bluuebunny/crossref_metadata_2025_split huggingface dataset:
P0082 Proteomic profiling of colonic mucosa in patients with ulcerative colitis: detection of molecular patterns of inflammation.
Authors: Iakovlev A A , Nukhova S , Tarasova G , Volkov A , Zubova A , Bashtovaya O , Piskovets V 
Published: January 2025

Abstract

Background
The mechanisms of recurrence and progression of ulcerative colitis (UC) require detailed study. Modern advances in proteomic analysis methods are ideal for studying the molecular characteristics of inflammation in the colonic mucosa (CM) of UC patients.

Methods
The study was comparative cohort with parallel design and included 88 patients (range from 22 to 35 years, 37 men and 51 women): 53 (60.2%) pancolitis and 35 (39.8%) left-sided UC, mild and moderate activity. The duration of UC was 5.3 years. The control group included 30 healthy individuals. Biosamples of CM in patients with UC in the active stage and in healthy persons were received by ileocolonoscopy with CM biopsy. The separation of individual proteins of CM was based on technologies of IEF, SDS-PAGE, 2DPAGE, by standard sets (MB-HIC C8 Kit, MB-IMAC Cu, MB-Wax Kit, «Bruker», USA). Automated mass spectrometry imaging was performed by MALDI-TOF-MS/MS, Ultraflex II, «Bruker», USA). The partially identified sequences were then submitted to “BLAST protein-protein” and screened against the Homo sapiens Swissprot database to check if this identification matched the MASCOT-identification (Matrix Science, UK). The data of the molecular interactions and functional features of proteins were received with STRING 10 database.

Results
Based on the data of standard methods of identification of UC and molecular phenotyping of colon mucosa we conducted new prognostic markers, molecular pathways of UC and diagnostic tests in patients with UC. We identified functional groups of peptides and proteins in molecular patterns of CM (fig. 1).
SMAD family member 2 (SMAD2) activates the transcription of TFG1β, that leads the development of fibrosis in colon submucosa in UC patients; the stimulation of the expression of apoС-III in affected CM in UC is associated with the activation of the FOXO1 signaling pathway that supports inflammatory processes; caspase 8 protects colonocytes from TNFα-induced cell death through a necroptosis mechanism via the blockade of the RIP3 expression. Significant decrease of the expression of PPARγ promotes the activation of STAT and AP-1 signaling pathways, that promotes the increase of the synthesis of IL-2, 6, 8, 12,TNFα, matrix metalloproteinases, the activity of immune and inflammation processes in colon mucosa. The reduction of expression of β-defensin-1 in cells of colon mucosa are accompanied with increased expression of CCR6, that promotes the formation of inflammatory infiltrates in colonic submucosa in UC.The molecular interactions of β-defensin-1 are presented on figure 2.

Conclusion
Bioinformatics analysis revealed the presence of the new potentially markers of the progression UC, that’s may provide for the development of novel diagnostic tests for UC.
P0083 Decisional needs among patients and physicians in Crohn's disease: A qualitative analysis
Authors: Cloots M , Hendrix E M B , Okegunna Y , Mingels S M B , van de Koppel I , Mujagic Z , Jeuring S , Dijkstra G , Duijvestein M , Römkens T E H , Dekker A L A J , Pierik M J , Fijten R R R 
Published: January 2025

Abstract

Background
Shared decision-making (SDM) is a collaborative process between patients and healthcare professionals (HCPs) that is essential to align treatment choices with patient values. The increasing variety of treatment options for Crohn’s Disease (CD) challenges the assessment and communication of risks and benefits for both patients and HCPs. Patient decision aids (PDAs) have been shown to be effective in enhancing patient-centered care across various decision-making contexts. This study aims to identify the informational needs of both patients and HCPs to develop an effective PDA for CD.

Methods
Qualitative semi-structured interviews were conducted with 7 CD patient representatives and 5 HCPs. Purposive sampling was used for recruitment of respondents. An empirical phenomenological approach was taken in the interviews to describe similarities and differences of experiences, needs, and preferences of CD patients and HCPs. Interviews were conducted face-to-face or digitally, audio recorded, and transcribed verbatim. Transcripts were thematically analysed through consecutive open, axial, and selective coding.

