bluuebunny/crossref_metadata_2025_split huggingface dataset:
DOP62 Medication use is increased in the decade prior to IBD diagnosis: A nationwide cohort study
Authors: Bonfils L , Karachalia Sandri A , Juul Poulsen G , Agrawal M , Ward D J , Jess T , Colombel J F , Allin K H 
Published: January 2023

Abstract

Background
There is increasing evidence of a pre-clinical phase of inflammatory bowel disease (IBD), but its length and progression with time is not well characterized. We here identified the use of any prescription medications within a decade prior to IBD diagnosis and compared their use in a matched population of individuals without IBD.

Methods
We harnessed the cross-linked nationwide Danish health registers to identify all individuals with incident IBD in Denmark from 2005 to 2018. Individuals with IBD were matched one to ten to individuals without IBD on age, sex, municipality of residence, and year of IBD diagnosis. Next, we examined their use of any prescription medication within the decade leading to IBD diagnosis or matching date. Prescription histories were compared and examined according to the WHO classification of medication by anatomical main group and therapeutical subgroup.

Results
We compared 29,219 individuals with IBD to 292,190 individuals without IBD. Up to a decade prior to IBD diagnosis, the IBD population had a significantly higher use of medications across all organ systems than the matched population. Medication use was more abundant in the IBD population at ten years before diagnosis/matching (p-value &lt;0·0001). This increased use was observed in 12 out of 14 main medication groups, covering most organ systems, and including medications used to treat gastrointestinal, cardiovascular, lung, infectious, neurological, and psychiatric diseases. For these 12 main medication groups, the proportion of users was 1.1- to 1.8-fold higher in the IBD population already ten years prior to IBD diagnosis (p-value &lt;0.0001). The pattern applied across IBD subtypes, sex, and age. The increased use by individuals with IBD became even more pronounced for several medication groups, the closer measurements were to a diagnosis of IBD. The IBD population had a steep increase in use of several medication groups in the two years imminent to diagnosis.

Conclusion
There is an increased use of a broad range of medications a decade before diagnosis of IBD. These findings further suggest a long pre-diagnostic phase of IBD, association of IBD with other immune-mediated diseases, and that IBD could be a multiorgan disease to a much larger extent than hitherto established. The long pre-diagnostic period is a window of opportunity for earlier detection, diagnosis, and intervention of IBD.
DOP67 A transcriptional module associated with neutrophil degranulation is highly conserved across species and is a core molecular pathway of treatment resistance in ulcerative colitis
Authors: Cozzetto D , Lo J , Powell N 
Published: January 2023

Abstract

Background
Advanced therapeutics are changing the treatment landscape in ulcerative colitis (UC), but drug resistance is still common. New strategies are needed to identify the molecular and cellular drivers of treatment resistance and inform the development of novel molecular diagnostics and therapies. In this study we analysed transcriptional modules conserved across species and different colitis models to look for fundamentally important pathways of disease.

Methods
We surveyed the colonic transcriptome in preclinical UC models, including the T-cell transfer, Il10-/-, DSS, DNBS, anti-CD40 mAb and TRUC (Tbx21-/- x Rag2-/- UC) models and multiple cohorts of patients with UC. Gene expression and pathway level changes were defined. Conserved gene and pathway level changes were defined and their relationship to treatment response with anti-TNF, ustekinumab and vedolizumab assessed in independent UC cohorts, including key registration trials.

Results
Principal component analysis showed clear separation between control and experimental colitis samples, which clustered according to the specific model and classification, such as chemically induced (DSS and DNBS), T-cell dependent (T-cell transfer model and Il10-/-, and T-cell independent, innate-mediated models (anti-CD40 mAb and TRUC models). Between 1700 and 8200 genes were differentially expressed (FDR &lt; 0.05) between the experimental models and the corresponding controls; 145 genes had expression levels at least doubled up in all cases. Pathway analysis highlighted significant shared effects (FDR&lt;0.05) on known cytokine-cytokine receptor interactions, signalling by interleukins and neutrophil degranulation. Genes expressed more specifically in the T-cell dependent models were enriched in immune processes such as the complement system, FCERI signalling and downstream activation of MAPK and NFKB, while those more specific to chemically-induced models were enriched in extracellular matrix functions like degradation and remodelling. A set of 21 genes involved in neutrophil degranulation, and over-expressed across all models of colitis, was also significantly enriched in the colon of patients with active UC. Moreover, the magnitude of enrichment of this gene list could differentiate between responders and non-responders to infliximab (difference in median -704.58, p=0.01) and ustekinumab (difference in median -771.08, p=2.19e-08) but not vedolizumab (difference in median 2212.71, p=0.37).

