all aspects of a disease like IBD, as denoted in the preceding chapters of this book.

The proper delivery of immune cells throughout the host's various tissues and organs is essential to health, and abnormalities in the type and quantity of leukocyte distribution is usually associated with disease. Because of its size and presence of a very large amount of immunocytes in the mucosa and mesenteric lymph nodes, the gut is the recipient of a constant influx of leukocytes, a process tightly regulated by multiple factors. These include cell adhesion molecules on the leukocytes and their counter-receptors on the microvascular endothelial cells in the bowel wall, a number of chemokines and cytokines that help attracting immune cells, platelets, bacterial products, danger signals, the size of the vascular and lymphatic beds and the process of leukocyte exit and circulation in the blood and lymphatic fluid. The disruption of any of the above regulatory mechanism can lead to inflammation, as is the case for inflammatory bowel disease. Learning how leukocyte and endothelial cells mutually function in health and what goes wrong in inflammation offers the opportunity to intervene therapeutically and re-establish the normal crosstalk between leukocytes and endothelial cells. (C) 2016 S. Karger AG, Basel

IBD is a chronic inflammatory condition of the gastrointestinal tract encompassing two main clinical entities: Crohn's disease and ulcerative colitis. Although Crohn's disease and ulcerative colitis have historically been studied together because they share common features (such as symptoms, structural damage and therapy), it is now clear that they represent two distinct pathophysiological entities. Both Crohn's disease and ulcerative colitis are associated with multiple pathogenic factors including environmental changes, an array of susceptibility gene variants, a qualitatively and quantitatively abnormal gut microbiota and a broadly dysregulated immune response. In spite of this realization and the identification of seemingly pertinent environmental, genetic, microbial and immune factors, a full understanding of IBD pathogenesis is still out of reach and, consequently, treatment is far from optimal. An important reason for this unsatisfactory situation is the currently limited comprehension of what are the truly relevant components of IBD immunopathogenesis. This article will comprehensively review current knowledge of the classic immune components and will expand the concept of IBD immunopathogenesis to include various cells, mediators and pathways that have not been traditionally associated with disease mechanisms, but that profoundly affect the overall intestinal inflammatory process.

The industrial revolution that began in the late 1800s has resulted in dramatic changes in the environment, human lifestyle, dietary habits, social structure, and so on. Almost certainly because this rapid evolution has outpaced the ability of the body to adapt to a number of environmental and behavioral changes, there has been a parallel emergence of several chronic inflammatory diseases, among which are inflammatory bowel diseases (IBD), primarily ulcerative colitis and Crohn's disease. The ability to treat these conditions has progressively improved in the last 50 years, particularly in the last couple of decades with the introduction of biological therapy targeting primarily soluble mediators produced by inflammatory cells. A large number of biologics are now available, but all of them induce similarly unsatisfactory (

Background Carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) displays multiple activities, among which pathogen binding and angiogenesis are particularly prominent. These same functions are also exerted by Toll- and NOD-like receptors (TLRs and NLRs), which are critical mediators of innate immune responses. We investigated whether a functional inter-relationship exists between CEACAM1 and TLRs and NLRs and its potential impact on induction of intestinal angiogenesis. Methods This hypothesis was tested using human intestinal microvascular endothelial cells, a unique cell population exposed to microbial products under physiological and pathological conditions. Results The results show that activation of TLR2/4, TLR4, NOD1, and NOD2 by specific bacterial ligands selectively and differentially upregulates the levels of cellular and soluble CEACAM1 produced by intestinal microvascular endothelial cells. The results also show that CEACAM1 regulates the migration, transmigration, and tube formation of these endothelial cells and mediates vessel sprouting induced by specific TLR and NLR bacterial ligands. Combined, these results demonstrate a close and reciprocal regulatory interaction between CEACAM1 and bacterial products in mediating multiple functions essential to new vessel formation in the gut mucosa. Conclusions A coordinated and reciprocal interaction of CEACAM1 and microbiota-derived factors is necessary to optimize angiogenesis in the gut mucosa. This suggests that a coordination of endogenous and exogenous innate immune responses is necessary to promote intestinal angiogenesis under physiological and inflammatory conditions such as inflammatory bowel disease.

