bluuebunny/crossref_metadata_2025_split huggingface dataset:
DOP87 Association of histologic measurement with endoscopic outcomes after one year of treatment with mirikizumab in patients with moderate to severe Crohn’s Disease
Authors: Magro F , De Hertogh G , Protic M , Chan L S , Pollack P , Feagan B G , Harpaz N , Pai R , Reinisch W 
Published: January 2022

Abstract

Background
There is a scarcity of data regarding the role of histopathology evaluation in Crohn’s disease (CD) and how it relates to endoscopy. Mirikizumab (miri) has shown efficacy in Ph2 studies in CD and ulcerative colitis (UC). Here we explore the agreement of histologic response and remission with endoscopic outcomes after 12 and 52 weeks of treatment with miri in a phase 2 randomized clinical trial (SERENTIY; NCT02891226) in patients with moderate-to-severe CD.

Methods
Patients were randomized 2:1:1:2 across 4 treatment arms (PBO, 200, 600, 1000mg miri) administered intravenously (IV) every four weeks (Q4W) at Weeks 0, 4, and 8. Those who received miri and achieved ≥1 point improvement from baseline (BL) at W12 in Simple Endoscopic Score for Crohn’s Disease (SES-CD) were re-randomized 1:1 into double-blind maintenance to continue their IV dose assignment Q4W (IV/IV) or to 300mg miri SC Q4W (IV/SC); due to small numbers, maintenance IV arms were pooled for analysis. W12 non-improvers and all induction PBO patients received 1000mg miri Q4W from W12 through W52. Biopsies were obtained during endoscopy at W0, 12 and 52 from the edge of the ulcers and the most inflamed mucosa in terminal ileum and 4 colonic segments (ascending, transverse, descending, rectum; N=10/patient, 2 per location with the more severe score used), and scored by central readers blind to study treatment, timepoint, and response status. Histologic endpoints were defined post-hoc but prior to performing the analyses (see Table footnotes for definitions). Cohen’s Kappa Coefficient was used to evaluate the degree of agreement of two measures.

Results
At Week 12, there was an overall 69.6% agreement in histologic and endoscopic response, and 84.2% agreement between histologic remission and endoscopic remission (Table 1). After 52 weeks of miri treatment, the agreement between histologic and endoscopic response was 61.9%, while the agreement between histologic and endoscopic remission was 70.6% (Table 2). Interestingly, in every comparison, the percentage of patients achieving the histologic outcome but not the endoscopic outcome was greater than that of patients achieving the endoscopic outcome but not the histologic outcome.

Conclusion
Histologic and endoscopic outcomes demonstrated fair association after both 12 and 52 weeks of miri treatment. Histologic endpoints, despite the stringent criteria, appear to be more sensitive to change than endoscopic endpoints. However, variability of biopsy sampling may be an additional factor contributing to these differences.
P002 Glial cell line-Derived Neurotrophic Factor (GDNF) improves intestinal wound healing – A new target for IBD treatment?
Authors: Kelm M , Burkard N , Hoerner M , Germer C T , Schlegel N , Flemming S 
Published: January 2022

Abstract

Background
Due to the rising incidence and socioeconomic relevance of Inflammatory Bowel Disease (IBD) worldwide, new therapeutic strategies are necessary to improve patient care. Since immunosuppressants are partially insufficient with relevant rates of side effects, novel concepts of treatment need to be developed. Mucosal and/or histological healing represent potential criteria to measure disease activity and are mentioned in current guidelines as favorable prognostic factors regarding disease outcomes. In previous studies, the soluble factor Glial cell line-Derived Neurotrophic Factor (GDNF) has been shown to be significantly reduced in tissue specimens from IBD patients and to be critically involved in intestinal epithelial barrier maturation. Therefore, the goal of this study was to further analyze the potential role of GDNF in IBD.

Methods
Intestinal wound healing was assessed in endoscopic biopsy-based wound assays as well as dextran sodium sulphate (DSS)-induced colitis in vivo. During the experiments, C57Bl/6 mice were either injected with GDNF or sodium chloride intraperitoneal while tissue samples were used for detailed molecular analyses. Further, scratch wound assays were performed in Caco2 monolayers to identify molecular pathways and cell mechanisms in vitro.