Conclusion
This transcriptional atlas provides a new lens to scrutinize fundamental biological pathways of gut inflammation and new opportunities to understand the core molecular features of the resistome. A set of neutrophil degranulation genes was associated with resistance to anti-cytokine therapies in UC.
DOP68 Autophagy induction in the intestinal epithelium protects against inflammation-induced barrier loss in vivo.
Authors: Saha K , Ganapathy A S , Wang A , Morris N , Yochum G , Koltun W , Ding W , Nighot M , Ma T , Nighot P 
Published: January 2023

Abstract

Background
Loss of the paracellular tight junction (TJ) barrier and defective autophagy in the gut are pathogenic factors for inflammatory bowel disease (IBD). Earlier, we demonstrated the role of autophagy in the degradation of the pore-forming claudin-2 protein and the resultant TJ barrier enhancement. Here, we investigated the role of autophagy in the regulation of the TJ barrier in vivo and in Crohn’s disease (CD) patient-derived tissues and patient-derived organoids.

Methods
Wild type and autophagy-deficient Atg7-/- mice were given intraperitoneal rapamycin injection to induce autophagy along with LPS or TNF-α to induce inflammation. Surgically resected tissues from CD patients were incubated with rapamycin and the paracellular barrier was measured by Ussing chambers. Autophagy was induced in human colonic organoids by incubation with either rapamycin or by nutrient starvation.

Results
Intraperitoneal rapamycin injection in WT mice successfully induced autophagy as evidenced through the degradation of the autophagy substrate p62/SQSTM. Rapamycin injection increased the colonic occludin levels and enhanced the paracellular TJ barrier as evidenced by the decreasing paracellular flux of inulin. Rapamycin prevented LPS and TNF-a induced colonic paracellular barrier loss and reduction in occludin levels in WT mice. Rapamycin reduced the LPS and TNF-a-induced increase in occludin’s association with caveolin-1 thereby preventing its caveolae-mediated endocytosis and degradation. The protective effect of rapamycin was dependent on autophagy. Conditional knockout of Atg7 (cAtg7) in mouse colon decreased baseline occludin levels and increased inulin flux in mouse colon. Furthermore, rapamycin failed to prevent the LPS and TNF-a-induced colonic barrier loss in the cAtg7 mice. Additionally, these mice lacking the ability to undergo autophagy in the colon were more susceptible to Dextran Sodium Sulphate (DSS)-induced colitis. In normal and inflamed colonic tissues from CD patients, incubation with rapamycin induced autophagy, evidenced through the reduction in p62/SQSTM1 protein levels, increased occludin levels and enhanced the paracellular TJ barrier. Autophagy induction by rapamycin or nutrient starvation also increased occludin levels and its membrane localization in patient-derived organoids.

Conclusion
Our data show that rapamycin successfully induced autophagy in WT mice’s colon and protected these mice from the barrier disruptive effect of both LPS and TNF-α, indicating the importance of autophagy in regulating the intestinal TJ barrier. Our data also highlights the application of autophagy induction as a potential therapeutic approach in the treatment of IBD.
DOP70 Crohn’s Disease Like Inflammation of The Pouch is a Distinct Type of Pouchitis
Authors: Kayal M , Tankelevich M , Guo Y , Fischer J , Jimenez D , Canales-Herrerias P , Livanos A , Colombel J F , Dubinsky M , Faith J , Ko H , Mehandru S 
Published: January 2023

Abstract

Background
Pouchitis occurs in up to 80% of patients with ulcerative colitis (UC) after total proctocolectomy (TPC) with ileal pouch anal anastomosis (IPAA). The pathogenesis of pouchitis is unclear, but is thought to involve a complex interaction between the microbiome and mucosal immune system. To examine the underlying pathophysiological mechanisms of pouchitis, the present study aims to simultaneously define immuno-histological and microbial parameters associated with different pouch phenotypes.

