Large-scale sequencing identifies multiple genes and rare variants associated with Crohn's disease susceptibility

Genome-wide association studies (GWASs) have identified hundreds of loci associated with Crohn's disease (CD). However, as with all complex diseases, robust identification of the genes dysregulated by noncoding variants typically driving GWAS discoveries has been challenging. Here, to complement GWASs and better define actionable biological targets, we analyzed sequence data from more than 30,000 patients with CD and 80,000 population controls. We directly implicate ten genes in general onset CD for the first time to our knowledge via association to coding variation, four of which lie within established CD GWAS loci. In nine instances, a single coding variant is significantly associated, and in the tenth, ATG4C, we see additionally a significantly increased burden of very rare coding variants in CD cases. In addition to reiterating the central role of innate and adaptive immune cells as well as autophagy in CD pathogenesis, these newly associated genes highlight the emerging role of mesenchymal cells in the development and maintenance of intestinal inflammation.

Accelerated waning of immunity to SARS-CoV-2 mRNA vaccines in patients with immune-mediated inflammatory diseases

BACKGROUNDLimited information is available on the impact of immunosuppressants on COVID-19 vaccination in patients with immune-mediated inflammatory diseases (IMID).METHODSThis observational cohort study examined the immunogenicity of SARS-CoV-2 mRNA vaccines in adult patients with inflammatory bowel disease, rheumatoid arthritis, ankylosing spondylitis, or psoriatic disease, with or without maintenance immunosuppressive therapies. Ab and T cell responses to SARS-CoV-2, including neutralization against SARS-CoV-2 variants, were determined before and after 1 and 2 vaccine doses.RESULTSWe prospectively followed 150 subjects, 26 healthy controls, 9 patients with IMID on no treatment, 44 on anti-TNF, 16 on anti-TNF with methotrexate/azathioprine (MTX/AZA), 10 on anti-IL-23, 28 on anti-IL-12/23, 9 on anti-IL-17, and 8 on MTX/AZA. Ab and T cell responses to SARS-CoV-2 were detected in all participants, increasing from dose 1 to dose 2 and declining 3 months later, with greater attrition in patients with IMID compared with healthy controls. Ab levels and neutralization efficacy against variants of concern were substantially lower in anti-TNF-treated patients than in healthy controls and were undetectable against Omicron by 3 months after dose 2.CONCLUSIONSOur findings support the need for a third dose of the mRNA vaccine and for continued monitoring of immunity in these patient groups.FUNDINGFunded by a donation from Juan and Stefania Speck and by Canadian Institutes of Health (CIHR)/COVID-Immunity Task Force (CITF) grants VR-1 172711 and VS1-175545 (to THW and ACG), CIHR FDN-143250 (to THW), GA2-177716 (to VC, ACG, and THW), and GA1-177703 (to ACG) and the CIHR rapid response network to SARS-CoV-2 variants, CoVaRR-Net (to ACG).

The Toronto IBD Global Endoscopic Reporting [TIGER] Score: A Single, Easy to Use Endoscopic Score for Both Crohn's Disease and Ulcerative Colitis Patients

BACKGROUND AND AIMS

We constructed the Toronto IBD Global Endoscopic Reporting [TIGER] score for inflammatory bowel disease [IBD]. The aim of our study was to develop and validate the TIGER score against faecal calprotectin [FC], C-reactive protein [CRP], and IBD Disk.

METHODS

A cross-sectional study was performed among 113 adult patients (60 Crohn's disease [CD] and 53 ulcerative colitis [UC]). In the development and usability phase, blinded IBD experts reviewed and graded ileocolonoscopy videos. In the validity phase the TIGER score was compared with: [1] the Simple endoscopic Score for CD [SES-CD] and the Mayo endoscopic score in CD and UC, respectively; [2] FC and CRP; and [3] IBD Disk.

RESULTS

Inter-observer reliability of the TIGER score per segment between reviewers was excellent: interclass correlation coefficient [ICC] = 0.94 [95% CI: 0.92-0.96]. For CD patients, overall agreement per segment between SES-CD and TIGER was 91% [95% CI: 84-95] with kappa coefficient 0.77 [95% CI: 0.63-0.91]. There was a significant correlation between TIGER and CRP [p <0.0083], and TIGER and FC [p <0.0001]. In addition, there was significant correlation between TIGER and IBD Disk [p <0.0001]. For UC patients, overall agreement per segment between Mayo endoscopic score and TIGER was 84% [95% CI: 74%-90%] and kappa coefficient 0.60 [95% CI: 0.42-0.808]. There was a significant correlation between TIGER and FC [p <0.0001]. There was a significant correlation between TIGER and IBD Disk [p <0.0001].

CONCLUSIONS

The TIGER score is a reliable and simple novel endoscopic score that can be used for both CD and UC patients and captures full endoscopic disease burden.

The Toronto IBD Global Endoscopic Reporting [TIGER] Score: A Single, Easy to Use Endoscopic Score for Both Crohn's Disease and Ulcerative Colitis Patients

BACKGROUND AND AIMS

We constructed the Toronto IBD Global Endoscopic Reporting [TIGER] score for inflammatory bowel disease [IBD]. The aim of our study was to develop and validate the TIGER score against faecal calprotectin [FC], C-reactive protein [CRP], and IBD Disk.

