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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.
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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
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Liu Y, Sun M, Xiong Y, Gu X, Zhang K, Liu L. Construction and Validation of Prognosis Nomogram for Metastatic Lung Squamous Cell Carcinoma: A Population-Based Study. Technol Cancer Res Treat 2022; 21:15330338221132035. [PMID: 36217877 PMCID: PMC9558863 DOI: 10.1177/15330338221132035] [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] [Indexed: 11/05/2022] Open
Abstract
Purpose: This study aimed to establish a nomogram to predict overall
survival in lung squamous cell carcinoma patients with metastasis for clinical
decision-making. Methods: We investigated lung squamous cell
carcinoma patients diagnosed with stage M1 in the Surveillance, Epidemiology,
and Final Results database between 2010 and 2015. They were divided into
training cohort and validation cohort. In the training cohort, statistically
significant prognostic factors were identified using univariate and multivariate
Cox regression analysis, and an individualized nomogram model was developed. The
model was evaluated by C-index, area under the curve, calibration plot, decision
curve analysis, and risk group stratification. Results: In total,
9910 patients were included in our study, including 6937 in the training cohort
and 2937 in the validation cohort. Factors containing age, T stage, N stage,
bone metastasis, brain metastasis, liver metastasis, surgery, chemotherapy, and
radiotherapy were independent prognostic factors for overall survival and were
used in the construction of the nomogram. The C-index in the training cohort and
validation cohort were 0.711 (95% confidenc interval: 0.705-0.717) and 0.707
(95% confidenc interval: 0.697-0.717), respectively. The time-dependent area
under the curve of both groups was higher than 0.7 within 5 years. Calibration
plots indicated that the nomogram-predicted survival was consistent with the
recorded 6-month, 1-year, and 2-year prognoses. Furthermore, decision curve
analysis revealed that the nomogram was clinically useful and had a better
discriminative ability to recognize patients at high risk than the TNM
criteria-based tumor staging. And then we developed an overall survival risk
classification system based on the nomogram total points for each patient, which
divided all patients into a high-risk group and a low-risk group. Finally, we
implemented this nomogram in a free online tool. Conclusion: We
constructed a nomogram and a corresponding risk classification system predicting
the overall survival of lung squamous cell carcinoma patients with metastasis.
These tools can assist in patients’ counseling and guide treatment
decision-making.
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Affiliation(s)
- Yuting Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong
University of Science and Technology, Wuhan, China
| | - Min Sun
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong
University of Science and Technology, Wuhan, China
| | - Ying Xiong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong
University of Science and Technology, Wuhan, China
| | - Xinyue Gu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong
University of Science and Technology, Wuhan, China
| | - Kai Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong
University of Science and Technology, Wuhan, China,Kai Zhang, Cancer Center, Union Hospital,
Tongji Medical College, Huazhong University of Science and Technology, Wuhan
430022, China. Li Liu, Cancer Center,
Union Hospital, Tongji Medical College, Huazhong University of Science and
Technology, Wuhan 430022, China.
| | - Li Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong
University of Science and Technology, Wuhan, China
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Yang Z, Wang H, Zhao Z, Jin Y, Zhang Z, Tan J, Hu F. Gene-microRNA Network Analysis Identified Seven Hub Genes in Association with Progression and Prognosis in Non-Small Cell Lung Cancer. Genes (Basel) 2022; 13:genes13081480. [PMID: 36011391 PMCID: PMC9407881 DOI: 10.3390/genes13081480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
Introduction: Lung cancer is the leading cause of cancer deaths in the world and is usually divided into non-small cell lung cancer (NSCLC) and small cell lung cancer. NSCLC is dominant and accounts for 85% of the total cases. Currently, the therapeutic method of NSCLC is not so satisfactory, and thus identification of new biomarkers is critical for new clinical therapy for this disease. Methods: Datasets of miRNA and gene expression were obtained from the NCBI database. The differentially expressed genes (DEGs) and miRNAs (DEMs) were analyzed by GEO2R tools. The DEG-DEM interaction was built via miRNA-targeted genes by miRWalk. Several hub genes were selected via network topological analysis in Cytoscape. Results: A set of 276 genes were found to be significantly differentially expressed in the three datasets. Functional enrichment by the DAVID tool showed that these 276 DEGs were significantly enriched in the term “cancer”, with a statistic p-value of 1.9 × 10−5. The subdivision analysis of the specific cancer types indicated that “lung cancer” occupies the largest category with a p-value of 2 × 10−3. Furthermore, 75 miRNAs were shown to be differentially expressed in three representative datasets. A group of 13 DEGs was selected by analysis of the miRNA–gene interaction of these DEGs and DEMs. The investigation of these 13 genes by GEPIA tools showed that eight of them had consistent results with NSCLC samples in the TCGA database. In addition, we applied the KMplot to conduct the survival analysis of these eight genes and found that seven of them have a significant effect on the prognosis survival of patients. We believe that this study could provide effective research clues for the prevention and treatment of non-small cell lung cancer.
