bluuebunny/crossref_metadata_2025_split huggingface dataset:
P065 Determination of the cytokine pattern of human colon organoids derived from Inflammatory Bowel Disease patients
Authors: Molnár T , Jójárt B , Resál T , Szántó K , Kata D , Földesi I , Molnár T , Maléth J , Farkas K 
Published: January 2022

Abstract

Background
Inflammatory bowel diseases (IBD) are characterized by chronic inflammation of the gastrointestinal tract which is associated with imbalanced pro- and anti-inflammatory cytokines. Anti-TNF-α therapy is widely used, but 10–30% of the patients are primarily not responding to the treatment or lose response over time. In vitro organoid cultures (OCs) generated from tissue specific adult stem cells can mimic cellular diversity and function of the organ of origin and might be used as a predictive tool for patient specific therapeutic response. However, the reductionist nature of the OCs and lack of knowledge about the proper representation of the disease features currently limit the utilization of the OCs as ex vivo IBD models.

Methods
Therefore our aims were to determine and compare cytokine profiles of colonic biopsies collected from IBD patients and OCs generated from the same biopsies, and to follow the changes of cytokine expression over time.
In this study samples from 20 IBD and 8 non-IBD patients were used. Biopsies were taken during colonoscopy from inflamed part of the colon of IBD patients. Crypts were isolated from biopsy samples to establish colon OCs. Total protein and RNA were isolated from biopsies and OCs. Cytokine Array was used to determine cytokine patterns in our samples. Gene expressions of control and IBD OCs after first passage was compared by qPCR. TNF-α concentrations and cellular expression was determined by EILSA and immunostainings, respectively in control and IBD OCs. To determine therapeutic response OCs were treated with anti-TNF-α therapy.

Results
Cytokine patterns of colon biopsies and OCs were remarkably similar until first passage. The major pro-inflammatory cytokines, IL-1β, IL-6, IL-8, were detected both in biopsies and OCs. After second passage the cytokine expression decreased or disappeared in OCs. TNF-α was also measurable in the OCs, however a similar decrease was observed, which was also confirmed by immunostaining. Gene expression analysis in IBD OCs showed an increased TNF-α, IL-1β and IL-6 levels compared to healthy control OCs after first passage. ELISA also showed higher TNF-α concentration in organoids from inflamed origin compared to controls. After anti-TNF-α treatment we detected a decrease in the IL-6 gene expression in treated OCs.

Conclusion
Our results suggest that colon OCs maintain the cytokine expression ex vivo until the 2nd passage and show inflammatory characteristics. Moreover, in vitro treatment induces changes in the cytokine expression. Based on these results the utility of patient-derived organoids to predict the therapeutic response can be investigated.
P066 Lower serum concentration of sulfated bile acids is associated with Primary Sclerosing Cholangitis Inflammatory Bowel Disease comorbidity and advanced liver fibrosis
Authors: Leibovitzh H , Nayeri S , Borowski K , Hernandez-Rocha C , Lee S H , Turpin W , Stempak J , Sandhu I , Milgrom R , Smith M I , Croitoru K , Hirschfield G M , Gulamhusein A , Silverberg M S 
Published: January 2022

Abstract

Background
Primary sclerosing cholangitis associated Inflammatory bowel disease (PSC-IBD) carries significant morbidity risk. Alterations in bile acid profiles has been shown to modulate chronic inflammation in IBD, but data in PSC-IBD comorbidity is scarce. We aimed to assess associations of serum and stool bile acids (BA) with PSC-IBD phenotype versus ulcerative colitis (UC) and the degree of liver fibrosis in PSC-IBD patients

Methods
In this cross-sectional study, bile acids were profiled in 52 PSC-IBD and 50 UC subjects. Quantitation of bile acids was performed by reversed phase ultrahigh performance liquid chromatography/multiple reaction monitoring mass spectrometry with negative ion detection (TMIC, Alberta, CA). After data filtering and normalization, 71 serum and 76 stool BA were available for analysis. Logistic regression was used to assess associations between BA levels and disease phenotype (PSC-IBD versus UC). Among the PSC-IBD group, linear regression was used to assess associations of fibrosis degree (severe (F4) versus no/mild (F0-3) fibrosis, measured by FibroScan®) with BA profile. Age, sex and ursodeoxycholic acid treatment were included as co-variates in all models and alkaline phosphatase (ALP) was added as co-variate for the liver fibrosis analysis. False discovery rate&lt;0.05 was considered significant

