1
|
Wei J, Wang X, Guo H, Zhang L, Shi Y, Wang X. Subclassification of lung adenocarcinoma through comprehensive multi-omics data to benefit survival outcomes. Comput Biol Chem 2024; 112:108150. [PMID: 39018587 DOI: 10.1016/j.compbiolchem.2024.108150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
OBJECTIVES Lung adenocarcinoma (LUAD) is the most common subtype of non-small cell lung cancer. Understanding the molecular mechanisms underlying tumor progression is of great clinical significance. This study aims to identify novel molecular markers associated with LUAD subtypes, with the goal of improving the precision of LUAD subtype classification. Additionally, optimization efforts are directed towards enhancing insights from the perspective of patient survival analysis. MATERIALS AND METHODS We propose an innovative feature-selection approach that focuses on LUAD classification, which is comprehensive and robust. The proposed method integrates multi-omics data from The Cancer Genome Atlas (TCGA) and leverages a synergistic combination of max-relevance and min-redundancy, least absolute shrinkage and selection operator, and Boruta algorithms. These selected features were deployed in six machine-learning classifiers: logistic regression, random forest, support vector machine, naive Bayes, k-Nearest Neighbor, and XGBoost. RESULTS The proposed approach achieved an area under the receiver operating characteristic curve (AUC) of 0.9958 for LR. Notably, the accuracy and AUC of a composite model incorporating copy number, methylation, as well as RNA- sequencing data for expression of exons, genes, and miRNA mature strands surpassed the accuracy and AUC metrics of models with single-omics data or other multi-omics combinations. Survival analyses, revealed the SVM classifier to elicit optimal classification, outperforming that achieved by TCGA. To enhance model interpretability, SHapley Additive exPlanations (SHAP) values were utilized to elucidate the impact of each feature on the predictions. Gene Ontology (GO) enrichment analysis identified significant biological processes, molecular functions, and cellular components associated with LUAD subtypes. CONCLUSION In summary, our feature selection process, based on TCGA multi-omics data and combined with multiple machine learning classifiers, proficiently identifies molecular subtypes of lung adenocarcinoma and their corresponding significant genes. Our method could enhance the early detection and diagnosis of LUAD, expedite the development of targeted therapies and, ultimately, lengthen patient survival.
Collapse
Affiliation(s)
| | - Xin Wang
- Qingdao University, Qingdao, China
| | | | - Ling Zhang
- Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Yao Shi
- Qingdao University, Qingdao, China.
| | | |
Collapse
|
2
|
Deng Y, Liu L, Xiao X, Zhao Y. A four-gene-based methylation signature associated with lymph node metastasis predicts overall survival in lung squamous cell carcinoma. Genes Genet Syst 2023; 98:209-219. [PMID: 37839873 DOI: 10.1266/ggs.22-00111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023] Open
Abstract
We aimed to identify prognostic methylation genes associated with lymph node metastasis (LNM) in lung squamous cell carcinoma (LUSC). Bioinformatics methods were used to obtain optimal prognostic genes for risk model construction using data from the Cancer Genome Atlas database. ROC curves were adopted to predict the prognostic value of the risk model. Multivariate regression was carried out to identify independent prognostic factors and construct a prognostic nomogram. The differences in overall survival, gene mutation and pathways between high- and low-risk groups were analyzed. Finally, the expression and methylation level of the optimal prognostic genes among different LNM stages were analyzed. FGA, GPR39, RRAD and TINAGL1 were identified as the optimal prognostic genes and were applied to establish a prognostic risk model. Significant differences were found among the different LNM stages. The risk model could predict overall survival, showing a moderate performance with AUC of 0.64-0.68. The model possessed independent prognostic value, and could accurately predict 1-, 3- and 5-year survival. Patients with a high risk score showed poorer survival. Lower gene mutation frequencies and enrichment of leukocyte transendothelial migration and the VEGF signaling pathway in the high-risk group may lead to the poor prognosis. This study identified several specific methylation markers associated with LNM in LUSC and generated a prognostic model to predict overall survival for LUSC patients.
