Establishment of a 5 DNA Methylation Site Prognostic Signature Associated with N6-Methyladenosine in Lung Adenocarcinoma

Abstract Background: There is a high incidence of lung adenocarcinoma (LUAD). Even with surgery, targeted therapy and immunotherapy, the survival rate of LUAD patients is still low. N6-methyladenosine (m6A) and DNA methylation markers can help with the diagnosis and treatment of LUAD patients. Therefore, it is necessary to identify a novel m6A-related DNA methylation sites signature to predict the survival of patients with LUAD. Methods: In this study, we screened 15 m6A-related genes and their 217 methylation sites. RNA sequencing data of 15 genes and the clinicopathological parameters of TCGA-LUAD were obtained from the TCGA database (http://cancergenome.nih.gov/). The LUAD-DNA CpG site information was obtained from the Illumina Human Methylation 450 BeadChip (Illumina, San Diego, CA, United States). The methylation sites related to prognosis were screened using univariate COX analysis, and the independent predictors of LUAD patients were identified using multivariate COX analysis of least absolute shrinkage and selection operator (LASSO) Cox regression analysis. Finally, a model with 5 methylation sites as the main body to predict the prognosis of OS in patients with LUAD was obtained. According to the risk grouping of the prediction model, Kaplan-Meier curve and the receiver operating characteristic (ROC) curve were performed in the test and training sets to assess the predicted capacity of the model. In addition, a nomogram constructed by combining the risk score of methylation group and other related clinicopathological factors to verify the reliability of our model.Results: We constructed a m6A-related 5-DNA methylation site model to predict OS in LUAD patients. According to the results of the Kaplan-Meier curve, both the test set and the training set, the high-risk group showed a worse prognosis. The AUCs of the 5 DNA methylation signature at 1, 5 and 10 years in test datasets were 0.730, 0.649 and 0.726, respectively, and 0.679, 0.656 and 0.732 in training datasets. Finally, we constructed a nomogram to further verify the reliability of the model.Conclusion: In this study, we analyzed the methylation sites of m6A-related genes and established a m6A-related 5-DNA methylation site model to predict OS in LUAD patients.

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Methylation and transcriptome analysis reveal lung adenocarcinoma-specific diagnostic biomarkers

Journal of Translational Medicine ◽

10.1186/s12967-019-2068-z ◽

2019 ◽

Vol 17 (1) ◽

Cited By ~ 7

Author(s):

Rui Li ◽

Yi-E Yang ◽

Yun-Hong Yin ◽

Meng-Yu Zhang ◽

Hao Li ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Lung Adenocarcinoma ◽

Cox Regression ◽

R Package ◽

Functional Enrichment ◽

Independent Effect ◽

Cox Regression Analysis ◽

Kaplan Meier ◽

Differentially Methylated Genes

Abstract Background DNA methylation can regulate the role of long noncoding RNAs (lncRNAs) in the development of lung adenocarcinoma (LUAD). The present study aimed to identify methylation-driven lncRNAs and mRNAs as biomarkers in the prognosis of LUAD using bioinformatics analysis. Methods Differentially expressed RNAs were obtained using the edge R package from 535 LUAD tissues and 59 adjacent non-LUAD tissues. Differentially methylated genes were obtained using the limma R package from 475 LUAD tissues and 32 adjacent non-LUAD tissues. Methylation-driven mRNA and lncRNA were obtained using the MethylMix R package from 465 LUAD tissues with matched DNA methylation and RNA expression and 32 non-LUAD tissues with DNA methylation. Gene ontology and ConsensusPathDB pathway analysis were performed to identify functional enrichment of methylation-driven mRNAs. Univariate and multivariate Cox regression analyses were performed to identify the independent effect of each variable for predicting the prognosis of LUAD. Kaplan–Meier curve analysis of DNA methylation and gene expression might provide potential prognostic biomarkers for LUAD patients. Results A total of 99 methylation-driven mRNAs and 17 methylation-driven lncRNAs were obtained. Univariate and multivariate Cox regression analysis showed that 6 lncRNAs (FOXE1, HOXB13-AS1_2, VMO1, HIST1H3F, AJ003147.8, ASXL3) were retrieved to construct a predictive model associated with overall survival in LUAD patients. Combined DNA methylation and gene expression survival analysis revealed that 4 lncRNAs (AC023824.1, AF186192.1, LINC01354 and WASIR2) and 8 mRNAs (S1PR1, CCDC181, F2RL1, EFS, KLHDC9, MPV17L, GKN2, ITPRIPL1) might act as independent biomarkers for the prognosis of LUAD. Conclusions Methylation-driven lncRNA and mRNA contribute to the survival of LUAD, and 4 lncRNAs and 8 mRNAs might be potential biomarkers for the prognosis of LUAD.

