A novel defined risk signature of cuproptosis-related long non-coding RNA for predicting prognosis, immune infiltration, and immunotherapy response in lung adenocarcinoma
Background: Cuproptosis is a newly discovered non-apoptotic form of cell death that may be related to the development of tumors. Nonetheless, the potential role of cuproptosis-related lncRNAs in tumor immunity formation and patient-tailored treatment optimization of lung adenocarcinoma (LUAD) is sti...
| Main Authors: | , , , , |
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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 Pharmacology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fphar.2023.1146840/full |
| _version_ | 1797739937956626432 |
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| author | Chao Ma Feng Li Zhuoyu Gu Yang Yang Yu Qi |
| author_facet | Chao Ma Feng Li Zhuoyu Gu Yang Yang Yu Qi |
| author_sort | Chao Ma |
| collection | DOAJ |
| description | Background: Cuproptosis is a newly discovered non-apoptotic form of cell death that may be related to the development of tumors. Nonetheless, the potential role of cuproptosis-related lncRNAs in tumor immunity formation and patient-tailored treatment optimization of lung adenocarcinoma (LUAD) is still unclear.Methods: RNA sequencing and survival data of LUAD patients were downloaded from The Cancer Genome Atlas (TCGA) database for model training. The patients with LUAD in GSE29013, GSE30219, GSE31210, GSE37745, and GSE50081 were used for validation. The proofed cuproptosis-related genes were extracted from the previous studies. The Pearson correlation was applied to select cuproptosis-related lncRNAs. We chose differentially expressed cuproptosis-related lncRNAs in the tumor and normal tissues and allowed them to go to a Cox regression and a LASSO regression for a lncRNA signature that predicts the LUAD prognosis. Kaplan–Meier estimator, Cox model, ROC, tAUC, PCA, nomogram predictor, decision curve analysis, and real-time PCR were further deployed to confirm the model’s accuracy. We examined this model’s link to other regulated cell death forms. Applying TMB, immune-related signatures, and TIDE demonstrated the immunotherapeutic capabilities of signatures. We evaluated the relationship of our signature to anticancer drug sensitivity. GSEA, immune infiltration analysis, and function experiments further investigated the functional mechanisms of the signature and the role of immune cells in the prognostic power of the signature.Results: An eight-lncRNA signature (TSPOAP1-AS1, AC107464.3, AC006449.7, LINC00324, COLCA1, HAGLR, MIR4435-2HG, and NKILA) was built and demonstrated owning prognostic power by applied to the validation cohort. Each signature gene was confirmed differentially expressed in the real world by real-time PCR. The eight-lncRNA signature correlated with 2321/3681 (63.05%) apoptosis-related genes, 11/20 (55.00%) necroptosis-related genes, 34/50 (68.00%) pyroptosis-related genes, and 222/380 (58.42%) ferroptosis-related genes. Immunotherapy analysis suggested that our signature may have utility in predicting immunotherapy efficacy in patients with LUAD. Mast cells were identified as key players that support the predicting capacity of the eight-lncRNA signature through the immune infiltrating analysis.Conclusion: In this study, an eight-lncRNA signature linked to cuproptosis was identified, which may improve LUAD management strategies. This signature may possess the ability to predict the effect of LUAD immunotherapy. In addition, infiltrating mast cells may affect the signature’s prognostic power. |
| first_indexed | 2024-03-12T14:04:23Z |
| format | Article |
| id | doaj.art-04b88021fca94e26b29f7c6c2f00239e |
| institution | Directory Open Access Journal |
| issn | 1663-9812 |
| language | English |
| last_indexed | 2024-03-12T14:04:23Z |
| publishDate | 2023-08-01 |
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| series | Frontiers in Pharmacology |
