Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade Glioma
Tumor mutation burden (TMB) is a useful biomarker to predict prognosis and the efficacy of immune checkpoint inhibitors (ICIs). In this study, we aimed to explore the prognostic value of TMB and the potential association between TMB and immune infiltration in lower-grade gliomas (LGGs). Somatic muta...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-08-01
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| Series: | Frontiers in Oncology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fonc.2020.01409/full |
| _version_ | 1818256935317667840 |
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| author | Wen Yin Xingjun Jiang Jun Tan Zhaoqi Xin Quanwei Zhou Chaohong Zhan Xianyong Fu Zhaoping Wu Youwei Guo Zhipeng Jiang Caiping Ren Caiping Ren Guihua Tang |
| author_facet | Wen Yin Xingjun Jiang Jun Tan Zhaoqi Xin Quanwei Zhou Chaohong Zhan Xianyong Fu Zhaoping Wu Youwei Guo Zhipeng Jiang Caiping Ren Caiping Ren Guihua Tang |
| author_sort | Wen Yin |
| collection | DOAJ |
| description | Tumor mutation burden (TMB) is a useful biomarker to predict prognosis and the efficacy of immune checkpoint inhibitors (ICIs). In this study, we aimed to explore the prognostic value of TMB and the potential association between TMB and immune infiltration in lower-grade gliomas (LGGs). Somatic mutation and RNA-sequencing (RNA-seq) data were downloaded from the Cancer Genome Atlas (TCGA) database. TMB was calculated and patients were divided into high- and low-TMB groups. After performing differential analysis between high- and low-risk groups, we identified six hub TMB and immune-related genes that were correlated with overall survival in LGGs. Then, Gene Set Enrichment Analysis was performed to screen significantly enriched GO terms between the two groups. Moreover, an immune-related risk score system was developed by LASSO Cox analysis based on the six hub genes and was validated with the Chinese Glioma Genome Atlas dataset. Using the TIMER database, we further systematically analyzed the relationships between mutants of the six hub genes and immune infiltration levels, as well as the relationships between the immune-related risk score system and the immune microenvironment in LGGs. The results showed that TMB was negatively correlated with OS and high TMB might inhibit immune infiltration in LGGs. Furthermore, the risk score system could effectively stratify patients into low- and high-risk groups in both the training and validation datasets. Multivariate Cox analysis demonstrated that TMB was not an independent prognostic factor, but the risk score was. Higher infiltration of immune cells (B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells) and higher levels of immune checkpoints (PD-1, CTLA-4, LAG-3, and TIM-3) were found in patients in the high-risk group. Finally, a novel nomogram model was constructed and evaluated to estimate the overall survival of LGG patients. In summary, our study provided new insights into immune infiltration in the tumor microenvironment and immunotherapies for LGGs. |
| first_indexed | 2024-12-12T17:35:39Z |
| format | Article |
| id | doaj.art-f78cef4493634ca5a3c39221a729af65 |
| institution | Directory Open Access Journal |
| issn | 2234-943X |
| language | English |
| last_indexed | 2024-12-12T17:35:39Z |
| publishDate | 2020-08-01 |
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| series | Frontiers in Oncology |
| spelling | doaj.art-f78cef4493634ca5a3c39221a729af652022-12-22T00:17:14ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2020-08-011010.3389/fonc.2020.01409555790Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade GliomaWen Yin0Xingjun Jiang1Jun Tan2Zhaoqi Xin3Quanwei Zhou4Chaohong Zhan5Xianyong Fu6Zhaoping Wu7Youwei Guo8Zhipeng Jiang9Caiping Ren10Caiping Ren11Guihua Tang12Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Neurosurgery, Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Neurosurgery, Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Neurosurgery, Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Neurosurgery, Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Neurosurgery, Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Neurosurgery, Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Neurosurgery, Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Neurosurgery, Xiangya Hospital of Central South University, Changsha, ChinaDepartment of Neurosurgery, Xiangya Hospital of Central South University, Changsha, ChinaThe Key Laboratory of Carcinogenesis of the Chinese Ministry of Health, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Xiangya Hospital, Central South University, Changsha, ChinaCancer Research Institute, Collaborative Innovation Center for Cancer Medicine, School of Basic Medical Science, Central South University, Changsha, ChinaDepartment of Clinical Laboratory, Hunan Provincial People's Hospital (First Affiliated Hospital of Hunan Normal University), Changsha, ChinaTumor mutation burden (TMB) is a useful biomarker to predict prognosis and the efficacy of immune checkpoint inhibitors (ICIs). In this study, we aimed to explore the prognostic value of TMB and the potential association between TMB and immune infiltration in lower-grade gliomas (LGGs). Somatic mutation and RNA-sequencing (RNA-seq) data were downloaded from the Cancer Genome Atlas (TCGA) database. TMB was calculated and patients were divided into high- and low-TMB groups. After performing differential analysis between high- and low-risk groups, we identified six hub TMB and immune-related genes that were correlated with overall survival in LGGs. Then, Gene Set Enrichment Analysis was performed to screen significantly enriched GO terms between the two groups. Moreover, an immune-related risk score system was developed by LASSO Cox analysis based on the six hub genes and was validated with the Chinese Glioma Genome Atlas dataset. Using the TIMER database, we further systematically analyzed the relationships between mutants of the six hub genes and immune infiltration levels, as well as the relationships between the immune-related risk score system and the immune microenvironment in LGGs. The results showed that TMB was negatively correlated with OS and high TMB might inhibit immune infiltration in LGGs. Furthermore, the risk score system could effectively stratify patients into low- and high-risk groups in both the training and validation datasets. Multivariate Cox analysis demonstrated that TMB was not an independent prognostic factor, but the risk score was. Higher infiltration of immune cells (B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells) and higher levels of immune checkpoints (PD-1, CTLA-4, LAG-3, and TIM-3) were found in patients in the high-risk group. Finally, a novel nomogram model was constructed and evaluated to estimate the overall survival of LGG patients. In summary, our study provided new insights into immune infiltration in the tumor microenvironment and immunotherapies for LGGs.https://www.frontiersin.org/article/10.3389/fonc.2020.01409/fulltumor mutation burden (TMB)lower-grade glioma (LGG)immune infiltrationimmune-related risk score systemnomogram |
| spellingShingle | Wen Yin Xingjun Jiang Jun Tan Zhaoqi Xin Quanwei Zhou Chaohong Zhan Xianyong Fu Zhaoping Wu Youwei Guo Zhipeng Jiang Caiping Ren Caiping Ren Guihua Tang Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade Glioma Frontiers in Oncology tumor mutation burden (TMB) lower-grade glioma (LGG) immune infiltration immune-related risk score system nomogram |
| title | Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade Glioma |
| title_full | Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade Glioma |
| title_fullStr | Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade Glioma |
| title_full_unstemmed | Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade Glioma |
| title_short | Development and Validation of a Tumor Mutation Burden–Related Immune Prognostic Model for Lower-Grade Glioma |
| title_sort | development and validation of a tumor mutation burden related immune prognostic model for lower grade glioma |
| topic | tumor mutation burden (TMB) lower-grade glioma (LGG) immune infiltration immune-related risk score system nomogram |
| url | https://www.frontiersin.org/article/10.3389/fonc.2020.01409/full |
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