ArticleJournal of Crohn's & colitis2022
Characterisation of the Circulating Transcriptomic Landscape in Inflammatory Bowel Disease Provides Evidence for Dysregulation of Multiple Transcription Factors Including NFE2, SPI1, CEBPB, and IRF2.
Article in Journal of Crohn's & colitis, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 49 citations in OpenAlex.
- Molecular pathways driving clarithromycin benefit in community-acquired pneumonia: analysis of the ACCESS randomised trial.EBioMedicine · 2026Trial
- Single-cell analysis of chromatin accessibility in the human intestine identifies regulatory programs and clarifies genetic associations in Crohn's disease.Nature genetics · 2026Article
- Identification of Gene Signatures and Molecular Mechanisms Underlying the Comorbidity of Alzheimer's Disease and Crohn's Disease Using Machine Learning.Psychiatry investigation · 2026Article
- Regulation of Inducible Nitric Oxide Synthase (NOS2) Expression in Healthy and Inflamed Bowel: A Narrative Review.International journal of molecular sciences · 2026Review
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- Immunoproteomic insights into inflammatory diseases of the critically endangered black rhinoceros (Diceros bicornis).Scientific reports · 2026Article
- Developmentally endothelial locus-1 facilitates intestinal inflammation resolution by suppressing the Cmpk2-cGAS-STING pathway and promoting reparatory macrophage transition.Journal of advanced research · 2026Article
- Pharmacogenomic Pathways Underlying Variable Vedolizumab Response in Crohn's Disease Patients: A Rare-Variant Analysis.Biomedicines · 2026Article
- Integrating polygenic signals and single-cell multiomics identifies cell-type-specific regulomes critical for immune- and aging-related diseases.Nature aging · 2026Article
- The Inflammatory Bowel Disease in South-Eastern Norway study: three decades of advancements in clinical understanding and scientific partnerships.Therapeutic advances in gastroenterology · 2026Review
- From Polymorphisms to Phenotypes:Genes · 2025Article
- Article
- Intestinal epithelialActa biochimica et biophysica Sinica · 2025Article
- Article
- Identification and Validation of Biomarkers to Predict Early Diagnosis of Inflammatory Bowel Disease and Its Progression to Colorectal Cancer.Biochemical genetics · 2025Article
- Regulatory role of CD177+ neutrophils in BMP signaling pathway and its implications for inflammatory bowel disease, sepsis, and intestinal tumors.Translational oncology · 2025Article
- Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data.Nature biotechnology · 2025Article
- Low Expression MCEMP1 Promotes Lung Adenocarcinoma Progression and its Clinical Value.Current cancer drug targets · 2025Article
- Integrative analysis of single-cell and microarray data reveals SPI1-centered macrophage regulatory signatures in ulcerative colitis.Frontiers in genetics · 2025Article
- Key Disease-Related Genes and Immune Cell Infiltration Landscape in Inflammatory Bowel Disease: A Bioinformatics Investigation.International journal of molecular sciences · 2024Article
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Authors and funding
16 authors at 9 institutions in 6 countries.
Funding
Abstract
aimTo assess the pathobiological and translational importance of whole-blood transcriptomic analysis in inflammatory bowel disease [IBD].
methodsWe analysed whole-blood expression profiles from paired-end sequencing in a discovery cohort of 590 Europeans recruited across six countries in the IBD Character initiative (newly diagnosed patients with Crohn's disease [CD; n = 156], ulcerative colitis [UC; n = 167], and controls [n = 267]), exploring differential expression [DESeq2], co-expression networks [WGCNA], and transcription factor involvement [EPEE, ChEA, DoRothEA]. Findings were validated by analysis of an independent replication cohort [99 CD, 100 UC, 95 controls]. In the discovery cohort, we also defined baseline expression correlates of future treatment escalation using cross-validated elastic-net and random forest modelling, along with a pragmatic ratio detection procedure.
resultsDisease-specific transcriptomes were defined in IBD [8697 transcripts], CD [7152], and UC [8521], with the most highly significant changes in single genes, including CD177 (log2-fold change [LFC] = 4.63, p = 4.05 × 10-118), MCEMP1 [LFC = 2.45, p = 7.37 × 10-109], and S100A12 [LFC = 2.31, p = 2.15 × 10-93]. Significantly over-represented pathways included IL-1 [p = 1.58 × 10-11], IL-4, and IL-13 [p = 8.96 × 10-9]. Highly concordant results were obtained using multiple regulatory activity inference tools applied to the discovery and replication cohorts. These analyses demonstrated central roles in IBD for the transcription factors NFE2, SPI1 [PU.1], CEBPB, and IRF2, all regulators of cytokine signalling, based on a consistent signal across cohorts and transcription factor ranking methods. A number of simple transcriptome-based models were associated with the need for treatment escalation, including the binary CLEC5A/CDH2 expression ratio in UC (hazard ratio = 23.4, 95% confidence interval [CI] 5.3-102.0).
conclusionsTranscriptomic analysis has allowed for a detailed characterisation of IBD pathobiology, with important potential translational implications.
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