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Affiliation(s)
- Zhiyuan Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
- Correspondence:
| | - Hongqi Wang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Zixin Zhao
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Yunlong Jin
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Zhengnan Zhang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Jiayi Tan
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Fuyan Hu
- Department of Statistics, Faculty of Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
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Sasa GBK, Xuan C, Chen M, Jiang Z, Ding X. Clinicopathological implications of lncRNAs, immunotherapy and DNA methylation in lung squamous cell carcinoma: a narrative review. Transl Cancer Res 2022; 10:5406-5429. [PMID: 35116387 PMCID: PMC8799054 DOI: 10.21037/tcr-21-1607] [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: 08/11/2021] [Accepted: 11/16/2021] [Indexed: 11/06/2022]
Abstract
Objective To explore the clinicopathological impact of lncRNAs, immunotherapy, and DNA methylation in lung squamous cell carcinoma (LUSC), emphasizing their exact roles in carcinogenesis and modes of action. Background LUSC is the second most prevalent form, accounting for around 30% of non-small cell lung cancer (NSCLC). To date, molecular-targeted treatments have significantly improved overall survival in lung adenocarcinoma patients but have had little effect on LUSC therapy. As a result, there is an urgent need to discover new treatments for LUSC that are based on existing genomic methods. Methods In this review, we summarized and analyzed recent research on the biological activities and processes of lncRNA, immunotherapy, and DNA methylation in the formation of LUSC. The relevant studies were retrieved using a thorough search of Pubmed, Web of Science, Science Direct, Google Scholar, and the university's online library, among other sources. Conclusions LncRNAs are the primary components of the mammalian transcriptome and are emerging as master regulators of a number of cellular processes, including the cell cycle, differentiation, apoptosis, and growth, and are implicated in the pathogenesis of a variety of cancers, including LUSC. Understanding their role in LUSC in detail may help develop innovative treatment methods and tactics for LUSC. Meanwhile, immunotherapy has transformed the LUSC treatment and is now considered the new standard of care. To get a better knowledge of LUSC biology, it is critical to develop superior modeling systems. Preclinical models, particularly those that resemble human illness by preserving the tumor immune environment, are essential for studying cancer progression and evaluating novel treatment targets. DNA methylation, similarly, is a component of epigenetic alterations that regulate cellular function and contribute to cancer development. By methylating the promoter regions of tumor suppressor genes, abnormal DNA methylation silences their expression. DNA methylation indicators are critical in the early detection of lung cancer, predicting therapy efficacy, and tracking treatment resistance. As such, this review seeks to explore the clinicopathological impact of lncRNAs, immunotherapy, and DNA methylation in LUSC, emphasizing their exact roles in carcinogenesis and modes of action.
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Affiliation(s)
- Gabriel B K Sasa
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Cheng Xuan
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Meiyue Chen
- The fourth affiliated hospital, Zhejiang University of Medicine, Hangzhou, China
| | - Zhenggang Jiang
- Department of Science Research and Information Management, Zhejiang Provincial Centers for Disease Control and Prevention, Hangzhou, China
| | - Xianfeng Ding
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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Zhao S, Liu Q, Li J, Hu C, Cao F, Ma W, Gao J. Construction and Validation of Prognostic Regulation Network Based on RNA-Binding Protein Genes in Lung Squamous Cell Carcinoma. DNA Cell Biol 2021; 40:1563-1583. [PMID: 34931870 DOI: 10.1089/dna.2021.0145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is a common histologic subtype of non-small cell lung cancer with a poor prognosis. RNA-binding proteins (RBPs) are key modulators in the posttranscriptional regulation and RBP alterations are commonly found in various cancer types. However, its roles in predicting the tumorigenesis and prognosis have not been identified in LUSC. To identify the roles of RBPs in the tumorigenesis and prognosis of LUSC, the RNA sequencing data of patients with LUSC were retrieved from The Cancer Genome Atlas (TCGA) databases. The differential expressed genes (DEGs) were evaluated and identified. The intersection of manually curated RBPs and tumorigenesis-related DEGs was filtered to the univariate Cox regression analysis. The intersection genes with prognostic value were defined as prognostic RNA-binding protein genes (PRBPGs). Based on them, the predicted model was constructed. Its accuracy was tested by the area under the curve (AUC) of the receiver operator characteristic curve and the risk score. In