bluuebunny/crossref_metadata_2025_split huggingface dataset:
P081 The integration of transcriptomic and microbiomic data links several intestinal bacterial families with key biological functions in the development of postoperative recurrence in Crohn's disease
Authors: Cabrer M , Suau R , Lopez-Siles M , Martinez-Medina M , Aterido A , Julià T , Zabana Y , Calafat M , Clua L , Lorén V , Domènech E , Mañosa M , Manyé J 
Published: January 2024

Abstract

Background
Crohn's disease (CD) is characterized by an imbalance between the microbiota and the host. The severity of CD leads to intestinal resection. However, more than half of the patients not receiving prophylaxis experience post-operative recurrence (POR) within one year. The main objective of this study has been to improve the knowledge of the pathophysiological bases of POR through the integration of transcriptome and microbiome data.

Methods
Samples of inflamed and microscopically non-inflamed ileal mucosa were collected from patients with CD undergoing intestinal resection. The severity of POR was classified according to the Rutgeerts endoscopic index: without recurrence (i0+i1, n=12) and with recurrence (i2+i3+i4, n=8). Samples of healthy ileal tissue were also obtained from patients with colorectal cancer (n=10). Gene expression was evaluated by microarrays and organized into co-expression modules. By sequencing the V3-V4 region of the 16S rRNA gene, intestinal bacteria were identified and classified at the genus and family taxonomic level. The differential expression and correlations between the two sources of omics information were studied. Next, the analysis of pathway enrichment and clustering was carried out according to the severity of the POR and the intestinal area affected or not (graphical abstract A).

Results
The results of the integrative analysis in the uninflamed area of patients without recurrence showed that Actinomycetales negatively correlated with COX6A1 and MTRF1L, related to mitochondrial respiration (GO:0098803; q=0.004) and protein synthesis (R-HSA-72766; q=0.034) (B). These genes and bacteria also played a key role in modules 3 and 25 related to the respiratory chain. In contrast, the inflamed area of recurrent patients showed a positive correlation of the Xanthomonadaceae family in the regulation of neutrophil granules (GO:0035579; q=0.011), with the key participation of the ITGAM transcript (C). This transcript was also related to integrins (R-HSA-216083; q=0.007) in the transcriptomic analyses. In addition, Porphyromonadaceae correlated with LSR and TFF1, involved in epithelium maintenance (GO:0010669; q=0.012) and A group in the Lachnospiradaceae family correlated with CDC20 and CDT1, linked to the cell cycle (q=0.019).

Conclusion
Bacterial families, involved in butyrate production, such as Porphyromonadaceae and Lachnospiradaceae, could influence functions that remember to epithelial regeneration in recurrent patients, while Actinomycetales are associated with a normalization in energy production in uninflamed areas of resections of patients without POR. These findings reveal a potential interaction between the microbiota and the pathophysiology of POR in patients with CD.
P085 Tc17 cells with a distinct immune signature do not correlate with response to therapy with ustekinumab or TNF antibodies in active Crohn’s Disease
Authors: Szentandrasi J , Hockenjos B , Reinscheid M , Thimme R , Bengsch B , Hasselblatt P , Mayer L S 
Published: January 2024

Abstract

Background
IL-17 producing CD8+ T cells (Tc17) expressing a specific immune signature (CD6high, CD39, CD69, PD-1, CD27low) were shown to be associated with active Crohn’s Disease (CD) and inform flare free survival. Here, we addressed the question whether Tc17 cells and their signature also correlate with response of CD patients to therapies with antibodies targeting TNFα or IL-12/23.

Methods
Peripheral blood mononuclear cells were longitudinally collected from CD patients prior to and up to 35 weeks after initiation of therapy with either TNF antibodies or ustekinumab and CD8+ T cells were analyzed by flow cytometry. Results were correlated with clinical outcomes.

Results
We analyzed dynamic changes during treatment in blood samples of 36 CD patients initiating anti-TNF (n = 14) or ustekinumab therapy (N = 22). Baseline Tc17 frequencies differed between ustekinumab and anti-TNF treatment groups, with significantly higher frequencies in the ustekinumab group. This may be due to differences in the baseline patient characteristics; while ustekinumab treated patients were all previously treated with anti-TNF-antibodies, most of the anti-TNF treated patients were naïve to biologics. Indeed, Tc17 frequencies increased during anti-TNF treatment, while Tc17 frequencies were reduced at follow up in the ustekinumab group. However, Tc17 frequencies in the peripheral blood at baseline did not correlate with response to either therapy, nor did the frequencies of Tc17 cells expressing Tc17 signature proteins. The expression of Tc17 signature proteins by IL-17A producing CD8+ T cells did not change significantly during follow up, suggesting that the Tc17 signature was preserved during anti-TNF and ustekinumab therapy. We did not observe major changes in the production of pro-inflammatory cytokines by Tc17 cells during therapy.