Results
PSC-IBD and UC group had similar age and sex distribution. In the multivariable logistic regression, 26 serum BA were significantly associated with PSC-IBD (Figure 1). Decreased concentrations of taurine/glycine-primary BA [odds ratio(OR)=0.97, 95% confidence interval (CI) 0.95–0.99], taurine/glycine-secondary BA [OR=0.98, 95%CI 0.97–0.99] and sulfated-BA [OR=0.96, 95%CI 0.95–0.98], and increased concentrations of conjugated-BA [OR=1.02, 95%CI 1.01–1.03] and glucuronidated-BA [OR=1.06, 95%CI 1.02–1.1] were associated with PSC-IBD phenotype (q&lt;0.05). Decreased sulfated-BA concentrations remained associated with PSC-IBD [OR=0.96, 95%CI 0.94–0.99, q=0.06] even among PSC-IBD subjects with normal ALP&lt;2XULN (n=67). In contrast, stool BA analysis did not show significant associations with PSC-IBD versus UC. Additionally, in the PSC-IBD group, F4 fibrosis degree compared to F0-3 was associated with lower serum concentrations of taurine/glycine- and sulfated-BA, and higher serum concentrations of conjugated-BA (q&lt;0.05)

Conclusion
Decreased concentration of sulfated-BA was associated with PSC-IBD phenotype with and without cholestasis compared to UC group. Lower sulfated-BA concentration was also associated with severe degree of liver fibrosis among PSC-IBD subjects. This inverse relationship between sulfated-BA levels and PSC-IBD and the degree of fibrosis should be further explored in future mechanistic studies
P076 Patients with Inflammatory Bowel Disease show IgG immune responses towards disease-associated small intestinal bacteria
Authors: Bourgonje A R , Roo-Brand G , Lisotto P , Sadaghian Sadabad M , Reitsema R D , de Goffau M C , Faber K N , Dijkstra G , Harmsen H J M 
Published: January 2022

Abstract

Background
Inflammatory bowel disease (IBD) is characterized by a disturbed gut microbiota composition. Patients with IBD have elevated levels of mucosal and serum levels of IgG-antibodies directed against bacterial antigens, including flagellins. In this study, we aimed to determine to which faecal bacteria the humoral immune response is directed to in patients with IBD.

Methods
Faecal and serum samples were collected from patients with IBD (n=55) and age- and sex-matched healthy controls (n=55). Faecal samples were incubated with autologous serum and IgG-coated fractions were isolated by magnetic-activated cell sorting (MACS) and the coating efficiency was assessed by flow cytometry. Bacterial composition of both untreated and IgG-sorted fecal samples was determined by 16S rRNA-gene Illumina sequencing.

Results
Serum IgG responses were primarily directed to typical small intestinal bacterial genera, including Streptococcus, Lactobacillus, Lactococcus, Enterococcus, Veillonella and Enterobacteriaceae, as well as against specific Lachnospiraceae bacteria, including Coprococcus and Dorea (all P&lt;0.001) (Figures), and to the species Ruminococcus gnavus (P&lt;0.05). In contrast, serological IgG responses against typical commensal, anaerobic and colonic microbial species were rather low, e.g. to the Lachnospiraceae members Roseburia and Blautia, to Faecalibacterium as well as to Bacteroides. IgG-sorted faecal samples were characterized by significantly lower microbial diversity. Patients with IBD showed more IgG-coating of Streptococcus, Lactobacillus and Lactococcus bacteria compared with healthy controls (all P&lt;0.05). No differences in IgG-coated bacterial fractions were observed between CD and UC, between active or non-active disease, nor between different disease locations in CD.

Conclusion
The IgG immune response is specifically targeted at typical small intestinal bacterial genera, whereas responses against commensal, rather colonic-type microbiota are lower in patients with IBD. These findings may be indicative of a strong immunological exposure to small intestinal bacteria in concordance with relative immune tolerance against commensal bacteria.
P092 Humoral and T cell responses to COVID-19 vaccination in IBD
Authors: Zhang E , Bond K , Nguyen O , Allen L , Kedzierski L , Kedzierka K , Christensen B 
Published: January 2022

Abstract

Background
The characteristics of SARS-CoV-2 vaccine-induced immunity in inflammatory bowel disease (IBD) patients on immune modifying agents has not been clearly defined due to their exclusion in vaccine trials. Emerging results suggest infliximab impairs antibody response compared to vedolizumab. However there has not been direct comparison to controls. We evaluated this with both humoral and T cell response in IBD patients.