Collapse
Affiliation(s)
- Yufei Deng
- Department of Pharmacy, Wuxi No.2 People's Hospital
| | - Lifeng Liu
- Department of Pharmacy, Wuxi No.2 People's Hospital
| | - Xia Xiao
- Department of Oncology, Wuxi No.2 People's Hospital
| | - Yin Zhao
- Department of Pharmacy, Wuxi No.2 People's Hospital
| |
Collapse
|
3
|
Xie X, Liang H, Jiangting W, Wang Y, Ma X, Tan Z, Cheng L, Luo Z, Wang T. Cancer-testis antigen CEP55 serves as a prognostic biomarker and is correlated with immune infiltration and immunotherapy efficacy in pan-cancer. Front Mol Biosci 2023; 10:1198557. [PMID: 37484531 PMCID: PMC10360201 DOI: 10.3389/fmolb.2023.1198557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 06/29/2023] [Indexed: 07/25/2023] Open
Abstract
Background: Centrosomal Protein 55 (CEP55) was initially described as a main participant in the final stage of cytokinesis. Further research identified CEP55 as a cancer-testis antigen (CTA) that is aberrantly expressed in different malignancies and a cancer vaccination candidate. The current study aimed to disclose the complete expression of CEP55, its effect on various malignancy prognoses, and its role in the tumor microenvironment. Methods: Transcriptional information regarding tumor and normal tissues, as well as externally validated and protein expression data were gathered from the Cancer Genome Atlas, Genotype-Tissue Expression project, Gene Expression Omnibus, and Human Protein Atlas. We examined the effect of CEP55 on tumor prognosis using Kaplan-Meier (KM) and univariate Cox regression analyses. In addition, we investigated the connections between CEP55 expression and hallmark cancer pathways, immune cell infiltration, and immune regulator expression across malignancies. We constructed and validated a CEP55-related risk model for hepatocellular carcinoma (HCC) and explored the correlations between CEP55 expression and HCC molecular subtypes. Finally, we investigated putative small-molecule drugs targeting CEP55 using a connectivity map (CMap) database and validated them using molecular docking analysis. Findings: CEP55 was aberrantly expressed in most cancers and revealed a prognostic value for several malignancies. Cancers with high CEP55 expression showed significantly enhanced cell cycle, proliferation, and immune-related pathways. For most malignancies, elevated CEP55 expression was associated with the infiltration of myeloid-derived suppressor cells (MDSCs) and Th2 cells. In addition, CEP55 expression was linked to immunomodulators and the potential prediction of immune checkpoint inhibitor (ICI) responses, and strongly associated with distinct molecular HCC subtypes, whereby the CEP55-based nomogram performed well in predicting short- and long-term HCC survival. Finally, we used connectivity map (CMap) and molecular docking analyses to discover three candidate small-molecule drugs that could directly bind to CEP55. Conclusion: CEP55 affected the occurrence and development of various cancers and possibly the regulation of the tumor immune microenvironment. Our findings suggest that CEP55 is a potential biomarker for prognosis and a powerful biomarker for ICI efficacy prediction.
Collapse
Affiliation(s)
- Xiaodong Xie
- Department of General Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
| | - Hongyin Liang
- Department of General Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
| | - Wushuang Jiangting
- Department of Anesthesiology, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
| | - Yu Wang
- Department of Microbiology, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xiao Ma
- Department of General Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
| | - Zhen Tan
- Department of General Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
| | - Long Cheng
- Department of General Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
- College of Medicine, The Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Zhulin Luo
- Department of General Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
- College of Medicine, The Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Tao Wang
- Department of General Surgery, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
- Department of General Surgery and Pancreatic Injury and Repair Key Laboratory of Sichuan Province, The General Hospital of Western Theater Command, Chengdu, Sichuan, China
- College of Medicine, The Southwest Jiaotong University, Chengdu, Sichuan, China
| |
Collapse
|
4
|
Li GS, Zhang W, Huang WY, He RQ, Huang ZG, Gan XY, Yang Z, Dang YW, Kong JL, Zhou HF, Chen G. CEP55: an immune-related predictive and prognostic molecular biomarker for multiple cancers. BMC Pulm Med 2023; 23:166. [PMID: 37173675 PMCID: PMC10182662 DOI: 10.1186/s12890-023-02452-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Centrosomal protein 55 (CEP55) plays a significant role in specific cancers. However, comprehensive research on CEP55 is lacking in pan-cancer. METHODS In-house and multi-center samples (n = 15,823) were used to analyze CEP55 in 33 cancers. The variance of CEP55 expression levels among tumor and control groups was evaluated by the Wilcoxon rank-sum test and standardized mean difference (SMD). The clinical value of CEP55 in cancers was assessed using receiver operating characteristic (ROC) curves, Cox regression analysis, and Kaplan-Meier curves. The correlations between CEP55 expression and the immune microenvironment were explored using Spearman's correlation coefficient. RESULTS The data of clustered regularly interspaced short palindromic repeats confirmed that CEP55 was essential for the survival of cancer cells in multiple cancer types. Elevated CEP55 mRNA expression was observed in 20 cancers, including glioblastoma multiforme (p < 0.05). CEP55 mRNA expression made it feasible to distinguish 21 cancer types between cancer specimens and their control samples (AUC = 0.97), indicating the potential of CEP55 for predicting cancer status. Overexpression of CEP55 was correlated with the prognosis of cancer individuals for 18 cancer types, exhibiting its prognostic value. CEP55 expression was relevant to tumor mutation burden, microsatellite instability, neoantigen counts, and the immune microenvironment in various cancers (p < 0.05). The expression level and clinical relevance of CEP55 in cancers were verified in lung squamous cell carcinoma using in-house and multi-center samples (SMD = 4.07; AUC > 0.95; p < 0.05). CONCLUSION CEP55 may be an immune-related predictive and prognostic marker for multiple cancers, including lung squamous cell carcinoma.