METHODS

A cross-sectional study was performed among 113 adult patients (60 Crohn's disease [CD] and 53 ulcerative colitis [UC]). In the development and usability phase, blinded IBD experts reviewed and graded ileocolonoscopy videos. In the validity phase the TIGER score was compared with: [1] the Simple endoscopic Score for CD [SES-CD] and the Mayo endoscopic score in CD and UC, respectively; [2] FC and CRP; and [3] IBD Disk.

RESULTS

Inter-observer reliability of the TIGER score per segment between reviewers was excellent: interclass correlation coefficient [ICC] = 0.94 [95% CI: 0.92-0.96]. For CD patients, overall agreement per segment between SES-CD and TIGER was 91% [95% CI: 84-95] with kappa coefficient 0.77 [95% CI: 0.63-0.91]. There was a significant correlation between TIGER and CRP [p <0.0083], and TIGER and FC [p <0.0001]. In addition, there was significant correlation between TIGER and IBD Disk [p <0.0001]. For UC patients, overall agreement per segment between Mayo endoscopic score and TIGER was 84% [95% CI: 74%-90%] and kappa coefficient 0.60 [95% CI: 0.42-0.808]. There was a significant correlation between TIGER and FC [p <0.0001]. There was a significant correlation between TIGER and IBD Disk [p <0.0001].

CONCLUSIONS

The TIGER score is a reliable and simple novel endoscopic score that can be used for both CD and UC patients and captures full endoscopic disease burden.

Time to Revisit Disease Classification in Inflammatory Bowel Disease: Is the Current Classification of Inflammatory Bowel Disease Good Enough for Optimal Clinical Management?

Inflammatory bowel disease (IBD), historically subdivided into Crohn's disease and ulcerative colitis, is a very heterogeneous condition. While the tendency in medicine is to try to reduce complexity, IBD is a disease that cannot justify a one-size-fits-all principle. Our current clinical classification tools are suboptimal and need further refinement to capture, at least in part, the variety of phenotypes encountered in daily clinical practice. Although these revised classification tools alone will not be sufficient and should be complemented by more detailed molecular subclassifications, optimized clinical phenotypes can contribute to improved trial designs, future translational research approaches, and better treatment outcomes. In the current review, we discuss key clinical features important in IBD disease heterogeneity, tackle limitations of the current classification systems, propose some potential improvements, and raise priorities for future research in this domain.

A235 ILEAL MICROBIOME ALPHA DIVERSITY REMAINS LOWER IN ENDOSCOPICALLY AND HISTOLOGICALLY INACTIVE CROHN’S DISEASE COMPARED TO ULCERATIVE COLITIS OR HEALTHY CONTROLS

Background

Crohn’s disease (CD) has been associated with a lower alpha diversity when compared to ulcerative colitis (UC) patients and healthy controls (HC), which also depends on disease location and endoscopic activity. However, it is unclear whether the resolution of histologic inflammation may influence mucosal alpha diversity in the ileum.

Aims

To characterize the ileal mucosa-associated microbiome diversity in subjects with ileal predominant CD (iCD) in endoscopic (ER) and endo-histologic (EHR) remission, compared to subjects with colonic predominant CD (cCD), UC and HC, respectively.

Methods

Data from a large cohort of subjects recruited at Mount Sinai Hospital Toronto (2009–2016) was analyzed. ER was defined as a segmental Simple Endoscopic Score for CD of &lt;3 in the ileum. EHR was defined as ER with the absence of active histologic inflammation in ileal biopsies. CD patients were divided according to the Montreal classification into iCD (L1 and L3) and cCD (L2) and compared against UC patients without backwash ileitis and HC. Patients with history of ileocecal resection and/or antibiotic use at baseline were excluded. Microbial 16S rRNA gene was sequenced using the Illumina MiSeq and processed using QIIME2. Alpha diversity was measured using the Shannon index and compared using Kruskal-Wallis test and further pairwise Wilcoxon with Holm correction. An adjusted p-value &lt; 0.05 was considered significant.

Results

We included 35 CD patients with ileal ER, 81 UC patients and 32 HC. Among CD patients, 20/35 (57.1%) and 15/35 (42.9%) had iCD and cCD, respectively. Ileal mucosal alpha diversity was significantly lower in iCD patients in ER compared with that of UC patients (q=0.004) and HC (q=0.001). No differences in ileal mucosal alpha-diversity were seen between iCD than cCD patients (q=0.12). When histology was included to classify CD and UC patients as EHR, the ileal alpha diversity of iCD patients remained reduced compared to UC patients and HC (q=0.008 and q=0.002, respectively). Again, ileal mucosal alpha-diversity was not significantly lower in iCD than cCD patients among those in ileal EHR (q=0.24).

Conclusions

Ileal mucosa of CD patients in ER and EHR have lower alpha diversity than UC and HC. These findings suggest that the ileal mucosa of CD patients remains dysbiotic despite achieving endoscopic and histologic remission.