Results
Preliminary results showed most patients were not actively involved but rather advised in their treatment decisions. Physicians typically preferred a particular treatment but regularly offered patients choices between similar medication options if they wanted more involvement. The primary concerns for patients were the reduction of medication related physical, mental, and social complaints that they often experienced from side effects, form of administration, and fear of surgery. This was reflected in the patients’ need for general disease information, treatment pros and cons, and patient experience stories. Physicians acknowledge that patients wish to be well-informed and believe they provide adequate information. However, many patients express feeling under-informed and frequently look for additional resources. Both groups find the idea of a PDA offering general and personalised information at varying stages in the treatment journey appealing, though physicians caution that personalised content may not be suitable for all patients.

Conclusion
This study highlights a barrier between the approach taken by physicians and patients’ desire for information and involvement in treatment. Providing a reliable and accessible source of information at key decision moments throughout the patient journey could help resolve this barrier. A well-designed PDA for CD patients with reliable information could empower them with confidence and support SDM. However, careful implementation is necessary to accommodate diverse patient needs and preferences.
P0084 Secreted inflammatory protein profiles of human inflammatory bowel disease explants following treatment ex-vivo with licenced biologic therapies and patients’ in-vivo response
Authors: Corcoran R , O'Connell F , Schellenberg N , O'Sullivan J , Kevans D 
Published: January 2025

Abstract

Background
Patient-derived inflammatory bowel disease (IBD) ex-plants have potential for biomarker and therapy discovery. Infliximab (IFX), ustekinumab (UST) and vedolizumab (VDZ) are biologic therapies licenced for the induction and maintenance of remission in ulcerative colitis (UC) and Crohn’s disease (CD). All have demonstrated efficacy in IBD despite differing mechanisms of action. IBD explants have the potential to be used as a precision medicine tool, to gain further insights into disease biology and therapeutic mechanisms of action.
We aimed to evaluate the effect of IFX, UST and VDZ on inflammatory protein secretion profiles in ex-vivo human IBD ex-plants, whilst comparing these explant secretome variations with in-vivo patient data of patients who commenced these therapies in clinic.

Methods
Patients with IBD due to commence in-vivo biologic therapy, undergoing endoscopy, were prospectively recruited. Endoscopic biopsies were collected from the sigmoid colon and IBD ex-plants generated as per previously described methods. IBD explants were then cultured for 24 hours with an IgG control vehicle, IFX, UST and VDZ. After 24 hours, tissue conditioned media (TCM) from IBD explants was collected. TCM secreted inflammatory protein profiles were quantified using 54 V-plex ELISA (Meso Scale Diagnostics, USA). Secreted inflammatory protein profiles were compared between IgG vehicle (control) and UST, IFX, VDZ treated ex-plants. Principal component analysis (PCA) was carried out to characterise the influence of biologics on ex-vivo explant secreted inflammatory profiles. Clinical responses of patients treated with biologics in-vivo were also compared with explants inflammatory profiles.

Results
37 patients with were included (51% CD, 49% UC); age (median, [IQR]) 41[33-53] years, 49% male; disease duration (median, [IQR]) 9 [5-14] years. 23 patients were subsequently commenced on either IFX, UST or VDZ in-vivo and followed over 2 years to determine therapy response. PCA identified significant variation in the CD and UC secretome. Biologic therapy ex-vivo resulted in significant alterations and clustering in the UC secretome compared to control.

Conclusion
The IBD explant model recapitulates expected IBD pathology. These data demonstrate that significant differences between the CD and UC secretome. Treatment with licenced biologic therapies ex-vivo significantly alters multiple pro-inflammatory cytokines, chemokines and secreted proteins in IBD explants. Further study is required to completely understand the effects of licenced biologic therapies on the IBD tissue microenvironment.
P0085 Faecalibacterium prausnitzii induces an anti-inflammatory response and a metabolic reprogramming in human monocytes
Authors: Rolhion N , Danne C , Creusot L , Formiga R , Marquet F , Sedda D , Hua L , Ruffié P , Pham H P , Alonso Salgueiro I , Brot L , Michel M L , Lefevre J , Sokol H 
Published: January 2025

Abstract

Background
Faecalibacterium prausnitzii, a highly abundant bacterium in the human gut microbiota, has been linked to overall health and is notably decreased in pathological conditions, such as Inflammatory Bowel Disease (IBD). F. prausnitzii has shown anti-inflammatory properties in human and mouse models, notably through the induction of IL-10 signaling. Here, we investigated which cell types from human blood and intestinal tissue are responsible for producing IL-10 induced by F. prausnitzii, and providing the first mechanistic insights.

