bluuebunny/crossref_metadata_2025_split huggingface dataset:
P0021 Long non-coding RNAs as predictors of response to anti-TNF therapy in Ulcerative Colitis patients
Authors: Heydari R , Tavassolifar M J , Derakhshan Nazari M H , Shahrokh S , Meyfour A 
Published: January 2025

Abstract

Background
Long non-coding RNAs (lncRNAs) are transcripts with more than 200 nucleotides that modulate molecular mechanisms in several ways, including epigenetic modification, transcription, post-transcription, translation, and post-translation. We have recently demonstrated the involvement of lncRNAs in the pathogenesis of inflammatory bowel disease (IBD) and their role in the accurate diagnosis of IBD patients 1,2. In this study, we aim to determine the potential of lncRNAs in predicting the response of ulcerative colitis (UC) patients to anti-TNF-α therapy.

Methods
Twenty-two UC patients who were naïve to Adalimumab biosimilar, CinnoRa enrolled in this prospective cohort study. Colonic tissue samples were collected at baseline and week 14 after treatment. Based on our previous reports, a list of important lncRNAs in IBD pathogenesis was prepared and their expression was evaluated by qRT-PCR. Machine learning algorithms were applied to evaluate the predictive potentiality of lncRNAs in differentiating UC non-responders (UCN) from UC Responders (UCR) at baseline.

Results
Among analyzed lncRNAs, significant dysregulation of H19 and TUG1 was observed in UCNs compared to UCRs before receiving anti-TNF therapy. Interestingly, this difference between the two patient groups was still detected in the 14th week after treatment. Machine learning algorithm results and receiver operating characteristic curve analysis demonstrated that these two lncRNAs could appropriately discriminate UCN patients from UCR with more than 90% accuracy and AUC &gt; 0.8.

Conclusion
We concluded that expression profiles of lncRNAs are different in pretreatment lesions of UC patients before receiving anti-TNF therapy. Importantly, lncRNAs are involved in the distinctive molecular response of UC patients to anti-TNF monoclonal antibodies. Furthermore, H19 and TUG1 can serve as biomarkers in predicting the response of UC patients to anti-TNF therapy at baseline.

References
1.
2. Heydari R, Karimi P, Meyfour A. Long non-coding RNAs as pathophysiological regulators, therapeutic targets and novel extracellular vesicle biomarkers for the diagnosis of inflammatory bowel disease. Biomed Pharmacother. Jul 2024;176:116868. doi:10.1016/j.biopha.2024.116868
P0022 Development of primary human fibroblast cell cultures for fibrosis modelling in Inflammatory Bowel Diseases
Authors: Kajári L , Szabó V , Jójárt B , Bacsur P , Molnár T , Farkas K , Maléth J ,   Epithelial Cell Signaling and Secretion Research Group
Published: January 2025

Abstract

Background
Inflammatory Bowel Diseases (IBD) are chronic immune-mediated diseases of the gastrointestinal tract. Fibrosis is frequent in IBD driven by inflammatory cytokines. During fibrosis, extracellular matrix proteins accumulate in the tissue, causing loss of epithelial function and stenosis, leading to malabsorption and intestinal motility problems. This can ultimately lead to serious complications, strictures, fistulas, or ileus. Anti-inflammatory drugs cannot target fibrosis, only surgical intervention can be used. No relevant primary in vitro cell culture model is available for intestinal fibrosis modelling. Therefore, we aimed to establish and optimize human primary fibroblast cell culture from intestinal biopsies of control and IBD patients. We characterized and compared the fibrosis phenotype and gene expression as well.

Methods
Fibroblast cell cultures were generated from colonic biopsy samples by enzymatic digestion. In a suitable medium, the cells attach to the bottom of the vessel and proliferate, at 90% confluence the cultures were passaged. The phenotype was confirmed by immunofluorescent staining. Target proteins: COL1A1 (Collagen type 1 alpha 1), TGF-ß1 (Transforming growth factor beta), PAI-1 (Plasminogen activator inhibitor type 1), α-SMA (Alpha smooth muscle actin), and PHH3 (Phosphohistone H3). For gene expression analysis RNA was isolated and qRT-PCR technique was used for the following target genes: COL1A1, ACTA2 (Actin alpha 2), TGF-ß1, FN1 (Fibronectin 1), PAI-1, H3C4 (H3 clustered histone 4). We evaluated the collected data and performed statistical analysis.

