scholarly journals An N6-methyladenosine and target genes-based study on subtypes and prognosis of lung adenocarcinoma

2021 ◽  
Vol 19 (1) ◽  
pp. 253-270
Author(s):  
Xiao Chu ◽  
◽  
Weiqing Wang ◽  
Zhaoyun Sun ◽  
Feichao Bao ◽  
...  

<abstract> <p><italic>Purpose:</italic> Lung adenocarcinoma (LUAD) is a highly lethal subtype of primary lung cancer with a poor prognosis. N6-methyladenosine (m<sup>6</sup>A), the most predominant form of RNA modification, regulates biological processes and has critical prognostic implications for LUAD. Our study aimed to mine potential target genes of m<sup>6</sup>A regulators to explore their biological significance in subtyping LUAD and predicting survival. <italic>Methods:</italic> Using gene expression data from TCGA database, candidate target genes of m<sup>6</sup>A were predicted from differentially expressed genes (DEGs) in tumor based on M<sup>6</sup>A2 Target database. The survival-related target DEGs identified by Cox-regression analysis was used for consensus clustering analysis to subtype LUAD. Uni-and multi-variable Cox regression analysis and LASSO Cox-PH regression analysis were used to select the optimal prognostic genes for constructing prognostic score (PS) model. Nomogram encompassing PS score and independent prognostic factors was built to predict 3-year and 5-year survival probability. <italic>Results:</italic> We obtained 2429 DEGs in tumor tissue, within which, 1267 were predicted to m<sup>6</sup>A target genes. A prognostic m<sup>6</sup>A-DEGs network of 224 survival-related target DEGs was established. We classified LUAD into 2 subtypes, which were significantly different in OS time, clinicopathological characteristics, and fractions of 12 immune cell types. A PS model of five genes (C1QTNF6, THSD1, GRIK2, E2F7 and SLCO1B3) successfully split the training set or an independent GEO dataset into two subgroups with significantly different OS time (p &lt; 0.001, AUC = 0.723; p = 0.017, AUC = 0.705).A nomogram model combining PS status, pathologic stage, and recurrence was built, showing good performance in predicting 3-year and 5-year survival probability (C-index = 0.708, 0.723, p-value = 0). <italic>Conclusion:</italic> Using candidate m<sup>6</sup>A target genes, we obtained two molecular subtypes and designed a reliable five-gene PS score model for survival prediction in LUAD.</p> </abstract>

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chunlei Wu ◽  
Quanteng Hu ◽  
Dehua Ma

AbstractLung adenocarcinoma (LUAD) is the main pathological subtype of Non-small cell lung cancer. We downloaded the gene expression profile and immune-related gene set from the TCGA and ImmPort database, respectively, to establish immune-related gene pairs (IRGPs). Then, IRGPs were subjected to univariate Cox regression analysis, LASSO regression analysis, and multivariable Cox regression analysis to screen and develop an 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 the GEO set was used to validate this signature. The relationship of 22 tumor-infiltrating immune cells (TIICs) to the immune risk score was also investigated. An IRGPs signature with 8 IRGPs was constructed. The AUC for 1- and 3-year overall survival in the TCGA set was 0.867 and 0.870, respectively. Similar results were observed in the AUCs of GEO set 1, 2 and 3 (GEO set 1 [1-year: 0.819; 3-year: 0.803]; GEO set 2 [1-year: 0.834; 3-year: 0.870]; GEO set 3 [1-year: 0.955; 3-year: 0.827]). Survival analysis demonstrated high-risk LUAD patients exhibited poorer prognosis. The multivariable Cox regression indicated that the risk score was an independent prognostic factor. The immune risk score was highly associated with several TIICs (Plasma cells, memory B cells, resting memory CD4 T cells, and activated NK cells). We developed a novel IRGPs signature for predicting 1- and 3- year overall survival in LUAD, which would be helpful for prognosis assessment of LUAD.


