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Background and Aims Historical and emerging data implicate fungi in Crohn’s disease [CD] pathogenesis. However, a causal link between mycobiota, dysregulated immunity, and any impact of NOD2 variants remains elusive. This study aims to evaluate associations between NOD2 variants and faecal mycobiota in CD patients and non-CD subjects. Methods Faecal samples were obtained from 34 CD patients [18 NOD2 mutant, 16 NOD2 wild-type] identified from the UK IBD Genetics Consortium. To avoid confounding influence of mucosal inflammation, CD patients were in clinical remission and had a faecal calprotectin Results CD was associated with higher numbers of fungal observed taxonomic units [OTUs] [p = 0.033]. Principal coordinates analysis using Jaccard index [p = 0.018] and weighted Bray-Curtis dissimilarities [p = 0.01] showed Candida spp. clustered closer to CD patients whereas Cryptococcus spp. clustered closer to non-CD. In CD, we found higher relative abundance of Ascomycota [p = 0.001] and lower relative abundance Basidiomycota [p = 0.019] phyla. An inverse relationship was found between bacterial and fungal Shannon diversity in NOD2 wild-type which was independent of CD [r = -0.349; p = 0.029]. Conclusions This study confirms compositional changes in the gut mycobiota in CD and provides evidence that fungi may play a role in CD pathogenesis. No NOD2 genotype-specific differences were observed in the faecal mycobiota.

BackgroundThe interleukin-22 cytokine (IL-22) has demonstrated efficacy in preclinical colitis models with non-immunosuppressive mechanism of action. Efmarodocokin alfa (UTTR1147A) is a fusion protein agonist that links IL-22 to the crystallisable fragment (Fc) of human IgG4for improved pharmacokinetic characteristics, but with a mutation to minimise Fc effector functions.MethodsThis randomised, phase 1b study evaluated the safety, tolerability, pharmacokinetics and pharmacodynamics of repeat intravenous dosing of efmarodocokin alfa in healthy volunteers (HVs; n=32) and patients with ulcerative colitis (n=24) at 30–90 µg/kg doses given once every 2 weeks or monthly (every 4 weeks) for 12 weeks (6:2 active:placebo per cohort).ResultsThe most common adverse events (AEs) were on-target, reversible, dermatological effects (dry skin, erythema and pruritus). Dose-limiting non-serious dermatological AEs (severe dry skin, erythema, exfoliation and discomfort) were seen at 90 μg/kg once every 2 weeks (HVs, n=2; patients, n=1). Pharmacokinetics were generally dose-proportional across the dose levels, but patients demonstrated lower drug exposures relative to HVs at the same dose. IL-22 serum biomarkers and IL-22-responsive genes in colon biopsies were induced with active treatment, and microbiota composition changed consistent with a reversal in baseline dysbiosis. As a phase 1b study, efficacy endpoints were exploratory only. Clinical response was observed in 7/18 active-treated and 1/6 placebo-treated patients; clinical remission was observed in 5/18 active-treated and 0/6 placebo-treated patients.ConclusionEfmarodocokin alfa had an adequate safety and pharmacokinetic profile in HVs and patients. Biomarker data confirmed IL-22R pathway activation in the colonic epithelium. Results support further investigation of this non-immunosuppressive potential inflammatory bowel disease therapeutic.Trial registration numberNCT02749630.

Background Conventional cellular phenotyping of intestinal cell populations by multi-parameter fluorescence cytometry is reliant on collection of fresh tissue for immediate enzymatic or mechanical disaggregation, or cryopreservation of samples. These factors limit widescale use of tissue for research, increase cost, and time for sample collection or preparation. Due to tissue disaggregation suspension cytometry does not provide data regarding spatial localisation of cells in tissue. Formalin fixed paraffin embedded (FFPE) tissue is widely collected at endoscopy and surgery for clinical histopathological assessment, and can be stored and transported at room temperature. Methods We aimed to develop a method for analysing FFPE intestinal tissue using Imaging Mass Cytometry (IMC) in combination with an analysis pipeline for cellular phenotyping and spatial characterisation that preserved multi-parameter, high dimensional phenotyping capabilities normally only afforded by suspension methodologies. FFPE blocks were accessed following written informed consent in accordance with research and ethics committee approval. Carrier-free antibodies specific to cell subsets of interest were selected based on conventional suspension fluorescence cytometry and immunohistochemistry data. Results Antibodies were conjugated to metal isotopes. Antigen retrieval and antibody dilution was optimised on 4µm tissue sections using Tris-EDTA pH 9 initially by immunofluorescence then in multiple assays by Hyperion (Fluidigm) IMC (Figure 1A). An analysis pipeline was developed based on the “Bodenmiller approach” using a combination of R, Python and MATLAB packages: CellProfiler and ilastik to segment single cells, and ImaCyte to explore the resident phenotypes and cellular neighbourhoods in diseased and healthy tissues. A staining panel with 25 antibodies was optimised to identify stromal, epithelial and leukocyte populations. Training algorithms allowed computational segmentation of nuclear, cytoplasmic and non-cellular regions (Figure 1B), cell mask, segmentation and spatial analysis (Figure 1C), and t-SNE (Figure 1D). Representative three parameter images created in MCD viewer (Fluidigm) are shown in Figure 1E to demonstrate cell populations and spatial localisation. Conclusion Quantifiable, multiparameter cellular phenotyping with spatial visualisation can be undertaken with FFPE intestinal tissue using IMC. Due to the existence of archival healthcare samples, the ease of tissue acquisition, processing and storage of FFPE specimens this provides a valuable resource for investigation, including mechanisms of disease pathogenesis, molecular biomarker discovery, and longitudinal pharmacodynamic analysis in clinical trials.

BACKGROUND & AIMS: Anti-tumor necrosis factor (anti-TNF) therapies are the most widely used biologic drugs for treating immune-mediated diseases, but repeated administration can induce the formation of anti-drug antibodies. The ability to identify patients at increased risk for development of anti-drug antibodies would facilitate selection of therapy and use of preventative strategies.METHODS: We performed a genome-wide association study to identify variants associated with time to development of anti-drug antibodies in a discovery cohort of 1240 biologic-naïve patients with Crohn's disease starting infliximab or adalimumab therapy. Immunogenicity was defined as an anti-drug antibody titer ≥10 AU/mL using a drug-tolerant enzyme-linked immunosorbent assay. Significant association signals were confirmed in a replication cohort of 178 patients with inflammatory bowel disease.RESULTS: The HLA-DQA1*05 allele, carried by approximately 40% of Europeans, significantly increased the rate of immunogenicity (hazard ratio [HR], 1.90; 95% confidence interval [CI], 1.60-2.25; P = 5.88 × 10-13). The highest rates of immunogenicity, 92% at 1 year, were observed in patients treated with infliximab monotherapy who carried HLA-DQA1*05; conversely the lowest rates of immunogenicity, 10% at 1 year, were observed in patients treated with adalimumab combination therapy who did not carry HLA-DQA1*05. We confirmed this finding in the replication cohort (HR, 2.00; 95% CI, 1.35-2.98; P = 6.60 × 10-4). This association was consistent for patients treated with adalimumab (HR, 1.89; 95% CI, 1.32-2.70) or infliximab (HR, 1.92; 95% CI, 1.57-2.33), and for patients treated with anti-TNF therapy alone (HR, 1.75; 95% CI, 1.37-2.22) or in combination with an immunomodulator (HR, 2.01; 95% CI, 1.57-2.58).CONCLUSIONS: In an observational study, we found a genome-wide significant association between HLA-DQA1*05 and the development of antibodies against anti-TNF agents. A randomized controlled biomarker trial is required to determine whether pretreatment testing for HLA-DQA1*05 improves patient outcomes by helping physicians select anti-TNF and combination therapies. ClinicalTrials.gov ID: NCT03088449.

