ArticleJournal of translational medicine2024
Integrating single-cell RNA-Seq and machine learning to dissect tryptophan metabolism in ulcerative colitis.
Article in Journal of translational medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- The gut microbiota-tryptophan metabolism-immune axis in inflammatory bowel disease: Mechanisms and therapeutic prospects.Human vaccines & immunotherapeutics · 2026Review
- Compensatory pathways in tryptophan metabolism and immune regulation following IDO inhibition.Molecular biology reports · 2026Review
- NFS1 activates PI3K/AKT/mTOR signaling to upregulate GPX4 expression and enhance ferroptosis resistance in osteosarcoma.Functional & integrative genomics · 2026Article
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- Identification of RPL4 as a biomarker associated with disulfidptosis and arachidonic acid metabolism in breast cancer.Discover oncology · 2026Article
- Analysis of PANoptosis-related genes in septic cardiomyopathy by bioinformatics, machine learning and experimental validation.Experimental and therapeutic medicine · 2026Article
- Epithelial cell-based multi-omics integration identifies SPINK5 and SRI as novel diagnostic biomarkers for ulcerative colitis.Frontiers in pharmacology · 2026Article
- Integrative Inflammation-Metabolism Indicator for Cardiovascular-Kidney-Metabolic Syndrome: Evaluating the C-Reactive Protein-Triglyceride Glucose Index for Risk Stratification and Progression Across Three National Cohorts.Mediators of inflammation · 2026Article
- Renshen-Baidu-San restores epithelial-immune crosstalk and drives type 2 immune repair in ulcerative colitis: an integrated multi-omics study.Frontiers in immunology · 2026Article
- Integrated Single Cell Spatial Analysis Reveals Dysregulated Basal Progenitor Cells in Ulcerative Colitis Pathogenesis: A Multi Omics Study.Health science reports · 2026Article
- A Single-Cell Transcriptomic Atlas Elucidates a Microglial Gene Signature Linking Ferroptosis to Mitochondrial Dysfunction in Epilepsy.Journal of inflammation research · 2026Article
- Proteome-wide Mendelian randomization and colocalization analyses identify potential biomarkers for schizophrenia.Frontiers in psychiatry · 2026Article
- Integrated single-cell and transcriptomic profiling identifies machine-learning-based pyroptosis biomarkers in IBD.Frontiers in immunology · 2026Article
- Implications of isonicotinylation-associated patterns in NK cells in the pathogenesis of Kawasaki disease: evidence from artificial intelligence-driven multi-omics and clinical validation.Frontiers in pediatrics · 2026Article
- Multi-omics analysis identifies macrophage immunometabolic signatures in ulcerative colitis.Frontiers in cellular and infection microbiology · 2026Article
- Article
- Integrative Single-Cell and Machine Learning Analysis Develops a Glutamine Metabolism-Based Prognostic Model and Identifies MSMO1 as a Therapeutic Target in Osteosarcoma.Biomolecules · 2025Article
- Article
- Identification of Key Genes Associated with Endoplasmic Reticulum Stress in Calcium Oxalate Kidney Stones.Genes · 2025Article
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Authors and funding
9 authors.
Funding
Abstract
backgroundUlcerative colitis (UC) is a persistent inflammatory bowels disease (IBD) characterized by immune response dysregulation and metabolic disruptions. Tryptophan metabolism has been believed as a significant factor in UC pathogenesis, with specific metabolites influencing immune modulation and gut microbiota interactions. However, the precise regulatory mechanisms and key genes involved remain unclear.
methodsAUCell, Ucell, and other functional enrichment algorithms were utilized to determine the activation patterns of tryptophan metabolism at the UC cell level. Differential analysis identified key genes associated with tryptophan metabolism. Five machine learning algorithms, including Random Forest, Boruta algorithm, LASSO, SVM-RFE, and GBM were integrated to identify and categorize disease-specific characteristic genes.
resultsWe observed significant heterogeneity in tryptophan metabolism activity across cell types in UC, with the highest activity levels in macrophages and fibroblasts. Among the key tryptophan metabolism-related genes, CTSS, S100A11, and TUBB were predominantly expressed in macrophages and significantly upregulated in UC, highlighting their involvement in immune dysregulation and inflammation. Cross-analysis with bulk RNA data confirmed the consistent upregulation of these genes in UC samples, highly indicating their relevance in UC pathology and potential as targets for therapeutic intervention.
conclusionsThis study is the first to reveal the heterogeneity of tryptophan metabolism at the single-cell level in UC, with macrophages emerging as key contributors to inflammatory processes. The identification of CTSS, S100A11, and TUBB as key regulators of tryptophan metabolism in UC underscores their potential as biomarkers and therapeutic targets.
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