bluuebunny/crossref_metadata_2025_split huggingface dataset:
DOP127 A novel epithelial junction gene associated with very early onset IBD: a mechanistic study using patient organoids and transgenic mouse models
Authors: Ma K , Deepak P , Ciorba M , Cao S 
Published: January 2025

Abstract

Background
Very early onset inflammatory bowel disease (VEO-IBD) is often associated with a severe disease course and unique characteristics including underlying monogenic etiologies in some cases. In this study, we mechanistically defined the function of CGNL1, an epithelial junctional protein gene whose pathogenic variants may contribute to VEO-IBD.

Methods
Whole exome sequencing (WES) was performed on the affected patient and all first-degree relatives. Intestinal epithelial organoids (IEOs) were generated from the patient’s mucosal biopsies and were characterized by microscopy, whole-mount immunostaining, transcriptomics and transmission electron microscopy (TEM). In addition, we generated a new Cgnl1-/- mice for dextran-sodium sulfate (DSS)-induced colitis and infection by Citrobacter rodentium which directly compromises intestinal epithelium. Integrated analysis was performed to determine CGNL1 expression in single-cell datasets.

Results
In this patient with VEO-IBD who required early total colectomy with pouch formation, coexistent primary sclerosing cholangitis (PSC) and celiac disease, WES identified two rare, novel, pathogenic variants in the CGNL1 gene. Both pathogenic variants were also present in the patient’s younger sister, who has a similar history including fulminant UC and PSC-autoimmune hepatitis overlap syndrome. Furthermore, multiple relatives of the patient suffer from IBD and other inflammatory conditions including celiac disease, eosinophilic esophagitis, and type-1 diabetes. The RNA and protein levels of CGNL1 were diminished in the patient’s intestinal epithelium compared to that of healthy individuals and other IBD patients. The patient’s IEOs from pouch body and pre-pouch ileum formed smaller 3D spheroids with altered cell composition and significantly impaired barrier function compared to those from normal controls (Figure 1). TEM demonstrated disrupted tight junctions and adherens junctions in the patient’s IEOs. Similarly, impaired junctional complexes in intestinal epithelial cells and elevated intestinal permeability were present in Cgnl1-/- mice, which also showed increased susceptibility to DSS-induced colitis (Figure 2) and C. rodentium infection. Single-cell analysis revealed diminished expression of CGNL1 in intestinal and hepatic epithelial cells from patients with IBD or PSC, respectively.

Conclusion
The pathogenic CGNL1 variants may contribute to VEO-IBD and other inflammatory GI disease by disrupting gut barrier integrity. This study expands our understanding of epithelial barrier impairment in the pathogenesis of VEO-IBD and suggests the intestinal epithelium as a therapeutic target for some IBD patients.
DOP131 Multi-ancestry genome-wide association study reveals new associated loci and nominates disease relevant cell types and novel effector genes for Crohn’s disease and ulcerative colitis
Authors: Fachal L , Zhang R ,   International IBD Genetics Consortium
Published: January 2025

Abstract

Background
Genome-wide association studies (GWAS) have identified 370 signals associated with inflammatory bowel disease (IBD) and its two main subtypes, Crohn’s disease (CD) and ulcerative colitis (UC). Revealing new association signals and the genes dysregulated by those significantly improves our biological understanding of the disease. However, nominating these genes remains challenging since they are predominantly located within the non-coding genome.

Methods
We performed a multi-ancestry GWAS meta-analysis of 67 cohorts, from European, East and South Asian populations. The final dataset comprised 125,992 IBD patients (59,734 with CD; 57,565 with UC) and &gt;1.2M population controls.
We ran fine-mapping (FM) analyses to define the most likely causal variants driving each signal.
To investigate whether the associated variants are preferentially located at cell-type specific regulatory regions, and thus infer cell-disease susceptibility relationships, we ran heritability enrichment analysis integrating ATAC-seq and single cell (sc) ATACseq data from five studies.
To nominate dysregulated genes, we combined cis expression QTL (eQTL) and sc-eQTL data for &gt;30 relevant tissues and cell types via colocalization analyses; as well as two large protein QTL studies implementing mendelian randomization (MR).

