Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer
Abstract Ferroptosis is an iron-dependent form of cell death induced by lipid oxidation with an essential role in diseases, including cancer. Since prognostic value of ferroptosis-dependent related genes (FDRGs) in colorectal cancer (CRC) remains unclear, we explored the significance of FDRGs in CRC...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-08-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-39412-y |
| _version_ | 1797576790794829824 |
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| author | Xiaochen Xu Xinwen Zhang Qiumei Lin Yuling Qin Yihao Liu Weizhong Tang |
| author_facet | Xiaochen Xu Xinwen Zhang Qiumei Lin Yuling Qin Yihao Liu Weizhong Tang |
| author_sort | Xiaochen Xu |
| collection | DOAJ |
| description | Abstract Ferroptosis is an iron-dependent form of cell death induced by lipid oxidation with an essential role in diseases, including cancer. Since prognostic value of ferroptosis-dependent related genes (FDRGs) in colorectal cancer (CRC) remains unclear, we explored the significance of FDRGs in CRC through comprehensive single-cell analysis. We downloaded the GSE161277 dataset for single-cell analyses and calculated the ferroptosis-dependent gene score (FerrScore) for each cell type. According to each cell type-specific median FerrScore, we categorized the cells into low- and high-ferroptosis groups. By analyzing differentially-expressed genes across the two groups, we identified FDRGs. We further screened these prognosis-related genes used to develop a prognostic signature and calculated its correlation with immune infiltration. We also compared immune checkpoint gene efficacy among different risk groups, and qRT-PCR was performed in colorectal normal and cancer cell lines to explore whether the signature genes could be used as clinical prognostic indicators. In total, 523 FDRGs were identified. A prognostic signature including five signature genes was constructed, and patients were divided into two risk groups. The high-risk group had poor survival rates and displayed high levels of immune infiltration. Our newly developed ferroptosis-based prognostic signature possessed a high predictive ability for CRC. |
| first_indexed | 2024-03-10T21:57:46Z |
| format | Article |
| id | doaj.art-bae51d5875a04ff380c7cc310cd440b1 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-10T21:57:46Z |
| publishDate | 2023-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-bae51d5875a04ff380c7cc310cd440b12023-11-19T13:03:37ZengNature PortfolioScientific Reports2045-23222023-08-0113111410.1038/s41598-023-39412-yIntegrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancerXiaochen Xu0Xinwen Zhang1Qiumei Lin2Yuling Qin3Yihao Liu4Weizhong Tang5Department of Gastrointestinal Surgery, Guangxi Medical University Cancer HospitalDepartment of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical UniversityDepartment of Clinical Laboratory, Guangxi Medical University Cancer HospitalDepartment of Clinical Laboratory, Guangxi Medical University Cancer HospitalDepartment of Gastrointestinal Surgery, Affiliated Hospital of Guilin Medical UniversityDepartment of Gastrointestinal Surgery, Guangxi Medical University Cancer HospitalAbstract Ferroptosis is an iron-dependent form of cell death induced by lipid oxidation with an essential role in diseases, including cancer. Since prognostic value of ferroptosis-dependent related genes (FDRGs) in colorectal cancer (CRC) remains unclear, we explored the significance of FDRGs in CRC through comprehensive single-cell analysis. We downloaded the GSE161277 dataset for single-cell analyses and calculated the ferroptosis-dependent gene score (FerrScore) for each cell type. According to each cell type-specific median FerrScore, we categorized the cells into low- and high-ferroptosis groups. By analyzing differentially-expressed genes across the two groups, we identified FDRGs. We further screened these prognosis-related genes used to develop a prognostic signature and calculated its correlation with immune infiltration. We also compared immune checkpoint gene efficacy among different risk groups, and qRT-PCR was performed in colorectal normal and cancer cell lines to explore whether the signature genes could be used as clinical prognostic indicators. In total, 523 FDRGs were identified. A prognostic signature including five signature genes was constructed, and patients were divided into two risk groups. The high-risk group had poor survival rates and displayed high levels of immune infiltration. Our newly developed ferroptosis-based prognostic signature possessed a high predictive ability for CRC.https://doi.org/10.1038/s41598-023-39412-y |
| spellingShingle | Xiaochen Xu Xinwen Zhang Qiumei Lin Yuling Qin Yihao Liu Weizhong Tang Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer Scientific Reports |
| title | Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer |
| title_full | Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer |
| title_fullStr | Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer |
| title_full_unstemmed | Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer |
| title_short | Integrated single-cell and bulk RNA sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer |
| title_sort | integrated single cell and bulk rna sequencing analysis identifies a prognostic signature related to ferroptosis dependence in colorectal cancer |
| url | https://doi.org/10.1038/s41598-023-39412-y |
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