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Inflammatory bowel diseases (IBDs) are chronic immune-mediated conditions characterized by significant gut tissue damage due to uncontrolled inflammation. Anti-inflammatory treatments have improved, but there are no current prorepair approaches. Organoids have developed into a powerful experimental platform to study mechanisms of human diseases. Here, we specifically focus on its role as a direct tissue repair modality in IBD. We discuss the scientific rationale for this, recent parallel advances in scientific technologies (CRISPR [clustered regularly interspaced short palindromic repeats]/Cas9 and metabolic programming), and in addition, the clinical IBD context in which this therapeutic approach is tractable. Finally, we review the translational roadmap for the application of organoids and the need for this as a novel direction in IBD.

SummaryObjectiveThere are few prospective data exploring the combined effect of genetic and lifestyle factors on the incidence of inflammatory bowel disease (IBD), and whether genetic risk of IBD may be mitigated by lifestyle remains unclear.DesignWe conducted a prospective cohort study based on the UK Biobank to examine the associations across genetic risk, modifiable lifestyle factors, and risk of Crohn’s disease (CD) and ulcerative colitis (UC). Genetic susceptibility to CD and UC was estimated by polygenic risk scores using common genetic variants identified by genome-wide association studies and was further categorized into high, intermediate, and low genetic risk categories. Weighted unhealthy lifestyle scores were constructed based on disease-related lifestyle factors, including ever smoking, unhealthy diet, physical inactivity, obesity, and abnormal sleep duration, and were categorized into ‘favorable’, ‘intermediate’, and ‘unfavorable’ categories. The Cox proportional hazard regression model was used to estimate the HRs and 95% CIs for their associations and accumulative risk for developing CD and UC were estimated for each risk group.ResultsDuring a median follow-up of 12.0 years, 707 CD and 1576 UC cases were diagnosed. Genetic risk and unhealthy lifestyle categories were monotonically associated with CD and UC risk and there was no multiplicative interaction between them. Compared with participants with low genetic risk, the hazard ratios (HRs) of CD and UC were 2.24 (95% confidence interval [CI] 1.75-2.86) and 2.15 (95% CI 1.82-2.53) for those with high genetic risk, respectively. The HRs of CD and UC for individuals in unfavorable lifestyle category were 1.94 (95% CI 1.61-2.33) and 1.98 (95% CI 1.73-2.27), respectively, compared with those in favorable category. When considering genetic risk and lifestyle jointly, the HRs of individuals with high genetic risk but a favorable lifestyle (2.33, 95% CI 1.58-3.44 for CD, and 2.05, 95% CI, 1.58-2.66 for UC) were reduced nearly by half comparing to those with high genetic risk but an unfavorable lifestyle (4.40, 95% CI, 2.91-6.66 for CD and 4.44, 95% CI, 3.34-5.91 for UC).ConclusionGenetic and lifestyle factors were independently associated with susceptibility to CD and UC. Participants at high genetic risk could reduce nearly 50% risk of CD and UC by adherence to a favorable lifestyle.FundingXL: the Natural Science Fund for Distinguished Young Scholars of Zhejiang Province (LR22H260001). XYW: National Natural Science Foundation of China (81970494) and Key Project of Research and Development Plan of Hunan Province(2019SK2041); SCL: the Swedish Heart-Lung Foundation (Hjärt-Lungfonden, 20210351), the Swedish Research Council (Vetenskapsrådet, 2019-00977), and the Swedish Cancer Society (Cancerfonden); ET: CRUK Career Development Fellowship (C31250/A22804); KFD: Project of the regional diagnosis and treatment center of the Health Planning Committee (No. JBZX-201903).What is already known on this topicPrevious studies have identified a number of genetic variants and several modifiable risk factors for IBD. However, there is a lack of studies on the combined effects of genetic and lifestyle factors on IBD risk.What this study addsIn this prospective cohort study, genetic risk and modifiable lifestyle factors were independently associated with the risk of incident Crohn’s disease and ulcerative colitis. Participants at high genetic risk could reduce nearly 50% of their genetic susceptibility to Crohn’s disease and ulcerative colitis by adherence to a favorable lifestyle.How this study might affect research, practice or policyPromoting a healthy lifestyle is an effective strategy to lower the incidence of these diseases, especially among those with high-risk genetic background.

Background MicroRNAs [miRNAs] are cell-specific small non-coding RNAs that can regulate gene expression and have been implicated in inflammatory bowel disease [IBD] pathogenesis. Here we define the cell-specific miRNA profiles and investigate its biomarker potential in IBD. Methods In a two-stage prospective multi-centre case control study, next generation sequencing was performed on a discovery cohort of immunomagnetically separated leukocytes from 32 patients (nine Crohn’s disease [CD], 14 ulcerative colitis [UC], eight healthy controls) and differentially expressed signals were validated in whole blood in 294 patients [97 UC, 98 CD, 98 non-IBD, 1 IBDU] using quantitative PCR. Correlations were analysed with phenotype, including need for early treatment escalation as a marker of progressive disease using Cox proportional hazards. Results In stage 1, each leukocyte subset [CD4+ and CD8+ T-cells and CD14+ monocytes] was analysed in IBD and controls. Three specific miRNAs differentiated IBD from controls in CD4+ T-cells, including miR-1307-3p [p = 0.01], miR-3615 [p = 0.02] and miR-4792 [p = 0.01]. In the extension cohort, in stage 2, miR-1307-3p was able to predict disease progression in IBD (hazard ratio [HR] 1.98, interquartile range [IQR]: 1.20–3.27; logrank p = 1.80 × 10–3), in particular CD [HR 2.81; IQR: 1.11–3.53, p = 6.50 × 10–4]. Using blood-based multimarker miRNA models, the estimated chance of escalation in CD was 83% if two or more criteria were met and 90% for UC if three or more criteria are met. Interpretation We have identified and validated unique CD4+ T-cell miRNAs that are differentially regulated in IBD. These miRNAs may be able to predict treatment escalation and have the potential for clinical translation; further prospective evaluation is now indicated.

