bluuebunny/crossref_metadata_2025_split huggingface dataset:
P0025 The effect of very small superparamagnetic nanoparticles on human blood cells as a diagnostic tool in Inflammatory Bowel Disease
Authors: Hussein S , Kühl A A , Golusda L , Plattner C , Heinze N , Sturm G , Freise C , Traube H , Trajanoski Z , Taupitz M , Schnorr J , Siegmund B , Paclik D 
Published: January 2025

Abstract

Background
The field of application of organic or inorganic nanoparticles (1-100 nm size) is extensive and involves their use in medicine. This includes using nanoparticles in human beings or animals (life-stock) which holds advantages but also bears risks. Therefore, nanoparticles used in diagnostics and therapy should be inert not affecting tissues or immune cells. Additionally, nanoparticles should not aggregate to form clusters exceeding the size of 100 nm or accumulate in sensitive structures like bone marrow or brain for long-term deposition.
We developed in-house very small superparamagnetic iron oxide nanoparticles (VSOP) with a size of 7 nm that were successfully used in preclinical magnetic resonance imaging (MRI) for the detection of intestinal inflammation and sclerosis. This study elucidates the effect of nanoparticles on human blood cells, including monocytes as well as monocyte-derived macrophages, in vitro as a first step toward clinical application in inflammatory bowel disease (IBD).

Methods
Whole blood of healthy donors and patients suffering from IBD as well as monocytes and monocyte-derived macrophages were treated with VSOP in vitro and analysed for changes in their transcriptome, phenotype and function. For transcriptome analysis, RNA sequencing was performed. Cell abundance, activation and proliferation were measured by mass cytometry. Migratory behavior of monocytes was analyzed by live microscopy. Cell metabolism was detected by Seahorse assay.

Results
RNA sequencing of monocytes showed that the most significantly regulated gene is encoding for the transferrin receptor (Tcfr). As a response to VSOP treatment and VSOP uptake thereby increasing the levels of intracellular iron, Tcfr is probably downregulated to restrict further iron uptake. While RNA sequencing of whole blood showed only significant differences in non-coding genes (C3orf86P, ENSG00000278996, ENSG00000259002), CyTOF analyses revealed that VSOP-treated monocytes are neither activated nor showing increased proliferation. Also, the migratory behavior is not influenced by VSOP uptake. Additionally, VSOP uptake resulted in an enhanced oxygen consumption rate and extracellular acidification rate. In comparison to the uptake of Latex beads, these increased rates are rather attributed to phagocytosis.

Conclusion
Analyses of our data with PBMC, monocytes and monocyte-derived macrophages suggest, that treatment with VSOP has no major affect on phenotype and function of immune cells. Therefore, VSOP are a promising tool for the early detection of IBD through MRI.
P0028 Discovery of GLP-2R agonists using computational molecular design techniques
Authors: Scagnoli B , Righino B , Pirolli D , Lopetuso L , Chieppa M , Mocci G , Petito V , Scaldaferri F , Gasbarrini A , Papa A , De Rosa M C 
Published: January 2025

Abstract

Background
Computational drug discovery is a powerful, cost-effective approach for accelerating drug development, providing key insights into modulating the GLP-2 receptor (GLP-2R), an important target for gastrointestinal diseases like short bowel syndrome1.

Methods
This study uses diverse in silico molecular design methods, mainly virtual screening2-3, to discover nonpeptidic small-molecule GLP-2R agonists that overcome the drawbacks of peptide-based treatments. The first strategy identifies virtual high-affinity binders on the contact surface between GLP-2 and GLP-2R, which may stabilize the GLP-2R/GLP-2 complex forming hydrogen bonds with both partners to enhance receptor activation. A second strategy uses fragment-based virtual screening to find critical fragments that bind strongly to GLP-2R residues essential for activation. The goal of using these fragments to screen various hit-like and lead-like molecule libraries is to discover small molecules with strong activation potential. Given the difficulty of targeting the large, shallow orthosteric site of GLP-2R with small molecules, a third computational approach focuses on finding small moleculesthat bind to allosteric sites, identified through computational modeling.

Results
In silico studies have led to the identification of a number of potential hit compounds that will undergo experimental testing to evaluate their effectiveness in activating GLP-2R.

Conclusion
This study lays the foundation for further lead optimization, where computational approaches will help find new drug candidates, that may advance specialized therapies for gastrointestinal disorders with limited treatment options.