Methods
Endoscopic biopsies from the pre-pouch ileum (PI) and the pouch body (PB) were obtained from 51 subjects age&gt;18 who underwent TPC with IPAA, n=48 for UC and n=3 for familial adenomatous polyposis (FAP). Mucosal mononuclear cells (MMC) were isolated from the intra-epithelial compartment (IEC) and lamina propria (LP) and examined for lymphoid, myeloid and innate immune subsets by multiparameter flow-cytometry (FC). Histological sections were examined by two pathologists, blinded to clinical identifiers and scored for inflammatory parameters that included neutrophilic activity, lymphoplasmacytic infiltration, eosinophilia, villous atrophy and submucosal fibrosis. Metagenomic sequencing of stool was performed and analyzed for microbial beta and alpha diversity.

Results
IPAA subjects were classified into the following phenotypes: normal pouch (NP) n=15 (29.4%), acute pouchitis (AP) n=9 (17.6%), chronic antibiotic dependent pouchitis (CADP) n=9 (17.6%), Crohn’s disease like pouch inflammation (CDLPI) n=15 (29.4%), and FAP NP n=3 (5.9%). Among subjects with NP, the PB had a higher frequency of naïve-CD4+ and CD8+ T cells, central memory- CD4+ T cells, and naïve B cells and a lower frequency of homeostatic IELs relative to the PI (Fig. 1A). Immune remodeling of the PB was further confirmed on histology that demonstrated increased lymphoid aggregates and decreased IELs. Subjects with CDLPI had significantly higher levels of inflammation, chronicity, and lymphoid aggregates but decreased IELs in the PI than NP or AP patients (Fig. 1B and 1C). In contrast to immune parameters, the composition of the microbiota in non-inflamed UC pouches was more similar to inflamed UC pouches than to FAP pouches. Alpha diversity and genus relative abundance differences between UC and FAP pouch stool samples were not statistically significant (Fig. 1D).

Conclusion
CDLPI represents a distinct entity of pouchitis that is associated with heightened levels of chronic inflammation relative to AP despite similarities in microbiota.
DOP71 TREM1, OSM and a co-expressed transcriptional module are core components of the molecular resistome to anti-cytokine therapy in Ulcerative Colitis
Authors: Saifuddin A , Madgwick M , Cozzetto D , Pavlidis P , Verstockt B , Hart A , Korcsmaros T , Powell N 
Published: January 2023

Abstract

Background
Molecular biomarkers are emerging as promising tools to predict response to advanced therapy in IBD. For instance, mucosal expression of Triggering Receptor Expressed on Myeloid cells-1 (TREM1) and oncostatin M (OSM) are associated with anti-TNF non-response in Ulcerative Colitis (UC). The specificity of such transcriptional features is poorly understood. We investigated whether mucosal expression of TREM1 and OSM influences ustekinumab response in UC.

Methods
UNIFI is a landmark, phase III, registration trial that evaluated the efficacy of ustekinumab as induction and maintenance therapy in patients with moderate to severe UC. In a subset of patients (n=358), colonic biopsies were sampled at baseline and gene expression profiled by RNA microarray (Affymetrix HT HG-U133+ PM). Normalised expression levels of TREM1 and OSM for responders and non-responders to induction (week 8 mucosal healing) were compared using Mann-Whitney U test on GraphPad Prism 9.2.0. Co-expressed transcripts were determined with Morpheus matrix visualisation software (Broad Institute, USA). Gene set variation analysis was used to calculate gene set enrichment scores (ES) within the expression data. Multivariable models were developed to construct receiver operating characteristic curve (ROC) analyses. Deeper biological insights of TREM1- and OSM-expressing cells were explored using single cell RNA sequencing and Gene Ontology over-representation analysis (R 4.2.2).

Results
Mucosal expression of TREM1 and OSM in inflamed colonic biopsies correlated highly (r = 0.81, p&lt;0.0001) and TREM1 was the third-highest correlate with OSM across the entire genome. Pathway analysis showed that a 20-gene module (GS1) of transcripts co-expressed with TREM1 and OSM was enriched for immune cell adhesion, migration and differentiation (Fig 1). Expression of TREM1 (median: 6.27 vs 5.55, p&lt;0.001), OSM (5.00 vs 4.72, p=0.002) and GS1 (ES: 0.00221 vs -0.496, p&lt;0.0001) were all significantly increased in ustekinumab non-responders compared to responders (Fig 2). Although key clinical parameters correlated weakly with TREM1 and OSM expression, they improved the performance of multivariate models to predict non-response (Fig 3). TREM1 and OSM were predominantly expressed by the same population of inflammatory monocytes accumulating in inflamed colon tissue (Fig 4).

