Development and Validation of a 23-Gene Signature for Prognosis Prediction in Lung Adenocarcinoma

Abstract Background: Lung cancer remains the most fatal tumorous disease in the worldwide. Among that, lung adenocarcinoma (LUAD) was the most common histological type. A precise and concise prognostic model was urgently needed of LUAD. We developed a 23-gene signature for prognosis prediction based on EMT, immune and stromal datasets.Methods: Univariate Cox regression analysis was performed to select genes which were significantly associated with overall survival (OS) of the TCGA LUAD cohorts. LASSO regression and multivariate Cox regression analysis was used to build the multi-gene signature. Enrichment analyses and a protein-protein interactions (PPI) network were performed to show the interaction and functions of the signature. A nomogram was developed based on risk score and other clinical features. Predictive performance of the signature was externally validated in two independent datasets from Gene Expression Omnibus (GSE37745 and GSE13213).Results: A total of 1334 EMT, immune and stromal associated genes were obtained. After LASSO regression and multivariate Cox regression analysis, a 23-gene signature for risk stratification was built. K-M curves showed that the patients with high risk had a poorer outcome. Finally, a nomogram was built to predict prognosis. The predictive performance of the 23-gene signature was confirmed in internal and external validation.Conclusion: We developed and verified a 23-gene signature based on EMT, immune and stromal gene sets. It provided a convenient and concise tool for risk stratificationand individual medicine.

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Prognostic Nomogram Based on Circular RNA-Associated Competing Endogenous RNA Network for Patients with Lung Adenocarcinoma

Oxidative Medicine and Cellular Longevity ◽

10.1155/2021/9978206 ◽

2021 ◽

Vol 2021 ◽

pp. 1-13

Author(s):

Yang Li ◽

Rongrong Sun ◽

Rui Li ◽

Yonggang Chen ◽

He Du

Keyword(s):

Overall Survival ◽

Regression Analysis ◽

Lung Adenocarcinoma ◽

Regulatory Mechanism ◽

Cox Regression ◽

Gene Signature ◽

Differentially Expressed ◽

Prognostic Signature ◽

Cox Regression Analysis ◽

Cerna Network

Evidence is increasingly indicating that circular RNAs (circRNAs) are closely involved in tumorigenesis and cancer progression. However, the function and application of circRNAs in lung adenocarcinoma (LUAD) are still unknown. In this study, we constructed a circRNA-associated competitive endogenous RNA (ceRNA) network to investigate the regulatory mechanism of LUAD procession and further constructed a prognostic signature to predict overall survival for LUAD patients. Differentially expressed circRNAs (DEcircRNAs), differentially expressed miRNAs (DEmiRNAs), and differentially expressed mRNAs (DEmRNAs) were selected to construct the ceRNA network. Based on the TargetScan prediction tool and Pearson correlation coefficient, we constructed a circRNA-associated ceRNA network including 11 DEcircRNAs, 8 DEmiRNAs, and 49 DEmRNAs. GO and KEGG enrichment indicated that the ceRNA network might be involved in the regulation of GTPase activity and endothelial cell differentiation. After removing the discrete points, a PPI network containing 12 DEmRNAs was constructed. Univariate Cox regression analysis showed that three DEmRNAs were significantly associated with overall survival. Therefore, we constructed a three-gene prognostic signature for LUAD patients using the LASSO method in the TCGA-LUAD training cohort. By applying the signature, patients could be categorized into the high-risk or low-risk subgroups with significant survival differences (HR: 1.62, 95% CI: 1.12-2.35, log-rank p = 0.009 ). The prognostic performance was confirmed in an independent GEO cohort (GSE42127, HR: 2.59, 95% CI: 1.32-5.10, log-rank p = 0.004 ). Multivariate Cox regression analysis proved that the three-gene signature was an independent prognostic factor. Combining the three-gene signature with clinical characters, a nomogram was constructed. The primary and external verification C -indexes were 0.717 and 0.716, respectively. The calibration curves for the probability of 3- and 5-year OS showed significant agreement between nomogram predictions and actual observations. Our findings provided a deeper understanding of the circRNA-associated ceRNA regulatory mechanism in LUAD pathogenesis and further constructed a useful prognostic signature to guide personalized treatment of LUAD patients.

