bluuebunny/crossref_metadata_2025_split huggingface dataset:
P0095 Human multi-lineage gut-on-chip to study near-physiological epithelial barrier function and directed secretion
Authors: Hensel I V , Steinhauer M , Éliás S , Neurath M F , Günther C , Resnik-Docampo M 
Published: January 2025

Abstract

Background
The human intestinal epithelium is composed of diverse cell types, enabling it to fulfil essential digestive functions such as absorption and secretion, while simultaneously acting as an immune interface. This epithelial barrier safeguards underlying immune cells in the lamina propria from luminal antigens by maintaining a mucus layer rich in antimicrobial peptides, preventing unwanted immune responses and allowing regulated cytokine and chemokine gradients. Despite advances in single-cell transcriptomics, understanding specific epithelial cell secretions remains limited.

Methods
To address this, we developed a human intestinal organ-on-chip (OoC) model, derived from human colon organoids, capable of forming a heterogenous, functional epithelial barrier without permeable supports. This OoC model provides concurrent access to luminal and basal compartments, allowing for mid- to high-throughput screenings, overcoming limitations of conventional transwell or 3D organoid cultures.

Results
In our study, we analysed barrier function by measuring transepithelial electrical resistance (TEER) and permeability as well as confirming tight junction assemble marked by ZO-1 and occludin. Cell type composition was modulated using distinct culture media, resulting in a heterogeneous cell composition including goblet cells, colonocytes, and enteroendocrine cells along with the proliferative compartment, evidenced by transcriptomic and protein analyses. Cytokine and chemokine secretions, notably CCL2, CCL20, IL-8, IL-18, and CXCL10, demonstrated cell type-dependent and spatially directed patterns, suggesting location-specific secretion along the crypt-surface axis in vivo. Under basal and stimulated conditions, our model retained responsiveness to bacterial stimuli, gluten-derived antigens, and pro-inflammatory conditions, confirming the important role of epithelial cells in immune response regulation.

Conclusion
Collectively, this OoC model offers a physiologically relevant platform for exploring human intestinal barrier function and epithelial-immune communication. This scalable, multi-lineage in vitro model advances our capacity to study directed secretion, barrier integrity, and epithelial cell type dependent immune response, supporting applications in disease modelling and personalized medicine development.
P0097 STING pathway drives cellular tryptophan degradation and pro-inflammatory responses in intestinal fibroblasts
Authors: Wu Q , Yang G , Xiang H , Shima K , Springer E , Bornhäuser J , Welz L , Aden K ,   AG Aden
Published: January 2025

Abstract

Background
Tryptophan metabolism is severely disrupted in IBD. Pro-inflammatory cytokines activate the first rate-limiting enzyme IDO1 leading to tryptophan degradation through the kynurenine pathway. Although Trp degradation typically support de novo NAD synthesis via KP activation, evidence suggests a metabolic block at the downstream enzyme QPRT in IBD. STING has been described as inducing the secretion of type I interferons and other inflammatory cytokines, suggesting its important role in regulating intestinal homeostasis. Several studies have reported an association between STING-mediated IDO1 activity and its role in promoting tumour immune evasion. However, the relationship between STING pathway and tryptophan metabolism in intestine has not be understood. This study aims to investigate the effect of STING signaling on tryptophan degradation and explore how the metabolic blockage in tryptophan-NAD axis may influence STING-mediated immune response.

Methods
To investigate the STING pathway's role in tryptophan metabolism in intestine, we utilized human colonic fibroblast cell line CCD-18co. Quantitative RT-PCR and Western blot were employed to measure mRNA and protein expression. Tryptophan metabolism was quantified via LC-MS. siRNA was performed to mediate QPRT knockdown. Intracellular NAD level were assessed by NAD-glo assay. Seahorse assay was conducted to evaluate mitochondrial function.