Results
Intraperitoneal injection of GDNF resulted in significantly enhanced wound closure in vivo. During the DSS-induced colitis model, mice treated with GDNF demonstrated significantly improved recovery from colitis in comparison to mice injected with sodium chloride. Similarly, application of GDNF in a scratch wound assay significantly enhanced wound closure in vitro. Mechanistically, molecular analysis revealed that GDNF application resulted in significantly increased cell proliferation. The effect of GDNF on cell proliferation was based on upregulation of LGR5-positive cells with increased phosphorylation of pSrc. Further studies demonstrated that the effect of GDNF on wound healing and cell proliferation could be inhibited by application of a Src-inhibitor.

Conclusion
GDNF significantly improves intestinal mucosal healing in vivo and in vitro which results in significantly enhanced recovery from colitis. While this effect is driven by increased cell proliferation due to upregulation of LGR5-positive cells and increased phosphorylation of pSrc, previous studies already demonstrated the critical impact of GDNF on epithelial barrier function. Following that, GDNF might have great potential in IBD treatment and could be a new target for future therapeutic approaches.
P004 Microbiota, not host origin drives ex vivo epithelial response in ulcerative colitis patients and non-IBD controls
Authors: Arnauts K , Sudhakar P , Verstockt S , Lapierre C , Potche S , Caenepeel C , Verstockt B , Raes J , Vermeire S , Sabino J , Verfaillie C , Ferrante M 
Published: January 2022

Abstract

Background
Host-microbial interactions in inflammatory bowel disease (IBD) are poorly understood. Furthermore, patients with IBD have microbial dysbiosis and their epithelial cells exhibit intrinsic defects. We aimed to unravel the effect of exposure to microbiota on epithelial cells from both patients with ulcerative colitis (UC) and non-IBD controls.

Methods
Confluent Transwell® organoid-derived monolayers of 8 UC patients and 8 non-IBD controls were co-cultured for 6 hours with microbiota (3.108 cells) derived from active UC patients (n=3, endoscopic Mayo score ≥2) or healthy volunteer (HV, n=1, selected on high microbial cell count and presence of selected phyla1). For this purpose, fresh faecal samples were filtered and frozen in 0.9% NaCl. Inflammation was re-induced with 100 ng/ml TNF-α, 20 ng/ml IL-1β, and 1 µg/ml flagellin in confluent Transwell® cultures, 24 hours prior to microbiota co-culture. Transepithelial electrical resistance (TEER), 4 kDa fluorescein isothiocyanate (FITC) dextran (2 mg/ml) measurements, and RNA sequencing by Truseq were performed on epithelial cells, and 16S rRNA sequencing on microbiota samples before and after co-culture.

Results
The transcriptomic response of epithelial cells to microbiota was clearly influenced by the type of microbiota stimulation (no, UC or HV microbiota). However, this response was not influenced by the origin of the epithelial cells (UC or non-IBD controls) (Figure 1A). TEER and FITC dextran measurements showed a strong decrease in epithelial integrity (in both UC and non-IBD epithelium) following stimulation with UC microbiota, in contrast to HV microbiota (Figure 1B). In UC epithelial cells, stimulation with microbiota from UC patients induced a stress induced phenotype including activation of EGR1 signalling, AP-1 family, FOSL genes, MAPK and JNK signalling (Figure 2). Activation of stress pathways (MAPK family cascades) and key markers (e.g. FOSB, FOSL1, MYC, EGR1, ATF3, NOTCH1) was lower after HV microbiota stimulation (Figure 3–4). Expression levels of key markers were UC microbiota specific and similar in epithelial cells of UC and non-IBD controls (Figure 4).

Conclusion
Not the host (UC vs non-IBD epithelial cells) but the microbial donor (UC vs HV) is driving the transcriptomic response. Epithelial cells from UC patients did not show an increased sensitivity towards microbiota stimulation compared to non-IBD epithelial cells. In contrast, exposure of epithelial cells to UC microbiota was sufficient to induce a strong stress response and barrier disruption. Further research on therapies to restore the microbial balance, to remove the constant trigger of dysbiosed microbiota, is required.
References
1. Vermeire, JCC, 2015
P007 ORMDL proteins shape homeostasis in the intestinal epithelium by regulating endoplasmic reticulum architecture and autophagy
Authors: Tran F , Stengel S , Yang H , Bernardes J P , Lopez-Agudelo V , Bordoni D , Falk-Paulsen M , Jentzsch M , Messner B , Schreiber S , Rosenstiel P 
Published: January 2022

Abstract

Background
ORM1-like protein 3 (ORMDL3) is an endoplasmic reticulum (ER)-resident protein that has been implicated in ER homeostasis and sphingolipid biosynthesis. Genome-wide association studies identified susceptibility loci around the ORMDL3 gene for inflammatory diseases, including asthma and IBD. Preliminary studies suggested a role of ORMDL proteins within the ER stress-induced unfolded protein response (UPR). Here, we set out to investigate the role of ORMDL proteins in intestinal inflammation.