The MUSIC study is a multi-centre, longitudinal study set in the real world IBD clinical setting to investigate and develop a new biomarker approach utilising mitochondrial DAMP and circulating DNA in assessing mucosal healing in Crohn’s disease. We present the study protocol (approved by East of Scotland Research Ethics Service, Scotland, United Kingdom - Reference No. 19/ES/0087) on 17th September 2019 and registered in ClinicalTrials.gov as NCT04760964 for this on-going project based in Scotland, UK.

— The coronavirus SARS-CoV-2 contributes to morbidity and mortality mainly as a result of immune-pathology in the lungs. Recent data has shown multi-system involvement with widespread viral tropism. Here we present a detailed intestinal protein characterisation of SARS-Cov-2 entry molecules ACE2 and TMPRSS2 in patients with inflammatory bowel disease ([IBD]; ulcerative colitis [UC] and Crohn’s disease [CD]) with age- and sex-matched non-IBD controls, and in those with fatal COVID-19 infection. In our dataset, ACE2 and TMPRSS2 displayed a membrane enterocyte staining in the ileum (due to presence of brush border/microvilli) in contrast to a cytoplasmic pattern in the colon. We also showed a high ACE2/low TMPRSS2 expression pattern in the ileum with a reverse trend in the colon. In UC, colonic ACE2 and TMPRSS2 are cytoplasmic in nature, with significantly higher ACE2 staining intensity compared to non-IBD controls. In inflamed and unaffected IBD mucosa, ileal and colonic enterocyte ACE2 and TMPRSS2 expressions are not modified in the histologic presence of inflammation. We observed immune cells within the lamina propria that expressed ACE2 and TMPRSS2, at higher frequencies in IBD when compared to non-IBD controls. These were identified as plasma cells with multiple myeloma oncogene 1/interferon regulatory factor 4 (MUM1/IRF4) expression. We further analysed the gut histology of six fatal COVID-19 cases, with no difference in colonic and ileal ACE2/TMRPSS2 staining (compared to non-IBD controls) and identified ACE2 + lamina propria plasma cells. Of interest, in this COVID-19 cohort, there was no histologic evidence gut inflammation despite known evidence of viral tropism within the enterocytes. Our data provides evidence for tissue expression of entry molecules ACE2 and TMPRSS2 including a close apposition to plasma cells — both pointing towards a role of the gut in the antecedent immune response to SARS-CoV-2 infection. Supplementary Information The online version contains supplementary material available at 10.1007/s10753-021-01567-z.

ObjectiveIBD prevalence is estimated to be rising, but no detailed, recent UK data are available. The last reported prevalence estimate in the UK was 0.40% in 2003. We aimed to establish the current, and project future, prevalence in Lothian, Scotland.DesignWe conducted an all-age multiparameter search strategy using inpatient IBD international classification of disease (ICD-10) coding (K50/51)(1997–2018), IBD pathology coding (1990–2018), primary and secondary care prescribing data (2009–2018) and a paediatric registry, (1997–2018) to identify ‘possible’ IBD cases up to 31/08/2018. Diagnoses were manually confirmed through electronic health record review as per Lennard-Jones/Porto criteria. Autoregressive integrated moving average (ARIMA) regression was applied to forecast prevalence to 01/08/2028.ResultsIn total, 24 601 possible IBD cases were identified of which 10 499 were true positives. The point prevalence for IBD in Lothian on 31/08/2018 was 784/100 000 (UC 432/100 000, Crohn’s disease 284/100 000 and IBD unclassified (IBDU) 68/100 000). Capture–recapture methods identified an additional 427 ‘missed’ cases (95% CI 383 to 477) resulting in a ‘true’ prevalence of 832/100 000 (95% CI 827 to 837).Prevalence increased by 4.3% per year between 2008 and 2018 (95% CI +3.7 to +4.9%, p80 years of age.ConclusionsWe report a rigorously validated IBD cohort with all-age point prevalence on 31/08/2018 of 1 in 125, one of the highest worldwide.

Subsets of mononuclear phagocytes, including macrophages and classical dendritic cells (cDC), are highly heterogeneous in peripheral tissues such as the intestine, with each subset playing distinct roles in immune responses. Understanding this complexity at the cellular level has proven difficult due to the expression of overlapping phenotypic markers and the inability to isolate leukocytes of the mucosal lamina propria (LP) effector site, without contamination by the isolated lymphoid follicles (ILFs), which are embedded in the mucosa and which are responsible for the induction of immunity. Here we exploit our novel method for separating lamina propria from isolated lymphoid follicles to carry out single-cell RNA-seq, CITE-seq and flow cytometry analysis of MNPs in the human small intestinal and colonic LP, without contamination by lymphoid follicles. As well as classical monocytes, non-classical monocytes, mature macrophages, cDC1 and CD103+cDC2, we find that a CD1c+CD103-cDC subset, which shares features of both cDC2 and monocytes, is similar to the cDC3 that have recently been described in human peripheral blood. As well as differing between the steady-state small intestine and colon, the proportions of the different MNP subsets change during different stages of inflammatory bowel disease (IBD) inflammation. Putative cDC precursors (pre-cDC) were also present in the intestine, and trajectory analysis revealed clear developmental relationships between these and subsets of mature cDC, as well as between tissue monocytes and macrophages. By providing novel insights into the heterogeneity and development of intestinal MNP, our findings should help develop targeted approaches for modulating intestinal immune responses.

