Integrating single-cell RNA-Seq and machine learning to dissect tryptophan metabolism in ulcerative colitis DOI Creative Commons
Guorong Chen,

Hongying Qi,

Li Jiang

и другие.

Journal of Translational Medicine, Год журнала: 2024, Номер 22(1)

Опубликована: Дек. 20, 2024

Ulcerative colitis (UC) is a persistent inflammatory bowels disease (IBD) characterized by immune response dysregulation and metabolic disruptions. Tryptophan metabolism has been believed as significant factor in UC pathogenesis, with specific metabolites influencing modulation gut microbiota interactions. However, the precise regulatory mechanisms key genes involved remain unclear. AUCell, Ucell, other functional enrichment algorithms were utilized to determine activation patterns of tryptophan at cell level. Differential analysis identified associated metabolism. Five machine learning algorithms, including Random Forest, Boruta algorithm, LASSO, SVM-RFE, GBM integrated identify categorize disease-specific characteristic genes. We observed heterogeneity activity across types UC, highest levels macrophages fibroblasts. Among metabolism-related genes, CTSS, S100A11, TUBB predominantly expressed significantly upregulated highlighting their involvement inflammation. Cross-analysis bulk RNA data confirmed consistent upregulation these samples, highly indicating relevance pathology potential targets for therapeutic intervention. This study first reveal single-cell level emerging contributors processes. The identification regulators underscores biomarkers targets.

Язык: Английский

Identification of the key tryptophan metabolic characteristics of Lactiplantibacillus plantarum for aryl hydrocarbon receptor activation and ulcerative colitis alleviation DOI

Xuemei Zuo,

Tingting Zhang, Xueqian Dong

и другие.

Food Research International, Год журнала: 2025, Номер 203, С. 115766 - 115766

Опубликована: Янв. 23, 2025

Язык: Английский

Процитировано

3
Tryptophan As a New Member of RNA‐Induced Silencing Complexes Prevents Colon Cancer Liver Metastasis DOI Creative Commons
Fangyi Xu, Yi Ren,

Yun Teng

и другие.

Advanced Science, Год журнала: 2024, Номер 11(31)

Опубликована: Июнь 20, 2024

Abstract Essential amino acids (EAA) and microRNAs (miRs) control biological activity of a cell. Whether EAA regulates the miR has never been demonstrated. Here, as proof‐of‐concept, tryptophan (Trp, an EAA) complex containing Argonaute 2 (Ago2) miRs including miR‐193a (Trp/Ago2/miR‐193a) is identified. Trp binds miR‐193a‐3p interacts with Ago2. Trp/Ago2/miR‐193a increases via enhancing RNase activity. Other miR‐103 miR‐107 in enhance by targeting same genes. Mechanistically, Trp‐binding pockets PIWI domain Ago2 to mediated This newly formed Ago2/Trp/miR‐193a‐3p more efficient than alone inhibiting expression targeted genes colon cancer liver metastasis. The findings show that through communication RNA‐induced silencing complexes (RISC), which provides basis for based therapy.

Язык: Английский

Процитировано

4
Multi-omics insights into anti-colitis benefits of the synbiotic and postbiotic derived from wheat bran arabinoxylan and Limosilactobacillus reuteri DOI

Lanqi Zhou,

Song Wei, Tianqi Liu

и другие.

International Journal of Biological Macromolecules, Год журнала: 2024, Номер 278, С. 134860 - 134860

Опубликована: Авг. 18, 2024

Язык: Английский

Процитировано

4
Rebalancing immune homeostasis in combating disease: the impact of medicine food homology plants and gut microbiome DOI

Lu Xia,

Chuangen Li, Jia Zhao

и другие.

Phytomedicine, Год журнала: 2024, Номер 136, С. 156150 - 156150

Опубликована: Окт. 24, 2024

Язык: Английский

Процитировано

3
Harnessing Cyber-Physical Social Systems for Comprehensive Bioeconomy Measurement DOI
Sebastián Leavy, Gabriela Allegretti, Elen Presotto

и другие.

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

0
Effects of different storage temperatures on the quality and metabolome of maize with high moisture content DOI Creative Commons
Yan Zhao,

Tianjie Qi,

Chaoyue Cui

и другие.

LWT, Год журнала: 2024, Номер unknown, С. 117117 - 117117

Опубликована: Ноя. 1, 2024

Язык: Английский

Процитировано

1
Integrating single-cell RNA-Seq and machine learning to dissect tryptophan metabolism in ulcerative colitis DOI Creative Commons
Guorong Chen,

Hongying Qi,

Li Jiang

и другие.

Journal of Translational Medicine, Год журнала: 2024, Номер 22(1)

Опубликована: Дек. 20, 2024

Ulcerative colitis (UC) is a persistent inflammatory bowels disease (IBD) characterized by immune response dysregulation and metabolic disruptions. Tryptophan metabolism has been believed as significant factor in UC pathogenesis, with specific metabolites influencing modulation gut microbiota interactions. However, the precise regulatory mechanisms key genes involved remain unclear. AUCell, Ucell, other functional enrichment algorithms were utilized to determine activation patterns of tryptophan at cell level. Differential analysis identified associated metabolism. Five machine learning algorithms, including Random Forest, Boruta algorithm, LASSO, SVM-RFE, GBM integrated identify categorize disease-specific characteristic genes. We observed heterogeneity activity across types UC, highest levels macrophages fibroblasts. Among metabolism-related genes, CTSS, S100A11, TUBB predominantly expressed significantly upregulated highlighting their involvement inflammation. Cross-analysis bulk RNA data confirmed consistent upregulation these samples, highly indicating relevance pathology potential targets for therapeutic intervention. This study first reveal single-cell level emerging contributors processes. The identification regulators underscores biomarkers targets.

Язык: Английский

Процитировано

1