Single-Cell RNA Sequencing, Cell Communication, and Network Pharmacology Reveal the Potential Mechanism of <i>Senecio scandens</i> Buch.-Ham in Hepatocellular Carcinoma Inhibition
Background: Hepatocellular carcinoma (HCC), a prevalent form of primary liver malignancy, arises from liver-specific hepatocytes. <i>Senecio scandens</i> Buch.-Ham(Climbing senecio) is a bitter-tasting plant of the Compositae family with anti-tumor properties. This study aims to identify...
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2024-12-01
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| author | Jiayi Jiang Haitao Wu Xikun Jiang Qing Ou Zhanpeng Gan Fangfang Han Yongming Cai |
| author_facet | Jiayi Jiang Haitao Wu Xikun Jiang Qing Ou Zhanpeng Gan Fangfang Han Yongming Cai |
| author_sort | Jiayi Jiang |
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| description | Background: Hepatocellular carcinoma (HCC), a prevalent form of primary liver malignancy, arises from liver-specific hepatocytes. <i>Senecio scandens</i> Buch.-Ham(Climbing senecio) is a bitter-tasting plant of the Compositae family with anti-tumor properties. This study aims to identify the molecular targets and pathways through which Climbing senecio regulates HCC. Methods: Active ingredients of Climbing senecio were collected from four online databases and mapped to relevant target databases to obtain predicted targets. After recognizing the key pathways through which Climbing senecio acts in HCC. Gene expression data from GSE54238 Underwent differential expression and weighted gene correlation network analyses to identify HCC-related genes. The “Climbing senecio-Hepatocellular Carcinoma Targets” network was constructed using Cytoscape 3.10.1 software, followed by topology analysis to identify core genes. The expression and distribution of key targets were evaluated, and the differential expression of each key target between normal and diseased samples was calculated. Moreover, single-cell data from the Gene Expression Omnibus (GSE202642) were used to assess the distribution of Climbing senecio’s bioactive targets within major HCC clusters. An intersection analysis of these clusters with pharmacological targets and HCC-related genes identified Climbing senecio’s primary targets for this disease. Cell communication, receiver operating characteristic (ROC)analysis, survival analysis, immune filtration analysis, and molecular docking studies were conducted for detailed characterization. Results: Eleven components of Climbing senecio were identified, along with 520 relevant targets, 300 differentially expressed genes, and 3765 co-expression module genes associated with HCC. <i>AKR1B1</i>, <i>CA2</i>, <i>FOS</i>, <i>CXCL2</i>, <i>SRC</i>, <i>ABCC1</i>, and <i>PLIN1</i> were identified within the intersection of HCC-related genes and Climbing senecio targets. TGFβ, IL-1, VEGF, and CXCL were identified as significant factors in the onset and progression of HCC. These findings underscore the anti-HCC potential and mode of action of Climbing senecio, providing insights into multi-targeted treatment approaches for HCC. Conclusions: This study revealed that Climbing senecio may target multiple pathways and genes in the process of regulating HCC and exert potential drug effects through a multi-target mechanism, which provides a new idea for the treatment of HCC. However, the research is predicated on network database analysis and bioinformatics, offering insights into HCC therapeutic potential while emphasizing the need for further validation. |
| format | Article |
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| institution | Kabale University |
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| language | English |
| publishDate | 2024-12-01 |
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| spelling | doaj-art-9654fee9408b41af940330fe0ac1b6852024-12-27T14:46:09ZengMDPI AGPharmaceuticals1424-82472024-12-011712170710.3390/ph17121707Single-Cell RNA Sequencing, Cell Communication, and Network Pharmacology Reveal the Potential Mechanism of <i>Senecio scandens</i> Buch.-Ham in Hepatocellular Carcinoma InhibitionJiayi Jiang0Haitao Wu1Xikun Jiang2Qing Ou3Zhanpeng Gan4Fangfang Han5Yongming Cai6School of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaSchool of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaSchool of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaSchool of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaSchool of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaSchool of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaSchool of Medical Information and Engineering, Guangdong Pharmaceutical University, Guangzhou 510006, ChinaBackground: Hepatocellular carcinoma (HCC), a prevalent form of primary liver malignancy, arises from liver-specific hepatocytes. <i>Senecio scandens</i> Buch.