Results
We can efficiently create and maintain human colon primary fibroblast cell cultures from colonic biopsies of healthy and CD origins. Cell morphology differences were observed from control and diseased patient samples. At the staining, the fluorescent intensity of fibrotic markers (COL1A1, TGF-ß1, PAI1) and the mitosis marker PHH3 were significantly higher in the CD samples, indicating that the cells maintained fibrotic phenotype, and the diseased fibroblasts had a higher proliferation rate. The myofibroblast marker, α-SMA didn’t show a significant difference. Interestingly, significant differences were not noted between the two groups in the qRT-PCR measurements.

Conclusion
In conclusion, we can generate primary human intestinal fibroblast cell cultures and maintain them to passage number 3. Fibrotic protein markers and morphology distinguish the diseased samples from the healthy subjects, therefore it could be useable for in vitro fibrosis modelling. However, the gene expression analysis doesn’t discriminate between the two groups at passage number 3. In the future, we would like to observe the fibrotic properties in earlier passage numbers.
P0024 Circadian regulator-mediated molecular subtypes depict the features of elderly ulcerative colitis
Authors: Zhang Y , Xu J , Cao S , Wang J , Lin Y , Liu Y 
Published: January 2025

Abstract

Background
The prevalence of UC in older individuals (i.e., aged &gt; 60 years) is increasing globally because of an ageing population and a subset of population with elderly-onset (i.e., onset aged ≥ 60 years) UC, which causes high burden on healthcare. Circadian rhythms are 24-h oscillations that control various biological processes in the living system and have been recognized to be associated with the development of autoimmune diseases and aging. However, the implication of circadian rhythm in elderly UC remains largely unknown.

Methods
We downloaded datasets from the Gene Expression Omnibus (GEO) database. The differential expression of circadian regulators between early adult (15-25 years old) and elderly (≥ 60 years old) UC patients was identified. We constructed and compared random forest (RF) and support vector machine (SVM) models. Feature genes were selected to develop a nomogram model with the superior model. The receiver operator characteristic (ROC) curves were used to validate the performances of predictive models and signature genes. The infiltration of 22 kinds of immune cells in elderly UC was analyzed by ssGSEA, and the relationship between feature circadian genes and the proportion of immune infiltration was studied. We identified circadian subtypes based on significantly differentially expressed circadian regulatory genes. Comprehensive evaluation of the two circadian patterns was performed, including immune characteristics and potential functions.

Results
The expression levels of circadian regulatory genes were extracted and a total of 44 differentially expressed circadian regulators were identified between early adult and elderly UC patients. Five feature circadian regulatory genes, AGT, EGF, NR3C2, PPY, and PYY were determined (p &lt; 0.05) to establish a nomogram model that can predict the incidence of elderly UC with the RF model. The signature circadian regulators were found to be correlated with activated memory CD4+ T cells, gamma delta T cells, and macrophages. We identified two circadian subtypes based on the five significant circadian regulatory genes. Cluster A had a higher immune infiltration of activated CD4+T cells, CD8+ T cells and B cells than cluster B (p &lt; 0.01). The signature circadian genes can also be used to predict the risk of elderly UC and have good diagnostic efficacy.

Conclusion
The circadian regulatory genes play non-negligible roles in elderly UC. A nomogram model developed by five feature circadian regulatory genes could be used to predict the incidence of elderly UC. Two circadian patterns were identified and evaluated comprehensively, which may provide insights into the classification of elderly UC patients and guide treatment.
P0033 GPR84, which is increased in Ulcerative Colitis patients, regulates the cytokine secretion of macrophages
Authors: Cejudo-Garcés A , Patel J , Jarén A , Macias-Ceja D , Navarro-Vicente F , Calatayud S , Barrachina M D , Ortiz-Masiá D , Cosín-Roger J 
Published: January 2025

Abstract

Background
Inflammatory Bowel Disease (IBD) is a gastrointestinal disorder comprising Ulcerative Colitis (UC) and Crohn´s Disease (CD) characterized by an exacerbated and chronic immune response. Although GPR84 has emerged as a proinflammatory receptor in some pathologies such as atherosclerosis or reflux esophagitis, its role in IBD remains unclear. We aim to analyze the protein expression of GPR84 in IBD patients and its role in the cytokine secretion in macrophages.

