ArticleGenome medicine2022
Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease.
Article in Genome medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
45 citing papers in PubMed, 1 synthesis or guideline pooled it, 59 citations in OpenAlex.
- Multi-Omics Biomarkers for Predicting Efficacy of Biologic and Small-Molecule Therapies in Adults With Inflammatory Bowel Disease: A Systematic Review.United European gastroenterology journal · 2025Pooled it
- Microbiome-metabolite signaling networks in gastrointestinal disease: systems biology, network rewiring, and precision therapeutics.Archives of microbiology · 2026Review
- Large-scale analysis of temporal gene expression variation in peripheral blood.Nature communications · 2026Article
- Decoding drug-responsive cell subpopulations in triple-negative breast cancer using single-cell multiomics.iScience · 2026Article
- A metabolic constraint in de novo NAD+ synthesis drives mucosal inflammation in IBD.Journal of Crohn's & colitis · 2026Article
- Epigenetic biomarkers in inflammatory bowel diseases-computational challenges and opportunities.Journal of Crohn's & colitis · 2026Review
- Predicting trajectories of illness using RNA velocity of whole blood.Nature communications · 2026Observational
- Advancing IBD Management: A Literature Review on the Role of Non-Invasive Blood-Based Biomarkers in Predicting and Assessing Pharmacodynamic Response to Treatment.Clinical and translational science · 2026Review
- Artificial intelligence in the management of inflammatory bowel disease: What's next?World journal of gastrointestinal pharmacology and therapeutics · 2026Review
- The role of ALOX15 in inflammation-related diseases.Frontiers in immunology · 2026Review
- Aimed at Subtype Discrimination but Yielding a Shared Marker: Integrative Analysis of Blood Transcriptomes Reveals UpregulatedClinical and experimental gastroenterology · 2026Article
- SEMA3B is associated with disease activity and infliximab response in IBD patients but does not contribute to the development of intestinal inflammationFrontiers in immunology · 2026Article
- Longitudinal omics data analysis: approaches and applications.Computational and structural biotechnology journal · 2026Review
- Review
- Risk stratification of IBD-associated liver disease using routinely collected biomarkers from a large-scale real-world dataset.BMJ open gastroenterology · 2025Observational
- Long-Term Intestinal Epithelial Remodeling Induced by Acute Protein-Energy Malnutrition.bioRxiv : the preprint server for biology · 2025Article
- Multiomics Integration Reveals Microbial Gene Interactions Shaping Host Responses in a DSS-Induced Colitis Mouse Model.Journal of microbiology and biotechnology · 2025Article
- Development and Validation of a Machine Learning Model to Predict Anti-Drug Antibody Formation During Infliximab Induction in Crohn's Disease.Biomedicines · 2025Article
- How "Sure" Are We About Precision Medicine in IBD?United European gastroenterology journal · 2025Article
- Pharmacoepigenetic Biomarkers in Inflammatory Bowel Diseases: A Narrative Review.The Yale journal of biology and medicine · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
24 authors at 7 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
BACKGROUND AND
aimsTreatment with tumor necrosis factor α (TNFα) antagonists in IBD patients suffers from primary non-response rates of up to 40%. Biomarkers for early prediction of therapy success are missing. We investigated the dynamics of gene expression and DNA methylation in blood samples of IBD patients treated with the TNF antagonist infliximab and analyzed the predictive potential regarding therapy outcome.
methodsWe performed a longitudinal, blood-based multi-omics study in two prospective IBD patient cohorts receiving first-time infliximab therapy (discovery: 14 patients, replication: 23 patients). Samples were collected at up to 7 time points (from baseline to 14 weeks after therapy induction). RNA-sequencing and genome-wide DNA methylation data were analyzed and correlated with clinical remission at week 14 as a primary endpoint.
resultsWe found no consistent ex ante predictive signature across the two cohorts. Longitudinally upregulated transcripts in the non-remitter group comprised TH2- and eosinophil-related genes including ALOX15, FCER1A, and OLIG2. Network construction identified transcript modules that were coherently expressed at baseline and in non-remitting patients but were disrupted at early time points in remitting patients. These modules reflected processes such as interferon signaling, erythropoiesis, and platelet aggregation. DNA methylation analysis identified remission-specific temporal changes, which partially overlapped with transcriptomic signals. Machine learning approaches identified features from differentially expressed genes cis-linked to DNA methylation changes at week 2 as a robust predictor of therapy outcome at week 14, which was validated in a publicly available dataset of 20 infliximab-treated CD patients.
conclusionsIntegrative multi-omics analysis reveals early shifts of gene expression and DNA methylation as predictors for efficient response to anti-TNF treatment. Lack of such signatures might be used to identify patients with IBD unlikely to benefit from TNF antagonists at an early time point.
Indexed as
Identifiers
What OpenQuestion holds
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.