Funding Agencies

IBD Genetics Consortium

A161 MUCOSAL TRANSCRIPTOMICS IN NON-INFLAMED ILEUM OF CROHN’S DISEASE PATIENTS SHOWS DIFFERENTIALLY EXPRESSED GENE PROFILE COMPARED TO ILEUM OF HEALTHY CONTROLS

Background

The terminal ileum is the most susceptible location to develop Crohn’s disease (CD) and therefore is a valuable tissue to investigate biological mechanisms underlying chronic inflammation. Gene expression is highly affected by the level of inflammation, however, data on ileal transcriptomic profile in the absence of active inflammation is limited.

Aims

To investigate the ileal mucosal transcriptomic profile of CD patients in endoscopic and histologic remission compared to healthy controls (HC).

Methods

Ileal biopsies were collected during colonoscopy from patients with CD and HC. Biopsies were classified as non-inflamed based on endoscopic appearance and histologic criteria. Endo-histologic remission (EHR) was defined as simple endoscopic score < 3 and absence of active histologic inflammation. We included CD patients with EHR and HC for the analysis of this study. CD phenotype was divided into isolated colonic CD (cCD) that included Montreal L2 and ileal predominant CD (iCD) that included Montreal L1 and L3. Total RNA was extracted from samples, sequenced using a HiSeq 2500 instrument (Illumina, San Diego, CA, USA) and differential expression analysis was performed in EdgeR. Genes that were differentially expressed at the average of 2-fold-change (FC) in mean expression and False Discovery Rate (FDR) < 0.05 were considered significant.

Results

Ileal samples from 14 CD patients in EHR and 29 HC were included in the analysis. CD patients were significantly younger (median age 28.5 years, interquartile range (IQR)=24–40) compared with HC (median age 56 years, IQR=51–64). There were no differences in gender distribution (42.9% males in CD and 55.2% males in HC). We found 101 differentially expressed genes in CD patients compared to HC (99 genes were up-regulated and two were down-regulated). Dual oxidase 2 (DUOX2) and complement C6 were respectively the most significant up-regulated (logFC=4.45, FDR=1.3e-8) and down-regulated (logFC=-2.73, FDR=0.0006) genes in non-inflamed ileum CD group when compared with HC. In a subgroup analysis comparing ileal samples of CD patients with cCD (n=8) versus iCD phenotype (n=6), no differentially expressed genes were identified.

Conclusions

The mucosal transcriptomic profile of patients with inactive endoscopic and histologic ileal CD shows significant differentially expressed gene profile compared to ileal mucosa of HC. The clinical relevance of these findings should be further investigated.

Funding Agencies

IBD Genetics Consortium

A156 MUCOSA-ASSOCIATED MICROBIOTA OF ILEOCOLONIC CROHN’S DISEASE PATIENTS IS DISTINCT FROM COLONIC CROHN’S DISEASE AND ULCERATIVE COLITIS PATIENTS INDEPENDENT OF BIOPSY SITE, ENDOSCOPIC INFLAMMATION AND HOST GENETICS

Background

Colonic IBD encompassing ulcerative colitis (UC) and isolated colonic Crohn’s disease (cCD) shows significant clinical, therapeutic response and genetic differences compared to ileocolonic CD (icCD). Elucidating the microbial signatures characterizing these subphenotypes could help to understand the causal factors underlying these clinical dissimilarities

Aims

We compared the mucosal microbial diversity and differential abundance (DA) among disease locations (UC, cCD and icCD) accounting for potential clinical, endoscopic, and genetic confounders

Methods

Healthy control (HC), UC, cCD and icCD patients (including ileal and ileocolonic involvement) underwent colonoscopy. Biopsy samples were obtained from terminal ileum (TI), ascending colon (AC) and sigmoid colon (SC) for 16s rRNA gene profiling. Patients with prior ileocecal resection, IBD-unclassified and antibiotic exposure within 3 months before colonoscopy were excluded. Endoscopic inflammation was defined as a segmental Mayo endoscopic subscore = 0 in UC and a simple endoscopic score ≤ 2 in CD. A blood sample was drawn for genotyping and a weighted genetic risk score (GRS) was built based on 169 IBD risk variants found in our cohort. Alpha diversity (Chao1) and DA between IBD subphenotypes were compared using a linear mixed-effects model with subjects as random effect and adjusted for biopsy site, endoscopic inflammation, age, sex, and GRS. For DA analysis, the MaAsLin2 protocol was applied. All p-values were corrected by false discovery rate (FDR) with < 0.05 considered significant

Results

A total of 199 IBD patients and 44 HC with a mean age of 37.2 ± 14 were recruited. Of these, 113 (46.5%) were female. At colonoscopy, 535 biopsy samples (TI = 178, AC = 123 and SC = 234) were obtained. Considering disease location, 254, 55 and 148 samples were obtained from UC, cCD and icCD patients, respectively. A total of 168 samples (31.4%) showed endoscopic inflammation. Alpha diversity was significantly reduced in icCD when compared to either HC, UC or cCD. MaAsLin2 identified that the genera Agathobacter and Faecalibacterium, as well as the family Ruminococacceae and the order Oscillospirales were significantly reduced in icCD when compared to either HC, UC or cCD. These findings were independent of age, sex, endoscopic inflammation, biopsied site, and GRS. UC and cCD did not show differences in their microbial profile

Conclusions

Mucosal samples from UC and cCD patients showed marked similarities in their microbial profile while icCD is characterized by a significant decrease in diversity and beneficial microbes. These data suggest that disease location is the main driver of the mucosal microbial landscape independent of IBD GRS

Funding Agencies

NoneNIDDK IBD Genetics Consortium

A236 ASSOCIATION OF STOOL METABOLOMIC PROFILE AND MICROBIOME COMPOSITION RISK SCORE WITH FUTURE ONSET OF CROHN’S DISEASE

Background

Microbial composition-based risk score (MRS) was recently developed and validated to predict future risk of developing Crohn’s disease (CD) among healthy first-degree relatives (FDR) of CD patients. We hypothesized that stool metabolomic profiles, some of which are linked to the gut microbiome, are associated with future risk of CD.