Collapse
Affiliation(s)
- Guo-Sheng Li
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Wei Zhang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Wan-Ying Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Rong-Quan He
- Department of Oncology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Xiang-Yu Gan
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Zhen Yang
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, 530021, Nanning, Guangxi, P. R. China
| | - Yi-Wu Dang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Jin-Liang Kong
- Division of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, No. 6, Shuangyong Road, 530021, Nanning, Guangxi, P. R. China
| | - Hua-Fu Zhou
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Guangxi Zhuang Autonomous Region, No. 6, Shuangyong Road, 530021, Nanning, P. R. China.
| |
Collapse
|
5
|
Li Y, Huang HQ, Huang ZH, Yu ND, Ye XL, Jiang MC, Chen LM. SNHG15 enhances cisplatin resistance in lung adenocarcinoma by affecting the DNA repair capacity of cancer cells. Diagn Pathol 2023; 18:33. [PMID: 36864456 PMCID: PMC9979449 DOI: 10.1186/s13000-023-01291-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/12/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is a prevalent malignancy. SNHG15 has been demonstrated to be oncogenic in many kinds of cancers, however the mechanism of SNHG15 in LUAD cisplatin (DDP) resistance remains unclear. In this study, we demonstrated the effect of SNHG15 on DDP resistance in LUAD and its related mechanism. METHODS Bioinformatics analysis was adopted to assess SNHG15 expression in LUAD tissues and predict the downstream genes of SNHG15. The binding relationship between SNHG15 and downstream regulatory genes was proved through RNA immunoprecipitation, chromatin immunoprecipitation and dual-luciferase reporter assays. Cell counting kit-8 assay was adopted to evaluate LUAD cell viability, and gene expression was determined by Western blot and quantitative real-time polymerase chain reaction. We then performed comet assay to assess DNA damage. Cell apoptosis was detected by Tunnel assay. Xenograft animal models were created to test the function of SNHG15 in vivo. RESULTS SNHG15 was up-regulated in LUAD cells. Moreover, SNHG15 was also highly expressed in drug-resistant LUAD cells. Down-regulated SNHG15 strengthened the sensitivity of LUAD cells to DDP and induced DNA damage. SNHG15 could elevate ECE2 expression through binding with E2F1, and it could induce DDP resistance by modulating the E2F1/ECE2 axis. In vivo experiments verified that the SNHG15 could enhance DDP resistance in LUAD tissue. CONCLUSION The results suggested that SNHG15 could up-regulate ECE2 expression by recruiting E2F1, thereby enhancing the DDP resistance of LUAD.
Collapse
Affiliation(s)
- Yong Li
- grid.411176.40000 0004 1758 0478Department of Respiration Medicine, Fujian Medical University Union Hospital, No.29 Xin Quan Road, Fuzhou, 350000 Fujian China
| | - Hui-Qin Huang
- grid.488150.0Fujian Provincial Key Laboratory of Medical Testing, Fujian Academy of Medical Sciences, Fuzhou, 350000 Fujian China
| | - Zheng-Hui Huang
- grid.411176.40000 0004 1758 0478Department of Respiration Medicine, Fujian Medical University Union Hospital, No.29 Xin Quan Road, Fuzhou, 350000 Fujian China
| | - Nan-Ding Yu
- grid.411176.40000 0004 1758 0478Department of Respiration Medicine, Fujian Medical University Union Hospital, No.29 Xin Quan Road, Fuzhou, 350000 Fujian China
| | - Xiang-Li Ye
- grid.411176.40000 0004 1758 0478Department of Respiration Medicine, Fujian Medical University Union Hospital, No.29 Xin Quan Road, Fuzhou, 350000 Fujian China
| | - Mei-Chen Jiang
- grid.411176.40000 0004 1758 0478Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, 350000 Fujian China
| | - Li-Min Chen
- Department of Respiration Medicine, Fujian Medical University Union Hospital, No.29 Xin Quan Road, Fuzhou, 350000, Fujian, China.
| |
Collapse
|
6
|
Sun D, Zhang H, Zhang C, Wang L. An evaluation of KIF20A as a prognostic factor and therapeutic target for lung adenocarcinoma using integrated bioinformatics analysis. Front Bioeng Biotechnol 2022; 10:993820. [PMID: 36619388 PMCID: PMC9816395 DOI: 10.3389/fbioe.2022.993820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022] Open
Abstract
The identification of prognostic and therapeutic biomarkers is essential to reduce morbidity and mortality from lung adenocarcinoma (LUAD). This study aimed to identify a reliable prognostic and therapeutic biomarker for LUAD using integrated bioinformatics. Based on the cancer genome atlas (TCGA) and genome-tissue expression (GTEx) analyses, KIF20A has been identified as the hub gene. Following validation using a series of cohorts, survival analysis, meta-analysis, and univariate Cox analysis was conducted. ESTIMATE and CIBERSORT algorithms were then used to study the association of KIF20A with the tumor microenvironment (TME) and the percentage of tumor-infiltrating immune cells (TICs). In vitro experiments were conducted to determine the function of KIF20A. Finally, there was a negative association between the expression of the KIF20A and overall survival, progression-free survival, and disease-free survival, which was confirmed by meta-analysis and COX analysis. Furthermore, KIF20A also had a potential role of altering the TME and TICs proportions in LUAD. Validations in vitro were performed on A549 and PC-9 cell lines, and we found that the knockdown of KIF20A exhibited inhibitory effects on cell proliferation, resulted in cell cycle arrest during the G2/M phase, and induced cellular apoptosis. Our study demonstrated that KIF20A could be utilized as a reliable prognostic marker and treatment target for LUAD. However, further studies are required to validate these findings.
