Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn’s disease by bioinformatics analysis and machine learning
Abstract Crohn’s disease (CD) is a chronic inflammatory bowel disease with an unknown etiology. Ubiquitination plays a significant role in the pathogenesis of CD. This study aimed to explore the functional roles of ubiquitination-related genes in CD. Differentially expressed ubiquitination-related g...
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Nature Portfolio
2025-01-01
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| Online Access: | https://doi.org/10.1038/s41598-025-88148-4 |
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| author | Wei Chen Zeyan Xu Haitao Sun Wen Feng Zhenhua Huang |
| author_facet | Wei Chen Zeyan Xu Haitao Sun Wen Feng Zhenhua Huang |
| author_sort | Wei Chen |
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| description | Abstract Crohn’s disease (CD) is a chronic inflammatory bowel disease with an unknown etiology. Ubiquitination plays a significant role in the pathogenesis of CD. This study aimed to explore the functional roles of ubiquitination-related genes in CD. Differentially expressed ubiquitination-related genes were identified by intersecting differentially expressed genes (DEGs) from the GSE95095 dataset in the Gene Expression Omnibus (GEO) database with a set of ubiquitination-related genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. Key genes were selected by combining hub genes from the protein-protein interaction (PPI) network with feature genes identified by Lasso and Random Forest (RF) algorithms. Additionally, the correlation between key genes and immune infiltration was assessed, and Gene Set Enrichment Analysis (GSEA) of key genes was conducted. The efficacy of key genes was validated using ROC curves in an external dataset, and their expression was confirmed in LPS-induced Caco-2 cells through RT-qPCR. A total of 32 ubiquitination-related DEGs were identified, and two key genes (UBE2R2, NEDD4L) were selected. The infiltration of M2 macrophages was reduced in CD patients, with UBE2R2 expression negatively correlated and NEDD4L expression positively correlated with M2 macrophage infiltration. GSEA indicated that UBE2R2 was enriched in terpenoid backbone biosynthesis, regulation of autophagy, and limonene and pinene degradation, while NEDD4L was enriched in lysosome, Wnt signaling, and calcium signaling pathways. ROC curves demonstrated superior efficacy for NEDD4L. In LPS-induced Caco-2 cells, UBE2R2 expression increased, while NEDD4L expression decreased. A comprehensive analysis of the functional relationship between ubiquitination-related genes and CD can enhance understanding of CD pathogenesis and suggest potential therapeutic targets. |
| format | Article |
| id | doaj-art-b7fe9bf1c7cd4ec58b6f7a615775bd95 |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
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| series | Scientific Reports |
| spelling | doaj-art-b7fe9bf1c7cd4ec58b6f7a615775bd952025-02-02T12:21:28ZengNature PortfolioScientific Reports2045-23222025-01-0115111110.1038/s41598-025-88148-4Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn’s disease by bioinformatics analysis and machine learningWei Chen0Zeyan Xu1Haitao Sun2Wen Feng3Zhenhua Huang4Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineDepartment of Gastroenterology, Zhongda Hospital, Southeast UniversityGeneral Surgery Department, Jiangsu University Affiliated People’s HospitalDepartment of Gastroenterology, Songjiang Hospital, Shanghai Jiao Tong University School of MedicineGeneral Surgery Department, Jiangsu University Affiliated People’s HospitalAbstract Crohn’s disease (CD) is a chronic inflammatory bowel disease with an unknown etiology. Ubiquitination plays a significant role in the pathogenesis of CD. This study aimed to explore the functional roles of ubiquitination-related genes in CD. Differentially expressed ubiquitination-related genes were identified by intersecting differentially expressed genes (DEGs) from the GSE95095 dataset in the Gene Expression Omnibus (GEO) database with a set of ubiquitination-related genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed. Key genes were selected by combining hub genes from the protein-protein interaction (PPI) network with feature genes identified by Lasso and Random Forest (RF) algorithms. Additionally, the correlation between key genes and immune infiltration was assessed, and Gene Set Enrichment Analysis (GSEA) of key genes was conducted. The efficacy of key genes was validated using ROC curves in an external dataset, and their expression was confirmed in LPS-induced Caco-2 cells through RT-qPCR. A total of 32 ubiquitination-related DEGs were identified, and two key genes (UBE2R2, NEDD4L) were selected. The infiltration of M2 macrophages was reduced in CD patients, with UBE2R2 expression negatively correlated and NEDD4L expression positively correlated with M2 macrophage infiltration. GSEA indicated that UBE2R2 was enriched in terpenoid backbone biosynthesis, regulation of autophagy, and limonene and pinene degradation, while NEDD4L was enriched in lysosome, Wnt signaling, and calcium signaling pathways. ROC curves demonstrated superior efficacy for NEDD4L. In LPS-induced Caco-2 cells, UBE2R2 expression increased, while NEDD4L expression decreased. A comprehensive analysis of the functional relationship between ubiquitination-related genes and CD can enhance understanding of CD pathogenesis and suggest potential therapeutic targets.https://doi.org/10.1038/s41598-025-88148-4BiomarkerBioinformaticsMachine learningUbiquitinationCrohn’s disease |
| spellingShingle | Wei Chen Zeyan Xu Haitao Sun Wen Feng Zhenhua Huang Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn’s disease by bioinformatics analysis and machine learning Scientific Reports Biomarker Bioinformatics Machine learning Ubiquitination Crohn’s disease |
| title | Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn’s disease by bioinformatics analysis and machine learning |
| title_full | Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn’s disease by bioinformatics analysis and machine learning |
| title_fullStr | Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn’s disease by bioinformatics analysis and machine learning |
| title_full_unstemmed | Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn’s disease by bioinformatics analysis and machine learning |
| title_short | Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn’s disease by bioinformatics analysis and machine learning |
| title_sort | identification of ubiquitination related key biomarkers and immune infiltration in crohn s disease by bioinformatics analysis and machine learning |
| topic | Biomarker Bioinformatics Machine learning Ubiquitination Crohn’s disease |
| url | https://doi.org/10.1038/s41598-025-88148-4 |
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