BACKGROUND: Anti-TNF drugs are effective treatments for the management of Crohn's disease but treatment failure is common. We aimed to identify clinical and pharmacokinetic factors that predict primary non-response at week 14 after starting treatment, non-remission at week 54, and adverse events leading to drug withdrawal. METHODS: The personalised anti-TNF therapy in Crohn's disease study (PANTS) is a prospective observational UK-wide study. We enrolled anti-TNF-naive patients (aged ≥6 years) with active luminal Crohn's disease at the time of first exposure to infliximab or adalimumab between March 7, 2013, and July 15, 2016. Patients were evaluated for 12 months or until drug withdrawal. Demographic data, smoking status, age at diagnosis, disease duration, location, and behaviour, previous medical and drug history, and previous Crohn's disease-related surgeries were recorded at baseline. At every visit, disease activity score, weight, therapy, and adverse events were recorded; drug and total anti-drug antibody concentrations were also measured. Treatment failure endpoints were primary non-response at week 14, non-remission at week 54, and adverse events leading to drug withdrawal. We used regression analyses to identify which factors were associated with treatment failure. FINDINGS:We enrolled 955 patients treated with infliximab (753 with originator; 202 with biosimilar) and 655 treated with adalimumab. Primary non-response occurred in 295 (23·8%, 95% CI 21·4-26·2) of 1241 patients who were assessable at week 14. Non-remission at week 54 occurred in 764 (63·1%, 60·3-65·8) of 1211 patients who were assessable, and adverse events curtailed treatment in 126 (7·8%, 6·6-9·2) of 1610 patients. In multivariable analysis, the only factor independently associated with primary non-response was low drug concentration at week 14 (infliximab: odds ratio 0·35 [95% CI 0·20-0·62], p=0·00038; adalimumab: 0·13 [0·06-0·28], p

Genome-wide association studies (GWAS) have identified hundreds of loci associated with Crohns disease (CD), however, as with all complex diseases, deriving pathogenic mechanisms from these non-coding GWAS discoveries has been challenging. To complement GWAS and better define actionable biological targets, we analysed sequenced data from more than 30,000 CD patients and 80,000 population controls. We observe rare coding variants in established CD susceptibility genes as well as ten genes where coding variation directly implicates the gene in disease risk for the first time.

BACKGROUND: Increased mucosa-associated E. coli are present in Crohn's disease, but their role in pathogenesis is uncertain. AIMS: To assess efficacy and safety of an antibiotic/hydroxychloroquine combination effective against E. coli inside macrophages. METHODS: Adults with moderately active disease (CDAI > 220-450 plus C reactive protein ≥ 5 mg/l and/or fecal calprotectin > 250 μg/g) were randomized to receive (open-label) oral budesonide (Entocort CR 9 mg/day 8 weeks, 6 mg/day 2 weeks, 3 mg/day 2 weeks) or oral ciprofloxacin 500 mg bd, doxycycline 100 mg bd, hydroxychloroquine 200 mg tds for 4 weeks, followed by doxycycline 100 mg bd and hydroxychloroquine 200 mg tds for 20 weeks. Primary endpoints were remission (CDAI ≤ 150) at 10 weeks, remission maintained to 24 weeks, and remission maintained to 52 weeks. Patients not responding (CDAI fall by > 70) by 10 weeks were invited to crossover onto the alternative therapy. RESULTS: Fifty-nine patients were recruited across 8 sites. Including crossover, 39 patients received antibiotics/hydroxychloroquine and 39 received budesonide. At 10 weeks, 24 weeks, and 52 weeks on initial therapy, only 2/27, 2/27, and 1/27 were in remission on antibiotics/hydroxychloroquine compared with 8/32, 1/32, and 1/32 on budesonide (P = 0.092 at 10 weeks). Withdrawals by 10 weeks due to adverse events were seen in 15 receiving antibiotics/hydroxychloroquine and 6 budesonide. Results including crossover were more promising with 9/24 patients receiving antibiotics/hydroxychloroquine per protocol in remission by 24 weeks. No correlation was seen between response to antibiotics/hydroxychloroquine and ASCA/OmpC antibody status or disease location. CONCLUSION: Overall results with this antibiotic/hydroxychloroquine combination were unimpressive, but long-term remission is seen in some patients and justifies further study.

Introduction Mucosal E. coli are increased in Crohn’s disease (CD). They replicate within macrophages and are then inaccessible to penicillins and gentamicin. Hydroxychloroquine is used with doxycycline to treat Whipple’s disease. It raises macrophage intra-vesicular pH and inhibits replication of bacteria that require acidic pH. Ciprofloxacin and doxycycline are also effective against E. coli within macrophages. Methods Adult patients with active CD (CDAI>220 plus CRP≥5 mg/l and/or faecal calprotectin >250 ugram/g) were randomised to receive (open label) either oral budesonide (Entocort CR 9 mg/day 8 weeks, then 6 mg/day 2 weeks and 3 mg/day 2 weeks) or antibiotics/hydroxychloroquine (AB/HCQ) - oral ciprofloxacin 500 mg bd, doxycycline 100 mg bd, hydroxychloroquine 200 mgs tds for 4 weeks, followed by doxycycline 100 mg bd and hydroxychloroquine 200 mgs tds for 20 weeks. Use of anti-TNF in the previous 3 months was an exclusion. Primary endpoints were remission (CDAI Results 59 patients were recruited across 8 sites, lower than target (100) as recruitment slowed due to widening access to biologics. Including cross-over, 39 patients received AB/HCQ and 39 received budesonide. No significant differences were seen comparing AB/HCQ with budesonide at 10, 24 or 52 weeks on either intention-to-treat or per protocol analysis (see table 1). Withdrawals by 10 weeks due to adverse events were seen in 16 AB/HCQ and 7 budesonide. When patients on AB/HCQ who responded at 10 weeks and later remitted were included, 9/24 patients were in remission at 24 weeks and 4/23 at 52 weeks. No correlation was seen between response to AB/HCQ and ASCA/OmpC status. Conclusions The long term remissions seen with AB/HCQ are encouraging and justify a phase 3 study.