Conclusion
Colonic expression of TREM1 and OSM is associated with resistance to both anti-TNF therapy and ustekinumab, supporting the notion that they constitute a core molecular resistome in UC patients treated with anti-cytokine agents. Their predominant co-expression in infiltrating, inflammatory monocytes indicates that treatment resistance is likely underpinned by biological pathways regulated by this cell population.
DOP73 Predicting endoscopic improvement in Ulcerative Colitis using the Ulcerative Colitis Severity Index (UCSI)
Authors: Wong E C L , Dulai P S , Marshall J K , Jairath V , Reinisch W , Narula N 
Published: January 2023

Abstract

Background
Scoring indices used in clinical trials for moderate-severe ulcerative colitis (UC) may lack specificity as a prognostic tool. We developed and internally validated a prognostic scoring index for UC patients on therapy that considers baseline patient-reported outcomes, biomarkers, endoscopy, and histology for achieving one-year endoscopic improvement (EI).

Methods
This post-hoc analysis of the UNIFI clinical trial (ClinicalTrials.gov identifier: NCT02407236) included 644 patients treated with ustekinumab induction therapy. Data were randomly split into 70% training and 30% testing cohorts. Baseline variables were assessed in multivariate analyses and variables with p &lt;0.05 were assigned weights according to their relative prognostic value for predicting one-year EI (Mayo endoscopic score (MES) ≤1). A cut-off was obtained by calculating the maximum Youden index and validated in the testing cohort.

Results
Prior biologic failure, albumin &lt; 40 g/L, CRP &gt; 5mg/L, Mayo stool frequency (SF) subscore, endoscopic erosions/ulcerations based on the UC Endoscopic Index of Severity, and histologic structural/architectural changes demonstrated significant associations with one-year EI and included in the final model. The Ulcerative Colitis Severity Index (UCSI) was generated (Table 1) and the median UCSI score among all participants was 10.4 (IQR 7-14.4, range: 2.2-20), which had acceptable discriminative ability for one-year EI in the training [AUC: 0.78 (95% CI: 0.70-0.86)] and testing cohort [AUC: 0.76 (95% CI: 0.68-0.85)] (Table 2). Compared to the UCSI, the Mayo score demonstrated poor accuracy [AUC: 0.49 (95% CI: 0.40-0.58)] for predicting one-year EI (p=0.0006). The UCSI also predicted one-year endoscopic healing (MES of 0), clinical remission (total Mayo score ≤2 and no subscore &gt;1), partial Mayo score (PMS) remission (PMS &lt; 2), and PRO-2 remission (SF and rectal bleeding subscore of 0) with significantly greater accuracy compared to the Mayo score. Similar findings were observed when the UCSI was compared with the adapted Mayo score. The maximum Youden index corresponded to a cut-off of 10. Participants with a UCSI ≥10 had a lower probability of one-year EI [27/104 (26%) vs. 40/76 (52.6%)]. Performance characteristics are detailed in Tables 3 and 4.

Conclusion
The UCSI is an internally validated prognostic scoring tool that accurately predicts one-year EI at baseline among patients with moderate-to-severe UC on active therapy. The UCSI demonstrated greater accuracy for one-year EI, EH, and clinical remission compared to the total and adapted Mayo score. The UCSI could improve disease management in UC by stratifying patients based on their predicted likelihood of long-term outcomes.
DOP80 Multi-omic sequencing reveals distinctive gene expression and DNA methylation alterations as potential predictors of primary sclerosing cholangitis development in treatment-naïve paediatric ulcerative colitis
Authors: Lawal O , Rodriguez-Sosa A , McDonnell C , Grant L , O'Brien J , Kel A , Dominik A , Stack R , Yochum G , Koltun W , Doherty G , Hussey S 
Published: January 2023

Abstract

Background
Primary sclerosing cholangitis (PSC) is a progressive choleostatic disease and up to 80% of patients also have ulcerative colitis (PSC-UC). This presents a clinical challenge owing to difficulty in diagnosis and increased risk for developing cancer. While several multifactorial processes including inflammation and microbial dysbiosis have been associated with PSC-UC pathogenesis, the precise molecular factors that regulate the phenotype of this disease subtype remain unknown.

Methods
Here, we applied methyl-capture sequencing and mRNA sequencing to colonic mucosal biopsies to identify transcriptomic and epigenetic alterations differentiating UC from PSC-UC. Samples were taken from 3 groups of treatment-naïve children at diagnosis who participated in the DOCHAS study (GEN-193/11) - UC (n=10), PSC-UC (n=10) and healthy controls(n=10).