Crohn’s Disease is a relapsing and remitting disease involving chronic intestinal inflammation that is often characterized by hypertrophy of visceral adipose tissue (VAT). While an increased ratio of VAT to subcutaneous fat (SQF) has previously been identified as a predictor of worse outcomes in Crohn’s Disease, bowel-proximal fat regions have also been hypothesized to play a role in inflammatory response. However, there has been no detailed study of VAT and SQF regions on MRI to determine their potential utility in assessing Crohn’s Disease severity or guiding therapy. In this paper we present a fully-automated algorithm to segment and quantitatively characterize VAT and SQF via routinely acquired diagnostic bowel MRIs. Our automated segmentation scheme for VAT and SQF regions involved a combination of morphological processing and connected component analysis, and demonstrated DICE overlap scores of 0.86±0.05 and 0.91±0.04 respectively, when compared against expert annotations. Additionally, VAT regions proximal to the bowel wall (on diagnostic bowel MRIs) demonstrated a statistically significantly, higher expression of four unique radiomic features in pediatric patients with moderately active Crohn’s Disease. These features were also able to accurately cluster patients who required aggressive biologic therapy within a year of diagnosis from those who did not, with 87.5% accuracy. Our findings indicate that quantitative radiomic characterization of visceral fat regions on bowel MRIs may be highly relevant for guiding therapeutic interventions in Crohn’s Disease.

International audience; The endothelial-to-mesenchymal transition (EndoMT) is a crucial cellular process during heart development necessary to the formation of cardiac valves. This embryonic process reappears in several pathological situations, such as vascular injury or organ fibrosis of various etiologies, as a mediator of extracellular matrix-producing cells. Because radiation induces both vascular damage and fibrosis, we investigated whether radiation exposure induces EndoMT in primary human intestinal microvascular endothelial cells (HIMECs) and whether EndoMT contributes to radiation-induced rectal damage in humans and in a preclinical model of radiation proctitis in mice. Irradiated HIMECs show phenotypic hallmarks of radiation-induced endothelial cell activation in vitro. Moreover, HIMECs undergo changes in molecular expression pattern compatible with EndoMT, with up-regulation of mesenchymal markers and down-regulation of endothelial markers via transforming growth factor/Smad pathway activation. In vivo, EndoMT readily occurs in the human rectum after radiation therapy for rectal adenocarcinoma. Finally, EndoMT was observed in rectal mucosal and submucosal microvessels in a preclinical model of radiation proctitis in Tie2-green fluorescent protein reporter-expressing mice all along radiation proctitis development, also associated with transforming growth factor/Smad pathway activation. In conclusion, radiation-induced cell activation and tissue inflammation constitute a setting that fosters the phenotypic conversion of endothelial cells into mesenchymal cells. Therefore, EndoMT is identified as a potential participant in radiation-induced gut damage and may represent an interesting therapeutic target in cases of radiation-induced pelvic disease. © 2015 American Society for Investigative Pathology.

Intestinal epithelial cell (IEC) death is typical of inflammatory bowel disease (IBD). We investigated: i) whether IEC–released necrotic cell products (proinflammatory mediators) amplify mucosal inflammation, ii) the capacity of necrotic cell lysates from HT29 cells or human IECs to induce human intestinal fibroblasts' (HIF) production of IL-6 and IL-8, and iii) whether IL-1α, released by injured colonocytes, exacerbated experimental IBD. Necrotic cell lysates potently induced HIF IL-6 and IL-8 production independent of Toll-like receptors 2 and 4, receptor for advanced glycation end-products, high-mobility group box 1, uric acid, IL-33, or inflammasome activation. IL-1α was the key IEC-derived necrotic cell product involved in HIF cytokine production. IL-1α–positive cells were identified in the epithelium in human IBD and dextran sulfate sodium (DSS)-induced colitis. IL-1α was detected in the stool of colitic mice before IL-1β. IL-1α enemas reactivated inflammation after DSS colitis recovery, induced IL-1 receptor expression in subepithelial fibroblasts, and activated de novo inflammation even in mice without overt colitis, after the administration of low-dose DSS. IL-1α amplifies gut inflammation by inducing cytokine production by mesenchymal cells. IL-1α–mediated IEC–fibroblast interaction may be involved in amplifying and perpetuating inflammation, even without obvious intestinal damage. IL-1α may be a target for treating early IBD or preventing the reactivation of IBD.

Inflammatory bowel disease (IBD) is presently one of the most investigated human disorders. Expansion of knowledge of its pathophysiology has helped in developing novel medications to combat gut inflammation with a considerably degree of success. Despite this progress, much more remains to be done in regard to gaining a more profound understanding of IBD pathogenesis, detecting inflammation before it clinically manifests, implementing lifestyle modifications, and developing agents that can modify the natural course of the disease. One of the limitations to achieve these goals is the lack of integration of the major components of IBD pathogenesis, that is the exposome, the genome, the gut microbiome, and the immunome. An “IBD integrome” approach that takes advantage of all functional information derived from the detailed investigation of each single pathogenic component through the use of systems biology may offer the solution to understand IBD and cure it.