Ethical guidance for genomic research is increasingly sought and perceived to be necessary. Although there are pressing ethical issues in genomic research – concerning for example the recruitment of patients/participants; the process of taking consent; data sharing; and returning results to patients/participants – there is still limited useful guidance available for researchers/clinicians or for the research ethics committees who review such projects. This report outlines the ethical principles and guidance for genomic research co-produced with stakeholders during two workshops which took place in the UK between November 2016 and May 2017. The stakeholders involved in these workshops included: healthcare professionals, genomic research teams, academics, patients, biobank managers, and representatives from the Health Research Authority (HRA), NHS Research Ethics Committees, patient support groups, pharmaceutical industry, and health policy think tanks. The co-produced principles and guidance are specifically aimed at researchers/clinicians and members of NHS Research Ethics Committees, and are formulated with the intention to be clear and accessible, both in terms of content and language, to these groups.

Background Inflammatory bowel disease (IBD) is characterised by gut dysbiosis, weakened epithelial barrier, and a dysregulated immune system. Interleukin-22 (IL-22), an IL-10 family cytokine, has demonstrated efficacy in animal IBD models by promoting intestinal epithelial repair, increasing antimicrobial peptide production, and increasing mucin production via goblet cells1. UTTR1147A is a fusion protein in which IL-22 is linked with the Fc portion of IgG4 to improve the pharmacokinetic (PK) characteristics. Methods A phase I study (NCT02749630) was conducted to evaluate the safety, tolerability, PK, and pharmacodynamics (PD) of repeat IV dosing of UTTR1147A in healthy volunteers (HV) and UC patients with centrally read Mayo endoscopic score ≥ 2. 38 HVs and 24 UC patients were given UTTR1147A or placebo at doses ranging from 30 to 90 µg/kg either biweekly or monthly (6:2 UTTR1147A: placebo per cohort). PK and serum PD (REG3A and CRP) were studied across multiple time points and the Mayo Clinic Score was evaluated at baseline, day 30 and day 85. Results Overall, UTTR1147A was safe and adequately tolerated in HV and UC patients. The most common adverse events were on-target dermatological effects (dry skin, erythema, and pruritus) that were manageable, monitorable and reversible. Dose-limiting non-serious dermatological toxicities (severe dry skin, erythema, exfoliation, and discomfort) were seen in two HVs and 1 UC patient dosed with 90ug/kg Q2wk. There were 2 unrelated serious adverse events (ankle fracture and cytomegalovirus infection) that eventually resolved. PK analyses showed that UTTR1147A exposures were, in general, dose proportional within HVs and within UC patients, with a mean elimination half-life of ~16 days and ~12 days, respectively. At the same dose level, UC patients showed relatively lower drug exposures than HVs, possibly due to faster drug clearance. Consistent with the Phase Ia2, UTTR1147A directly induced production of serum PD biomarkers REG3A and CRP at all dose cohorts tested compared with placebo. Notably, UC patients appear to have attenuated serum PD responses compared with HV. Clinical response was observed in 7/18 patients, and clinical remission in 5/18 patients treated with UTTR1147A compared with 1/6 and 0/6 placebo patients, respectively. Conclusion UTTR1147A demonstrated adequate safety and PK profile in healthy volunteers and UC patients. PD biomarker data demonstrated pharmacological activity of UTTR1147A providing evidence of IL-22R pathway activation. Together with the preliminary signals of efficacy, these data support further investigation of this potential, novel non-immunosuppressive therapy in IBD.

Introduction We have previously shown that altering dietary ferrous iron consumption exacerbates murine models of inflammatory bowel disease (Mahalhal et al., 2018) and is associated with dysbiosis. We have now investigated the effect of oral ferric maltol and ferrous sulphate on the microbiome of patients with iron deficiency anaemia (IDA) and on mice treated with dextran sodium sulphate (DSS) to induce colitis. We report results of changes at the phylum level. Methods Studies were performed on three groups of wild-type mice: acute colitis was induced with 2% DSS for 5 days, followed by 5 further days on water while mice were fed one of three diets (from day-1 of DSS treatment): normal diet (200ppm iron ferrous sulphate) [ND (n=8)], 400ppm iron ferrous sulphate [FS (n=16)] or 400ppm iron ferric maltol [FM (n=16)]. Clinical and pathological data were compared at day-1 and day-10, when faecal samples were collected. 16 patients with IDA were also recruited: 10 were treated with FS and 6 with FM supplements for 4 weeks: paired faecal samples (pre and post-treatment) were collected. Faecal bacterial gDNA was extracted from murine and human samples and the microbiota composition was determined from the sequence of V4 region of 16S rDNA. Statistical inferences were made using Welch’s t-test with post-hoc analysis: Shannon Diversity Index (SDI) and Principal Component Analysis (PCA) were used to compare population and phylum-level changes. Results DSS-induced colitis was worse in ND and FS mice than FM mice (determined by weight loss [3, 7 & 0%, at day-8 respectively] and histology [median score 2, 2 & 1 at day-10]). FS supplementation was associated with an increase in Bacteroidetes (15% in mice, 4% in humans) whereas FM led to a reduction in Bacteroidetes (3% in mice and 15% in humans). There was a 4% increase in Firmicutes with FM supplementation in mice and 20% in humans whereas FS led to a 15% reduction in Firmicutes in mice and 5% in humans. Conclusion This study has demonstrated differential and unique influences of ferric maltol and ferrous sulphate supplements on the faecal microbiome of mice with DSS induced colitis and patients with iron deficiency. These differences might contribute to the difference in side effects that are associated with these preparations.

Background Mucosal E. coli are increased in Crohn’s disease (CD). They replicate within macrophages where they are inaccessible to penicillins and gentamicin. Hydroxychloroquine is successfully used together with doxycycline, typically for 12 months, to treat Whipple’s disease. It raises macrophage intra-vesicular pH and inhibits replication of bacteria , including E. coli that require an acid pH. Ciprofloxacin and doxycycline are also effective against E. coli replicating inside macrophages. Methods Adult patients with active CD (CDAI>220 plus CRP≥5mg/l and/or faecal calprotectin >250 μg/g) were randomised to receive either standard oral budesonide (Entocort CR 9mg/day for 8 weeks, 6mg/day for 2 weeks, 3mg/day for 2 weeks) or antibiotics/hydroxychloroquine (AB/HCQ) - oral ciprofloxacin 500mg bd, doxycycline 100mg bd, hydroxychloroquine 200 mg tds for 4 weeks, followed by continuation of doxycycline 100 mg bd and hydroxychloroquine 200 mg tds for a further 20 weeks. The use of anti-TNF in the previous 3 months was an exclusion. Primary endpoint parameters were remission at 10 weeks, remission maintained through to 24 weeks, and remission maintained through to 52 weeks. Secondary endpoints included remission and/or response (fall in CDAI of >70) at 10 weeks and remission at 4 weeks. Patients who failed to respond by 10 weeks were invited to cross-over onto the alternative therapy. Results 59 patients were recruited across 8 sites, lower than target (100) because recruitment slowed due to widening access to biologics. Including cross-over, 39 patients received AB/HCQ and 39 received budesonide. No significant differences were seen comparing AB/HCQ with budesonide at 10, 24 or 52 weeks on either intention-to-treat or per-protocol analysis (see table). Withdrawals by 10 weeks due to adverse events were seen in 16 AB/HCQ, - including nausea (3), photosensitivity (2), Achilles pain (2) and activity of CD (4); and 7 budesonide. Although not significant when analysed per protocol, when patients on AB/HCQ who responded at 10 weeks and later remitted were included, 9/24 patients were in remission at 24 weeks and 4/23 at 52 weeks. No correlation was seen between response to AB/HCQ and ASCA/OmpC status. Conclusion The longer-term remissions seen in some patients receiving AB/HCQ are encouraging and a larger phase 3 study is justified.