Aims

To assess the association of stool metabolomic profile with onset of CD and to determine the correlation between stool metabolites and the MRS

Methods

Healthy FDR of CD patients were recruited as part of the nested case-control cohort of the CCC-GEM Project. Healthy FDRs who later developed CD (n=56) were matched approximately 1:1 by age, sex, follow-up duration, and geographical location with control FDRs remaining healthy (n=66). Stool metabolomics were assessed using the Metabolon’s DiscoveryHD4™ platform, and the stool microbiome characterised by 16s rDNA amplicon sequencing. We fitted a multivariable conditional logistic regression model on the disease status as a function of individual stool metabolites. We additionally performed Spearman correlation between each stool metabolite and the MRS.

Results

Among 1,029 stool metabolites that were analyzed, 79 were associated with future risk of CD (p&lt;0.05); however, none remained significant after multiple testing correction (FDR correction). Considering the exploratory nature of this study with limited sample size, we focused on the top seven metabolites associated with CD onset (p&lt;0.01). Of these, two stool metabolites (dimethylglycine, methylmyristate) were associated with increased risk of CD onset while five (cytosine, guanine, cytidine, hydroxyglutarate, nervonate) were associated with decreased risk of developing CD. The two metabolites positively associated with CD onset were positively correlated with the MRS, while the five metabolites negatively associated with CD onset, were negatively correlated with the MRS. Meanwhile, 24 stool metabolites had significant correlation with MRS (FDR-corrected p&lt;0.2). Among those, a total of four stool metabolites (cytosine, guanine, methymyristate, cytidine) overlapped with the top seven stool metabolites associated with CD onset.

Conclusions

Stool metabolite profiles may predict future risk of CD. A subset of these metabolites have significant correlation with the MRS with consistent direction of effect. This may suggest that stool metabolites mediate the putative effect of the gut microbiome on CD risk. Further validation in the full GEM cohort is warranted.

Funding Agencies

CCC, CIHRThe Leona M. and Harry B. Helmsley Charitable Trust; Kenneth Croitoru is the recipient of the Canada Research Chair in Inflammatory Bowel Diseases; Sun-Ho Lee is a recipient of the Imagine/ CIHR/CAG Fellowship Award; Sun-Ho Lee, Juan Antonio Raygoza Garay, and Williams Turpin are recipients of fellowship awards from the Department of Medicine, Mount Sinai Hospital, Toronto, Canada.

Patients With Low Drug Levels or Antibodies to a Prior Anti-Tumor Necrosis Factor Are More Likely to Develop Antibodies to a Subsequent Anti-Tumor Necrosis Factor

Therapeutic drug monitoring (TDM) with measurement of serum drug and antidrug antibodies (ADAb) is used widely to confirm therapeutic exposure, rule out immunogenicity, and optimize treatment of biologics in patients with inflammatory bowel diseases.¹ A recent genome-wide association study found the variant HLA-DQA1∗05 to increase the risk of development of antibodies against infliximab (IFX) and adalimumab (ADM) 2-fold, regardless of concomitant immunomodulator use.^2,3 However, there is currently limited evidence showing whether patients who develop antibodies to 1 anti-tumor necrosis factor (TNF) are prone to develop antibodies to the subsequent anti-TNF. Our aim was to investigate the risk of subsequent antibody development in cases (with ADAb to prior anti-TNF) versus control subjects (without ADAb to prior anti-TNF) using a large cohort of patients with inflammatory bowel diseases who underwent TDM with a drug-tolerant assay.

Combined Histo-endoscopic Remission but not Endoscopic Healing Alone in Ulcerative Colitis is Associated with a Mucosal Transcriptional Profile Resembling Healthy Mucosa

BACKGROUND AND AIMS

A composite endpoint of histological and endoscopic remission is proposed to be the most complete measure of mucosal healing in ulcerative colitis [UC]. We aim to establish the prognosis, and transcriptional and microbial features of histo-endoscopic remission and activity.

METHODS

A cross-sectional endoscopic rectosigmoid colon sample collection from UC patients and healthy controls [HC] was performed for histopathology and host genome-wide RNA-sequencing. Histo-endoscopic remission and histo-endoscopic activity were defined as Mayo endoscopic subscore [MES] 0-1 with and without histological activity, respectively. UC relapse, defined as symptomatic and endoscopic worsening, was retrospectively recorded for survival analysis. Unsupervised and differential gene expression analyses were performed, and the interaction between transcriptomics and mucosal gut microbiota was analysed based on the 16S rRNA gene sequencing profile.