Personalized medicine is variably defined as a new system aimed at providing optimal medical care by using comprehensive pathophysiology-based information on all aspects and components of a disease process to prevent, diagnose and treat in ways that are custom-made for the individual patient. The need for personalized medicine derives from the realization that today's most challenging medical conditions are chronic complex diseases with multiple pathogenic components that interact with each other. Complexity and interaction together create unique molecular pathways that are only relevant to certain disease subtypes, but not to the entire population of patients with the same diagnosis. Thus, complex diseases cannot be properly controlled, and much less cured, by modulating single components at sporadic time points in the course of the disease or administering the same treatment to all patients, as we currently do in the management of inflammatory bowel disease (IBD). The implementation of personalized medicine requires entirely novel and methodologically sophisticated bioinformatics-based approaches that use comprehensive and detailed information on the various components (‘omes') of the disease process. This requires identifying the key controllers (‘hubs') of pathogenic pathways in a totally unbiased fashion and discovering highly specific agents that can selectively block or even revert pathogenic events. IBD is a perfect example of a condition with multiple causes and multiple mechanisms, and IBD patients will unquestionably benefit from the adoption of personalized medicine in the near future.

SummaryBackground There is an urgent need for cheap, reproducible, easy to perform and specific biomarkers for diagnosis, differentiation and stratification of inflammatory bowel disease (IBD) patients. Technical advances allow for the determination of volatile organic compounds in the human breath to differentiate between health and disease. Aim Review and discuss medical literature on volatile organic compounds in exhaled human breath in GI disorders, focusing on diagnosis and differentiation of IBD. Methods A systematic search in PubMed, Ovid Medline and Scopus was completed using appropriate keywords. In addition, a bibliography search of each article was performed. Results Mean breath pentane, ethane, propane, 1-octene, 3-methylhexane, 1-decene and NO levels were elevated (P

Despite unquestionable progress in the management of inflammatory bowel disease (IBD) and the much improved clinical results achievable today in Crohn's disease (CD) and ulcerative colitis (UC) patients, the overall therapeutic outcome remains far from optimal. The main reason of this partial success is that all current medications only block individual components of a highly complex disease process that results from the integration of multiple and incompletely identified pathogenic components. Thus, if further progress is to be achieved in IBD therapeutics and we want to move from the current success rate to nearly 100%, bold new ideas must be entertained and new approaches put into practice. Both are necessary because in IBD we are dealing with a prototypical complex disease superimposed to the background of the extreme biological diversity of humans in response to injury. An unresolved challenge mandates the adoption of new solutions specifically designed to address the unique features of that challenge. Translated to a disease condition, and IBD in particular, the unresolved challenges of CD and UC demand bold new thinking leading to the conception and implementation of totally innovative therapies. In this article, we propose that one such new thinking is the notion of network medicine for IBD, and that the development of brand new treatments should be based on the identification of the molecular structure of the IBD interactome with the purpose of targeting its controlling elements (central nodes or hubs). This specific targeting of the underlying molecular disease modules will lead to the disruption of the IBD interactome and foster the resolution of intestinal inflammatory process.

In the last 10 years, we have learned much about the pathogenesis, diagnosis, and management of intestinal fibrosis in patients with inflammatory bowel diseases. Just a decade ago, intestinal strictures were considered to be an inevitable consequence of long-term inflammation in patients who did not respond to anti-inflammatory therapies. Inflammatory bowel diseases−associated fibrosis was seen as an irreversible process that frequently led to intestinal obstructions requiring surgical intervention. This paradigm has changed rapidly, due to the antifibrotic approaches that may become available. We review the mechanisms and diagnosis of this serious complication of inflammatory bowel diseases, as well as factors that predict its progression and management strategies.

International audience; Crohn’s disease (CD) and ulcerative colitis (UC) are chronic inflammatory bowel diseases (IBDs) of unknown etiology that are associated with an aberrant mucosal immune response. Neoangiogenesis and vascular injury are observed in IBD along with increased lymphangiogenesis. While the pathogenic role of angiogenesis in IBD is well characterized, it is not clear how or if increased lymphangiogenesis promotes disease. Here, we determined that enhancing lymphangiogenesis and lymphatic function reduces experimental IBD. Specifically, we demonstrated that adenoviral induction of prolymphangiogenic factor VEGF-C provides marked protection against the development of acute and chronic colitis in 2 different animal models. VEGF-C–dependent protection was observed in combination with increased inflammatory cell mobilization and bacterial antigen clearance from the inflamed colon to the draining lymph nodes. Moreover, we found that the VEGF-C/VEGFR3 pathway regulates macrophage (MΦ) plasticity and activation both in cultured MΦs and in vivo, imparting a hybrid M1-M2 phenotype. The protective function of VEGF-C was meditated by the so-called resolving MΦs during chronic experimental colitis in a STAT6-dependent manner. Together, these findings shed light on the contribution of lymphatics to the pathogenesis of gut inflammation and suggest that correction of defective lymphatic function with VEGF-C has potential as a therapeutic strategy for IBD.