SummaryBackgroundAnti-tumour necrosis factor (anti-TNF) therapies are the most widely used biologic therapies for treating immune-mediated diseases. Their efficacy is significantly reduced by the development of anti-drug antibodies which can lead to treatment failure and adverse reactions. The biological mechanisms underlying antibody development are unknown but the ability to identify subjects at higher risk would have significant clinical benefits.MethodsThe PANTS cohort consists of Crohn’s disease patients recruited prior to first administration of anti-TNF, with serial measurements of anti-drug antibody titres. We performed a genome-wide association study across 1240 individuals from this cohort to identify genetic variants associated with anti-drug antibody development.FindingsThe Human Leukocyte Antigen allele, HLA-DQA1*05, carried by approximately 40% of Europeans, significantly increased the rate of anti-drug antibody development (hazard ratio [HR], 1.90; 95% confidence interval [CI], 1.60 to 2.25; P=5.88×10-13). This association was consistent for patients treated with adalimumab (HR, 1.89; 95% CI, 1.32 to 2.70) and infliximab (HR, 1.92; 95% CI, 1.57 to 2.33), and for patients treated with mono-(HR, 1.75; 95% CI, 1.37 to 2.22) or combination therapy with immunomodulators (HR, 2.0; 95% CI, 1.57 to 2.58).InterpretationHLA-DQA1*05 is significantly associated with an increased rate of anti-drug antibody formation in patients with Crohn’s disease treated with infliximab and adalimumab. Pre-treatment HLA-DQA1*05 genetic testing may help personalise the choice of anti-TNF therapy and allow the targeted use of immunomodulator therapy to minimise risk and maximise response.

Background Recent findings suggest that αE expression is enriched on effector T cells and that intestinal αE+ T cells have increased expression of inflammatory cytokines. αE integrin expression is a potential predictive biomarker for response to etrolizumab, a monoclonal antibody against β7 integrin that targets both α4β7 and αEβ7. We evaluated the prevalence and localization of αE+ cells as well as total αE gene expression in healthy and inflammatory bowel disease patients. Methods αE+ cells were identified in ileal and colonic biopsies by immunohistochemistry and counted using an automated algorithm. Gene expression was assessed by quantitative reverse-transcriptase polymerase chain reaction. Results In both healthy and inflammatory bowel disease patients, significantly more αE+ cells were present in the epithelium and lamina propria of ileal compared with colonic biopsies. αE gene expression levels were also significantly higher in ileal compared with colonic biopsies. Paired biopsies from the same patient showed moderate correlation of αE expression between the ileum and colon. Inflammation did not affect αE expression, and neither endoscopy nor histology scores correlated with αE gene expression. αE expression was not different between patients based on concomitant medication use except 5-aminosalicylic acid. Conclusion αE+ cells, which have been shown to have inflammatory potential, are increased in the ileum in comparison with the colon in both Crohn’s disease and ulcerative colitis, as well as in healthy subjects. In inflammatory bowel disease patients, αE levels are stable, regardless of inflammatory status or most concomitant medications, which could support its use as a biomarker for etrolizumab.

Introduction In Newcastle Hospitals, we care for up to 3000 IBD patients including complex patients from around the North East (NE) of England although in the absence of a database the number is an estimate. We have designed an IBD database, based on the IBD Bioresource database so that we can audit and improve the management of our patients. Methods Together with the IT team at Newcastle upon Tyne Hospitals, we created a bespoke IBD database embedded in the Cerner e-record system used by the trust. Data are entered by clinicians and began in June 2016, results are shown to early Feb 2018. Data from this database have been uploaded onto the national Bioresource database. Results Total number of patients included on database is 1358; Crohn’s 756, Ulcerative Colitis 574, IBDU (Unclassified) 28. There are 723 Female patients. A positive family history of IBD was recorded for 328 patients (24.1%). Current drug usage:Biologics: Infliximab 188, Adalimumab 144 and Vedolizumab 22 Immunomodulators: Azathioprine 348, 6MP (Mercaptopurine) 73 and Methotrexate 73 Adverse drug side effects: A significant number of patients have experienced adverse drug side effects requiring dose reduction or cessation: Azathioprine: Nausea 59, Deranged Liver Function Test (LFT’s) 50, Vomiting 41, Leucopaenia 28, Pancreatitis 18 6MP: Deranged LFT’s 16, Nausea 10, Leucopaenia 3, Pancreatitis 2 Methotrexate: Nausea 31, Deranged LFT’s 13, Vomiting 10, Neutropaenia 2 Infliximab: Rash 16, Arthralgia 6, Infection 6, Drug induced lupus 3, Anaphylaxis 2 Adalimumab: Rash 8, Demyelination 2, Deranged LFT’s 2, Drug induced lupus 1, Arthralgia 1. Conclusions Newcastle Hospitals is a tertiary regional centre managing complex IBD cases covering the NE of England. This novel database is embedded within the Cerner e-record system. IBD clinicians have the opportunity of seeing all patient details in a snap shot instead of having to hunt through voluminous clinic notes. It creates a very convenient tool to monitor various aspects of patient care, e.g. keeping a close track of patients on biologics and Immunomodulators. This database will enable us to audit our performance against agreed national parameters. As with all databases keeping it up to date will be crucial for its usefulness.

Background and aimsAlthough genome-wide association studies (GWAS) in inflammatory bowel disease (IBD) have identified a large number of common disease susceptibility alleles for both Crohn’s disease (CD) and ulcerative colitis (UC), a substantial fraction of IBD heritability remains unexplained, suggesting that rare coding genetic variants may also have a role in pathogenesis. We used high-throughput sequencing in families with multiple cases of IBD, followed by genotyping of cases and controls, to investigate whether rare protein altering genetic variants are associated with susceptibility to IBD.MethodsWhole exome sequencing was carried out in 10 families in which 3 or more individuals were affected with IBD. A stepwise filtering approach was applied to exome variants to identify potential causal variants. Follow-up genotyping was performed in 6,025 IBD cases (2,948 CD; 3,077 UC) and 7,238 controls.ResultsOur exome variant analysis revealed coding variants in the NLRP7 gene that were present in affected individuals in two distinct families. Genotyping of the two variants, p.S361L and p.R801H, in IBD cases and controls showed that the p.S361L variant was significantly associated with an increased risk of ulcerative colitis (odds ratio 4.79, p=0.0039) and IBD (odds ratio 3.17, p=0.037). A combined analysis of both variants showed suggestive association with an increased risk of IBD (odds ratio 2.77, p=0.018).ConclusionsThe results suggest that NLRP7 signalling and inflammasome formation may be a significant component in the pathogenesis of IBD.

