bluuebunny/crossref_metadata_2025_split huggingface dataset:
P039 Identifying Key Genes in CROHN'S DISEASE and Acute Pancreatitis: A Bioinformatics and Systems Biology Approach
Authors: Wu H , Su T , Zhi M , Yao J 
Published: January 2024

Abstract

Background
Previous studies have shown acute pancreatitis (AP) to be the most common pancreatic disease in inflammatory bowel disease (IBD) patients, with Crohn's disease (CD) patients exhibiting significantly higher incidence than ulcerative colitis (UC) patients. However, the shared biological mechanisms remain elusive. This study aimed to identify the differentially expressed genes (DEGs) between CD and AP and explore their associated molecular mechanisms using bioinformatics approaches.

Methods
Microarray datasets GSE75214 and GSE194331 were obtained from the Gene Expression Omnibus (GEO) database. Comprehensive bioinformatics analyses, including functional annotation, pathway enrichment analysis, expression validation, drug-gene prediction, construction of TF-mRNA-miRNA regulatory networks, comparative analysis of immune infiltration between CD and AP, and correlation assessment between key genes and infiltrating immune cells, were performed after identifying the common DEGs and hub genes.

Results
55 upregulated and 12 downregulated common DEGs were screened from the datasets. Functional and enrichment analyses of these genes indicated their shared pathogenic mechanisms may be relevant to immunity, inflammation, and lipid metabolism. Fifteen hub genes (MNDA, AQP9, S100A12, FPR1, ITGAX, CSF3R, CXCR1, IL1RN, NCF2, VNN2, S100A8, S100A9, IL1B, FCGR2A, and CXCL8) were filtered by constructing the protein-protein interaction (PPI) network. Further bioinformatics analysis of the hub genes highlighted the importance of the immune system in both CD and AP again. Two overlapped immune cells, including upregulated neutrophils and downregulated T cells CD8, were discovered between CD and AP.

Conclusion
Taken together, this study revealed the common hub genes between CD and AP for the first time and constructed a miRNA-gene regulatory network. The analysis of hub genes and immune cell landscape indicated the shared biological mechanisms between CD and acute AP, providing potential therapeutic targets for acute pancreatitis in Crohn's disease patients.
P063 Interleukin-8 mucosal transcript as predictor of response to Vedolizumab treatment in Ulcerative Colitis: preliminary results from a prospective study
Authors: Bota A D , Mușa A M , Dinu M C , Săftoiu A , Mușa M , Coman S , Dobre M , Milanesi E , Țieranu C G 
Published: January 2024

Abstract

Background
Vedolizumab (VDZ) is a safe, well tolerated and efficient biologic agent used for the treatment of inflammatory bowel disease (IBD), as confirmed by phase 3 randomised controlled trials. However, primary non-response and secondary loss-of-response to VDZ represent a clinically significant problem. The objectives of the present study are to assess the differences in mucosal gene expression profiles of patients with Ulcerative Colitis (UC) prior to VDZ initiation and to identify transcriptomic biomarkers capable of discriminating responders and non-responders to VDZ treatment.

Methods
Mucosal samples were collected during colonoscopy from patients with UC prior to VDZ initiation. The minimum extension of disease for study inclusion was left-sided colitis (E2 Montreal), and patients had at least moderate flare of clinical activity based on the total Mayo Score. Patients were dichotomized based on clinical response at week 10 in responders and non-responders. Clinical response at week 10 was defined as a decrease with &gt;50 percent for both rectal bleeding score and stool frequency score according to the latest STRIDE-II recommendations for short-term targets. A commercially available panel of primers for 84 genes associated with IBD were assessed on mucosal samples through quantitative PCR.

Results
Eight patients with previous failure to anti-TNF agents, were sampled prior to VDZ initiation. We identified 3 responders and 5 primary non-responders at week 10 after VDZ treatment initiation. We found 15 genes up-regulated in non-responders compared to responders with a trend towards statistical significance (p=0.057). The highest fold-change was obtained for CXCL8.

Conclusion
We identified 15 mucosal transcripts differentially expressed in VDZ primary non-responder UC patients. Of those, the highest fold change was observed for CXCL8. Enlarging the cohort might contribute to achievement of statistical significance for the data presented. CXCL8 up-regulation seems to predict lack of response to VDZ treatment and represents an interesting future therapeutic target in UC.
P067 Volumetric Assessment of Treatment Response in Newly Diagnosed Crohn Disease: A Pilot Study
Authors: Derinkuyu B E , Bard A , Naim I , Tkach J A , Denson L A , Dillman J R 
Published: January 2024

Abstract

Background
Traditionally, mural thickness and disease length have been the radiological standards for assessing Crohn's Disease (CD) severity and treatment response. Our study aimed to evaluate and compare these linear measurements with volumetric ones in newly diagnosed pediatric CD, as well as to assess the concordance between manual and semi-automated volumetric methods.

