bluuebunny/crossref_metadata_2025_split huggingface dataset:
OP17 Impact of phenotypic and genetic factors on Crohn’s Disease evolution in a cohort of 13,926 patients
Authors: Zhang Q , Fachal L , Shawky R , Parkes M , Anderson C , Raine T 
Published: May 2021

Abstract

Background
Patients with Crohn’s disease (CD) can develop complications including stricturing and penetrating disease [1, 2]. Although reliable baseline predictors of disease progression are urgently needed to inform management strategies, few studies have comprehensively explored the phenotypic and genetic determinants of disease progression in a sufficiently powered cohort.

Methods
We used data from 13,926 patients with CD in the UK IBD BioResource to investigate the effects of clinical phenotypes and genetics on CD progression. Median follow-up was 10.6 years and total follow-up was 193,033 patient-years. We applied the Montreal classification system to define disease as B1 (inflammatory), B2 (stricturing) and B3 (penetrating). Patients with B2 or B3 disease (N = 5,185) were compared to patients with B1 disease (N = 8,471) in a multivariate model fitted with both phenotype data and a polygenic score that we developed. Associations with q-values (false discovery rate adjusted p-values) less than 0.05 were defined as statistically significant.

Results
CD progression occurred over time from diagnosis (Figure 1). Consistent with previous findings, we confirmed factors including smoking, disease location and perianal disease were associated with disease progression [3] (Table 1). The impact of a genetic influence on disease progression was confirmed and shown to be independent of genetic effects on disease location [4]. Early prescription of medications showed a protective effect on disease progression: Infliximab, adalimumab and thiopurines significantly reduced the chance of B2/B3 progression when prescribed within two years of diagnosis. Additionally, we observed a decreased progression to B2/B3 disease in patients diagnosed recently (between 2012–2020) compared to those diagnosed before 2012. This finding persisted after conditioning on exposure to biologics and correcting for follow-up time and interval to first thiopurine prescription, and thus may be indicative of other improvements in standards of care in recent years.

Conclusion
Using a large, well-characterised cohort we confirm the importance of disease location, smoking status and genetics on disease progression. We highlight the positive impact of early medication prescription on disease progression and discover an independent signal relating to potential improvements in the standard of care in CD over time. These results create the framework for reliable predictors of CD progression that may better guide future CD management strategies.

References
OP31 RESTORE: Interim analysis of a Phase 2 study of QBECO SSI for the induction and maintenance of clinical and endoscopic remission in subjects with Moderate to Severe Crohn’s Disease
Authors: Bressler B , Marshall J K , Atkinson K , Sutcliffe S , Pankovich J , Jones M , Kalyan S , Gunn H 
Published: May 2021

Abstract

Background
Innate immune defects play a role in the pathogenesis of CD. Enhancing innate immune competency and restoring mucosal barrier function provide a novel approach to treat CD. QBECO SSI is a first-in-class immunotherapy designed to correct innate immune dysfunction underlying CD. This analysis is from subjects in the open label portion of a planned controlled trial. Objectives were to assess endoscopic response at Wks 16 and 26, and select the optimal induction timepoint for the RCT. Safety and treatment compliance were also evaluated.

Methods
20 pts with moderate-to-severe CD were enrolled and received QBECO SSI by sc injection every other day for up to 52 wks. Minimum eligibility: Simple Endoscopic Score for CD (SES-CD) ≥7 (ileitis ≥4), abdominal pain (AP) score &gt;21 (11-point scale) or liquid/very soft stools (SF) (BFS Type 6 or 7) &gt;10 for 7 consecutive days during screening. Pts were evaluated for clinical symptoms and endoscopy at Wks 16, 26, and 52. After evaluation at the induction period (Wk 26) pts could continue in maintenance up to Wk 52. Endoscopies were evaluated by central blinded read and pts reported daily symptoms. Endoscopic response defined as ≥50% reduction in SES-CD from baseline. Clinical remission defined as AP and SF ≤21.

Results
Mean age was 43.6 (SD 13.6) yrs; 60% men and 60% previously treated with biologics. Mean yrs since CD diagnosis was 14.4 (10.1), AP score 30.4 (15.8), SF score 36.2 (19.1) and mean SES-CD at baseline was 12.5 (6.7) indicating a more difficult to treat population. Endoscopic response rate by central read during the induction period was 30% (6/20) overall, 38% (3/8) for biologic naïve and 25% (3/12) biologic experienced pts (ITT analysis). Similar number of pts achieved endoscopic response at Wk 16 (4 pts) as 26 (3 pts). Mean SES-CD improved through Wk 26 with a 0.6 point greater reduction at Wk 26 compared to 16. Change in SES-CD from baseline in biologic naïve pts was -2.9 (5.8) at Wk 16 and -4.1 (6.7) at 26. Clinical remission was achieved by 45% (9/20) of pts at Wk 16 and 40% (8/20) at Wk 26; 16 pts continued into the maintenance phase of the study. By central evaluation, 13% (2/16) were in endoscopic response at Wk 52. QBECO SSI was very well tolerated. 8/20 (40%) pts reported AEs related to treatment. Most frequency reported related AE was injection site erythema (2/20, 10% pts). Majority of AEs were mild and no other related AE was reported by more than 1 patient.