Methods
Mice with constitutive and conditional knockouts (KO) of Ormdl1, Ormdl2 and Ormdl3 in intestinal epithelial cells were generated. From these, intestinal organoids were generated to perform functional assessment of ER stress, autophagy, and inflammatory responses. We performed 3’-single cell RNA sequencing (scRNAseq) of small intestine tissue of animals with triple conditional knockout of Ormdl1/Ormdl2/Ormdl3 (“Ormdl123-VilCre”) vs. wildtype to identify cell type-specific effects of epithelial ablation of ORMDL proteins. 16S rDNA sequencing was performed on stool samples from these animals.

Results
Mice deficient for ORMDL displayed reduced body weight dependent on the number of knockouts. Ormdl1/2/3-KO mice are embryonically lethal while Ormdl1/2/3-VilCre animals were viable without signs of spontaneous inflammation. Ormdl1- and Ormdl3-KO animals displayed reduced number of Paneth and goblet cells in the small intestine, accompanied by massive dilation/ballooning of the ER. This phenotype was strongly pronounced in Ormdl1/3-KO and Ormdl1/2/3-VilCre animals. ORMDL3 co-localises and co-precipitates with LC3, indicating a direct interaction with autophagy proteins, while loss of ORMDL proteins impaired autophagic flux. Interestingly, UPR and Cxcl1 expression were insufficiently induced in intestinal organoids from Ormdl1/2/3-VilCre animals treated with tunicamycin. scRNAseq analysis of small intestine tissue surprisingly revealed compensatory induction of antimicrobial peptides in non-Paneth cells and vice versa downregulation of apoptosis regulating gene in Ormdl1/2/3-VilCre mice. We observed an expansion of myeloid and plasma cells in Ormdl1/2/3-VilCre mice, while no changes in epithelial cell proportions can be identified. These findings were accompanied by dysbiosis of the stool microbiome (β-diversity, Bray-Curtis dissimilarity) of Ormdl1/2/3-VilCre animals.

Conclusion
Our data suggest a critical regulatory role of the IBD risk gene ORMDL3 in the ER-autophagy axis in intestinal epithelial cells, shaping the mucosa homeostasis on cellular and microbiome level. Functional assessment of inflammation in Ormdl1/2/3-VilCre animals (e.g., DSS colitis model) will be performed to understand the role of ORMDL in intestinal inflammation.
P012 The effect of Oncostatin M on human intestinal organoids
Authors: Filidou E , Kandilogiannakis L , Kokkotis G , Tarapatzi G , Arvanitidis K , Drygiannakis I , Valatas V , Paspaliaris V , Kolios G , Bamias G 
Published: January 2022

Abstract

Background
We have previously shown that human subepithelial myofibroblasts (SEMFs), which are of mesenchymal origin, express the receptor of Oncostatin M (OSM), which is further induced when SEMFs are previously exposed to IL-1α and TNF-α. Human Intestinal Organoids (HIOs), derived from embryonic stem cells (ESC), form epithelial crypts consisting of several subtypes of epithelial cells and are surrounded by cells of mesenchymal origin. Recently, we reported that the mesenchymal component of HIOs is gradually reduced, as culture passages increase. The aim of our study was to examine the effect of exogenous OSM on fibrotic and pro-inflammatory marker expression of HIOs, with and without the combined presence of IL-1α and TNF-α.

Methods
The human ESC line (H1)-derived HIOs were developed using a commercially available kit and characterized by immunofluorescence in all differentiation stages. HIOs from passage 2 were stimulated with either 100ng/ml OSM for 12 hours or 5ng/ml IL-1α and 50ng/ml TNF-α for 24 hours and then with 100ng/ml OSM for 12 hours. mRNA expression of fibrotic markers, Collagen Type I, III, and Fibronectin, and pro-inflammatory markers, CCL2, CXCL10 and CXCL11 were examined by reverse transcription quantitative PCR.

