Rewiring the altered tryptophan metabolism as a novel therapeutic strategy in inflammatory bowel diseases.

OBJECTIVE: The extent to which tryptophan (Trp) metabolism alterations explain or influence the outcome of inflammatory bowel diseases (IBDs) is still unclear. However, several Trp metabolism end-products are essential to intestinal homeostasis. Here, we investigated the role of metabolites from the kynurenine pathway. DESIGN: Targeted quantitative metabolomics was performed in two large human IBD cohorts (1069 patients with IBD). Dextran sodium sulphate-induced colitis experiments in mice were used to evaluate effects of identified metabolites. In vitro, ex vivo and in vivo experiments were used to decipher mechanisms involved. Effects on energy metabolism were evaluated by different methods including Single Cell mEtabolism by profiling Translation inHibition. RESULTS: In mice and humans, intestinal inflammation severity negatively correlates with the amount of xanthurenic (XANA) and kynurenic (KYNA) acids. Supplementation with XANA or KYNA decreases colitis severity through effects on intestinal epithelial cells and T cells, involving Aryl hydrocarbon Receptor (AhR) activation and the rewiring of cellular energy metabolism. Furthermore, direct modulation of the endogenous tryptophan metabolism, using the recombinant enzyme aminoadipate aminotransferase (AADAT), responsible for the generation of XANA and KYNA, was protective in rodent colitis models. CONCLUSION: Our study identified a new mechanism linking Trp metabolism to intestinal inflammation and IBD. Bringing back XANA and KYNA has protective effects involving AhR and the rewiring of the energy metabolism in intestinal epithelial cells and CD4+ T cells. This study paves the way for new therapeutic strategies aiming at pharmacologically correcting its alterations in IBD by manipulating the endogenous metabolic pathway with AADAT.

A Scoring System to Determine Patients' Risk of Colectomy Within 1 Year After Hospital Admission for Acute Severe Ulcerative Colitis.

BACKGROUND & AIMS: There is consensus on the criteria used to define acute severe ulcerative colitis (ASUC) and on patient management, but it has been a challenge to identify patients at risk for colectomy based on data collected at hospital admission. We aimed to develop a system to determine patients' risk of colectomy within 1 y of hospital admission for ASUC based on clinical, biomarker, and endoscopy data. METHODS: We performed a retrospective analysis of consecutive patients with ASUC treated with corticosteroids, ciclosporin, or tumor necrosis factor (TNF) antagonists and admitted to 2 hospitals in France from 2002 through 2017. Patients were followed until colectomy or loss of follow up. A total of 270 patients with ASUC were included in the final analysis, with a median follow-up time of 30 months (derivation cohort). Independent risk factors identified by Cox multivariate analysis were used to develop a system to identify patients at risk for colectomy 1 y after ASUC. We developed a scoring system based on these 4 factors (1 point for each item) to identify high-risk (score 3 or 4) vs low-risk (score 0) patients. We validated this system using data from an independent cohort of 185 patients with ASUC treated from 2006 through 2017 at 2 centers in France. RESULTS: In the derivation cohort, the cumulative risk of colectomy was 12.3% (95% CI, 8.6-16.8). Based on multivariate analysis, previous treatment with TNF antagonists or thiopurines (hazard ratio [HR], 3.86; 95% CI, 1.82-8.18), Clostridioides difficile infection (HR, 3.73; 95% CI, 1.11-12.55), serum level of C-reactive protein above 30 mg/L (HR, 3.06; 95% CI, 1.11-8.43), and serum level of albumin below 30 g/L (HR, 2.67; 95% CI, 1.20-5.92) were associated with increased risk of colectomy. In the derivation cohort, the cumulative risks of colectomy within 1 y in patients with scores of 0, 1, 2, 3, or 4 were 0.0%, 9.4% (95% CI, 4.3%-16.7%), 10.6% (95% CI, 5.6%-17.4%), 51.2% (95% CI, 26.6%-71.3%), and 100%. Negative predictive values ranged from 87% (95% CI, 82%-91%) to 92% (95% CI, 88%-95.0%). Findings from the validation cohort were consistent with findings from the derivation cohort. CONCLUSIONS: We developed a scoring system to identify patients at low-risk vs high-risk for colectomy within 1 y of hospitalization for ASUC, based on previous treatment with TNF antagonists or thiopurines, C difficile infection, and serum levels of CRP and albumin. The system was validated in an external cohort.