Results
We screened a range of established IDO1-inducing cytokines (IFNγ, TNFα, etc.) and compared their effects on IDO1 expression with STING agonists diABZI, dsDNA and 2’3’cGAMP. STING agonists induced significantly higher IDO1 expression than any of the cytokines tested. While cultivation of in presence of Anifrolumab (type I IFN receptor antagonist) and Tofacitinib (pan-JAK inhibitor) strongly inhibited STING-induced IDO1 upregulation. LC-MS showed upregulation of IDO1 drive tryptophan into kynurenine pathway, which was again inhibited by Anifrolumab and Tofacitinib. To mimic the reduced QPRT expression in IBD, we performed QPRT knockdown. QPRT deficiency led to STING pathway overactivation upon diABZI treatment, resulting in elevated expression of pro-inflammatory cytokines and phosphorylation of STING and TBK1. QPRT-deficient cells exhibited reduced intracellular NAD level and impaired mitochondrial function. Supplementation with the nicotinamide riboside restored NAD levels, which effectively reduced the elevated cytokine expression caused by QPRT knockdown.

Conclusion
Our data provide a novel link of how STING activation in intestinal fibroblasts drives tryptophan degradation via KP pathway. Additionally, QPRT-related metabolic blockage enhance STING-mediated pro-inflammatory response, which can be mitigated by NAD precursor supplementation
P0103 Systems biology analysis of cytokine signalling in IBD highlights the importance of TYK2-dependent pathways
Authors: Desch N , Petrakis I , Singh N , Tang J , Sirota-Madi A , Schuster R , Davidzohn N , Wyrobnik I , Shen-Orr S S , Chowers Y , Panchal P , Wennbo H , Thakker P , Arunachalam V 
Published: January 2025

Abstract

Background
Ulcerative colitis (UC) and Crohn’s disease (CD), collectively inflammatory bowel disease (IBD), are characterized by chronic gastrointestinal tract inflammation. Recently, there has been interest in the use of selective oral tyrosine kinase 2 (TYK2) inhibitors for IBD treatment, which inhibit signalling downstream of multiple pro-inflammatory cytokines and may have an improved safety profile relative to non-specific Janus kinase (JAK) inhibition. Here, we use a transcriptomic approach to assess the involvement of TYK2-dependent signalling pathways in IBD, and how these are impacted by currently available treatments.

Methods
TYK2-dependent gene signatures were characterized using cytokine stimulation studies and co-expression analysis. Involvement of signature modules in IBD was assessed using disease model data generated from 4059 biopsy samples from 2993 unique patients in 15 UC and 38 CD clinical studies, including assessments of golimumab, infliximab, ustekinumab, and vedolizumab. Pathway differential expression analysis was performed using Gene Set Enrichment Analysis (GSEA) and single-sample GSEA methods.1,2

Results
Seven TYK2-dependent gene signature modules were defined, including two for type I interferon (IFN), three for IL-23, and two for IL-12. Type I IFN signatures were strongly enriched in both UC and CD, while enrichment of IL-23 was stronger for UC than for CD, and enrichment of IL-12 was stronger for CD than for UC. In each case, gene signature module enrichment was associated with greater disease severity. Pathway enrichment analysis of data from individual clinical studies demonstrated that specific type I IFN and IL-12 modules were significantly reduced, but not completely ameliorated, following treatment with golimumab, infliximab, ustekinumab, or vedolizumab. Further assessment of response to therapy in these studies showed that enrichment of type I IFN, IL-23, and IL-12 signature modules was associated with non-response to golimumab, infliximab, and vedolizumab.

Conclusion
Enrichment of TYK2-dependent gene signatures, including type I IFN, IL-23, and IL-12, is associated with both UC and CD. These TYK2-dependent enrichments are not fully mitigated through currently available treatments, and may be associated with non-response to treatment. It is important that all three signalling pathways are considered in the development of future treatment options.

References
1.Barbie DA, Tamayo P, Boehm JS, et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. Nov 5 2009;462(7269):108-12. doi:10.1038/nature08460
2.Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. Oct 25 2005;102(43):15545-50. doi:10.1073/pnas.0506580102
P0112 Cannabidiol (CBD) targeting of colorectal cancer cells is mutation-independent and via CB2 receptor
Authors: Moniruzzaman M , Janjua T , Begun J , Popat A 
Published: January 2025

Abstract

Background
Cannabidiol (CBD) is a non-neurotoxic, phytocannabinoid from cannabis with reported medicinal properties including anti-epileptic and anti-inflammatory activity. Several in vitro and in vivo studies have shown that CBD has antitumour potential against colorectal cancer (CRC), the third deadliest cancer in the world. However, as different mutations influence the antitumour effects and CBD can bind a variety of receptors, it is yet to be determined whether specific CRC mutations affect CBD’s efficacy in treatment of CRC.