Collapse
Affiliation(s)
- Dongjie Sun
- College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Haiying Zhang
- Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Chi Zhang
- Department of Anesthesiology, The First Hospital of Jilin University, Changchun, China
| | - Lina Wang
- Department of Pediatric Respiration, The First Hospital of Jilin University, Changchun, China,*Correspondence: Lina Wang,
| |
Collapse
|
7
|
Huang X, Su B, Wang X, Zhou Y, He X, Liu B. A network-based dynamic criterion for identifying prediction and early diagnosis biomarkers of complex diseases. J Bioinform Comput Biol 2022; 20:2250027. [PMID: 36573886 DOI: 10.1142/s0219720022500275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lung adenocarcinoma (LUAD) seriously threatens human health and generally results from dysfunction of relevant module molecules, which dynamically change with time and conditions, rather than that of an individual molecule. In this study, a novel network construction algorithm for identifying early warning network signals (IEWNS) is proposed for improving the performance of LUAD early diagnosis. To this end, we theoretically derived a dynamic criterion, namely, the relationship of variation (RV), to construct dynamic networks. RV infers correlation [Formula: see text] statistics to measure dynamic changes in molecular relationships during the process of disease development. Based on the dynamic networks constructed by IEWNS, network warning signals used to represent the occurrence of LUAD deterioration can be defined without human intervention. IEWNS was employed to perform a comprehensive analysis of gene expression profiles of LUAD from The Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) database. The experimental results suggest that the potential biomarkers selected by IEWNS can facilitate a better understanding of pathogenetic mechanisms and help to achieve effective early diagnosis of LUAD. In conclusion, IEWNS provides novel insight into the initiation and progression of LUAD and helps to define prospective biomarkers for assessing disease deterioration.
Collapse
Affiliation(s)
- Xin Huang
- School of Mathematics and Information Science, Anshan Normal University, Anshan, Liaoning 114007, P. R. China
| | - Benzhe Su
- School of Computer Science and Technology, Dalian University of Technology, Dalian, Liaoning 116024, P. R. China
| | - Xingyu Wang
- School of Mathematics and Information Science, Anshan Normal University, Anshan, Liaoning 114007, P. R. China
| | - Yang Zhou
- Liaoning Clinical Research Center for Lung Cancer, The Second Hospital of Dalian Medical University Dalian, Liaoning 116023, P. R. China
| | - Xinyu He
- School of Computer and Information Technology, Liaoning Normal University, Dalian, Liaoning 116029, P. R. China
| | - Bing Liu
- School of Mathematics and Information Science, Anshan Normal University, Anshan, Liaoning 114007, P. R. China
| |
Collapse
|
8
|
Li G, Wu L, Yu J, Zhai S, Deng H, Wang Q. Identification and Validation of Three-Gene Signature in Lung Squamous Cell Carcinoma by Integrated Transcriptome and Methylation Analysis. JOURNAL OF ONCOLOGY 2022; 2022:9688040. [PMID: 36193204 PMCID: PMC9525794 DOI: 10.1155/2022/9688040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 11/21/2022]
Abstract
Since DNA methylation (DNAm) is associated with the carcinogenesis of various cancers, this study aimed to explore potential DNAm prognostic signatures of lung squamous cell carcinoma (LUSC). First, transcriptomic and methylation profiles of LUSC were obtained from The Cancer Genome Atlas database (TCGA). DNAm-related genes were screened by integrating DNAm and transcriptome profiles via MethylMix package. Subsequently, a prognostic signature was conducted with the least absolute shrinkage and selector operation (LASSO) Cox analysis. This signature combined with the clinicopathological parameters was then utilized to construct a prognostic nomogram via the rms package. A signature based on three DNAm-related genes claudin 1 (CLDN1), ATP-binding cassette subfamily C member 5 (ABCC5), and cystatin A (CSTA) that were hypomethylated and upregulated in LUSC was constructed. Univariate and multivariate Cox regression analysis suggested that this signature, combined with age and TNM.N stage, was significantly correlated with survival rate. Time-dependent receiver operating characteristics and calibration curves suggested the nomogram constructed with age and TNM.N stage variables could accurately evaluate the 3- and 5-year outcome of LUSC. Finally, the average mRNA and protein expression levels of CLDN1, ABCC5, and CSTA in LUSC were verified to be significantly higher than those in paracancerous tissues. Moreover, silencing CLDN1, ABCC5, and CSTA expressions could significantly reduce the carcinogenesis of the A549 cell line. The DNAm-driven prognostic signature consists of CLDN1, ABCC5, and CSTA incorporated with age and TNM. N stage could facilitate the prediction outcome of LUSC.
