bluuebunny/crossref_metadata_2025_split huggingface dataset:
DOP128 Spatial transcriptomic analysis reveals evolutionary dynamics in colitis-associated colorectal cancer
Authors: Kim Y , Lee Y , Lee M , Yoon D K , Baek J , Hwang S W , Lee J L , Park S H , Yang D H , Kim J , Yang S K , Han B , Song K , Yoon Y S , Ye B D , Lee H S 
Published: January 2025

Abstract

Background
Colitis-associated colorectal cancer (CAC) is a severe complication of inflammatory bowel disease, particularly ulcerative colitis. Despite its clinical significance, the spatiotemporal dynamics of neoplastic progression in CAC remain poorly understood. This study aimed to elucidate the evolutionary trajectory of CAC using spatial transcriptomics.

Methods
We employed spatial transcriptomics to analyze four tissue samples from three patients with ulcerative colitis at various stages of neoplastic progression. Whole-slide spatial transcriptomics RNA sequencing was performed, enabling simultaneous analysis of gene expression and tissue architecture. Integrated spatial transcriptomic data revealed recurring epithelial programs along the progression of copy number alteration.

Results
Our analysis using copy number variation (CNV) score and Hematoxylin and Eosin (H&E) staining image revealed progressive changes in gene expression patterns as tissue transitioned from non-tumor to pre-tumor and finally to tumor states. This progression was quantified using beta coefficient values, allowing us to track gradual alterations in gene expression across the disease continuum. We identified a core set of 48 genes that exhibited consistent changes across all four analyzed samples. Among these, 40 genes showed a progressive decrease in expression, while eight genes, including CLDN1, E2F1, and RECQL4, demonstrated a gradual increase in expression as the tissue advanced towards a tumorous state. These upregulated genes pointed to potential oncogenic drivers or compensatory mechanisms activated during tumor development. Pathway analysis of the 48 genes revealed enrichment in key cellular processes, including p53 signaling, transcriptional regulation by E2F factors, and role of PKR in interferon induction and antiviral response. Upstream Regulator analysis revealed YAP1 and TGFB1 as the most significant regulators, highlighting the importance of transcriptional control and growth factor signaling in CAC development.

Conclusion
This study provides unprecedented insights into the spatiotemporal dynamics of CAC progression. By leveraging spatial transcriptomics, we have mapped the evolutionary trajectory of CAC at high resolution, revealing key molecular events and spatial features associated with disease progression. These findings not only enhance our understanding of CAC pathogenesis but also highlight potential targets for early intervention and personalized treatment strategies.
DOP133 Spatiotemporal analysis of Crohn’s disease reveals PECAM2 signaling at the basis of inflammation-to-fibrosis transition
Authors: Ungaro F , Massimino L , Parigi T L , Riva M , Nicolò S , Spanò S , Mino S , Bugatti M , Frontali A , Scarfò F , Vignali A , Municchi A , Villanacci V , Albarello L , Ponzoni M , Solitano V , Jairath V , Peyrin-Biroulet L , Sileri P , Danese S 
Published: January 2025

Abstract

Background
Crohn’s disease is a chronic inflammatory disease of the bowel often complicated by fibrotic strictures(1,2,3). Medical treatment is lacking, and surgery is commonly required(3). The mechanisms underlying the progression from chronic inflammation to fibrosis are not yet defined. We aim to unravel Crohn’s disease pathogenesis using cutting-edge computational and bioinformatics tools (Figure 1).

Methods
Spatial transcriptomics was performed on 13 surgical specimens of inflamed and fibrotic Crohn’s disease and healthy controls. Spatial transcriptomics results were integrated with single-cell data to track the cellular and molecular evolution from healthy intestine to fibrosis by employing CellChat(4) and pseudotime analysis. Computational data were confirmed by immunostaining of tissues from an independent cohort of Crohn’s patients.

Results
We demonstrated that intestinal cytoarchitecture was rearranged while chronic inflammation progressed. Crohn’s disease-associated fibrosis evolved within the mesenchymal compartment, driven by PECAM2 signaling through PECAM1-CD38 interaction. Notably, CD38 positivity was found in the mesenchymal compartment in an independent cohort of Crohn’s disease patients. In parallel, ApoA signaling, particularly APOA1-ABCA interaction, emerged as relevant for maintaining epithelial and stromal homeostasis, while its downregulation was associated with fibrosis development (Figure 2).

