bluuebunny/crossref_metadata_2025_split huggingface dataset:
P014 Identification of Crohn’s disease immunopathotypes
Authors: Baer H M , MacDonald E , Ferguson A , Scott A M , Khan M I , Bain K A , Ijaz U Z , Cole J , Ramanujam M , Nibbs R J B , Gaya D R , Milling S W F 
Published: January 2020

Abstract

Background
Crohn’s disease (CD) is a chronic inflammatory gastrointestinal condition, with globally increasing incidence. Patients with CD suffer from a loss of tolerance towards their commensal microbiota causing an aberrant immune response, occurring in a protracted relapse and remission cycle. Although a variety of frontline therapies is currently available, including targeted therapies such as biologic drugs, 30–40% of CD patients still require surgery to manage the disease. At present, the immunobiology of CD is not fully understood. However, differences in immune responses between patients might play an important role in diverse treatment responses. The aim of this study was to identify differences in peripheral and local immune responses of CD to understand differences in disease behaviour and treatment outcome.

Methods
Peripheral blood mononuclear cells and plasma were isolated from whole blood of a cross-sectional CD patient cohort (nCD = 12) and normal controls (NC, nNC = 28). Flow cytometry analysis and multiplex assays were used to quantify immune cell populations and cytokine levels, respectively. The local immune response was analysed by bulk RNA sequencing of mucosal colonic biopsies either from inflamed CD or normal tissue. Gene signatures were then followed up by validation in publicly deposited gene expression datasets (nCD = 36, nNC = 24), and by measurement of specific proteins using our archived samples.

Results
Peripheral immunophenotyping of the initial cross-sectional study displayed three different types of CD patients, characterised by either a decrease in leukocyte populations, an increase of cytokines, or a change in both. Analysis of the RNAseq data derived from colonic biopsies revealed four distinct clusters in genes associated with the immune response in CD patients. Further pathway analysis showed one cluster with an enriched B cell signature and another cluster with an elevated macrophage and neutrophil response. We utilised publicly available gene expression datasets to validate these signatures in a larger cohort and identified a selection of patients with an up-regulated pro-inflammatory macrophage response. Using correlation analysis, we suggest an immunopathotype with increased macrophage activation which is potentially associated with a more severe form of the disease.

Conclusion
We have identified distinct immunopathotypes in both the peripheral and local immune response of CD patients. Further investigation will correlate these distinct immune responses in CD with clinical parameters, to understand associations between diverse treatment responses and disease behaviours.
P031 Therapeutic effect of OPS-2071 in a murine model of Crohn’s disease and in in vitro anti-inflammatory assays
Authors: Takagi H , Sato M , Kazuyuki F , Shibuya I , Oka D , Yamaya N , Inagaki K 
Published: January 2020

Abstract

Background
OPS-2071 is a novel fluoroquinolone that is currently in Phase 2 clinical trials for the evaluation of Crohn’s disease (CD) as an add-on therapy to standard of care. OPS-2071 has broad and potent antibacterial activity with low systemic absorption. It was previously investigated for the treatment of enteric infections, including Clostridium difficile. CD is an immune-mediated condition of unknown aetiology; however, studies suggest that an abnormal immune response against certain intestinal bacteria may trigger the development of chronic inflammation. In this study, we have evaluated the effect of OPS-2071 on both the murine T-cell-mediated colitis as well as its in vitro effect on the activity of immune cells.

Methods
Transfer of naïve T cells (CD4+CD62L+CD44−) into immunodeficiency mice induces autoimmune colitis. Two weeks following T-cell transfer, OPS-2071, sulfasalazine and anti-IL12/23 p40 antibody were administered for 3 weeks, followed by assessment of efficacy evaluation by histological score and inflammatory index. In vitro inhibitory action for TNF-α production was assayed using LPS-stimulated human peripheral blood cells and THP-1 macrophages. The effect on T-cell activation and cytokine production (TNF-α, IFN-γ) was examined using anti-CD2/CD3/CD28 antibody-loaded beads-stimulated human peripheral blood mononuclear cells. In vitro activity against bacteria considered to be a potential cause of IBD such as M. avium sub. paratuberculosis, Klebsiella pneumonia, etc., was also tested.