Increased incidence of systemic serious viral infections in patients with inflammatory bowel disease associates with active disease and use of thiopurines.

Background: The magnitude and drivers of the risk of serious viral infections in Inflammatory Bowel diseases (IBD) are unclear. Objective: The objective of this study was to assess the incidence and risk factors for systemic serious viral infections in IBD patients. Methods: Using MICISTA, a database detailing prospective characteristics and complications of IBD, we identified patients that were followed for IBD in 2005-2014 outside the context of organ transplantation, HIV infection or chronic viral hepatitis. We estimated incidences of systemic serious viral infections, defined by the need for hospitalization or permanent organ damage. Standardized incidence ratios (SIRs) were calculated using the French hospital database. We performed a case-control study nested in MICISTA for assessing the role of exposure to IBD drugs and IBD clinical activity in the risk of developing infection. Results: We identified 31 patients with serious viral infections among 2645 patients followed for 15,383 person-years. We observed 13 cases of cytomegalovirus, 10 Epstein-Barr virus, 5 varicella zoster virus and 3 herpes simplex virus infections. No deaths occurred. The incidence rate of infections in patients with IBD was 2.02/1000 person-years, and the SIR was 3.09 (95% confidence interval (CI), 1.98-4.20; p = 0.0002) in the study population. By multivariate analysis, increased risk of infection was associated with exposure to thiopurines (odds ratio (OR), 3.48; 95% CI, 1.36-8.90; p = 0.009), and clinically active IBD at onset of infection (OR, 3.35; 95% CI, 1.23-9.23; p = 0.02). Conclusions: The incidence of systemic serious viral infections in patients with IBD is tripled compared to general population. Clinically active IBD and exposure to thiopurines are the main drivers of the risk.

Increased risk of permanent stoma in Crohn's disease associated with hidradenitis suppurativa: a case-control study.

BACKGROUND: Crohn's disease (CD) and hidradenitis suppurativa (HS), a chronic inflammatory skin disease, induce similar inflammatory lesions of the groin and gluteal area. Both diseases are characterised by an inadequate immune response to commensal bacteria in genetically predisposed subjects and can be associated. AIM: To assess whether HS was associated with clinical and prognostic factors in CD. METHODS: A retrospective case-control study included 4645 patients with CD referred to Saint-Antoine Hospital gastroenterology tertiary care centre between 2003 and 2016. Matching variables were sex, age, age and the presence of perianal lesions at CD diagnosis, follow-up quality. HS was confirmed by dermatological examination; location, phenotype and severity (Hurley staging) were recorded. RESULTS: Hidradenitis suppurativa prevalence was 0.95% (44 cases); 80% of patients displayed Hurley stage II or III disease. CD preceded HS in 70% of cases with a median interval of 9 years (IQR 5.25-12.75). CD with HS was more active (56% vs 40% years with active disease, P < 0.001) and required more anti-TNF agents (39% vs 23% years spent with anti-TNF treatment, P < 0.001) than CD without HS. HS was associated with a higher risk of permanent stoma, 16.8% (IQR 7.5-33.3) vs 2.5% (IQR 0.8-7.4) in the control group (P = 0.002). Multivariate analysis confirmed HS as independent risk factor for permanent stoma (odds ratio 6.19; 95% CI, 2.30-38.33; P < 0.001). CONCLUSIONS: Hidradenitis suppurativa is associated with worse CD prognosis, more active disease and increased risk of permanent stoma, despite a higher use of anti-TNF agents.

Fecal microbiota transplantation to maintain remission in Crohn's disease: a pilot randomized controlled study.