Background: Anti-tumour necrosis factor (TNF) drugs have revolutionised Crohn's disease management but treatment failure is common. We sought clinical and pharmacokinetic factors that predict and mitigate primary non-response at week 14, non-remission at week 54, and adverse events leading to drug withdrawal. Methods: We conducted a prospective observational UK-wide study in 1610 biologic naive patients with active luminal Crohn's disease (955 infliximab [753 Remicade; 202 biosimilar CT-P13] and 655 adalimumab). Findings: Primary non-response (PNR) occurred in 23·8% (95% CI 21·4%-26·2%), non-remission in 63·1% (95% CI 60·3%-65·8%), and adverse events curtailed treatment in 7·8% (95% CI 6·6%-9·2%) patients. The only independent risk factor for PNR was low drug level. The optimal week 14 drug levels associated with remission at weeks 14 and 54 were 7 mg/L and 12 mg/L for infliximab and adalimumab, respectively. Continuing standard dosing regimens after PNR was rarely helpful: only 12·4% (14/113; 95% CI 6·9%-19·9%) entered remission by week 54. Obesity, smoking, low albumin levels, higher baseline markers of disease activity, and development of anti-drug antibodies were associated with low drug levels, which mediated week 54 non-remission. Immunogenicity rates at week 54 were 62·8% (95% CI 59·0-66·3%) for infliximab and 28·5% (95% CI 24·0-32·7%) for adalimumab. For both drugs, sub-optimal week 14 drug levels were the main determinant of immunogenicity; whilst subsequent anti-drug antibody formation was the principle factor accounting for low drug levels. Combination thiopurine or methotrexate therapy mitigated this risk with similar effect sizes for both anti-TNF drugs and for infliximab led to lower week 54 non-remission rates. Interpretation: Anti-TNF treatment failure is common and associated with low drug levels, partly mediated by immunogenicity Clinical trials are required to investigate whether personalised induction regimens and treatment-to-target dose intensification improve outcomes. Funding: Charities: CORE, CCUK, C3. Unrestricted grants: Abbvie, Merck Sharp & Dohme, NAPP, Pfizer and Celltrion. Declaration of Interest: All authors have completed and submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest and declare: N.A.K has consulted for Falk and received honoraria from Falk, Allergan, Pharmacosmos and Takeda for unrelated topics and is a deputy editor of Alimentary Pharmacology & Therapeutics Journal; G.A.H reports non-financial support from AbbVie, outside the submitted work; and that he is now an employee of AbbVie and owns stock in the company; M.R. is an employee of AbbVie and owns stock in the company; D.G. reports honoraria from AbbVie; G.J.W has consulted for AbbVie and received honoraria from Falk and AbbVie for unrelated topics and a fellowship from NIHR; A.H has served as consultant, advisory board member or speaker for AbbVie, Atlantic, Bristol-Myers Squibb, Celltrion, Falk, Ferring, Janssen, MSD, Napp Pharmaceuticals, Pfizer, Pharmacosmos, Shire and Takeda and also serves on the Global Steering Committee for Genentech outside the submitted work;. S.S reports personal fees from AbbVie, Merck, Takeda, grants from Takeda, Tillotts, AbbVie, Merck, outside the submitted work; P.M.I reports personal fees from Abbvie, Janssen, Pfizer, Sandoz, VH squared, Samsung Bioepis, and Ferring , grants from MSD, grants and personal fees from Takeda, non-financial support from Falk, outside the submitted work; D.McG reports grants from NIH and Helmsley Charitable Trust, during the conduct of the study; grants and personal fees from Janssen, Precision IBD Inc, Second Genome, Qu Biologics, Pfizer, Gilead and Takeda, outside the submitted work; C.W.L reports grants and personal fees from Abbvie and Gilead personal fees from GSK, Janssen, Takeda, Amgen, Pfizer, Samsung Bioepis, Celgene, grants outside the submitted work; J.R.F.C reports personal fees from Abbvie, grants and personal fees from Takeda, Hospira and Biogen, personal fees from Janssen, MSD, Celltrion, NAPP, and Sandoz, outside the submitted work; J.L has served as consultant, advisory board member or speaker for Shire (International/UK) AbbVie, Atlantic, BMS, Celltrion, Falk, Ferring (International/UK), Janssen, MSD, Napp Pharmaceuticals, Pfizer, GSK, Allergan, Cornerstone US, and Takeda and has received travel support from AbbVie, Warner Chilcot, Takeda and Pfizer outside the submitted work; R.K.R reports honoraria from Abbvie, Ferring , Therakos and Celltrion, grants from Nestec, outside the submitted work; J.R.G received honoraria from Falk, Abbvie and Shield therapeutics for unrelated topics. T.A has received unrestricted research grants, advisory board fees, speaker honorariums and support to attend international meetings from AbbVie, Merck, Janssen, Takeda, Ferring, Tillotts, Ferring, Pfizer, NAPP, Celltrion, Hospira for unrelated topics, no financial relationships with any organizations that might have an interest in the submitted work in the previous three years; no other relationships or activities that could appear to have influenced the submitted work. H.G, B.H, C.B, M.H.P, T.M, A.T, R.N, 473 S.B, N.C, N.M.H, P.H, S.L, M.P, J.C.M have no conflicts of interest to declare. Ethical Approval: The South West Research Ethics committee approved the study (REC Reference: 12/SW/0323) in January 2013.

Background and Aims Although genome-wide association studies [GWAS] in inflammatory bowel disease [IBD] have identified a large number of common disease susceptibility alleles for both Crohn’s disease [CD] and ulcerative colitis [UC], a substantial fraction of IBD heritability remains unexplained, suggesting that rare coding genetic variants may also have a role in pathogenesis. We used high-throughput sequencing in families with multiple cases of IBD, followed by genotyping of cases and controls, to investigate whether rare protein-altering genetic variants are associated with susceptibility to IBD. Methods Whole-exome sequencing was carried out in 10 families in whom three or more individuals were affected with IBD. A stepwise filtering approach was applied to exome variants, to identify potential causal variants. Follow-up genotyping was performed in 6025 IBD cases [2948 CD; 3077 UC] and 7238 controls. Results Our exome variant analysis revealed coding variants in the NLRP7 gene that were present in affected individuals in two distinct families. Genotyping of the two variants, p.S361L and p.R801H, in IBD cases and controls showed that the p.S361L variant was significantly associated with an increased risk of ulcerative colitis [odds ratio 4.79, p = 0.0039] and IBD [odds ratio 3.17, p = 0.037]. A combined analysis of both variants showed suggestive association with an increased risk of IBD [odds ratio 2.77, p = 0.018]. Conclusions The results suggest that NLRP7 signalling and inflammasome formation may be a significant component in the pathogenesis of IBD.