PGE2 inhibits Tregs and promotes intestinal inflammation through actions on mononuclear phagocytes and the gut microbiota., The gut microbiota fundamentally regulates intestinal homeostasis and disease partially through mechanisms that involve modulation of regulatory T cells (Tregs), yet how the microbiota-Treg cross-talk is physiologically controlled is incompletely defined. Here, we report that prostaglandin E2 (PGE2), a well-known mediator of inflammation, inhibits mucosal Tregs in a manner depending on the gut microbiota. PGE2 through its receptor EP4 diminishes Treg-favorable commensal microbiota. Transfer of the gut microbiota that was modified by PGE2-EP4 signaling modulates mucosal Treg responses and exacerbates intestinal inflammation. Mechanistically, PGE2-modified microbiota regulates intestinal mononuclear phagocytes and type I interferon signaling. Depletion of mononuclear phagocytes or deficiency of type I interferon receptor diminishes PGE2-dependent Treg inhibition. Together, our findings provide emergent evidence that PGE2-mediated disruption of microbiota-Treg communication fosters intestinal inflammation.

Analysis of immunofluorescence is commonly confounded by autofluorescence and non-specific staining in the colorectum, particularly within highly inflamed samples. There is no consensus on how to definitively prevent this, and study protocols are variable. Our laboratory identified strong immunofluorescence within negative control samples stained for numerous target antigens, including CD3. Following methodical attempts to ensure there was no reagent contamination, we concluded that this was autofluorescence/ non-specific staining. Significant optimisation was subsequently performed. In this protocol, we report our optimised methodology for immunofluorescence experiments on formalin fixed paraffin embedded (FFPE) tissue sections, stained for identification of CD3+ lymphocytes. We hope this protocol acts as a template to help other laboratories optimise their own immunofluorescence protocols for similar antibodies.

Background Success in personalized medicine in complex disease is critically dependent on biomarker discovery. We profiled serum proteins using a novel proximity extension assay [PEA] to identify diagnostic and prognostic biomarkers in inflammatory bowel disease [IBD]. Methods We conducted a prospective case-control study in an inception cohort of 552 patients [328 IBD, 224 non-IBD], profiling proteins recruited across six centres. Treatment escalation was characterized by the need for biological agents or surgery after initial disease remission. Nested leave-one-out cross-validation was used to examine the performance of diagnostic and prognostic proteins. Results A total of 66 serum proteins differentiated IBD from symptomatic non-IBD controls, including matrix metallopeptidase-12 [MMP-12; Holm-adjusted p = 4.1 × 10–23] and oncostatin-M [OSM; p = 3.7 × 10–16]. Nine of these proteins are associated with cis-germline variation [59 independent single nucleotide polymorphisms]. Fifteen proteins, all members of tumour necrosis factor-independent pathways including interleukin-1 (IL-1) and OSM, predicted escalation, over a median follow-up of 518 [interquartile range 224–756] days. Nested cross-validation of the entire data set allowed characterization of five-protein models [96% comprising five core proteins ITGAV, EpCAM, IL18, SLAMF7 and IL8], which define a high-risk subgroup in IBD [hazard ratio 3.90, confidence interval: 2.43–6.26], or allowed distinct two- and three-protein models for ulcerative colitis and Crohn’s disease respectively. Conclusion We have characterized a simple oligo-protein panel that has the potential to identify IBD from symptomatic controls and to predict future disease course. Further prospective work is required to validate our findings.

Summary Ulcerative colitis (UC) is an inflammatory disease of the large bowel which is characterised by dysregulated immunity and death to epithelial cells in the bowel, leading to prolonged inflammation. This can ultimately lead to surgery to remove the large bowel, with a risk of cancer developing if inflammation persists. Current therapies – which target the incoming immune cells or the cytokines they produce – are improving significantly but they are expensive and are immunosuppressive, leading to risk of infection. Here, we discuss a new trial which targets an early inducer of inflammation – the production of reactive oxygen species (ROS) by mitochondria. Previous work has shown that excessive mitochondrial ROS induces inflammatory signalling through the cGAS-STING pathway, leading to dysregulated immunity and death of epithelial cells. In this MARVEL trial (Mitochondrial Anti-oxidant therapy to Resolve Inflammation in Ulcerative Colitis) individuals with an active UC flare-up will be given a mitochondrial anti-oxidant (MitoQ) or placebo tablet in addition to standard medical treatment, in order to suppress inflammation as it develops. This phase 2b trial will repurpose MitoQ, which has been previously tested in other large trials in different disease settings, and will measure clinical response and markers of inflammation over 24 weeks. It is hoped that this trial will develop a new target for UC through re-purposing a relatively cheap, non-toxic and well-characterised drug.

SummaryBackgroundSuccess in personalised medicine in complex disease is critically dependent on biomarker discovery. We profiled serum proteins using a novel proximity extension assay (PEA) to identify diagnostic and prognostic biomarkers in inflammatory bowel disease (IBD).MethodsWe conducted a prospective case-control study in an inception cohort of 552 patients (328 IBD, 224 non-IBD), profiling proteins recruited across 6 centres. Treatment escalation was characterised by the need for biological agents or surgery after initial disease remission. Nested leave-one-out cross validation was used to examine the performance of diagnostic and prognostic proteins.ResultsA total of 66 serum proteins differentiated IBD from symptomatic non-IBD controls including Matrix Metalloproteinase-12 (Holm adjusted p=4.1×10−23) and Oncostatin-M (OSM, p=3.7×10−16). Nine of these proteins associate with cis- germline variation (59 independent SNPs). Fifteen proteins, all members of TNF independent pathways including interleukin-1 and OSM predicted escalation, over a median follow-up of 518 (IQR 224-756) days. Nested cross-validation of the entire data set allows characterisation of 5-protein-models (96% comprising five core proteins ITGAV, EpCAM, IL18, SLAMF7, and IL8) which define a high-risk subgroup in IBD (HR 3.90, 95% CI: 2.43-6.26), or allows distinct 2, and 3 protein models for UC and CD respectively.ConclusionWe have characterised a simple oligo-protein panel that has the potential to identify IBD from symptomatic controls and predicts the evolution of disease over time. The technology could be suitable as a point of care testing in defining risk. Further prospective work is required to characterise the utility of the approach.