BACKGROUND: The role of the gut microbiota in Crohn's disease (CD) is established and fecal microbiota transplantation (FMT) is an attractive therapeutic strategy. No randomized controlled clinical trial results are available. We performed a randomized, single-blind, sham-controlled pilot trial of FMT in adults with colonic or ileo-colonic CD. METHOD: Patients enrolled while in flare received oral corticosteroid. Once in clinical remission, patients were randomized to receive either FMT or sham transplantation during a colonoscopy. Corticosteroids were tapered and a second colonoscopy was performed at week 6. The primary endpoint was the implantation of the donor microbiota at week 6 (Sorensen index > 0.6). RESULTS: Eight patients received FMT and nine sham transplantation. None of the patients reached the primary endpoint. The steroid-free clinical remission rate at 10 and 24 weeks was 44.4% (4/9) and 33.3% (3/9) in the sham transplantation group and 87.5% (7/8) and 50.0% (4/8; one patient loss of follow-up while in remission at week 12 and considered in flare at week 24) in the FMT group. Crohn's Disease Endoscopic Index of Severity decreased 6 weeks after FMT (p = 0.03) but not after sham transplantation (p = 0.8). Conversely, the CRP level increased 6 weeks after sham transplantation (p = 0.008) but not after FMT (p = 0.5). Absence of donor microbiota engraftment was associated with flare. No safety signal was identified. CONCLUSION: The primary endpoint was not reached for any patient. In this pilot study, higher colonization by donor microbiota was associated with maintenance of remission. These results must be confirmed in larger studies (NCT02097797). Video abstract.

Nancy Index Scores of Chronic Inflammatory Bowel Disease Activity Associate With Development of Colorectal Neoplasia.

BACKGROUND & AIMS: The degree of histologic and endoscopic disease activity has been associated with an increased risk of colorectal neoplasia (CRN) in patients with inflammatory bowel diseases (IBDs), but no histologic scoring systems have been validated for determining risk of CRN. We investigated the association between histologic and endoscopic disease activity and risk of first CRN in patients with IBD who had negative findings from a surveillance colonoscopy. METHODS: We performed a retrospective analysis of consecutive patients who underwent at least 2 colonoscopies at Saint Antoine Hospital in France from January 1, 1996, through March 1, 2015, and whose first procedure was a surveillance colonoscopy. Histologic IBD activity was assessed by the Nancy histologic index. Patients were followed up for a mean 5.7 ± 3.3 years. Logistic regression and generalized estimating equations were used to identify clinical, endoscopic, and histologic factors associated with detection of neoplasia in the inflamed colon mucosa. RESULTS: Among 398 patients who underwent 1277 colonoscopies, we identified 45 patients with CRN. Factors associated with CRN were primary sclerosing cholangitis (odds ratio [OR], 2.65; 95% CI, 1.06-6.61; P = .04), age (OR per 1-year increase, 1.04; 95% CI, 1.01-1.07; P = .003), and mean Nancy histologic index during follow-up evaluation (per 1-unit increase, OR, 1.69; 95% CI, 1.29-2.21; P < .001). After adjustment for established factors, chronic disease activity defined as detection of ulcerations at more than 50% of colonoscopies was not associated with an increased risk of CRN (OR, 1.24; 95% CI, 0.53-2.91; P = .62). CONCLUSIONS: In addition to established risk factors, we associated Nancy histologic index scores with development of CRN. Histologic findings based on the Nancy histologic index therefore should be included in determining the risk of colonic neoplasia in patients with IBD.

Impact of Aphthous Colitis at Diagnosis on Crohn's Disease Outcomes.