Collapse
Affiliation(s)
- Guanghua Li
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150000, China
| | - Libo Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Hainan Medical College, Haikou 570100, China
| | - Jiaxing Yu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150000, China
| | - Siyang Zhai
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150000, China
| | - Hailong Deng
- Department of Thoracic Surgery, Hailun People's Hospital, Hailun 152300, China
| | - Qiushi Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin 150000, China
| |
Collapse
|
9
|
Construction of Lymph Node Metastasis-Related Prognostic Model and Analysis of Immune Infiltration Mode in Lung Adenocarcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:3887857. [PMID: 35836921 PMCID: PMC9274234 DOI: 10.1155/2022/3887857] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/09/2022] [Indexed: 01/10/2023]
Abstract
Background Lung adenocarcinoma (LUAD) is a major cause for global cancer-related deaths. Research reports demonstrate that lymph node metastasis (LNM) is pertinent to the survival rate of LUAD patients, and crux lies in the lack of biomarkers that could distinguish patients with LNM. We aimed to verify the LNM-related prognostic biomarkers in LUAD. Methods We firstly accessed the expression data of mRNA from The Cancer Genome Atlas (TCGA) database and then obtained samples with LNM (N+) and without LNM (N-). Differential expression analysis was conducted to acquire differentially expressed genes (DEGs). Univariate-LASSO-multivariate Cox regression analyses were performed on DEGs to build a risk model and obtain optimal genes. Afterwards, effectiveness and independence of risk model were assessed based on TCGA-LUAD and GSE31210 datasets. Moreover, a nomogram was established combining clinical factors and riskscores. Nomogram performance was measured by calibration curves. The infiltration abundance of immune cells was scored with CIBERSORT to explore the differences between high- and low-risk groups. Lastly, gene set enrichment analysis (GSEA) was used to investigate differences in immune features between the two risk groups. Results Nine optimal feature genes closely related to LNM in LUAD were identified to construct a risk model. Prognostic ability of the risk model was verified in independent databases. Patients were classified into high- and low-risk groups in accordance with their median riskscores. CIBERSORT score displayed differences in immune cell infiltration like T cells CD4 memory resting between high/low-risk groups. LNM-related genes may also be closely relevant to immune features. Additionally, GSEA indicated that differential genes in the two risk groups were enriched in genes related to immune cells. Conclusion This research built a risk model including nine optimal feature genes, which may be potential biomarkers for LUAD.
Collapse
|
10
|
He C, Huang D, Yang F, Huang D, Cao Y, Peng J, Luo X. High Expression of lncRNA HEIH is Helpful in the Diagnosis of Non-Small Cell Lung Cancer and Predicts Poor Prognosis. Cancer Manag Res 2022; 14:503-514. [PMID: 35173484 PMCID: PMC8841735 DOI: 10.2147/cmar.s320965] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background This study aims to investigate the expression and clinical value of long non-coding RNA (lncRNA) HEIH in peripheral blood of patients with non-small cell lung cancer (NSCLC). Methods Healthy subjects (N=70), patients with lung squamous cell carcinoma (LUSC, N=70) and patients with lung adenocarcinoma (LUAD, N=80) were included. LncRNA HEIH expression in peripheral blood of included subjects was detected using RT-qPCR. According to the median expression of lncRNA HEIH, LUSC and LUAD patients were allocated into lncRNA HEIH high/low expression groups. The correlation between lncRNA HEIH and clinical indicators of patients was analyzed; Logistic multifactor regression was used to analyze the independent risk factors influencing lncRNA HEIH level. Receiver-operating characteristic (ROC) curve was used to evaluate the diagnostic efficacy of lncRNA HEIH and carcinoembryonic antigen (CEA) in LUSC/LUAD patients. MedCalc-Comparison of ROC curves was used to compare the area under ROC curve. The cumulative survival rates of lncRNA HEIH high/low expression group were analyzed by Kaplan–Meier curve. COX multivariate analysis was used to assess the independent factors affecting prognosis of NSCLC. Results LncRNA HEIH in peripheral blood of LUSC/LUAD patients was higher than that in healthy controls, with no evident difference between LUSC and LUAD groups. In LUSC/LUAD patients, TNM stage, lymph node metastasis, distal metastasis, and CEA were independent risk factors affecting lncRNA HEIH; patients with high lncRNA HEIH expression had larger pack-years and tumor size, higher CEA level and tumor stage, and higher risk of lymph node metastasis and distal metastasis. LncRNA HEIH had higher diagnostic efficiency than CEA in NSCLC patients. High expression of lncRNA HEIH predicted poor prognosis in patients with NSCLC and was an independent risk factor for prognosis of NSCLC. Conclusion High expression of lncRNA HEIH is helpful in the diagnosis of NSCLC and predicts poor prognosis.