Conclusion
Our results provide insights into CD38-driven fibrosis and suggest that PECAM2 signaling blockade could reduce the development of strictures in patients with Crohn’s disease, potentially offering a new treatment target.

References
1.Torres J, Mehandru S, Colombel J-F, et al. Crohn’s disease. Lancet 2017;389:1741–1755.
2.Lichtenstein GR, Loftus EV, Isaacs KL, et al. ACG clinical guideline: management of crohn’s disease in adults. Am. J. Gastroenterol. 2018;113:481–517.
3.Rieder F, Kessler S, Sans M, et al. Animal models of intestinal fibrosis: new tools for the understanding of pathogenesis and therapy of human disease. Am. J. Physiol. Gastrointest. Liver Physiol. 2012;303:G786-801.
4.Jin S, Plikus MV, Nie Q. CellChat for systematic analysis of cell-cell communication from single-cell and spatially resolved transcriptomics. BioRxiv 2023.
P0010 Characterization of proliferating memory CD4⁺ T cells reveals a distinct immune signature in anti-α4β7 integrin therapy non-responders Inflammatory Bowel Disease patients
Authors: Cancino C , Horn V , Obermayer B , Fritz K , Nguyen A , Juhran K , Bösel D , Conrad T , Sonnenberg E , Weidinger C , Siegmund B , Thurley K , Hegazy A 
Published: January 2025

Abstract

Background
Failure to respond to the anti-α4β7 integrin therapy, vedolizumab, is observed in a subset of inflammatory bowel disease (IBD) patients, potentially linked to distinct T cell activation profiles. This study aims to characterize the transcriptional and phenotypic features of circulating memory CD4⁺ T cells in vedolizumab non-responders and their association with treatment resistance.

Methods
We performed multidimensional flow cytometry and single-cell RNA sequencing to analyze IBD patients' circulating memory CD4⁺ T cell compartment, comparing pre- and post-treatment peripheral blood samples from vedolizumab responders and non-responders. Proteogenomic analysis and TCR repertoire profiling of CD4⁺ T cells were conducted using matched peripheral blood samples. Flow cytometry characterized T cell subsets based on surface markers, migration receptors, transcription factors, and cytokine expression, focusing on differences in activation and migration profiles.

Results
Ki67⁺ cells were enriched in the memory CD4⁺ T cell population of vedolizumab non-responders in both UC and CD, confirmed by two independent cohorts. TCR repertoire analysis showed increased diversity in memory CD4⁺ T cells post-treatment. Single-cell sequencing and proteomics revealed these Ki67⁺ cells had a high activation and proliferation profile (HLA-DR, CD40LG, MKI67) with reduced IL7R and SELL expression. They displayed elevated integrins (α4, β1, β7) and gut-homing receptors (CXCR3, CCR6). Upregulated T-bet, EOMES, and RORγt and increased IL-17A, indicated a pro-inflammatory Th1/Th17 phenotype in non-responders.

Conclusion
Ki67⁺ memory CD4⁺ T cells are significantly enriched in the peripheral blood of vedolizumab non-responders, displaying a distinct transcriptional and phenotypic profile characterized by Th1/Th17 polarization, high integrin α4β1 expression, and enhanced gut-homing capacity. These findings indicate that proliferating effector memory CD4⁺ T cells could contribute to therapy resistance in IBD, emphasizing the need for alternative therapeutic strategies targeting these cells in anti-α4β7 integrin therapy non-responders.
P0014 Mesenteric inflammation-associated fibroblasts are critical in the pathogenesis of Crohn’s disease
Authors: Park J , Joo Y H , Song E M , Park Y , Noh G T , Choi E , Byun J , Byun J R , Kim H S , Ahn Y H , Jung S A 
Published: January 2025

Abstract

Background
The Mesentery, initially considered as a structure support of abdominal organs, has emerged as an active participant in the inflammatory processes of Crohn's disease (CD). It serves as a central hub for immune cell activity, including macrophages, T cells, and B cells, driving the propagation of inflammation. Additionally, mesenteric fibroblasts play a crucial role in CD-associated fibrosis. These fibroblasts are activated by pro-fibrotic cytokines such as TGF-β and IL-13, leading to excessive extracellular matrix (ECM) deposition, which contributes to intestinal wall thickening and the formation of strictures. In this study, we aim to explore the specific role of mesenteric fibroblasts in the pathogenesis of CD.