BACKGROUND: The natural history of intestinal lesions in Crohn's disease [CD] is not fully understood. Although the extent of lesions at diagnosis usually defines the extent of the disease, some lesions seen at diagnosis, particularly aphthous ulcers [AUs], may resolve before follow-up. The aim of this study was to evaluate the outcomes of CD patients with colonic AUs seen at diagnosis. METHODS: CD patients with aphthous colitis at diagnosis who had been followed since 2001 were included in a case control study matched with two groups of controls: one without colonic involvement at diagnosis and a second group with colonic lesions more severe than AUs at diagnosis. RESULTS: Seventy-five patients were included, with a median follow-up of 7.3 years [interquartile range 2.7-9.8]. Seventy-one per cent of those having a second colonoscopy at least 6 months after diagnosis were stable or healed. Medical treatments were similar between the three groups. The AU group's rate of ileal surgery was similar to those without colitis. In multivariate analysis, the independent factors associated with ileal resection were ileal involvement (odds ratio [OR]: 8.8; 95% confidence interval [CI] [7.68-33.75]; p = 0.002) and the presence of severe colitis (OR = 0.5; 95% CI [0.32-0.79], p = 0.003). The risk of ileal surgery was not influenced by the presence of aphthous colitis (OR: 0.63; 95% CI [0.37-1.1]; p = 0.1). CONCLUSION: Aphthous colitis at diagnosis seems to resolve in most patients. This suggests that these lesions are of little clinical significance and may not need to be considered prior to ileal resection in CD or when making other important therapeutic decisions.

Clinical activity is an independent risk factor of ischemic heart and cerebrovascular arterial disease in patients with inflammatory bowel disease.

BACKGROUND AND AIMS: In inflammatory bowel disease (IBD), the impact of established cardiovascular risk factors and disease-related factors on the risk of acute arterial events is still unclear. We aimed to identify risk factors of acute arterial events in patients with IBD. METHODS: All consecutive patients followed at Saint-Antoine Hospital between 1996 and 2015 with subsequent occurrence of acute arterial events (acute coronary syndrome or ischemic stroke) were identified. Traditional cardiovascular risk factors, treatment exposure, systemic inflammation (mean serum CRP level greater than or equal to 5 mg/L) and IBD clinical activity were assessed. A nested case-control study was performed including cases and controls without arterial ischemic event, matched on age, gender, and disease extent. RESULTS: A total of 30 patients (median age at acute vascular event occurrence: 42 years (interquartile range: 25-59)) developed acute coronary syndrome (n = 22) or ischemic stroke (n = 8). In univariate analysis, clinical disease activity and the persistence of systemic inflammation, diabetes, dyslipidemia and hypertension were significantly associated with an increased risk of acute arterial events. Neither protective nor aggravating effects associated with treatment exposure were identified. In multivariate analysis, the presence of diabetes (Odds ratio (OR): 14.5, 95% confidence interval (CI): 1.1-184.7) and clinical disease activity (OR: 10.4, 95% CI: 2.1-49.9) remained significantly associated with the risk of acute arterial event. CONCLUSION: Disease activity may have an independent impact on the risk of acute arterial events in patients with IBD. These findings may highlight new potential benefits of optimizing anti-inflammatory treatment in patients with persisting clinical activity.

Inter-kingdom effect on epithelial cells of the N-Acyl homoserine lactone 3-oxo-C12:2, a major quorum-sensing molecule from gut microbiota.

BACKGROUND AND AIMS: N-acyl homoserine lactones (AHLs), which are autoinducer quorum-sensing molecules involved in the bacterial communication network, also interact with eukaryotic cells. Searching for these molecules in the context of inflammatory bowel disease (IBD) is appealing. The aims of our study were to look for AHL molecules in faecal samples from healthy subjects (HS) and IBD patients to correlate AHL profiles with the microbiome and investigate the effect of AHLs of interest on epithelial cells. METHODS: Using mass spectrometry, we characterised AHL profiles in faecal samples from HS (n = 26) and IBD patients in remission (n = 24) and in flare (n = 25) and correlated the presence of AHLs of interest with gut microbiota composition obtained by real-time qPCR and 16S sequencing. We synthesised AHLs of interest to test the inflammatory response after IL1ß stimulation and paracellular permeability on Caco-2 cells. RESULTS: We observed 14 different AHLs, among which one was prominent. This AHL corresponded to 3-oxo-C12:2 and was found significantly less frequently in IBD patients in flare (16%) and in remission (37.5%) versus HS (65.4%) (p = 0.001). The presence of 3-oxo-C12:2 was associated with significantly higher counts of Firmicutes, especially Faecalbacterium prausnitzii, and lower counts of Escherichia coli. In vitro, 3-oxo-C12:2 exerted an anti-inflammatory effect on Caco-2 cells. Interestingly, although 3-oxo-C12, the well-known AHL from Pseudomonas aeruginosa, increased paracellular permeability, 3-oxo-C12:2 did not. CONCLUSIONS: We identified AHLs in the human gut microbiota and discovered a new and prominent AHL, 3-oxo-C12:2, which correlates with normobiosis and exerts a protective effect on gut epithelial cells.