The gut microbiota fundamentally regulates intestinal homeostasis and disease partially through mechanisms that involve modulation of regulatory T cells (Tregs), yet how the microbiota-Treg crosstalk is physiologically controlled is incompletely defined. Here, we report that prostaglandin E2 (PGE2), a well-known mediator of inflammation, inhibits mucosal Tregs in a manner depending on the gut microbiota. PGE2 through its receptor EP4 diminishes Treg-favorable commensal microbiota. Transfer of the gut microbiota that was modified by PGE2-EP4 signaling modulates mucosal Treg responses and exacerbates intestinal inflammation. Mechanistically, PGE2-modified microbiota regulates intestinal mononuclear phagocytes and type I interferon signaling. Depletion of mononuclear phagocytes or deficiency of type I interferon receptor contracts PGE2-dependent Treg inhibition. Taken together, our findings provide emergent evidence that PGE2-mediated disruption of microbiota-Treg communication fosters intestinal inflammation.

Inflammatory bowel diseases are common, complex, immune-mediated conditions with a sharply rising global prevalence. While major advances since 2000 have provided strong mechanistic clues implicating a de-regulation in the normal interaction among host genetics, immunity, microbiome, and the environment, more recent progress has generated entirely new hypotheses and also further refined older disease concepts. In this review, we focus specifically on these novel developments in the pathogenesis of ulcerative colitis.

Despite significant recent therapeutic advances, complete mucosal healing remains a difficult treatment target for many patients with inflammatory bowel diseases (IBD) to achieve. Our review focuses on the translational concept of promoting resolution of inflammation and repair as a necessary adjunctive step to reach this goal. We explore the roles of inflammatory cell apoptosis and efferocytosis to promote resolution, the new knowledge of gut monocyte-macrophage populations and their secreted prorepair mediators, and the processes of gut epithelial repair and regeneration to bridge this gap. We discuss the need and rationale for this vision and the tangible steps toward integrating proresolution therapies in IBD.

Switching from Remicade to CT-P13 allows for significant cost savings and has been shown to be non-inferior to continued therapy with Remicade for the treatment of Crohn’s disease. The aim of this work was to prospectively evaluate clinical outcomes in a cohort of patients with Crohn’s disease switching from Remicade to CT-P13. A prospective service evaluation was performed. The Harvey-Bradshaw index, CRP, faecal calprotectin and serum for infliximab/antibody levels were collected prior to patients' final Remicade infusion and at 6 and 12 months after switching to CT-P13 as part of routine clinical care. All adverse events during follow-up were also recorded. One hundred and ten patients on Remicade switched to CT-P13. No significant difference was observed between the Harvey-Bradshaw Index (p = 0.07), CRP (p = 0.13), faecal calprotectin (p = 0.25) or trough infliximab levels (p = 0.47) comparing before and at 6 and 12 months after the switch to CT-P13. Seven patients developed new infliximab antibodies after switching from Remicade to CT-P13. The majority of patients remained on CT-P13 at 12 months (84.5%) and the rate of adverse events and serious adverse events was 53.8 and 13.5 per 100 patient-years of follow-up, respectively. Switching to CT-P13 resulted in a cost saving of approximately 46.4%. The transition to CT-P13 from Remicade for the treatment of Crohn’s disease is safe and has no negative effect on clinical outcomes at 12 months.

Adalimumab is an established treatment for Crohn's disease. Limited data are available regarding the relationship between adalimumab drug levels and serum/fecal markers of gut inflammation. We therefore aimed to characterize the relationship between adalimumab levels and biologic remission during maintenance therapy.A single-center prospective cross-sectional study was undertaken on Crohn's disease patients who had received adalimumab therapy for a minimum of 12 weeks after induction. Data on clinical activity (Harvey-Bradshaw Index), C-reactive protein (CRP), adalimumab drug and antibody levels, and fecal calprotectin were collected. Biologic remission was defined as a CRP5 mg/L and fecal calprotectin250 µg/g. Adalimumab drug and antibody levels were processed using the Immundiagnostik monitor enzyme-linked immunosorbent assay.One hundred fifty-two patients had drug and antibody samples matched with CRP and fecal calprotectin. Patients in biologic remission had significantly higher adalimumab levels compared with others (12.0 µg/mL vs 8.0 µg/mL, P0.0001). Receiver operating characteristic curve analysis demonstrated an optimal adalimumab level of8.5 µg/mL (sensitivity, 82.2%; specificity, 55.7%; likelihood ratio, 1.9) for predicting biologic remission. Multivariable logistic regression revealed that adalimumab levels8.5 µg/mL were independently associated with biologic remission (odds ratio, 5.27; 95% confidence interval, 2.43-11.44; P0.0001).Higher adalimumab levels are associated with biologic remission. An optimal level of8.5 µg/mL was identified.

Introduction Intravenous steroids remain the standard first line treatment for patients with acute ulcerative colitis (UC). However, 30% of patients fail to respond and require second line therapies and/or surgery. The purpose of this study was to determine if day 1 parameters could identify a group at high risk of failing first line therapies. Methods All admissions for acute UC (ICD-10 K51) to hospitals within NHS Lothian (4 sites) from 1st November 2015 to 31st October 2016 were obtained from the regional coding department. Inclusion was limited to patients with UC as the primary reason for admission. Case record review confirmed diagnosis and clinical data were collected. Response to steroids was defined as discharge from hospital with no further acute medical or surgical treatment. The following parameters were recorded up to the first 10 days post admission: haemoglobin, platelet count, CRP, albumin, stool frequency, faecal calprotectin and abdominal x-ray results. Each patient was later attributed a score based on CRP ( 50 mg/dL=1), albumin (>30 g/L=0; 450×109/L=1). Results From 1 st November 2015 to 31 st October 2016 61 admissions with acute UC were identified; 37 (60%) of which responded to steroids, 24 (40%) patients were non-responders. 3 (12.5%) non-responders received infliximab as second line therapy, 1 (4.2%) adalimumab and 20 (83.3%) ciclosporin; 11 (45.8%) of the non-responders required surgery, 100% of whom had been previously treated with ciclosporin. On univariate analysis, the albumin, platelet count and CRP differed significantly between responders and non-responders (p≤0.05), whereas on multivariate analysis only CRP and albumin were significant. No difference was seen for haemoglobin and stool frequency. 88.9% of patients with concurrent hypoalbuminaemia, high CRP and high platelets (score=3) were non-responders. Conclusions 82.4% of patients with a score of 2 or more will fail first line medical therapy. The combination of these readily available parameters identifies a high-risk population who may benefit from earlier second line medical or surgical intervention.

