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Liu R, Yang G, Guo H, Chen F, Lu S, Zhu H. Roles of naïve CD4 + T cells and their differentiated subtypes in lung adenocarcinoma and underlying potential regulatory pathways. J Transl Med 2024; 22:781. [PMID: 39175022 PMCID: PMC11340134 DOI: 10.1186/s12967-024-05530-y] [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: 04/04/2024] [Accepted: 07/23/2024] [Indexed: 08/24/2024] Open
Abstract
BACKGROUND Naïve CD4+ T cells and their differentiated counterparts play a significant regulatory role in the tumor immune microenvironment, yet their effects on lung adenocarcinoma (LUAD) are not fully understood. METHODS We utilized Mendelian randomization to assess the causal association between naïve CD4+ T cells and LUAD. Employing a modified single-sample Gene Set Enrichment Analysis (ssGSEA) algorithm with The Cancer Genome Atlas (TCGA) database, we determined the infiltration levels of naïve CD4+ T cells and their differentiation subtypes and investigated their correlation with clinical characteristics. Potential regulatory pathways of T helper cells were identified through Mantel tests and Kyoto Encyclopedia of Genes and Genomes (KEGG) database enrichment analysis. RESULTS Mendelian randomization analysis revealed an inhibitory effect of naïve CD4+ T cells on LUAD (false discovery rate < 0.05), which was corroborated by observational experiments using TCGA database. Specifically, T helper cell type 2 demonstrated a promotive effect on LUAD in terms of overall, disease-free, and progression-free survival (p < 0.05). Moreover, regulatory T cells exhibited a protective effect on LUAD in terms of disease-specific survival (p < 0.01). Concurrently, we explored the overall impact of naïve CD4+ T cell differentiation subtypes on LUAD, revealing upregulation in pathways such as neutrophil degranulation, MAPK family signaling pathways, and platelet activation, signaling, and aggregation. CONCLUSION Naïve CD4+ T cells and their differentiated counterparts play essential regulatory roles in the tumor immune microenvironment, demonstrating bidirectionality in their effects.Thus, elucidating the mechanisms and developing novel cell differentiation-inducing agents will benefit anti-cancer therapy.
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Affiliation(s)
- Runze Liu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Guangjian Yang
- Department of Respiratory Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Hongbo Guo
- Department of Thoracic Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Feihu Chen
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Shuangqing Lu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Hui Zhu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China.
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Han X, Zhu Y, Ke J, Zhai Y, Huang M, Zhang X, He H, Zhang X, Zhao X, Guo K, Li X, Han Z, Zhang Y. Progression of m 6A in the tumor microenvironment: hypoxia, immune and metabolic reprogramming. Cell Death Discov 2024; 10:331. [PMID: 39033180 PMCID: PMC11271487 DOI: 10.1038/s41420-024-02092-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/23/2024] Open
Abstract
Recently, N6-methyladenosine (m6A) has aroused widespread discussion in the scientific community as a mode of RNA modification. m6A comprises writers, erasers, and readers, which regulates RNA production, nuclear export, and translation and is very important for human health. A large number of studies have found that the regulation of m6A is closely related to the occurrence and invasion of tumors, while the homeostasis and function of the tumor microenvironment (TME) determine the occurrence and development of tumors to some extent. TME is composed of a variety of immune cells (T cells, B cells, etc.) and nonimmune cells (tumor-associated mesenchymal stem cells (TA-MSCs), cancer-associated fibroblasts (CAFs), etc.). Current studies suggest that m6A is involved in regulating the function of various cells in the TME, thereby affecting tumor progression. In this manuscript, we present the composition of m6A and TME, the relationship between m6A methylation and characteristic changes in TME, the role of m6A methylation in TME, and potential therapeutic strategies to provide new perspectives for better treatment of tumors in clinical work.