-Ham(Climbing senecio) is a bitter-tasting plant of the Compositae family with anti-tumor properties. This study aims to identify the molecular targets and pathways through which Climbing senecio regulates HCC. Methods: Active ingredients of Climbing senecio were collected from four online databases and mapped to relevant target databases to obtain predicted targets. After recognizing the key pathways through which Climbing senecio acts in HCC. Gene expression data from GSE54238 Underwent differential expression and weighted gene correlation network analyses to identify HCC-related genes. The “Climbing senecio-Hepatocellular Carcinoma Targets” network was constructed using Cytoscape 3.10.1 software, followed by topology analysis to identify core genes. The expression and distribution of key targets were evaluated, and the differential expression of each key target between normal and diseased samples was calculated. Moreover, single-cell data from the Gene Expression Omnibus (GSE202642) were used to assess the distribution of Climbing senecio’s bioactive targets within major HCC clusters. An intersection analysis of these clusters with pharmacological targets and HCC-related genes identified Climbing senecio’s primary targets for this disease. Cell communication, receiver operating characteristic (ROC)analysis, survival analysis, immune filtration analysis, and molecular docking studies were conducted for detailed characterization. Results: Eleven components of Climbing senecio were identified, along with 520 relevant targets, 300 differentially expressed genes, and 3765 co-expression module genes associated with HCC. <i>AKR1B1</i>, <i>CA2</i>, <i>FOS</i>, <i>CXCL2</i>, <i>SRC</i>, <i>ABCC1</i>, and <i>PLIN1</i> were identified within the intersection of HCC-related genes and Climbing senecio targets. TGFβ, IL-1, VEGF, and CXCL were identified as significant factors in the onset and progression of HCC. These findings underscore the anti-HCC potential and mode of action of Climbing senecio, providing insights into multi-targeted treatment approaches for HCC. Conclusions: This study revealed that Climbing senecio may target multiple pathways and genes in the process of regulating HCC and exert potential drug effects through a multi-target mechanism, which provides a new idea for the treatment of HCC. However, the research is predicated on network database analysis and bioinformatics, offering insights into HCC therapeutic potential while emphasizing the need for further validation.https://www.mdpi.com/1424-8247/17/12/1707<i>Senecio Scandens</i> Buch.-Hamhepatocellular carcinomanetwork pharmacology<i>SRC</i><i>FOS</i> |
| spellingShingle | Jiayi Jiang Haitao Wu Xikun Jiang Qing Ou Zhanpeng Gan Fangfang Han Yongming Cai Single-Cell RNA Sequencing, Cell Communication, and Network Pharmacology Reveal the Potential Mechanism of <i>Senecio scandens</i> Buch.-Ham in Hepatocellular Carcinoma Inhibition Pharmaceuticals <i>Senecio Scandens</i> Buch.-Ham hepatocellular carcinoma network pharmacology <i>SRC</i> <i>FOS</i> |
| title | Single-Cell RNA Sequencing, Cell Communication, and Network Pharmacology Reveal the Potential Mechanism of <i>Senecio scandens</i> Buch.-Ham in Hepatocellular Carcinoma Inhibition |
| title_full | Single-Cell RNA Sequencing, Cell Communication, and Network Pharmacology Reveal the Potential Mechanism of <i>Senecio scandens</i> Buch.-Ham in Hepatocellular Carcinoma Inhibition |
| title_fullStr | Single-Cell RNA Sequencing, Cell Communication, and Network Pharmacology Reveal the Potential Mechanism of <i>Senecio scandens</i> Buch.-Ham in Hepatocellular Carcinoma Inhibition |
| title_full_unstemmed | Single-Cell RNA Sequencing, Cell Communication, and Network Pharmacology Reveal the Potential Mechanism of <i>Senecio scandens</i> Buch.-Ham in Hepatocellular Carcinoma Inhibition |
| title_short | Single-Cell RNA Sequencing, Cell Communication, and Network Pharmacology Reveal the Potential Mechanism of <i>Senecio scandens</i> Buch.-Ham in Hepatocellular Carcinoma Inhibition |
| title_sort | single cell rna sequencing cell communication and network pharmacology reveal the potential mechanism of i senecio scandens i buch ham in hepatocellular carcinoma inhibition |
| topic | <i>Senecio Scandens</i> Buch.-Ham hepatocellular carcinoma network pharmacology <i>SRC</i> <i>FOS</i> |
| url | https://www.mdpi.com/1424-8247/17/12/1707 |
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