Conclusion
Our data suggest that despite playing a pathogenic role in CD, Tc17 cells with a distinct immune signature do not directly correlate with response to therapy with anti-TNF agents or ustekinumab. However, anti-TNF therapy may skew CD8 T cell differentiation towards a Tc17 phenotype, which may have an impact on long term disease outcomes and should be investigated further.
P086 Identification of a Novel Immunometabolic Target and Agonist for PLXDC2 for Amelioration of DSS Colitis Model in Mice
Authors: Abdurahiman S , Mosig R , Cataldi F , Vermeire S , Verstockt B 
Published: January 2024

Abstract

Background
PLXDC2 is expressed on the cell surface of macrophage, dendritic and specific mesenchymal and epithelial cells whose activation shifts cellular metabolism and reduces oxidative stress to rebalance the immune response and decrease inflammation. It’s role in IBD pathogenesis is unknown. PLXDC2 activation improves disease severity in rheumatoid arthritis models1, while loss of PLXDC2 exacerbates the severity of disease in DSS colitis2. PX-04 is a novel, first-in-class, orally active PLXDC2 agonist. Here, we report on the consequences of activating PLXDC2 using PX-04 in an acute DSS colitis model.

Methods
Mice were given DSS in drinking water for seven days to induce disruption of the epithelial layer. At project initiation, mice were 8 weeks of age and began once daily dosing with 20mg/kg of PX-04 24 hours after being placed on DSS. Mice were weighed and scored daily for 15 symptoms of disease (weight loss, diarrhea, rectal bleeding, rectal inflammation, pain, & overall behavior). Colons were collected and digested, and the resultant cellular suspensions were filtered to produce single cell suspensions. Colonic Lamina Propria Immune cells were isolated by Percoll gradient centrifugation. Cells were labeled with mixtures of extracellular (CD45, CD3, CD4, CD8, CD19, NK1.1, CD25, F4/80, CD11b, Gr1, CX3CR1, CD64) and intracellular (Tbet, RORγT, FOXP3, IFNγ, IL17, IL10, TNFα) antibodies in a sequential live staining in 96-well plates. Data was acquired using a FACS Celesta flow cytometer with FACSDiva software.

Results
Oral PX-04 treatment decreased the cumulative disease activity of mice challenged with DSS (FIG 1A). Immunologically, PX-04 affected both the adaptive and innate immune responses. First, PX-04 greatly decreased Th17 cells in the colon, while providing a slight increase to regulatory CD4+ T cells (FIG. 1C). A lower proportion of Natural Killer (NK) cells (FIG. 7D) produced IFNγ. Meanwhile, the proportion of TNF producing dendritic cells was decreased by PX-04 treatment.

Conclusion
Conclusion: PLXDC2 is expressed in cells relevant to IBD pathogenesis. PX-04, which binds to and activates PLXDC2, effectively decreases levels of effector T cells and myeloid cells, as well as overall disease severity in acute DSS colitis, warranting further investigation.
1Tubau-Juni et al. J Immunol 206(Supp)
2Tubau-Juni et al. Sci Rep 10(1)
P102 Neuron-specific gene-2 aggravates colitis and colon tumorigenesis by controlling microbial composition
Authors: Han Y M , Jo K , Lee C H , Yu H , Kim K W , Kang H W , Kim J W , Koh S J 
Published: January 2024

Abstract

Background
Previous studies have shown that Neuron Specific Gene-2 (NSG-2) plays a role in exacerbating murine colitis and colitis-associated tumorigenesis. This study aimed to elucidate the role of Nsg-2 in the pathogenesis of intestinal inflammation by controlling microbial composition.

Methods
The effect of NSG-2 in acute murine colitis was evaluated using both wild-type (WT) and Nsg-2 knock-out (KO) mice. The effect of NSG-2 on colitis-associated tumorigenesis was evaluated using an azoxymethane (AOM) and 3% dextran sodium sulfate (DSS)-induced murine model. The co-housing method was used to assess the role of microbiome in colitis and colitis-associated tumorigenesis. Microbial composition was analyzed using 16S rRNA between the two groups before and after co-housing.