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Affiliation(s)
- Xuan Han
- First Clinical College of Changzhi Medical College, Changzhi, China
| | - Yu Zhu
- Linfen Central Hospital, Linfen, China
| | - Juan Ke
- Linfen Central Hospital, Linfen, China
| | | | - Min Huang
- Linfen Central Hospital, Linfen, China
| | - Xin Zhang
- Linfen Central Hospital, Linfen, China
| | | | | | | | | | | | - Zhongyu Han
- School of Medicine and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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3
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Yu M, Pan Y, Li H, Liu X, Chen Z, Chen H, Ma S, Zeng W. N6-methyladenosine methylation regulatory pattern of pulmonary lymphoepithelioma-like carcinoma based on exosomal transcriptome analysis. Mol Carcinog 2023; 62:1846-1859. [PMID: 37589421 DOI: 10.1002/mc.23619] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/26/2023] [Accepted: 08/02/2023] [Indexed: 08/18/2023]
Abstract
Pulmonary lymphoepithelioma-like carcinoma (pLELC) is a rare malignancy that lacks specific biomarkers. N6-methyladenosine (m6 A) is the most widespread internal modification of messenger RNA (mRNA), and its dysregulation is involved in the development of many cancers. However, the expression of m6 A genes in pLELC and their roles are unknown. We obtained an exosomal transcriptome data set of patients diagnosed with pLELC and healthy controls using RNA sequencing and identified differentially expressed genes (DEGs) in the two groups using R software. The differential expression of the 37 m6 A genes in the two sets of samples was further analyzed, and receiver operating characteristic (ROC) curves were plotted for each gene to identify their grouping ability. The STRING database was used to construct a protein-protein interaction network for m6 A genes. An mRNA-miRNA regulatory network of m6 A-related DEGs was constructed using the miRNet database, and a prediction score formula was established. A nomogram was constructed based on the candidate m6 A genes and prediction scores. The expression of key genes was determined through the immunohistochemical (IHC) staining of clinical tissue sections. Using ROC curves, nine m6 A genes were revealed to have classification efficacy in both groups of samples. We screened seven m6 A-related DEGs (MAN2C1, HNRNPCL1, FUS, EIF6, DIP2A, COA3, and BUD13) that were beneficial for grouping and constructed nomogram models. Through IHC, we identified FUS and EIF6 as being possibly involved in the occurrence and development of pLELC. The m6 A gene expression patterns in pLELC-derived exosomes were significantly different from those in healthy controls. We screened several key genes to facilitate the development of diagnostic markers for pulmonary lymphoepithelioma.
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Affiliation(s)
- Mengge Yu
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Yiyun Pan
- Department of Oncology, Ganzhou Cancer Hospital, Gannan Medical University, Ganzhou, Jiangxi, P.R. China
| | - Huahua Li
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Xiaomei Liu
- Department of Surgical Oncology, Ganzhou Cancer Hospital, Gannan Medical University, Ganzhou, Jiangxi, P.R. China
| | - Zhengcong Chen
- Department of Surgical Oncology, Ganzhou Cancer Hospital, Gannan Medical University, Ganzhou, Jiangxi, P.R. China
| | - Hailong Chen
- Department of Oncology, Ganzhou Cancer Hospital, Gannan Medical University, Ganzhou, Jiangxi, P.R. China
| | - Shudong Ma
- Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Wen Zeng
- Department of Surgical Oncology, Ganzhou Cancer Hospital, Gannan Medical University, Ganzhou, Jiangxi, P.R. China
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4
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Yang S, Li K, Zhang J, Liu J, Liu L, Tan Y, Xu C. Link between m6A modification and infiltration characterization of tumor microenvironment in lung adenocarcinoma. Exp Biol Med (Maywood) 2023; 248:2273-2288. [PMID: 38166412 PMCID: PMC10903232 DOI: 10.1177/15353702231214266] [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: 05/11/2023] [Accepted: 08/30/2023] [Indexed: 01/04/2024] Open
Abstract
N6-methyladenosine (m6A) RNA methylation plays a pivotal role in immune responses and the onset and advancement of cancer. Nonetheless, the precise impact of m6A modification in lung adenocarcinoma (LUAD) and its associated tumor microenvironment (TME) remains to be fully elucidated. Here, we distinguished distinct m6A modification patterns within two separate LUAD cohorts using a set of 21 m6A regulators. The TME characteristics associated with these two patterns align with the immune-inflamed and immune-excluded phenotypes, respectively. We identified 2064 m6A-related genes, which were used as a basis to divide all LUAD samples into three distinct m6A gene clusters. We applied a scoring system to evaluate the m6A gene signature of the m6A modification pattern in individual patients. To authenticate the categorization significance of m6A modification patterns, we established a correlation between m6A score and TME infiltration profiling, tumor somatic mutations, and responses to immunotherapy. A high level of m6A modification may be associated with the aggressiveness and poor prognosis of LUAD. Further studies should investigate the mechanism of action of m6A regulators and m6A-related genes to improve the diagnosis and treatment of patients with LUAD.