Methods
Antibody and T cell response were analysed in IBD patients who received BNT162b2 (Pfizer–BioNTech) or ChAdOx1 nCoV-19 (Oxford–AstraZeneca) vaccination from a single Australian centre. The control group were healthcare workers (HCW) without IBD. Blood samples were taken at 4 time points: at baseline V0 (before vaccination); V1 (7–14 days after vaccine 1); V2 (7–14 days after vaccine 2); V3 (21–42 days after vaccine 2). Antibodies to the S1/2 IgG subunit and receptor-binding protein (RBD) were measured and reported here.

Results
88 (28 ulcerative colitis, 50 Crohn’s disease) IBD patients were included and compared to 53 healthy controls (Table 1). IBD patients medications included 6 5ASA (6.8%), 6 immunomodulator monotherapy (6.8%), 14 anti-TNF monotherapy (15.9%), 32 anti-TNF combination therapy with immunomodulator (36%), 16 IL12/23 (18%) and 13 vedolizumab (14%). Pre-vaccine baseline sera showed absence of anti-RBD antibodies in all participants. 84 patients (87%) received BNT162b2 and 4 (4.5%) received ChAdOx1 nCoV-19 vaccines. Geometric mean [SD] anti-S1/2 antibody concentrations at 4 weeks after second vaccination (V3) were significantly lower in IBD TNF treated patients (162.6[1.7]) compared to IBD non TNF treated patients (325.2[1.3]), and healthy controls (325.2[1.3]), p&lt;0.0001 (Figure 1). There was no difference between non-TNF treated patients including those on vedolizumab or IL12/23 compared to controls. Similarly there was a significant difference between anti-RBD IgG titres between TNF and non-TNF IBD patients at V3 but not when compared to controls (Figure 2). There was no difference in RBD IgG and anti-S1/2 antibodies between anti-TNF monotherapy and combination anti-TNF with immunomodulator. All IBD and healthy controls seroconverted at V3 (Figure 3).

Conclusion
TNF agents influence SARS-CoV-2 vaccine-induced antibody response in IBD patients, with lower anti-S1/2 IgG concentrations compared to non-TNF IBD patients and healthy controls. However, there was no difference in RBD IgG titres between controls and IBD patients overall. It is unclear whether these subtle differences in antibody response in IBD patients on TNF agents is biologically meaningful, as all groups seroconverted after second dose vaccination. Neutralising antibody and T cell data (CD4+/CD8+) from this study to come.
P094 Transcriptomic and small RNA sequencing profile in ileal resections from complicated Crohn′s Disease patients
Authors: Seco-Cervera M , Bauset C , Santana-Plata C , Civera-Barrachina M , Ortiz-Masià D , Calatayud S , Barrachina M D 
Published: January 2022

Abstract

Background
Crohn′s disease is a chronic inflammatory disorder of gastrointestinal tract that is classified into three different behaviours: the inflammatory (B1), the stenotic (B2) or the penetrating (B3). We pretend to identify differences in transcriptomic and non-long coding RNA expression profiles associated to damaged and no-damaged surgical ileal resections from complicated CD patients.

Methods
We conducted both RNA and small RNA sequencing profiling on ileal surgical resections from CD patients with structuring (n=10) or penetrating (n=10) behaviour; from each patient we obtained a sample from affected tissue (B2A and B3A, respectively) and the paired non-affected ileum (B2C and B3C, respectively). Ten ileal resections (control samples) were obtained from non-affected ileum of patients with right colorectal cancer (IL). Enrichment scores of the GO terms and KEGG pathways were used to functional analysis investigated in this study. Gene expression and miRNA profiles were validated by RT-qPCR.