Methods
Immune cells isolated from human blood and intestinal lamina propria of patients with IBD and non-inflamed controls, were stimulated with F. prausnitzii EXL01 strain or Escherichia coli lipopolysaccharide (LPS) and analysed by Legendplex, ELISA, flow cytometry, RNA-sequencing (RNAseq), and Seahorse analyser.

Results
F. prausnitzii EXL01 strain induced the direct and dose-dependent production of IL-10 in CD14+ monocytes from the systemic circulation and intestinal tissue of IBD patients and non-inflamed controls, without inducing a pro-inflammatory response as compared to LPS stimulation. RNAseq analysis corroborated these results and revealed that F. prausnitzii EXL01 strain differentially affects cell energy metabolism compared to LPS. The anti-inflammatory response induced by F. prausnitzii in monocytes was dependent on mitochondrial respiration.

Conclusion
F. prausnitzii induces an anti-inflammatory response and rewires energy metabolism in human monocytes, which might explain its beneficial impact on intestinal inflammation and human health in general. These results provide new insight into the mechanisms underlying the anti-inflammatory effects of F. prausnitzii and are crucial for a better understanding of its potential use in the treatment of IBD. The well-characterised F. prausnitzii EXL01 is already in clinical development in Crohn's disease (NCT05542355), and the results of the first phase 1/2A study involving 8 patients will be available in early 2025.
P0086 The role of enteric glial cells in patients with ulcerative colitis.
Authors: Miyazaki H , Ogino T , Sekido Y , Takeda M , Hata T , Miyoshi N , Uemura M , Mizushima T , Doki Y , Eguchi H 
Published: January 2025

Abstract

Background
Enteric glial cells (EGCs) have traditionally been regarded as supportive cells within the enteric nervous system. However, recent studies indicate that, beyond their involvement in neural circuit formation, EGCs possess antigen-presenting capabilities and actively contribute to mucosal defense. In the mouse myenteric plexus, inflammation-inducing stimuli have been shown to trigger the expression of MHC class II on glial cells, which subsequently influences the differentiation of helper T-cell and regulatory T-cell subtypes, thereby maintaining immune homeostasis under inflammatory conditions. Nevertheless, research on EGCs in humans remains limited. Thus, this study aimed to elucidate the function and involvement of EGCs in the pathogenesis of ulcerative colitis (UC).

Methods
Normal colonic mucosa was obtained from histologically and macroscopically intact areas of patients with colorectal cancer (n=6). Colonic mucosa from UC patients, diagnosed based on established clinical, bacteriological, radiologic, and endoscopic criteria, was also obtained from surgically resected specimens (n=7). Lamina propria mononuclear cells were isolated through enzymatic digestion, and mesenchymal stromal fractions (CD31-CD45-EPCAM-CD90+), containing glial cells, were further isolated using flow cytometry for single-cell RNA sequencing (scRNA-seq) analysis and T cell differentiation assay.

Results
We identified a specific EGC population (Cluster 3: PDPN+ HLA-DR high) with high antigen-presenting capacity, which was selectively elevated at inflamed sites in UC. scRNA-seq analysis, transcription factor activity analysis, and gene-enriched pathway analysis indicated that IFNγ-STAT1 signaling activation within Cluster 3 enhances MHC class II expression. To assess T-cell effects, naive CD4+ T-cells were co-cultured with PDPN+ HLA-DR high cells isolated from UC samples. This co-culture induced differentiation into IL-10+ IL-17A+ CD4+ T-cells, with a positive correlation observed between the proportions of IL-10+ IL-17A+ CD4+ T-cells and PDPN+ HLA-DR high cells. Bulk RNA sequencing and qPCR analysis further demonstrated that PDPN+ HLA-DR high cells highly express the IL-27 subunit EBI3 and the TGF-β activator integrin αvβ8. To evaluate clinical relevance, we also examined the correlation between PDPN+ HLA-DR high cell numbers and clinical factors in 45 UC patients. Immunofluorescence staining for the glial marker CDH2 and HLA-DR revealed a negative correlation between CDH2+ HLA-DR+ cell numbers and preoperative Mayo endoscopic scores.