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Development of a novel prognostic signature for predicting the overall survival of bladder cancer patients

Bioscience Reports ◽

10.1042/bsr20194432 ◽

2020 ◽

Vol 40 (6) ◽

Author(s):

Huamei Tang ◽

Lijuan Kan ◽

Tong Ou ◽

Dayang Chen ◽

Xiaowen Dou ◽

...

Keyword(s):

Dna Methylation ◽

Overall Survival ◽

Bladder Cancer ◽

Cancer Patients ◽

Cox Regression ◽

Test Group ◽

Training Group ◽

The Cancer Genome Atlas ◽

Methylation Site ◽

Cox Regression Analysis

Abstract Background: Bladder cancer is one of the most common malignancies. So far, no effective biomarker for bladder cancer prognosis has been identified. Aberrant DNA methylation is frequently observed in the bladder cancer and holds considerable promise as a biomarker for predicting the overall survival (OS) of patients. Materials and methods: We downloaded the DNA methylation and transcriptome data for bladder cancer from The Cancer Genome Atlas (TCGA), a public database, screened hypo-methylated and up-regulated genes, similarly, hyper-methylation with low expression genes, then retrieved the relevant methylation sites. Cox regression analysis was used to identify a nine-methylation site signature of a training group. Predictive ability was validated in a test group by receiver operating characteristic (ROC) analysis. Results: We identified nine bladder cancer-specific methylation sites as potential prognostic biomarkers and established a risk score system based on the methylation site signature to evaluate the OS. The performance of the signature was accurate, with area under curve was 0.73 in the training group and 0.71 in the test group. Taking clinical features into consideration, we constructed a nomogram consisting of the nine-methylation site signature and patients’ clinical variables, and found that the signature was an independent risk factor. Conclusions: Overall, the significant nine methylation sites could be novel prediction biomarkers, which could aid in treatment and also predict the overall survival likelihoods of bladder cancer patients.

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NDRG2 combined with EGFR improved its prognostic value for lung adenocarcinoma

10.21203/rs.2.14181/v1 ◽

2019 ◽

Author(s):

Bo Yang ◽

Xiao-Ping Li ◽

Hong-Gang Zhou ◽

Tao Jiang ◽

Ting Xiao ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Cox Regression ◽

Growth Factor Receptor ◽

Prognostic Indicators ◽

Clinicopathological Parameters ◽

Clinical Value ◽

Cox Regression Analysis ◽

Egfr Expression ◽

Serum Carcinoembryonic Antigen ◽

Prediction Of Prognosis

Abstract Background N-Myc downstream-regulated gene2 (NDRG2) plays an important role in lung adenocarcinoma (LUAD). Epidermal growth factor receptor (EGFR) mutation has significantly improved prognosis in patients with adenocarcinoma. We aimed to elucidate the clinical value of NDRG2/EGFR as a prediction of prognosis in patients with lung adenocarcinoma.Materials and Methods Immunohistochemistry and western blot analysis were conducted to detect the expression of NDRG2 protein. Association between NDRG2/EGFR expression and clinicopathological parameters of the patients were examined. Serum Carcinoembryonic antigen (CEA) level was examined prior to treatment in patients with LUAD. Patients’ survival rate was assessed by Kaplan–Meier. Candidates for independent prognostic biomarkers were analyzed using a COX proportional hazard model.Results NDRG2 levels were significantly decreased in patients with lung adenocarcinoma. NDRG2 levels were positively correlated with CEA and EGFR. Advanced stages were significantly associated with low expression of NDRG2. Patients with NDRG2-high combined with EGFR-positive expression had the best prognosis during the 5-year follow-up period. Meanwhile, COX regression analysis showed that the conjoined expressions of NDRG2-low/EGFR-positive, NDRG2-high/EGFR-positive and vascular invasion were independent prognostic indicators for lung adenocarcinoma.Conclusion NDRG2 is of more prognosis value as the biomarker for lung adenocarcinoma when analyzed combined with the EGFR expression.