Results
DSS-treated WT mice showed severe colitis compared to DSS-treated Nsg-2 -/- mice. In addition, WT mice exposed to AOM/DSS exhibited higher tumor burdens than Nsg-2-/- mice. After co-housing using WT and Nsg-2 -/- mice, the severity of colitis and colitis-associated tumorigenesis was not different between the two groups, suggesting that microbiome may play a key role in Nsg-2-related aggravation of colitis and tumorigenesis. The microbial taxonomy differed between the two groups in 16S rRNA analysis of stools collected before and after co-housing. Before co-housing, Nsg-2-/- mice showed higher α-diversity than WT mice. Significant differences exist in the Sangeribacter Muris and Lactobacillus Taiwanensis proportion between the two groups. PCoA of beta diversity showed that the microbiome profiles between the two groups were separated before co-housing. However, after co-housing, the difference between the two groups significantly decreased.

Conclusion
Nsg-2 intensifies colitis resulting in colon tumorigenesis through microbial interaction, which suggests that Nsg-2 may have the potential as a therapeutic target for intestinal inflammation.
P130 High serum lipocalin-2 expression at the diagnosis in children with ulcerative colitis: a pilot study
Authors: D'Arcangelo G , Petrella C , Zucconi F , Fiore M , Distante M , Aloi M 
Published: January 2024

Abstract

Background
The identification of new biomarker is a main challenge in inflammatory boweldisease. Lipocalin-2 (LCN-2) is a pleiotropic mediator of various inflammatory processes. We determined the serum levels of LCN-2 in a cohort of newly diagnosed UC children, and we compared them with healthy controls.

Methods
Prospective cross-sectional observational study conducted at the Pediatric Gastroenterology, hepatology, and nutrition Unit of the Umberto I Hospital in Rome and at the IBBC – Institute of Biochemistry and Cell Biology – CNR in Rome. All children aged 6-18 years of age, newly diagnosed with UC at the Pediatric Gastroenterology and Liver Unit, Sapienza University of Rome, were consecutively enrolled. Blood withdrawal was conducted upon diagnosis. Human serum LCN-2 (Cat. No. DY1757) was measured using a sandwich enzyme-linked-immunosorbent assay (ELISA) kits (R&D Systems, Minneapolis, MN, USA), according to the protocols provided by the manufacturer. Clinical, demographic, biochemical and endoscopic data were recorded.

Results
Thirty-two children with a new diagnosis of UC [11 (34%) female, mean age 12,7 ± 4] and 38 age- and sex-matched healthy control [21 (55%) females, mean age 11.71 ± 4] were consecutively enrolled. Serum LCN-2 levels were significantly higher in cases compared to controls (280 ± 152 ng/mL vs 66 ± 55 ng/mL), p &lt; 0,001]. Among UC children, significantly higher LCN2 levels were measured in pancolitis (363.7± 155.2 ng/mL) compared to proctitis, left-sided and extensive colitis (184.9 ± 74.65 ng/mL; p = 0.0003). A significant inverse correlation was observed between LCN-2 and albumin levels at the diagnosis by the Spearman coefficient correlation (r = −0.455; P = 0.03) and a significant direct correlation was observed between LCN-2 and CRP values at the diagnosis (r = 0.44; p &lt;0.05).

Conclusion
Serum LCN-2 levels are significantly higher in children with UC compared to the healthy control group, with the highest levels observed in children with the most extensive disease. Such results as well as and its correlation with the actual disease monitoring tool, make this protein an interesting candidate biomarker.
P135 Mixed probiotics containing Bifidobacterium longum and its metabolites inhibit the formation of NLRP3 inflammasomes by suppressing GBP5 expression in macrophages in ulcerative colitis
Authors: Zhou H , Wu T , Wang F , Zhang T , Lin J , Shi Y , Liang J 
Published: January 2024

Abstract

Background
Ulcerative Colitis (UC) is a non-specific chronic inflammation of the intestine. As an intestinal disease with a gradually increasing incidence in recent years and increasingly valued by medical staff, UC has a close relationship with intestinal flora. At present, domestic and foreign guidelines point out that probiotics can be used to induce remission in ulcerative colitis, but there are no clear instructions on the selection of probiotics, the use of dosage forms, and the dosage of probiotics, and there is a lack of relevant clinical and basic research. This study aims to explore the distinct therapeutic effects of mixed probiotics and individual strains of probiotics (Bifidobacterium longum), as well as elucidate the underlying mechanisms responsible for these variations.