2021 ◽  
Author(s):  
Chenxi Yuan ◽  
Qingwei Wang ◽  
Xueting Dai ◽  
Yipeng Song ◽  
Jinming Yu

Abstract Background: Lung adenocarcinoma (LUAD) and skin cutaneous melanoma (SKCM) are common tumors around the world. However, the prognosis in advanced patients is poor. Because NLRP3 was not extensively studied in cancers, so that we aimed to identify the impact of NLRP3 on LUAD and SKCM through bioinformatics analyses. Methods: TCGA and TIMER database were utilized in this study. We compared the expression of NLRP3 in different cancers and evaluated its influence on survival of LUAD and SKCM patients. The correlations between clinical information and NLRP3 expression were analyzed using logistic regression. Clinicopathologic characteristics associated with overall survival in were analyzed by Cox regression. In addition, we explored the correlation between NLRP3 and immune infiltrates. GSEA and co-expressed gene with NLRP3 were also done in this study. Results: NLRP3 expressed disparately in tumor tissues and normal tissues. Cox regression analysis indicated that up-regulated NLRP3 was an independent prognostic factor for good prognosis in LUAD and SKCM. Logistic regression analysis showed increased NLRP3 expression was significantly correlated with favorable clinicopathologic parameters such as no lymph node invasion and no distant metastasis. Specifically, a positive correlation between increased NLRP3 expression and immune infiltrating level of various immune cells was observed. Conclusion: Together with all these findings, increased NLRP3 expression correlates with favorable prognosis and increased proportion of immune cells in LUAD and SKCM. These conclusions indicate that NLRP3 can serve as a potential biomarker for evaluating prognosis and immune infiltration level.


Author(s):  
Yongmei Wang ◽  
Guimin Zhang ◽  
Ruixian Wang

Background: This study aims to explore the prognostic values of CT83 and CT83-related genes in lung adenocarcinoma (LUAD). Methods: We downloaded the mRNA profiles of 513 LUAD patients (RNA sequencing data) and 246 NSCLC patients (Affymetrix Human Genome U133 Plus 2.0 Array) from TCGA and GEO databases. According to the median expression of CT83, the TCGA samples were divided into high and low expression groups, and differential expression analysis between them was performed. Functional enrichment analysis of differential expression genes (DEGs) was conducted. Univariate Cox regression analysis and LASSO Cox regression analysis were performed to screen the optimal prognostic DEGs. Then we established the prognostic model. A Nomogram model was constructed to predict the overall survival (OS) probability of LUAD patients. Results: CT83 expression was significantly correlated to the prognosis of LUAD patients. A total of 59 DEGs were identified, and a predictive model was constructed based on six optimal CT83-related DEGs, including CPS1, RHOV, TNNT1, FAM83A, IGF2BP1, and GRIN2A, could effectively predict the prognosis of LUAD patients. The nomogram could reliably predict the OS of LUAD patients. Moreover, the six important immune checkpoints (CTLA4, PD1, IDO1, TDO2, LAG3, and TIGIT) were closely correlated with the Risk Score, which was also differentially expressed between the LUAD samples with high and low-Risk Scores, suggesting that the poor prognosis of LUAD patients with high-Risk Score might be due to the immunosuppressive microenvironments. Conclusion: A prognostic model based on six optimal CT83 related genes could effectively predict the prognosis of LUAD patients.


2021 ◽  
Vol 12 ◽  
Author(s):  
Guomin Wu ◽  
Qihao Wang ◽  
Ting Zhu ◽  
Linhai Fu ◽  
Zhupeng Li ◽  
...  

This study aimed to establish a prognostic risk model for lung adenocarcinoma (LUAD). We firstly divided 535 LUAD samples in TCGA-LUAD into high-, medium-, and low-immune infiltration groups by consensus clustering analysis according to immunological competence assessment by single-sample gene set enrichment analysis (ssGSEA). Profile of long non-coding RNAs (lncRNAs) in normal samples and LUAD samples in TCGA was used for a differential expression analysis in the high- and low-immune infiltration groups. A total of 1,570 immune-related differential lncRNAs in LUAD were obtained by intersecting the above results. Afterward, univariate COX regression analysis and multivariate stepwise COX regression analysis were conducted to screen prognosis-related lncRNAs, and an eight-immune-related-lncRNA prognostic signature was finally acquired (AL365181.2, AC012213.4, DRAIC, MRGPRG-AS1, AP002478.1, AC092168.2, FAM30A, and LINC02412). Kaplan–Meier analysis and ROC analysis indicated that the eight-lncRNA-based model was accurate to predict the prognosis of LUAD patients. Simultaneously, univariate COX regression analysis and multivariate COX regression analysis were undertaken on clinical features and risk scores. It was illustrated that the risk score was a prognostic factor independent from clinical features. Moreover, immune data of LUAD in the TIMER database were analyzed. The eight-immune-related-lncRNA prognostic signature was related to the infiltration of B cells, CD4+ T cells, and dendritic cells. GSEA enrichment analysis revealed significant differences in high- and low-risk groups in pathways like pentose phosphate pathway, ubiquitin mediated proteolysis, and P53 signaling pathway. This study helps to treat LUAD patients and explore molecules related to LUAD immune infiltration to deeply understand the specific mechanism.