Methods
To investigate this, we selected four CRC cell lines, including HCT116, HT-29, LS174T, and LS153 which harbour distinct mutations. Cells were treated with a range of concentrations of CBD to evaluate its cytotoxic effects and impact on cell proliferation, migration, and invasion using a live-cell imaging system. IC50 values were then calculated for each parameter. The level of endoplasmic reticulum (ER) stress pathway markers was also measured using qRTPCR. The requirements for CB1 or CB2 receptor-medicated signalling was investigated using the selective inhibitors AM251 and SR144528, respectively.

Results
Our results demonstrate that CBD induces apoptosis and halts proliferation, migration, and invasion of CRC cells in a concentration dependent manner. CBD showed potent antitumour effects in the tested cell lines with no obvious effect of different mutations such as KRAS, BRAF, APC, PTEN etc. CBD also induced ER stress in CRC cells but not the healthy intestinal organoids. Co-treatment with SR144528 inhibited the effects of indicating involvement of CB2 receptor activation in the anticancer effects of CBD.

Conclusion
Together, these results demonstrated that CBD could be effective for CRC regardless of the underlying mutation through CB2 receptor activation.
P0114 Tracking Crohn’s Disease Progression through Extracellular Matrix Remodeling: A Longitudinal Study of Pre- and Post-Resection Samples
Authors: Poulsen A , Alexdóttir M S , Buhl Riis L , Ovesen P D , Rasmussen J , Wewer M D , Lin V , Lagström R M B , Al-Sheikh M , Dahl E , Ries A , Porsbjerg L , Katranara Tsapanou T , Pehrsson M , Gögenur I , Krarup P M , Burisch J , Mortensen J H , Seidelin J B 
Published: January 2025

Abstract

Background
Crohn's disease (CD) is a chronic inflammatory condition that can lead to irreversible intestinal damage. Fibrosis, caused by imbalanced extracellular matrix (ECM) remodeling, is difficult to manage, as current anti-inflammatory treatments do not prevent or reverse these processes. ECM fragments released during remodeling may serve as biomarkers for transmural disease activity and fibrosis burden. This study evaluated the correlation of serum C3M, PRO-C3, and PRO-C16 levels and their potential to differentiate between stenosing and luminal CD.

Methods
In this prospective cohort study 62 patients with stenosing CD requiring resection without residual disease and 49 with luminal CD managed medically were included. Phenotype was assessed by diagnostic imaging and/or endoscopy at inclusion. Serum levels of C3M, PRO-C3, and PRO-C16 were measured pre- and post-resection, Neo-epitope specific biomarkers of type III collagen degradation (C3M) and type III and XVI collagen formation (PRO-C3, PRO-C16) were measured in serum using a competitive ELISA. To compare the stenotic and luminal groups, the Wilcoxon signed-rank test was used, and for pre- and post-resection ECM marker values, one-way ANOVA with Tukey’s post hoc was applied.

Results
Baseline levels of PRO-C3 were significantly higher in patients with stenosing CD compared to those with luminal CD (57.3 (IQR: 47.7-75.7)) vs 43.4 (36.0-52.9) ng/ml, p&lt;0.001). Conversely, PRO-C16 levels were higher in the luminal group compared to the stenotic group (2961.5 (2780.8-3264.3) vs 2677.0 (2407.5-2904.5), p&lt;0.001). C3M levels showed no difference at baseline between stenotic and luminal patients (596.0 (546.0-677.5) vs 585.0 (538.5-643.3), p=0.394). Post-resection, C3M and PRO-C3 levels decreased initially (p=0.003 and &lt;0.001), then showed an increase at one month, stabilizing from three to twelve months. The median PRO-C16 value decreased significantly the day after surgery and subsequently increased throughout the first year to levels exceeding pre-resection values (Figure 1).