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Affiliation(s)
- Sha Yang
- Guizhou University Medical College, Guiyang 550025, China
| | - Ke Li
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Jiqin Zhang
- Department of Anesthesiology, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Jian Liu
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Lin Liu
- Department of Respiratory and Critical Care Medicine, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Ying Tan
- Department of Neurosurgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
| | - Chuan Xu
- Department of Thoracic Surgery, Guizhou Provincial People’s Hospital, Guiyang 550002, China
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Sun NA, Wang YU, Chu J, Han Q, Shen Y. Bayesian Approaches in Exploring Gene-environment and Gene-gene Interactions: A Comprehensive Review. Cancer Genomics Proteomics 2023; 20:669-678. [PMID: 38035701 PMCID: PMC10687732 DOI: 10.21873/cgp.20414] [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: 09/19/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Rapid advancements in high-throughput biological techniques have facilitated the generation of high-dimensional omics datasets, which have provided a solid foundation for precision medicine and prognosis prediction. Nonetheless, the problem of missing heritability persists. To solve this problem, it is essential to explain the genetic structure of disease incidence risk and prognosis by incorporating interactions. The development of the Bayesian theory has provided new approaches for developing models for interaction identification and estimation. Several Bayesian models have been developed to improve the accuracy of model and identify the main effect, gene-environment (G×E) and gene-gene (G×G) interactions. Studies based on single-nucleotide polymorphisms (SNPs) are significant for the exploration of rare and common variants. Models based on the effect heredity principle and group-based models are relatively flexible and do not require strict constraints when dealing with the hierarchical structure between the main effect and interactions (M-I). These models have a good interpretability of biological mechanisms. Machine learning-based Bayesian approaches are highly competitive in improving prediction accuracy. These models provide insights into the mechanisms underlying the occurrence and progression of complex diseases, identify more reliable biomarkers, and develop higher predictive accuracy. In this paper, we provide a comprehensive review of these Bayesian approaches.
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Affiliation(s)
- N A Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, P.R. China
| | - Y U Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, P.R. China
| | - Jiadong Chu
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, P.R. China
| | - Qiang Han
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, P.R. China
| | - Yueping Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, P.R. China
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Yu M, Ji W, Yang X, Tian K, Ma X, Yu S, Chen L, Zhao X. The role of m6A demethylases in lung cancer: diagnostic and therapeutic implications. Front Immunol 2023; 14:1279735. [PMID: 38094306 PMCID: PMC10716209 DOI: 10.3389/fimmu.2023.1279735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
m6A is the most prevalent internal modification of eukaryotic mRNA, and plays a crucial role in tumorigenesis and various other biological processes. Lung cancer is a common primary malignant tumor of the lungs, which involves multiple factors in its occurrence and progression. Currently, only the demethylases FTO and ALKBH5 have been identified as associated with m6A modification. These demethylases play a crucial role in regulating the growth and invasion of lung cancer cells by removing methyl groups, thereby influencing stability and translation efficiency of mRNA. Furthermore, they participate in essential biological signaling pathways, making them potential targets for intervention in lung cancer treatment. Here we provides an overview of the involvement of m6A demethylase in lung cancer, as well as their potential application in the diagnosis, prognosis and treatment of the disease.