Conclusion
Week 26 was the optimal endoscopic evaluation timepoint for QBECO SSI treatment and will be utilized in the larger RCT. Both biologics naïve and experienced patients showed response to QBECO SSI treatment by Weeks 26 and 52, with higher response rates in biologics naïve patients. QBECO SSI was well tolerated.
OP32 Stool microbiome communities predict remission in treatment-naïve Pediatric Crohn’s Disease patients
Authors: Verburgt C , Dunn K , Bielawski J , Otley A , Heyman M , Sunseri W , Shouval D , Levine A , de Meij T , Hyams J , Denson L , Kugathasan S , Benninga M , de Jonge W , Van Limbergen J 
Published: May 2021

Abstract

Background
Early relapse in paediatric Crohn’s Disease (CD) is associated with severe disease course that heavily impairs quality of life. Changes in gut microbiome composition have been linked to active CD and disease course. This has led to development of microbiome-based prediction models for diagnosis and response to treatment. Our aim was to identify community-level microbiome signatures of treatment-naïve children with mild-to-moderate CD who did not require anti-TNF or surgery at diagnosis, with the goal of predicting need for re-induction or treatment escalation within the first year after diagnosis.

Methods
We selected de novo, treatment-naïve paediatric CD patients from the RISK cohort(Gevers 2014). Taxonomic labels were assigned to the 16s rRNA amplicon data using QIIME and closed OTU-picking. A hierarchical Bayesian model for microbial community structure was used to learn how baseline gut microbiomes differed according to treatment outcome. Model predictions were assessed using a leave-one-out analysis. We compared 16S rRNA sequences of CD patients with non-IBD controls(Gevers 2014) and healthy siblings of CD patients(Turpin 2016).

Results
Metadata and 16S rRNA amplicon data were available from 197 stool samples of de novo paediatric CD patients from the RISK cohort. We selected 44 out of 197 samples of patients that were treatment-naïve. Prior to treatment, PCDAI scores were similar between patients reaching remission and those that did not at 6 months. Bayesian analysis characterized 4 assemblages that accounted for 93% of the posterior probability distribution. The Bayesian model on pre-treatment stool microbiomes was able to predict 6-month outcome of patients that maintained remission and those that did not from the pre-treatment microbiome in 81% and 75% of samples (AUC=0.79). When comparing CD samples to 28 non-IBD controls (many with GI symptoms but negative for IBD during endoscopy, e.g. Irritable Bowel Syndrome), 6 assemblages were characterized with 44% of distributions shared between groups (AUC=0.61). In contrast, in CD samples compared to 728 healthy sibling samples (with increased genetic susceptibility), shared distribution within 4 characterized assemblages was less than 1% (AUC=1).

Conclusion
A Bayesian approach predicted clinical course in treatment-naïve children with CD in the first year after diagnosis with high accuracy, when ensuring only treatment-naïve faecal samples in the analysis. This classification level is comparable to previous findings using mucosal samples. Further study is needed to validate these pre-treatment microbiome signatures of newly diagnosed paediatric CD patients to allow identification of patients with mild-to-moderate disease who are most likely to require treatment escalation.
OP34 AJM300, an Oral Antagonist of α4-Integrin, as induction therapy for patients with Moderately Active Ulcerative Colitis: A Phase 3, randomized, double-blind, placebo-controlled induction study
Authors: Watanabe M , Matsuoka K , Ohmori T , Nakajima K , Ishida T , Ishiguro Y , Kanke K , Kobayashi K , Hirai F , Watanabe K , Hibi T 
Published: May 2021

Abstract

Background
AJM300 (INN; carotegrast methyl), an orally active small molecule antagonist of the α4 subunit of α4β1/α4β7 integrins, demonstrated the efficacy and safety in patients with moderately active ulcerative colitis (UC) in a phase 2 study. The phase 3 study (NCT 03531892) of AJM300 as induction therapy was conducted in patients with moderately active UC.