Background Due to common evolutionary origins, mitochondrial DNA (mtDNA) shares many similarities with immunogenic bacterial DNA. MtDNA is recognized as a pro-inflammatory damage-associated molecular pattern (DAMP) with a pathogenic role in several inflammatory diseases. We hypothesised that mtDNA is released during active disease, serving as a key pro-inflammatory factor in inflammatory bowel disease (IBD). Methods Between 2014 and 2015, we collected plasma separated within 2 hours of sampling from 97 prospectively recruited IBD patients (67 ulcerative colitis [UC] and 30 Crohn’s disease [CD]) and 40 non-IBD controls. We measured circulating mtDNA using quantitative polymerase chain reaction (amplifying mitochondria COXIII/ND2 genes) and also in mouse colitis induced by dextran sulfate-sodium (DSS). We used a mass spectometry approach to detect free plasma mitochondrial formylated peptides. Furthermore, we examined for mitochondrial damage using electron microscopy (EM) and TLR9 expression, the target for mtDNA, in human intestinal IBD mucosa. Results Plasma mtDNA levels were increased in UC and CD (both P < 0.0001) compared with non-IBD controls. These levels were significantly correlated to blood (C-reactive protein, albumin, white cell count), clinical and endoscopic markers of severity, and disease activity. In active UC, we identified 5 mitochondrial formylated peptides (the most abundant being fMMYALF with known chemoattractant function) in plasma. We observed mitochondrial damage in inflamed UC mucosa and significantly higher fecal MtDNA levels (vs non-IBD controls [P < 0.0001]), which supports gut mucosal mitochondrial DAMP release as the primary source. In parallel, plasma mtDNA levels increased during induction of acute DSS colitis and were associated with more severe colitis (P < 0.05). In active IBD, TLR9+ lamina propria inflammatory cells were significantly higher in UC and CD compared with controls (P < 0.05). Conclusions We present the first evidence to show that mtDNA is released during active IBD. MtDNA is a potential mechanistic biomarker, and our data point to mtDNA-TLR9 as a therapeutic target in IBD.

Ulcerative colitis (UC) and Crohn’s disease (CD) represent the two major forms of inflammatory bowel disease (IBD). UC is a chronic idiopathic inflammatory condition affecting the colon and rectum. A complex interplay between components of the innate immune system and environmental factors, notably the microflora, regulates colonic mucosal homeostasis which is dysregulated in UC. In this chapter, we review current concepts of the epidemiology, pathogenesis, clinical features and management of UC.

Anti-tumor necrosis factor α (anti-TNF) therapy has revolutionised the treatment of Crohn’s disease (CD). However, primary nonresponse occurs in an estimated 13-40% of patients1 and secondary loss of response in 23%-46% of patients after 12 months2. A challenging and important aspect of anti-TNF management is therefore to avoid the development of nonresponse, and identify/manage secondary nonresponse if it occurs.

The completion of the human genome project in 2003 represented a major scientific landmark, ushering in a new era with hopes and expectations of fresh insights into disease mechanisms and treatments. In inflammatory bowel disease (IBD), many important discoveries soon followed, notably the identification of >200 genetic susceptibility loci and characterization of the gut microbiome. As “big data”, driven by advances in technology, becomes increasingly available and affordable, individuals with IBD and clinicians alike yearn for tangible outcomes from the promise of “precision medicine”—precise diagnosis, monitoring, and treatment. Here, we provide a commentary on the prospects and challenges of precision medicine and biomarkers in IBD. We focus on the three key areas where precision IBD will have the most impact: (1) disease susceptibility, activity, and behavior; (2) prediction of drug response and adverse effects; and (3) identification of subphenotypic mechanisms to facilitate drug discovery and selection of new treatments in IBD.

Endogenous damage-associated molecular patterns (DAMPs) are released during tissue damage and have increasingly recognized roles in the etiology of many human diseases. The inflammatory bowel diseases (IBD), ulcerative colitis (UC) and Crohn’s disease (CD), are immune-mediated conditions where high levels of DAMPs are observed. DAMPs such as calprotectin (S100A8/9) have an established clinical role as a biomarker in IBD. In this review, we use IBD as an archetypal common chronic inflammatory disease to focus on the conceptual and evidential importance of DAMPs in pathogenesis and why DAMPs represent an entirely new class of targets for clinical translation.

In August 1999, a 26-year-old Caucasian woman presented with abdominal pain, diarrhoea and weight loss. Active small bowel Crohn's disease (CD) was diagnosed on barium follow-through and confirmed histologically following ileal resection in October 1999. Subsequent radiological and endoscopic investigations demonstrated extensive small bowel and foregut involvement with stricturing disease. Despite treatment with 6-mercaptopurine (6-MP) (1.25 mg/kg/day) and corticosteroids, control of disease activity was suboptimal and four further laparotomies were required. (or stricturoplasties and adhesiolysis). Between January and July 2004, she had received four infliximab (Remicade®, Schering-Plough) (5 mg/kg) infusions with limited efficacy. In June 2007 the humanized anti-tumour necrosis factor (TNF) agent, adalimumab (Humira®, Abbott Ltd.), was commenced (80 mg loading dose, then 40 mg every second week) with good clinical effect. In October 2007, she presented with ‘pins and needles’ affecting the fingertips of her left hand and the right side of her face. These symptoms evolved over 2 weeks to include parasthesias affecting her left arm and intermittent diplopia. Her left hand became clumsy and her left leg weak. In addition to adalimumab she was also treated with mercaptopurine, ketamine, gabapentin, esomeprazole, folic acid and loperamide. Her mother suffered from rheumatoid arthritis. Clinical examination revealed bilateral internuclear ophthalmoplegia with associated horizontal nystagmus. There was reduced sensation to light touch and pin prick in the left upper and lower limbs. There was mild pyramidal weakness on the left arm and leg with finger–nose ataxia, predominantly right-sided. Reflexes were brisk throughout and there was an upgoing left plantar response. She was afebrile and demonstrated no signs of sepsis. Haematological and biochemical parameters including full blood count, renal and thyroid function, vitamin B12, folate and C reactive protein were normal. Rheumatoid factor, anti-nuclear and anti-neutrophil cytoplasmic antibodies were negative. MRI scanning of the central nervous system (CNS) demonstrated a number of white matter lesions …