Results
We identified 290 new independent disease signals. While most association signals are shared between CD and UC ~38% were subtype-specific.
IBD susceptibility variants were significantly enriched within regulatory elements of blood and tissue resident T cells, macrophages, and B cells. In contrast, we observed a larger enrichment of UC variants, when compared to CD variants, in regulatory elements of intestinal epithelial cells.
Combining FM, colocalization and MR, we prioritised 626 genes (Table). This set is enriched in well-established pairs of receptor-ligands, such as SERPINE1-ITGAV or VTN-PLAUR. Thirteen of the nominated genes have been previously linked to monogenic forms of IBD, such as CARD11, SHARPIN or IL10RB. Orthogonal lines of evidence provide further support for the effect (and the direction of effect) of the causal variant on disease susceptibility mediated through the molecular phenotype (Fig). For example, three novel risk signals (2 in CD, 1 in UC) mediate higher levels of expression of PDCD1, SELL, and MMP10, respectively. This was echoed by our MR analysis, which suggests that higher levels in serum of PDCD1 and SELL have a causal effect on CD-risk, and MMP10 on IBD-risk.

Conclusion
This study provides new insights into the cellular types by which genetic variants influence disease and nominates genes regulated by disease susceptibility variants, expanding the list of targets to prioritise for therapeutic interventions.
DOP134 Uncovering genetic archetypes to explain patient heterogeneity in IBD
Authors: Gaite-Reguero A , Sanchez-Mayor M , Lao O , Mars Z , Bujanda L , Marigorta U M 
Published: January 2025

Abstract

Background
Genome-wide association studies (GWAS) have identified 300 loci linked to inflammatory bowel disease (IBD) risk, underscoring the genetic complexity of the disease. But these findings do not explain the significant clinical heterogeneity observed across IBD patients. Without clear biomarkers to define subtypes, the clinical impact of these genetic variants remains limited. We hypothesized that distinct genetic archetypes underlie the variability in symptoms observed among patients. We developed a battery of polygenic risk scores to capture these genetic profiles and explore their potential for more precise patient stratification.

Methods
We applied a three-step strategy to develop partitioned polygenic risk scores (PRS) to characterize distinct genetic profiles. First, we used a phenome-wide association approach to classify genetic risk variants into non-overlapping clusters based on their association with traits related with IBD. Second, we used functional genomics datasets to identify partitioned PRSs based on similarity in gene enhancer landscapes, gene expression changes across IBD-relevant tissues, co-expression networks in patients, and publicly available gene ontologies and biological pathways. Finally, we used a genetic algorithm to integrate the abovementioned molecularly-based PRSs and assign patients into independent clusters. This algorithm utilized artificial intelligence principles based on genetic programming, focusing on optimizing the discovery of groups of patients with most genetic differences among them.

Results
Our analyses identified distinct genetic archetypes in IBD patients, revealing clusters associated with specific biological pathways. The phenome-wide approach classified genome-wide significant variants into seven non-overlapping clusters, some linked to inflammatory (e.g. multiple sclerosis) and behavioral traits (e.g. sedentary behaviour) that are relevant to the comorbidity patterns observed in each patient. Through functionally-informed partitioning of genetic risk, we proposed 18,470 novel pathway-specific risk scores adapted for IBD. Notably, 25% of them significantly differentiated patients from controls. Finally, the genetic algorithm integrating these pathway-specific PRSs uncovered patient clusters with unique genetic profiles, highlighting the diverse biological underpinnings of IBD heterogeneity.

Conclusion
By combining GWAS results, functional genomics, and AI algorithms, we uncovered distinct genetic archetypes in IBD patients that reflect diverse biological pathways, including inflammatory and behavioral traits. This strategy improves our understanding of the genetic underpinnings of IBD heterogeneity and may serve to lay the groundwork for more precise patient stratification.
P0001 Single-cell profiling reveals distinct γδ T cell subsets with protective and pathogenic roles in Ulcerative Colitis
Authors: Mayer L S , Arnold J , Reuter N , Pattekar A , Ohtani T , Bruder K , Ribeiro M , Siwicki R , Obwegs D , Stahl E , Kolter J , Mansoori Moghadam Z , Alaswad A , Li Y , Lewis J D , Wu G D , Bewtra M , Tomov V T , Bengsch B , Thimme R , Hasselblatt P , Picelli S , Hofmann M , Sagar S 
Published: January 2025

