Dataset Information

Systematic construction and validation of an immune prognostic model for lung adenocarcinoma.

ABSTRACT: Lung adenocarcinoma (LUAD), the most common non-small-cell lung cancer, is characterized by a dense lymphocytic infiltrate, which indicates that the immune system plays an active role in the development and growth of this cancer. However, no investigations to date have proposed robust models for predicting survival outcome for patients with LUAD in terms of tumour immunology. A total of 761 LUAD patients were included in this study, in which the database of The Cancer Genome Atlas (TCGA) was utilized for discovery, and the Gene Expression Omnibus (GEO) database was utilized for validation. Bioinformatics analysis and R language tools were utilized to construct an immune prognostic model and annotate biological functions. Lung adenocarcinoma showed a weakened immune phenotype compared with adjacent normal tissues. Immune-related gene sets were profiled, an immune prognostic model based on 2 immune genes (ANLN and F2) was developed with the TCGA database to distinguish cases as having a low or high risk of unfavourable prognosis, and the model was verified with the GEO database. The model was prognostically significant in stratified cohorts, including stage I-II, stage III-IV and epidermal growth factor receptor (EGFR) mutant subsets, and was considered to be an independent prognostic factor for LUAD. Furthermore, the low- and high-risk groups showed marked differences in tumour-infiltrating leucocytes, tumour mutation burden, aneuploidy and PD-L1 expression. In conclusion, an immune prognostic model was proposed for LUAD that is capable of independently identifying patients at high risk for poor survival, suggesting a relationship between local immune status and prognosis.

SUBMITTER: Luo C

PROVIDER: S-EPMC6991688 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Systematic construction and validation of an immune prognostic model for lung adenocarcinoma.

Luo Chenghan C Lei Mengyuan M Zhang Yixia Y Zhang Qian Q Li Lifeng L Lian Jingyao J Liu Shasha S Wang Liping L Pi Guofu G Zhang Yi Y

Journal of cellular and molecular medicine 20191128 2

Lung adenocarcinoma (LUAD), the most common non-small-cell lung cancer, is characterized by a dense lymphocytic infiltrate, which indicates that the immune system plays an active role in the development and growth of this cancer. However, no investigations to date have proposed robust models for predicting survival outcome for patients with LUAD in terms of tumour immunology. A total of 761 LUAD patients were included in this study, in which the database of The Cancer Genome Atlas (TCGA) was uti ...[more]

