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pmid:37622116
Identification of cuproptosis and immune-related gene prognostic signature in lung adenocarcinoma.
Wentao Zhang · Haizeng Qu · Xiaoqing Ma · Liang Li · Yanjun Wei · Ye Wang · Renya Zeng · Yuanliu Nie · Chenggui Zhang · Ke Yin · Fengge Zhou · Zhe Yang
Frontiers in immunology · 2023 doi:10.3389/fimmu.2023.1179742
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Complete file
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It is a promising new target for cancer therapy. Additionally, immune-related genes play a crucial role in cancer progression and patient prognosis. Therefore, our study aimed to create a survival prediction model for lung adenocarcinoma patients based on cuproptosis and immune-related genes. This model can be utilized to enhance personalized treatment for patients.\nMethods: RNA sequencing (RNA-seq) data of lung adenocarcinoma (LUAD) patients were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The levels of immune cell infiltration in the GSE68465 cohort were determined using gene set variation analysis (GSVA), and immune-related genes (IRGs) were identified using weighted gene coexpression network analysis (WGCNA). Additionally, cuproptosis-related genes (CRGs) were identified using unsupervised clustering. Univariate COX regression analysis and least absolute shrinkage selection operator (LASSO) regression analysis were performed to develop a risk prognostic model for cuproptosis and immune-related genes (CIRGs), which was subsequently validated. Various algorithms were utilized to explore the relationship between risk scores and immune infiltration levels, and model genes were analyzed based on single-cell sequencing. Finally, the expression of signature genes was confirmed through quantitative real-time PCR (qRT-PCR), immunohistochemistry (IHC), and Western blotting (WB).\nResults: We have identified 5 Oncogenic Driver Genes namely CD79B, PEBP1, PTK2B, STXBP1, and ZNF671, and developed proportional hazards regression models. The results of the study indicate significantly reduced survival rates in both the training and validation sets among the high-risk group. 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE68465", "GSE72094", "GSE37745", "GSE131907", "GSE168410"], "resolved_accessions": ["GSE68465", "GSE72094", "GSE37745", "GSE131907", "GSE168410"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/ Supplementary Material ."], "basis": "The paper names GSE68465, GSE72094, GSE37745, GSE131907, GSE168410 in National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database and the accession resolves in the repository. 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Methods: RNA sequencing (RNA-seq) data of lung adenocarcinoma (LUAD) patients", "ersonalized treatment for patients. Methods: RNA sequencing (RNA-seq) data of lung adenocarcinoma (LUAD)", "dditionally, we batch-corrected and combined RNA-seq data from the GSE68465 and TCGA LUAD cohorts"], "order_basis": "paper_text_order:575", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ure genes was confirmed through quantitative real-time PCR (qRT-PCR), immunohistochemistry (IHC), and W"], "order_basis": "paper_text_order:1560", "id": "assay:2"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["hrough quantitative real-time PCR (qRT-PCR), immunohistochemistry (IHC), and Western blotting (WB). Results: W", "al-time PCR (qRT-PCR), immunohistochemistry (IHC), and Western blotting (WB). Results: We hav"], "order_basis": "paper_text_order:1585", "id": "assay:3"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["R (qRT-PCR), immunohistochemistry (IHC), and Western blotting (WB). Results: We have identified 5 Oncogeni"], "order_basis": "paper_text_order:1617", "id": "assay:4"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Univariate Cox analysis was performed on CIRGs to screen out genes related to survival with statistical significance (P<0.05)."], "order_basis": "consumes_earlier_output", "id": "assay:5"}]}