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Development of an immune-related gene pairs signature for predicting clinical outcome in lung adenocarcinoma

10.21203/rs.3.rs-26948/v1 ◽

2020 ◽

Author(s):

Chunlei Wu ◽

Quanteng Hu ◽

Dehua Ma

Keyword(s):

Regression Analysis ◽

Lung Adenocarcinoma ◽

Cox Regression ◽

Characteristic Curve ◽

Lasso Regression ◽

Related Gene ◽

Cox Regression Analysis ◽

Gene Pairs ◽

Immune Related Gene ◽

Pathological Subtype

Abstract Background Lung adenocarcinoma (LUAD) is the main pathological subtype of Non-small cell lung cancer. The aim of this study was to establish an immune-related gene pairs (IRGPs) signature for predicting the prognosis of LUAD patients.Methods We downloaded the gene expression profile and immune-related gene set from TCGA and ImmPort database, respectively, to establish IRGPs. Then, IRGPs subjected to univariate Cox regression analysis, LASSO regression analysis and multivariable Cox regression analysis to screen and develop a IRGPs signature. The receiver operating characteristic curve (ROC) was applied for evaluating the predicting accuracy of this signature by calculating the area under ROC (AUC) and data from GEO was used to validate this signature.Results A IRGPs signature with 8 IRGPs was constructed. The AUC for 1- and 3-year overall survival in TCGA set was 0.867 and 0.870, respectively. Similar result was observed in the AUC of GEO set and Total set (GEO set [1-year: 0.819; 3-years: 0.803]; Total set [1-year: 0.845; 3-years: 0.801]). Survival analysis of three sets demonstrated high-risk LUAD patients exhibited poorer prognosis. The multivariable Cox regression indicated that risk score was independent prognostic factors.Conclusions We developed a novel IRGPs signature for predicting prognosis of LUAD.

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Identification of a circadian gene signature that predicts overall survival in lung adenocarcinoma

PeerJ ◽

10.7717/peerj.11733 ◽

2021 ◽

Vol 9 ◽

pp. e11733

Author(s):

Xinliang Gao ◽

Mingbo Tang ◽

Suyan Tian ◽

Jialin Li ◽

Wei Liu

Keyword(s):

Overall Survival ◽

Regression Analysis ◽

Lung Adenocarcinoma ◽

Circadian Clock ◽

Cox Regression ◽

Gene Signature ◽

Differentially Expressed ◽

Circadian Gene ◽

Cox Regression Analysis ◽

Circadian Genes

Background Lung adenocarcinoma (LUAD) is one of the most common subtypes of lung cancer which is the leading cause of death in cancer patients. Circadian clock disruption has been listed as a likely carcinogen. However, whether the expression of circadian genes affects overall survival (OS) in LUAD patients remains unknown. In this article, we identified a circadian gene signature to predict overall survival in LUAD. Methods RNA sequencing (HTSeq-FPKM) data and clinical characteristics were obtained for a cohort of LUAD patients from The Cancer Genome Atlas (TCGA). A multigene signature based on differentially expressed circadian clock-related genes was generated for the prediction of OS using Least Absolute Shrinkage and Selection Operator (LASSO)-penalized Cox regression analysis, and externally validated using the GSE72094 dataset from the GEO database. Results Five differentially expressed genes (DEGs) were identified to be significantly associated with OS using univariate Cox proportional regression analysis (P < 0.05). Patients classified as high risk based on these five DEGs had significantly lower OS than those classified as low risk in both the TGCA cohort and GSE72094 dataset (P < 0.001). Multivariate Cox regression analysis revealed that the five-gene-signature based risk score was an independent predictor of OS (hazard ratio > 1, P < 0.001). Receiver operating characteristic (ROC) curves confirmed its prognostic value. Gene set enrichment analysis (GSEA) showed that Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to cell proliferation, gene damage repair, proteasomes, and immune and autoimmune diseases were significantly enriched. Conclusion A novel circadian gene signature for OS in LUAD was found to be predictive in both the derivation and validation cohorts. Targeting circadian genes is a potential therapeutic option in LUAD.