PMID: 31779055

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Project description:BackgroundLung adenocarcinoma (LUAD) originates mainly from the mucous epithelium and glandular epithelium of the bronchi. It is the most common pathologic subtype of non-small cell lung cancer (NSCLC). At present, there is still a lack of clear criteria to predict the efficacy of immunotherapy. The 5-year survival rate for LUAD patients remains low.MethodsAll data were downloaded from The Cancer Genome Atlas (TCGA) database. We used Gene Set Enrichment Analysis (GSEA) database to obtain immune-related mRNAs. Immune-related lncRNAs were acquired by using the correlation test of the immune-related genes with R version 3.6.3 (Pearson correlation coefficient cor = 0.5, P < 0.05). The TCGA-LUAD dataset was divided into the testing set and the training set randomly. Based on the training set to perform univariate and multivariate Cox regression analyses, we screened prognostic immune-related lncRNAs and given a risk score to each sample. Samples were divided into the high-risk group and the low-risk group according to the median risk score. By the combination of Kaplan-Meier (KM) survival curve, the receiver operating characteristic (ROC) (AUC) curve, the independent risk factor analysis, and the clinical data of the samples, we assessed the accuracy of the risk model. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed on the differentially expressed mRNAs between the high-risk group and the low-risk group. The differentially expressed genes related to immune response between two risk groups were analyzed to evaluate the role of the model in predicting the efficacy and effects of immunotherapy. In order to explain the internal mechanism of the risk model in predicting the efficacy of immunotherapy, we analyzed the differentially expressed genes related to epithelial-mesenchymal transition (EMT) between two risk groups. We extracted RNA from normal bronchial epithelial cell and LUAD cells and verified the expression level of lncRNAs in the risk model by a quantitative real-time polymerase chain reaction (qRT-PCR) test. We compared our risk model with other published prognostic signatures with data from an independent cohort. We transfected LUAD cell with siRNA-LINC0253. Western blot analysis was performed to observed change of EMT-related marker in protein level.ResultsThrough univariate Cox regression analysis, 24 immune-related lncRNAs were found to be strongly associated with the survival of the TCGA-LUAD dataset. Utilizing multivariate Cox regression analysis, 10 lncRNAs were selected to establish the risk model. The K-M survival curves and the ROC (AUC) curves proved that the risk model has a fine predictive effect. The GO enrichment analysis indicated that the effect of the differentially expressed genes between high-risk and low-risk groups is mainly involved in immune response and intercellular interaction. The KEGG enrichment analysis indicated that the differentially expressed genes between high-risk and low-risk groups are mainly involved in endocytosis and the MAPK signaling pathway. The expression of genes related to the efficacy of immunotherapy was significantly different between the two groups. A qRT-PCR test verified the expression level of lncRNAs in LUAD cells in the risk model. The AUC of ROC of 5 years in the independent validation dataset showed that this model had superior accuracy. Western blot analysis verified the change of EMT-related marker in protein level.ConclusionThe immune lncRNA risk model established by us could better predict the prognosis of patients with LUAD.

Project description:BackgroundAutophagy related genes (ARGs) regulate lysosomal degradation to induce autophagy, and are involved in the occurrence and development of a variety of cancers. The expression of ARGs in tumor tissues has a great prospect in predicting the survival of patients. The aim of this study was to construct a prognostic risk score model for lung adenocarcinoma (LUAD) based on ARGs.Methods5,786 ARGs were obtained from GeneCards database. Gene expression profiles and clinical data of 395 LUAD patients were collected from The Cancer Genome Atlas (TCGA) database. All ARGs expression data were extracted, and The ARGs differentially expressed were identified by R software. Survival analysis of differentially expressed ARGs was performed to screen for ARGs with prognostic value, and functional enrichment analysis was performed. The least absolute selection operator (LASSO) regression and Cox regression model were used to construct a prognostic risk scoring model for ARGs. The receiver operating characteristic (ROC) curve was drawn to obtain the optimal cut-off value of risk score. According to the cut-off value, the patients were divided into high-risk group and low-risk group. The area under curve (AUC) and the Kaplan-Meier survival curve was plotted to evaluate the model performance, which was verified in external data sets. Finally, univariate and multivariate Cox regression analysis was applied to evaluate the independent prognostic value of the model, and its clinical relevance was analyzed.ResultsSurvival analysis, Lasso regression and Cox regression analysis were used to construct a LUAD prognostic risk score model with five ARGs (ADAM12, CAMP, DKK1, STRIP2 and TFAP2A). The survival time of patients with low-risk score in this model was significantly better than that of patients with high-risk score (P<0.001). The model showed good prediction performance for LUAD in both the training set (AUCmax=0.78) and two external validation sets (AUCmax=0.88). Risk score was significantly associated with the prognosis of LUAD patients in univariate and multivariate Cox regression analyses, suggested that risk score could be a potential independent prognostic factor for LUAD. Correlation analysis of clinical characteristic showed that high risk score was closely associated with high T stage, high tumor stage and poor prognosis.ConclusionsWe constructed a LUAD risk score model consisting of five ARGs, which can provide a reference for predicting the prognosis of LUAD patients, and may be used in combination with tumor node metastasis (TNM) staging for prognosis prediction of LUAD patients in the future.

