David Kevans

Association of host genome with intestinal microbial composition in a large healthy cohort

Intestinal microbiota is known to be important in health and disease. Its composition is influenced by both environmental and host factors. Few large-scale studies have evaluated the association between host genetic variation and the composition of microbiota. We recruited a cohort of 1,561 healthy individuals, of whom 270 belong in 123 families, and found that almost one-third of fecal bacterial taxa were heritable. In addition, we identified 58 SNPs associated with the relative abundance of 33 taxa in 1,098 discovery subjects. Among these, four loci were replicated in a second cohort of 463 subjects: rs62171178 (nearest gene UBR3) associated with Rikenellaceae, rs1394174 (CNTN6) associated with Faecalibacterium, rs59846192 (DMRTB1) associated with Lachnospira, and rs28473221 (SALL3) associated with Eubacterium. After correction for multiple testing, 6 of the 58 associations remained significant, one of which replicated. These results identify associations between specific genetic variants and the gut microbiome.

Characterization of Intestinal Microbiota in Ulcerative Colitis Patients with and without Primary Sclerosing Cholangitis

BACKGROUND AND AIMS There is an unexplained association between ulcerative colitis [UC] and primary sclerosing cholangitis [PSC], with the intestinal microbiota implicated as an important factor. The study aim was to compare the structure of the intestinal microbiota of patients with UC with and without PSC. METHODS UC patients with PSC [PSC-UC] and without PSC [UC] were identified from biobanks at Oslo University Hospital, Foothills Hospital Calgary and Mount Sinai Hospital Toronto. Microbial DNA was extracted from colonic tissue and sequencing performed of the V4 region of the 16S rRNA gene on Illumina MiSeq. Sequences were assigned to operational taxonomic units [OTUs] using Quantitative Insights Into Microbial Ecology [QIIME]. Microbial alpha diversity, beta diversity, and relative abundance were compared between PSC-UC and UC phenotypes. RESULTS In all, 31 PSC-UC patients and 56 UC patients were included. Principal coordinate analysis [PCoA] demonstrated that city of sample collection was the strongest determinant of taxonomic profile. In the Oslo cohort, Chao 1 index was modestly decreased in PSC-UC compared with UC [p = 0.04] but did not differ significantly in the Calgary cohort. No clustering by PSC phenotype was observed using beta diversity measures. For multiple microbial genera there were nominally significant differences between UC and PSC-UC, but results were not robust to false-discovery rate correction. CONCLUSIONS No strong PSC-specific microbial associations in UC patients consistent across different cohorts were identified. Recruitment centre had a strong effect on microbial composition. Future studies should include larger cohorts to increase power and the ability to control for confounding factors.

Determinants of Intestinal Permeability in Healthy First-Degree Relatives of Individuals with Crohnʼs Disease

Background:The Genetics, Environmental, Microbial Project is a multicenter study assessing etiological factors in Crohns disease by studying healthy first-degree relatives (FDRs) of individuals affected by Crohns disease. We aimed to evaluate the contribution of genetic, microbial, and environmental factors to the determination of intestinal permeability in healthy FDRs. Methods:IP was assessed using the lactulose-mannitol ratio (LacMan ratio). FDRs were genotyped for 167 inflammatory bowel disease-associated single nucleotide polymorphisms. Taxonomic profile of the fecal microbiota was determined by Illumina MiSeq pyrosequencing of 16S ribosomal RNA. The associations of LacMan ratio with demographic factors, inflammatory bowel disease-associated single nucleotide polymorphisms and the fecal microbiota were assessed. Results:One hundred ninety-six white FDRs were included. Eleven percent of FDRs had an elevated LacMan ratio (≥0.03). A multivariate analysis demonstrated that younger subjects and nonsmokers had higher LacMan ratios, P = 3.62 × 10−4 and P = 0.03, respectively. The LacMan ratio was not significantly heritable, H2r, 0.13, P = 0.13. There was no association between any of the 167 inflammatory bowel disease-associated risk variants and LacMan ratio nor was there a correlation between fecal microbial composition and the LacMan ratio. Conclusions:We did not find LacMan ratio to be significantly heritable suggesting that the contribution of genetic factors to the determination of intestinal permeability in healthy FDRs is modest. Environmental factors, such as smoking, are likely more important determinants. The effect of age on intestinal barrier function has been underappreciated.

IBD Genetic Risk Profile in Healthy First-Degree Relatives of Crohn's Disease Patients.