Methods
In this single-center, prospective study, 20 children with newly diagnosed ileal CD treated with anti-TNF therapy from Dec 2018 to Oct 2021 (8 females; median age=14.5 years) underwent dedicated research MRI examinations at three timepoints – diagnosis (baseline) as well as 6 weeks and 6 months into therapy. For each exam and using T2-weighted Single Shot Fast Spin Echo (SSFSE) images, a single radiologist measured maximum bowel wall thickness (BWT, mm) and length of disease (cm). The inflamed ileum was manually segmented to measure tissue volume (ml) (Entrolytics; Motilent, London, UK). Semi-automated 3D volumetric measurements of the inflamed ileum (GI Seg tool) were created using the same platform. Estimated maximum BWT also was automatically calculated from manually-edited algorithmically generated masks. Mixed-effects models evaluated measurement changes over time. Intra-class correlation assessed absolute agreement between manual and automated volumetric assessments.

Results
BWT decreased over time with treatment (0.76 vs. 0.58 vs. 0.45 cm; p&lt;0.0001), with a 24% decrease from baseline to 6 weeks and a 41% decrease from baseline to 6 months. Similarly, there was a significant decrease in length of disease over time (19.2 vs. 12.2 vs. 8.0 cm; p=0.002), with a 36% decrease from baseline to 6 weeks and a 58% decrease from baseline to 6 months. Manual volumetric measurements also showed a significant treatment response (19.8 vs. 11.6 vs. 5.1 ml; p&lt;0.0001), with a 41% decrease from baseline to 6 weeks and a 74% decrease from baseline to 6 months. Using the semi-automated segmentation tool, the volume of inflamed bowel also decreased significantly over time (24.0 vs. 15.1 vs. 9.1 ml; p=0.0007), decreasing 37% between baseline and 6 weeks and 62% between baseline and 6 months. There was good agreement between manual and semi-automated volumetric bowel assessments (ICC=0.78 [95% CI: 0.57-0.88]). ICC between manual and code-estimated Max BWT was 0.60 [95% CI: 0.42, 0.72] with a strong positive correlation (r=0.839; p &lt;0.001) between these two methods as shown in the Figure.

Conclusion
Volumetric assessments, along with automatic measurements of bowel wall thickness, show promise in accurately assessing treatment response in pediatric CD. These methods might provide more consistent and repeatable measurements, essential for long-term disease monitoring and management.
P068 Recapitulation of human colonocytes in situ by human colon organoids in vitro and after orthotopic transplantation
Authors: Hausmann A , Post F , Clement D L , Skov J , Steenholdt C , Mund A , Nielsen O H , Mann M , Jensen K B 
Published: January 2024

Abstract

Background
The intestinal epithelium plays a central role in human health and disease, and several chronic inflammatory disorders associate with a weakened epithelial barrier. The organoid model allows the cultivation, expansion and analysis of non-immortalized intestinal epithelial cells and has been instrumental in studying epithelial behavior in homeostasis and disease. Recent advances in human organoid transplantation into mouse and human lay the base for models to study human epithelial cell behavior within the intestinal tissue context, and promise novel therapeutic approaches for diseases such as short bowel syndrome and inflammatory bowel disease. It remained unclear how organoid transplantation into the colon would affect epithelial phenotypes and protein expression, which is key to assess the suitability of this model to study human epithelial cells in situ and safety aspects upon transplantation into human recipients.

Methods
To address this, we employed state-of-the-art deep visual proteomics to compare human colonic epithelial stem and differentiated cells in vivo, upon transplantation in situ, and to organoids cultured in vitro.

Results
We find that organoids transplanted into the murine colon closely resemble human intestinal epithelial cells in vivo compared to organoids grown in vitro, indicating that organoid culture induces a transient shift in epithelial phenotypes, which is reversible upon reintroduction into the mucosa. Phenotypic differences between epithelial cells in vitro and in situ/in vivo were largely driven by hallmarks of high proliferation and lower functional differentiation in organoids, likely due to culture conditions.