Methods
Magnetic-activated cell sorting was utilized to isolate mesenteric inflammation-associated fibroblasts (IAFs) and normal fibroblasts (NFs) from surgical samples of patients with Crohn's disease (CD) and noncancerous colonic polyps (control group). Various cell-based assays, including cell viability, invasion, and collagen contraction assays, were conducted to investigate phenotypic differences between NFs and IAFs. To assess the impact of NFs and IAFs on colonic epithelium, Co-culture experiments were performed with the isolated fibroblasts and Caco-2 and HT-29 colorectal cancer cell lines using transwell and 3D Matrigel culture systems.

Results
IAFs exhibited a significantly faster growth rate than NFs (Figure 1B; fold change [FC] 1.60 ± 0.04, P &lt; 0.001). Furthermore, IAFs showed markedly higher wound healing (Figure 1C; FC 1.44 ± 0.15, P = 0.004), invasion (Figure 1D; FC 1.45 ± 4.7, P = 0.035), and collagen contraction activities (Figure 1E; FC 1.26 ± 4.73, P = 0.007) compared to NFs. In a 3D Matrigel co-culture system with Caco-2 spheres, abnormal lumen formation with invasive structures of Caco-2 spheres was significantly higher in IAFs compared to NFs (Figure 2A; FC 1.3 ± 0.08, P &lt; 0.001). Similarly, a fluorescein transport assay using a transwell co-culture system revealed that IAFs caused significantly greater epithelial disruption compared to NFs (Figure 2B; FC 1.25 ± 0.04, P = 0.04). Conditioned media from IAFs upregulated the expression of mesenchymal markers, such as ZEB1 (FC 2.67 ± 0.2, P &lt; 0.01) and CDH2 (FC 2.11 ± 0.54, P &lt; 0.05), in Caco-2 cells when compared with NFs (Figure 2C).

Conclusion
These findings suggest that mesenteric IAFs play an active role in the inflammatory and fibrotic processes in the pathogenesis of CD. Targeting mesenteric IAFs and their associated pathways may provide a promising therapeutic approach for managing CD.
P0015 The local intestinal interstitial cytokine profile provides an insight into inflamed bionaive patients with Ulcerative Colitis
Authors: Rogoll E , Seeger A , Zigra G , Wilhelm A , Kräker K , Müller D N , Siegmund B , Haag L M 
Published: January 2025

Abstract

Background
Proinflammatory cytokines identified in the mucosal microenvironment at the site of inflammation are involved in the pathophysiology of chronic inflammatory bowel diseases such as ulcerative colitis (UC). We hypothesize that the local cytokine production is significantly altered in inflamed regions of the intestine and cannot be predicted by plasma measurements. Our goal is to identify personalized cytokine signatures in UC patients' interstitial space depending on their disease progression. This can significantly advance our understanding of UC and support the development of more personalized treatment strategies as cytokine signaling is already a target of current therapies.

Methods
We isolated interstitial fluid (IF) from the intestinal mucosa using the tissue elution method in bionaive UC patients (mild activity (UCEIS 1-4) n = 6; inflamed (UCEIS 5-8) n = 6) and healthy controls (n = 25). We took biopsies from 4 different intestinal segments (rectum, descending colon, ascending colon and ileum) with an average weight of 13,4 mg in 400 mg NaCl for 2h elution in 4°C. Obtained IF was used for multiplex immunoassays of 18 proinflammatory cytokines in the same way as plasma cytokines.

Results
Cytokines such as VEGF, IL-16 and IL-12p40 are present in healthy controls and inflamed patients in the IF. Depending on the disease's severity, more cytokines can be detected. Cytokine concentrations decrease in the more aboral localizations of the colon with the rectum showing a unique cytokine pattern. Cytokines that can be detected in plasma show much lower concentrations compared to IF. Inflamed patients can be distinguished from mild activity in local interstitial profiles. In plasma, different cytokines appear to drive inflammation – those can be identified by linear discriminant analysis, and their composition differs from that in the rectum. Moreover, plasma and rectal interstitial mucosa cytokine patterns correlate well with endoscopic and clinical UC scores.