Collapse
Affiliation(s)
- Chaowen He
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
- Correspondence: Chaowen He, Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, No. 187 Guanlan Avenue, Longhua District, Shenzhen, 518110, Guangdong, People’s Republic of China, Tel +86-18123964996, Email
| | - Dongxuan Huang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
| | - Fan Yang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
| | - Dongsheng Huang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
| | - Yahui Cao
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
| | - Jianfeng Peng
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
| | - Xiaohua Luo
- Department of Pulmonary and Critical Care Medicine, Shenzhen Longhua District Central Hospital, Shenzhen, 518110, Guangdong, People’s Republic of China
| |
Collapse
|
11
|
Liu P, Li H, Liao C, Tang Y, Li M, Wang Z, Wu Q, Zhou Y. Identification of key genes and biological pathways in Chinese lung cancer population using bioinformatics analysis. PeerJ 2022; 10:e12731. [PMID: 35178291 PMCID: PMC8812315 DOI: 10.7717/peerj.12731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 12/11/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Identification of accurate prognostic biomarkers is still particularly urgent for improving the poor survival of lung cancer patients. In this study, we aimed to identity the potential biomarkers in Chinese lung cancer population via bioinformatics analysis. METHODS In this study, the differentially expressed genes (DEGs) in lung cancer were identified using six datasets from Gene Expression Omnibus (GEO) database. Subsequently, enrichment analysis was conducted to evaluate the underlying molecular mechanisms involved in progression of lung cancer. Protein-protein interaction (PPI) and CytoHubba analysis were performed to determine the hub genes. The GEPIA, Human Protein Atlas (HPA), Kaplan-Meier plotter, and TIMER databases were used to explore the hub genes. The receiver operating characteristic (ROC) analysis was performed to evaluate the diagnostic value of hub genes. Reverse transcription quantitative PCR (qRT-PCR) was used to validate the expression levels of hub genes in 10 pairs of lung cancer paired tissues. RESULTS A total of 499 overlapping DEGs (160 upregulated and 339 downregulated genes) were identified in the microarray datasets. DEGs were mainly associated with pathways in cancer, focal adhesion, and protein digestion and absorption. There were nine hub genes (CDKN3, MKI67, CEP55, SPAG5, AURKA, TOP2A, UBE2C, CHEK1 and BIRC5) identified by PPI and module analysis. In GEPIA database, the expression levels of these genes in lung cancer tissues were significantly upregulated compared with normal lung tissues. The results of prognostic analysis showed that relatively higher expression of hub genes was associated with poor prognosis of lung cancer. In HPA database, most hub genes were highly expressed in lung cancer tissues. The hub genes have good diagnostic efficiency in lung cancer and normal tissues. The expression of any hub gene was associated with the infiltration of at least two immune cells. qRT-PCR confirmed that the expression level of CDKN3, MKI67, CEP55, SPAG5, AURKA, TOP2A were highly expressed in lung cancer tissues. CONCLUSIONS The hub genes and functional pathways identified in this study may contribute to understand the molecular mechanisms of lung cancer. Our findings may provide new therapeutic targets for lung cancer patients.
Collapse
Affiliation(s)
- Ping Liu
- Department of Respiratory Medicine, The First Hospital of Changsha, Changsha, China
| | - Hui Li
- Department of Respiratory Medicine, The First Hospital of Changsha, Changsha, China
| | - Chunfeng Liao
- Department of Cardiology, The First Hospital of Changsha, Changsha, China
| | - Yuling Tang
- Department of Respiratory Medicine, The First Hospital of Changsha, Changsha, China
| | - Mengzhen Li
- MyGene Diagnostics Co., Ltd., Guangzhou, China
| | - Zhouyu Wang
- MyGene Diagnostics Co., Ltd., Guangzhou, China
| | - Qi Wu
- Department of Emergency, The First Hospital of Changsha, Changsha, China
| | - Yun Zhou
- Department of Spinal Surgery, The First Hospital of Changsha, Changsha, China
| |
Collapse
|
12
|
Zhang Y, Wang X, Cheng XK, Zong YY, He RQ, Chen G, Qin YJ. Clinical significance and effect of lncRNA BBOX1-AS1 on the proliferation and migration of lung squamous cell carcinoma. Oncol Lett 2021; 23:17. [PMID: 34820016 PMCID: PMC8607367 DOI: 10.3892/ol.2021.13135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 10/19/2021] [Indexed: 12/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have a role in the occurrence and development of lung squamous cell carcinoma (LUSC). lncRNA γ-butyrobetaine hydroxylase 1 (BBOX1)-antisense 1 (AS1) may contribute to disease development. However, there are no studies on the role of BBOX1-AS1 in LUSC to date. In the present study, an in-house gene microarray analysis was performed to detect the differentially expressed lncRNAs and mRNAs between three pairs of LUSC and normal lung tissues. Only one lncRNA, BBOX1-AS1, was differentially expressed in the in-house microarray and The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and ArrayExpress databases. Reverse transcription-quantitative PCR (RT-qPCR) was then performed and the original RNA-sequencing data from the TCGA, GEO and ArrayExpress datasets were used to determine the expression and clinical value of BBOX1-AS1 in LUSC. In addition, a Cell Counting Kit-8 assay, cell cycle analysis and scratch assay were performed to explore whether BBOX1-AS1 expression affected the proliferation and migration of LUSC cells in vitro. The results of the RT-qPCR analysis and data obtained from the TCGA database, GEO datasets, in-house gene microarray and standard mean deviation analysis all supported the upregulated expression level of BBOX1-AS1 in LUSC. Furthermore, silencing of BBOX1-AS1 inhibited the proliferation and migration of LUSC cells according to in vitro assays. In addition, the cells were arrested in S-phase after knockdown of BBOX1-AS1. In conclusion, the expression level of BBOX1-AS1 was upregulated in LUSC tissues. BBOX1-AS1 may exert an oncogenic effect on LUSC by regulating various biological functions. However, additional functional experiments should be performed to verify the exact mechanism.