Fundings
2.1 "Rafforzamento e potenziamento della ricerca biomedica del SSN", finanziato dall’Unione europea – NextGenerationEU, CUP C53C22001140007. 2022 PNRR Project"Changing the future of intestinal failure in intestinal chronic inflammation: towards innovative predictive factors and therapeutic targets" code: PNRR-MAD-2022-12376791.

References
1.Johnson TO, Akinsanmi AO, Ejembi SA, et al. Modern drug discovery for inflammatory bowel disease: The role of computational methods. World J Gastroenterol. 2023;29(2):310-331. doi:10.3748/wjg.v29.i2.310
2.Tripathi NM, Bandyopadhyay A. High throughput virtual screening (HTVS) of peptide library: Technological advancement in ligand discovery. Eur J Med Chem. 2022;243:114766. doi:10.1016/j.ejmech.2022.114766
3.Pirolli D, Righino B, Camponeschi C, Ria F, Di Sante G, De Rosa MC. Virtual screening and molecular dynamics simulations provide insight into repurposing drugs against SARS-CoV-2 variants Spike protein/ACE2 interface [published correction appears in Sci Rep. 2023 Feb 15;13(1):2707. doi: 10.1038/s41598-023-29766-8]. Sci Rep. 2023;13(1):1494. Published 2023 Jan 27. doi:10.1038/s41598-023-28716-8
P0032 Human Extrachromosomal Circular DNA (EccDNA) is a Novel Biomarker in Inflammatory Bowel Disease
Authors: Di Vincenzo F , Petito V , Gerovska D , Piazzesi A , Russo A , Turchini L , Masi L , Lopetuso L R , Regenberg B , Gasbarrini A , Putignani L , Aruzo-Bravo M J , Scaldaferri F 
Published: January 2025

Abstract

Background
Inflammatory Bowel Diseases (IBD), comprising Ulcerative Colitis (UC) and Crohn’s Disease (CD), are chronic, relapsing-remitting disorders of the gastrointestinal tract with unclear etiology. Identifying reliable biomarkers for predicting disease progression and treatment response remains a priority. Extrachromosomal circular DNA (eccDNA) has shown promise as a diagnostic and prognostic biomarker in oncology, but its potential in IBD patients, including the gene fragments involved, has not been extensively studied.

Methods
This monocentric, observational case-control study enrolled IBD patients and healthy controls (HC) undergoing colonoscopy for colorectal cancer screening at our center. IBD disease activity was assessed using the Partial Mayo Score and Mayo Endoscopic Subscore (MES) for UC, and the Harvey-Bradshaw Index and Simple Endoscopic Score (SES-CD) for CD. Colonic biopsies were collected from both inflamed and healthy mucosa of IBD patients, and from HCs. eccDNA was purified using the Circle-Seq method; detection was performed with the Circle Finder pipeline. The study analyzed differences in eccDNA abundances between IBD patients and HCs, focusing on Differentially Produced per Gene eccDNAs (DPpGCs).

Results
In total, 93 IBD patients (38 CD, 39 UC) and 16 HC were included. IBD patients showed a significantly higher abundance of eccDNAs compared to HC, with this increase observed across all chromosomes, suggesting a global upregulation of eccDNA production throughout the human genome. There was also a statistically significant trend towards larger eccDNA fragments in IBD biopsies. Notably, even when considering only eccDNA derived from genic elements ("genic eccDNAs") IBD patients exhibited a significantly higher abundance of eccDNA compared to HCs. Analysis of DPpGCs (fold change &gt;1 log2, p &lt; 0.01) identified 152 genes enriched in IBD, including GRID2 and NRG1. In CD patients, 70 genes, such as FGF14, SOX5, and ZBTB20, were enriched, while UC patients had 123 enriched genes, including NRG1, SPOCK3, and ATP13A4.
Patients in endoscopic remission (SES-CD&lt; 3, MES 0-1) exhibited fewer eccDNAs, though this reduction was not statistically significant. Among identified DPpGCs, key genes included FARS2, HERC3, and PNK2. When analyzing UC and CD seperately, we found a statistically significant increase of eccDNA production in active UC, but not in CD, with NRG1 being notably overrepresented, suggesting its potential as a UC-specific biomarker.