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Clinicopathological and Prognostic Characteristics of CD276 (B7-H3) Expression in Adrenocortical Carcinoma

Disease Markers ◽

10.1155/2020/5354825 ◽

2020 ◽

Vol 2020 ◽

pp. 1-10

Author(s):

Jiayu Liang ◽

Zhihong Liu ◽

Tianjiao Pei ◽

Yingming Xiao ◽

Liang Zhou ◽

...

Keyword(s):

Adrenocortical Carcinoma ◽

Cox Regression ◽

Therapeutic Option ◽

Immunohistochemical Analysis ◽

Endocrine Tumor ◽

The Cancer Genome Atlas ◽

Clinicopathological Parameters ◽

Cox Regression Analysis ◽

Regression Methods ◽

Kaplan Meier

Background. Adrenocortical carcinoma (ACC) is a rare malignant endocrine tumor with a high tumor recurrence rate and poor postoperative survival. Recent studies suggest that CD276- (B7-H3) targeted therapy represents a promising therapeutic option for solid tumors. However, little is known about the expression status of CD276 or its association with progression and prognosis of ACC. Methods. Clinical data were retrospectively analyzed from patients who underwent resection of ACC at our institution (n=48). Archived, formalin-fixed, and paraffin-embedded samples were collected for immunohistochemical analysis, and the correlation between CD276 expression and clinicopathological parameters was evaluated. Kaplan–Meier and univariate/multivariate Cox regression methods were implemented to identify any prognostic effects. Data from The Cancer Genome Atlas (TCGA) ACC cohort (n=77) were retrieved for quantitative validation analysis. Results. Positive expression of CD276 was detected on the cell membrane and in the cytoplasm of cancer cells or tumor-associated vascular cells in 91.67% (44/48) of ACCs. Vascular expression of CD276 was associated with local aggression (higher T stage, P=0.029) and advanced ENSAT stage (P=0.02). Specifically, patients with a higher CD276-positive cancer cell density exhibited significantly worse overall survival and recurrence-free survival in our cohort (HR=2.8, P=0.01, and HR=7.52, P<0.001, respectively) and in the validation cohort (HR=2.4, P=0.033, and HR=3.7, P<0.001, respectively). The prognostic association remained significant in multivariate Cox regression analysis. Further analysis indicated that CD276 participates in regulating the immune response as well as in the malignant biological behaviors of ACC. Conclusion. These findings highlight the immune checkpoint factor CD276 as an independent prognostic factor and a potential therapeutic target in ACC.

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Lepidic component identifies a subgroup of lung adenocarcinoma with a distinctive prognosis: a multicenter propensity-matched analysis

Therapeutic Advances in Medical Oncology ◽

10.1177/1758835920982845 ◽

2020 ◽

Vol 12 ◽

pp. 175883592098284

Author(s):

Erjia Zhu ◽

Chenyang Dai ◽

Huikang Xie ◽

Hang Su ◽

Xuefei Hu ◽

...

Keyword(s):