Conclusion
Baseline biomarker differences between stenosing and luminal CD suggest their potential to distinguish disease phenotypes. However, a sustained post-operative change in ECM markers linked to fibrostenotic phenotype was not observed in patients, challenging this explanation. Day one post-resection ECM marker changes likely reflected wound healing, while subsequent dynamics may indicate collagen processes relevant to stenosis formation without being primary local drivers. These findings underscore the need for longitudinal and cross-sectional studies to clarify ECM biomarkers' role in tissue repair and fibrosis in CD.
P0124 Therapeutic Potential of Adipose-Derived Extracellular Vesicles for Inflammation Modulation and Mucosal Healing in Crohn’s Disease
Authors: Clua L , Suau R , Monfort-Ferré D , Boronat-Toscano A , Menacho M , Caro A , Mañas M J , Mañosa M , Domènech E , Manyé J , Serena C 
Published: January 2025

Abstract

Background
Crohn’s disease (CD) is a chronic, idiopathic inflammatory bowel disease characterised by discontinuous lesions and transmural inflammation that can affect the entire gastrointestinal tract. Despite recent therapeutic advancements, around 50% of patients with CD require at least one surgical intervention within ten years of diagnosis, with 80% of these patients developing new lesions following surgery.1 Emerging evidence highlights that the therapeutic efficacy of mesenchymal stem cells (MSCs) is predominantly attributed to the extracellular vesicles (EVs) they secrete.2 These nanovesicles have gained recognition as critical mediators of anti-inflammatory responses and tissue repair. This research seeks to develop MSC-derived EV-based acellular therapy to regulate the immune response, heal the intestinal mucosa, restore gut microbiota balance, and ultimately reduce disease severity and recurrence.

Methods
Inclusion criteria for selecting healthy donors for obtaining EVs derived from subcutaneous adipose tissue MSCs include sex, age &lt;40 years, and BMI &lt;25 kg/m². Exclusion criteria include smokers, alcohol consumers, and patients with cancer or other chronic conditions. EV isolation was performed using size-exclusion chromatography, and characterisation was conducted via flow cytometry and electron microscopy (Cryo-TEM). To assess the therapeutic properties of the EVs, biopsies of inflamed perilesional adipose tissue and intestinal mucosa from CD patients were treated with a dose of 150 µg/mL for 20 hours. Finally, the gene expression profile of pro-inflammatory markers (TNFα, IL1B, IL6, and CCL2) and anti-inflammatory markers (IL10) was analysed by qPCR.

Results
The isolation and characterization of EVs were successfully demonstrated, along with their functional efficacy in both adipose and intestinal explant models. Explants treatment with EVs resulted in a significant reduction in pro-inflammatory cytokines, with IL-1β and TNF-α expression decreased by up to 200-fold compared to untreated explants, while also promoting a notable increase in the anti-inflammatory marker IL-10.

Conclusion
Adipose tissue-derived EVs could regulate inflammation and promote the regeneration of the intestinal barrier, thus reducing the severity of CD and lowering the risk of post-surgical recurrence.

References
1Golovics PA, Mandel MD, Lovasz BD, Lakatos PL. Inflammatory bowel disease course in Crohn’s disease: Is the natural history changing? World J Gastroenterol. 2014;20(12):3198-3207.
2.Zhou Y, Yamamoto Y, Xiao Z, Ochiya T. The immunomodulatory functions of mesenchymal stromal/stem cells mediated via paracrine activity. J Clin Med. 2019;8(1)
P0126 Single-cell analysis reveals enrichment of mucosal Th17-polarized T cells in Acute Severe Ulcerative Colitis
Authors: Bourgonje A R , Meringer H , Roudko V , Jha D , Canales-Herrerias P , Livanos A E , Cossarini F , Tankelevich M , D'Souza D , Nie K , Kim-Schulze S , Petralia F , Kayal M , Colombel J F , Mehandru S 
Published: January 2025

Abstract

Background
Acute severe ulcerative colitis (ASUC), a severe and potentially life-threatening manifestation of ulcerative colitis (UC) affects up to 25% of patients over their lifetime and requires urgent medical intervention. T cell subsets and myeloid cells play a critical role in the pathogenesis of mucosal inflammation. In this study, we aimed to perform an unbiased analysis of mucosal immune cell populations in patients with ASUC and to identify ASUC-specific cell type alterations.