Results
OPS-2071 and anti-IL12/23 p40 antibody significantly reduced both histological score (control: 9.0, OPS: 4.7, anti-IL12: 4.3, p &lt; 0.01) and inflammatory index (control: 58.3 ± 3.7 mg/cm, OPS: 25.9 ± 1.4 mg/cm, anti-IL12: 41.1 ± 2.4 mg/cm, p &lt; 0.01) at a dose of 10 and 25 mg/kg, respectively. OPS-2071 suppressed TNF-α production in T cells, as well as macrophage activity in a dose-dependent fashion. OPS-2071 also suppressed human T-cell activation and proliferation. At high OPS-2071 concentrations, these effects were comparable to prednisolone. The minimum inhibitory concentration against IBD-related bacteria for: OPS-2071, ciprofloxacin, and metronidazole were 0.015–0.5, 0.25–8 and 0.03–&gt;128 mg/ml, respectively.

Conclusion
OPS-2071 demonstrated significant therapeutic effect on colonic inflammation, suppressed TNF-α production in vitro and showed in vitro activity against bacteria related to CD. From these in vitro results, it can be concluded that OPS-2071 has anti-inflammatory activity, independent of its antibacterial activity. The dual effects demonstrated by this novel agent, OPS-2071, provided a rationale for exploring the impact of this compound on human CD in clinical trials.
P036 A novel p53-mediated mouse model of inflammatory bowel disease-associated colorectal cancer
Authors: Churchhouse A M , Billard C V , Arends M J , Myant K B 
Published: January 2020

Abstract

Background
Current mouse models of colitis-associated cancer often utilise a combination of APC mutation, Dextran sulphate sodium (DSS) and azoxymethane administration. However, only 13% of human inflammatory bowel disease (IBD)-associated cancers is associated with an APC mutation1. Instead, they are frequently associated with mutation of p53 (occurring in 63% of human cancers1). Whilst some models of IBD-associated cancer using either global p53 loss or mutant p53 have been described, we felt that a more pathophysiologically relevant model would be represented using p53 loss solely in the colonic epithelium.

Methods
Colonic epithelial p53 floxing in Vil-CreERT2p53fl/fl mice was achieved through intraperitoneal injection of 120 and 80 mg/kg tamoxifen on two consecutive days. After 16 days, mice were started on a chronic DSS treatment protocol. Chronic DSS-induced colitis involved three 5-day cycles of low-dose DSS (1.5% initially and subsequently 1% for the remaining two cycles), interspersed with normal drinking water for 2 weeks to facilitate recovery. After three cycles of DSS, mice were aged to 164 days.

Results
At 164 days post induction of DSS, 100% of mice had developed adenomata with low-grade dysplasia (n = 4). Adenomata in 50% of these mice (n = 2) also had features of high-grade dysplasia. There were between one and three adenomata in each animal. No features of invasive adenocarcinoma were demonstrated. There was partial β-catenin nuclear localisation in these tumours. Background chronic colitis was evident, even though the experiment ended over 3 months after the DSS treatment finished.

Conclusion
To the best our knowledge, this is the first mouse model of colitis-associated cancer using p53 loss in the colonic epithelium together with chronic colitis induction using DSS. The experiment ended over 3 months after the DSS treatment finished, showing that the resultant chronic colitis can persist long after the initial insult is given. The fact that β-catenin is partially, but not fully nuclear localised suggests an alternative pathway to tumour formation in this p53fl/fl model, and may therefore be more pathophysiologically relevant to human IBD-associated colorectal cancers. Further work is now being carried out to both validate and further evaluate this novel mouse model, including assessment of stem cell dynamics in response to colitis in the context of p53 loss.

Reference
P052 Nuclear magnetic resonance metabolomic profiling of IBD patients under anti-TNF treatment. Are the pathways network deregulated?
Authors: Notararigo S , Martin-Pastor M , Dominguez Munoz J E , Barreiro-de Acosta M 
Published: January 2020

Abstract

Background
The deregulation of immune system cell response implies loss of T-cell apoptosis, high rate of proinflammatory cytokines production and subsequent exacerbate activation of TNF-α pathway. The use of biologic antibody decrease inflammation rate and symptoms, but it remains unclear if it has a direct effect on the pathways activation/inactivation on peripheral blood mononuclear cells (PBMCs). The aim of this study is evaluate the role of nuclear magnetic resonance spectroscopy (NMR) applied to the metabolomic study of serum samples isolated from fresh blood from inflammatory bowel disease (IBD) patients under IFX treatment to understand the activated/inactivated pathways of PBMCs.