Conclusion
Isolation of IF is a valuable approach to assessing inflammation in UC patients, improving our understanding of mild residual activity and more severe conditions compared to traditional plasma measurements. We can identify cytokines that drive inflammation in UC and characterize the inflammatory cytokine profile in the intestinal interstitial space associated with a healthy gut. Future targeted therapies should also consider the unique cytokine profiles of individual patients being expressed in the rectum. Comparing bionaive cytokine profiles with profiles from patients treated with biologicals, will allow us to demonstrate how the network changes in response to immunosuppression.
P0016 Comprehensive Characterization of local Cytokine Signatures in Ulcerative Colitis in Deep Remission
Authors: Rogoll E , Seeger A , Gluschke H , Zigra G , Wilhelm A , Kräker K , Kühl A A ,   I.C. The TRR2415, Müller D N , Siegmund B , Haag L M 
Published: January 2025

Abstract

Background
Ulcerative colitis (UC) is a chronic relapsing-remitting disease characterized by distinct molecular patterns and proinflammatory pathways. Through advances in therapy and monitoring-strategies, long lasting remission can be achieved in an increasing number of patients. Our aim is to investigate cytokine signatures in the interstitial microenvironment at protein and RNA level in UC patients showing deep remission (DR) to better understand the response to existing therapies. We hypothesize that the DR forms a distinct group that differs in its local intestinal cytokine profile from mild activity and non-IBD controls.

Methods
Two cohorts of UC patients along with non-IBD controls were characterized. We isolated interstitial fluid (IF) from the rectum and colonic mucosa of 14 UC patients in DR (UCEIS 0 + Mayo 0), 11 in mild activity (UCEIS 1-4 and/or Mayo 1-4) and 25 non-IBD controls as part of the InFlame study (DRKS00031203). Obtained IF was used for multiplex immunoassays of 18 proinflammatory cytokines in the same way as plasma cytokines of this cohort. RNA isolates of colonic biopsies of the other cohort (IBDome) (DR n=22; mild activity n=14, non-IBD controls n=18) underwent bulk RNA sequencing. After normalization, expression profiles of genes corresponding to measured cytokines were compared.

Results
RNA expression of genes corresponding to IL-15, IL-17 and VEGF were significantly upregulated in DR versus non-IBD samples in colonic samples. On the contrary, there were no significant differences in cytokine levels in the IF of the rectum and colon. 14 out of 18 (78 %) genes were differentially expressed between DR and mild activity. Cytokine levels of IL-8, IL-10, IL-15, IL-16, IL-17, IFN-gamma and TNF-a were also upregulated in the IF. VEGF and IL-12B were only significantly upregulated at the protein level. DR and non-IBD controls could not be satisfyingly distinguished in PCA clustering based on interstitial cytokines or the corresponding gene expression. However, PCA clustering could separate DR from mild activity in both datasets. Within the mild activity group, patients with a higher clinical score appeared further away from the DR group. Generally, the characterization of disease activity in the interstitial space was significantly more robust in the rectum than in the descending colon. At the plasma level, DR cannot be distinguished from mild activity, and neither can the healthy state.

Conclusion
Cytokines in the IF can reliably differentiate between UC in different activity stages. Furthermore, RNA expression of corresponding cytokines is correlating. Nevertheless, DR with very stringent criteria seems to resemble non-IBD controls more than UC with mild activity.
P0017 Single-cell transcriptomic analysis reveals insights into the mechanism of action and immune modulation by granulocyte-monocyte apheresis
Authors: Kioroglou D , Cabriada J L , Marigorta U M , Rodríguez-Lago I 
Published: January 2025

Abstract

Background
Granulocyte-monocyte apheresis (GMA) with Adacolumn® is a non-pharmacological therapy used for ulcerative colitis (UC). Despite its clinical efficacy, the precise immunological mechanisms of GMA have not been completely characterized. This study aimed to uncover the immune cell composition and signalling changes induced by GMA using single-cell RNA sequencing (scRNA-Seq) of peripheral blood mononuclear cells (PBMCs) in UC patients.

Methods
Patients with steroid-dependent UC receiving GMA were included. scRNA-Seq was performed on PBMCs obtained at a) immediately pre-treatment, b) post-first session (outflow catheter), and c) 1 month after induction GMA. We applied an in-house standard pipeline for quality control, including batch correction and data integration, followed by differential gene expression analyses to ascertain the alterations in immune cell profiles and regulatory pathways induced by GMA.