Specificities of the intestinal microbiota in patients with inflammatory bowel disease and Clostridium difficile infection.

Clostridium difficile infection (CDI) is a common complication in inflammatory bowel disease (IBD) and has been associated with poor IBD outcome. Intestinal microbiota composition in IBD patients with CDI has not been specifically evaluated to date. The fecal microbiota of 56 IBD patients, including 8 in flare with concomitant CDI, 24 in flare without CDI, and 24 in remission, as well as 24 healthy subjects, was studied using 16S sequencing. Analysis was performed using the Qiime pipeline. Compared to IBD patients without CDI, IBD patients with CDI had more pronounced dysbiosis with higher levels of Ruminococcus gnavus and Enterococcus operational taxonomic units (OTUs) and lower levels of Blautia and Dorea OTUs. Correlation network analysis suggested a disrupted ecosystem in IBD patients in flare, particularly in those with CDI. In patients with IBD, CDI is associated with a more pronounced intestinal dysbiosis with specific alterations in intestinal microorganisms.

Clostridium difficile infection in acute flares of inflammatory bowel disease: A prospective study.

OBJECTIVES: Clostridium difficile infection (CDI) is a common complication in inflammatory bowel disease (IBD) and has been associated with poor IBD outcome. The aims of our study were to look for predictive factors of CDI in patients hospitalized for IBD flare and to evaluate a rapid testing strategy in this population. METHODS: Consecutive patients hospitalized for IBD flare in Saint-Antoine Hospital (Paris, France) were prospectively tested for CDI with a defined strategy involving rapid testing and reference methods. Risk factors for CDI were investigated and performances of diagnostic tests were evaluated. RESULTS: C. difficile testing was performed at admission in 461 hospitalizations for IBD flare. CDI was diagnosed in 35 cases (7.6%) and non-toxigenic C. difficile was identified in 10 cases (2.2%). In multivariate analysis, UC phenotype was associated with CDI (OR 2.2, 95% CI 1.03-4.6, p=0.047). Glutamate dehydrogenase (GDH) test had a 97.1% sensitivity and a 100% negative predictive value for CDI diagnosis but a positive predictive value of 79.1%. Enzyme immunoassay (EIA)-based toxin detection (C. Diff Quik Chek complete®, Alere) had a poor sensitivity and diagnosis was rescued by toxin PCR in 100% of cases. CONCLUSION: CDI is frequent in patients hospitalized for IBD flare. Clinical parameters do not help for the diagnosis and rapid testing should be performed in all patients. Currently, a negative result of an EIA-based toxin search associated with a positive GDH test cannot rule out a CDI and should not delay initiation of specific treatment in case of severe symptoms or high presumption.

Fungal microbiota dysbiosis in IBD.

OBJECTIVE: The bacterial intestinal microbiota plays major roles in human physiology and IBDs. Although some data suggest a role of the fungal microbiota in IBD pathogenesis, the available data are scarce. The aim of our study was to characterise the faecal fungal microbiota in patients with IBD. DESIGN: Bacterial and fungal composition of the faecal microbiota of 235 patients with IBD and 38 healthy subjects (HS) was determined using 16S and ITS2 sequencing, respectively. The obtained sequences were analysed using the Qiime pipeline to assess composition and diversity. Bacterial and fungal taxa associated with clinical parameters were identified using multivariate association with linear models. Correlation between bacterial and fungal microbiota was investigated using Spearman's test and distance correlation. RESULTS: We observed that fungal microbiota is skewed in IBD, with an increased Basidiomycota/Ascomycota ratio, a decreased proportion of Saccharomyces cerevisiae and an increased proportion of Candida albicans compared with HS. We also identified disease-specific alterations in diversity, indicating that a Crohn's disease-specific gut environment may favour fungi at the expense of bacteria. The concomitant analysis of bacterial and fungal microbiota showed a dense and homogenous correlation network in HS but a dramatically unbalanced network in IBD, suggesting the existence of disease-specific inter-kingdom alterations. CONCLUSIONS: Besides bacterial dysbiosis, our study identifies a distinct fungal microbiota dysbiosis in IBD characterised by alterations in biodiversity and composition. Moreover, we unravel here disease-specific inter-kingdom network alterations in IBD, suggesting that, beyond bacteria, fungi might also play a role in IBD pathogenesis.

