A novel necroptosis-related long noncoding RNA model for predicting clinical features, immune characteristics, and therapeutic response in clear cell renal cell carcinoma
BackgroundNecroptosis is an immune-related cell death pathway involved in the regulation of the tumor microenvironment (TME). Here, we aimed to explore the role of necroptosis in clear cell renal cell carcinoma (ccRCC) and construct a necroptosis-related lncRNA (NRL) model to assess its potential as...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-08-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1230267/full |
| _version_ | 1797756536021319680 |
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| author | Lei Zhang Lei Zhang Yongquan Chen Yongquan Chen Weijing Hu Bo Wu Linfeng Ye Dongwen Wang Dongwen Wang Tao Bai |
| author_facet | Lei Zhang Lei Zhang Yongquan Chen Yongquan Chen Weijing Hu Bo Wu Linfeng Ye Dongwen Wang Dongwen Wang Tao Bai |
| author_sort | Lei Zhang |
| collection | DOAJ |
| description | BackgroundNecroptosis is an immune-related cell death pathway involved in the regulation of the tumor microenvironment (TME). Here, we aimed to explore the role of necroptosis in clear cell renal cell carcinoma (ccRCC) and construct a necroptosis-related lncRNA (NRL) model to assess its potential association with clinical characteristics and immune status.MethodsGene expression profiles and clinical data for ccRCC patients were obtained from the Cancer Genome Atlas (TCGA). Pearson’s correlation, univariate Cox, and least absolute shrinkage and selection operator analyses were used to develop an NRL model. Kaplan–Meier (K-M) and receiver operating characteristic (ROC) curve analyses were used to determine the prognostic value of the NRL model. The clinical information was used to assess the diagnostic value of the NRL model. The TME, immune function, immune cell infiltration, and immune checkpoints associated with the NRL model risk score were studied using the ESTIMATE, GSEA, ssGSEA, and CIBERSORT algorithms. The immunophenoscore (IPS) and half-maximal inhibitory concentration (IC50) were used to compare the efficacies of immunotherapy and chemotherapy based on the NRL model. Finally, in vitro assays were performed to confirm the biological roles of NRLs.ResultsA total of 18 necroptosis-related genes and 285 NRLs in ccRCC were identified. A four-NRL model was constructed and showed good performance in the diagnosis and prognosis of ccRCC patients. The ESTIMATE scores, tumor mutation burden, and tumor stemness indices were significantly correlated with NRL model risk score. Immune functions such as chemokine receptors and immune receptor activity showed differences between different risk groups. The infiltration of immunosuppressive cells such as Tregs was higher in high-risk patients than in low-risk patients. High-risk patients were more sensitive to immunotherapy and some chemotherapy drugs, such as sunitinib and temsirolimus. Finally, the expression of NRLs included in the model was verified, and knocking down these NRLs in tumor cells affected cell proliferation, migration, and invasion.ConclusionNecroptosis plays an important role in the progression of ccRCC. The NRL model we constructed can be used to predict the clinical characteristics and immune features of ccRCC patients. |
| first_indexed | 2024-03-12T18:01:54Z |
| format | Article |
| id | doaj.art-e1b96edb3ec9448588ed83642e497ebd |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-03-12T18:01:54Z |
| publishDate | 2023-08-01 |
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| series | Frontiers in Immunology |
| spelling | doaj.art-e1b96edb3ec9448588ed83642e497ebd2023-08-02T09:53:02ZengFrontiers Media S.A.Frontiers in Immunology1664-32242023-08-011410.3389/fimmu.2023.12302671230267A novel necroptosis-related long noncoding RNA model for predicting clinical features, immune characteristics, and therapeutic response in clear cell renal cell carcinomaLei Zhang0Lei Zhang1Yongquan Chen2Yongquan Chen3Weijing Hu4Bo Wu5Linfeng Ye6Dongwen Wang7Dongwen Wang8Tao Bai9Department of Urology, First Hospital of Shanxi Medical University, Taiyuan, ChinaDepartment of the First Clinical Medical College, Shanxi Medical University, Taiyuan, ChinaDepartment of Urology, First Hospital of Shanxi Medical University, Taiyuan, ChinaDepartment of the First Clinical Medical College, Shanxi Medical University, Taiyuan, ChinaDepartment of the First Clinical Medical College, Shanxi Medical University, Taiyuan, ChinaDepartment of Urology, First Hospital of Shanxi