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Affiliation(s)
- Mengjiao Yu
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Wenqian Ji
- College of International Studies, Southwest University, Chongqing, China
| | - Xu Yang
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Kai Tian
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Xinyi Ma
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Shali Yu
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
| | - Lin Chen
- Nantong Institute of Liver Diseases, Nantong Third People’s Hospital Affiliated Nantong Hospital of Nantong University, Nantong, China
| | - Xinyuan Zhao
- Department of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China
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7
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Diao MN, Zhang XJ, Zhang YF. The critical roles of m6A RNA methylation in lung cancer: from mechanism to prognosis and therapy. Br J Cancer 2023; 129:8-23. [PMID: 36997662 PMCID: PMC10307841 DOI: 10.1038/s41416-023-02246-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/05/2023] [Accepted: 03/17/2023] [Indexed: 04/03/2023] Open
Abstract
Lung cancer, a highly malignant disease, greatly affects patients' quality of life. N6-methyladenosine (m6A) is one of the most common posttranscriptional modifications of various RNAs, including mRNAs and ncRNAs. Emerging studies have demonstrated that m6A participates in normal physiological processes and that its dysregulation is involved in many diseases, especially pulmonary tumorigenesis and progression. Among these, regulators including m6A writers, readers and erasers mediate m6A modification of lung cancer-related molecular RNAs to regulate their expression. Furthermore, the imbalance of this regulatory effect adversely affects signalling pathways related to lung cancer cell proliferation, invasion, metastasis and other biological behaviours. Based on the close association between m6A and lung cancer, various prognostic risk models have been established and novel drugs have been developed. Overall, this review comprehensively elaborates the mechanism of m6A regulation in the development of lung cancer, suggesting its potential for clinical application in the therapy and prognostic assessment of lung cancer.
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Affiliation(s)
- Mei-Ning Diao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Xiao-Jing Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China
| | - Yin-Feng Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China.
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Ren Q, Zhang P, Lin H, Feng Y, Chi H, Zhang X, Xia Z, Cai H, Yu Y. A novel signature predicts prognosis and immunotherapy in lung adenocarcinoma based on cancer-associated fibroblasts. Front Immunol 2023; 14:1201573. [PMID: 37325647 PMCID: PMC10264584 DOI: 10.3389/fimmu.2023.1201573] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Background Extensive research has established the significant correlations between cancer-associated fibroblasts (CAFs) and various stages of cancer development, including initiation, angiogenesis, progression, and resistance to therapy. In this study, we aimed to investigate the characteristics of CAFs in lung adenocarcinoma (LUAD) and develop a risk signature to predict the prognosis of patients with LUAD. Methods We obtained single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data from the public database. The Seurat R package was used to process the scRNA-seq data and identify CAF clusters based on several biomarkers. CAF-related prognostic genes were further identified using univariate Cox regression analysis. To reduce the number of genes, Lasso regression was performed, and a risk signature was established. A novel nomogram that incorporated the risk signature and clinicopathological features was developed to predict the clinical applicability of the model. Additionally, we conducted immune landscape and immunotherapy responsiveness analyses. Finally, we performed in vitro experiments to verify the functions of EXO1 in LUAD. Results We identified 5 CAF clusters in LUAD using scRNA-seq data, of which 3 clusters were significantly associated with prognosis in LUAD. A total of 492 genes were found to be significantly linked to CAF clusters from 1731 DEGs and were used to construct a risk signature. Moreover, our immune landscape exploration revealed that the risk signature was significantly related to immune scores, and its ability to predict responsiveness to immunotherapy was confirmed. Furthermore, a novel nomogram incorporating the risk signature and clinicopathological features showed excellent clinical applicability. Finally, we verified the functions of EXP1 in LUAD through in vitro experiments. Conclusions The risk signature has proven to be an excellent predictor of LUAD prognosis, stratifying patients more appropriately and precisely predicting immunotherapy responsiveness. The comprehensive characterization of LUAD based on the CAF signature can predict the response of LUAD to immunotherapy, thus offering fresh perspectives into the management of LUAD patients. Our study ultimately confirms the role of EXP1 in facilitating the invasion and growth of tumor cells in LUAD. Nevertheless, further validation can be achieved by conducting in vivo experiments.