Multivariate Analysis ◽

Lung Adenocarcinoma ◽

Cox Regression ◽

Survival Rates ◽

Prognostic Impact ◽

Data Set ◽

Cox Regression Analysis ◽

T Stage ◽

Kaplan Meier ◽

T Classification

Background: Our aim was to investigate the prognostic impact of the lepidic component on T stage in patients with lung adenocarcinoma (LUAD). Methods: A retrospective data set including 863 cases of LUAD with lepidic component and 856 cases without lepidic component was used to identify matched lepidic-positive and lepidic-negative cohorts ( n = 376 patients per group) using a propensity-score matching. Primary outcome variables included recurrence-free survival (RFS) and overall survival (OS). Prognostic factors were assessed by Cox regression analysis and Kaplan–Meier estimates. Results: Multivariate analysis revealed that lepidic component presence was an independent prognostic factor for prolonged RFS ( p < 0.001) and OS ( p < 0.001). Furthermore, lepidic ratio (LR) >25% or ⩽25% were confirmed to be independent prolonged survival predictors. No survival differences were observed between patients with LUAD with LR >25% or ⩽25% (RFS p = 0.333; OS p = 0.078). The 5-year OS rates of patients with LUAD with a lepidic component were 90% regardless of the T stage, and these survival rates were significantly better than those of patients with LUAD without a lepidic component in the corresponding T stage. Multivariate analysis confirmed that T stage was associated with survival only in patients with LUAD without a lepidic component. Conclusions: Lepidic component presence identifies a LUAD subgroup with an excellent prognosis independent of the LR, pathological T classification. Considering the lepidic component presence may improve prognostic predictions for patients with LUAD.

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A methylation-based nomogram for predicting survival in patients with lung adenocarcinoma

BMC Cancer ◽

10.1186/s12885-021-08539-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xuelong Wang ◽

Bin Zhou ◽

Yuxin Xia ◽

Jianxin Zuo ◽

Yanchao Liu ◽

...

Keyword(s):

Risk Factors ◽

Dna Methylation ◽

Overall Survival ◽

Regression Analysis ◽

Lung Adenocarcinoma ◽

Risk Score ◽

Cox Regression ◽

Risk Group ◽

Clinical Risk Factors ◽

Cox Regression Analysis

Abstract Background DNA methylation alteration is frequently observed in Lung adenocarcinoma (LUAD) and may play important roles in carcinogenesis, diagnosis, and prognosis. Thus, this study aimed to construct a reliable methylation-based nomogram, guiding prognostic classification screening and personalized medicine for LUAD patients. Method The DNA methylation data, gene expression data and corresponding clinical information of lung adenocarcinoma samples were extracted from The Cancer Genome Atlas (TCGA) database. Differentially methylated sites (DMSs) and differentially expressed genes (DEGs) were obtained and then calculated correlation by pearson correlation coefficient. Functional enrichment analysis and Protein-protein interaction network were used to explore the biological roles of aberrant methylation genes. A prognostic risk score model was constructed using univariate Cox and LASSO analysis and was assessed in an independent cohort. A methylation-based nomogram that included the risk score and the clinical risk factors was developed, which was evaluated by concordance index and calibration curves. Result We identified a total of 1362 DMSs corresponding to 471 DEGs with significant negative correlation, including 752 hypermethylation sites and 610 hypomethylation sites. Univariate cox regression analysis showed that 59 DMSs were significantly associated with overall survival. Using LASSO method, we constructed a three-DMSs signature that was independent predictive of prognosis in the training cohort. Patients in high-risk group had a significant shorter overall survival than patients in low-risk group classified by three-DMSs signature (log-rank p = 1.9E-04). Multivariate cox regression analysis proved that the three-DMSs signature was an independent prognostic factor for LUAD in TCGA-LUAD cohort (HR = 2.29, 95%CI: 1.47–3.57, P = 2.36E-04) and GSE56044 cohort (HR = 2.16, 95%CI: 1.19–3.91, P = 0.011). Furthermore, a nomogram, combining the risk score with clinical risk factors, was developed with C-indexes of 0.71 and 0.70 in TCGA-LUAD and GSE56044 respectively. Conclusions The present study established a robust three-DMSs signature for the prediction of overall survival and further developed a nomogram that could be a clinically available guide for personalized treatment of LUAD patients.

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Expression Status and Prognostic Value of m6A RNA Methylation Regulators in Lung Adenocarcinoma

Life ◽

10.3390/life11070619 ◽

2021 ◽

Vol 11 (7) ◽

pp. 619

Author(s):

Xiuhong Li ◽

Zian Feng ◽

Rui Wang ◽

Jie Hu ◽

Xiaodong He ◽

...