Collapse
Affiliation(s)
- Yu Zhang
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, P.R. China
| | - Xiao Wang
- Department of Orthopedics, Shandong Second Provincial General Hospital, Shandong Provincial ENT Hospital, Jinan, Shandong 250000, P.R. China
| | - Xian-Kui Cheng
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, P.R. China
| | - Yuan-Yuan Zong
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, P.R. China
| | - Rong-Quan He
- Department of Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Ye-Jun Qin
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250000, P.R. China
| |
Collapse
|
13
|
Li M, Liu Y, Jiang X, Hang Y, Wang H, Liu H, Chen Z, Xiao Y. Inhibition of miR-144-3p exacerbates non-small cell lung cancer progression by targeting CEP55. Acta Biochim Biophys Sin (Shanghai) 2021; 53:1398-1407. [PMID: 34435195 DOI: 10.1093/abbs/gmab118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence has indicated that microRNA dysregulation is closely related to the occurrence and development of cancers. Herein, we investigated the relationship between miR-144-3p and CEP55 expression. We then evaluated the association between miR-144-3p and CEP55 expression and proliferation, invasion and apoptosis of non-small cell lung cancer (NSCLC) cells. Real-time quantitative PCR results revealed that CEP55 was over-expressed whereas miR-144-3p was under-expressed in NSCLC tissues. CCK-8 assay, wound healing assay, and flow cytometry further revealed that overexpression of miR-144-3p significantly inhibited proliferation and migration, but promoted apoptosis of A549 cells. Conversely, inhibition of miR-144-3p promoted proliferation and migration but suppressed apoptosis of H460 cells. Dual-luciferase reporter assay revealed that miR-144-3p modulated malignant properties of cancer cells by targeting CEP55. Overexpression of CEP55 partially blocked the inhibitory effect of miR-144-3p on proliferation and migration of A549 cells and induced apoptosis of A549 cells. CEP55 knockdown modulated the increase in proliferation and migration and the decrease in apoptosis of H460 cells following miR-144-3p inhibition. These findings demonstrated that miR-144-3p suppresses NSCLC development by inhibiting CEP55 expression.
Collapse
Affiliation(s)
- Ming Li
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 418000, China
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, China
- Scientific Research Institute, Hunan Yueyang Maternal & Child Health-Care Hospital, Yueyang 414000, China
- Guangxi Province Postgraduate Co-training Base for Cooperative Innovation in Basic Medicine, Guilin Medical University and Yueyang Women & Children’s Medical Center, Yueyang 414000, China
| | - Yannan Liu
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 418000, China
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, China
| | - Xinglin Jiang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 418000, China
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, China
| | - Yuanxin Hang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 418000, China
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, China
| | - Haiying Wang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 418000, China
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, China
| | - Hang Liu
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 418000, China
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, China
| | - Zhuo Chen
- Scientific Research Institute, Hunan Yueyang Maternal & Child Health-Care Hospital, Yueyang 414000, China
- Guangxi Province Postgraduate Co-training Base for Cooperative Innovation in Basic Medicine, Guilin Medical University and Yueyang Women & Children’s Medical Center, Yueyang 414000, China
| | - Yubo Xiao
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, Hunan University of Medicine, Huaihua 418000, China
- School of Public Health and Laboratory Medicine, Hunan University of Medicine, Huaihua 418000, China
| |
Collapse
|
14
|
Li Y, Sun R, Li R, Chen Y, Du H. Prognostic Nomogram Based on Circular RNA-Associated Competing Endogenous RNA Network for Patients with Lung Adenocarcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:9978206. [PMID: 34497684 PMCID: PMC8421160 DOI: 10.1155/2021/9978206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/14/2021] [Indexed: 11/29/2022]
Abstract
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.
Collapse
Affiliation(s)
- Yang Li
- Department of Central Laboratory, Affiliated Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou 221009, China
| | - Rongrong Sun
- Department of Medical Oncology, Affiliated Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou 221009, China
| | - Rui Li
- Department of Central Laboratory, Affiliated Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou 221009, China
| | - Yonggang Chen
- Department of Clinical Pharmacy, Xuzhou Central Hospital, Clinical School of Xuzhou Medical University, Xuzhou 221009, China
| | - He Du
- Department of Medical Oncology, Affiliated Shanghai Pulmonary Hospital, Tongji University, Shanghai 200433, China
| |
Collapse
|
15
|
Xu F, Huang X, Li Y, Chen Y, Lin L. m 6A-related lncRNAs are potential biomarkers for predicting prognoses and immune responses in patients with LUAD. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 24:780-791. [PMID: 33996259 PMCID: PMC8094594 DOI: 10.1016/j.omtn.2021.04.003] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/03/2021] [Indexed: 02/05/2023]
Abstract
Lung adenocarcinoma (LUAD) is the most frequent subtype of lung cancer worldwide. However, the survival rate of LUAD patients remains low. N6-methyladenosine (m6A) and long noncoding RNAs (lncRNAs) play vital roles in the prognostic value and the immunotherapeutic response of LUAD. Thus, discerning lncRNAs associated with m6A in LUAD patients is critical. In this study, m6A-related lncRNAs were analyzed and obtained by coexpression. Univariate, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses were conducted to construct an m6A-related lncRNA model. Kaplan-Meier analysis, principal-component analysis (PCA), functional enrichment annotation, and nomogram were used to analyze the risk model. Finally, the potential immunotherapeutic signatures and drug sensitivity prediction targeting this model were also discussed. The risk model comprising 12 m6A-related lncRNAs was identified as an independent predictor of prognoses. By regrouping the patients with this model, we can distinguish between them more effectively in terms of the immunotherapeutic response. Finally, candidate compounds aimed at LUAD subtype differentiation were identified. This risk model based on the m6A-based lncRNAs may be promising for the clinical prediction of prognoses and immunotherapeutic responses in LUAD patients.