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Affiliation(s)
- Qianhe Ren
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Pengpeng Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haoran Lin
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanlong Feng
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, China
| | - Xiao Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhijia Xia
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University, Munich, Germany
| | - Huabao Cai
- Department of Neurosurgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yue Yu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Li D, Chen T, Li QG. Identification of a m 6A-related ferroptosis signature as a potential predictive biomarker for lung adenocarcinoma. BMC Pulm Med 2023; 23:128. [PMID: 37072786 PMCID: PMC10111681 DOI: 10.1186/s12890-023-02410-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 03/31/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Both N6-methyladenosine (m6A) and ferroptosis-related genes are associated with the prognosis of lung adenocarcinoma. However, the predictive value of m6A-related ferroptosis genes remains unclear. Here, we aimed to identify the prognostic value of m6A-related ferroptosis genes in lung adenocarcinoma. METHODS Lung adenocarcinoma sample data were downloaded from the University of California Santa Cruz Xena and Gene Expression Omnibus databases. Spearman's correlation analysis was used to screen for m6A-related ferroptosis genes. Univariate Cox regression, Kaplan-Meier, and Lasso analyses were conducted to identify prognostic m6A-related ferroptosis genes, and stepwise regression was used to construct a prognostic gene signature. The predictive value of the gene signature was assessed using a multivariate Cox analysis. In the validation cohort, survival analysis was performed to verify gene signature stability. The training cohort was divided into high- and low-risk groups according to the median risk score to assess differences between the two groups in terms of gene set variation analysis, somatic mutations, and tumor immune infiltration cells. RESULTS Six m6A-related ferroptosis genes were used to construct a gene signature in the training cohort and a multivariate Cox analysis was conducted to determine the independent prognostic value of these genes in lung adenocarcinoma. In the validation cohort, Kaplan-Meier and receiver operating characteristic analyses confirmed the strong predictive power of this signature for the prognosis of lung adenocarcinoma. Gene set variation analysis showed that the low-risk group was mainly related to immunity, and the high-risk group was mainly related to DNA replication. Somatic mutation analysis revealed that the TP53 gene had the highest mutation rate in the high-risk group. Tumor immune infiltration cell analysis showed that the low-risk group had higher levels of resting CD4 memory T cells and lower levels of M0 macrophages. CONCLUSION Our study identified a novel m6A-related ferroptosis-associated six-gene signature (comprising SLC2A1, HERPUD1, EIF2S1, ACSL3, NCOA4, and CISD1) for predicting lung adenocarcinoma prognosis, yielding a useful prognostic biomarker and potential therapeutic target.
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Affiliation(s)
- Dongdong Li
- Medical College of Nanchang University, Nanchang, 330006, Jiangxi, P. R. China
- Department of Pulmonary and Critical Care Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330006, Jiangxi, P. R. China
| | - Ting Chen
- Department of Pulmonary and Critical Care Medicine, Wuhan Wuchang Hospital, Wuhan, 430063, Hubei, P. R. China
| | - Qiu-Gen Li
- Medical College of Nanchang University, Nanchang, 330006, Jiangxi, P. R. China.
- Department of Pulmonary and Critical Care Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330006, Jiangxi, P. R. China.
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10
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Xu L, Zhou L, Yan C, Li L. Emerging role of N6-methyladenosine RNA methylation in lung diseases. Exp Biol Med (Maywood) 2022; 247:1862-1872. [PMID: 36278325 PMCID: PMC9679358 DOI: 10.1177/15353702221128564] [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: 12/29/2022] Open
Abstract
In recent years, with the increase of air pollution, smoking, aging, and respiratory infection, the incidence rate and mortality of lung diseases are increasing annually, which has become a major hazard to human health. N6-methyladenosine (m6A) RNA methylation is the most abundant modifications in eukaryotes, and such modified RNA can be specifically recognized and combined by m6A recognition proteins and then mediate RNA splicing, maturation, enucleation, degradation, and translation. More and more studies have revealed that the m6A modification is involved in the pathogenesis and development of some diseases; however, the mechanisms of m6A in lung diseases are poorly understood. In this review, we summarize the latest progress in the biological function of m6A modifications in lung diseases and discuss the potential therapeutic and prognostic strategies. The dysregulation of global m6A levels and m6A regulators may affect the occurrence and development of asthma, chronic obstructive pulmonary disease, lung cancer, and other lung diseases through inflammation and immune function. In lung cancer, this modification has an important impact on malignant cell proliferation, migration, invasion, and drug resistance. In addition, abnormally changed m6A-modified proteins in lung cancer tissue samples and circulating tumor cells (CTCs) may be used as diagnostic and prognostic markers of lung cancer. Models composed of multiple m6A regulators can be used to evaluate the risk prediction or prognosis of asthma and pulmonary fibrosis. In general, the in-depth study of m6A modifications is a frontier direction in disease research. It provides novel insights for understanding of the molecular mechanisms underlying disease occurrence, development, and drug resistance, as well as for the development of effective novel therapeutics.