| spelling | doaj.art-04b88021fca94e26b29f7c6c2f00239e2023-08-21T14:25:17ZengFrontiers Media S.A.Frontiers in Pharmacology1663-98122023-08-011410.3389/fphar.2023.11468401146840A novel defined risk signature of cuproptosis-related long non-coding RNA for predicting prognosis, immune infiltration, and immunotherapy response in lung adenocarcinomaChao MaFeng LiZhuoyu GuYang YangYu QiBackground: Cuproptosis is a newly discovered non-apoptotic form of cell death that may be related to the development of tumors. Nonetheless, the potential role of cuproptosis-related lncRNAs in tumor immunity formation and patient-tailored treatment optimization of lung adenocarcinoma (LUAD) is still unclear.Methods: RNA sequencing and survival data of LUAD patients were downloaded from The Cancer Genome Atlas (TCGA) database for model training. The patients with LUAD in GSE29013, GSE30219, GSE31210, GSE37745, and GSE50081 were used for validation. The proofed cuproptosis-related genes were extracted from the previous studies. The Pearson correlation was applied to select cuproptosis-related lncRNAs. We chose differentially expressed cuproptosis-related lncRNAs in the tumor and normal tissues and allowed them to go to a Cox regression and a LASSO regression for a lncRNA signature that predicts the LUAD prognosis. Kaplan–Meier estimator, Cox model, ROC, tAUC, PCA, nomogram predictor, decision curve analysis, and real-time PCR were further deployed to confirm the model’s accuracy. We examined this model’s link to other regulated cell death forms. Applying TMB, immune-related signatures, and TIDE demonstrated the immunotherapeutic capabilities of signatures. We evaluated the relationship of our signature to anticancer drug sensitivity. GSEA, immune infiltration analysis, and function experiments further investigated the functional mechanisms of the signature and the role of immune cells in the prognostic power of the signature.Results: An eight-lncRNA signature (TSPOAP1-AS1, AC107464.3, AC006449.7, LINC00324, COLCA1, HAGLR, MIR4435-2HG, and NKILA) was built and demonstrated owning prognostic power by applied to the validation cohort. Each signature gene was confirmed differentially expressed in the real world by real-time PCR. The eight-lncRNA signature correlated with 2321/3681 (63.05%) apoptosis-related genes, 11/20 (55.00%) necroptosis-related genes, 34/50 (68.00%) pyroptosis-related genes, and 222/380 (58.42%) ferroptosis-related genes. Immunotherapy analysis suggested that our signature may have utility in predicting immunotherapy efficacy in patients with LUAD. Mast cells were identified as key players that support the predicting capacity of the eight-lncRNA signature through the immune infiltrating analysis.Conclusion: In this study, an eight-lncRNA signature linked to cuproptosis was identified, which may improve LUAD management strategies. This signature may possess the ability to predict the effect of LUAD immunotherapy. In addition, infiltrating mast cells may affect the signature’s prognostic power.https://www.frontiersin.org/articles/10.3389/fphar.2023.1146840/fulllung adenocarcinomalncRNAsignaturecuproptosiscoppertumor microenvironment |
| spellingShingle | Chao Ma Feng Li Zhuoyu Gu Yang Yang Yu Qi A novel defined risk signature of cuproptosis-related long non-coding RNA for predicting prognosis, immune infiltration, and immunotherapy response in lung adenocarcinoma Frontiers in Pharmacology lung adenocarcinoma lncRNA signature cuproptosis copper tumor microenvironment |
| title | A novel defined risk signature of cuproptosis-related long non-coding RNA for predicting prognosis, immune infiltration, and immunotherapy response in lung adenocarcinoma |
| title_full | A novel defined risk signature of cuproptosis-related long non-coding RNA for predicting prognosis, immune infiltration, and immunotherapy response in lung adenocarcinoma |
| title_fullStr | A novel defined risk signature of cuproptosis-related long non-coding RNA for predicting prognosis, immune infiltration, and immunotherapy response in lung adenocarcinoma |
| title_full_unstemmed | A novel defined risk signature of cuproptosis-related long non-coding RNA for predicting prognosis, immune infiltration, and immunotherapy response in lung adenocarcinoma |
| title_short | A novel defined risk signature of cuproptosis-related long non-coding RNA for predicting prognosis, immune infiltration, and immunotherapy response in lung adenocarcinoma |
| title_sort | novel defined risk signature of cuproptosis related long non coding rna for predicting prognosis immune infiltration and immunotherapy response in lung adenocarcinoma |
| topic | lung adenocarcinoma lncRNA signature cuproptosis copper tumor microenvironment |
| url | https://www.frontiersin.org/articles/10.3389/fphar.2023.1146840/full |
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