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Prognostic Nomograms Based on Ground Glass Opacity and Subtype of Lung Adenocarcinoma for Patients with Pathological Stage IA Lung Adenocarcinoma

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.769881 ◽

2021 ◽

Vol 9 ◽

Author(s):

Wenyu Zhai ◽

Dachuan Liang ◽

Fangfang Duan ◽

Wingshing Wong ◽

Qihang Yan ◽

...

Keyword(s):

Regression Analysis ◽

High Risk ◽

Lung Adenocarcinoma ◽

Cox Regression ◽

Ground Glass Opacity ◽

Predictive Performance ◽

Pathological Stage ◽

Invasive Adenocarcinoma ◽

Cox Regression Analysis ◽

Stage Ia

The value of lung adenocarcinoma (LUAD) subtypes and ground glass opacity (GGO) in pathological stage IA invasive adenocarcinoma (IAC) has been poorly understood, and reports of their association with each other have been limited. In the current study, we retrospectively reviewed 484 patients with pathological stage IA invasive adenocarcinoma (IAC) at Sun Yat-sen University Cancer Center from March 2011 to August 2018. Patients with at least 5% solid or micropapillary presence were categorized as high-risk subtypes. Independent indicators for disease-free survival (DFS) and overall survival (OS) were identified by multivariate Cox regression analysis. Based on these indicators, we developed prognostic nomograms of OS and DFS. The predictive performance of the two nomograms were assessed by calibration plots. A total of 412 patients were recognized as having the low-risk subtype, and 359 patients had a GGO. Patients with the low-risk subtype had a high rate of GGO nodules (p < 0.001). Multivariate Cox regression analysis showed that the high-risk subtype and GGO components were independent prognostic factors for OS (LUAD subtype: p = 0.002; HR 3.624; 95% CI 1.263–10.397; GGO component: p = 0.001; HR 3.186; 95% CI 1.155–8.792) and DFS (LUAD subtype: p = 0.001; HR 2.284; 95% CI 1.448–5.509; GGO component: p = 0.003; HR 1.877; 95% CI 1.013–3.476). The C-indices of the nomogram based on the LUAD subtype and GGO components to predict OS and DFS were 0.866 (95% CI 0.841–0.891) and 0.667 (95% CI 0.586–0.748), respectively. Therefore, the high-risk subtype and GGO components were potential prognostic biomarkers for patients with stage IA IAC, and prognostic models based on these indicators showed good predictive performance and satisfactory agreement between observational and predicted survival.

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A 5-mRNA-Based Prognostic Signature of Survival in Lung Adenocarcinoma

10.21203/rs.3.rs-547271/v1 ◽

2021 ◽

Author(s):

qianlin xia ◽

Weimo Yu ◽

Qiuyue Li ◽

Jin Wang ◽

Yuzhen Du

Keyword(s):