Genetic association studies have identified 215 risk loci for inflammatory bowel disease, thereby uncovering fundamental aspects of its molecular biology. We performed a genome-wide association study of 25,305 individuals and conducted a meta-analysis with published summary statistics, yielding a total sample size of 59,957 subjects. We identified 25 new susceptibility loci, 3 of which contain integrin genes that encode proteins in pathways that have been identified as important therapeutic targets in inflammatory bowel disease. The associated variants are correlated with expression changes in response to immune stimulus at two of these genes (ITGA4 and ITGB8) and at previously implicated loci (ITGAL and ICAM1). In all four cases, the expression-increasing allele also increases disease risk. We also identified likely causal missense variants in a gene implicated in primary immune deficiency, PLCG2, and a negative regulator of inflammation, SLAMF8. Our results demonstrate that new associations at common variants continue to identify genes relevant to therapeutic target identification and prioritization.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access. Protein-truncating variants protective against human disease provide in vivo validation of therapeutic targets. Here we used targeted sequencing to conduct a search for protein-truncating variants conferring protection against inflammatory bowel disease exploiting knowledge of common variants associated with the same disease. Through replication genotyping and imputation we found that a predicted protein-truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF=up to 0.78%) in RNF186, a single-exon ring finger E3 ligase with strong colonic expression, protects against ulcerative colitis (overall P=6.89 × 10(-7), odds ratio=0.30). We further demonstrate that the truncated protein exhibits reduced expression and altered subcellular localization, suggesting the protective mechanism may reside in the loss of an interaction or function via mislocalization and/or loss of an essential transmembrane domain. National Institute of Diabetes and Digestive and Kidney Disease (NIDDK) DK064869 DK062432 National Human Genome Research Institute (NHGRI) DK064869 DK043351 HG005923 Crohns and Colitis Foundation 3765 Leona M. & Harry B. Helmsley Charitable Trust 2015PG-IBD001 Amgen 2013583217 CCFA 3765 Cedars-Sinai F. Widjaja Foundation, info:eu-repo/grantAgreement/EC/FP7/305479, European Union DK062413 AI067068 U54DE023789-01 Leona M. and Harry B. Helmsley Charitable Trust Crohn's and Colitis Foundation of America NIH DK062431 U01 DK062429 U01 DK062422 R01 DK092235 U01 DK062420 Medical Research Council, UK MR/J00314X/1 Wellcome Trust WT091310 098051 Inflammatory Bowel Disease Genetic Research Chair at the University of Pittsburgh PO1DK046763

Several risk factors for Crohn's disease have been identified in recent genome-wide association studies. To advance gene discovery further, we combined data from three studies on Crohn's disease ( a total of 3,230 cases and 4,829 controls) and carried out replication in 3,664 independent cases with a mixture of population-based and family-based controls. The results strongly confirm 11 previously reported loci and provide genome-wide significant evidence for 21 additional loci, including the regions containing STAT3, JAK2, ICOSLG, CDKAL1 and ITLN1. The expanded molecular understanding of the basis of this disease offers promise for informed therapeutic development.

Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with diseaseIRGM for Crohns disease, HLA for Crohns disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetesalthough in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases. © 2010 Macmillan Publishers Limited. All rights reserved.

Genetic association studies have identified 210 risk loci for inflammatory bowel disease1–7, which have revealed fundamental aspects of the molecular biology of the disease, including the roles of autophagy and Th17 cell signaling and development. We performed a genome-wide association study of 25,305 individuals, and meta-analyzed with published summary statistics, yielding a total sample size of 59,957 subjects. We identified 26 new genome-wide significant loci, three of which contain integrin genes that encode molecules in pathways identified as important therapeutic targets in inflammatory bowel disease. The associated variants are also correlated with expression changes in response to immune stimulus at two of these genes (ITGA4, ITGB8) and at two previously implicated integrin loci (ITGAL, ICAM1). In all four cases, the stimulus-dependent expression increasing allele also increases disease risk. We applied summary statistic fine-mapping and identified likely causal missense variants in the primary immune deficiency genePLCG2and the negative regulator of inflammation,SLAMF8. Our results demonstrate that new common variant associations continue to identify genes and pathways of relevance to therapeutic target identification and prioritization.

Background and Aims: The αEβ7 integrin is crucial for retention of T lymphocytes at mucosal surfaces through its interaction with E-cadherin. Pathogenic or protective functions of these cells during human intestinal inflammation, such as ulcerative colitis [UC], have not previously been defined, with understanding largely derived from animal model data. Defining this phenotype in human samples is important for understanding UC pathogenesis and is of translational importance for therapeutic targeting of αEβ7–E-cadherin interactions. Methods: αEβ7+ and αEβ7− colonic T cell localization, inflammatory cytokine production and expression of regulatory T cell-associated markers were evaluated in cohorts of control subjects and patients with active UC by immunohistochemistry, flow cytometry and real-time PCR of FACS-purified cell populations. Results: CD4+αEβ7+ T lymphocytes from both healthy controls and UC patients had lower expression of regulatory T cell-associated genes, including FOXP3, IL-10, CTLA-4 and ICOS in comparison with CD4+αEβ7− T lymphocytes. In UC, CD4+αEβ7+ lymphocytes expressed higher levels of IFNγ and TNFα in comparison with CD4+αEβ7− lymphocytes. Additionally the CD4+αEβ7+ subset was enriched for Th17 cells and the recently described Th17/Th1 subset co-expressing both IL-17A and IFNγ, both of which were found at higher frequencies in UC compared to control. Conclusion: αEβ7 integrin expression on human colonic CD4+ T cells was associated with increased production of pro-inflammatory Th1, Th17 and Th17/Th1 cytokines, with reduced expression of regulatory T cell-associated markers. These data suggest colonic CD4+αEβ7+ T cells are pro-inflammatory and may play a role in UC pathobiology.

Previous work has shown that the gene DMBT1, which encodes a large secreted epithelial glycoprotein known as salivary agglutinin, gp340, hensin or muclin, is an innate immune defence protein that binds bacteria. A deletion variant of DMBT1 has been previously associated with Crohn's disease, and a DMBT1(-/-) knockout mouse has increased levels of colitis induced by dextran sulphate. DMBT1 has a complex copy number variable structure, with two, independent, rapidly mutating copy number variable regions, called CNV1 and CNV2. Because the copy number variable regions are predicted to affect the number of bacteria-binding domains, different alleles may alter host-microbe interactions in the gut. Our aim was to investigate the role of this complex variation in susceptibility to Crohn's disease by assessing the previously reported association. We analysed the association of both copy number variable regions with presence of Crohn's disease, and its severity, on three case-control cohorts. We also reanalysed array comparative genomic hybridisation data (aCGH) from a large case-control cohort study for both copy number variable regions. We found no association with a linear increase in copy number, nor when the CNV1 is regarded as presence or absence of a deletion allele. Taken together, we show that the DMBT1 CNV does not affect susceptibility to Crohn's disease, at least in Northern Europeans.European Journal of Human Genetics advance online publication, 27 January 2016; doi:10.1038/ejhg.2015.280.