2021 ◽  
Vol 11 ◽  
Author(s):  
Peng Liu ◽  
Jinhong Wei ◽  
Feiyu Mao ◽  
Zechang Xin ◽  
Heng Duan ◽  
...  

Hepatocellular carcinoma (HCC) is one of the most common types of cancer worldwide and its incidence continues to increase year by year. Endoplasmic reticulum stress (ERS) caused by protein misfolding within the secretory pathway in cells and has an extensive and deep impact on cancer cell progression and survival. Growing evidence suggests that the genes related to ERS are closely associated with the occurrence and progression of HCC. This study aimed to identify an ERS-related signature for the prospective evaluation of prognosis in HCC patients. RNA sequencing data and clinical data of patients from HCC patients were obtained from The Cancer Genome Atlas (TCGA) and The International Cancer Genome Consortium (ICGC). Using data from TCGA as a training cohort (n=424) and data from ICGC as an independent external testing cohort (n=243), ERS-related genes were extracted to identify three common pathways IRE1, PEKR, and ATF6 using the GSEA database. Through univariate and multivariate Cox regression analysis, 5 gene signals in the training cohort were found to be related to ERS and closely correlated with the prognosis in patients of HCC. A novel 5-gene signature (including HDGF, EIF2S1, SRPRB, PPP2R5B and DDX11) was created and had power as a prognostic biomarker. The prognosis of patients with high-risk HCC was worse than that of patients with low-risk HCC. Multivariate Cox regression analysis confirmed that the signature was an independent prognostic biomarker for HCC. The results were further validated in an independent external testing cohort (ICGC). Also, GSEA indicated a series of significantly enriched oncological signatures and different metabolic processes that may enable a better understanding of the potential molecular mechanism mediating the progression of HCC. The 5-gene biomarker has a high potential for clinical applications in the risk stratification and overall survival prediction of HCC patients. In addition, the abnormal expression of these genes may be affected by copy number variation, methylation variation, and post-transcriptional regulation. Together, this study indicated that the genes may have potential as prognostic biomarkers in HCC and may provide new evidence supporting targeted therapies in HCC.


2019 ◽  
Author(s):  
Xu-gang Hu ◽  
De-min Jiao ◽  
You-liang Si ◽  
Jun Chen ◽  
Xia-li Tang ◽  
...  

Abstract Background: Tobacco exposure is the most important risk factor for the occurrence and death of lung cancer. Fibrinogen beta chain (FGB), the most abundant coagulation factor in plasma, is putatively involved in tumor progression. This study aimed to evaluate the expression pattern and prognostic value of FGB in lung adenocarcinoma with tobacco exposure. Methods: FGB expression in lung adenocarcinoma (LUAD) and corresponding normal lung tissues was compared in The Cancer Genome Atlas (TCGA) database. Stratified analysis was conducted to investigate the expression of FGB in LUAD patients with different tobacco exposure. Kaplan-Meier analysis and Cox-regression analysis were performed to evaluate the prognostic significance of FGB. The same survival analyses were conducted in the KM plotter database to validate the prognostic value of FGB. Results: FGB expression was significantly increased in LUAD tissues than in normal tissues (P<0.001). The FGB expression in smoker group was higher than those in non-smoker group (P<0.001). High FGB expression was associated with advanced N stage (P=0.033) and TNM stage (P=0.046). The smoker group possessed higher level of FGB both in LUAD patients without (P=0.003) or (P =0.045) with lymph node metastasis. However, in early TNM stages, the smoker group showed elevated expression of FGB compared with non-smoker group (P=0.0004), and in advanced TNM stages, there was no significant difference between the two groups (P=0.350). In survival analyses, patients with high FGB expression had remarkably worse overall survival (P=0.007) and progression-free survival ((P=0.007) than those with low FGB expression. In smoker group, high level of FGB expression predicted worse OS (P=0.003) and PFS (P=0.029). Cox-regression analysis indicated that FGB was an independent prognostic factor for LUAD patients’ OS (HR= 1.616, P=0.017) and PFS (HR= 1.710, P=0.028). In smoking group, FGB also served as a promising prognostic biomarker for OS (HR= 1.806, P=0.027) and PFS (HR= 2.181, P=0.013). Similar survival curves were generated in the KM plotter cohort. Conclusions: Our study demonstrated that elevated expression of FGB may identify an aggressive subgroup in LUAD with tobacco exposure and serve as an independent prognostic indicator in these patients.