Methods
Surgical resections from UC (n=5) and CD patients (n=5) were obtained. Healthy colon and ileum from colon-carcinoma patients (n=10) were used as controls. Protein expression of GPR84 and CD68 was analyzed by WesternBlot and immunohistochemistry. U937 monocytes were differentiated into macrophages with PMA (0,01μM) during 48 hours and treated with the GPR84 agonist decanoic acid (50-250μM) and a proinflammatory cocktail (0,1μM LPS + 20ng/mL IFNγ) during 24 hours. Some of them were treated with the GPR84 antagonist (10μM) or transiently silenced with a specific siRNA-GPR84. RNA was isolated and gene expression of pro- and anti-inflammatory cytokines was quantified by qPCR. Cytokine levels in supernatant were also quantified by Luminex. Data were expressed as fold induction vs control (mean±SEM) and compared by t-test. A p-value&lt;0.05 was considered statistically significant.

Results
Protein levels of GPR84 were significantly increased in UC patients (150.3±11.75 vs 100.0±11.85), while no differences were observed in CD patients vs healthy ileums. Immunohistochemistry revealed a slight staining of this receptor in intestinal epithelial cells, whereas several cells of the lamina propria were strongly stained. Double immunohistochemistry confirmed that intestinal CD68 macrophages expressed GPR84 in both UC and CD patients. U937-derived macrophages treated with decanoic acid showed a significant increased expression of IL1b (2.68±0.86) and IL8 (2.44±0.48) vs vehicle-treated macrophages (0.998±0.23 and 1.05±0.17, respectively). In addition, IL1b levels in supernatant from macrophages treated with decanoic acid were significantly increased compared with the supernatant from vehicle-treated macrophages (4.50±1.05 vs 1.00±0.19). Moreover, the cotreatment with decanoic acid and GPR84 antagonist significantly reduced the expression of IL1b (0.99±0.29) vs vehicle-treated macrophages (1.94±0.26) and the transiently silencing of this receptor significantly reduced the expression of IL8 (0.89±0.25) vs siCtrl macrophages (4.02±1.59).

Conclusion
GPR84 is increased in UC patients and expressed in intestinal CD68+ macrophages. It regulates the expression of several cytokines pointing GPR84 as a promising pharmacological target for UC patients.
P0034 Glycosylation as new molecular mechanism underlying Pediatric Inflammatory Bowel Disease
Authors: Amorim R , Santos-Pereira B , Dias A M , Sousa Pinto B , Lefeber D J , Espinheira C , Trindade E , Carneiro F , Gaifem J , Pinho S 
Published: January 2025

Abstract

Background
Pediatric Inflammatory Bowel Disease (IBD) can be a highly disabling chronic condition. Genetic, immune and microbial factors have been associated with the development of IBD. Recent studies have shown that changes in glycosylation increase the susceptibility to immune-mediated diseases in adults, including IBD. This study aims to investigate, for the first time in pediatric population, if changes in glycosylation play a role in the immunopathogenesis of IBD, envisioning the identification of novel biomarkers and therapeutic targets.

Methods
We designed a cross-sectional study in which blood samples and fresh colonic biopsies from pediatric patients, either with Crohn’s Disease (CD) or Ulcerative Colitis (UC) or without IBD, were collected at the time of colonoscopy or outpatient visit in a tertiary hospital. T lymphocytes were isolated from colonic tissue and blood, and their glycosylation profile was analyzed by fluorescence-activated cell sorting using specific lectins that recognize different glycans structures and surface antibodies as markers of immune cells (CD45, CD4, CD8).

Results
A total of 80 participants were included, 24 without IBD and 56 with IBD. Among the IBD patients, 23 were diagnosed with Ulcerative Colitis (UC) and 33 with Crohn's Disease (CD). We observed that T lymphocytes from patients with CD exhibit a glycosylation profile alteration distinct from that seen in patients with UC and children without IBD, both at the level of the colon mucosa and in circulation (blood). The levels of a specific free glycan in peripheral blood circulation were higher in patients with Crohn's Disease compared to those with UC and non-IBD (p&lt;0.05).