Regression Analysis ◽

Lung Adenocarcinoma ◽

Prediction Models ◽

Risk Model ◽

Cox Regression ◽

External Validation ◽

Assessment Tools ◽

Normal Lung ◽

Survival Prognosis ◽

Cox Regression Analysis

Abstract Background: Lung adenocarcinoma (LUAD) is the most common non-small cell lung cancer, with an increasing incidence and poor prognosis. To evaluate the prognosis of LUAD patients and optimize treatment, effective clinical research prediction models are urgently needed. Methods : In this study, we thoroughly mined LUAD genomic data from GEO (GSE43458, GSE32863, and GSE27262) and TCGA datasets, including 698 LUAD and 172 healthy (or adjacent normal) lung tissue samples. Single-factor Cox and LASSO regression analyses were used to screen DEGs related to patient prognosis, and multivariate Cox regression analysis was applied to establish the risk score equation and construct the survival prognosis model. Receiver operating characteristic (ROC) curve and Kaplan-Meier (KM) survival analyses with clinically independent prognostic parameters were performed to verify the predictive power of the model and further establish a prognostic nomogram. Results: A total of 380 DEGs were identified in LUAD tissues through GEO and TCGA datasets, and 5 DEGs (TCN1, CENPF, MAOB, CRTAC1 and PLEK2) were screened out by multivariate Cox regression analysis, indicating that the prognostic risk model could be used as an independent prognostic factor (HR = 1.520, P < 0.001). Internal and external validation of the model confirmed that the prediction model had good sensitivity and specificity (AUC = 0.754, 0.737). Combining genetic models and clinical prognostic factors, nomograms can also predict overall survival more effectively. Conclusion: A 5-mRNA-based model was constructed to predict the prognosis of lung adenocarcinoma, which may provide clinicians with reliable prognostic assessment tools and help clinical treatment decisions.

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Development of an Immune-Related Gene Pairs Signature for Predicting Clinical Outcome in Lung Adenocarcinoma

10.21203/rs.3.rs-43696/v1 ◽

2020 ◽

Author(s):

Chunlei Wu ◽

Quanteng Hu ◽

Dehua Ma

Keyword(s):

Regression Analysis ◽

Lung Adenocarcinoma ◽

Cox Regression ◽

Characteristic Curve ◽

Lasso Regression ◽

Related Gene ◽

Cox Regression Analysis ◽

Gene Pairs ◽

Immune Related Gene ◽

Pathological Subtype

Abstract Background: Lung adenocarcinoma (LUAD) is the main pathological subtype of Non-small cell lung cancer. The aim of this study was to establish an immune-related gene pairs (IRGPs) signature for predicting the prognosis of LUAD patients.Methods: We downloaded the gene expression profile and immune-related gene set from TCGA and ImmPort database, respectively, to establish IRGPs. Then, IRGPs were subjected to univariate Cox regression analysis, LASSO regression analysis and multivariable Cox regression analysis to screen and develop a IRGPs signature. The receiver operating characteristic curve (ROC) was applied for evaluating the predicting accuracy of this signature by calculating the area under ROC (AUC) and data from GEO was used to validate this signature. Results: A IRGPs signature with 8 IRGPs was constructed. The AUC for 1- and 3-year overall survival in TCGA set was 0.867 and 0.870, respectively. Similar result was observed in the AUC of GEO set and Total set (GEO set [1-year: 0.819; 3-years: 0.803]; Total set [1-year: 0.845; 3-years: 0.801]). Survival analysis of three sets demonstrated high-risk LUAD patients exhibited poorer prognosis. The multivariable Cox regression indicated that risk score was independent prognostic factors.Conclusions: We developed a novel IRGPs signature for predicting prognosis of LUAD.

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N6-Methyladenosine-Related RNA Signature Predicting the Prognosis of Ovarian Cancer

Recent Patents on Anti-Cancer Drug Discovery ◽

10.2174/1574892816666210615164645 ◽

2021 ◽

Vol 16 ◽

Author(s):

Jiao Jiao ◽

Longyang Jiang ◽

Yang Luo

Keyword(s):