The complexity of IBD is well recognized as are the putative four major components of its pathogenesis, i.e. environment, genetic makeup, gut microbiota and mucosal immune response. Each of these components is extremely complex on its own, and at present should be more appropriately defined by the terms ‘exposome', ‘genome', ‘microbiome' and ‘immunome', respectively, based on the ‘ome' suffix that refers to a totality of some sort. None of these ‘omes' is apparently capable of causing IBD by itself; it is instead the intricate and reciprocal interaction among them, through the so-called ‘IBD interactome', that results in the emergence of IBD, or more appropriately the ‘IBD integrome'. To deal with and understand such overwhelming biological complexity, new approaches and tools are needed, and these are represented by ‘omics', defined as the study of related sets of biological molecules in a comprehensive fashion, such as genomics, transcriptomics, proteomics, metabolomics, and so on. Numerous bioinformatics-based tools are available to explore and take advantage of the massive amount of information that can be generated by the analysis of the various omes and their interactions, aiming at identifying the molecular interactome underlying any particular status of health and disease. These novel approaches are fully applicable to IBD and allow us to achieve the ultimate goal of developing and applying personalized medicine and far more effective therapies to individual patients with Crohn's disease and ulcerative colitis. For the practicing gastroenterologist, an omics-based delivery of healthcare may be intimidating, but it must be accepted and implemented if he or she is to provide the best possible care to IBD patients.

The review summarizes the current knowledge of the roles played by the vascular and lymphatic endothelium throughout the gut in the pathogenesis of inflammatory bowel disease (IBD) and gives an update on emerging strategies targeting both vasculatures.Enormous efforts have been made to understand the mechanisms underlining the origin, development and maintenance of intestinal chronic inflammation. In particular, new studies focused their attention on the role played by the microvascular and lymphatic endothelium in the pathogenesis of IBD. During inflammation, whereas the microvasculature is responsible for the entry and distribution of immune cells in the mucosa, the lymphatic system controls leukocyte exit, bacterial clearance and edema absorption. The study of these events, which are aberrant during chronic inflammation, has resulted in the identification and validation of several targets for the treatment of experimental colitis, some of which have translated into effective treatments for patients with IBD.Although much attention has been paid to the microvascular endothelium and to antiangiogenic therapies, specific studies on the lymphatic vasculature and its functions in IBD are still at the initial stage, and other molecular mechanisms, genes, molecules and new pathways must definitely be explored.

The clinical course of inflammatory bowel disease (IBD) is highly heterogeneous and often unpredictable, with multiple and serious complications that range from stricture formation to bowel obstruction or perforation, fistula formation and the need for surgery. All these problems are manifestations of tissue remodeling, a secondary but universal response to the insults of chronic inflammation. The factors involved in tissue remodeling are several, including the site and duration of inflammation, soluble molecules, the gut microbiota, and the type of mesenchymal cell response. The prototypical and most common type of tissue remodeling in IBD, and Crohn's disease (CD) in particular, is a fibrotic response, and this review will focus on the factors and mechanisms involved in fibrogenesis, and speculate on what is needed for the development of a rational treatment of intestinal fibrosis.

OBJECTIVES: The accuracy of available noninvasive biomarkers for diagnosis, stratification, and prediction of inflammatory bowel disease (IBD) courses is limited. We analyzed volatile organic compounds (VOCs) in the breath of IBD patients and controls for diagnosis and differentiation of IBD as well as their link with disease location, activity, and phenotype. METHODS: A prospective study of diagnostic testing was conducted, recruiting Crohn's disease (CD), ulcerative colitis (UC), other inflammatory gastrointestinal diseases (OGDs), and healthy controls (HCs), as well as subjects with ileal pouch anal anastomosis (IPAA). The breath VOC profile was analyzed using selective ion flow tube-mass spectrometry. RESULTS: One hundred and twenty-four subjects (n=24 CD, n=11 UC, n=6 OGD, n=53 HC, n=30 IPAA) were included. The breath metabolome was significantly different in patients with IBD, CD, or UC compared with OGD and HC (7 out of 22 VOCs), but not between CD and UC. No link between the level of VOCs with complications, disease location, and clinical or radiologic disease activity, as well as lab parameters or type of medication was found. Breath VOCs were markedly different in patients with IPAA compared with any other group (17 out of 22 VOCs) and the presence of pouch inflammation did not alter the VOC levels. CONCLUSIONS: A specific breath metabolome is associated with IBD and markedly changes in patients with IPAA. Analysis of a broader spectrum of VOCs can potentially aid in the development of breath prints to diagnose or differentiate inflammatory bowel disorders.