Methods
Ten adult ASUC patients (defined by the Truelove and Witts criteria), 7 patients with active UC (not fulfilling ASUC criteria), and 5 normal volunteers (NV) were recruited (Fig. 1A). Intestinal mononuclear cells were isolated from endoscopically obtained intestinal biopsies and analyzed by single-cell RNA-sequencing (scRNA-seq). Linear mixed-effects models were applied to compare lineage-normalized cell type fractions across groups, while adjusting for relevant covariates including age, sex, and body mass index.

Results
Unsupervised clustering of 127,795 cells, expressing 38,224 unique genes, identified 45 distinct cell types (Fig. 1B). Among the salient findings specific to lymphoid cells, re-clustering of the T cell/NK cell compartment identified 9 cell subsets (Fig. 1C-D). Notably, TH17 cells (RORA, CTSH, CXCR6, and CCL20) and cycling TH17 cells (MKI67, PCLAF, SMC4, NUSAP1, and RRM2) were significantly enriched in patients with ASUC compared to those with active UC (adjusted P=0.019 and P=0.027, respectively) and NV (adjusted P&lt;0.001 for both) (Fig. 1E-F). Among myeloid cells, of the 11 delineated subsets, patients with ASUC showed a significant reduction in lineage-normalized fractions of type 2 conventional dendritic cells (cDC2s) (CD1C, FCER1A) relative to both active UC and NV (adjusted P=0.017 for both) (Fig. 1G). Additionally, a cluster of CD14+ monocytes (CD14, FCN1, and LYZ) was significantly elevated in patients with ASUC compared to NV (adjusted P=0.032).

Conclusion
Elevated TH17 cell frequencies distinguish ASUC from UC. While further investigations, including protein-level validation of transcriptomic data and an assessment of the impact of cellular perturbation on treatment outcome, are ongoing, these findings shed light on a potentially underappreciated role for TH17-polarized T cells in ASUC.
P0127 Fistula-derived fibroblasts express genes associated with a dysfunctional wound healing process
Authors: Van Os B , Su J , Bruckner R , Zhou Z , van der Meulen-de Jong A , Hawinkels L , Barnhoorn M 
Published: January 2025

Abstract

Background
Approximately a third of patients with Crohn’s Disease will develop perianal fistulas. Perianal fistulas greatly impact the quality of life by causing pain, discharge and faecal incontinence. Current drug treatments in combination with surgery are not very effective in curing fistulas, and only a low number of patients with complex fistulas reach complete remission. One of the main reasons for the lack of treatment options is our limited understanding of the formation of these fistulas. In this study we investigated the role of fibroblasts in the formation of perianal fistulas by evaluating their expression profiles compared to healthy colonic fibroblasts.

Methods
To gain more insight into the characteristics of fistula fibroblasts, fibroblasts were isolated from fistula scrapings derived during drainage surgery from both CD (n = 8) and non-CD patients (n = 6) and from healthy colon tissue of non-IBD patients (n = 18). After expanding the fibroblasts in vitro, they were subjected to mRNA sequencing. After sequence alignment, gene set enrichment and pathway activation analysis was performed. Differentially regulated processes were further investigated in vitro to confirm these results.

Results
Remarkably, fibroblasts isolated from CD and non-CD fistulas share a similar transcriptional profile, with only 25 differentially expressed genes (DEGs) found between them. Comparing fistula derived fibroblasts with healthy colon fibroblasts revealed 3606 DEGs. Pathway analysis revealed increased extracellular matrix remodelling and proliferation but reduced inflammation in fistula fibroblasts compared to healthy colon. Strikingly, although collagen type 1 production was increased, myofibroblast-associated genes such as ACTA2, LRRC17, LRRC32, NKX2-3 and RSPO3 were decreased in fistula fibroblasts. We confirmed these observations in vitro.

Conclusion
Currently, CD and non-CD fistulas are treated differently. Whereas surgical removal is the main treatment for non-CD fistulas, CD fistulas are primarily treated with the combination of surgery and medication targeting inflammation. However, our results suggest that at least the fibroblasts isolated these fistulas are very much similar on a transcriptional level. We found these fibroblasts display a signature that seems to point at aberrant wound-healing. Further research in 3D co-cultures, comparing the role of fistula and healthy fibroblasts, will elucidate the role of these cells in the formation of fistulas.