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Affiliation(s)
- Limin Xu
- Huzhou Central Hospital, Affiliated Hospital of Huzhou Normal University, Huzhou 313000, China,Huzhou Hospital, Zhejiang University, Huzhou 313000, China
| | - Lingyan Zhou
- Huzhou Central Hospital, Affiliated Hospital of Huzhou Normal University, Huzhou 313000, China,Huzhou Hospital, Zhejiang University, Huzhou 313000, China
| | - Chenxin Yan
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China
| | - Liqin Li
- Huzhou Central Hospital, Affiliated Hospital of Huzhou Normal University, Huzhou 313000, China,Huzhou Hospital, Zhejiang University, Huzhou 313000, China,Liqin Li.
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11
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Lu L, Zheng D, Qu J, Zhuang Y, Peng J, Lan S, Zhang S, Huang F. METTL16 predicts a favorable outcome and primes antitumor immunity in pancreatic ductal adenocarcinoma. Front Cell Dev Biol 2022; 10:759020. [PMID: 36158188 PMCID: PMC9500295 DOI: 10.3389/fcell.2022.759020] [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: 08/15/2021] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
Pancreatic carcinogenesis is a complicated and multi-step process. It is substantially assisted by N6-methyladenosine (m6A) RNA modification, especially when mutations of driver genes (KRAS, TP53, CDKN2A, and SMAD4) occur. However, the underlying mechanism remains obscure. In this research, we identified m6A regulators as potential biomarkers when mutations of driver genes occur, and investigated the role of these m6A candidates in pancreatic ductal adenocarcinoma (PDA). We first estimated the abnormal expression patterns of potential m6A regulators when all the driver genes are mutated, using The Cancer Genome Atlas and Gene Expression Omnibus databases. METTL16, an m6A“writer,” was chosen as a unique candidate of PDA, owing to its markedly differential expression under mutations of all driver genes (KRAS, TP53, CDKN2A, and SMAD4) and its favorable prognostic value. Moreover, METTL16 was under-expressed in PDA tissues and cell lines. Consistently, gain- and loss-of-function experiments indicated that it had a tumor suppressor role in vitro and in vivo. Further, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that METTL16 may have an effect on the tumor microenvironment. Notably, a markedly positive association between METTL16 expression and infiltration of B cells and CD8+ T cells was observed according to the CIBERSORT and TIMER databases. Enhanced expression of immune checkpoints and cytokines was elicited in patients with over-expression of METTL16. Notably, decreased expression of PD-L1 was observed when upregulation of METTL16 expression occurred in MIA PaCa-2 cells, while increased expression of PD-L1 existed when downregulation of METTL16 happened in HPAF-II cells. Collectively, these findings highlight the prognostic value of METTL16, and indicate that it is a potential immunotherapy target that could be used to regulate the tumor microenvironment and promote antitumor immunity in PDA.