Background & aimsGenome-wide association studies have identified 200 inflammatory bowel disease (IBD) loci, but the genetic architecture of Crohn's disease (CD) and ulcerative colitis remain incompletely defined. Here, we aimed to identify novel associations between IBD and functional genetic variants using the Illumina ExomeChip (San Diego, CA).MethodsGenotyping was performed in 10,523 IBD cases and 5726 non-IBD controls. There were 91,713 functional single-nucleotide polymorphism loci in coding regions analyzed. A novel identified association was replicated further in 2 independent cohorts. We further examined the association of the identified single-nucleotide polymorphism with microbiota from 338 mucosal lavage samples in the Mucosal Luminal Interface cohort measured using 16S sequencing.ResultsWe identified an association between CD and a missense variant encoding alanine or threonine at position 391 in the zinc transporter solute carrier family 39, member 8 protein (SLC39A8 alanine 391 threonine, rs13107325) and replicated the association with CD in 2 replication cohorts (combined meta-analysis P= 5.55× 10(-13)). This variant has been associated previously with distinct phenotypes including obesity, lipid levels, blood pressure, and schizophrenia. We subsequently determined that the CD risk allele was associated with altered colonic mucosal microbiome composition in both healthy controls (P= .009) and CD cases(P= .0009). Moreover, microbes depleted in healthycarriers strongly overlap with those reduced in CD patients (P=9.24× 10(-16)) and overweight individuals (P=6.73×10(-16)).ConclusionsOur results suggest that anSLC39A8-dependent shift in the gut microbiome could explain itspleiotropic effects on multiple complex diseases includingCD.

The two major forms of IBD, Crohn's disease (CD) and UC, are chronic inflammatory disorders, the pathogenesis of which involves a complex interplay of multiple factors.1 ,2 The introduction of biological agents has substantially expanded and improved the therapeutic options for IBD, but a large proportion of patients still do not respond or achieve remission in the short term or long term. Thus, there is still a considerable need to improve the treatment of IBD, and significant research efforts are underway to address this unmet need. During the last two decades, the period of time over which the biologics as well as other new drugs for IBD have entered the market, the number of therapies that have failed is remarkably high. This is significant, and understanding the reasons for such failure should lead to a better drug development process and pave the way for alternate and more efficient drug development strategies. Traditionally, the drug development process initially involves target discovery and selection, and then biological confirmation in cellular and animal models. This is followed by phase I testing in healthy volunteers to check for safety and pharmacokinetics, then phase II testing in patient volunteers to obtain preliminary safety, clinical efficacy and dosing data, and finally phase III clinical studies in patients to obtain a more comprehensive characterisation of the safety and efficacy profile of a drug. This traditional pathway of drug development has had relatively limited success in generating new forms of treatment for IBD. Results have been impacted by predictable high clinical response rates in the placebo groups, a lack of objective end points, trial design with arbitrary definitions of induction and maintenance phases and outcomes, and not taking into account key components of IBD pathogenesis.3 Moreover, a lack of strict criteria to ensure the presence …

Inflammatory bowel diseases (IBD) are characterized by chronic relapsing inflammation of the gastrointestinal tract. The pathogenesis of IBD involves the alteration of innate and adaptive immune systems by environmental and microbial factors in genetically susceptible hosts. A number of immune based therapies are used for treatment of IBD including steroids; immunomodulators like thiopurines, methotrexate, cyclosporine; tumor necrosis factor inhibitors like infliximab, adalimumab, certolizumab, golimumab; and anti-integrin antibodies like vedolizumab. New drugs that target various aspects of the immune system are being investigated. In this chapter, we aim to summarize immune regulatory pathways in IBD, current therapies and their mechanism of action, and briefly highlight agents that are in the pipeline for the treatment of IBD.