Methods
A total of 90 patients with ulcerative colitis (UC) were enrolled in our center, who were subsequently divided into three groups: control group, single strain probiotic group (Bifidobacterium longum), and mixed probiotic group. After three months of adjuvant probiotic therapy, serum and fecal samples were collected for comparative analysis of therapeutic effects using ELISA and fecal 16s rDNA and metabolome sequence analysis. Mixed probiotic and Bifidobacterium longum were cultured in BHIs in an anaerobic chamber. The supernatant obtained after bacterial cultivation was subjected to metabolome sequence analysis. Human colonic organoids and Caco-2 cells were co-cultured with mixed probiotic and Bifidobacterium longum subsequent to inflammation induction, and cytotoxicity, permeability, and inflammatory cytokine release were assessed. THP1 cells were also to co-cultured with mixed probiotic and Bifidobacterium longum, and expression of virulence genes was analyzed using RT-qPCR, transcriptome sequencing, and western blot. GBP5 gene manipulated cell and mouse model were used to evaluate inflammation and apoptosis.

Results
The utilization of mixed probiotic therapy in patients with UC demonstrated significantly superior therapeutic efficacy compared to those receiving a single strain probiotic (Bifidobacterium longum). Differential metabolite 8-Deoxylactucinwas identified among various groups through the metabolome sequence analysis of clinical patients’ feces, bacterial culture supernatant, and mouse feces. Through in vitro and in vivo experiments, it has been demonstrated that 8-Deoxylactucin exhibits inhibitory effects on the expression of GBP5 in THP-1 cells and ameliorates inflammation.

Conclusion
Collectively, these findings indicate that mixed probiotics and its metabolites suppress GBP5 expression in macrophages in ulcerative colitis.
P137 Salivary calprotectin: a potential biomarker in inflammatory bowel disease?
Authors: Rodrigues C , Gomes A , Leal J , Mendes K , Correia M J , Pereira P , Martins R , Nélio V , Rosa N , Soares C , Ministro P 
Published: January 2024

Abstract

Background
Background: Biomarkers are used frequently for evaluation and monitoring of IBD. Fecal calprotectin (FCP) is an already established biomarker in IBD, nevertheless patients often do not feel comfortable with stool manipulation. A saliva sample collection is particularly interesting due to its noninvasiveness and readiness of collection. We aimed to assess if salivary calprotectin (SCP) could be used as a new biomarker to assess disease activity.

Methods
In this observational cohort study, saliva was collected through the passive drool technique from adult IBD patients. All patients were submitted to a previous oral examination performed by a dentist. Recent history of antibiotic treatment (within the preceding month), proton pump inhibitors or non-steroidal anti-inflammatory drugs were exclusion criteria. Determination of FCP and SCP levels was accomplished using Elia Stool Extraction Kit and Elia Calprotectin 2 test. Intestinal disease activity was assessed with fecal calprotectin levels and the Harvey-Bradshaw Index (HBI) or Partial Mayo score (PMS). Ethical approval was obtained.

Results
92 patients (56 with CD and 36 with UC) were included. Clinical characteristics are presented in Table 1. Patients had a median FCP of 45 mg/Kg and a median SCP of 206.5 mg/Kg. No significant correlations between SCP and FCP, CRP (C-reactive protein), ferritin and ESR (erythrocyte sedimentation rate) were found. However, there was a significant correlation between fecal calprotectin and CRP (p&lt;0.001) and ESR (p=0.011). Disease activity scores did not correlate significantly with SCP, although there was a significant correlation between FCP and PMS (p=0.006).
IBD patients were stratified based on a composite criterion for inactive disease HBI score &lt;5 for CD or a PMS ≤ 2 for UC, and FCP cutoff value of 150 mg/Kg), with no significant difference in SCP between the two groups, despite the significant difference in FCP (p&lt;0.001). No significant differences between different treatments groups or no treatment in salivary calprotectin concentration were found using Kruskal–Wallis H tests (CD (χ2(4) = 6.211, p = 0.184; UC group (χ2(3) = 1.201, p = 0.753)). 77% of patients with IBD do not have periodontal health. Nonetheless, there was no significant difference in the median SCP value between patients with or without periodontal health. Although the median SCP value was higher in patients with UC without periodontal health, the difference was not statistically significant (0.484).

Conclusion
SCP does not correlate with FCP and do not represent a reliable biomarker to distinguish disease activity in patients with IBD patients. Moreover, according to our results, it cannot be used as a marker of lack of oral health, namely periodontitis.
P157 Differentiation of Tonsil-derived mesenchymal stem cells to intestinal stem cells-like cells for cell therapy of inflammatory bowel disease
Authors: Song E M , Joo Y H , Byeon J , Choe A R , Park Y , Moon C M , Kim S E , Jung S A 
Published: January 2024

Abstract

Background
Tonsil-derived mesenchymal stem cells (TMSCs) were found to exhibit a faster growth rate compared to mesenchymal stem cells derived from other tissues. This is attributed to the relatively younger age of the tonsil tissue donors. Moreover, it has been verified that TMSCs possess the capability to undergo differentiation into endoderm lineages, giving rise to cell types like parathyroid glands and insulin-producing cells. In this study, we explored the possibility of differentiation of TMSCs into intestinal stem cells-like cells (ISC-like cells), a cell type of endoderm lineages for utilizing these cells for therapeutic applications in inflammatory bowel disease (IBD).