Ovarian Cancer ◽

Regression Analysis ◽

Cox Regression ◽

Prognostic Indicator ◽

Gene Signature ◽

Genetic Alterations ◽

Lasso Regression ◽

Cox Regression Analysis ◽

Rna Methylation ◽

M6a Rna Methylation

Background: N6-Methyladenosine (m6A) RNA methylation is the most universal mRNA modification in eukaryotic cells. M6A mRNA modification affects almost every phases of RNA processing, including splicing, decay, export, translation and expression. Several patents have reported the application of m6A mRNA modification in cancer diagnosis and treatment. Ovarian cancer is the leading cause of death among all gynecological cancers. It is urgent to identify new biomarkers for early diagnosis and prognosis of ovarian cancer. Objective: In the current study, we aimed to evaluate the m6A RNA methylation regulators and m6A related genes and establish a new gene signature panel for prognosis of ovarian cancer. Method: We downloaded the Mutations data, FPKM data and corresponding clinical information of 373 patients with ovarian cancer (OC) from the TCGA database. We performed LASSO regression analysis and multivariate cox regression analysis to develop a risk-identifying gene signature panel. Results: A total of 317 candidate m6A RNA methylation related genes were obtained. Finally, 12 -genes (WTAP, LGR6, ZC2HC1A, SLC4A8, AP2A1, NRAS, CUX1, HDAC1, CD79A, ACE2, FLG2 and LRFN1) were selected to establish the signature panel. We analyzed the genetic alterations of the selected 12 -genes in OC using cBioPortal database. Among the 373 patients, 368 patients have mutations. The results showed that all queried genes were altered in 137 of 368 cases (37.23%). The 12-gene signature panel was confirmed as an independent prognostic indicator (P =2.29E-18, HR = 1.699, 95% CI = 1.508-1.913). Conclusion: We established an effective m6A-related gene signature panel consisted of 12 -genes, which can predict the outcome of patients with OC. The high risk score indicates unfavorable survival. Our study provided novel insights into the relationship between m6A and OC. This gene signature panel will be helpful in identifying poor prognostic patients with OC and could be a promising prognostic indicator in clinical practice.

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A Five-Gene Signature for Recurrence Prediction of Hepatocellular Carcinoma Patients

BioMed Research International ◽

10.1155/2020/4037639 ◽

2020 ◽

Vol 2020 ◽

pp. 1-13

Author(s):

Zeyu Wang ◽

Ningning Zhang ◽

Jiayu Lv ◽

Cuihua Ma ◽

Jie Gu ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Regression Analysis ◽

Cox Regression ◽

Early Stage ◽

Gene Signature ◽

Functional Enrichment ◽

High Recurrence Rate ◽

Lasso Regression ◽

Cox Regression Analysis ◽

Recurrence Prediction

Background. Hepatocellular carcinoma (HCC) is one of the most aggressive malignancies with poor prognosis. There are many selectable treatments with good prognosis in Barcelona Clinic Liver Cancer- (BCLC-) 0, A, and B HCC patients, but the most crucial factor affecting survival is the high recurrence rate after treatments. Therefore, it is of great significance to predict the recurrence of BCLC-0, BCLC-A, and BCLC-B HCC patients. Aim. To develop a gene signature to enhance the prediction of recurrence among HCC patients. Materials and Methods. The RNA expression data and clinical data of HCC patients were obtained from the Gene Expression Omnibus (GEO) database. Univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were conducted to screen primarily prognostic biomarkers in GSE14520. Multivariate Cox regression analysis was introduced to verify the prognostic role of these genes. Ultimately, 5 genes were demonstrated to be related with the recurrence of HCC patients and a gene signature was established. GSE76427 was adopted to further verify the accuracy of gene signature. Subsequently, a nomogram based on gene signature was performed to predict recurrence. Gene functional enrichment analysis was conducted to investigate the potential biological processes and pathways. Results. We identified a five-gene signature which performs a powerful predictive ability in HCC patients. In the training set of GSE14520, area under the curve (AUC) for the five-gene predictive signature of 1, 2, and 3 years were 0.813, 0.786, and 0.766. Then, the relative operating characteristic (ROC) curves of five-gene predictive signature were verified in the GSE14520 validation set, the whole GSE14520, and GSE76427, showed good performance. A nomogram comprising the five-gene signature was built so as to show a good accuracy for predicting recurrence-free survival of HCC patients. Conclusion. The novel five-gene signature showed potential feasibility of recurrence prediction for early-stage HCC.