Methods
A case–control study was performed. Inclusion criteria were IBD patients under IFX treatment. Blood samples were obtained in Crohn’s disease (CD) and ulcerative colitis (UC) patients before IFX and in healthy controls (CTRL). CD patients were divided into subgroups according to the gut affected, in Ileocolic (IC), ileum and colon. NMR samples of the serum were collected and measured according to Standard Operation Procedures. Three types of NMR spectra were measured for each serum sample (1Hnoepresat, 1Hcpmgpresat and 1HDfilterpresat). The signal in each NMR spectrum was integrated in a series of equidistant little portion of the spectrum called buckets of a constant width of 0.04 ppm, covering the complete 1H NMR spectral window from −5 to 14 ppm. Buckets in regions depleted from signal at the two extremes of the spectrum were discarded as well as those in the proximity of the water peak at ca. 4.7 ppm which was affected by the presaturation. The vectors corresponding to a number of samples of two or more groups can be rapidly analysed using Multivariant Statistical Analysis methods.

Results
Twenty-two IBD patients (12 CD and nine UC) were included, 10 CTRL were also included. The metabolomic analyses of the NMR spectra of the serum of the different patients and control groups by the fingerprinting and targeting profiling strategies provided OPLS-DA statistical models (Figure 1) that permitted the successful classification of certain groups of samples which are summarised in Table 1.

Conclusion
The results of this pilot NMR metabolomic study of serum samples of IBD found a series of spectral fingerprints that are able to discriminate between groups of patients CTRL and CD, which underlines its potential use for the diagnosis of the disease.
P059 Cytokine responsive transcriptional networks in inflammatory bowel disease
Authors: Treveil A , Pavlidis P , Tsakmaki A , Bewick G , Korcsmaros T , Powell N 
Published: January 2020

Abstract

Background
Interactions between the immune system and the intestinal epithelium play an important role in the pathogenesis of chronic immune mediated inflammatory diseases, including inflammatory bowel disease (IBD). In IBD, debilitating symptoms and complications including abscesses and cancer are associated with aberrant cytokine production and resulting intestinal epithelial damage. Despite the advent of biological therapies targeting key pathogenic cytokines, like tumour necrosis α (TNF), only 18% of IBD patients will achieve complete disease control and mucosal healing. Here, we provide new insights into the epithelial response to cytokines using network analysis of transcriptomics data from colonic organoids (colonoids).

Methods
We generated an atlas of the transcriptomic effects of cytokines by treating human-derived colonoids with IFNg, IL13, IL9, IL17A and TNF (independently). By integrating the observed transcriptional changes with previously published signalling and regulatory interactions, we generated causal networks to elucidate the effect of cytokine cues on epithelial cells. These networks comprised experimentally verified protein–protein and transcription factor (TF)–target gene interactions, forming signalling pathways linking cytokines to TFs and from TFs to differentially expressed genes.

Results
With this analysis, we identified previously unrecognised levels of shared and distinct transcriptional regulation of colonic epithelial function by different cytokines. While IL9 had a negligible impact on the transcriptome, the transcripts with differential expression induced by IFNg, IL13, IL17A or TNF were consistent with their recognised function in other tissues. IFNg and TNF exhibited similar magnitude and directional effects on key immune pathways while IL13 had the opposite effect. Using a network approach, we found that regulatory effects of cytokines are primarily transduced through unique signalling routes, some of which converge on the same key transcription factors; CEBPA, E2F1, E2F2, ETS1, FOS, IRF1 and MAZ. We observed independent regulatory mechanisms of the different cytokines as well as complementarity in the epithelial responses regulated by different canonical cytokines.