Methods
Eligible patients were moderately active Japanese UC, defined as total Mayo Clinic scores (MCS) of 6–10, endoscopic subscores (ES) ≥2, and rectal bleeding subscores (RBS) ≥1, who had inadequate response or intolerance to oral 5-ASA. Followed by a 2-week single-blind placebo (PBO) run-in phase, patients were randomized 1:1 to receive AJM300 960 mg or PBO 3 times daily for 8 weeks. Responders or remitters were allowed to receive AJM300 960 mg again at the subsequent relapse (open-label). The primary endpoint was clinical response at week 8, defined as reduction of the MCS of ≥3-pts and ≥30%, reduction in RBS of ≥1-pt or RBS of ≤1, and ES ≤1.

Results
The randomized 203 patients had moderately active endoscopic evidence at baseline with median UC duration of 6.1 years and MCS of 7.8. For the primary endpoint, 45.1% (46/102) and 20.8% (21/101) of patients in the AJM300 and PBO groups, respectively, achieved clinical response at week 8 (OR=3.30 [95% CI, 1.73–6.29]; p=0.0003). Symptomatic remission, endoscopic improvement and endoscopic remission were also statistically significant for AJM300 vs PBO (Table). In case of episodic AJM300 treatment, AJM300 exhibited similar response to initial treatment. Overall, the incidence of AEs and serious AEs were similar between AJM300 and PBO. There were no deaths or cases of progressive multifocal leukoencephalopathy.

Conclusion
AJM300 induced clinical response as well as endoscopic remission with good tolerability. AJM300 may become a novel therapeutic option for patients who had inadequate response or intolerance to oral 5-ASA.
OP39 The effect of phenotype and genotype on the plasma proteome in patients with Inflammatory Bowel Disease
Authors: Bourgonje A R , Hu S , Spekhorst L M , Zhernakova D V , Vich Vila A , Li Y , Voskuil M D , van Berkel L A , Bley Folly B , Charrout M , Mahfouz A , Reinders M J T , van Heck J I P , Joosten L A B , Visschedijk M C , van Dullemen H M , Faber K N , Samsom J N , Festen E A M , Dijkstra G , Weersma R K 
Published: May 2021

Abstract

Background
Protein profiling in patients with inflammatory bowel diseases (IBD) for diagnostic and therapeutic purposes is underexplored. Assessment of interactions between genetics and the plasma proteome could lead to identification of novel disease-associated molecular pathways. In this study, we performed the largest gene-protein association analysis thus far in patients with IBD, taking into account relevant phenotypic covariates and integrating information from multiple biological data layers.

Methods
Ninety-two (92) inflammation-related proteins were quantified in plasma of 1,028 patients with IBD (567 Crohn’s disease [CD]; 461 ulcerative colitis [UC]) and 148 healthy individuals to assess proteome-phenotype associations. Both whole-exome sequencing (WES) and global screening array (GSA) data of 919 patients with IBD were included to study associations between over 8 million genetic variants and protein levels (protein quantitative trait loci [pQTL]). Cis-pQTLs were defined within ± 1 Mb of the region of each protein-coding gene center, whereas trans-pQTLs were outside of that region. After adjusting for phenotypic covariates, a step-wise conditional analysis was used to identify all independent pQTLs in CD and UC separately, followed by a meta-analysis. Intestinal mucosal RNA sequencing and fecal metagenomic data were used for complementary analyses.

Results
Thirty-four (34) proteins were differentially abundant between IBD and healthy individuals, of which 24 proteins independent of active inflammation. (Figure 1) Seventy-two (72) proteins were significantly associated to 14 phenotypic factors, including age, sex, medication use, and surgical history. (Figure 2) Fibroblast growth factor-19 (FGF-19) levels were decreased in CD patients with ileal disease or a history of ileocecal resection. Thirteen (13) novel cis-pQTL variants were identified and 10 replicated from previous studies, together affecting 21 different plasma proteins. One trans-pQTL variant of the FUT2 gene (rs602662) and two independent cis-pQTL variants of the CCL25 gene significantly affected plasma C-C motif chemokine ligand 25 (CCL25) levels. (Figure 3) Intestinal gene expression data revealed an overlapping cis-expression (e)QTL-variant (rs3745387) of the CCL25 gene. The FUT2 rs602662 trans-pQTL variant associated significantly with reduced abundances of multiple fecal butyrate-producing bacteria, including the genus Blautia and the species Faecalibacterium prausnitzii.

