ArticleInflammatory bowel diseases2023
Assessing Cellular and Transcriptional Diversity of Ileal Mucosa Among Treatment-Naïve and Treated Crohn's Disease.
Article in Inflammatory bowel diseases, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 27 citations in OpenAlex.
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- Multi-omics reveals fibroblast subtypes with distinct roles in inflammatory bowel disease.Biology direct · 2026Article
- Single-cell RNA sequencing of intestinal Behçet's disease identifies putative pathogenic programs and potential therapeutic targets.Biomolecules & biomedicine · 2026Article
- Transglutaminase 2 modulates inflammatory angiogenesis via vascular endothelial growth factor receptor 2 pathway in inflammatory bowel disease.Journal of advanced research · 2026Article
- The SWI/SNF chromatin-remodeling subunit DPF2 regulates macrophage inflammation in intestinal injury via the CACNA1D-mediated MAPK pathway.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Cell-type-resolved genetic regulatory variation shapes inflammatory bowel disease risk.medRxiv : the preprint server for health sciences · 2025Article
- Integrated Single-Cell Transcriptome Analysis Reveals Novel Insights into the Role of Opioid Signaling in the Pathophysiology of Inflammatory Bowel Disease.Biomedicines · 2025Article
- Gut-on-a-chip platforms: Bridging in vitro and in vivo models for advanced gastrointestinal research.Physiological reports · 2025Review
- Altered inflammatory mucosal signatures within their spatial and cellular context during active ileal Crohn's disease.JCI insight · 2025Article
- Decoding the mosaic of inflammatory bowel disease: Illuminating insights with single-cell RNA technology.Computational and structural biotechnology journal · 2024Review
- Single-cell transcriptomics of rectal organoids from individuals with perianal fistulizing Crohn's disease reveals patient-specific signatures.Scientific reports · 2024Article
- Impaired activation of succinate-induced type 2 immunity and secretory cell production in the small intestines of Ptk6-/- male mice.Cell death & disease · 2024Article
- Longitudinal single-cell data informs deterministic modelling of inflammatory bowel disease.NPJ systems biology and applications · 2024Article
- Challenges in IBD Research 2024: Preclinical Human IBD Mechanisms.Inflammatory bowel diseases · 2024Review
- BEST4American journal of physiology. Cell physiology · 2024Review
- Concordant B and T Cell Heterogeneity Inferred from the Multiomic Landscape of Peripheral Blood Mononuclear Cells in a Crohn's Disease Cohort.Journal of Crohn's & colitis · 2024Article
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16 authors at 2 institutions in 1 country.
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Abstract
backgroundCrohn's disease is a lifelong disease characterized by chronic inflammation of the gastrointestinal tract. Defining the cellular and transcriptional composition of the mucosa at different stages of disease progression is needed for personalized therapy in Crohn's.
methodsIleal biopsies were obtained from (1) control subjects (n = 6), (2) treatment-naïve patients (n = 7), and (3) established (n = 14) Crohn's patients along with remission (n = 3) and refractory (n = 11) treatment groups. The biopsies processed using 10x Genomics single cell 5' yielded 139 906 cells. Gene expression count matrices of all samples were analyzed by reciprocal principal component integration, followed by clustering analysis. Manual annotations of the clusters were performed using canonical gene markers. Cell type proportions, differential expression analysis, and gene ontology enrichment were carried out for each cell type.
resultsWe identified 3 cellular compartments with 9 epithelial, 1 stromal, and 5 immune cell subtypes. We observed differences in the cellular composition between control, treatment-naïve, and established groups, with the significant changes in the epithelial subtypes of the treatment-naïve patients, including microfold, tuft, goblet, enterocyte,s and BEST4+ cells. Surprisingly, fewer changes in the composition of the immune compartment were observed; however, gene expression in the epithelial and immune compartment was different between Crohn's phenotypes, indicating changes in cellular activity.
conclusionsOur study identified cellular and transcriptional signatures associated with treatment-naïve Crohn's disease that collectively point to dysfunction of the intestinal barrier with an increase in inflammatory cellular activity. Our analysis also highlights the heterogeneity among patients within the same disease phenotype, shining a new light on personalized treatment responses and strategies.
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