Abstract

Background
Comprising about 40% of mucosal lymphocytes, γδ T cells represent a significant lineage in the gut, and thus are key players in the intestinal immune homeostasis. In contrast to αβ TCRs, γδ TCRs are able to recognize antigen independent from MHC-restricted antigen presentation. While antigens recognized by γδ TCRs are largely undefined, activation of γδ T cells is initiated by phospho-antigens and members of the butyrophilin (BTN) family. Data from both murine and human studies suggest a protective role of γδ T cells in the pathogenesis of inflammatory bowel diseases (IBD). However, significant species-specific variations of γδ T cells demand more detailed investigation of human intestinal γδ T cells. To date, no single-cell study has comprehensively assessed subset-related roles of γδ T cells in ulcerative colitis (UC).

Methods
In this study, we performed multimodal profiling of intestinal γδ T cells in ulcerative colitis (UC) at single-cell resolution using FLASH-seq (healthy donors (HD) n=2, active UC n=5) and cytometry by time of flight (CyTOF, HD n=29, inactive UC n=26, active UC n=24). FLASH-seq analysis of additional samples is ongoing. Peripheral blood samples were analyzed in a subset of patients.

Results
Our analysis revealed that healthy gut epithelium is predominantly populated by CD103+ intraepithelial γδ lymphocytes (γδ IELs). However, in the inflamed intestinal environment, two distinct although clonally related γδ T cell subsets emerge: one TCF-1+ PD-1+ memory-like subset, resembling stem-like αβ T cells previously described in chronic infections and cancer, and the other exhibiting a cytotoxic phenotype, characterized by increased expression of GZMB, PRF1, and TBX21. The decline in CD103+ γδ T cells, coupled with the expansion of these two subsets, was associated with reduced expression of butyrophilin-like (BTNL) molecules, BTNL3 and BTNL8, and increased expression of BTN3A1 and BTN3A3, along with transcriptional and metabolic changes associated with enhanced γδ T cell-mediated killing in intestinal epithelial cells. Patients responding to therapies showed a return to a healthy γδ T cell subset composition, with the contraction of these subsets after remission, further supporting their pathogenic role. Additionally, significant opposing phenotypic changes were observed in peripheral blood γδ T cell subsets in UC.

Conclusion
Overall, our data provide a comprehensive single-cell landscape of γδ T cells in UC, identifying novel subsets that differentially carry out protective and pathogenic roles. These subsets may serve as valuable biomarkers, and may represent novel therapeutic targets.
P0006 Developmentally endothelial locus-1 promotes intestinal inflammation resolution through inhibition of the Cmpk2-cGAS-STING pathway and regulates reparatory macrophage transition
Authors: Tao M , Chen C , Fu Y 
Published: January 2025

Abstract

Background
Abnormalities in inflammation resolution function are closely associated with chronic inflammation, and proresolution therapies may provide new opportunities for the treatment of inflammatory bowel disease (IBD). Developmental endothelial locus 1 (DEL-1) is an important endogenous molecule that regulates tissue immune homeostasis and promotes resolution of inflammation, but its effect on IBD remains unknown. Here, we aimed to explore the expression and roles of DEL-1 in IBD.

Methods
DEL-1 levels were examined in patients with IBD, mice with colitis, and LPS-induced RAW264.7 cells. DEL-1 overexpression plasmids and/or DEL-1-Fc intervened in cells and mice to explore it effects in the acute and recovery phases of inflammation. Moreover, flow cytometry, RNA-Seq, chromatin immunoprecipitation (ChIP), dual-luciferase reporter assays and 16S rRNA were used to illustrate the potential mechanism of DEL-1 in colitis.