Conclusion
Our data suggest that CD patients may have a distinctive glycosignature that can be detected in circulation. This may represent a promising tool to discriminate CD patients from UC and non IBD, thus reducing the need for invasive exams in these patients. Overall, our findings may contribute to the identification of a novel diagnostic biomarker with clinical impact in decision-making algorithms, as well as therapeutic targets to improve disease control.
P0036 NRG1, a gene significantly detected from intestinal mucosa eccDNA, may predict therapeutic response in Inflammatory Bowel Disease
Authors: Emoli V , Foscarini E , Di Vincenzo F , Masi L , Troisi S , Pane C , Migliore G , Piazzesi A , Turchini L , Pugliese D , Laterza L , Lopetuso L R , Papa A , Cammarota G , Putignani L , Gasbarrini A , Scaldaferri F , Petito V 
Published: January 2025

Abstract

Background
Many patients with Inflammatory Bowel Diseases do not respond to biological therapies. Extrachromosomal circular DNA(eccDNA) has been showed to play a role in the pathophysiology of IBD, as there is a higher presence of eccDNA in the intestinal mucosa of these patients. By characterizing the gene content of eccDNA, up-regulation of certain genes is observed; one of these is NRG1 (Neuregulin 1), an EGF ligand that guides tissue repair after injury and is associated with tissue plasticity. This gene is located on chromosome 8p12 and it is expressed in macrophages, Paneth cells, and stromal mesenchymal cells of the stem cell niche. In the context of IBD, where chronic inflammation is a hallmark, NRG1 could potentially modulate the immune response to reduce inflammation and promote healing. It is important to understand whether its expression within eccDNA may correlate with a particular course of the disease.

Methods
eccDNA was extracted from intestinal mucosa samples derived from patients diagnosed with IBD and amplified using the Circle-Seq analysis. Following sequencing, bioinformatic interpretation of the data was performed, through which a list of gene fragments present on the circles of individual patients and their localization was obtained. Finally, the presence of the gene found up-regulated by the bioinformatic analysis was confirmed using Real Time PCR.

Results
Starting from 99 intestinal mucosa samples from IBD patients, whose eccDNA was sequenced, circles containing fragments of NRG1 were found in 22 of them; its presence was compared to samples of diseased mucosa biopsies versus healthy mucosa from the same IBD patient. The number of circles from NRG1 is greater in diseased mucosa samples compared to healthy ones, in both UC and CD patients. Furthermore stratifying patients by response to therapy, about 70% of responders to IBD-therapy were NRG1- , with Odds Ratio &lt;1.

Conclusion
Preliminary results show that NRG1, a gene significantly detected from intestinal mucosa eccDNA, may predict therapeutic response in Inflammatory Bowel Disease. Further analysis are needed to confirm these data.

References
1.Di Vincenzo F, Yadid Y, Petito V. et al. Circular and Circulating DNA in Inflammatory Bowel Disease: From Pathogenesis to Potential Molecular Therapies. Cells. 2023 Jul 27;12(15):1953.
2.Møller H.D., Bojsen RK., Tachibana C. et al. Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells. J Vis Exp. 2016 Apr 4;(110):e54239
3.Møller H.D., Mohiyuddin M., Prada-Luengo I. et al. Circular DNA elements of chromosomal origin are common in healthy human somatic tissue. Nat Commun 9, 1069 (2018).
P0041 Assessment of real-world effectiveness of risankizumab in patients with moderate-severe Crohn’s disease in a global setting
Authors: Dignass A , Joshi N , Lukanova R , Dawod F , Jones W , Kligys K , Zambrano J A , Song A , Griffith J , Jairath V , Bossuyt P 
Published: January 2025

Abstract

Background
The primary treatment goals in Crohn’s disease (CD) are to control symptoms, such as abdominal pain and diarrhea, and induce long-term endoscopic remission. The biologic risankizumab (RZB) was approved in 2022 for the treatment of adult patients with moderate-severe CD. As data on RZB utilization and effectiveness are limited, this study aimed to assess the impact of RZB on disease remission and symptom control for optimizing treatment outcomes in patients with CD.

Methods
Data were drawn from the Adelphi Real World CD Disease Specific Programme, a cross-sectional survey with retrospective data collection of gastroenterologists (GIs) in France, Germany, Italy, Spain, the UK, and the USA from Feb 2023–Oct 2024. GIs provided data on their consulting patients with subjectively classified at RZB initiation moderate-severe CD reported demographics, clinical characteristics and symptoms at RZB initiation and at most recent consultation. Analyses were descriptive, Wilcoxon signed rank and McNemar tests were used to compare severity and symptoms at RZB initiation and at most recent consultation, respectively.