addition, to explore the key regulatory network, the relationship among PRBPGs, target RNA, and absolute quantification of 50 hallmarks of cancer was also identified by Pearson correlation analysis. A total of 311 genes were filtered as the intersection of 1542 manually curated RBPs and tumorigenesis-related DEGs and the results revealed 17 PRBPGs. Based on them, we constructed the predict model with a relatively high accuracy (AUC: 0.739). The Kaplan-Meier survival curve showed the significant prognostic value of risk score (p < 0.001). Moreover, we uncovered the regulatory networks of PHF5A-TOMM22-oxidative phosphorylation, TLR3-CTSO inflammation-related pathway, SECISBP2L-targeted RNA (ADGRF5, TGFBR2, CD302, AC096921.2, AHCYL2, RPS6KA2, SLC34A2, and SFTPB) angiogenesis, and SECISBP2L-AKAP13 signaling (DNA repair, MTORC1 signaling, and MYC targets). The regulation mechanisms and cellular location of key PRBPGs were validated by assay for targeting accessible chromatin with high-throughput sequencing and single-cell RNA sequencing. Our study identifies PRBPGs as reliable indexes in predicting the tumorigenesis and prognosis of patients with LUSC and provides a well-applied model for predicting the overall survival for patients with LUSC. Besides, we also identified the regulatory network among PRBPGs, target RNA, and cancer gene sets in mediating the LUSC tumorigenesis.
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Affiliation(s)
- Shilong Zhao
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiuhong Liu
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junlu Li
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunling Hu
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fengan Cao
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wentao Ma
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing Gao
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Huang G, Zhang J, Gong L, Liu D, Wang X, Chen Y, Guo S. Specific Lung Squamous Cell Carcinoma Prognosis-Subtype Distinctions Based on DNA Methylation Patterns. Med Sci Monit 2021; 27:e929524. [PMID: 33661858 PMCID: PMC7942209 DOI: 10.12659/msm.929524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Lung squamous cell carcinoma (LUSC) is one of the major types of non-small-cell lung cancer. Epigenetic alterations, such as DNA methylation, have been recognized to be closely associated with the tumorigenesis and progression. Material/Methods In this study, we investigated the prognosis subgroups and assessed their correlation with clinical characteristics in LUSC using a methylation array acquired from The Cancer Genome Atlas (TCGA) database. Results A total of 196 DNA methylation sites exhibited a significant association with patient prognosis, and patients were further stratified into 7 prognosis subgroups based upon the consensus clustering. The patients in every subgroup were different in terms of prognosis and TNM stage. In addition, we found these 196 significant methylation sites corresponded to 258 genes. The function enrichment analysis revealed that these 258 genes enriched in biological pathways were closely related to cancers, such as DNA methylation and demethylation, cell cycle DNA replication, regulation of signal transduction by p53 class mediator, and genetic imprinting. Subsequently, we determined the levels of methylation sites in 7 subgroups, and found 24 intra-subgroup-specific methylation sites. Meanwhile, we selected 3 subgroups-specific methylation sites to construct the prognosis model for LUSC patients using multivariate Cox proportional risk regression model analysis. This model can effectively predict the prognosis of LUSC patients. Conclusions Our study identified a new classification of LUSC into 7 prognosis subgroups on the basis of DNA methylation data in TCGA, which demonstrated that molecular subtypes are independent factor for prognosis in LUSC. This may provide a more detailed explanation for LUSC heterogeneity. Additionally, this classification will contribute to discovery of new biomarkers of LUSC and provide more accurate subdivision of LUSC. Furthermore, these specific DNA methylation sites and corresponding genes can serve as biomarkers for early diagnosis, accurate therapy, and prognosis prediction.
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Affiliation(s)
- Guichuan Huang
- Department of Pulmonary and Critical Care Medicine, The First People's hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China (mainland)
| | - Jing Zhang
- Department of Pulmonary and Critical Care Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China (mainland)
| | - Ling Gong
- Department of Pulmonary and Critical Care Medicine, The First People's hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China (mainland)
| | - Daishun Liu
- Department of Pulmonary and Critical Care Medicine, The First People's hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, Guizhou, China (mainland)
| | - Xin Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China (mainland)
| | - Yi Chen
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China (mainland)
| | - Shuliang Guo
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China (mainland)
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