Background: Inflammatory bowel diseases (IBDs) are a result of interactions between luminal pathogens and the intestinal immune response. Cyclooxygenase-2 (COX-2) plays a key role in the regulation of the inflammatory response upon stimulation by luminal pathogens via Toll-like receptors. Methods: Genotypes of the COX-2/PTGS2/PGHS2 A-1195G (rs689466), G-765C (rs20417), and T8473C (rs5275) polymorphisms were assessed in a Scottish and Danish case–control study including 732 Crohn's disease (CD) cases, 973 ulcerative colitis (UC) cases, and 1157 healthy controls using logistic regression. Results: Carriers of the COX-2 A-1195G variant allele had increased risk of UC (odds ratio [OR], 95% confidence interval [CI] = 1.25 [1.02–1.54], P = 0.03) and of both UC and IBD among never smokers (OR [95% CI] = 1.47 [1.11–1.96], P = 0.01 and OR [95% CI] = 1.37 [1.06–1.77], P = 0.02, respectively). Furthermore, this variant genotype was associated with increased risk of diagnosis of UC before age 40 years and with extensive UC (OR [95% CI] = 1.34 [1.11–1.62], P = 0.002 and OR [95% CI] = 1.32 [1.03–1.69], P = 0.03, respectively). Conclusions: COX-2 A-1195G polymorphism was associated with the risk of UC, especially among never-smokers, suggesting that low activity of COX-2 may predispose to UC. Our results suggest that inclusion of smoking status may be essential for the evaluation of the role of genetic predisposition to IBD. (Inflamm Bowel Dis 2011)

Summary Background Adalimumab is a second generation humanized anti-tumour necrosis factor (TNF) monoclonal antibody with established efficacy in Crohn’s disease (CD). Aims To evaluate the efficacy and safety of adalimumab on a nationwide clinical setting. Methods We used the Scottish Society of Gastroenterology network to identify and follow up the clinical outcomes of patients with CD treated with adalimumab over a 4-year period (2004–2008). Results A total of 98 patients received adalimumab - 100.5 patient follow-up years were recorded (64.3% females; median age at diagnosis of 20.7 years; 88.8% treated with 80/40 mg induction regimen. Eighty eight (89.8%) had previous infliximab with 29 (32.9%) primary nonresponders; 32 (32.6%) were corticosteroid-dependent; 47 (47.9%) were intolerant/resistant to most immunosuppressive therapies (two or more). In all, 60% of patients were in clinical remission at 1-year follow-up, with 30% and 55% requiring dose escalation to weekly therapy at 1-and 2-year follow-up respectively. Overall, 29 (29.6%) patients developed complications with eight nonfatal serious (8.2%) adverse events and 2 (2.0%) case fatalities (sepsis following perforation and disseminated colorectal cancer, respectively). Conclusions Adalimumab is efficacious in severe and refractory CD in the clinical setting, although there remain significant therapy- and disease-related risks of serious complications.

Summary Background Anti-TNF agents are now widely used in Crohn’s disease (CD), and in ulcerative colitis (UC). Aim To review the safety profile of anti-TNF agents in all patients treated with infliximab in Edinburgh from 1999 to 2007. Methods Complete data were available on 202/207 patients comprising 157 CD, 42 UC and three coeliac disease. Median follow-up was 2.4 years (1.0–4.9) with a total of 620 patient-years follow-up. About 19.1% of CD patients were subsequently treated with adalimumab. Results Seven deaths (3.3%) occurred in follow-up; only one death was

IntroductionThere is an unmet need for novel blood based biomarkers that offer timely and accurate diagnostic and prognostic testing in Inflammatory Bowel Diseases (IBD). We aimed to investigate the diagnostic and prognostic utility of serum calprotectin (SC) in IBD.MethodsA total of 171 patients (n=96 IBD, n=75 non-IBD) were prospectively recruited. A multi biomarker model was derived using multivariable logistic regression analysis. Cox proportional hazards model was derived to assess the contribution of each variable to disease outcomes.ResultsSC correlated strongly with current biomarkers including faecal calprotectin (FC) (n=50, rho= 0.50, p=1.6x10-437 ). SC was the strongest individual predictor of IBD diagnosis (odds ratio (OR): 9.37(95%CI: 2.82-34.68), p=4.00×10-438 ) compared with other markers (CRP: OR 8.52(95%CI: 2.75-28.63), p=2.80×10-439 ); albumin: OR 6.12(95%CI: 1.82-22.16), p=0.004). In a subset of 50 patients with paired SC and FC, the area under receiver operating characteristic discriminating IBD from controls was better for FC than SC (0.99, (95% CI 0.87-1.00) and 0.87 (95% CI:0.78-0.97) respectively; p=0.01).43 At follow up (median 342 days; IQR: 88-563), SC predicted treatment escalation and/or44 surgery in IBD (HR 2.7, 95% CI: 1.1-4.9), in particular CD (HR 4.2, 95% CI 1.2-15.3).Page 2 of 73ScholarOne, 375 Greenbrier Drive, Charlottesville, VA, 22901American Journal of GastroenterologyFor Peer Review3A model incorporating SC and either CRP or albumin has a positive likelihood 45 ratio of 24.1446 for IBD. At 1 year, our prognostic model can predict treatment escalation in IBD in 65% of47 cases (95% CI: 43-79%) and 80% (95% CI: 31-94%) in CD if 2 or more blood marker48 criteria are met.49 Conclusions50 A diagnostic and prognostic model that combines SC and other blood-based biomarkers51 accurately predicts the inflammatory burden in IBD and has the potential to predict disease52 and its outcomes. Our data warrants further detailed exploration and validation in large multi53centre cohorts.

Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. We replicate the top DMP (RPS6KA2) and DMRs (VMP1, ITGB2 and TXK) in an independent cohort. Using paired genetic and epigenetic data, we delineate methylation quantitative trait loci; VMP1/microRNA-21 methylation associates with two polymorphisms in linkage disequilibrium with a known IBD susceptibility variant. Separated cell data shows that IBD-associated hypermethylation within the TXK promoter region negatively correlates with gene expression in whole-blood and CD8+ T cells, but not other cell types. Thus, site-specific DNA methylation changes in IBD relate to underlying genotype and associate with cell-specific alteration in gene expression., Epigenetic perturbations may be an important factor in diseases where both genes and environment play a role. Here, Ventham and colleagues show that DNA methylation changes in inflammatory bowel disease are related to the underlying genotype, and are associated with cell-specific changes to gene expression.

Summary Background Adalimumab is a humanized monoclonal antibody targeting tumour necrosis factor-α. Recent clinical trials have demonstrated its efficacy in Crohn’s disease; however, experience in clinical practice remains limited. Aim To investigate the efficacy and safety of adalimumab in the clinical setting. Methods The clinical outcomes of patients with medically refractory Crohn’s disease treated with adalimumab in the Western General Hospital Edinburgh, over a 3-year period (2003–2006), were studied. Results Twenty-two (14 females; age at therapy: 32.6 years) patients were treated using an 80/40 mg induction regimen followed by fortnightly 40 mg treatment. All had proven refractory/intolerant to corticosteroids and immunosuppression. Twenty patients had had previous infliximab infusions – of these eight (36%), six (27%), three (14%) had previous infusion reactions, no response and lost response to infliximab, respectively. Over a period of 1.0 years (IQR: 0.62–2.5), Kaplan–Meier analyses showed that 68% (seven nonresponders) were in clinical remission and 67% (five surgery – discounting oral CD) avoided further surgery for active disease. 59% required dose escalation to 40 mg weekly (0.55 years; IQR: 0.22–1.4). Three (50%) primary nonresponders to infliximab achieved remission. Two patients developed serious infective complications and one patient developed lung cancer. Conclusions Adalimumab is efficacious in refractory Crohn’s disease, with benefit observed in infliximab primary nonresponders. However, many patients require escalation of dosing regimen.

The discovery of nucleotide-binding oligomerization domain 2/caspase recruitment domain-containing protein 15 (NOD2/CARD15) as the first susceptibility gene in Crohn's disease (CD) has shifted the focus of research into the pathogenesis of inflammatory bowel disease (IBD) firmly to the innate immune response and the integrity of the epithelial barrier. The subsequent implication in IBD of variant alleles of OCTN, DLG5, MDR1, and TLRs has provided further support for a new, more complex model of innate immunity function in the gastrointestinal tract. In this review, we examine the recent advances in our understanding of the influence of genetics of the innate immune response on IBD. We will focus on germline variation of genes encoding pathogen-recognition receptors, proteins involved in epithelial homeostasis and secreted antimicrobial proteins. Copyright © 2006 Crohn's & Colitis Foundation of America, Inc.

Several lines of evidence suggest a role for the multidrug resistance gene (ABCB1/MDR1) and its product, P-glycoprotein 170, in the pathogenesis of inflammatory bowel disease (IBD). In addition, P-glycoprotein activity determines bioavailability of many drugs used regularly in many medical specialities, and ABCB/ MDR1 variation appears to be a critical pharmacogenetic determinant. We have utilized a gene-wide haplotype tagging approach to further define the identity of germ-line variations in the ABCB1/MDR1 gene contributing to IBD susceptibility. Six haplotype tagging single nucleotide polymorphisms (tSNPs) representing the haplotypic variations of the ABCB1/MDR1 gene were identified initially following the characterization of the haplotype structure of this gene in 24 Centre d'Etude du Polymorphisme Humain Caucasian trios. Genotyping was performed in 249 ulcerative colitis (UC) and 179 Crohn's disease (CD) patients and 260 healthy controls. Using log-likelihood analysis, we observed a highly significant association between the common haplotypes and UC (P = 4.22 x 10 -7 ) but not CD (P = 0.22). This significant association was critically dependent on one tSNP, intronic variant rs3789243. All haplotypes with this variant retained a highly significant association (P = 3.2 x 10 -7 -3.6 x 10 -12 ), whereas significance was lost when rs3789243 was dropped in systematic haplotypic analysis. The effect of this tSNP was independent of C3435T SNP, previously suggested to be the critical variant in disease susceptibility and drug transport. The association with UC was shown to be strongest with the phenotype of extensive disease (P = 1.7 x 10 -7 ). This 'candidate gene' approach provides compelling evidence to support the contribution of the ABCB1/MDR1 gene in determining risk to UC but not to CD and provides new insights into the localization of the critical susceptibility determinants within the gene. In addition, these findings have potentially important implications in the application of pharmacogenetics across a range of common diseases, including HIV, epilepsy and colorectal cancer.