Results
DEL-1 levels were remarkably lower in IBD patients, colitis mice, and LPS-induced RAW264.7 cells, while the levels increased with inflammation to resolve. Transfection with DEL-1 overexpression plasmid and/or DEL-1-Fc intervention reduces levels of inflammatory cytokines in both phases and upregulates reparative gene levels in the recovery phase. Mechanistically, we demonstrated that DEL-1 inhibits Cytosine monophosphate kinase 2 (Cmpk2)-dependent mtDNA synthesis, thereby inhibiting the cGAS-STING pathway to ameliorate intestinal inflammation. Moreover, DEL-1 promoted reparative macrophage transition in the repair model of colitis. Spi1 was identified as a transcription factor that regulates Cmpk2 and the reparative gene Il10. Intervention with overexpression plasmid of Spi1 or Cmpk2 or the STING agonist DMXAA reverses the effects of DEL-1. DEL-1 also inhibits neutrophil recruitment, repairs the intestinal barrier, and improves intestinal microbiota dysbiosis.

Conclusion
This is the first study to show that DEL-1 effectively attenuates colonic inflammation in mice with DSS-induced colitis by inhibits the Cmpk2-cGAS-STING pathway and regulates reparatory macrophage transition, thus providing a novel therapeutic target for IBD.
P0009 Comparative analysis of ileal mucus in healthy individuals and Crohn’s Disease patients using scanning electron microscopy suggests changes in network structure
Authors: Mönch P W , Kramer C , Timm S , Kerkhoff Y , Ludwig K , Ochs M , Siegmund B 
Published: January 2025

Abstract

Background
Ileal mucus is vital for intestinal health, acting as a mesh-like barrier against pathogens while permitting nutrient absorption [1,2]. Structural changes in mucus are linked to diseases like Crohn’s disease (CD) [3,4]. This study used scanning electron microscopy (SEM) to qualitatively and quantitatively compare the ultrastructure of ileal mucus in healthy individuals and CD patients.

Methods
Ileal mucus samples from five healthy donors and three CD patients were collected during colonoscopies and analyzed via SEM. Systematic random sampling ensured unbiased, representative image collection. Images were captured at predefined intervals using a meandering scan pattern. Morphological parameters, including pore diameter and filament properties, were measured manually with ImageJ using an unbiased counting frame. An automated tool was also employed for comparison. Rheological measurements estimated mucus mesh size, which was compared to SEM-derived pore diameters.

Results
Automated analysis of CD samples showed smaller median pore diameters (28.93 nm vs. 33.86 nm in healthy samples) and thicker filaments (71.58 nm vs. 36.73 nm). CD samples also had longer filaments (120.51 nm vs. 93.53 nm) and a mean pore diameter of 46.19 nm, slightly larger than healthy samples (43.73 nm). Structural differences, including altered cellular components like echinocytes, were observed in CD samples. The calculated mesh size from rheological measurements trends aligned with SEM pore diameters, validating the findings. Healthy samples were analyzed manually so far, while CD samples were analyzed using an automated tool under validation for airway mucus.

Conclusion
The study reveals significant structural differences in ileal mucus between healthy individuals and CD patients, offering a robust method for advancing mucosal biology research.

References
1.Johansson, M. E. V., Sjövall, H., & Hansson, G. C. (2013). The gastrointestinal mucus system in health and disease. Nature Reviews Gastroenterology & Hepatology, 10(6), 352-361. https://doi.org/10.1038/nrgastro.2013.35
2.Bansil, R., & Turner, B. S. (2018). The biology of mucus: Composition, synthesis and organization. Advanced Drug Delivery Reviews, 124, 3-15. https://doi.org/10.1016/j.addr.2017.09.019
3.Kramer, C., RulD, H., Ziegler, J. F., et al. (2024). Ileal mucus viscoelastic properties diDer in Crohn’s disease. Mucosal Immunology, 17(4), 713-722. https://doi.org/10.1038/s41385-023-00567-9
4.Atreya, R., Siegmund, B. (2021). Location is important: differentiation between ileal and colonic Crohn’s disease. Nature Reviews Gastroenterology & Hepatology, 18(8), 544-558. https://doi.org/10.1038/s41575-021-00452-3
P0020 Type 1 and CD103+ type 2 conventional dendritic cells are decreased in patients with active ulcerative colitis but not with Crohn’s disease.
Authors: Bernardo D , Arribas-Rodríguez E , G de Castro C , Fiz-López A , De Prado A , Martín-Muñoz A , Fernández-Salazar L , Barrio J , Izquierdo S , García-Alonso F J , de Andrés B , García-Abril J M , Romero A , Sánchez-González J , Arranz E , Chaparro M , Gisbert J P , Garrote J A 
Published: January 2025

Abstract

Background
Human intestinal conventional dendritic cells (cDC) maintain the mechanisms of immune tolerance in health. However, their specific contribution to the development of inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn´s disease (CD) remains elusive

Methods
Human intestinal cDC were identified by flow cytometry in the human intestinal mucosal, and divided into CD103- cDC2, CD103+ cDC2 and cDC1. Their phenotype was determined in health and IBD, together with their stimulatory capacity over naïve T-cells.

