ArticleThe Journal of clinical investigation2014
Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.
Article in The Journal of clinical investigation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. It is linked to trial NCT03378167 (PediCRaFT), which is not on this map. Cited by 324 papers, 4 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
PediCRaFT: Pediatric Crohn's Disease Fecal Microbiota Transplant Pilot Study
Who cites it
324 citing papers in PubMed, 4 syntheses or guidelines pooled it, 522 citations in OpenAlex.
- Specific alterations in the gut microbiome and metabolome across disease locations of Crohn's disease: a systematic review.BMC gastroenterology · 2026Pooled it
- Fecal Microbial Community Profiling Allows Discrimination of Phenotype and Treatment Response in Pediatric Crohn's Disease and Ulcerative Colitis-An International Meta-Analysis.Inflammatory bowel diseases · 2025Pooled it
- Meta-analysis defines predominant shared microbial responses in various diseases and a specific inflammatory bowel disease signal.Genome biology · 2022Pooled it
- Gut Microbiota Profile in Pediatric Patients With Inflammatory Bowel Disease: A Systematic Review.Frontiers in pediatrics · 2021Pooled it
- Epithelial Cell Biomarkers Are Predictive of Response to Biologic Agents in Crohn's Disease.Inflammatory bowel diseases · 2021Trial
- Luminal microbiota related to Crohn's disease recurrence after surgery.Gut microbes · 2020Trial
- Defining the Celiac Disease Transcriptome using Clinical Pathology Specimens Reveals Biologic Pathways and Supports Diagnosis.Scientific reports · 2019Trial
- Neonatal Vitamin A Supplementation and Vitamin A Status Are Associated with Gut Microbiome Composition in Bangladeshi Infants in Early Infancy and at 2 Years of Age.The Journal of nutrition · 2019Trial
- Lachnospiraceae in the Food-Gut Axis: A Critical Review of Dietary Modulation, Immune Regulation, and Translational Barriers.Comprehensive reviews in food science and food safety · 2026Review
- Concerted changes in the pediatric single-cell intestinal ecosystem before and after anti-TNF blockade.eLife · 2026Article
- Toll-like receptor 2 impacts small intestinal villus capillarization through epithelial dual oxidase 2.Redox biology · 2026Article
- Tuft cells protect against intestinal inflammation through histone deacetylase 3.Mucosal immunology · 2026Article
- Therapeutic zinc targets dysregulated GC-C signaling and restores ileal defects in a preclinical model of familial diarrheal disease.American journal of physiology. Gastrointestinal and liver physiology · 2026Article
- TENTACLES: a consensus machine learning tool for robust biomarker discovery in heterogeneous data.BioData mining · 2026Article
- OTOP2 proton channel couples luminal pH sensing to intestinal immune homeostasis.The Journal of biological chemistry · 2026Article
- Tissue transcriptional programs stratify Crohn's disease by therapeutic response and clinical outcomes.Scientific reports · 2026Article
- An IL-17-DUOX2 axis controls gastrointestinal colonization by Candida albicans.Nature communications · 2026Article
- Epithelial SLPI expression in severe inflammatory bowel disease relates to high IL-17 and neutrophil programming.JCI insight · 2026Article
- TET1 deficiency amplifies macrophage inflammatory signaling associated with Crohn's disease.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026Article
- Short Ileal Microvillus Length Phenotype Associates with Progression from Inflammatory to Complicated Disease Behavior in Pediatric Crohn's Disease.Inflammatory bowel diseases · 2026Article
264 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
- Erratum issued
Authors and funding
24 authors at 14 institutions in 3 countries.
Funding
Abstract
Interactions between the host and gut microbial community likely contribute to Crohn disease (CD) pathogenesis; however, direct evidence for these interactions at the onset of disease is lacking. Here, we characterized the global pattern of ileal gene expression and the ileal microbial community in 359 treatment-naive pediatric patients with CD, patients with ulcerative colitis (UC), and control individuals. We identified core gene expression profiles and microbial communities in the affected CD ilea that are preserved in the unaffected ilea of patients with colon-only CD but not present in those with UC or control individuals; therefore, this signature is specific to CD and independent of clinical inflammation. An abnormal increase of antimicrobial dual oxidase (DUOX2) expression was detected in association with an expansion of Proteobacteria in both UC and CD, while expression of lipoprotein APOA1 gene was downregulated and associated with CD-specific alterations in Firmicutes. The increased DUOX2 and decreased APOA1 gene expression signature favored oxidative stress and Th1 polarization and was maximally altered in patients with more severe mucosal injury. A regression model that included APOA1 gene expression and microbial abundance more accurately predicted month 6 steroid-free remission than a model using clinical factors alone. These CD-specific host and microbe profiles identify the ileum as the primary inductive site for all forms of CD and may direct prognostic and therapeutic approaches.
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Registered trials
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.