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Affiliation(s)
- Liting Lu
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Dandan Zheng
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Junchi Qu
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanyan Zhuang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Juanfei Peng
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sihua Lan
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shineng Zhang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- *Correspondence: Shineng Zhang, ; Fengting Huang,
| | - Fengting Huang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
- *Correspondence: Shineng Zhang, ; Fengting Huang,
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12
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Zhang C, Sun Q, Zhang X, Qin N, Pu Z, Gu Y, Yan C, Zhu M, Dai J, Wang C, Li N, Jin G, Ma H, Hu Z, Zhang E, Tan F, Shen H. Gene amplification-driven RNA methyltransferase KIAA1429 promotes tumorigenesis by regulating BTG2 via m6A-YTHDF2-dependent in lung adenocarcinoma. Cancer Commun (Lond) 2022; 42:609-626. [PMID: 35730068 PMCID: PMC9257983 DOI: 10.1002/cac2.12325] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 05/09/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022] Open
Abstract
Background Epigenetic alterations have been shown to contribute immensely to human carcinogenesis. Dynamic and reversible N6‐methyladenosine (m6A) RNA modification regulates gene expression and cell fate. However, the reasons for activation of KIAA1429 (also known as VIRMA, an RNA methyltransferase) and its underlying mechanism in lung adenocarcinoma (LUAD) remain largely unexplored. In this study, we aimed to clarify the oncogenic role of KIAA1429 in the tumorigenesis of LUAD. Methods Whole‐genome sequencing and transcriptome sequencing of LUAD data were used to analyze the gene amplification of RNA methyltransferase. The in vitro and in vivo functions of KIAA1429 were investigated. Transcriptome sequencing, methylated RNA immunoprecipitation sequencing (MeRIP‐seq), m6A dot blot assays and RNA immunoprecipitation (RIP) were performed to confirm the modified gene mediated by KIAA1429. RNA stability assays were used to detect the half‐life of the target gene. Results Copy number amplification drove higher expression of KIAA1429 in LUAD, which was correlated with poor overall survival. Manipulating the expression of KIAA1429 could regulate the proliferation and metastasis of LUAD. Mechanistically, the target genes of KIAA1429‐mediated m6A modification were confirmed by transcriptome sequencing and MeRIP‐seq assays. We also revealed that KIAA1429 could regulate BTG2 expression in an m6A‐dependent manner. Knockdown of KIAA1429 significantly decreased the m6A levels of BTG2 mRNA, leading to enhanced YTH m6A RNA binding protein 2 (YTHDF2, the m6A “reader”)‐dependent BTG2 mRNA stability and promoted the expression of BTG2; thus, participating in the tumorigenesis of LUAD. Conclusions Our data revealed the activation mechanism and important role of KIAA1429 in LUAD tumorigenesis, which may provide a novel view on the targeted molecular therapy of LUAD.
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Affiliation(s)
- Chang Zhang
- Department of Epidemiology, School of Public Health, Southeast University, Nanjing, Jiangsu, 210009, P. R. China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Qi Sun
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Xu Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Na Qin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Zhening Pu
- Center of Clinical Research, Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, 214023, P. R. China
| | - Yayun Gu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Caiwang Yan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Meng Zhu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Juncheng Dai
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Cheng Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Ni Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, P. R. China
| | - Guangfu Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Hongxia Ma
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Zhibin Hu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Gusu School, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China
| | - Fengwei Tan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, P. R. China
| | - Hongbing Shen
- Department of Epidemiology, School of Public Health, Southeast University, Nanjing, Jiangsu, 210009, P. R. China.,Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Gusu School, Nanjing Medical University, Nanjing, Jiangsu, 211166, P. R. China.,Research Unit of Prospective Cohort of Cardiovascular Diseases and Cancers, Chinese Academy of Medical Sciences, Beijing, 100142, P. R. China
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13
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Mo L, Meng L, Huang Z, Yi L, Yang N, Li G. An analysis of the role of HnRNP C dysregulation in cancers. Biomark Res 2022; 10:19. [PMID: 35395937 PMCID: PMC8994388 DOI: 10.1186/s40364-022-00366-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/20/2022] [Indexed: 12/21/2022] Open
Abstract
Heterogeneous nuclear ribonucleoproteins C (HnRNP C) is part of the hnRNP family of RNA-binding proteins. The relationship between hnRNP C and cancers has been extensively studied, and dysregulation of hnRNP C has been found in many cancers. According to existing public data, hnRNP C could promote the maturation of new heterogeneous nuclear RNAs (hnRNA s, also referred to as pre-mRNAs) into mRNAs and could stabilize mRNAs, controlling their translation. This paper reviews the regulation and dysregulation of hnRNP C in cancers. It interacts with some cancer genes and other biological molecules, such as microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and double-stranded RNAs (dsRNAs). Even directly binds to them. The effects of hnRNP C on biological processes such as alternative cleavage and polyadenylation (APA) and N6-methyladenosine (m6A) modification differ among cancers. Its main function is regulating stability and level of translation of cancer genes, and the hnRNP C is regarded as a candidate biomarker and might be valuable for prognosis evaluation.