Results
cDC1 (minority) and cDC2 (majority) did not change their proportion throughout the healthy gut. However, CD103+ cDC2 were the main subset in the duodenum as opposed to CD103- cDC2 which were predominant in the colon and ileum. CD103+ cDC2 displayed higher levels of PD-L1 together with an enhanced production of IL-10. CD103+ cDC2 also increased their proportion following culture, referred to their CD103- cDC2 precursors, being this process abrogated in the presence of LPS. All human intestinal cDC subsets primed the generation of IL-10+ helper T-cells, being ileal cDC more stimulatory than their colonic counterparts. In IBD, cDC had a constitutive lower expression of SIRPα irrespectively of IBD type (CD/UC) or condition (inflamed/not-inflamed). Of note, the inflamed colon from UC patients, but not from CD, displayed a specific reduction of both cDC1 and CD103+ cDC2, while colonic cDC from CD patients were more stimulatory and primed IL-17+ T-cells in the inflamed tissue.

Conclusion
All human intestinal cDC subsets prime the generation of IL-10+ helper T-cells. The specific reduction of cDC1 and CD103+ cDC2 in the inflamed mucosa from UC, but not CD, suggests the presence of different pathogenic mechanisms occurring in IBD.
P0023 Methionine Restriction Promotes Intestinal Mucosal Repair by Regulating Selenbp1 and Modulating Macrophage Polarization
Authors: Wu L , Chen Y , Chen R , Tang W , Liu Y 
Published: January 2025

Abstract

Background
Intestinal epithelial homeostasis is critical for maintaining gut integrity and function. Methionine is an essential amino acid involved in various cellular processes, and its dietary regulation may impact intestinal injury and repair mechanisms. Selenbp1, an oxidase of the methionine metabolite methanethiol, plays an important role in this process. This study investigates the role of methionine intake and Selenbp1 in colonic injury and epithelial repair.

Methods
Animal models with radiation-induced intestinal injury were used to assess the effects of methionine restriction and supplementation. Intestinal epithelial-specific knockout of Selenbp1 and control mice were used for in vivo experiments. Colonic organoids, macrophage co-culture assays, and biochemical assays, including qPCR, immunoblotting, and flow cytometry, were employed to study epithelial proliferation, SUMOylation of Satb2, and macrophage polarization. Clinical samples from patients with Crohn's disease were also analyzed for macrophage markers, as well as Satb2 and SUMO2/3 expression levels.

Results
Methionine restriction alleviated radiation-induced colonic injury in mice, as evidenced by improved histological scores and reduced inflammatory markers. In contrast, high methionine levels decreased Selenbp1 expression in the colon. Intestinal epithelial-specific Selenbp1 knockout exacerbated radiation-induced colonic mucosal injury, with significantly lower organoid survival rates and budding efficiency post-irradiation. However, this detrimental effect of Selenbp1 knockout was reversed upon methionine restriction, demonstrating the potential of dietary modulation. Furthermore, methionine supplementation led to a reduction in the SUMOylation of Satb2, a key regulator of intestinal epithelial homeostasis. The lower the level of Satb2 SUMOylation, the higher the clinical pathological features of Crohn's disease, such as disease activity. In co-culture assays, methionine supplementation enhanced M1 polarization of macrophages, further indicating a role of methionine in modulating immune responses. In clinical Crohn's disease (CD) specimens, we also found that a higher proportion of M1 macrophages correlated with lower expression levels of Selenbp1.

Conclusion
Methionine restriction promotes intestinal mucosal repair by regulating Selenbp1 and macrophage polarization, suggesting its potential as a therapeutic strategy for colonic repair.