2021 ◽  
Vol 11 ◽  
Author(s):  
Lu Lu ◽  
Le-Ping Liu ◽  
Qiang-Qiang Zhao ◽  
Rong Gui ◽  
Qin-Yu Zhao

Lung adenocarcinoma (LUAD) is a highly heterogeneous malignancy, which makes prognosis prediction of LUAD very challenging. Ferroptosis is an iron-dependent cell death mechanism that is important in the survival of tumor cells. Long non-coding RNAs (lncRNAs) are considered to be key regulators of LUAD development and are involved in ferroptosis of tumor cells, and ferroptosis-related lncRNAs have gradually emerged as new targets for LUAD treatment and prognosis. It is essential to determine the prognostic value of ferroptosis-related lncRNAs in LUAD. In this study, we obtained RNA sequencing (RNA-seq) data and corresponding clinical information of LUAD patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database and ferroptosis-related lncRNAs by co-expression analysis. The best predictors associated with LUAD prognosis, including C5orf64, LINC01800, LINC00968, LINC01352, PGM5-AS1, LINC02097, DEPDC1-AS1, WWC2-AS2, SATB2-AS1, LINC00628, LINC01537, LMO7DN, were identified by Least Absolute Shrinkage and Selection Operator (LASSO) Cox regression analysis, and the LUAD risk prediction model was successfully constructed. Kaplan-Meier analysis, receiver operating characteristic (ROC) time curve analysis and univariate and multivariate Cox regression analysis and further demonstrated that the model has excellent robustness and predictive ability. Further, based on the risk prediction model, functional enrichment analysis revealed that 12 prognostic indicators involved a variety of cellular functions and signaling pathways, and the immune status was different in the high-risk and low-risk groups. In conclusion, a risk model of 12 ferroptosis related lncRNAs has important prognostic value for LUAD and may be ferroptosis-related therapeutic targets in the clinic.


2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Yang Li ◽  
Rongrong Sun ◽  
Rui Li ◽  
Yonggang Chen ◽  
He Du

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.


2021 ◽  
Author(s):  
Fei Li ◽  
Dongcen Ge ◽  
Shu-lan Sun

Abstract Background. Ferroptosis is a newly discovered form of cell death characterized by iron-dependent lipid peroxidation. The aim of this study is to investigate the relationship between ferroptosis and the prognosis of lung adenocarcinoma (LUAD).Methods. RNA-seq data was collected from the LUAD dataset of The Cancer Genome Altas (TCGA) database. We used ferroptosis-related genes as the basis, and identify the differential expression genes (DEGs) between cancer and paracancer. The univariate Cox regression analysis were used to screen the prognostic-related genes. We divided the patients into training and validation sets. Then, we screened out key genes and built a 5 genes prognostic prediction model by the applications of the least absolute shrinkage and selection operator (LASSO) 10-fold cross-validation and the multi-variate Cox regression analysis. We divided the cases by the median value of risk score and validated this model in the validation set. Meanwhile, we analyzed the somatic mutations, and estimated the score of immune infiltration in the high- and low-risk groups, as well as performed functional enrichment analysis of DEGs.Results. The result revealed that the high-risk score triggered the worse prognosis. The maximum area under curve (AUC) of the training set and the validation set of in this study was 0.7 and 0.69. Moreover, we integrated the age, gender, and tumor stage to construct the composite nomogram. The charts indicated that the AUC of cases with survival time of 1, 3 and 5 years are 0.698, 0.71 and 0.73. In addition, the mutation frequency of patients in the high-risk group was higher than that in the low-risk group. Simultaneously, DEGs were mainly enriched in ferroptosis-related pathways by analyzing the functional results.Conclusion. This study constructed a novel LUAD prognosis prediction model base on 5 ferroptosis-related genes, which can provide a prognostic evaluation tool for the clinical therapeutic decision.


2020 ◽  
Author(s):  
Chunlei Wu ◽  
Quanteng Hu ◽  
Dehua Ma

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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