It is becoming increasingly evident that the old paradigm of disease pathogenesis where a given genotype would determine a phenotype and this would lead to a particular disease is no longer acceptable. Many novel components are now recognized to be involved in the predisposition, triggering, progression and outcome of chronic inflammatory diseases like inflammatory bowel disease (IBD). Accordingly, investigation of IBD must recognize this complexity and take all potential components into account, if a full understanding of disease pathophysiology is to be reached and truly effective therapies developed based on this new global understanding. Essential to this approach is the notion of functional integration. Groups of functionally related pathogenic components must be assembled and studied as ‘omes’ like, for instance, the genome and the microbiome; at the same time all relevant ‘omes’ must be functionally and meaningfully integrated into the ‘interactome’, while the ‘epigenome’ should be used to dissect and understand the connections underlying the interactome. This is an ideal but also realistic scenario for the immediate future, as some of the ‘omes’ are already being explored in greater depth and their interactions examined through investigation of gene-gene (GXG) and gene-environment (GXE) interactions. Current knowledge of GXG and GXE and their impact on IBD pathogenesis is the focus of this review.

The major histocompatibility complex (MHC) on chromosome 6p is an established risk locus for ulcerative colitis (UC) and Crohn's disease (CD). We aimed to better define MHC association signals in UC and CD by combining data from dense single-nucleotide polymorphism (SNP) genotyping and from imputation of classical human leukocyte antigen (HLA) types, their constituent SNPs and corresponding amino acids in 562 UC, 611 CD and 1428 control subjects. Univariate and multivariate association analyses were performed, controlling for ancestry. In univariate analyses, absence of the rs9269955 C allele was strongly associated with risk for UC (P = 2.67 × 10(-13)). rs9269955 is a SNP in the codon for amino acid position 11 of HLA-DRβ1, located in the P6 pocket of the HLA-DR antigen binding cleft. This amino acid position was also the most significantly UC-associated amino acid in omnibus tests (P = 2.68 × 10(-13)). Multivariate modeling identified rs9269955-C and 13 other variants in best predicting UC vs control status. In contrast, there was only suggestive association evidence between the MHC and CD. Taken together, these data demonstrate that variation at HLA-DRβ1, amino acid 11 in the P6 pocket of the HLA-DR complex antigen binding cleft is a major determinant of chromosome 6p association with UC.

In addition to mesenchymal cells, endothelial cells may contribute to fibrosis through the process of endothelial-to-mesenchymal transition (EndoMT). We investigated whether human intestinal microvascular endothelial cells (HIMEC) undergo EndoMT and contribute to fibrosis in human and experimental inflammatory bowel disease (IBD). HIMEC were exposed to TGF-β1, IL-1β, and TNF-α or supernatants of lamina propria mononuclear cells (LPMC) and evaluated for morphological, phenotypic, and functional changes compatible with EndoMT. Genomic analysis was used to identify transcription factors involved in the transformation process. Evidence of in situ and in vivo EndoMT was sought in inflamed human and murine intestine. The combination of TGF-β1, IL-1β and TNF-α, or activated LPMC supernatants induced morphological and phenotypic changes consistent with EndoMT with a dominant effect by IL-1. These changes persisted after removal of the inducing agents and were accompanied by functional loss of acetylated LDL-uptake and migratory capacity, and acquisition of de novo collagen synthesis capacity. Sp1 appeared to be the main transcriptional regulator of EndoMT. EndoMT was detected in microvessels of inflammatory bowel disease (IBD) mucosa and experimental colonic fibrosis of Tie2–green fluorescent protein (GFP) reporter–expressing mice. In conclusion, chronic inflammation induces transdifferentiation of intestinal mucosal microvascular cells into mesenchymal cells, suggesting that the intestinal microvasculature contributes to IBD-associated fibrosis through the novel process of EndoMT.

Exposure of esophageal mucosa to hydrochloric acid (HCl) is a crucial factor in the pathogenesis of reflux disease. We examined supernatant of HCl-exposed rabbit mucosa for inflammatory mediators enhancing migration of leukocytes and production of H2O2as an indicator of leukocyte activation. A tubular segment of rabbit esophageal mucosa was tied at both ends to form a sac, which was filled with HCl-acidified Krebs buffer at pH 5 (or plain Krebs buffer as control) and kept oxygenated at 37°C. The medium around the sac (supernatant) was collected after 3 h. Rabbit peripheral blood leukocytes (PBL) were isolated, and sac supernatant was used to investigate PBL migration and H2O2production. HCl-exposed esophageal mucosa released substance P (SP), CGRP, platelet-activating factor (PAF), and IL-8 into the supernatant. PBL migration increased in response to IL-8 or to supernatant of the HCl-filled mucosal sac. Supernatant-induced PBL migration was inhibited by IL-8 antibodies and by antagonists for PAF (CV3988) or neurokinin 1 (i.e., SP), but not by a CGRP antagonist. Supernatant of the HCl-filled mucosal sac increased H2O2release by PBL that was significantly reduced by CV3988 and by a SP antagonist but was not affected by IL-8 antibodies or by a CGRP antagonist. We conclude that IL-8, PAF, and SP are important inflammatory mediators released by esophageal mucosa in response to acid that promote PBL migration. In addition, PAF and SP induce production of H2O2by PBL. These findings provide a direct link between acid exposure and recruitment and activation of immune cells in esophageal mucosa.