RESULTS

UC patients with histo-endoscopic remission showed a significantly lower risk of relapse compared to histo-endoscopic activity. Unsupervised analysis of the transcriptomic profile showed that histo-endoscopic remission and histo-endoscopic activity samples clustered with HC and MES 2-3 samples, respectively. A total of 452 host genes enriched for humoral immune response, antimicrobial defence, chemokine and TH17 signalling pathway were upregulated in histo-endoscopic activity compared to histo-endoscopic remission. A set of host genes with antimicrobial properties showed significant associations with mucosal microbiota.

CONCLUSIONS

The rectosigmoid mucosa transcriptional profile of UC patients in histo-endoscopic remission resembles that of HC mucosa and confers a lower risk of relapse. These data support that the combination of histo-endoscopic remission could be the most appropriate definition of mucosal healing in UC.

Serum Analyte Profiles Associated With Crohn's Disease and Disease Location

BACKGROUND

Crohn's disease (CD) can affect any segment of the digestive tract but is most often localized in the ileal, ileocolonic, and colorectal regions of the intestines. It is believed that the chronic inflammation in CD is a result of an imbalance between the epithelial barrier, the immune system, and the intestinal microbiota. The aim of the study was to identify circulating markers associated with CD and/or disease location in CD patients.

METHODS

We tested 49 cytokines, chemokines, and growth factors in serum samples from 300 patients with CD and 300 controls. After quality control, analyte levels were tested for association with CD and disease location.

RESULTS

We identified 13 analytes that were higher in CD patients relative to healthy controls and that remained significant after conservative Bonferroni correction (P < 0.0015). In particular, CXCL9, CXCL1, and interleukin IL-6 had the greatest effect and were highly significant (P < 5 × 10-7). We also identified 9 analytes that were associated with disease location, with VEGF, IL-12p70, and IL-6 being elevated in patients with colorectal disease (P < 3 × 10-4).

CONCLUSIONS

Multiple serum analytes are elevated in CD. These implicate the involvement of multiple cell types from the immune, epithelial, and endothelial systems, suggesting that circulating analytes reflect the inflammatory processes that are ongoing within the gut. Moreover, the identification of distinct profiles according to disease location supports the existence of a biological difference between ileal and colonic CD, consistent with previous genetic and clinical observations.

Treatment of pouchitis, Crohn's disease, cuffitis, and other inflammatory disorders of the pouch: consensus guidelines from the International Ileal Pouch Consortium

Pouchitis, Crohn's disease of the pouch, cuffitis, polyps, and extraintestinal manifestations of inflammatory bowel disease are common inflammatory disorders of the ileal pouch. Acute pouchitis is treated with oral antibiotics and chronic pouchitis often requires anti-inflammatory therapy, including the use of biologics. Aetiological factors for secondary pouchitis should be evaluated and managed accordingly. Crohn's disease of the pouch is usually treated with biologics and its stricturing and fistulising complications can be treated with endoscopy or surgery. The underlying cause of cuffitis determines treatment strategies. Endoscopic polypectomy is recommended for large, symptomatic inflammatory polyps and polyps in the cuff. The management principles of extraintestinal manifestations of inflammatory bowel disease in patients with pouches are similar to those in patients without pouches.

Anti-Microbial Antibody Response is Associated With Future Onset of Crohn's Disease Independent of Biomarkers of Altered Gut Barrier Function, Subclinical Inflammation, and Genetic Risk

BACKGROUND AND AIMS

Altered host immune reactivity to microbial antigens is hypothesized to trigger the onset of Crohn's disease (CD). We aimed to assess whether increased serum anti-microbial antibody response in asymptomatic first-degree relatives (FDRs) of CD patients is an independent risk factor for future CD development.

METHODS

We measured host serum antibody response to 6 microbial antigens at enrollment (Prometheus enzyme-linked immunosorbent assay test: anti-Saccharomyces cerevisiae antibodies immunoglobulin A/immunoglobulin G, anti-OmpC, anti-A4-Fla2, anti-FlaX, anti-CBir1) and derived the sum of positive antibodies (AS). We used samples at enrollment of prospectively followed healthy FDRs from a nested case-control cohort of the Crohn's and Colitis Canada Genetics Environment Microbial Project. Those who later developed CD (n = 77) were matched 1:4 by age, sex, follow-up duration, and geographic location with control FDRs remaining healthy (n = 307). To address our research aims, we fitted a multivariable conditional logistic regression model and performed causal mediation analysis.

RESULTS

High baseline AS (≥2) (43% of cases, 11% of controls) was associated with higher risk of developing CD (adjusted odds ratio, 6.5; 95% confidence interval, 3.4-12.7; P < .001). Importantly, this association remained significant when adjusted for markers of gut barrier function, fecal calprotectin, C-reactive protein, and CD-polygenic risk score, and in subjects recruited more than 3 years before diagnosis. Causal mediation analysis showed that the effect of high AS on future CD development is partially mediated (42%) via preclinical gut inflammation.