Medical University, Taiyuan, ChinaDepartment of Otorhinolaryngology-Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan, ChinaDepartment of the First Clinical Medical College, Shanxi Medical University, Taiyuan, ChinaCancer Hospital Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, ChinaDepartment of Pathology, First Hospital of Shanxi Medical University, Taiyuan, ChinaBackgroundNecroptosis is an immune-related cell death pathway involved in the regulation of the tumor microenvironment (TME). Here, we aimed to explore the role of necroptosis in clear cell renal cell carcinoma (ccRCC) and construct a necroptosis-related lncRNA (NRL) model to assess its potential association with clinical characteristics and immune status.MethodsGene expression profiles and clinical data for ccRCC patients were obtained from the Cancer Genome Atlas (TCGA). Pearson’s correlation, univariate Cox, and least absolute shrinkage and selection operator analyses were used to develop an NRL model. Kaplan–Meier (K-M) and receiver operating characteristic (ROC) curve analyses were used to determine the prognostic value of the NRL model. The clinical information was used to assess the diagnostic value of the NRL model. The TME, immune function, immune cell infiltration, and immune checkpoints associated with the NRL model risk score were studied using the ESTIMATE, GSEA, ssGSEA, and CIBERSORT algorithms. The immunophenoscore (IPS) and half-maximal inhibitory concentration (IC50) were used to compare the efficacies of immunotherapy and chemotherapy based on the NRL model. Finally, in vitro assays were performed to confirm the biological roles of NRLs.ResultsA total of 18 necroptosis-related genes and 285 NRLs in ccRCC were identified. A four-NRL model was constructed and showed good performance in the diagnosis and prognosis of ccRCC patients. The ESTIMATE scores, tumor mutation burden, and tumor stemness indices were significantly correlated with NRL model risk score. Immune functions such as chemokine receptors and immune receptor activity showed differences between different risk groups. The infiltration of immunosuppressive cells such as Tregs was higher in high-risk patients than in low-risk patients. High-risk patients were more sensitive to immunotherapy and some chemotherapy drugs, such as sunitinib and temsirolimus. Finally, the expression of NRLs included in the model was verified, and knocking down these NRLs in tumor cells affected cell proliferation, migration, and invasion.ConclusionNecroptosis plays an important role in the progression of ccRCC. The NRL model we constructed can be used to predict the clinical characteristics and immune features of ccRCC patients.https://www.frontiersin.org/articles/10.3389/fimmu.2023.1230267/fullnecroptosislncRNAccRCCprognosistumor microenvironmentimmunotherapy |
| spellingShingle | Lei Zhang Lei Zhang Yongquan Chen Yongquan Chen Weijing Hu Bo Wu Linfeng Ye Dongwen Wang Dongwen Wang Tao Bai A novel necroptosis-related long noncoding RNA model for predicting clinical features, immune characteristics, and therapeutic response in clear cell renal cell carcinoma Frontiers in Immunology necroptosis lncRNA ccRCC prognosis tumor microenvironment immunotherapy |
| title | A novel necroptosis-related long noncoding RNA model for predicting clinical features, immune characteristics, and therapeutic response in clear cell renal cell carcinoma |
| title_full | A novel necroptosis-related long noncoding RNA model for predicting clinical features, immune characteristics, and therapeutic response in clear cell renal cell carcinoma |
| title_fullStr | A novel necroptosis-related long noncoding RNA model for predicting clinical features, immune characteristics, and therapeutic response in clear cell renal cell carcinoma |
| title_full_unstemmed | A novel necroptosis-related long noncoding RNA model for predicting clinical features, immune characteristics, and therapeutic response in clear cell renal cell carcinoma |
| title_short | A novel necroptosis-related long noncoding RNA model for predicting clinical features, immune characteristics, and therapeutic response in clear cell renal cell carcinoma |
| title_sort | novel necroptosis related long noncoding rna model for predicting clinical features immune characteristics and therapeutic response in clear cell renal cell carcinoma |
| topic | necroptosis lncRNA ccRCC prognosis tumor microenvironment immunotherapy |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2023.1230267/full |
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