Results
Differential gene expression between UC and PSC-UC identified disease-associated genes that were either up- or down-regulated in UC or PSC relative to controls. Furthermore, expression of these genes was intricately regulated by master transcriptional regulators (pro-caspases, IL7RA) and transcription factors (AR, p53, JUND, CEBPA). Importantly, gene expression comparison between UC vs PSC-UC revealed 4 up-regulated genes in PSC-UC (RAB31, TENM3, KLHL17 and COL7A1). Notably, RAB31 and TENM3 are also significantly up-regulated in gastrointestinal (GI) cancers. We also identified 4 down-regulated genes in PSC-UC (H3C15, SLC37A2, SLC14A2 and IL20RA).
Differential methylation analysis between healthy control biopsies vs PSC-UC and UC demonstrated &gt;1000 differentially methylated regions (DMRs, 5Kb), with majority of these sites displaying hypermethylation. Interestingly, PSC-UC vs UC analysis identified 53 regions and 59 DMRs that are hyper- and hypomethylated respectively in PSC-UC, with a large proportion of these DMRs located in gene promoters and putative enhancer regions and notably impacted gene expression of differentially expressed genes identified from the mRNAseq analysis.

Conclusion
Taken together, our study for the first time identifies distinct gene expression and DNA methylation alterations that differentiate UC from PSC-UC at diagnosis in treatment-naïve paediatric patients, some of which are associated with GI cancers. Their potential utility as predictive biomarkers of PSC development in UC or dysplasia risk in PSC-UC warrants further validation through larger patient cohorts.
DOP88 Understanding the molecular mechanisms of anti-TNF treatment failure: Whole blood DNA methylation changes associated with primary non-response to anti-TNF treatment in patients with Crohn’s disease
Authors: Lin S , Hannon E , Waring J F , Reppell M , Smaoui N , Pivorunas V L , Guay H , Chanchlani N , Bewshea C , Bai B Y H , Kennedy N A , Goodhand J R , Mill J , Ahmad T 
Published: January 2023

Abstract

Background
Anti-TNF treatment failure in patients with IBD is common and frequently related to low drug concentrations. DNA methylation sites from whole blood have been identified as effective biomarkers predicting treatment response to methotrexate and etanercept in patients with rheumatoid arthritis. We sought to define differences in DNA methylation associated with primary non-response (PNR) to anti-TNF treatment in patients with Crohn’s disease.

Methods
The Personalised Anti-TNF Therapy in Crohn’s disease (PANTS) study is a prospective UK-wide study investigating anti-TNF treatment failure in patients with active luminal Crohn’s disease. DNA methylation from whole blood was assessed using the Illumina EPIC Beadchip at baseline, weeks 14, 30 and 52. We compared DNA methylation profiles in a subset of adalimumab- and infliximab-treated patients who experienced PNR at week 14 and were not in remission at week 54 (infliximab = 99, adalimumab = 94) with patients who responded at week 14 and were in remission at week 54 (infliximab = 99, adalimumab = 93).
Low anti-TNF drug concentration was defined as an infliximab level &lt;3mg/L and adalimumab level &lt;5mg/L.
Epigenome-wide association (EWAS) analysis was performed using linear mixed models, where p values &lt; 9 x 10-8 were considered significant. Because we observed significant changes in CD4 and CD8 T cells, B cells, NK cells, monocytes and granulocytes following anti-TNF treatment we adjusted our models for derived cell proportions (Figure 1).

Results
Overall, between baseline and week 14, we observed 4999 differentially methylated probes (DMPs) annotated to 2376 genes. Pathway analysis identified 108 significant gene ontology terms enriched in biological processes related to immune system processes and responses (Figure 2).
EWAS analysis at baseline identified 48 DMPs annotated to 36 genes associated with PNR (Figure 3). The majority of DMPs (40/48) were hypermethylated (p &lt; 0.001): of those annotated to genes, 25 were located in the gene body, 5 in the 5’ untranslated regions (UTR), 4 in transcription start sites and the remaining in 3’UTR. When EWAS analysis at baseline was stratified by anti-TNF drug concentration, 27 DMPs annotated to 17 genes were associated with PNR and low drug concentration. Of these, 11 DMPs were independently associated with low anti-TNF drug concentration at week 14 (Figure 4). We did not identify any DMPs associated with PNR with adequate drug concentration.

Conclusion
Our data suggests that baseline DNA methylation profiles may be used as a predictor for anti-TNF drug concentration at week 14.