CONCLUSIONS

Our results suggest that increased anti-microbial antibody responses are associated with risk of future development of CD, independent of biomarkers of abnormal gut barrier function, subclinical inflammation, and CD-related genetic risks. This suggests that anti-microbial antibody responses are an early predisease event in the development of CD.

A Role for CXCR3 Ligands as Biomarkers of Post-Operative Crohn's Disease Recurrence

BACKGROUND AND AIMS

Crohn's disease [CD] recurrence following ileocolic resection [ICR] is common. We sought to identify blood-based biomarkers associated with CD recurrence.

METHODS

CD patients undergoing ICR were recruited across six centres. Serum samples were obtained at post-operative colonoscopy. A multiplex immunoassay was used to analyse 92 inflammation-related proteins [Olink Proteomics]. Bayesian analysis was used to identify proteins associated with increasing Rutgeerts score. Identified proteins were used in receiver operating characteristic [ROC] analysis to examine the ability to identify CD recurrence [Rutgeerts score ≥i2]. Existing single cell data were interrogated to further elucidate the role of the identified proteins.

RESULTS

Data from 276 colonoscopies in 213 patients were available. Median time from surgery to first and second colonoscopy was 7 (interquartile range [IQR] 6-9) and 19 [IQR 16-23] months, respectively. Disease recurrence was evident at 60 [30%] first and 36 [49%] second colonoscopies. Of 14 proteins significantly associated with Rutgeerts score, the strongest signal was seen for CXCL9 and MMP1. Among patients on anti-tumour necrosis factor drugs, CXCL9 and CXCL11 were most strongly associated with Rutgeerts score. Both are CXCR3 ligands. Incorporation of identified proteins into ROC analysis improved the ability to identify disease recurrence as compared to C-reactive protein alone: area under the curve [AUC] 0.75 (95% confidence interval [CI]: 0.66-0.82] vs 0.64 [95% CI 0.56-0.72], p = 0.012. Single cell transcriptomic data provide evidence that innate immune cells are the primary source of the identified proteins.

CONCLUSIONS

CXCR3 ligands are associated with CD recurrence following ICR. Incorporation of novel blood-based candidate biomarkers may aid in identification of CD recurrence.

Post-Induction High Adalimumab Drug Levels Predict Biological Remission at Week 24 in Patients With Crohn's Disease

INTRODUCTION

We investigated whether early adalimumab drug levels (ADL) at week 4 predicted biological remission at week 24.

METHODS

In a prospective study, we assessed clinical and biological remission at weeks 0, 4, 12, and 24 after induction of adalimumab in 33 patients with Crohn's disease. Disease activity was determined by the Harvey-Bradshaw Index, ileocolonoscopy reports, cross-sectional imaging, C-reactive protein (CRP), and fecal calprotectin (FC) levels. Clinical remission was defined as Harvey-Bradshaw Index <5. Biological remission was defined as a combination of FC < 200 μg/g and CRP <5 μg/mL. ADL trough levels were tested using a liquid phase, mobility shift assay.

RESULTS

At 24 weeks, 18/33 (55%) of the patients were with biological remission. Ten (30%) patients required dose escalation or withdrawal from adalimumab by week 24 because of lack of response and exhibited significantly higher FC (P = 0.003) and CRP (P = 0.002). ADL levels at week 4 (19.8 μg/mL vs 10.2 μg/mL, P = 0.001) were significantly higher in patients with biological remission vs nonresponders at week 24. ADL levels at week 4 were a good predictor of biological remission at week 24, with area under the curve 0.86, 95% confidence interval (1.1; 1.67) and for combined biological and clinical remission, with area under the curve 0.8. The best ADL cutoff at week 4 that predicted biological remission at week 24 was 13.9 μg/mL (sensitivity 94.4% and specificity 73.3%).

DISCUSSION

In individuals with Crohn's disease, higher adalimumab drug levels at week 4 (>13.9 μg/mL) were significantly associated with biological remission at week 24.

Comparative effectiveness of higher adalimumab maintenance therapy versus standard dose in anti-tumor necrosis factor experienced Crohn's disease patients: A propensity-score matched cohort analysis

BACKGROUND AND AIM

Crohn's disease (CD) patients who previously failed anti-tumor necrosis factor (TNF) therapy are at higher risk of treatment failure with subsequent biologics. This study aims to determine the effectiveness and safety of higher maintenance dose regimens of adalimumab compared with standard doses in CD patients who failed anti-TNF.

METHODS

In this retrospective observational study, CD patients who failed anti-TNF and received adalimumab were categorized according to their post-induction maintenance regimen; 40 mg subcutaneous (sc) weekly or 80 mg sc every other week were defined as a high-dose (HD) maintenance regimen, and 40 mg sc every other week was defined as a standard-dose (SD) maintenance regimen. The primary outcome was time to treatment failure. Cox proportional hazards regression was used to adjust for confounders. Sensitivity analysis was conducted using propensity scores to create a cohort of matched participants with similar distribution of baseline covariates.

RESULTS

Forty patients started on HD regimens following induction, and 77 patients received the SD regimen. The median time to failure in the HD group was 6.6 years (interquartile range [IQR] 4.0-9.6) and 3.0 years (IQR 0.9-9.4) in the SD group (log-rank test P = 0.006). Patients on HD adalimumab had a lower hazard rate of treatment failure (hazard ratio: 0.27; 95% confidence interval [0.12, 0.62]; P = 0.002) compared with SD patients. No difference in adverse events was identified between groups (30% vs 31.2%, P = 1.0). Results were similar in the propensity score-matched cohort.