Methods
TMSCs were cultivated in DMEM (10% FBS) and used in the experiment when 90-100% confluency was observed. Adipose-derived mesenchymal stem cells (AMSCs) were used as the control for assessing the differentiation efficacy of TMSCs. The morphology of cells was verified at each differentiation stage, and the expression of endoderm and intestinal stem cell markers was confirmed using real-time PCR (qPCR), western blotting, and immunofluorescence (IF) staining.

Results
Subjected to 100ng/ml of Activin A for endoderm differentiation and cultured for 2 to 5 days, TMSCs exhibited an upregulation in endoderm markers (SOX17, FOXA2), as confirmed by real-time PCR. Specifically, under the influence of Activin A at 100ng/ml and cultured for 5 days, there was a significant increase in the expression of SOX17 (pre-differentiation vs. endoderm-differentiation, 0.999 vs. 3.610, P=0.0394) and FOXA2 (1.047 vs. 3.912, P=0.0297). Following the endoderm differentiation phase, the medium was changed to include 500ng/ml of FGF4 and 500ng/ml of Wnt3a for a 7-day period. Post-culture, the expression level of Lgr5, an intestinal stem cell (ISC) marker, was significantly increased in TMSCs (1.061 vs. 134.0, P&lt;0.001). Notably, AMSCs displayed a lower expression rate compared to TMSCs (TMSCs vs. AMSCs, 134.0 vs. 9.819, P&lt;0.001). Moreover, the spheroids formation was observed 7 days after the initiation of FGF4 and Wnt3a treatment, a phenomenon absent in AMSCs differentiation. Immunofluorescence staining for differentiation markers further validated these findings: the expression of SOX17, an endoderm marker, and the fluorescence density of LGR5, an ISC marker, were notably higher in TMSCs compared to AMSCs. Protein expression levels also confirmed the upregulation of each marker in TMSCs.

Conclusion
This study validated the potential of TMSCs to differentiate into ISC-like cells, with a higher efficiency observed compared to AMSCs. The prospect of differentiating into ISC positions TMSCs as promising candidates for use as a tool in IBD.
P160 Integrative transcriptional analysis to identify predictive biomarkers for IBD severity and subtyping
Authors: Balasubramanian B , Patel S , Gall L , Parker S , Carpenter A , Hannan N , Pin C , Moran G , Ordóñez Morán P 
Published: January 2024

Abstract

Background
Conventional diagnostic strategies for Inflammatory Bowel Diseases (IBD) heavily rely on invasive biopsy procedures and subjective questionnaires, thereby introducing intrinsic limitations in the context of precision medicine. By understanding the molecular mechanisms behind IBD disease biology, we aim to identify certain signalling pathways relevant for epithelial tissue regeneration under chronic inflammation conditions.

Methods
To address these limitations, we compared gene expression in a large cohort of IBD patients, utilizing the IBD Plexus database (Crohn’s & Colitis Foundation, US) as well as other publicly available datasets. We further validated our results derived from the transcriptional programs by using patient derived advanced 3D-organoid models (Hospital of Nottingham, UK). These models, derived from ulcerated and normal tissue regions of IBD patients, serve as a sophisticated platform for robust validation, bridging the gap between molecular insights and clinical applications.

Results
Our primary objective was to discern putative biomarkers that are capable of effectively stratifying IBD subtypes. We further identified the genes that were upregulated exclusively in each subtypes and the gene signature that is elevated in inflamed samples compared to non-inflamed samples. We found that either the chemokine and interleukin (IL-17) signalling pathways which have known roles in recruitment of immune cells thereby perpetuating chronic inflammation and several key chemokines influence the integrity of the epithelial barrier function and regeneration. We are also analysing non-invasive biomarkers by using samples such as blood, plasma and stool and employ machine learning methods to correlate with established clinical indicators such as sCDAI, PRO2, PRO3, and MAYO categories.

Conclusion
Hence, in identifying specific targets we can introduce novel therapeutic strategies to mitigate inflammation and restore integrity of the gut epithelial barrier. With this research we aim to improve the current IBD diagnostics landscape as well propels it towards precision medicine by offering precise subtyping and predictive markers for disease severity, ultimately contributing to more personalised and effective therapeutics interventions.