Keyword(s):

Regression Analysis ◽

Survival Analysis ◽

Lung Adenocarcinoma ◽

Roc Curve ◽

Cox Regression ◽

Cox Regression Analysis ◽

Rna Methylation ◽

Kaplan Meier ◽

M6a Rna Methylation ◽

Prediction Efficiency

N6-methyladenosine (m6A) RNA modification is the most abundant modification method in mRNA, and it plays an important role in the occurrence and development of many cancers. This paper mainly discusses the role of m6A RNA methylation regulators in lung adenocarcinoma (LUAD) to identify novel prognostic biomarkers. The gene expression data of 19 m6A methylation regulators in LUAD patients and its relevant clinical parameters were extracted from The Cancer Genome Atlas (TCGA) database. We selected three significantly differentially expressed m6A regulators in LUAD to construct the risk signature, and evaluated its prognostic prediction efficiency using the receiver operating characteristic (ROC) curve. Kaplan–Meier survival analysis and Cox regression analysis were used to identify the independent prognostic significance of the risk signature. The ROC curve indicated that the area under the curve (AUC) was 0.659, which means that the risk signature had a good prediction efficiency. The results of the Kaplan–Meier survival analysis and Cox regression analysis showed that the risk score can be used as an independent prognostic factor for LUAD. In addition, we explored the differential signaling pathways and cellular processes related to m6A methylation regulators in LUAD.

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N6-Methyladenosine-Regulated mRNAs: Potential Prognostic Biomarkers for Patients With Lung Adenocarcinoma

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.705962 ◽

2021 ◽

Vol 9 ◽

Author(s):

Junjun Sun ◽

Yili Ping ◽

Jingjuan Huang ◽

Bingjie Zeng ◽

Ping Ji ◽

...

Keyword(s):

Lung Adenocarcinoma ◽

Mrna Expression ◽

Cox Regression ◽

Interaction Network ◽

Prognostic Biomarkers ◽

Cox Regression Analysis ◽

Receiver Operating Characteristic Curves ◽

Network Analyses ◽

Kaplan Meier ◽

Selection Operator

Aberrant regulation of m6A mRNA modification can lead to changes in gene expression, thus contributing to tumorigenesis in several types of solid tumors. In this study, by integrating analyses of m6A methylation and mRNA expression, we identified 84 m6A-regulated mRNAs in lung adenocarcinoma (LUAD). Although the m6A methylation levels of total RNA in LUAD patient tumor tissue were reduced, the majority (75.2%) of m6A-regulated mRNAs were hypermethylated. The m6A-hypermethylated mRNAs were mainly enriched in terms related to transcription factor activity. We established a 10-m6A-regulated-mRNA signature score system through least absolute shrinkage and selection operator Cox regression analysis, with its predictive value validated by Kaplan–Meier curve and time-dependent receiver operating characteristic curves. RFXAP and KHDRBS2 from the signature also exhibited an independent prognostic value. The co-expression and interaction network analyses demonstrated the strong correlation between m6A regulators and the genes in the signature, further supporting the results of the m6A methylation modification patterns. These findings highlight the potential utility of integrating multi-omics data (m6A methylation level and mRNA expression) to accurately obtain potential prognostic biomarkers, which may provide important insights into developing novel and effective therapies for LUAD.

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IL-11RA is a Prognostic Biomarker and Correlated with Immune Infiltration in Lung Adenocarcinoma

10.21203/rs.3.rs-673757/v1 ◽

2021 ◽

Author(s):

Aitao Nai ◽

SHOAIB BASHIR ◽

Ling Jin ◽

Zirui He ◽

Shuwen Zeng ◽

...