CONCLUSIONS

High-dose maintenance regimens were associated with longer time-to-failure as compared with SD regimens in CD patient who failed anti-TNF.

Higher adalimumab maintenance regimen is more effective than standard dose in anti-TNF experienced Crohn's disease patients

BACKGROUND

Many Crohn's disease patients treated with anti-tumor necrosis factor (TNF) therapies suffer from loss of response over time and require dose escalation. The aim of this study was to evaluate the efficacy and safety of treating anti-TNF experienced Crohn's disease patients with higher maintenance regimens of adalimumab.

METHODS

In a retrospective observational study, Crohn's disease patients receiving adalimumab were categorized according to their maintenance regimen; 40 mg weekly, 80 mg every other week or greater were defined as a high-dose maintenance regimen and 40 mg every other week was defined as a standard maintenance regimen. The primary outcome was time to treatment failure.

RESULTS

Thirty-nine patients were started on high-dose regimens following induction and 40 patients received the standard regimen. According to a Kaplan-Meier survival curve analysis, time to treatment failure was significantly longer in patients in the high-dose group (P = 0.0015). Patients on high-dose adalimumab had a lower treatment failure rate (hazard ratio 0.21; P = 0.0005) when compared to patients on the standard regimen, after adjusting for induction dose and concomitant immunomodulator use. No difference in adverse events was identified between the groups (31 vs. 30%; P = 0.94).

CONCLUSION

High-dose maintenance regimens were more effective than the standard adalimumab maintenance protocol with better short and long-term clinical outcomes.

Diagnosis and classification of ileal pouch disorders: consensus guidelines from the International Ileal Pouch Consortium

Restorative proctocolectomy with ileal pouch-anal anastomosis is an option for most patients with ulcerative colitis or familial adenomatous polyposis who require colectomy. Although the construction of an ileal pouch substantially improves patients' health-related quality of life, the surgery is, directly or indirectly, associated with various structural, inflammatory, and functional adverse sequelae. Furthermore, the surgical procedure does not completely abolish the risk for neoplasia. Patients with ileal pouches often present with extraintestinal, systemic inflammatory conditions. The International Ileal Pouch Consortium was established to create this consensus document on the diagnosis and classification of ileal pouch disorders using available evidence and the panellists' expertise. In a given individual, the condition of the pouch can change over time. Therefore, close monitoring of the activity and progression of the disease is essential to make accurate modifications in the diagnosis and classification in a timely manner.

Early Changes in Serum Albumin Predict Clinical and Endoscopic Outcomes in Patients With Ulcerative Colitis Starting Anti-TNF Treatment

BACKGROUND

Up to 60% of patients with ulcerative colitis (UC) ultimately fail anti-tumor necrosis factor (TNF) treatment. We aimed to investigate early predictive markers of clinical and endoscopic outcomes in patients with UC who were anti-TNF-naïve commencing anti-TNF treatment, with particular focus on changes in albumin and C-reactive protein levels in the first 2 weeks of treatment.

METHODS

We retrospectively investigated 210 patients with UC who started infliximab or adalimumab between 2009 and 2016 (male, 62.4%; median age at diagnosis, 37.9 years [interquartile range, 25.5-48.9 years]; median follow-up duration, 3.3 years [1.9-5.0 years]). Logistic and Cox proportional-hazards regressions were performed to identify variables associated with primary nonresponse (PNR), endoscopic outcomes, time-to-colectomy, and anti-TNF failure.

RESULTS

Forty-one patients (19.5%) experienced PNR; week 0/week 2 ratio serum albumin was associated with PNR (adjusted odds ratio [aOR], 1.8; 95% confidence interval [CI], 1.1-2.9, per interquartile range increase). Week 0/week 2 ratio albumin was also associated with endoscopic response (aOR, 0.28; 95% CI, 0.31-0.82) and endoscopic remission (aOR, 0.61; 95% CI, 0.39-0.96) at weeks 8 to 14, time-to-colectomy (adjusted hazard ratio, 2.12; 95% CI, 1.29-3.49) and time-to-anti-TNF failure (adjusted hazard ratio, 1.54; 95% CI, 1.22-1.96), regardless of age, disease severity, or in-patient status. Association with time-to-colectomy and anti-TNF failure was externally validated in an independent cohort of inpatients with UC starting infliximab.

CONCLUSIONS

Change in serum albumin within the first 2 weeks of anti-TNF treatment is predictive of PNR, endoscopic outcomes, time-to-colectomy, and anti-TNF failure in patients with UC. Timely access to this biomarker enables early identification of patients with UC at risk of anti-TNF failure and may guide early optimization of anti-TNF treatment to improve disease outcomes.

Serum Ustekinumab Concentrations Are Associated With Remission in Crohn's Disease Defined by a Serum-Based Endoscopic Healing Index

Background

Optimal ustekinumab levels (UST) in Crohn disease (CD) treatment have not been defined. We set out to define the optimal UST to differentiate between remission and active CD, as defined using the serum-based endoscopic healing index (EHI).