Collapse
Affiliation(s)
- Feng Xu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Xiaoling Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yangyi Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yongsong Chen
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
- Department of Endocrinology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
- Corresponding author: Yongsong Chen, Department of Endocrinology, The First Affiliated Hospital of Shantou University Medical College, No. 57 Changping Road, Shantou, Guangdong 515041, China.
| | - Ling Lin
- Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
- Department of Rheumatology, The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
- Corresponding author: Ling Lin, Department of Rheumatology, The First Affiliated Hospital of Shantou University Medical College, No. 57 Changping Road, Shantou, Guangdong 515041, China.
| |
Collapse
|
16
|
Li Z, Yu B, Qi F, Li F. KIF11 Serves as an Independent Prognostic Factor and Therapeutic Target for Patients With Lung Adenocarcinoma. Front Oncol 2021; 11:670218. [PMID: 33968780 PMCID: PMC8103954 DOI: 10.3389/fonc.2021.670218] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 03/24/2021] [Indexed: 12/31/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is challenging in clinical practice due to the poor understanding of molecular mechanisms and limited therapeutic targets. Herein, the work aimed to use bioinformatics to identify a promising molecular target for LUAD therapy. Methods Differentially expressed genes (DEGs) from the Cancer Genome Atlas (TCGA) dataset were used for a weighted gene co-expression network analysis (WGCNA) to screen the hub gene. After a prognostic estimation with meta-analysis and COX regression analysis, we performed a function analysis on the corresponding gene. The ESTIMATE and CIBERSORT methods were adopted to analyze the association of the hub gene with the tumor microenvironment (TME). A cohort of functional assays was conducted to establish the functional roles of the hub gene in A549 and PC-9 cells. Results Our screen identified KIF11 as a prognostic factor, which indicated the poor overall survival and the worse progression-free survival in LUAD patients. Additionally, KIF11 was primarily involved in cell cycle, TME alteration and tumor-infiltrating immune cells proportions. KIF11 knockdown exerted inhibitory effects on cell proliferation, migration, and invasion. Results of the flow cytometry analysis revealed that KIF11 knockdown induced a G2/M phase arrest and improved apoptosis in LUAD cells. Conclusions KIF11 is essential for LUAD cell proliferation and metastasis, and it may serve as an independent prognostic factor as well as a promising therapeutic target for LUAD patients.
Collapse
Affiliation(s)
- Zhaodong Li
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, China
| | - Bingxin Yu
- Department of Ultrasonography, The Third Hospital of Jilin University, Changchun, China
| | - Fangyuan Qi
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, China
| | - Fan Li
- Department of Pathogenobiology, The Key Laboratory of Zoonosis, Chinese Ministry of Education, College of Basic Medicine, Jilin University, Changchun, China.,The Key Laboratory for Bionics Engineering, Ministry of Education, China, Jilin University, Changchun, China.,Engineering Research Center for Medical Biomaterials of Jilin Province, Jilin University, Changchun, China.,Key Laboratory for Biomedical Materials of Jilin Province, Jilin University, Changchun, China.,State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, China
| |
Collapse
|
17
|
Cao B, Wang P, Gu L, Liu J. Use of four genes in exosomes as biomarkers for the identification of lung adenocarcinoma and lung squamous cell carcinoma. Oncol Lett 2021; 21:249. [PMID: 33664813 PMCID: PMC7882885 DOI: 10.3892/ol.2021.12510] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
The determination of biomarkers in the blood specific for lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) is crucial for the selection of effective treatment strategies and the prediction of prognosis. The purpose of the present study was to analyze the differentially expressed genes (DEGs) in LUSC and LUAD from The Cancer Genome Atlas (TCGA) database. In order to identify the potential biomarkers for non-small cell lung cancer (NSCLC) for clinical diagnosis, bioinformatics was used to analyze the DEGs of two subtypes of NSCLC, LUAD and LUSC. Exosomes were isolated from the serum of patients with LUAD or LUSC and identified using transmission electron microscopy, nanoparticle tracking analysis and western blot analysis. A total of four differential exosomal mRNAs were selected for validation with serum samples from 70 patients with NSCLC via reverse transcription-quantitative polymerase chain reaction. Receiver operating characteristic curves were established to evaluate the clinical diagnostic value of four DEGs for patients with LUAD and LUSC. The analysis based on TCGA data revealed the DEGs in LUSC and LUAD: A total of 1,619 genes were differentially expressed in patients with LUSC and LUAD. DEGs analyzed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that inflammation-related signaling pathways, such as complement pathways, and multiple autoimmune diseases, such as systemic lupus erythematosus and asthma were mainly enriched in LUAD. The cell cycle, Hippo signaling pathway, Rap1 signaling pathway and Wnt signaling pathway were the main signaling pathways enriched in LUSC. The combination of tumor protein P63 (TP63), keratin 5 (KRT5), CEA cell adhesion molecule 6 (CEACAM6) and surfactant protein B (SFTPB) improved the specificity and sensitivity in the diagnosis of different lung cancer subtypes. Exosomal TP63, KRT5, CEACAM6 and SFTPB mRNAs can thus be used as biomarkers to differentiate between LUSC and LUAD, and may provide a novel strategy for their differential diagnosis and treatment.
Collapse
Affiliation(s)
- Bingji Cao
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Pengyu Wang
- Department of Clinical Laboratory, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Lina Gu
- Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| | - Junfeng Liu
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei 050011, P.R. China
| |
Collapse
|