Results
Our comparative bioinformatic analysis of RNA sequencing showed that the comparation of IL and the non-affected ileum from CD patients (B2C+B3C) revealed that only 11 genes were significantly altered and any miRNA with significative expression. The comparative analysis between B2A+B3A vs B2C+B3C showed: a) 2562 genes differentially regulated and the GO enrichment analysis determined that inflammation, cell activation, and regulation of the extracellular matrix (EM) were the main biological processes altered (Figure 1a). KEGG analysis showed that cytokine-receptor interaction and MAPK and Ras signalling were the most affected pathways (Figure 1b). Among the top ten up-regulated genes we found several immunoglobulins (such as IGHG4, IGHG3, and IGHG1), proteins of the extracellular matrix EM (such as EPYC, COMP, and CHI3L1), and transcription factors (such as PRRX1). When the analysis was performed by CD behaviour, results revealed that most of these genes were significantly increased in both, B2 and B3 CD; b) 103 miRNAs with differential expression, 56 were up-regulated and 47 were down-regulated. Negative and significant correlations were detected between the RNA expression of ECM components and some miRNA expression.

Figure 1. Bar plot of enrichment analysis with differential expressed genes between B2A+B3A vs B2C+B3C. A) Biological Process (BP), Cellular Component (CC), and Molecular Function (MF) of Gene Ontology (GO) enrichment analysis. B) Enrichment of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis.

Conclusion
The correlation detected between extracellular matrix components and some miRNA suggest an epigenetic regulation in the affected ileum of complicated CD patients.
P099 Serum proteomic analysis reveals novel biomarkers associated with disease activity in pediatric patients with Crohn’s disease
Authors: Werner L , Weiss B , Matar M , Shamir R , Shouval D 
Published: January 2022

Abstract

Background
Although Crohn’s disease (CD) is associated with a marked hyper-inflammatory response, identifying serum biomarkers associated with disease activity and outcomes is considered challenging, given lack of sensitivity of different assays. Our aim was to identify novel markers using Olink, a novel technology based on proximity extension assay, enabling detection of minute amounts of proteins.

Methods
Serum samples were obtained from pediatric patients with CD at the time of diagnosis and following induction therapy, and from control subjects, consisting of pediatric patients with normal endoscopic procedures, without past or present history of an immune-mediated disorder (e.g. celiac, diabetes). Serums were subjected to Olink (two panels used, consisting of 184 proteins), and analysis was performed on a Normalized Protein eXpression file by supervised, multivariate, principal component analysis and verification by univariate ANOVA with Benjamini-Hochberg and post-hoc Tukey analysis.

Results
Eighty-eight serum samples were collected: 30 from control subjects and 58 from 32 patients with CD (24 of them pre- and post-induction therapy). The median age of patients in the control and CD groups was 13.9 years (IQR 11.1–16.6) and 14.6 years (IQR 12.2–16.9), respectively (P=0.32). Twenty-four patients were treated with anti-TNFa agents and 8 with EEN. The median pediatric Crohn’s Disease Activity Index (PCDAI) decreased from 35 (22.5–42.5) to 5 (0–12.5, P&lt;0.001) following induction therapy. We identified 72 proteins that significantly differed between patients and controls, and many of them were associated with CRP or ESR levels. String analysis identified several important nodes linking different proteins, including MMPs, MPO, EGFR and TNFRSF1A. Many proteins, such as resistin and different MMPs, showed a strong positive correlation with disease activity, based on PCDAI, while others, such as EGFR, showed a negative correlation. Several novel markers were identified to be highly expressed in the serum of patients with CD, including LRIG1, an intestinal stem cell marker, that was highly correlated with disease activity among the patients.

Conclusion
We identified novel serum markers that are associated with disease activity in pediatric patients with CD. These findings should be validated in future studies, and be complemented with expression and functional studies to define their role in mediating intestinal immune responses.
P105 Treatment of the lower gastrointestinal tract Klebsiella infections by recombinant bacteriocin KvarIa
Authors: Karaliute I , Ramonaite R , Kupcinskas J , Misiunas A , Denkovskiene E , Gleba Y , Razanskiene A , Skieceviciene J 
Published: January 2022

Abstract

Background
Hospital-acquired infections (HAI) are one of the leading worldwide health care issues. The most prevalent HAI are the Klebsiella species. K. quasipneumoniae strains tend to colonize the gastrointestinal tract (GI) and show high rates of resistance against antibiotics. Orally delivered recombinant bacteriocins, like klebicins, could be employed as oral antimicrobials to eradicate multidrug-resistant Klebsiella from the intestinal tract prior to/during hospitalization.