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Identification of the Signature Associated With m6A RNA Methylation Regulators and m6A-Related Genes and Construction of the Risk Score for Prognostication in Early-Stage Lung Adenocarcinoma

Frontiers in Genetics ◽

10.3389/fgene.2021.656114 ◽

2021 ◽

Vol 12 ◽

Author(s):

Bingzhou Guo ◽

Hongliang Zhang ◽

Jinliang Wang ◽

Rilige Wu ◽

Junyan Zhang ◽

...

Keyword(s):

Regression Analysis ◽

Lung Adenocarcinoma ◽

Risk Score ◽

Cox Regression ◽

Test Group ◽

Gene Signature ◽

Cox Regression Analysis ◽

Rna Methylation ◽

Chi Square Analysis ◽

Random Survival Forest

BackgroundN6-methyladenosine (m6A) RNA modification is vital for cancers because methylation can alter gene expression and even affect some functional modification. Our study aimed to analyze m6A RNA methylation regulators and m6A-related genes to understand the prognosis of early lung adenocarcinoma.MethodsThe relevant datasets were utilized to analyze 21 m6A RNA methylation regulators and 5,486 m6A-related genes in m6Avar. Univariate Cox regression analysis, random survival forest analysis, Kaplan–Meier analysis, Chi-square analysis, and multivariate cox analysis were carried out on the datasets, and a risk prognostic model based on three feature genes was constructed.ResultsRespectively, we treated GSE31210 (n = 226) as the training set, GSE50081 (n = 128) and TCGA data (n = 400) as the test set. By performing univariable cox regression analysis and random survival forest algorithm in the training group, 218 genes were significant and three prognosis-related genes (ZCRB1, ADH1C, and YTHDC2) were screened out, which could divide LUAD patients into low and high-risk group (P < 0.0001). The predictive efficacy of the model was confirmed in the test group GSE50081 (P = 0.0018) and the TCGA datasets (P = 0.014). Multivariable cox manifested that the three-gene signature was an independent risk factor in LUAD. Furthermore, genes in the signature were also externally validated using the online database. Moreover, YTHDC2 was the important gene in the risk score model and played a vital role in readers of m6A methylation.ConclusionThe findings of this study suggested that associated with m6A RNA methylation regulators and m6A-related genes, the three-gene signature was a reliable prognostic indicator for LUAD patients, indicating a clinical application prospect to serve as a potential therapeutic target.

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Prognosis Implication of a Novel Metabolism-Related Gene Signature in Ewing Sarcoma

Journal of Oncology ◽

10.1155/2021/3578949 ◽

2021 ◽

Vol 2021 ◽

pp. 1-14

Author(s):

Zhuo-Yuan Chen ◽

Huiqin Yang ◽

Jie Bu ◽

Qiong Chen ◽

Zhen Yang ◽

...

Keyword(s):

Regression Analysis ◽

Ewing Sarcoma ◽

Cox Regression ◽

Roc Curves ◽

Gene Signature ◽

Gene Expression Omnibus ◽

Prognostic Indicators ◽

Immune Checkpoints ◽

Lasso Regression ◽

Cox Regression Analysis

Ewing sarcoma (ES) is one of the most common bone cancers in adolescents and children. Growing evidence supports the view that metabolism pathways play critical roles in numerous cancers (He et al. (2020)). However, the correlation between metabolism-associated genes (MTGs) and Ewing sarcoma has not been investigated systematically. Here, based on the univariate Cox regression analysis, we get survival genes from differentially expressed genes (DEGs) from Gene Expression Omnibus (GEO) cohort. Multivariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were employed to establish the MTG signature. Comprehensive survival analyses including receiver operating characteristic (ROC) curves and Kaplan–Meier analysis were applied to estimate the independent prognostic value of the signature. The ICGC cohort served as the validation cohort. A nomogram was constructed based on the risk score of the MTG signature and other independent clinical variables. The CIBERSORT algorithm was applied to estimate immune infiltration. In addition, we explored the correlation between MTG signature and immune checkpoints. Collectively, this work presents a novel MTG signature for prognostic prediction of Ewing sarcoma. It also suggests six genes that are potential prognostic indicators and therapeutic targets for ES.

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