Conclusion
PDPN+ HLA-DR high glial cells are increased in inflamed areas of UC patients, suggesting a role in anti-inflammatory processes and the maintenance of immune homeostasis.
P0087 Calprotectin contributes to refractory Crohn’s disease fistula through dysregulation of epithelial wound healing responses
Authors: Becker M , Koelink P , Ouahoud S , Meisner S , Muncan V , Frei A , Nabozny G , li F , Saris J , Bemelman W , D'Haens G , Buskens C , Wildenberg PhD M 
Published: January 2025

Abstract

Background
Refractory perianal fistula in Crohn’s disease (CD) still present an unmet clinical need with a high disease burden. Despite increasing interest, pathophysiology leading to the refractory phenotype remains unclear, with only epithelial-to-mesenchymal-transitioning (EMT) commonly mentioned as a contributing factor. Using a systematic approach comparing therapy refractory CD fistula, therapy responsive non-IBD fistula and normal rectum, we aimed to differentiate between general healing responses and dysregulation thereof in refractory CD fistula.

Methods
Total RNASeq (n=51), single cell RNASeq (n=31) and spatial transcriptomic (n=8) analysis were performed on the internal opening and tract of CD fistula and idiopathic fistula. Results were validated using immunohistochemistry. Functional studies were performed in human adult organoid cultures and intestinal cell lines.

Results
In the fistula tracts we identified development of a squamous epithelium characterized by expression of WFDC2, keratin 5 and keratin 13. Although some EMT markers were expressed in the squamous epithelium or its intermediates, no activation of a complete EMT program could be detected in any of the tissue types, regardless of the underlying diagnosis. Upstream analysis indicated TNFα, IL6 and TGFβ as inducers of WFDC2+ epithelium, and human adult colon organoids stimulated with these cytokines (but not TGFβ alone) indeed showed a transciptional profile similar to the fistula epithelium, confirming redifferentiation potential. While WFDC2+ epithelium did occur in CD fistula, abundance was strongly decreased compared to non-IBD fistula. In addition, those WFDC2+ cells present had a more pro-inflammatory profile and were morphologically disorganized. Surprisingly, pseudotime analysis indicated epithelial calprotectin (S100A8/9) as a key factor in the aberrant development of WFDC2+ tissue in CD. Normal intestinal epithelium does not express calprotectin, but a mix of cytokines present in fistula induced clear intracellular expression of S100A8/9 in both epithelial cell lines and primary colon organoids. In CD fistula, calprotectin expression was particularly intranuclear, suggesting a transcriptional role. CHIP analysis indeed showed binding of calprotectin to various inflammatory genes and knockdown of calprotectin abrogated expression of these genes supporting a crucial regulatory role.

Conclusion
These data identify redifferentiation of rectal mucosa to a squamous phenotype as a normal damage response during fistula formation. However, in CD patients, transcriptional effects of calprotectin derail this process, resulting in disorganized inflammatory tissue not amenable for surgical closure and contributing to refractory disease.
P0088 3D tissue-level analysis of intestinal T cell dynamics reveals dual effects of etrasimod on recruitment and tissue exit in experimental colitis
Authors: Fontes V , Müller T , Derdau J , Schett G , Neurath M F , Zundler S , Uderhardt S 
Published: January 2025

Abstract

Background
Sphingosin-1-phosphate (S1P) receptor (S1PR) agonists are a novel class of anti-trafficking agents approved for the treatment of ulcerative colitis. These compounds induce T lymphocyte sequestration in secondary lymphoid organs, reducing their availability in peripheral blood and presumably in inflamed intestinal tissue. However, direct evidence for their effects on T cell dynamics within intestinal tissue is lacking. Moreover, while S1PR-dependent mechanisms regulate T cell egress from the gut, it remains unclear whether S1PR agonists modulate this process. This limited understanding of tissue-specific effects presents a crucial barrier to comprehending their full therapeutic mechanism.

Methods
We developed a comprehensive volumetric imaging platform to investigate tissue-level mechanisms of colitis within the complex three-dimensional architecture of the intestine. Using the T cell transfer colitis model, mice were treated with etrasimod or vehicle control. Full-thickness colon samples underwent tissue clearing and whole-mount immunofluorescence for T cell markers. Advanced light-sheet and volumetric confocal microscopy, combined with machine learning-based image analysis, enabled three-dimensional reconstruction of T cell distributions and lymphatic networks, allowing for quantitative histocytometry and spatial mapping of immune cell dynamics.