Background and aims The course of ulcerative colitis (UC) following orthotopic liver transplantation (OLT) for primary sclerosing cholangitis (PSC) is unclear. We documented the nationwide experience of the course of UC, before and after OLT for PSC. Methods and results A total of 470 liver transplants were performed for 413 patients between 1992 and 2003, in the Scottish Liver Transplantation Unit, UK. Twenty-six patients had co-existing UC/PSC. Of these, data from 20 patients were studied over a median period of 11.9 years before OLT and 4.4 years after OLT; of the others, four patients required colectomy prior to OLT, one died within 7 days of transplant, and one developed UC after transplant. A significantly higher relapse rate (number of relapses/year of follow-up) was seen after OLT (median 1.0 versus 0.3; interquartile range, 0.10–1.42 and 0.01–0.40, respectively; P=0.007). The corticosteroids requirement (number of courses/year of follow-up) after OLT was also significantly higher (0.40 versus 0.10; interquartile range, 0.51–1.13 and 0.05–0.12, respectively; P=0.003). Twenty per cent of patients (4/20) became corticosteroid dependent after OLT. Thirty-five per cent of patients (7/20) underwent colectomy after OLT: three for severe disease and four for neoplasia/dysplasia. Five patients (19%) developed neoplasia following OLT. Conclusion Despite immunosuppression, UC follows a more aggressive clinical course after OLT and is associated with a high rate of neoplasia.

Background & Aims: Recent data suggest that polymorphisms in the organic cation transporter (OCTN) genes OCTN1 (SLC22A4) and OCTN2 (SLC22A5) represent disease-causing mutations within the IBD5 locus (chromosome 5q31). We investigated associations with disease susceptibility, phenotype, and evidence for epistasis with CARD15 in 679 patients with Crohn’s disease (CD) or ulcerative colitis (UC). Methods: A total of 374 patients with CD, 305 patients with UC, and 294 healthy controls (HCs) were studied. Genotyping for single nucleotide polymorphisms IGR2096, IGR2198, and IGR2230, OCTN1 variant (SLC22A4 1672C→T), and OCTN2 variant (SLC22A5 −207G→C) was performed using the TaqMan system. Results: The IBD5 OCTN1 and OCTN2 polymorphisms were in strong linkage disequilibrium (D′, >0.959). IGR2198 variant allele frequency (49.1% vs 40.8%; P = .0046) and homozygosity (21% vs 14.8%; P = .044) were associated with CD versus HCs. Variant allelic frequency of OCTN1 (53.6% vs 43%; P = .0008) and OCTN2 (56.1% vs 48.4%; P = .0092) polymorphisms and homozygosity for the OCTN1/2-TC haplotype (28.4% vs 16%; P = .0042) were associated with CD versus HCs. IGR2198 homozygosity and TC homozygosity were associated with stricturing/penetrating disease at follow-up (P = .011 and P = .011, respectively) and disease progression (P = .038 and P = .049, respectively) on univariate analysis and with need for surgery on multivariate analysis (P = .016 and P = .004, respectively). In the absence of the IBD5 risk haplotype, no association of OCTN1/2 variants with CD was detected. No associations were seen with UC. Conclusions: The IBD5 locus influences susceptibility, progression, and need for surgery in CD. However, the contribution of OCTN1/2 variants is not independent of the IBD5 haplotype; a causative role for these genes remains plausible but is not yet proven. Further genetic, functional, and expression data are now required.

The chronic idiopathic inflammatory bowel diseases (IBDs), Crohn’s disease (CD) and ulcerative colitis (UC), are characterized by an overly aggressive cell-mediated immune response to luminal commensal bacteria in genetically susceptible individuals. 1,2 Several lines of evidence now suggest a role for the multidrug resistance (MDR1) gene and its product P-glycoprotein 170 (PgP) in the regulation of host– bacteria interaction and in the pathogenesis of IBD. PgP functions as an ATP-dependent efflux transporter pump and is highly expressed in the epithelial surfaces of intestine, biliary ductules, proximal tubules of kidneys, and central nervous system, where it forms the basis of the blood–brain barrier. 3–5 Interindividual variability of PgP expression in the intestine plays a role in the determining the pharmacokinetics of a wideranging number of substrates. 6 The exact physiological role in the gut remains unknown. The high constitutive levels of expression of PgP in the gut suggest a role in protection against xenobiotics and bacterial products. 7 This review focuses on the current data (animal studies, gene expression, and genetic studies) on the possible role of MDR1 in IBD and also future directions and implications of our current knowledge of this gene.

Background & Aims: The MDR1 gene encodes P-glycoprotein 170, an efflux transporter that is highly expressed in intestinal epithelial cells. The MDR1 exonic single nucleotide polymorphisms (SNPs) C3435T and G2677T have been shown to correlate with activity/expression of P-glycoprotein 170. Methods: This was a case-control analysis of MDR1 C3435T and G2677T SNPs in a large well-characterized Scottish white cohort (335 with ulcerative colitis [UC], 268 with Crohn's disease [CD], and 370 healthy controls). We conducted 2-locus haplotype and detailed univariate and multivariate genotypic-phenotypic analyses. Results: The MDR1 3435 TT genotype (34.6% vs 26.5%; P = .04; odds ratio [OR], 1.60; 95% confidence interval [95% CI], 1.04–2.44) and T-allelic frequencies (58.2% vs 52.8%; P = .02; OR, 1.28; 95% CI, 1.03–1.58) were significantly higher in patients with UC compared with controls. No association was seen with CD. The association was strongest with extensive UC (TT genotype: 42.4% vs 26.5%; P = .003; OR, 2.64; 95% CI, 1.34–4.99; and T allele: 63.9% vs 52.8%; P = .009; OR, 1.70; 95% CI, 1.24–2.29), and this was also confirmed on multivariate analysis ( P = .007). The G2677T SNP was not associated with UC or CD. These 2 SNPs lie in linkage disequilibrium in our population (D′, .8–.9; r 2 , .7–.8). Two-locus haplotypes showed both positive (3435T/G2677 haplotype: P = .03; OR, 1.44) and negative (C3435/2677T haplotype: P = .002; OR, .35) associations with UC. Homozygotes for the haplotype 3435T/G2677 were significantly increased in UC ( P = .017; OR, 8.88; 95% CI, 1.10–71.45). Conclusions: Allelic variations of the MDR1 gene determine disease extent as well as susceptibility to UC in the Scottish population. The present data strongly implicate the C3435T SNP, although the 2-locus haplotype data underline the need for further detailed haplotypic studies.