Keyword(s):

Overall Survival ◽

Lung Adenocarcinoma ◽

Cox Regression ◽

Progression Free Survival ◽

Clinicopathological Parameters ◽

Free Survival ◽

Cox Regression Analysis ◽

Immune Infiltration ◽

Potential Biomarker

Abstract Background: Interleukin-11 receptor subunit alpha (IL-11RA) contributes to multiple biological processes in various tumors. However, the role of IL-11RA in Lung adenocarcinoma (LUAD) is still undetermined. The study aims to explore the role of IL-11RA in LUAD via an integrated bioinformatics analysis. Methods: TIMER, GEPIA, TCGA and HPA databases analysis were used to detect IL-11RA expression. UALCAN database was used to analysis the correlation between IL-11RA expression and clinicopathological parameters of LUAD. Kaplan-Meier Plotter, TCGA and GEO databases were used to analysis overall survival (OS) and progression-free survival (PFS) of the LUAD patients. Univariate Cox regression analysis was used to assess the prognostic value of IL-11RA in different clinical characteristics. GSEA, and TIMER were used to investigate the relationship between IL-11RA and immune infiltration.Results: The expression of IL-11RA was down-regulated in LUAD tissues. Furthermore, IL-11RA expression was closely associated with clinical stage, lymph node stage and smoking habits. The patients with lower IL-11RA expression had poorer overall survival (OS) and progression-free survival (PFS). Lower IL-11RA expression was significantly associated with its hypermethylation, and the hypermethylation of CpG site at cg14609668 and cg21504624 was obviously correlated with poorer OS. Then, we found that IL-11RA may play an important role in LUAD progression and immune regulations. Notably, High expression of IL-11RA may suppress the progression of LUAD through inhibiting cell proliferation and immune cell infiltration, especially in B cells, CD4+ T cells, and Dendritic Cell. Conclusions: Decreased IL-11RA expression correlates with poor prognosis and immune infiltration in LUAD. Our work highlights IL-11RA might be a potential biomarker for prognosis and provide a new therapeutic target for LUAD patients.

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A Methylation-based nomogram for predicting survival in patients with lung adenocarcinoma

10.21203/rs.3.rs-75403/v1 ◽

2020 ◽

Author(s):

Xuelong Wang ◽

Bin Zhou ◽

Yuxin Xia ◽

Jianxin Zuo ◽

Yanchao Liu ◽

...

Keyword(s):

Risk Factors ◽

Dna Methylation ◽

Overall Survival ◽

Regression Analysis ◽

Lung Adenocarcinoma ◽

Risk Score ◽

Cox Regression ◽

Risk Group ◽

Clinical Risk Factors ◽

Cox Regression Analysis

Abstract Background DNA methylation alteration is frequently observed in Lung adenocarcinoma (LUAD) and may play important roles in carcinogenesis, diagnosis, and prognosis. Thus, this study aimed to construct a reliable methylation-based nomogram, guiding prognostic classification screening and personalized medicine for LUAD patients. Method: The DNA methylation data, gene expression data and corresponding clinical information of lung adenocarcinoma samples were extracted from The Cancer Genome Atlas (TCGA) database. Differentially methylated sites (DMSs) and differentially expressed genes (DEGs) were obtained and then calculated expression correlation by pearson correlation coefficient. Functional enrichment analysis and Protein-protein interaction network were used to explore the biological roles of aberrant methylation genes. A prognostic risk score model was constructed using univariate Cox and LASSO analysis and was assessed in an independent cohort. A methylation-based nomogram that included the risk score and the clinical risk factors was developed, which was evaluated by concordance index and calibration curves. Result We identified a total of 1362 DMSs corresponding to 471 DEGs with significant negative correlation, including 752 hypermethylation sites and 610 hypomethylation sites. Univariate cox regression analysis showed that 59 DMSs were significantly associated with overall survival. Using LASSO method, we constructed a three-DMSs signature that was independent predictive of prognosis in the training cohort. Patients in high-risk group had a significant shorter overall survival than patients in low-risk group classified by three-DMSs signature (log-rank p = 1.9E-04). Multivariate cox regression analysis proved that the three-DMSs signature was an independent prognostic factor for LUAD in TCGA-LUAD cohort (HR = 2.29, 95%CI: 1.47–3.57, P = 2.36E-04) and GSE56044 cohort (HR = 2.16, 95%CI: 1.19–3.91, P = 0.011). Furthermore, a nomogram, combining the risk score with clinical risk factors, was developed with C-indexes of 0.71 and 0.70 in TCGA-LUAD and GSE56044 respectively. Conclusions The present study established a robust three-DMSs signature for the prediction of overall survival and further developed a nomogram that could be a clinically available guide for personalized treatment of LUAD patients.

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