Understanding Microbiome Data: A Primer for Clinicians.

The human gut contains 1014 bacteria and many other micro-organisms such as Archaea, viruses and fungi. This gut microbiota has co-evolved with host determinants through symbiotic and co-dependent relationships. Bacteria, which represent 10 times the number of human cells, form the most depicted part of this black box owing to new tools. Re-evaluating the gut microbiota showed how this entity participates in gut physiology and beyond this in human health. Studying and handling this real 'hidden organ' remains a challenge for clinicians. In this review, we aimed to bring information about gut microbiota, its structure, its roles and the way to capture and measure it. After bacterial colonization in infant, intestinal microbial composition is unique for each individual although more than 95% can be assigned to 4 major phyla. Besides its biodiversity, the major characteristics of gut microbiota are stability over time and resilience after perturbation. In pathological situations, dysbiosis (i.e. imbalance in gut microbiota composition) is observed with a loss in overall diversity. Dysbiosis associated with inflammatory bowel disease was specified with the reduction in biodiversity, the decreased representation of different taxa in the Firmicutes phylum and an increase in Gammaproteobacteria. Beyond depicting gut microbial composition, metagenomics allows the description of the combined genomes of the microorganisms present in the gut, giving access to their potential functions. In fact, each individual overall microbial metagenome outnumbers the size of human genome by a factor of 150. Besides a functional core in which there is redundancy for mandatory functions assuring the robustness of the ecosystem, human gut contains an important diversity and high number of non-redundant bacterial genes. Clinical data, treatment and all the factors able to influence microbiome should enter integrated big data sets to put in light pathways of interplay within the supra organism composed of gut microbiome and host. A better understanding of dynamics within human gut microbiota and microbes-host interaction will allow new insight into gut pathophysiology especially regarding resilience mechanisms and dysbiosis onset and maintenance. This will lead to description of biomarkers of diseases, development of new probiotics/prebiotics and new therapies.

Portomesenteric vein thrombosis in patients with inflammatory bowel disease.

BACKGROUND: Inflammatory bowel disease (IBD) is associated with a high risk of deep venous thromboembolism. However, few data are available so far on portomesenteric vein thrombosis (PMVT). The aim of this study was to describe the characteristics of PMVT in patients with IBD. METHODS: A retrospective study was conducted at 13 GETAID (Groupe d'Etude Thérapeutique des Affections Inflammatoires du Tube Digestif) centers from January 1995 to June 2010. The following data were collected, using a standardized questionnaire: characteristics of IBD, disease status at the time of PMVT, PMVT characteristics and mode of discovery, concomitant prothrombotic disorders, anticoagulant therapy, and evolution of PMVT. RESULTS: Fifty cases (29 men and 21 women; median age, 41 years) were identified, including 14 patients with ulcerative colitis and 36 with Crohn's disease. Thirty-one patients (62%) presented with acute PMVT. Twenty-four patients had previously undergone surgical treatment, and IBD was active in 23 cases (77%) of acute thrombosis. The discovery of PMVT was fortuitous in 40% of our cases. Among the 43 patients screened for a prothrombotic disorder, abnormalities were observed in 17 patients (40%) (mainly hyperhomocysteinemia, n = 12). Forty-four patients (88%) were treated with anticoagulants. Recanalization of the vein was significantly more successful in patients with acute thrombosis (65% versus 37%, P = 0.05). CONCLUSIONS: PMVT can occur when IBD is inactive, and its diagnosis was fortuitous in 40% of our cases. Screening for prothrombotic disorders is essential because it is positive in more than one third of cases.