Conclusion
Taken together, we demonstrate that transplanted epithelial cells in situ represent a physiological, relevant model for studying functional aspects of mature colonocytes compared to the organoid model. We furthermore show that the proliferative phenotype of organoids in vitro is a transient state driven by culture conditions, which is reversible upon reintroduction into the mucosal environment. This is an important consideration regarding the safety of organoid transplantation into humans as a potential therapeutic strategy.
P076 Dock2 acts as a tumour suppressor via immune cell regulation of IDO1 in Inflammatory Bowel Disease–associated colorectal cancer
Authors: Churchhouse MD A , Billard C V , Pohl S Ö , Donnelly K , Suzuki T , Von Kriegsheim A , Arends M J , Coffelt S B , Myant K B 
Published: January 2024

Abstract

Background
Inflammatory Bowel Disease-associated colorectal cancer (IBDCRC) is a known and serious complication of Inflammatory Bowel Disease (IBD) affecting the colon. However, relatively little is known about the pathogenesis of IBD-associated colorectal cancer in comparison with its sporadic cancer counterpart. Mutations in Dock2 occur in around 10% of IBD-associated colorectal cancers.

Methods
We used an APC-mediated mouse model of inflammation-associated tumourigenesis. VilApcfl/+Dock2tm1b/tm1b and VilApcfl/+ (control) mice were subjected to chronic dextran sodium sulphate (DSS) colitis and aged. After tamoxifen induction, mice were given two seven-day rounds of 0.5% DSS, interspersed with normal drinking water, and then aged to 47 days before culling for analysis. Additionally in vitro, Apc deficient, tumourigenic colonic organoids were generated by deleting Apc from wild type and Dock2tm1a/tm1a colonic organoids using CRISPR/Cas9.

Results
We found that loss of Dock2 increases tumourigenesis (both in terms of tumour number and tumour burden) via immune dysregulation in an APC-mediated model of inflammation-induced tumourigenesis in vivo. The increased tumourigenesis observed is associated with a CD3 and gamma delta (γδ) T-positive immune cell infiltrate, an interferon gamma signature, and a significant upregulation of Ido1 (which catalyses the conversion of amino acid tryptophan to kynurenine). In tumours from VilApcfl/+Dock2tm1b/tm1b mice, tryptophan is reduced whilst the metabolite xanthurenate is increased, demonstrating IDO activity. Separately in vitro, we showed that epithelial IDO1 is induced by administration of interferon gamma. We demonstrated a source of this interferon gamma as γδ T cells, which are increased in tumours of mice lacking Dock2. Critically, inhibition of IDO1 (with 1-L-MT) abrogated the increased tumourigenesis observed as a result of Dock2 loss in mice.

Conclusion
Overall, we have identified a role for γδ T cells in promoting tumour initiation via Ido1 expression, using a Dock2 model to accentuate this phenotype.Further work is now needed to both fully characterise this novel pathway in IBDCRC, and establish how immune dysregulation promotes tumourigenesis, but it opens exciting potential for a therapeutic strategy in preventing cancer as a result of Inflammatory Bowel Disease.
P087 IFN-γ-Induced Intestinal Epithelial Cell Type-Specific Cytotoxic Responses of Human Enteroids: PANoptosis and The Protective Role of Selective JAK1 Inhibitors
Authors: Hong S N , Chansu L , Minjee K , Yujin L , Songee B , Ji Eun K , Young-Ho K 
Published: January 2024

Abstract

Background
Interferon-gamma (IFN-γ) plays an important role in the development of intestinal injury and inflammatory bowel disease (IBD). Using human intestinal organoid (enteorid) models, this study was investigated 1) what is the major response of intestinal epithelial cells (IECs) induced by IFN-γ to elucidate; 2) which programmed cell death (PCD) pathways cause IFN-γ-induced cell death on IECs in the absence of intestinal microbiota and immune cells; 3) how the expression of cell-cell adhesion molecules in epithelial cells is altered by IFN-γ; 4) how epithelial cell differentiation is altered by IFN-γ; 5) whether there is a difference in IFN-γ-induced PCD between different epithelial cell types; and 6) which molecules can block IFN-γ-induced PCD in IECs.

Methods
Using human enteroids, the major response of IECs induced by IFN-γ was evaluated, focusing on the IFN-γ-induced PCD pathway. The intestinal epithelial cell type-specific response to IFN-γ was assessed by bulk and single-cell RNA sequencing (RNA-seq). Furthermore, the molecules to block IFN-γ-induced PCD in IECs were evaluated.

