A novel endothelial-related prognostic index by integrating single-cell and bulk RNA sequencing data for patients with kidney renal clear cell carcinoma
Background: Endothelial cells in the tumor microenvironment play an important role in the development of kidney renal clear cell carcinoma (KIRC). We wanted to further identify the function of endothelial cells in KIRC patients by integrating single-cell and bulk RNA sequencing data.Methods: Online...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-03-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1096491/full |
| _version_ | 1811155501145128960 |
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| author | Deng-Xiong Li Qing-Xin Yu Chui-Xuan Zeng Lu-Xia Ye Yi-Qing Guo Jun-Fei Liu Hai-Hong Zheng Dechao Feng Wuran Wei |
| author_facet | Deng-Xiong Li Qing-Xin Yu Chui-Xuan Zeng Lu-Xia Ye Yi-Qing Guo Jun-Fei Liu Hai-Hong Zheng Dechao Feng Wuran Wei |
| author_sort | Deng-Xiong Li |
| collection | DOAJ |
| description | Background: Endothelial cells in the tumor microenvironment play an important role in the development of kidney renal clear cell carcinoma (KIRC). We wanted to further identify the function of endothelial cells in KIRC patients by integrating single-cell and bulk RNA sequencing data.Methods: Online databases provide the original data of this study. An endothelial-related prognostic index (ERPI) was constructed and validated by R version 3.6.3 and relative packages.Results: The ERPI consisted of three genes (CCND1, MALL, and VWF). Patients with high ERPI scores were significantly correlated with worse prognosis than those with low ERPI scores in the TCGA training group, TCGA test group, and GSE29609 group. A positive correlation was identified between the ERPI score and poor clinical features. The results of functional analysis indicated that ERPI was significantly associated with immune-related activities. We suggested that patients with high ERPI scores were more likely to benefit from immunotherapy based on the results of immune checkpoints, tumor microenvironment, stemness index, and TCIA, while patients with low ERPI scores were sensitive to gemcitabine, docetaxel, paclitaxel, axitinib, pazopanib, sorafenib, and temsirolimus according to the results of the “pRRophetic” algorithm. Therefore, this ERPI may help doctors choose the optimal treatment for patients with KIRC.Conclusion: By integrating single-cell and bulk RNA sequencing data from KIRC patients, we successfully identified the key genes from the perspective of endothelial cells in the tumor microenvironment and constructed ERPIs that had positive implications in precision medicine. |
| first_indexed | 2024-04-10T04:34:29Z |
| format | Article |
| id | doaj.art-98d709540efe4bbba5c86e5b2e86f566 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-04-10T04:34:29Z |
| publishDate | 2023-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-98d709540efe4bbba5c86e5b2e86f5662023-03-10T04:39:39ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-03-011410.3389/fgene.2023.10964911096491A novel endothelial-related prognostic index by integrating single-cell and bulk RNA sequencing data for patients with kidney renal clear cell carcinomaDeng-Xiong Li0Qing-Xin Yu1Chui-Xuan Zeng2Lu-Xia Ye3Yi-Qing Guo4Jun-Fei Liu5Hai-Hong Zheng6Dechao Feng7Wuran Wei8Department of Urology, West China Hospital, Institute of Urology, Sichuan University, Chengdu, Sichuan, ChinaDepartment of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang, ChinaDepartment of Urology, Sichuan Cancer Hospital and Institute, Chengdu, Sichuan, ChinaDepartment of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang, ChinaDepartment of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang, ChinaDepartment of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang, ChinaDepartment of Pathology, Taizhou Hospital, Wenzhou Medical University, Linhai, Zhejiang, ChinaDepartment of Urology, West China Hospital, Institute of Urology, Sichuan University, Chengdu, Sichuan, ChinaDepartment of Urology, West China Hospital, Institute of Urology, Sichuan University, Chengdu, Sichuan, ChinaBackground: Endothelial cells in the tumor microenvironment play an important role in the development of kidney renal clear cell carcinoma (KIRC). We wanted to further identify the function of endothelial cells in KIRC patients by integrating single-cell and bulk RNA sequencing data.Methods: Online databases provide the original data of this study. An endothelial-related prognostic index (ERPI) was constructed and validated by R version 3.6.3 and relative packages.Results: The ERPI consisted of three genes (CCND1, MALL, and VWF). Patients with high ERPI scores were significantly correlated with worse prognosis than those with low ERPI scores in the TCGA training group, TCGA test group, and GSE29609 group. A positive correlation was identified between the ERPI score and poor clinical features. The results of functional analysis indicated that ERPI was significantly associated with immune-related activities. We suggested that patients with high ERPI scores were more likely to benefit from immunotherapy based on the results of immune checkpoints, tumor microenvironment, stemness index, and TCIA, while patients with low ERPI scores were sensitive to gemcitabine, docetaxel, paclitaxel, axitinib, pazopanib, sorafenib, and temsirolimus according to the results of the “pRRophetic” algorithm. Therefore, this ERPI may help doctors choose the optimal treatment for patients with KIRC.Conclusion: By integrating single-cell and bulk RNA sequencing data from KIRC patients, we successfully identified the key genes from the perspective of endothelial cells in the tumor microenvironment and constructed ERPIs that had positive implications in precision medicine.https://www.frontiersin.org/articles/10.3389/fgene.2023.1096491/fullendothelial cellskidney renal clear cell carcinomasingle-cellprecision medicinetumor microenvironment |
| spellingShingle | Deng-Xiong Li Qing-Xin Yu Chui-Xuan Zeng Lu-Xia Ye Yi-Qing Guo Jun-Fei Liu Hai-Hong Zheng Dechao Feng Wuran Wei A novel endothelial-related prognostic index by integrating single-cell and bulk RNA sequencing data for patients with kidney renal clear cell carcinoma Frontiers in Genetics endothelial cells kidney renal clear cell carcinoma single-cell precision medicine tumor microenvironment |
| title | A novel endothelial-related prognostic index by integrating single-cell and bulk RNA sequencing data for patients with kidney renal clear cell carcinoma |
| title_full | A novel endothelial-related prognostic index by integrating single-cell and bulk RNA sequencing data for patients with kidney renal clear cell carcinoma |
| title_fullStr | A novel endothelial-related prognostic index by integrating single-cell and bulk RNA sequencing data for patients with kidney renal clear cell carcinoma |
| title_full_unstemmed | A novel endothelial-related prognostic index by integrating single-cell and bulk RNA sequencing data for patients with kidney renal clear cell carcinoma |
| title_short | A novel endothelial-related prognostic index by integrating single-cell and bulk RNA sequencing data for patients with kidney renal clear cell carcinoma |
| title_sort | novel endothelial related prognostic index by integrating single cell and bulk rna sequencing data for patients with kidney renal clear cell carcinoma |
| topic | endothelial cells kidney renal clear cell carcinoma single-cell precision medicine tumor microenvironment |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1096491/full |
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