Modern studies of inflammatory bowel disease (IBD) pathogenesis have been pursued for about four decades, a period of time where the pace of progress has been steadily increasing. This progress has occurred in parallel with and is largely due to developments in multiple basic scientific disciplines that range from population and social studies, genetics, microbiology, immunology, biochemistry, cellular and molecular biology, and DNA engineering. From this cumulative and constantly expanding knowledge base the fundamental pillars of IBD pathogenesis appear to have been identified and consolidated during the last couple of decades. Presently there is a general consensus among basic IBD investigators that both Crohn's disease (CD) and ulcerative colitis (UC) are the result of the combined effects of four basic components: global changes in the environment, the input of multiple genetic variations, alterations in the intestinal microbiota, and aberrations of innate and adaptive immune responses. There is also agreement on the conclusion that none of these four components can by itself trigger or maintain intestinal inflammation. A combination of various factors, and most likely of all four factors, is probably needed to bring about CD or UC in individual patients, but each patient or set of patients seems to have a different combination of alterations leading to the disease. This would imply that different causes and diverse mechanisms underlie IBD, and this could also explain why every patient displays his or her own clinical manifestations and a personalized response to therapy, and requires tailored approaches with different medications. While we are becoming increasingly aware of the importance of this individual variability, we have only a superficial notion of the reasons why this occurs, as hinted by the uniqueness of the genetic background and of the gut flora in each person. So, we are apparently facing the paradox of having to deal with the tremendous complexity of the mechanisms responsible for chronic intestinal inflammation in the setting of each patient's individuality in the response to this biological complexity. This obviously poses considerable challenges to reaching a full understanding of IBD pathogenesis, but being aware of the difficulties is the first step in finding answers to them.

Hyaluronan (RA) occurs in the body as a large, hydrating, space-filling, carbohydrate polymer in the extracellular matrix; it has both anti-angiogenic and immunosuppressive properties. Cleavage of HA results in the generation of variably sized fragments that stimulate multiple angiogenic and inflammatory responses in a size-specific manner. in this study, we report that platelets, as well as their megakaryocyte precursors, are unusual among somatic cells in that they contain only hyaluronidase 2 (HYAL2) but not HYAL1. Platelet HYAL2 is sufficient to cleave HA into fragments that are specific for inflammatory and angiogenic signaling; this process occurs in the absence of HYAL1, which is necessary in all other tissues to perform further HA degradation. Platelets can bind to RA, some of which derives from the stressed microvessel endothelial cell surface. Platelet-derived HYAL2 cleaves RA into fragments that stimulate mononuclear leukocytes in the immediate microenvironment to produce proinflammatory cytokines, including interleukin-6 and interleukin-8. Platelets, thus, are not only involved in hemostasis, the earliest step in wound healing, but are also important in the signaling of subsequent inflammatory and angiogenic steps. We hypothesize that aberrations in these sequential steps can promote chronic inflammation, as found in inflammatory bowel disease. The platelet may thus provide an interface between acute and chronic inflammation, wound healing, and their subsequent fibrotic responses. (Am J Pathol 2009, 174:2254-2264; DOI: 10.2353/ajpath.2009.080831)

The rapid accumulation of new knowledge on the genes, gene variations and genetic loci associated with both forms of inflammatory bowel disease (IBD), e.g. Crohn’s disease (CD) and ulcerative colitis (UC), is shedding new light on the immunopathogenic mechanisms underlying these conditions. After the initial report of the association of NOD2 mutations with ileal CD, a large number of additional genetic variants and loci has been found to be associated with both CD and UC, CD alone and, quite recently, UC-associated variants have also emerged. Much of this progress is due to the use of methods such as genome-wide associations (GWA) based on large numbers of reasonably well-characterized patient groups. Among several others, some of the most pathophysiologically relevant associations reported so far are with gene variants related to innate immunity, autophagy, apoptosis, Th1 and Th17 responses, T cell activation, and immunosuppression. Some of these associations have lent further support to previously construed disease mechanisms or disclosed brand new mechanisms, like in the case of the autophagy pathway. While this much progress is obviously welcome, it also brings new challenges. These include the fact that all the gene mutations uncovered so far only account for a minority of all IBD cases, the variable distribution of gene mutations among worldwide IBD populations, and the still unknown effects of gene-gene and gene-environment interactions. Nevertheless, there is no question that genetic information will be quickly utilized not only for a better understanding of IBD pathogenesis, but it will also soon be incorporated into the armamentarium of better diagnostic and therapeutic tools.