BACKGROUND Family history provides important information on risk of developing inflammatory bowel disease [IBD], and genetic profiling of first-degree relatives [FDR] of Crohns disease [CD]- affected individuals might provide additional information. We aimed to delineate the genetic contribution to the increased IBD susceptibility observed in FDR. METHODS N = 976 Caucasian, healthy, non-related FDR; n = 4997 independent CD; and n = 5000 healthy controls [HC]; were studied. Genotyping for 158 IBD-associated single nucleotide polymorphisms [SNPs] was performed using the Illumina Immunochip. Risk allele frequency [RAF] differences between FDR and HC cohorts were correlated with those between CD and HC cohorts. CD and IBD genetic risk scores [GRS] were calculated and compared between HC, FDR, and CD cohorts. RESULTS IBD-associated SNP RAF differences in FDR and HC cohorts were strongly correlated with those in CD and HC cohorts, correlation coefficient 0.63 (95% confidence interval [CI] 0.53 - 0.72), p = 9.90 x 10(-19). There was a significant increase in CD-GRS [mean] comparing HC, FDR, and CD cohorts: 0.0244, 0.0250, and 0.0257 respectively [p < 1.00 x 10(-7) for each comparison]. There was no significant difference in the IBD-GRS between HC and FDR cohorts [p = 0.81]; however, IBD-GRS was significantly higher in CD compared with FDR and HC cohorts [p < 1.00 x 10(-10) for each comparison]. CONCLUSION FDR of CD-affected individuals are enriched with IBD risk alleles compared with HC. Cumulative CD-specific genetic risk is increased in FDR compared with HC. Prospective studies are required to determine if genotyping would facilitate better risk stratification of FDR.

Genetics and Innate and Adaptive Immunity in IBD

Inflammatory bowel disease (IBD) is an abnormal inflammatory response within the gut to a trigger that has yet to be identified. The family history in many patients, especially those with Crohns disease, suggests a genetic predisposition. It has been hypothesized that the abnormal inflammatory response is due in part to genetic alterations in the normal homeostatic processes that regulate host interactions with the normal gut microbes. Genetic studies have identified increasing numbers of genetic risk factors that involve a diverse series of pathways such as receptors of innate immune response, defects in epithelial barrier function, immune- and cytokine-related genes and genes involved in autophagy. Studies further suggest that abnormal immune responses in IBD patients are directed against the intestinal microbiota, with activation of both innate and adaptive immune responses. Indeed, studies have shown bacterial-derived antigen as drivers of T cell immune responses. More recently, Th17, regulatory T cells and unconventional innate-like T cells have been implicated in the induction and regulation of intestinal inflammation. The seminal discoveries of pathogen recognition receptors including Toll-like receptors and nucleotide-binding oligomerization domain receptors have changed our understanding of how immune cells respond to microbes and the role this may play in IBD pathogenesis. Understanding these mechanism will lead to new strategies in the treatment and prevention of IBD.

Serological markers associated with disease behavior and response to anti‐tumor necrosis factor therapy in ulcerative colitis

Information is limited on the relationship between serological markers and disease behavior and anti‐tumor necrosis factor‐α (anti‐TNF) therapy response in ulcerative colitis (UC). This study aimed to determine the association between serological markers and unfavorable UC behavior defined as need for colectomy or UC‐related hospitalization. The association between serological markers and requirement for and outcome of anti‐TNF therapy was also evaluated.

Sa1234 RNA-Seq Derived Whole Blood Gene Expression Signature As a Biomarker for Differential Diagnosis and Intestinal Inflammation in Inflammatory Bowel Disease

Introduction: In the last two decades the therapeutic paradigm of Crohns disease (CD) has changed dramatically thanks to the use of biological drugs. In this scenario, we must consider the pivotal role of tumor necrosis factor-alpha (TNF-α), a pro-inflammatory cytokine, in the pathogenesis and relapse of CD. High levels of TNF-α have been associated with the development of intestinal inflammation in CD and blocking this cytokine with anti-TNF-α molecules may result in mucosal healing. In addition several studies have shown increased TNF-α levels in the serum and in the intestinal mucosa of patients with CD. However, little is known about the course of TNF-α levels and their relationship with disease recurrence in CD patients during maintenance treatment with Adalimumab. Aim: We assessed TNF-α levels in patients with CD who were in maintenance treatment with ADA and correlated them with clinical and endoscopic disease activity. Methods: In this prospective observational cohort study, performed at a single tertiary referral center, 23 [14M/9F; mean age 41 (range 21-66) infliximab-Naive patients with CD in maintenance treatment with ADA were included and followed-up. Blood samples were drawn at standardized time points (i.e. at 6, 12, 18, 24 months and in case of CD relapse) just before ADA injection. Antibodies against ADA (AAA) were measured using an homogenous mobility shift assay (HMSA; Prometheus Lab, San Diego, United States). Blood samples were considered positive for AAA presence if ≥1.7 U/mL. Disease activity was assessed at the same points by means of the Harvey-Bradshaw Index (HBI, remission 16). Moreover, endoscopic activity was assessed at baseline and at the time of relapse by means of CD endoscopic index (CDEIS 5 responder, CDEIS<3 complete endoscopic remission and mucosal healing). Results: We have data from 133 blood samples. AAA were observed in 26/133 (19.5%) samples, and 10/26 (38.5%) had a value of AAA ≥1.7 U/mL. TNF-α levels were present in all samples assessed (Mean 4.4, range 027.2). As shown in the figure, per-patient median TNF-α levels were strongly correlated with median HBI scores (r2=0.702, p<0.0001). Moreover, TNF levels were also correlated with CDEIS (r2=0.350, p=0.001). Conclusion: TNF-α levels strongly correlated with disease activity based on HBI and CDEIS indices in patients with CD in maintenance treatment with ADA. Indeed, moderate to severe patients often have high sustained TNF-α levels.