Conclusion
Our study unveils a unique pattern of eccDNA production in IBD. We showed that circles harboring specific genes can distinguish UC and CD from HCs with statistical significance (p&lt;0.01), indicating that eccDNA profiling may represent a novel diagnostic tool for IBD patients.
P0042 Hydrogel-integrated millifluidic system enhances function in primary small intestinal epithelial cells
Authors: Alzain N , Almalla A , Gerbeth L , Ziegler J , Kramer C , Glauben R , Weinhart M , Siegmund B 
Published: January 2025

Abstract

Background
The intestinal epithelium is protected by a vital mucus layer which is essential for maintaining gut homeostasis and regulating host-microbial interactions. However, studying this mucus layer in vitro has been challenging due to the lack of physiologically relevant models.

Methods
We hypothesized that culturing human adult intestinal stem cells (ISCs) under flow conditions on a biomimetic scaffold could better recapitulate in vivo epithelial differentiation and mucus production. To test this, we developed a hydrogel-integrated millifluidic chamber, where ISCs were cultured on decellularized and methacrylated porcine small intestinal submucosa (dSIS-MA) under both static and dynamic (laminar flow) conditions. RNA bulk sequencing was used later to explore gene expression profiles across early and late time points to assess the impact of dSIS-MA and fluid flow on ISC differentiation and function over time.

Results
Our results reveal significant changes in pathways related to epithelial lineage commitment and intestinal barrier function on dSIS-MA compared to tissue culture plastic and in dynamic compared to static conditions, highlighting the critical influence of matrix structure and fluid flow.

Conclusion
In summary, we have successfully established a model that mimics in vivo conditions and reveals that surface and shear stress strongly impact intestinal epithelial cell development and function. This advanced in vitro approach enhances our understanding of molecular processes underlying epithelial cell behavior in conditions closely resembling the gut environment, with applications in gut health and disease research.
P0045 Serologic levels of fatty acids as promising biomarkers for the severity of Inflammatory Bowel Disease
Authors: Cejudo-Garcés A , Patel J , Jarén A , Macias-Ceja D , Boscá-Watts M M , Boronat L , Calatayud S , Barrachina M D , Ortiz-Masiá D , Cosín-Roger J 
Published: January 2025

Abstract

Background
Inflammatory Bowel Disease (IBD) is a chronic and autoimmune disease which affects the gastrointestinal tract. Several changes in the metabolomic profile have been described in urine, blood and feces samples of IBD patients. However, little is known regarding the relationship between these metabolic changes and the severity of IBD. Therefore, we aim to characterize the metabolomic profile, specifically the fatty acid profile, in serum from both active and in remission IBD patients.

Methods
Blood samples from UC active patients (n=20), UC patients in remission (n=20), CD active patients (n=21), CD patients in remission (n=21) and non-IBD controls (n=21) were obtained. UC and CD patients were classified in active or remission according to the Mayo-score and Harvey-Bradshaw Index, respectively. Serum was obtained after centrifugation of the fresh blood. Metabolomic analysis was performed using Liquid Chromatography High-Resolution Mass Spectrometry. Data were expressed as mean±SEM (μg/mL) and compared by a t-test or ANOVA. A p-value&lt;0.05 was considered statistically significant.

Results
A total of 42 fatty acids were quantified and results are shown in Table 1. 23 of them showed significant differences, either Control vs UC, Control vs CD, or CD vs UC. In addition, 9 fatty acids showed significant differences between active CD vs remission CD patients (FA 15:0, FA 16:1n10, FA 17:0, FA 18:0, FA 18:1n12 + FA 18:1n13 + FA 18:1n9trans, FA 20:0, FA 20:3n9, FA 20:4n6, FA 22:4n6). In case of UC, 24 fatty acids showed significant differences in active vs remission patients, especially those with large and very large chain (FA 14:0, FA 15:0, FA 16:1n10, FA 16:1n9, FA 17:0, FA 18:1n12 + FA 18:1n13 + FA 18:1n9trans, FA 18:1n7trans, FA 18:1n9, FA 18:2n6trans, FA 18:3n6, FA 19:0, FA 20:0, FA 20:1n9, FA 20:2n6, FA 20:3n3 + FA 20:3n6, FA 20:3n9, FA 20:4n6, FA 22:0, FA 22:1n9, FA 22:2n6, FA 22:3n3 + FA 22:3n6 + FA 22:3n9, FA 22:4n6, FA 22:5n6 and FA 24:1n9). Moreover, 4 fatty acids, specifically FA 20:0, FA 22:0, FA 22:1n9 and FA 22:4n6, showed areas under the curve higher than 0.8 in the ROC curves (0.87, 0.84, 0.89 and 0.81 respectively).