Results
OSM alone significantly downregulated both Collagen Type I and III mRNA expression, and had no effect on Fibronectin expression. When HIOs were previously exposed to IL-1α and TNF-α, however, OSM stimulation resulted in significant upregulation of Collagen Type I and Fibronectin, and had no effect on Collagen Type III. Regarding the pro-inflammatory marker expression, OSM alone induced the expression of CCL2, CXCL10 and CXCL11, with a greater effect observed when HIOs were previously exposed to IL-1α and TNF-α.

Conclusion
Our findings indicate that OSM induces the expression of both fibrotic and pro-inflammatory factors in early passages of HIOs, previously exposed to IL-1a and TNF-a, as has been previously observed on SEMFs. Since the mesenchymal cell component of HIOs is strongly present in early passages and OSM’s receptor is mainly found to be expressed in these cells, our results suggest OSM affects HIOs via the cells that are of mesenchymal origin.
P015 Detection of endoscopic lesions from limited quality annotations in colonoscopy videos
Authors: Alali S , Chaussard J , Li-Thiao-Té S , Ogier-Denis É , Percy-du-sert A , Treton X , Zaag H 
Published: January 2022

Abstract

Background
Ulcerative colitis is an idiopathic inflammatory disorder affecting the mucosa of the colon with superficial erosion and ulcers associated with bleeding. Severity assessment using current scoring schemes such as UCEIS and MAYO relies on the subjective interpretation of the physician and fails to take into account the size of the lesions, their number and distribution. Automatic lesion detection methods can enable fine-grained assessment of lesion severity, but require training stage based on time-consuming manual annotation. Most methods currently use generic datasets that are biased towards capsule endoscopy and are not adapted to locally available hardware.

Methods
We learn automatic bleeding and ulcer detectors on a local data set created by the Gastroenterology group at the Bichat and Beaujon hospitals. The patients’ videos were anonymous, analysed after obtaining their consent. The study was approved by the local research study committee. To minimise expert annotation burden, only rectangular annotations are provided instead of a precise delineation of lesion boundaries (Figure 1). This leads to many mislabelled pixels, especially in the corners, and affects the evaluation of the models’ performance and our ability to find correct models. Standard sensitivity and specificity cannot be used effectively on this data-set. We propose to evaluate model sensitivity on the annotation level and keep specificity at the pixel level. On the training set, we consider that a model correctly identifies a lesion if it agrees with the expert on a subset of the annotation, and count the detected annotations weighted by their area. For robustness and ease of interpretation, we explore the set of linear classifiers, and propose an efficient sampling scheme that rejects trivial models. This method is evaluated on a database of 10 colonoscopy videos (5 training videos and 5 test videos).

Results
In spite of the limited quality of the annotations, we find lesion detectors with a good annotation-level sensitivity (Table 1) and visual performance (see Figure 1). The detector’s performance is computed reliably. We evaluate sensitivity and specificity on 20 random subsets containing 10\% of the images, and obtain similar performance for the same patient for all models (cf Figure 2).

Conclusion
Despite mislabeled pixels, we obtain lesion detectors with good performance, and we show that the performance is computed reliably. However, the inter-patient performance is variable and the best models fail on some patients (sensitivity below 20\% in some cases Figure 2). This suggests that the models are not universal and that the appearance of bleeding and ulcers should be normalised further before automatic detection.
P017 Transcriptional characterization of lymphocytic colitis and comparison to collagenous colitis
Authors: Koch S , Münch A , Escudero-Hernández C 
Published: January 2022

Abstract

Background
Lymphocytic colitis (LC) is an inflammatory disease of the large intestine that causes chronic, watery, non-bloody diarrhoea. LC is characterized by infiltration of lymphocytes in the colonic mucosa. To better understand LC pathophysiology on a molecular level, we performed genome-wide RNA sequencing (RNA-seq) analysis on LC mucosal samples.

Methods
We collected colonic biopsies from healthy controls (Hc), and LC patients with active disease. Collagenous colitis (CC) samples were included as a separate control. Total RNA was isolated from biopsies for bulk RNA-seq. Whole-genome expression data were analysed by principal component analysis (PCA), differential gene expression (DGE), and gene-set variation analysis (GSVA) using R statistical software. Benjamini-Hochberg FDR was used to adjust p values, considering &lt;0.05 as statistically significant. Gene-set enrichment analysis (GSEA) was performed using GSEA software and visualized in Cytoscape.