Results
As the concentration of IFN-γ in the culture media increased, disruption of organoid structure, growth arrest, and cell death were observed in IFN-γ-treated enteroids on organoid reconstitution, MTT, and EdU assay. Bulk RNA-seq and western blot were identified the activation of pyroptosis, apoptosis, and necroptosis to form the collective inflammatory cell death pathway of PANoptosis. Single-cell RNA-seq indicated that IFN-γ altered epithelial cell differentiation in human enteroids, including expansion of the intstinal stem cell (ISC) population and depletion of the enterocyte population. PCD-associated gene expression was upregulated in enterocytes and goblet cells, but not in ISCs and paneth cells. Individual PCD inhibitors may be insufficient to prevent IFN-γ-induced cytotoxicity, whereas upadacitinib interferes with the downstream signaling of IFN-γ by inhibiting the activity of JAK1 kinase, resulting in effective blocking of PANoptosis.

Conclusion
PANoptosis is the major mechanism of IFN-γ-induced IEC damage, which was blocked by a selective JAK1 inhibitor. ECs were particularly susceptible to IFN-γ-induced PANoptosis.
* This work was supported by the National Research Foundation of Korea(NRF) grant funded by the Korea government(MSIT) (2022R1A2B5B02002092 and 2021R1C1C2095192) and Future Medicine 2030 Project of the Samsung Medical Center (SMO1230011).
P096 Human extrachromosomal circular DNA is an emerging biomarker in Inflammatory Bowel Disease
Authors: Petito V , DI VINCENZO F , Gerovska D , Piazzesi A , Russo A , Turchini L , Masi L , Lopetuso L R , Abreu M T , Regenberg B , Gasbarrini A , Putignani L , Bravo Araúzo M J , Scaldaferri F 
Published: January 2024

Abstract

Background
Inflammatory Bowel Diseases (IBD) are chronic multifactorial disorders, which affect the gastrointestinal tract, including Ulcerative Colitis (UC) and Crohn’s Disease (CD). The existence of extrachromosomal circular DNA fragments (eccDNA) is well established, and it arises from all parts of the genome. eccDNA has mainly been studied in the context of cancer and not in relation to other diseases, and it has become a promising diagnostic and prognostic biomarker for different types of cancer. Herein, we investigate for the first time the role of eccDNA in IBD.

Methods
Forty consecutive IBD patients (19 CD, 21 UC) and 13 HC were enrolled, who underwent screening colonoscopy were prospectively enrolled at our center in this observational, case-controlled study. In IBD patients, disease activity was assessed using PMS and MES for UC, and HBI and SES-CD for CD. Colonic biopsies were collected from both inflamed and healthy mucosa in IBD patients and from HC. eccDNA was enriched, sequenced, and identified with Circle Finder from intestinal biopsies.

Results
Colonic mucosal samples from IBD patients showed increased average of eccDNAs, across all chromosomes than samples from HC. Furthermore, there was a slight yet significant tendency for larger eccDNAs in IBDs compared to HCs. Focusing on eccDNA coming from genic elements ("genic eccDNAs"), approximately 60% were fragments from protein coding genes, 32% from non-coding RNAs and 8% from pseudogenes. IBD patients had, on average, significantly more genic eccDNAs in their intestines as compared to HC. Moreover, IBD in remission had fewer eccDNAs in their intestines than active disease, although not statistically significant. eccDNAs from phosphodiesterase genes and genes involved in lipid metabolism were enriched in patients with active IBD than patients in remission. eccDNA from inflamed mucosa (both in UC and in CD) show an enrichment of genes related to inflammatory and immune pathways, such as MAPK, mTOR, ErB, Rap-1 and cGMP (SPOKE3, GRID2, DLEU1, ITGA8, NRG1).

Conclusion
We are the first to uncover an IBD-specific pattern of eccDNA production. Furthermore, we identified genic hotspots which characterize active vs. inactive disease and inflamed vs. healthy colonic tissue. We propose that eccDNA identification could be a promising new diagnostic marker for IBD patients.
P100 Salivary exosomes aggravate colitis via oral-gut axis
Authors: Yang C , Chen J , Wu J , Zhao Y , Xu Y , You P , Xu J , Chen N 
Published: January 2024

Abstract

Background
Inflammatory bowel disease (IBD) is a chronic intestinal immune-dysfunctional disease, while the presence of persistent triggering factors leading to relapsing and remitting inflammation in IBD remains undetermined. The oral cavity is one of the most frequently affected extraintestinal organ in IBD, and literature highlights the oral cavity's influence on gastrointestinal conditions. The understanding of alternative mechanisms in the long-distance interaction between the oral cavity and gut is limited. Exosomes exist in various bodily fluids and facilitate intercellular communication. Thus, we aimed to further explore the role of salivary exosomes in aggravating colitis via bridging oral cavity and gut.