Conclusion
Differences in serum levels of fatty acids were detected between active and remission patients of both CD and UC. The ROC curves of some of them point these fatty acids as potential biomarkers indicating the severity of IBD in these patients.
Table 1. Levels of the fatty acids in serum of both non-IBD and IBD patients.
P0048 Alterations in circulating T-cell subpopulations reflect disease activity in Ulcerative Colitis
Authors: Profeta F , Rumi G , Notarnicola D , Capobianco I , Masi L , Emoli V , Troisi S , Varuolo M M , Turchini L , Lopetuso L R , Laterza L , Pugliese D , Papa A , Gasbarrini A , Petito V , Scaldaferri F 
Published: January 2025

Abstract

Background
Ulcerative colitis (UC) is a chronic condition characterised by dysregulation of the immune response and consequent uncontrolled inflammation. Circulating T cells play a crucial role in maintaining immune balance and their dysfunction contributes to disease progression1. This study aims to evaluate the expression of circulating T-cell subpopulations in UC patients and explore their association with disease activity.

Methods
Blood samples were collected from UC patients with active disease (partial Mayo score (PMS) &gt; 1), UC patients in clinical remission (PMS 0-1) and healthy controls (HC). A cytofluorimetric analysis using the BD FACSLyric Flow Cytometry system was performed for T-cell subpopulations analysis [table 1]. ANOVA test was used to compare the expression levels of subpopulations across the three groups, while t-tests were conducted for pairwise analysis.

Results
21 UC patients (11 in clinical remission and 10 with active disease) and 10 HC were enrolled. Central memory CD4 T cells resulted significantly reduced in active UC compared to UC in remission and HC (p&lt; 0.05), while effector memory and effector CD4 T cells were markedly elevated in active UC compared to UC in remission and HC. Similarly, central memory CD8 T cells were reduced in active UC, while effector memory CD8 T cells and effector CD8 T cells showed significant increase in active patients compared to patients in remission and HC (p&lt; 0.01). Notably, regulatory T cells were significantly higher in remission UC compared to active disease (p&lt; 0.05) [figure 1]. No significant differences were observed among other subpopulations analysed.

Conclusion
This study demonstrates significant alterations in circulating T-cell subpopulations in UC compared to controls, with distinct differences based on disease activity status. The progression of T cells toward effector phenotypes parallels increased inflammatory activity, linking T-cell differentiation and immune aging to disease progression. These findings underscore the potential of circulating T-cell subpopulations as non-invasive biomarkers for disease activity and as promising therapeutic targets.

References
Casalegno Garduño R, Däbritz J. New Insights on CD8+ T Cells in Inflammatory Bowel Disease and Therapeutic Approaches. Front Immunol. 2021 Oct 11;12:738762. doi: 10.3389/fimmu.2021.738762. PMID: 34707610; PMCID: PMC8542854.
P0049 Bile acid profiling of ileal fluid in Crohn’s disease using metabolomics
Authors: De Greef I , Loopmans S , Bislenghi G , D'Hoore A , Terrasson I , Verstockt B , Sabino J , Ferrante M , Ghesquière B , Vermeire S , Verstockt S 
Published: January 2025

Abstract

Background
An ileal resection is known to cause bile acid malabsorption in Crohn’s disease (CD) 1, but its impact on the bile acid landscape remains understudied. Therefore, we studied bile acid composition in ileal fluid of CD and control patients using targeted metabolomics, and assessed the impact of sample preparation.

Methods
Ileal fluid was collected from CD patients (n=10) and non-IBD controls (n=10) having an ileostomy (patient characteristics in Table 1). Targeted metabolomics (LC-MS/MS) was applied on full ileal fluid samples as well as on their supernatants (ie. after centrifugation of a full fluid sample aliquot). Bile acid raw abundances were normalised to sample weight (g), and only bile acids detected in at least 40% of all samples (per sample type) were included for further analysis. A comparative analysis between full ileal fluid and its supernatants across all samples was assessed by Spearman correlations, while the bile acid abundances between CD and controls was compared using Mann-Whitney U tests. A nominal p value &lt; 0.05 was considered significant.