Results
Overall, 206 GIs reported data on 333 patients with moderate-severe CD receiving RZB. Mean (standard deviation; SD) patient age was 40.8 (13.0), disease duration was 4.7 (5.8) years; 54% were advanced therapy (AT, comprising biologics and small molecule therapies) naïve and 46% AT experienced (Table 1). Among all patients, 85% received RZB as a monotherapy; 6% received RZB with corticosteroids and 9% with 5-aminosalicylates and/or immunomodulators for; mean (SD) time on RZB among those with a known treatment duration (n=299) was 7.5 (7.5) months.
Among patients receiving RZB for &gt;6 months (n=140), 55% were in GI-reported clinical remission at most recent consultation. Among all patients, GI-reported moderate-severe disease severity significantly reduced from RZB initiation (100% of patients) to most recent consultation (55%; p&lt;0.0001; Fig 1A). Key symptoms experienced at RZB initiation (abdominal pain, 87%; bloody diarrhoea, 29%; non-bloody diarrhoea, 59%; fatigue, 54%; bowel urgency, 41%) significantly reduced at most recent consultation with continued RZB treatment (48%, 9%, 35%, 38%, 20%, respectively; p&lt;0.0001; Fig 1B).

Conclusion
In a real-world global setting, patients with moderate-severe CD treated with RZB experienced a significant reduction in GI-reported disease severity and improvement in key symptoms, and over half of patients were in GI-reported clinical remission. The improvement in symptoms and severity were greater among patients who were treated for a longer duration with RZB. These results highlight the real-world effectiveness of RZB in managing disease activity and symptom burden among patients over time.
P0043 Fecal extracellular vesicles from healthy individuals: A novel therapeutic approach for patients with Inflammatory Bowel Disease
Authors: Ghandian A , Heydari R , Shahrokh S , Meyfour A 
Published: January 2025

Abstract

Background
Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disease that consists of two main types: Crohn's disease and ulcerative colitis. One of the main causes of this disease is the disruption of the diversity of the gut microbiome and dysregulation of the interactions between microbes and the human immune system. So far, no definitive cure has been identified for the disease, and current treatments are only for temporary suppression of severe inflammatory responses. One treatment option currently being investigated in clinical trials is fecal transplants from healthy donors to patients with IBD. Extracellular vesicles (EVs), released by various cell types and microbes residingt in the gastrointestinal tract, can play an important role in the disease progression and treatment of IBD. In this study, we investigate the therapeutic potential of extracellular vesicles extracted from the feces of healthy individuals in the in vitro model of inflammatory bowel disease.

Methods
An in vitro model of IBD was established using a transwell co-culture system of Caco-2 intestinal epithelial cells and RAW264.7 macrophages. Inflammation was induced in macrophages using lipopolysaccharide (LPS). Stool samples were obtained from healthy donors and IBD patients. Stools were suspended in Tris-EDTA-based buffer in a 1:5 ratio and centrifuged. The supernatant was filtered and centrifuged at 100,000 x g to isolate EVs. Dynamic light scattering (DLS) and Transmission electron microscopy (TEM) were performed to characterize EVs in size and shape. The effects of EVs isolated from healthy individuals and IBD patients on the intestinal cells and expression of epithelial barrier markers were investigated in the in vitro IBD model.

Results
DLS results revealed that the size of isolated EVs was mainly distributed around 100-200 nm. TEM results showed that the EVs were round- or oval-shaped and their structures did not alter by ultracentrifugation. Inflammation induction using LPS led to changes in the morphology of intestinal cells. However, the shape of cells after treatment with EVs derived from feces of healthy donors was similar to the control group. Intriguingly, the cell shapes shifted toward the inflammatory phase when they were treated with stool-derived EVs of IBD patients. Molecular findings showed that stool-derived EVs of healthy individuals could restore the expression of epithelial cell markers in the inflamed intestinal cells, preserving epithelial barrier function, similar to what was observed in the non-inflamed cells.

Conclusion
Stool-derived EVs of healthy individuals can be introduced as a new solution for the treatment of IBD patients, although further studies on animal models are needed to enter the clinic.