Conclusion
The generated cytokine transcriptional atlas provides a unique insight into the immune-epithelial interactome by allowing the identification of shared and distinct transcriptional pathways across different types of immunity at the mucosal barrier. In addition, it provides the unique opportunity to study cytokine responses in the context of human disease and generate novel hypotheses.
P063 B-cell receptor signalling in lymphoid tissues may be regulated by CEACAM1
Authors: Nagaishi T , Tsugawa N , Yamada D , Watabe T , Onizawa M , Watanabe M 
Published: January 2020

Abstract

Background
It has been recently shown that the carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) expressed in T cells may regulate immune responses in the gut. Moreover, it has also been reported that the treatments with either an agonistic monoclonal antibody (mAb) or natural ligands for this molecule can suppress colitis severity in murine models of inflammatory bowel diseases (IBD). On the other hand, in addition to T cells, B cells are also an important population in the gut-associated lymphoid tissues (GALT) that orchestrate mucosal homeostasis. However, the role of CEACAM1 in B cells has not been elucidated.

Methods
We analysed primary B-cell subsets in the lymphoid tissues of wild-type C57BL6 mice as well as a murine B-cell line, A20, to determine the expressions and functions of CEACAM1.

Results
FACS analysis of the lymphocyte subsets isolated from secondary lymphoid tissues such as spleen, mesenteric lymph nodes and Peyer’s patches of C57BL6 revealed higher expression level of CEACAM1 on B-cell surface than that of T cells. Bone marrow analysis showed that such CEACAM1 expression was increased during maturation and differentiation process of B cells. When isolated splenic B cells were stimulated with LPS, anti-CD40 or anti-μ chain Abs in the presence of agonistic anti-CEACAM1 mAb, the usual increased cytokine productions (such as IL-4 and IL-5 by activation via B cell receptor (BCR) signalling) were specifically suppressed by CEACAM1 signalling rather than B-cell activations via either TLR4 or CD40 signalling. Immunofluorescent studies using confocal microscopy revealed co-localisation of CEACAM1 and BCR when B cells were activated with anti-μ chain Ab. Given these results, A20 cells were transfected with CEACAM1 cDNA. Biochemical analysis showed that an inducible overexpression of CEACAM1 suppressed the BCR signalling in these cells when compared with that of vector alone-transfected control. Moreover, the overexpression of CEACAM1 in these cells resulted in reduced expressions of activation markers such as CD69, CD80, CD86, MHC-I and -II on the cell surface. These observations were associated with decreased Ca2+ influx and suppressed cytokine production by the overexpression of CEACAM1 after BCR signal activation.

Conclusion
These results suggest that CEACAM1 can regulate B-cell activation and differentiation specifically via BCR signalling in the lymphoid tissues. Therefore, this molecule can be a therapeutic target in IBD by regulating of both T-cell and B-cell activation in GALT.
P081 The structure of the proteomic profile and gut microbiota in patients with primary immunodeficiency, common variable immunodeficiency and inflammatory bowel disease
Authors: Iakovlev A A , Volkov A , Bashtovaya O , Shcherbakova I , Ghazudin T , Leonova G , Tarasova G 
Published: January 2020

Abstract

Background
Infringement of intestinal microbiota in patients with primary immunodeficiency (PID), common variable immunodeficiency (CVID) and ulcerative colitis (UC) continues to be studied. The aim of the research is a comprehensive study of the structure of gut microbiota and mucosal protein profile (MPP) in patients with PID, CVID and UC in different phases of the disease course.

Methods
The research included 15 patients with PID, 22 CVID and 46 UC (28 with relapse and 18 with persistent remission of the disease), control group—20 healthy volunteers. Estimation of gut microbiota was performed by bacteriological seeding, hydrogen breath test (HBT) with lactulose. Content of short-chain fatty acids (SCFAs) and microbial lipid markers (MLM) in faeces and colon mucosa was determined by gas–liquid chromatographic and gas chromatography–mass spectrometry (GC–MS). MPP was based on isoelectric focusing techniques (SDS–PAGE, 2DGE). Mass spectrograms were obtained using MALDI-TOF-MS/MS (Bruker, USA).