Results
For the CD group, the median [min-max] length of resected ileum was 15.0 [0.0-33.5] cm and 0.0 [0.0-15.0] cm for the control group (Table 1). Ten primary, 6 secondary and 2 modified bile acids were present in full ileal fluid as well as in the corresponding supernatants. While bile acid abundances were 1.2 to 6.0 times higher in full ileal fluid compared to paired supernatants (Figure 1A), the overall bile acid profiles remained highly consistent. In particular, 13 out of 18 bile acids showed a strong correlation between both sample types (r&gt;0.8, p&lt;0.05), and the remaining 5 showed moderate but significant correlations (r=0.5-0.7, p&lt;0.05). Lastly, while the abundances between the full CD and control groups were similar, a subanalysis comparing CD patients with an ileal resection (n=5) to controls with a total mesorectal excision (n=6), revealed an increase in primary bile acids glycocholic acid (GCA) (p=0.052) and glycochenodeoxycholic acid (GCDCA) (p=0.056) in the CD subgroup (Figure 1B).

Conclusion
In this pilot metabolomics study, we detected both primary and secondary bile acids in the ileal fluid of CD patients and controls. Bile acid composition in full ileal fluid aligns well with its derived supernatant, suggesting supernatant as a viable alternative for measurements, simplifying sample preparation. GCA and GCDCA, both primary bile acids typically reabsorbed in the ileum, tended to be increased after ileal resection in CD patients. A broader screening of bile acid and microbiota metabolites in ileal fluid on a larger scale may unravel novel targets contributing to disease recurrence after resection.

References
(1)Vitek L. Bile acid malabsorption in inflammatory bowel disease. Inflamm Bowel Dis. 2015;21(2):476-83
P0052 Enhancing gut epithelial integrity and reducing epithelial inflammation through supplementation of fecal metabolites, guided by novel ex vivo functional prioritization and testing
Authors: Elwahidi L , Abbas-Egbariya H , Braun T , Amir A , Haberman Y 
Published: January 2025

Abstract

Background
Inflammatory bowel disease (IBD) pathogenesis involves the gut epithelia, showing intensified inflammatory signals and a "leaky gut". However, there are no interventions targeting the epithelia. We aimed to prioritize and test whether fecal content from IBD patients, supplemented with metabolites directed by our functional assays, can reduce epithelial inflammation and improve integrity.

Methods
We established a model system utilizing whole human fecal samples from Crohn's disease (CD), Ulcerative colitis (UC), and healthy control subjects that were co-cultured with Caco-2 epithelial cells. Transepithelial electrical resistance (TEER) measured epithelial barrier integrity, and ELISA measured CXCL1 secretion. 16Sseq characterized fecal bacteria and metabolites were characterized using a semi-targeted predefined library (n=550).

Results
Fecal samples were processed by separating the supernatant, heat-killing the bacteria, and rejoining them. (Fig. 1A). We generated three pools per group (CD p#1-3, UC p#1-3, Controls p#1-3). All p#1 pools included samples from ten subjects, and p#2-3 each included samples from additional five independent subjects. Microbial characterization indicated that the fecal content pools captured the overall variations with separation between IBD and control samples (Fig. 1B). Co-culturing with p#1 revealed a significant increase in CXCL1 proinflammatory chemokine secretion to the media (Fig. 1C), and reduction in TEER (Fig. 1D) which was lower with pools obtained from CD and UC patients compared to the healthy pools. Independent validation with fecal pools p#2 and p#3 showed largely similar results (Fig. 1E-F). Characterizing metabolite levels in the nine pools and correlating them with disease state (IBD vs. controls) and the measured TEER outcomes highlighted several metabolites higher in controls and with improved TEER outcomes (Fig. 2A-B). Supplementing these prioritized metabolites with fecal contents pools, UC p#3 and CD p#2, which were linked with poorer epithelial outcomes, improved epithelial integrity, showing higher TEER when compared with original CD and UC pools (Fig. 2C). Similarly, supplementing UC p#3 and CD p#2 with those same metabolites mix significantly reduced CXCL1 secretion from epithelia in the model (Fig. 2D).

Conclusion
Fecal content from CD and UC patients was associated with more pathologic epithelial signals, which was improved in part with the addition of specific prioritized metabolites. This pipeline and model system highlights the potential future use of metabolite supplementations to improve epithelial function and outcome in IBD.