Methods

Paired serum UST and EHI tests were analyzed. Remission was defined as EHI <20. Active disease was defined as EHI ≥50. The proportion of patients in remission was compared across UST quartiles. UST in subjects with EHI <20 and EHI ≥50 were compared. An area under receiver operating characteristic curve was generated to identify an optimal UST to differentiate between active disease and remission.

Results

A total of 337 unique patients were identified; median UST and EHI were 5.0 µg/mL [interquartile range (IQR) 2.7-9.1] and 37 (IQR 26-53), respectively. EHI <20 (remission) was found in 57 (16.9%) patients. EHI ≥50 (active disease) was found in 97 (28.8%) patients. Higher proportions of subjects were in remission for increasing UST quartiles, P = 0.01. Median UST in patients with EHI <20 and EHI ≥50 were 7.5 µg/mL (IQR 4.6-10.9) and 3.1 µg/mL (IQR 1.8-6.6), respectively, P < 0.001. An UST threshold of 3.75 µg/mL optimally differentiated between active disease and remission (area under the curve 0.725). UST levels >3.75 µg/mL were associated with a lower proportion of subjects with active disease (EHI ≥50; 18.9%) compared with UST levels ≤3.75 µg/mL (45.6%, P < 0.001).

Conclusions

Using the EHI, we identified a threshold UST level of 3.75 µg/mL to optimally differentiate between active and quiescent CD. These data suggest that UST serum concentrations of >3.75 µg/mL are optimally associated with endoscopic remission in CD.

Integrative Analysis of Colonic Biopsies from Inflammatory Bowel Disease Patients Identifies an Interaction Between Microbial Bile Acid-inducible Gene Abundance and Human Angiopoietin-like 4 Gene Expression

BACKGROUND AND AIMS

Microbial-derived bile acids can modulate host gene expression, and their faecal abundance is decreased in active inflammatory bowel disease [IBD]. We analysed the impact of endoscopic inflammation on microbial genes involved in bile acid biotransformation, and their interaction with host transcriptome in the intestinal mucosa of IBD patients.

METHODS

Endoscopic mucosal biopsies were collected from non-inflamed and inflamed terminal ileum, ascending and sigmoid colon of IBD patients. Prediction of imputed metagenome functional content from 16S rRNA profile and real-time quantitative polymerase chain reaction [qPCR] were utsed to assess microbial bile acid biotransformation gene abundance, and RNA-seq was used for host transcriptome analysis. Linear regression and partial Spearman correlation accounting for age, sex, and IBD type were used to assess the association between microbial genes, inflammation, and host transcriptomics in each biopsy location. A Bayesian network [BN] analysis was fitted to infer the direction of interactions between IBD traits and microbial and host genes.

RESULTS

The inferred microbial gene pathway involved in secondary bile acid biosynthesis [ko00121 pathway] was depleted in inflamed terminal ileum of IBD patients compared with non-inflamed tissue. In non-inflamed sigmoid colon, the relative abundance of bile acid-inducible [baiCD] microbial genes was positively correlated with the host Angiopoietin-like 4 [Angptl4] gene expression. The BN analysis suggests that the microbial baiCD gene abundance could affect Angptl4 expression, and this interaction appears to be lost in the presence of inflammation.

CONCLUSIONS

Endoscopic inflammation affects the abundance of crucial microbial bile acid-metabolising genes and their interaction with Angptl4 in intestinal mucosa of IBD patients.

An expert consensus to standardise clinical, endoscopic and histologic items and inclusion and outcome criteria for evaluation of pouchitis disease activity in clinical trials

BACKGROUND

Pouchitis is a condition with large unmet medical needs and no approved therapies. Lack of validated instruments to measure disease activity and treatment response is a major barrier to drug development.

AIM

To conduct a modified RAND/University of California Los Angeles appropriateness process to produce a standardised assessment of pouchitis disease activity in clinical trials.

METHODS

A list of 164 items generated upon a systematic review and expert opinion were rated based on a 9-point scale (appropriate, uncertain and inappropriate), by a panel including 16 gastroenterologists, surgeons and histopathologists.

RESULTS

Items rated as appropriate to evaluate in pouchitis clinical trials were: (a) clinical: stool frequency and faecal urgency; (b) endoscopic: primary assessment in the pouch body according to the percentage of affected area (<50%, 50%-75% and >75%), evaluation of the presence of ulcers/erosions according to size (erosions <5 mm, ulcers ≥5 mm to 2 cm and large ulcers >2 cm) and ulcerated area (<10%, 10%-30% and >30%); (c) histologic: two biopsies from each segment, from the ulcer's edge when present, or endoscopically normal areas, assessment of lamina propria chronic inflammation, epithelial and lamina propria neutrophils, epithelial damage, erosions and ulcers; and (d) clinical trial inclusion/outcome criteria: minimum histologic disease activity for inclusion, a primary endpoint based on stool frequency and assessment of clinical, endoscopic and histologic response and remission. The overall majority of items surveyed (100/164) were rated 'uncertain'.

CONCLUSION

We conducted a RAND/UCLA appropriateness process to help inform measurement of pouchitis disease activity within clinical trials and foster the development of novel therapies.