Results
HBT showed a 4.5-, 8- and 11-fold increase in hydrogen production on a 150th-minute study. SCFA showed a 6-, 9- and 11-fold decrease in propionic and butyric acids, mainly in patients with PID and UC: 0.2 + 0.1, 0.14 + 0.03 and 0.04 + 0.02 mg/g, respectively. Microbiological analysis showed a decrease in titers of E. coli, bifido- and lactobacilli on average 4.6 + 0.8 Lg. The conditionally pathogenic microflora was represented by E. coli, lactose-negative strains (n = 51,105/g) and haemolytic strains (n = 34,104/g, Proteus spp. (n = 48,105/g), Staphylococcus spp. (n = 29,105–6/g), Candida (n = 51,104–6/g) and Clostridium spp. (n = 38,104/g) in stool culture. MLN GS-MS results showed a 5.5-, 3- and 6-fold increase in total bacterial load in patients with PID, CVID and UC, respectively, which was represented by resident anaerobic microflora: Streptococcus mutants, Clostridium difficile, Candida albicans. Results of MPP (detection rate of 75% or more) of the colon mucosa in patients with PID were detected: 1, 2, 4 okkludin, kininogen 1, interleukin-1B, interleukin 8, B2-glycoprotein, heat shock protein 27, in patients with CVID—translational elongation factor, apolipoprotein C-III. In patients with UC—NF-kB, alipoprotein C-III, TNF-α, interleukin-2 and 8 were presented.

Conclusion
In patients with PID, CVID and UC markers of colon excess growth and significant decrease in SCFA are recorded during the relapse period. MPP in patients with PID, CVID and UC was characterised by proteins characteristic of inflammation, apoptosis, proliferation and proteins reflecting the activity of the autoimmune process. Patients with UC in the remission have recovery trend of gut microbiota, production of SCFA, disappearance of specific components of altered MPP.
P083 Characterisation of T-cell receptor repertoire patterns of circulating a4b7 positive memory T cells in ulcerative colitis
Authors: Gamliel A , Werner L , Salamon N , Pinsker M , Weiss B , Shouval D 
Published: January 2020

Abstract

Background
Memory T cells play an important role in mediating inflammatory responses in IBD. The integrin a4b7 is highly expressed on activated T cells, and is thought to direct homing of lymphocytes to the intestine, following its binding to MADCAM-1 expressed exclusively on intestinal endothelial cells. Since UC is characterised by oligoclonal expansion of specific T-cell clonotypes, we hypothesised that circulating memory T cells with gut-homing potential would exhibit unique T-cell receptor repertoire features.

Methods
Peripheral blood mononuclear cells were collected from 5 control subjects and 6 pediatric patients with active UC. Following CD3 MACS sorting cells were FACS sorted into a4b7 positive and a4b7 negative CD3+CD45RO+ memory T cells. DNA was Isolated from each subset and subjected to next-generation sequencing of the TCRB. This high-throughput platform employs massive parallel sequencing to process millions of rearranged T-cell receptor (TCR) products simultaneously, and permits an in-depth analysis of individual TCRs at the nucleotide level. Comparisons of different indices of diversity, CDR3 length and clonal biochemical characteristics were performed between a4b7 positive and a4b7 negative populations for each subject, and between controls and UC patients.

Results
PBMCs were isolated from active UC patients during endoscopic assessment. Four patients had a Mayo endoscopic score of 2, and two patients had a score of 1. Only one patient was treated with an immunosuppressive medication (azathioprine), and five out of six patients were treated with 5ASAs. Percentages of memory T cells (43.8 ± 12.3% vs. 32.2 ± 13.1%, p = 0.17) and a4b7 positive T cells (33.6 ± 15.7% vs. 36.0 ± 17.6%, p = 0.81) were comparable between controls and UC patients. Interestingly, a4b7 positive memory T cells displayed a polyclonal distribution, in both control subjects and in UC patients, without expansion of specific clones. Different indices of diversity, including shanon’s H, clonality index and entropy, were similar among controls and patients, both for a4b7 positive and a4b7 negative populations. Finally, clonal overlap between a4b7 positive and a4b7 negative memory T cells, for each subject was high, ranging between 30–50% for controls and 27–48% for UC patients.

Conclusion
a4b7 expressing memory T cells exhibited a polyclonal repertoire in both control subjects and patients with active UC, with high rates of overlap with a4b7 negative memory T cells. Our study, along with additional recent reports, challenge the dogma of the importance of a4b7 expression for T-cell migration to the gut, and may suggest that vedolizumab’s suppresses intestinal inflammation by blocking the trafficking of innate immune subsets.