Results
Five patients were included and 12 samples were analysed, averaging 8,997 cells and 19,424 genes each. We observed pervasive modulations in immune cell composition, most notably reductions in classical monocytes and expansions in plasmacytoid dendritic cells (pDCs) and Natural Killer (NK) cells. The pathway analyses highlighted downregulation of NF-κB and IL6/JAK/STAT3 signalling across multiple immune cell types, implying widespread decrease in inflammatory activity. This downregulation was particularly pronounced in samples collected immediately after the first session (outflow catheter), suggesting an acute suppression of inflammatory signalling.
Classical monocytes showed reduced expression of key pro-inflammatory genes, including TNF, NFKBIZ, and NFKBIA, indicating suppressed pro-inflammatory potential. In turn, non-classical monocytes displayed upregulation of anti-inflammatory markers such as IL1R2, suggesting a reorientation toward balanced immune control.
By the second visit (one month after induction), we observed a marked return to homeostasis. This included increased expression of immunoglobulin-related genes, such as IGHA1 and IGKC, across various T cell subsets, such as regulatory T cells (Tregs) and tissue-resident memory T cells (Trm). These patterns suggest a heightened capacity for immune regulation and improved balance within the immune response over time.

Conclusion
This first single-cell transcriptomic analysis of GMA in UC patients reveals selective impacts on immune cell composition and signalling, with sustained reductions in inflammation and enhanced regulatory balance over time. Our work underscores the potential of GMA as a targeted therapeutic approach to managing immune dysregulation in UC, paving the way for future exploration into its application and optimization in immune-mediated diseases.
P0018 Fat rich dietary habits: Further increasing IBD risk in first degree relatives
Authors: Koentgen S , Cosier D , Tavakoli P , Leach S T , Dutt S , Ghaly S , Connor S J , Lemberg D A , Lambert K , Hold G L 
Published: January 2025

Abstract

Background
Western diets characterised by high intake of meat and processed food, are implicated in IBD development1. Dietary habits are often shared amongst family members however, where familial diets diverge a difference in IBD risk may arise, compounding in members adhering to western diets. In this study, we compared macronutrient intake and dietary patterns between unaffected first degree relatives (FDRs), their IBD relatives and healthy controls (HCs).

Methods
70 FDRs were recruited within the Australian IBD Microbiome (AIM) study. FDRs were matched ~1:3 to healthy participants (HC; n=200), IBD relatives (adult; n=25 and paediatric; n=25; no other groups contained paediatric participants) were also included for comparison. Macronutrient intake was assessed from 3-day food records. Dietary patterns were computed using principal component analysis (PCA) of food frequency questionnaires (FFQ).

Results
There was no difference in mean daily energy (KJ), total fat or protein intake (g/day) between groups. Paediatric IBD patients matched FDRs in energy intake (8031KJ; □□□□=2788 and 8046KJ; □□□□= 2741 respectively, p&gt;0.9999). Carbohydrate intake (g/day) was significantly higher in the paediatric IBD group than FDRs (p=0.0408), however variance in daily intake was high (paediatric IBD; 210g, □□□□=108g). FDRs had the lowest percentage of energy from carbohydrate intake compared to all other groups (36.4%, p&lt;0.0004). Energy contribution from total fat was highest in FDRs (38.2%); significantly higher than HCs (35.1%, p=0.0063). Energy from protein consumption was consistent among groups (~20%). PCA of FFQs (all participants) produced 5 distinct dietary patterns from 27 food groups, explaining 47.6% of the total variance. These patterns were described as ‘Ultra-Processed’, ‘Balanced Whole Foods’, ‘Processed High Fat’, ‘Meat Centric’, and ‘Sweetened Beverages & Low Fibre’. Adherence to the ‘Processed High Fat’ dietary pattern was significantly higher in paediatric IBD patients and FDRs than HCs (p&lt;0.0362). This dietary pattern was characterised by high consumption of butters/creams, processed meats, pizzas, savoury pastries, sauces/condiments and red meat.

Conclusion
FDRs have unique macronutrient intake and habitual dietary pattern adherence, diverging significantly from HCs. Similarity in adherence to the ‘Processed High Fat’ dietary pattern between paediatric IBD and FDR cohorts may reflect food decision-making by parental FDRs. Macronutrient and dietary pattern analysis indicate fat-rich dietary habits in FDRs; Increased IBD risk may in part be due to fat rich dietary habits.

References
1.Kaplan GG, Ng SC. Understanding and Preventing the Global Increase of Inflammatory Bowel Disease. Gastroenterology. 2017;152(2):313-321. doi:10.1053/j.gastro.2016.10.020