Methods
This study aimed to investigate the antimicrobial efficacy of orally delivered Eudragit - coated klebicin (KvarIa) in a murine lower gastrointestinal tract model of K. quasipneumoniae infection. Four study groups were used (3 animals/group) to test the antimicrobial efficacy of orally delivered klebicin KvarIa: vehicle-only group (control, phosphate-buffered saline), and other three groups with bacteria, antibiotic therapy, and 100 µg of uncoated Kvarla, 100 µg coated KvarIa, 1000 µg coated KvarIa. Faecal and tissue samples were used for Klebsiella haemolysin gene (khe) analysis using RT-PCR.

Results
The gastrointestinal K. quasipneumoniae colonization was achieved only in the antibiotic-treated mice groups ((i) penicillin, streptomycin or (ii) penicillin, streptomycin, and metronidazole) followed by the introduction of K. quasipneumoniae. Analysis of the antimicrobial efficacy of Kvarla showed that coated-KvarIa significantly reduced colonization of K. quasipneumoniae in both mice groups compared to the control group. The amounts of K. quasipneumoniae changed from 6.3 x 107 CFU/50mg on the 18th day to 3.9 x 105 CFU/50mg on the 22nd day (p = 0.01) in the Eudragit S100-coated KvarIa 100 µg group and from 4.0 x 107 CFU/50mg on the 18th day to 1.6 x 105 CFU/50mg on 22nd day (p = 0.009) in the Eudragit S100-coated KvarIa 1000 µg group.

Conclusion
Our study demonstrates that colonization of mice intestinal tract by K. quasipneumoniae can be achieved after eradication of resident gut microbiota with antibiotics. Furthermore, using this murine model, we showed that orally delivered encapsulated klebicins substantially reduce K. quasipneumoniae colonization in the lower gastrointestinal tract.
P110 Risk Factors of Clinical Relapses in Pediatric Luminal Crohn’s Disease, a Retrospective Cohort Study
Authors: Sassine S , Djani L , Cambron-Asselin C , Savoie-Robichaud M , Lin Y F , Qaddouri M , Fadela-Zekhnine S , Grzywacz K , Groleau V , Dirks M , Drouin É , Halac U , Marchand V , Girard C , Courbette O , Patey N , Dal Soglio D , Deslandres C , Jantchou P 
Published: January 2022

Abstract

Background
Few risk factors are associated with the risk of relapses of Crohn’s disease in children. The aims of this retrospective cohort study were to describe the rate of relapses in children with Crohn’s disease, its evolution over the past decade and to determine risk factors associated with relapse.

Methods
Patients under 18 years old and diagnosed between 2009 and 2019 were included. Patients clinical, endoscopic, histological, and laboratory characteristics, as well as their treatments, where collected from their medical records and the prospective CHU Sainte-Justine inflammatory bowel disease registry. Survival analyses and Cox regression models were used to assess the impact of those risk factors on relapse.

Results
639 patients were included. There was a decrease in the clinical relapse rate over the past decade: 70.9% of patients diagnosed between 2009 and 2014 experienced a relapse compared to 49.1% of patients diagnosed between 2015 and 2019 (p&lt;0.0001). The following variables were associated with clinical relapse: female sex (adjusted hazard ratio (aHR)= 1.51, p=0.0009), high PCDAI (aHR= 1.02, p=0.04) and SES-CD (aHR= 1.03, p=0.03) scores at diagnosis, upper digestive tract involvement (aHR= 1.59, p=0.0003), exposure to oral 5-ASA (aHR= 1.91, p=0.0003), use of immunomodulatory agents compared to TNF-alpha inhibitors (methotrexate aHR= 1.91, p=0.0006; thiopurines aHR= 2.06, p&lt;0.0001), presence of granulomas (aHR= 1.27, p=0.04) and increased eosinophils on intestinal biopsies (aHR= 1.34, p=0.02), high levels of C-reactive protein (aHR= 1.01, p&lt;0.0001) and fecal calprotectin (aHR=1.09, p&lt;0.0001) during clinical remission and low serum infliximab levels during maintenance (aHR for mean serum infliximab level under 7ug/mL = 2.48, p=0.005).
Figure 1: Kaplan-Meier curve representing patients time to relapse according to the first maintenance treatment administered.

Conclusion
Relapse risk was significantly associated with baseline clinical, endoscopic, histological and laboratory data and treatment strategies. These results could help better select treatment options for pediatric Crohn’s disease at induction and maintenance.
Figure 2: Kaplan-Meier curve representing patients time to relapse according to the mean infliximab level in post-induction.