Crohn's disease and ulcerative colitis are chronic inflammatory disorders affecting the gastrointestinal tract. Faecal calprotectin is a protein complex of the S-100 family of calcium-binding proteins present in inflammatory cells that can be measured in stool samples, which act as a biomarker for bowel inflammation. Elevated faecal calprotectin has been shown to reflect the presence of ongoing mucosal inflammation, which improves with mucosal healing. The aim of this review was to evaluate the available evidence on the ability of faecal calprotectin to predict a relapse in inflammatory bowel disease. Multiple retrospective studies have shown that patients who relapse have significantly higher levels of calprotectin in their stool compared with non-relapsers, especially in ulcerative colitis. Elevated faecal calprotectin postoperatively in Crohn's disease was also shown to be indicative of a relapse. However, the association of a raised faecal calprotectin and relapse is not universal and may be explained by the different patterns of mucosal inflammatory activity that exist. In conclusion, we put forward our hypothesis that changes such as a rise in faecal calprotectin levels may be more predictive of a relapse than absolute values.

There is a rising incidence of several sexually transmitted infections (STIs), many of which can present with proctitis. Causative organisms include Neisseria gonorrhoeae, Chlamydia trachomatis, herpes simplex virus, Treponema pallidum (syphilis), Giardia lamblia (giardiasis) and Entamoeba histolytica (amoebiasis). This paper outlines important clinical discriminators and key investigations to distinguish these organisms from non-infective pathology that include inflammatory bowel disease, solitary rectal ulcer syndrome and Behçet's syndrome. Management of these infections is described and suggestions are made for successful gastroenterology clinical consultation when an STI is suspected.

Genome-wide association studies and candidate gene studies in ulcerative colitis have identified 18 susceptibility loci. We conducted a meta-analysis of six ulcerative colitis genome-wide association study datasets, comprising 6,687 cases and 19,718 controls, and followed up the top association signals in 9,628 cases and 12,917 controls. We identified 29 additional risk loci (P < 5 x 10(-8)), increasing the number of ulcerative colitis-associated loci to 47. After annotating associated regions using GRAIL, expression quantitative trait loci data and correlations with non-synonymous SNPs, we identified many candidate genes that provide potentially important insights into disease pathogenesis, including IL1R2, IL8RA-IL8RB, IL7R, IL12B, DAP, PRDM1, JAK2, IRF5, GNA12 and LSP1. The total number of confirmed inflammatory bowel disease risk loci is now 99, including a minimum of 28 shared association signals between Crohn's disease and ulcerative colitis.

Crohn's disease and ulcerative colitis are chronic relapsing gastrointestinal conditions characterised by an influx of inflammatory cells to the affected gut mucosa. The mainstay of diagnosing and re-evaluating these conditions in clinical practice and research is by invasive serological, radiological, endoscopic and histological assessment. In clinical trials, disease activity is often evaluated using a combination of the above tests plus clinical indices such as the Crohn's Disease Activity Index and Ulcerative Colitis Activity Index. These tools rely on subjective assessment of symptoms and so, often, do not correlate with mucosal inflammation or mucosal healing, which may be the preferred therapeutic end point for long-term inflammatory bowel disease (IBD) management. The faecal biomarkers calprotectin and lactoferrin are neutrophil derived proteins that are stable in faeces and can be detected by quantitative ELISA in small stool samples. Concentrations of both are raised in patients with gastrointestinal mucosal inflammation. They provide a unique, inexpensive, non-invasive method of testing for active inflammatory disease. They can be used to screen for IBD and as a surrogate marker of mucosal healing they are useful in monitoring the response to therapeutic intervention or surgery. They may also predict the clinical course of the disease. This clinical review aims to discuss the current evidence, limitations and potential future uses of these biomarkers in IBD.

DNA polymorphisms in a region on chromosome 5q33.1 which contains two genes, immunity related GTPase related family, M (IRGM) and zinc finger protein 300 (ZNF300), are associated with Crohn's disease (CD). The deleted allele of a 20 kb copy number variation (CNV) upstream of IRGM was recently shown to be in strong linkage disequilibrium (LD) with the CD-associated single nucleotide polymorphisms and is itself associated with CD (P < 0.01). The deletion was correlated with increased or reduced expression of IRGM in transformed cells in a cell line-dependent manner, and has been proposed as a likely causal variant. We report here that small insertion/deletion polymorphisms in the promoter and 5' untranslated region of IRGM are, together with the CNV, strongly associated with CD (P = 1.37 x 10(-5) to 1.40 x 10(-9)), and that the CNV and the 5'-untranslated region variant -308(GTTT)(5) contribute independently to CD susceptibility (P = 2.6 x 10(-7) and P = 2 x 10(-5), respectively). We also show that the CD risk haplotype is associated with a significant decrease in IRGM expression (P < 10(-12)) in untransformed lymphocytes from CD patients. Further analysis of these variants in a Japanese CD case-control sample and of IRGM expression in HapMap populations revealed that neither the IRGM insertion/deletion polymorphisms nor the CNV was associated with CD or with altered IRGM expression in the Asian population. This suggests that the involvement of the IRGM risk haplotype in the pathogenesis of CD requires gene-gene or gene-environment interactions which are absent in Asian populations, or that none of the variants analysed are causal, and that the true causal variants arose after the European-Asian split.

Elevated blood pressure is a common, heritable cause of cardiovascular disease worldwide. To date, identification of common genetic variants influencing blood pressure has proven challenging. We tested 2.5 million genotyped and imputed SNPs for association with systolic and diastolic blood pressure in 34,433 subjects of European ancestry from the Global BPgen consortium and followed up findings with direct genotyping (N ≤ 71,225 European ancestry, N ≤ 12,889 Indian Asian ancestry) and in silico comparison (CHARGE consortium, N = 29,136). We identified association between systolic or diastolic blood pressure and common variants in eight regions near the CYP17A1 (P = 7 × 10(-24)), CYP1A2 (P = 1 × 10(-23)), FGF5 (P = 1 × 10(-21)), SH2B3 (P = 3 × 10(-18)), MTHFR (P = 2 × 10(-13)), c10orf107 (P = 1 × 10(-9)), ZNF652 (P = 5 × 10(-9)) and PLCD3 (P = 1 × 10(-8)) genes. All variants associated with continuous blood pressure were associated with dichotomous hypertension. These associations between common variants and blood pressure and hypertension offer mechanistic insights into the regulation of blood pressure and may point to novel targets for interventions to prevent cardiovascular disease.

There has been considerable recent success in the detection of gene-disease associations. We consider here the development of tools that facilitate the more detailed characterization of the effect of a genetic variant on disease. We replace the simplistic classification of individuals according to a single binary disease indicator with classification according to a number of subphenotypes. This more accurately reflects the underlying biological complexity of the disease process, but it poses additional analytical difficulties. Notably, the subphenotypes that make up a particular disease are typically highly associated, and it becomes difficult to distinguish which genes might be causing which subphenotypes. Such problems arise in many complex diseases. Here, we concentrate on an application to Crohn disease (CD). We consider this problem as one of model selection based upon log-linear models, fitted in a Bayesian framework via reversible-jump Metropolis-Hastings approach. We evaluate the performance of our suggested approach with a simple simulation study and then apply the method to a real data example in CD, revealing a sparse disease structure. Most notably, the associated NOD2.908G--R mutation appears to be directly related to more severe disease behaviors, whereas the other two associated NOD2 variants, 1007L--FS and 702R--W, are more generally related to disease in the small bowel (ileum and jejenum). The ATG16L1.300T--A variant appears to be directly associated with only disease of the small bowel.