Project description:Necroptosis is a new form of cell death. Since the discovery that long non-coding RNAs can affect the proliferation of lung adenocarcinoma, much has been learned about it, yet those of necroptosis-related long non-coding RNAs (NRlncRNAs) in lung adenocarcinoma (LUAD) remain enigmatic. This study aims to explore novel biomarkers and therapeutic targets for LUAD. The LUAD data was downloaded from The Cancer Genome Atlas, and necroptosis-related genes were retrieved from published literature. Co-expression analysis, univariate Cox analysis, least absolute shrinkage and selection operator regression analysis were used to identify necroptosis-related prognostic long non-coding RNAs. A comprehensive evaluation of tumor immunity for necrosis-related features was performed, and we identified a 9-NRlncRNA signature. Kaplan-Meier and Cox regression analyses confirmed that the signature was an independent predictor of LUAD outcome in the test and train sets (all P < 0.05). The areas of 1-, 2-, and 3-year overall survival under the time-dependent receiver operating characteristics (ROC) curve (AUC) were 0.754, 0.746, and 0.720, respectively. The GSEA results showed that 9 NRlncRNAs were associated with multiple malignancy-associated and immunoregulatory pathways. Based on this model, we found that the immune status and level of response to chemotherapy and targeted therapy were significantly different in the low-risk group compared with the high-risk group. qRT-PCR assay revealed that 9 NRlncRNAs were involved in the regulation of tumor cell proliferation and may affect the expression of programmed cell death 1 (PD1) and CD28 at human immune checkpoints. Our results indicated that the novel signature involving 9 NRlncRNAs (AL031600.2, LINC01281, AP001178.1, AL157823.2, LINC01290, MED4-AS1, AC026355.2, AL606489.1, FAM83A-AS1) can predict the prognosis of LUAD and are associated with the immune response. This will provide new insights into the pathogenesis and development of therapies for LUAD.

Project description:BackgroundTumor metabolism and immune response can affect the biological behavior of tumor cells. There is an obvious relationship between glycolysis and immune response. However, the association between metabolism and immune response and prognosis in lung adenocarcinoma (LUAD) has not yet been examined in a comprehensive and detailed manner. The establishment of reliable models for predicting the prognosis of LUAD based on glycolysis ability and immune status is still highly anticipated.MethodsThe expression of genes were obtained from online databases, and the differentially expressed genes in LUAD tissues and adjacent tissues were identified. We used LUAD samples in The Cancer Genome Atlas (TCGA) database as training set and the Gene Expression Omnibus (GEO) databases as validation sets. The best predictive model was constructed using least absolute selection and shrinkage operator (LASSO) regression and Cox regression. The receiver operator characteristic (ROC) curve is used to verify the accuracy of the model. The expression status of the Glycolysis-related genes (GRGs) and the status of the immune cells in LUCD patients were further analyzed. The protein levels of the 3 identified genes were then tested in LUAD patients.ResultsWe identified 3 GRGs and immune-related genes (i.e., fibroblast growth factor 2, hyaluronan-mediated motor receptor, and nuclear receptor 0B2) and constructed a stable comprehensive index of glycolysis and immunity (CIGI) prediction model. The validation results for this CIGI model were quite stable across different datasets and patient subgroups and the CIGI score can be included as an independent prognostic factor for LUAD patients. The area under the curve (AUC) values of 1-, 3- and 5-year of the finally established nomogram model are 0.767, 0.735 and 0.769. Further analysis showed that LUAD patients in the low-risk group had lower levels of glycolytic gene expression than those in the high-risk group and exhibited an immunosuppressed state. Finally, hyaluronan-mediated motor receptor may play a role in inhibiting cancer, while fibroblast growth factor 2 and nuclear receptor 0B2 may play roles in promoting cancer.ConclusionsIn this study, we established a new prognostic prediction model for LUAD patients that combines glycolysis ability and immune status.

Dataset Information

Systematic construction and validation of an immune prognostic model for lung adenocarcinoma.

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Systematic construction and validation of an immune prognostic model for lung adenocarcinoma.

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