ArticlePloS one2022
Profound gene expression changes in the epithelial monolayer of active ulcerative colitis and Crohn's disease.
Article in PloS one, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 41 citations in OpenAlex.
- Single-cell analysis of chromatin accessibility in the human intestine identifies regulatory programs and clarifies genetic associations in Crohn's disease.Nature genetics · 2026Article
- Regulation of Inducible Nitric Oxide Synthase (NOS2) Expression in Healthy and Inflamed Bowel: A Narrative Review.International journal of molecular sciences · 2026Review
- Epithelial Chloride and Bicarbonate Transport in Intestinal Barrier Failure: A Molecular Target-Validation Assessment of CFTR and SLC26A3/DRA in Inflammatory Bowel Disease.International journal of molecular sciences · 2026Review
- Review
- The nascent transcriptome delineates the regulatory landscape in human health and disease.bioRxiv : the preprint server for biology · 2026Article
- Identifying subtype-specific molecular pathways in Crohn's disease through RNA-seq and protein-protein interaction network analysis.Journal of translational autoimmunity · 2026Article
- Reference-guided genome assembly of long non-coding rna transcripts reveals target genes associated with Crohn's disease.Scientific reports · 2026Article
- UC-associated autoantibodies to αvβ6 inhibit mucosal TGFβ activation and predispose to intestinal inflammation.bioRxiv : the preprint server for biology · 2026Article
- Pharmacogenomic Pathways Underlying Variable Vedolizumab Response in Crohn's Disease Patients: A Rare-Variant Analysis.Biomedicines · 2026Article
- Reference-guided Genome Assembly of Long Non-coding RNA Transcripts Reveals Target Genes Associated With Crohn's Disease.bioRxiv : the preprint server for biology · 2025Article
- Cell type heterogeneity in gene co-expression networks: implications for toxicological research.Briefings in bioinformatics · 2025Review
- A 3D Genome Atlas of Genetic Variants and Their Pathological Effects in Cancer.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Genome-Wide DNA Methylation Identifies Potential Disease-Specific Biomarkers and Pathophysiologic Mechanisms in Irritable Bowel Syndrome, Inflammatory Bowel Disease, and Celiac Disease.Neurogastroenterology and motility · 2025Article
- The Cell-Specific Effects of JAK1 Inhibitors in Ulcerative Colitis.Journal of clinical medicine · 2025Review
- Proteomic profile of human colon organoids: effects of a multi-mineral intervention alone and in the presence of pro-inflammatory and anti-inflammatory treatments.Frontiers in gastroenterology (Lausanne, Switzerland) · 2025Article
- Correction: Profound gene expression changes in the epithelial monolayer of active ulcerative colitis and Crohn's disease.PloS one · 2025Article
- Single-cell transcriptomics of rectal organoids from individuals with perianal fistulizing Crohn's disease reveals patient-specific signatures.Scientific reports · 2024Article
- Establishment of an ulcerative colitis model using colon organoids derived from human induced pluripotent stem cells.iScience · 2024Article
- A living organoid biobank of patients with Crohn's disease reveals molecular subtypes for personalized therapeutics.Cell reports. Medicine · 2024Article
- Exposure of Colon-Derived Epithelial Monolayers to Fecal Luminal Factors from Patients with Colon Cancer and Ulcerative Colitis Results in Distinct Gene Expression Patterns.International journal of molecular sciences · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In recent years it has become apparent that the epithelium is highly involved in inflammatory bowel disease (IBD) pathophysiology. The majority of gene expression studies of IBD are generated from heterogeneous biopsies, providing no distinction between immune cells, the epithelium and other mucosal cells. By using laser capture microdissection (LCM) coupled with RNA sequencing, we aimed to characterize the expressional changes of the isolated colonic epithelial monolayer from ulcerative colitis (UC) and Crohn's disease (CD) patients compared to healthy controls (HC). The analysis identified 3706 genes as differentially expressed between active IBD epithelium and HC. Weighted gene co-expression network analysis was used to stratify genes into modules, which were subsequently characterized using enrichment analysis. Our data show a distinct upregulation of the antigen presentation machinery during inflammation, including major histocompatibility complex class II molecules (e.g. HLA-DPA1, HLA-DPB1, HLA-DRA) and key transcription factors/activators (STAT1, IRF1, CIITA). We also see an epithelial downregulation of retinoic acid-responsive nuclear receptors (RARA, RARB, RXRA), but upregulation of retinoid-metabolizing enzymes (RDH11, ALDH1A2, ALDH1A3), which together suggest a perturbation of epithelial vitamin A signaling during active IBD. Lastly, we identified a cluster of stress-related genes, including activator protein 1 components JUNB and ATF3, as significantly upregulated in active UC but not in CD, revealing an interesting aspect of IBD heterogeneity. The results represent a unique resource for enhanced understanding of epithelial involvement in IBD inflammation and is a valuable tool for further studies on these processes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.