Background Therapy targeted at tumour necrosis factor-alpha has an established role in Crohn's disease. Lenalidomide, an analogue of thalidomide, is an oral immunomodulatory agent with powerful antitumour necrosis factor-alpha properties. It is licensed for myeloma and myelodysplastic syndrome. Based upon reports of thalidomide efficacy, lenalidomide was evaluated in Crohn's disease.Aim To evaluate the efficacy and safety of lenalidomide in subjects with moderately severe active Crohn's disease.Methods In a multicentre, double-blind, placebo-controlled parallel group study 89 subjects were randomized to lenalidomide 25 mg daily, 5 mg daily or placebo. Subjects were treated for 12 weeks. The primary end point was a 70-point reduction in Crohn's Disease Activity Index.Results The overall clinical response rate was not significantly different between the three groups: lenalidomide 25 mg 26%, lenalidomide 5 mg 48% and placebo 39%. Lenalidomide was generally well tolerated with only one serious adverse event, a deep vein thrombosis, being attributed to treatment.Conclusion Lenalidomide, an oral agent with antitumour necrosis factor-alpha properties, was not effective in active Crohn's disease in contrast to reports of benefit from thalidomide. The reasons for this lack of efficacy are speculative, other physiological activities may offset its action on inflammatory cytokines, or its antitumour necrosis factor-alpha action without apoptosis may be insufficient for activity in Crohn's disease.

Background & Aims: A genome-wide association scan of nonsynonymous DNA polymorphisms identified association of a threonine-to-alanine substitution (T300A) in the autophagy-related 16-like gene ATG16L1 with Crohn's disease. We investigated this association in independent U.K. cohorts of Crohn's disease and ulcerative colitis. Methods: The T300A variant (rs2241880) was genotyped in an independent sample of 727 Crohn's disease and 877 ulcerative colitis cases, and in 579 controls. We then performed an extension analysis combining these data with the U.K. data from the initial study to give a total of 1236 U.K. Crohn's disease cases and 1235 controls to estimate disease risk and test for interaction with the CARD15 and IBD5 risk loci and for association with disease subtypes. Results: The association of T300A was replicated in the independent sample of 727 Crohn's disease cases ( P = .001), and was strongly associated in the extended analysis of 1236 Crohn's cases ( P = 2.4 × 10 −6 ). The 300A/A genotype conferred a 1.65-fold risk of Crohn's disease, with a 2.2-fold risk of ileal disease. Analysis of the interaction of ATG16L1 with CARD15 and IBD5 indicated that all 3 loci contribute independently to disease risk. Homozygosity for the risk allele at all 3 loci conferred a combined risk of 20.4 (95% confidence interval: 8.71, 47.7) for Crohn's disease. The ATG16L1 risk genotype showed a modest but significant association with ulcerative colitis ( P = .026). Conclusions: The association of ATG16L1 with Crohn's disease and possibly with ulcerative colitis supports a role for autophagy in the pathogenesis of inflammatory bowel disease.

A common haplotype spanning 250 kb on chromosome 5q31 is strongly associated with Crohn disease (CD). Recently, two functional variants within the SLC22A4 and SLC22A5 genes at this locus (IBD5), L503F (c.1507C > T) and G-207C (c.-207G > C), have been proposed to contribute directly to susceptibility to CD. However, extensive linkage disequilibrium at the IBD5 locus has complicated efforts to distinguish causal variants from association of the general risk haplotype. We genotyped the SLC22A4 and SLC22A5 variants and other polymorphisms across the risk haplotype in four populations of European origin, and applied regression-based haplotype analysis to over 1,200 fully genotyped case-control pairs, modeling case/control status on the presence of one or more SNPs to test for conditional association and to identify risk haplotypes. We found highly significant association of SNPs at the IBD5 locus with Crohn disease in all populations tested. However, the frequencies of L503F and G-207C in individuals who did not carry the general IBD5 risk haplotype were not significantly different in cases and controls, with associated disease odds ratios (ORs) of 0.90 (95% CI, 0.57-1.40) and 0.90 (95% CI, 0.65-1.23), respectively. Haplotype analysis showed that addition of the SLC22A4 and SLC22A5 variants to a null model that included the background risk haplotype did not significantly improve the model fit. In addition to the common risk haplotype, several rare haplotypes had an increased frequency in cases compared to controls. This study suggests that the molecular basis for Crohn disease susceptibility at the IBD5 locus remains to be defined, and highlights the challenge of the identification of causal variants in a complex disease in regions of extensive linkage disequilibrium.

This article aims to offer an updated review of the effects of smoking on inflammatory bowel disease, and provide a review of the methods of achieving smoking cessation. A systematic review of Embase and Medline databases was conducted. Smoking causes opposing effects on ulcerative colitis and Crohn's disease. The odds ratio of developing ulcerative colitis for smokers compared with lifetime non-smokers is 0.41. Conversely, smokers with Crohn's disease have a more aggressive disease requiring more therapeutic intervention. Smoking cessation is associated with a 65% reduction in the risk of a relapse as compared with continued smokers, a similar magnitude to that obtained with immunosuppressive therapy. Although difficult to achieve smoking cessation can best be encouraged by accessing appropriate counselling services, nicotine replacement therapy and bupropion. Using a combination of these treatments there is an improved chance of success of up to 20% compared with an unassisted quit attempt. Smoking cessation unequivocally improves the course of Crohn's disease and should be a primary therapeutic aim in smokers with Crohn's disease.

The chemokine gene cluster [CCL22, CX3CL1, CCL17] (previously known as [SCYA22, SCYD1, SCYA17]) is a candidate locus for one of the susceptibility genes for inflammatory bowel disease that are located in the peri-centromeric region of chromosome 16. Screening for sequence variation at this locus led to the detection of 14 single nucleotide polymorphisms (SNPs). An efficient experimental and computational approach was developed to estimate allele frequencies and pairwise linkage disequilibrium relationships between SNPs at this locus, and to test them for association with inflammatory bowel disease. The 12 common SNPs were assigned to 5 distinct linkage disequilibrium groups. Genotyping of one SNP from each linkage disequilibrium group in a large cohort of families with inflammatory bowel disease did not provide convincing evidence of association with either Crohn's disease or ulcerative colitis. We describe an efficient experimental design from SNP screening to association testing. This strategy can be used to test candidate genes for involvement in susceptibility to complex disease.

The immunoglobulin superfamily 6 gene (IGSF6) on chromosome 16p11-p12 has been investigated as a positional and functional candidate for inflammatory bowel disease (IBD) susceptibility. Screening of the six exons of IGSF6 for single nucleotide polymorphisms (SNPs) detected four novel SNPs, and validated three of six SNPs listed in the international SNP database (dbSNP). The seven SNPs in IGSF6 formed five distinct linkage disequilibrium groups. There was no evidence for association of the common SNPs with disease in a large cohort of patients with IBD. The novel SNPs and the linkage disequilibrium map will be a useful resource for the analysis of IGSF6 in other immune disorders.