Results
PCA of all samples identified 2 principal components that explained 65% of the transcriptional variation and separated sample groups into distinct clusters of gene expression. Subsequent analysis revealed differential expression of 5045 genes in patients with active LC compared to Hc, which were mainly involved in DNA and telomere repair, in ubiquitinylation and proteasomal degradation, response to viruses and interleukin (IL)-12 signalling according to GSEA. Compared to CC samples, we identified 384 differentially expressed genes (DEGs) with LC. Pathway analysis displayed an enrichment in cell adhesion and proliferation genes in LC, whereas DEGs related to microbial response, collagen and wound healing processes, chemotaxis, and epithelial biology (e.g. ion channels, epithelial cell proliferation) were enriched for CC samples. Estimations of infiltrating immune cells performed by GSVA indicated a possible role for professional antigen-presenting cells (i.e. macrophages and inactive dendritic cells) as well as T regulatory cells in LC pathogenesis.

Conclusion
LC is a transcriptionally homogeneous disease that can be characterised by increased expression of cell adhesion and proliferation-related genes. Furthermore, our analyses confirm an elevated immune response in LC, particularly involving macrophages, dendritic and T regulatory cells. Comparison of LC and CC gene expression additionally supports that these diseases are pathobiologically distinct.
P018 Proteomic profile of serum and urine in newly diagnosed patients with Inflammatory Bowel Disease: new approach for biomarker discovery
Authors: Baldan-Martin M , Azkargorta M , Iloro I , Ortega Moreno L , Aldars Garcia L , Soleto Fernández I , Ramirez C , Riestra S , Rivero M , Gutierrez A , Rodríguez-Lago I , Fernández-Salazar L , Ceballos D , Benítez J M , Aguas M , Bastón-Rey I , Bermejo F , Casanova M J , Llorente R , Ber Y , Royo V , Esteve M , Elortza F , Chaparro M , Gisbert J P 
Published: January 2022

Abstract

Background
Currently, endoscopy is the gold standard for the evaluation of disease activity and inflammation in clinical practice. However, it is an invasive procedure for the patient, costly and time-consuming. Therefore, there is an urgent need to identify non-invasive biomarkers with the potential clinical utility to diagnose inflammatory bowel disease (IBD) patients, improve the patient′s quality of life and increase efficiency in the Health Systems.

Methods
A label-free quantitative proteomics method was used to profile the urinary and serum proteomes of 100 patients with newly diagnosed IBD, before starting any treatment [50 patients with Crohn′s disease (CD) and 50 patients with ulcerative colitis (UC)] and 50 healthy controls (HC). The resulting peptides were separated by NanoLC (EVOSEP ONE) and coupled online by electrospray to Trapped Ion Mobility Spectrometry (TIMS) TOF Pro for tandem mass spectrometry analysis. Mass spectrometry data were processed and analyzed with MaxQuant and Perseus software. Proteins with p≤0.05 and ratio&gt;1.5 in any sense, were considered as significantly dysregulated. Bioinformatic analysis of differentially expressed proteins was performed to characterize involved biological processes, molecular functions, cell locations and proteins pathways (PANTHER and STRING v11.5).

Results
A total of 2,500 proteins were identified in the urine, and 468 proteins were identified in the serum with at least two different peptides at FDR&lt;1%. Of the urine proteins, 110 were significantly changed in UC versus HC, 50 proteins were differentially expressed between CD and HC, and a total of 31 proteins were significantly changed in CD compared with UC patients (Figure 1). In serum samples, a total of 45 differentially expressed proteins were identified in the comparison between UC and HC groups, 32 proteins significantly expressed in CD versus HC, and 12 proteins in CD compared with UC (Figure 2). Finally, biological information analysis was performed according to these differential proteins. The molecular functions, biological processes, and pathways enriched mainly involved the neutrophil degranulation, complement and coagulation cascades and immune system responses (Figures 3 and 4).

Conclusion
Proteome profiling revealed significantly differences in newly diagnosed patients with CD or UC. Both serum and urine seem to be appropriate biological matrixes for this approach. Next steps of our research will be to understand the role of candidate proteins as well as to validate those with potential as biomarkers in independent cohort.