Accelerated Clearance of Infliximab is Associated With Treatment Failure in Patients With Corticosteroid-Refractory Acute Ulcerative Colitis

Background and Aims A significant proportion of patients with corticosteroid-refractory acute ulcerative colitis [UC] fail therapy. We aimed to assess the pharmacokinetics [PK] of infliximab [IFX] in patients with corticosteroid-refractory acute UC and determine the association between induction IFX PK and short- and long-term therapy outcome. Methods A population PK model was developed using data from 51 patients with UC [n = 42] and Crohns disease [n = 9]. A subset of patients [n = 36] with acute corticosteroid-refractory UC (median Mayo score 11 [range 8-12]; 33 of 36 hospitalized; median corticosteroid dose at study entry 50mg prednisolone equivalent IV/oral) commencing IFX were studied to assess further correlations between PK from the first induction dose and therapy outcomes. Serial induction drug levels from the 36 UC patients were collected, facilitating population-based PK analysis. IFX and antibodies-to-infliximab [ATIs] concentrations were determined using AnsrTM IFX assay [Prometheus Inc.]. Results The Week 14 clinical response and Week 54 corticosteroid-free remission rates were 78% [28/36] and 53% [19/36], respectively. The estimated effective IFX half-life [T1/2] (median [range]) and clearance (median [range]) were 8.42 [3.94-22.03] days and 0.50 [0.19-1.41] L/day respectively. Longer induction IFX T1/2 and lower clearance were associated with the Week 14 clinical response [p = 0.005] and the Week 54 corticosteroid-free remission rates [p = 0.007]. Conclusions Accelerated IFX clearance occurs in corticosteroid-refractory acute UC and is associated with therapy failure. These data support the use of accelerated IFX induction regimens in patients with corticosteroid-refractory acute UC failing conventional dosing regimens.

Mo1324 Association of a Panel of Anti-Microbial Antibodies With Disease Behavior and Response to Anti-TNF Therapy in a Cohort of Patients With Ulcerative Colitis

Infliximab is highly efficacious in induction as well as maintenance of remission in patients with Crohns disease (CD). However, the cost and potential serious side-effects is concerning for continuing the medication on a long-term. Primary aim of this meta-analysis was to determine the outcome in patients with CD in whom infliximab was discontinued while in remission. Secondary aim was to assess the results of re-treatment with anti-TNF agents following a relapse and identify the factors associated with a relapse. MethodsWe searched Medline, Scopus, conference proceedings and Google scholar for Infliximab related trials in Crohns disease. Studies where the information on status of remission prior to discontinuation of infliximab was unclear or the clinical outcome following the discontinuation of infliximab was unavailable were excluded. For studies which provided complete data over at least 3 years, the median remission rate was calculated using Kaplan-Meier method. For studies which provided median remission rate, an average of the remission rates was calculated. ResultsA total of 398 patients in six different studies were included in the final analysis. The average relapse rates over 1st, 2nd, 3rd, 4th and 6th year following the cessation of infliximab were 35%, 48%, 62%, 69% and 76% respectively. The results of Kaplan-Meier analysis for the 4 studies (219 patients) with detailed data over at least 3 years data are given in Table-1. Following relapse, retreatment with infliximab results in remission in 91100% (89 patients). Medication reaction following retreatment with infliximab occurred in only one patient. ConclusionMajority of patients who discontinue infliximab while in remission will relapse and most relapses will occur in first 3 years following cessation of infliximab. Retreatment with infliximab is however favorable and risk of re-treatment reaction is not increased. Kaplan Meier Statistics