Conclusion
This study shows that both genotype and multiple disease phenotypes strongly associate with the plasma proteome in patients with IBD and identifies disease-associated pathways that may help to improve disease management in the future.
P010 GSDMB-mediated pyroptosis exacerbates intestinal inflammation by destroying intestinal epithelium in Crohn’s disease
Authors: Gong W , Liu P , Ren J 
Published: May 2021

Abstract

Background
Intestinal epithelial injury acts an essential role in the pathogenesis and development of Crohn’s disease (CD). Recent studies indicated that gasdermin D (GSDMD) mediated pyroptosis in intestinal epithelial cell (IEC) contributes to the epithelial injury during intestinal inflammation. However, how gasdermin B (GSDMB) mediated pyroptosis regulates intestinal epithelial injury in CD remains unknown.

Methods
We studied the characteristics of GSDMB mediated pyroptosis in CD patients and intestinal epithelial cells (Caco-2, HT-29 and primary IECs). The CD8+ T cells were extracted from intestinal mucosa of CD patients and health controls, and then co cultured with normal primary IECs to observe the pyroptosis of IECs. We further analyzed the CD8+ T cell subsets that promote pyroptosis in intestinal biopsies of CD patients. In addition, we screened out four single nucleotide polymorphism (SNP) of GSDMB that related to disease risk of CD in the public IBD exomes database (https://ibd.broadinstitute.org/), and investigated their effects on pyroptosis.

Results
GSDMB mediated pyroptosis was notably increased in intestinal mucosa of active human CD, and only existed in intestinal epithelial cells (Figure 1). Granzyme A (GrzA) initiated the killing results by the cleavage of GSDMB in intestinal epithelial cells, and interferon gamma (IFN-γ) up-regulated GSDMB expression in intestinal epithelial cells and promoted pyroptosis (Figure 2). GSDMB in primary IECs was significantly cleaved when co cultured with CD8+ T cells from active CD patients, while the phenomenon weakened a lot when GrzA in CD8+ T cells or GSDMB in epithelial cells was knocked down (Figure 3). We also found that IL26 possive CD8+ T cells were the main CD8+ T cells subsets secreting GrzA (Figure 3). We screened out two SNP of GSDMB related to increased disease risk of CD (rs2305480 and rs11078928) and two related to decreased disease risk (rs35104165 and rs143933205), and constructed these four mutant plasmids. Compared with wild type of GSDMB, rs2305480 promoted the cleavage while rs35104165 blocked the cleavage (Figure 4).

Conclusion
GSDMB-mediated pyroptosis results in intestinal epithelial injury, which will exacerbate intestinal inflammation. Modulation of the GSDMB-mediated pyroptosis emerges as a potential therapeutic strategy to target epithelium damage and treat CD.
P030 SUCNR1 mediates inflammasome activation: Relevance in Ulcerative Colitis
Authors: Bauset C , Lis-López L , Ortiz-Masia D , Gisbert-Ferrándiz L , Coll S , Calatayud S , Barrachina M D , Cosín-Roger J 
Published: May 2021

Abstract

Background
Ulcerative colitis (UC) is characterized by a diffuse, continuous, and chronic inflammation of mucosa and submucosa layers in the colon1. Inflammasome complex is involved in the intestinal homeostasis regulation, but its role in UC has not been established yet. We have recently reported that SUCNR1 mediates intestinal inflammation and fibrosis2. We aim to analyze the role of SUCNR1 in inflammasome activation and UC.

Methods
Intestinal resections from UC and non-IBD patients were obtained. HT29 cells were treated with succinate 1mM and an inflammasome activator cocktail (TNF-α 25ng/ml, IFN-γ 20 ng/ml and LPS 1µg/ml) for 24 hours and transfected with SUCNR1 siRNA. Chronic DSS-colitis was induced in wild-type (WT) and SUNCR1-/- (KO) mice with 4 cycles of DSS. Gene expression and protein levels of SUCNR1 and inflammasome markers were analyzed by qPCR, WesternBlot and ELISA. Histology of murine tissue was analyzed by Hematoxylin-Eosin staining. Results were expressed as fold induction (mean±SEM, n≥5). Statistical analysis was performed with one-way ANOVA followed by Newman-Keuls test. Correlations were analyzed with the Spearman coefficient.