Intestinal fibrosis is a potentially serious complication of inflammatory bowel disease and its pathophysiology is still unclear. This review will discuss recent developments relating to sources of fibroblasts in intestinal inflammation, mediators that modulate fibroblast activation and function, as well as new clinical, laboratory, endoscopic and radiological studies aimed at improving diagnosis and management of intestinal fibrosis in inflammatory bowel disease.The fibroblast remains the central cell responsible for intestinal fibrosis in inflammatory bowel disease and transforming growth factor-beta1 is still the most potent pro-fibrogenic cytokine. Novel mediators, however, are being identified that modulate fibroblast function, such as interleukin-13, interleukin-21, galectin-3, osteopontin, Wnt and toll-like receptor ligands, and anti-tumor necrosis factor-alpha agents. New fibroblast sources are being identified, such as fibrocytes, and new mechanisms of fibroblast generation, like epithelial- and endothelial-to-mesenchymal transition. Animal models of intestinal fibrosis are still few, but new ways to induce gut fibrosis are being explored. Serological markers indicating a clinically complicated course that includes intestinal fibrosis are promising and are being tested in adult and pediatric populations, particularly in Crohn's disease. Video capsule endoscopy, the Given Patency capsule, double balloon enteroscopy, and computed tomographic enteroscopy are some of the new modalities being developed to assess the risk and improve the diagnosis of intestinal fibrosis. Novel therapeutic approaches include endoscopic balloon dilatation with conventional and double balloon enteroscopy, and local injection of glucocorticoids and tumor necrosis factor-alpha blockers, showing partial but encouraging success.More studies are needed to improve knowledge of the pathophysiology of intestinal fibrosis if better preventive, diagnostic and therapeutic measures are to be expected in the near future.

Increased hyaluronan (HA) deposition is a common feature of inflamed tissues, including inflammatory bowel disease (IBD)-involved intestines. However, whether HA accumulation promotes or is the result of intestinal inflammation is unknown. Using the mouse dextran sulfate sodium (DSS)-induced experimental model of colitis, we investigated changes in HA deposition in the colon over time in conjunction with evolving pathological changes of tissue architecture. Profound changes in colon HA deposition occurred within 3-7 days of oral DSS administration and, more important, they preceded the inflammatory infiltrate. Interestingly, HA deposition within blood vessels of the colon is observed as early as 3 days during the course of colitis induction, well before any significant inflammatory infiltrate. HA deposition is also observed in blood vessels of inflamed human colon of IBD patients. We determined that human intestinal endothelial cells generate HA in response to proinflammatory stimuli by demonstrating a TNF-alpha-induced increase in hyaluronan synthase-3 mRNA expression and the accumulation of HA cable-like structures that are adhesive for leukocytes. Additionally, IBD mucosal endothelial cells produce higher levels of cell surface HA in response to TNF-alpha than non-IBD control cells. Therefore, HA deposition is an early event in inflamed gut tissue, preceding and likely promoting leukocyte infiltration.

At the “4th International Meeting on Inflammatory Bowel Diseases: on the Way to New Therapies,” Capri, 2006, genetics, bacteria–host interactions, immunomodulation, and tissue response were discussed deeply in order to understand, rationalize, and develop novel therapies. About genetics, the importance of a better understanding of the nature of known loci and of the putative associations was stressed. It was confirmed that genotype–phenotype associations in inflammatory bowel disease (IBD) have important clinical and therapeutic implications. The importance of the search for dominant bacterial antigens in chronic immune-mediated intestinal inflammation emerged, as well as knowledge of cellular and molecular mechanisms of bacterial–host interactions. It was discussed how innate and adaptive immunity signaling events can perpetuate chronic inflammation. Signal transduction pathways provide an intracellular mechanism by which cells respond and adapt to environmental stress. The identification of these signals have led to a greater understanding of the pathogenesis of IBD and pointed to potential therapeutic targets. It was shown that immune homeostasis is lost in IBD, resulting in a complex tissue response involving the action of immune and nonimmune cells. The nonimmune tissue response in IBD could be regarded as a new target for control of chronic intestinal inflammation. The changing role of biotherapy in IBD was widely discussed and in particular the anti-TNF-α monoclonal antibodies. Granulocyte-colony stimulating factor (GM-CSF) and stem cells therapies were also discussed. The risk-to-benefit ratio of the novel therapies was analyzed in detail. Finally, future directions for basic science and the unmet needs for clinical practice were presented. (Inflamm Bowel Dis 2007)