Methods
Salivary exosomes were obtained from active IBD patients, remission IBD patients, and healthy donors using ultracentrifugation. In vivo, we established a dextran sulfate sodium (DSS)-induced colitis model to investigate the possible role and mechanisms of salivary exosomes. In vitro, THP-1 cells and Caco-2 cells were stimulated with salivary exosomes respectively and the expression of related inflammatory factors was detected. Moreover, our investigated the immune regulatory mechanism of salivary exosomes by analyzing their microRNA profiles.

Results
DIL-labeled salivary exosomes accumulated in mouse colon at 6 hours post-gavage, indicating their ability to reach and accumulate in the colon through the "oral-gut axis" (Figure 1A). Salivary exosomes of active IBD patients (active IBD-Sexos) exacerbated colitis in DSS mouse, while salivary exosomes derived from remission IBD patients or healthy donors not (Figure1B). The potential mechanisms may include remodeling of macrophage phenotypes by activating the NF-κB signaling pathway (Figure1D-F), impairment of intestinal mucosal barrier function (Figure1C), and modulation of the intestinal microbiota. Co-culture of THP-1 cells and Caco-2 cells with active IBD-Sexos were shown to raise inflammation in macrophages, which lead to increased release of inflammatory factors and promoted macrophage M1 polarization(Figure1G-K). We found 35 differentially expressed microRNAs in active IBD-Sexos compared to exosomes from both remission IBD patients and healthy donors (Figure1L). Specifically, miR-223 regulates the inflammatory response of IBD. MiR-119b-5p and miR-203-5p impact the NF-κB signaling pathway.These microRNAs promote inflammation, suggesting a possible role of salivary exosome delivery in IBD pathogenesis.

Conclusion
In conclusion, our study provides evidence that salivary exosomes play a significant role in the communication between the oral cavity and gut, beyond microorganisms or immune cells, with the potential to exacerbate intestinal inflammation in IBD (Figure1M).
P110 Heterogeneous response of colonoid-derived monolayers to TNFα and IFNγ exposure: functional and morphological characterization
Authors: Parente I , Chiara L , Gaiani F , de’Angelis G L , Barocelli E , Bertoni S 
Published: January 2024

Abstract

Background
Despite the progress made in the diagnosis and treatment of inflammatory bowel diseases (IBD), incidence and prevalence are still growing. Considering the lack of human preclinical studies, reliable models that mimic the inflamed intestinal epithelium are increasingly explored. Patient-derived colonoids are a powerful tool that recapitulate, in vitro,many physiological features of the human colon. The present work aims to characterize, functionally and morphologically, colonoid-derived monolayers (CDMs) and the changes induced by TNFα and IFNγ, comparing their effects with Caco-2 monolayers.

Methods
Colonic crypts, isolated from biopsies of 5 healthy volunteers undergoing colonoscopy for reasons other than IBD, were embedded in 70% (v/v) Matrigel® and grown for 5-7 days. IntestiCultTM OGM was used to generate cystic-like colonoids, further expanded in suspension cultures. After dissociation, cells were seeded at 7.5x105 cells/cm2 onto 24-well inserts coated with Matrigel® (1:50). The integrity of the epithelial barriers was monitored by TEER. When monolayers reached confluence (TEER≥100 Ω·cm2), IntestiCultTM OGM was switched to ODM. Differentiated CDMs were exposed for 24h to 25ng/mL TNFα and 25ng/mL IFNγ. Changes in cell morphology and viability, IL8 and NF-kB p65 levels, and FITC-D4 apparent permeability (Papp) were determined. Caco-2 cells, seeded at 5x104 cells/cm2, were exposed after 21 days to the same cytokine cocktail for 24h: TEER was monitored and IL8 release was quantified.

Results
CDMs developed into robust epithelial barriers, with TEER values increasing over time, indicating that tight junctions were formed. Immunocytochemistry (ICC) staining for villin and MUC2 revealed that cells were polarized and differentiated. Exposure to TNFα and IFNγ impaired significantly, although heterogeneously, the barrier integrity of CDMs and increased the release of IL8. When the barrier damage was more severe, FITC-D4 Papp and NF-kB p65 levels also raised, while cell viability was reduced. ICC images showed a large number of apoptotic cells near the basal side, and a decrease in the expression of villin and MUC2, suggesting that cell polarity and differentiation were impaired. In Caco-2 monolayers, cytokine exposure induced a mild damage on the barrier integrity and a significantly lower release of IL8, when compared to CDMs.

Conclusion
CDMs from different patients formed functional barriers that showed heterogenous sensitivity to TNFα and IFNγ exposure. In essence, all CDMs showed compromised epithelial barriers, altered cell morphology, and increased IL-8 levels. Differences between the IL8 released by Caco-2 and CDMs highlight the variation in the inflammatory response of the two models.