Results
T cell transfer colitis induced substantial lymphocyte infiltration in the colon, with T cells forming both distinct clusters and diffuse distributions throughout the tissue. The presence of numerous T cells within lymphatic vessels indicated active tissue egress, suggesting that T cell accumulation reflects a dynamic balance between recruitment and exit (Figure 1). Etrasimod treatment not only reduced overall T cell infiltration but also markedly altered their spatial distribution pattern. Notably, we observed a decreased proportion of T cells within lymphatic vessels, coupled with increased accumulation of T cells in proximity to lymphatic structures, indicating a previously unrecognized effect on tissue exit dynamics.

Conclusion
Our advanced volumetric imaging approach revealed novel insights into a potential dual mechanism of etrasimod in inflammatory bowel disease. Beyond reducing lymphocyte recruitment, etrasimod appears to create a tissue exit block, effectively trapping T cells within the intestinal compartment. These findings raise important questions about how enforced tissue residency influences local inflammatory circuits and may guide optimization of therapeutic strategies.
P0094 The Role Of Sdf2l1 On Intestinal Physiology And Inflammatory Bowel Disease
Authors: Thies M , Schuran F A , Mishra N , Pimenta Bernardes J , Hinrichsen F , Rosenstiel P 
Published: January 2025

Abstract

Background
The intestinal tract, as the body's largest mucosal surface, is exposed to various factors, requiring specialized epithelial and immune cell interactions to maintain homeostasis. These interactions, along with a dynamic microenvironment, induce endoplasmic reticulum (ER) stress. While the ER employs coping mechanisms to preserve cellular integrity, unresolved ER stress is a key driver in the development and progression of chronic inflammatory bowel disease (IBD).1 An important player in the ER-resident unfolded protein response is stromal derived growth factor 2-like 1 (Sdf2l1), a chaperone protein that ensures proper protein folding and prevents the accumulation of misfolded proteins.2,3 Furthermore, Sdf2l1 is highly expressed in the intestine, thus we hypothesize that Sdf2l1 plays a pivotal role in the pathogenesis of IBD.

Methods
To investigate the role of Sdf2l1 in the gastrointestinal system, we used wildtype or conditional Sdf2l1 knockout mice lacking Sdf2l1 in intestinal epithelial cells (Sdf2l1ΔIE) and ex vivo organoid systems.

Results
No baseline differences were found in the intestinal mucosa of Sdf2l1-deficient mice, but molecular differences in ER stress responses were evident in small intestinal organoids. When ER stress was induced with IL-22, Sdf2l1ΔIE organoids showed significantly higher NFκB expression, suggesting enhanced UPR activation or compromised stress coping. Under tunicamycin treatment, Sdf2l1-deficient organoids had increased Hspa5/Grp78 expression, indicating elevated ER stress. Sdf2l1 is needed for proper UPR initiation, as it forms a complex with GRP78. In these deficient organoids, IRE1 signaling was impaired, as shown by reduced Xbp1s expression.

Conclusion
Insufficient activation of the UPR due to Sdf2l1 deficiency and the associated ER stress potentially leads to inflammatory reactions in the cells. Impaired cell integrity disrupts intestinal homeostasis and can lead to an imbalance of pro- and anti-inflammatory processes, thus favoring the pathophysiology of IBD.

References
1. Eugene SP, Reddy VS, Trinath J. Endoplasmic Reticulum Stress and Intestinal Inflammation: A Perilous Union. Front Immunol. 2020 Nov 25;11:543022. doi: 10.3389/fimmu.2020.543022. PMID: 33324392; PMCID: PMC7723926.
2. Kim J-S, Mochida K, Shinozaki K. ER Stress and the Unfolded Protein Response: Homeostatic Regulation Coordinate Plant Survival and Growth. Plants. 2022; 11(23):3197. https://doi.org/10.3390/plants11233197
3. Sasako, T., Ohsugi, M., Kubota, N. et al. Hepatic Sdf2l1 controls feeding-induced ER stress and regulates metabolism. Nat Commun 10, 947 (2019). https://doi.org/10.1038/s41467-019-08591-6