Results
In UC patients, gene expression of SUCNR1 (4.47±1.70), Nlrp3 (1.97±0.38), Caspase-1 (2.08±0.33) and IL-1β (6.90±2.02) were significantly increased vs non-IBD. SUCNR1 positively correlates with the expression of Caspase-1 (r=0.46) and ASC (r=0.45). Protein levels of SUCNR1 (151.00±8.29), Nlrp3 (215.20±53.35) and Caspase-1 (518.30±231.50) were increased in UC vs non-IBD. HT29 cells treated with succinate and inflammasome cocktail showed an increased gene expression of SUCNR1 (4.45±1.17), Nlrp3 (3.13±0.29), Caspase-1 (70.40±16.14), ASC (2.38±0.37), IL-18 (2.52±0.31) and IL-1β (2.32±0.18). Of interest, siSUCNR1 cells treated with the cocktail and succinate showed a significant reduction in the expression of Nlrp3 (1.00±0.15), IL-1β (0.98±0.21), and ASC (1.19±0.14). In parallel, protein levels of Caspase-1 in siSUCNR1 cells treated with cocktail and succinate were significantly reduced (609.00±116.20) vs non-transfected cells (1095.00±148.30). IL-1β levels were also significantly reduced in siSUCNR1 cells (148.60±16.13) vs non-transfected cells (744.70±94.06). Finally, WT-DSS mice exhibited a worse colon histology and an increased protein expression of Caspase-1 (170.60±32.20), compared with KO-DSS (61.39±4.59).

Conclusion
SUCNR1 is increased and positively correlates with the expression of inflammasome components in UC patients. Moreover, SUCNR1 mediates inflammasome activation and its absence ameliorates chronic DSS-colitis. Hence, SUCNR1 might be a potential pharmacological target for UC treatment.

Reference
P041 CDKN2B-AS1 (ANRIL) expression is decreased in Inflammatory Bowel Disease epithelia and in Celiac, and its reduction is linked with induced cells proliferation
Authors: Benshoshan M , Sosnovski K E , Braun T , Amir A , Anikster Y , Haberman Ziv Y 
Published: May 2021

Abstract

Background
Long non-coding RNAs (lncRNAs) have attenuated expression in several immune-mediated disorders. Using mRNAseq of intestinal biopsies, we identified a widespread dysregulation of 459 lncRNAs in the ileum of treatment-naïve pediatric Crohn Disease (CD) patients. We noted that large fraction of downregulated lncRNAs were correlated with epithelial functions. CDKN2B-AS1 (ANRIL) is one of the top most down-regulated lncRNA in CD, and showed decreased expression in Ulcerative Colitis (UC) colon tissues in recent studies.

Methods
Transcriptomics data is used to evaluate CDKN2B-AS1 expression in mucosal biopsies datasets and in gut epithelia. siRNA oligonucleotides targeting most CDKN2B-AS1 transcripts using Lipofectamine RNAiMAX is used to modulate CDKN2B-AS1 function, and RT-PCR to evaluate mRNA expression. xCELLigence system with gold microelectrodes in plate base is used to measure the impedance as an indicator for cell index.

Results
CDKN2B-AS1 is down-regulated in bulk mucosal biopsies obtained from CD ileum [fold change (FC) -8, corrected p=1.6E-5], in UC rectum (FC -9.4, corrected p=3.9E-18), and in celiac duodenum (FC -2.3, corrected p=0.03) in comparison to controls. CDKN2B-AS1 is detected under basal conditions in HT-29 cells. Two sets of CDKN2B-AS1 siRNA oligonucleotides (targeting most transcripts) achieved up to 60% reduction in CDKN2B-AS1 expression in HT-29 cells (p=1E-04) as confirmed by RT-PCR using two sets of primers. CDKN2B-AS1 reduction significantly increased cell index as measured by xCELLigence (doubled the index, p=1.7E-03). mRNAseq of the CDKN2B-AS1 reduced HT-29, showed reduction of the tumor suppressor gene APC in CDKN2B-AS1 siRNA treated cells (FC=-1.75, p=0.04) and of TGFBR2 (FC=-1.75, p=0.04). In contrast, reduction of CDKN2B-AS1 resulted in increase in WNT11 (FC=2.1, p=0.02) and TGFB1 (FC=1.9, p=0.04), and induction of the replication associated topoisomerase TOP1MT (FC=2.7, p=0.001). We confirmed these mRNAseq results using RT-PCR. Finally, mimicking inflammation by treating HT-29 with IL1β and LPS, reduced CDKN2B-AS1 expression (by 70%, p=6.3E-04) and doubled the cell index (p=1.8E-03).

Conclusion
We detected reduced CDKN2B-AS1 expression in three inflammatory disease affecting the gut in different location along the GI tract. Using HT-29 model system we were able to show, as was previously shown, an increase in cell index in CDKN2B-AS1 siRNA treated cells. We supplement those showing effect on down-stream genes that may be relevant in controlling cell proliferation. We further show that upon inflammatory triggering of HT-29 cells, CDKN2B-AS1 expression is reduced and cell index is increased, which may suggest a potential role in epithelial renewal in inflammation.