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Affiliation(s)
- Liyi Mo
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lijuan Meng
- Department of Ultrasonography, Second Affiliated Hospital, University of South China, Hengyang, 421001, Hunan, China
| | - Zhicheng Huang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Lan Yi
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Nanyang Yang
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
| | - Guoqing Li
- The Hengyang Key Laboratory of Cellular Stress Biology, Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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14
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Liao J, Wei Y, Liang J, Wen J, Chen X, Zhang B, Chu L. Insight into the structure, physiological function, and role in cancer of m6A readers—YTH domain-containing proteins. Cell Death Dis 2022; 8:137. [PMID: 35351856 PMCID: PMC8964710 DOI: 10.1038/s41420-022-00947-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/24/2022] [Accepted: 03/15/2022] [Indexed: 12/14/2022]
Abstract
YT521-B homology (YTH) domain-containing proteins (YTHDF1-3, YTHDC1-2) are the most crucial part of N6-methyladenosine (m6A) readers and play a regulatory role in almost all stages of methylated RNA metabolism and the progression of various cancers. Since m6A is identified as an essential post-transcriptional type, YTH domain-containing proteins have played a key role in the m6A sites of RNA. Hence, it is of great significance to study the interaction between YTH family proteins and m6A-modified RNA metabolism and tumor. In this review, their basic structure and physical functions in RNA transcription, splicing, exporting, stability, and degradation as well as protein translation are introduced. Then we discussed the expression regulation of YTH domain-containing proteins in cancers. Furthermore, we introduced the role of the YTH family in cancer biology and systematically demonstrated their functions in various aspects of tumorigenesis and development. To provide a more institute understanding of the role of YTH family proteins in cancers, we summarized their functions and specific mechanisms in various cancer types and presented their involvement in cancer-related signaling pathways.
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15
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Xie L, Dai R, Wang X, Xie G, Gao Z, Xu X. Comprehensive Analysis Revealed the Potential Implications of m6A Regulators in Lung Adenocarcinoma. Front Mol Biosci 2022; 9:806780. [PMID: 35419413 PMCID: PMC8995862 DOI: 10.3389/fmolb.2022.806780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/22/2022] [Indexed: 11/24/2022] Open
Abstract
Background: The biological significance of RNA N6-methyladenosine (m6A) decoration in tumorigenicity and progression has been highlighted in recent studies, but whether m6A modification plays a potential role in tumor microenvironment (TME) formation and immune regulation in lung adenocarcinoma (LUAD) remains unclear. Methods: m6A modification features were evaluated by analyzing the multi-omics features of 17 m6A regulators in over 1900 LUAD samples, and at the same time, the correlation between these modification patterns and TME characteristics was analyzed. An m6A score signature–based principal component analysis (PCA) algorithm was constructed to assess the prognosis and responses of individual patients to immunotherapeutic and targeted therapies. Results: Three different m6A modification patterns were determined in 1901 LUAD samples, which were found to be related to diverse clinical outcomes via different biological pathways. Based on the m6A score extracted from the m6A-associated signature genes, LUAD patients were separated into high- and low-m6A score groups. It was discovered that patients with high m6A scores had longer survival, lower tumor mutation loads, and low PD-L1/PDCD1/CTLA4/TAG3 expression level. In addition, LUAD patients with high m6A scores displayed lower IC50 to some targeted drugs, including nilotinib, erlotinib, imatinib, and lapatinib. Conclusion: m6A modification was significantly associated with the TME and clinical outcomes. These findings may help gain more insights into the role of m6A decoration in the molecular mechanism of LUAD, thus facilitating the development of more effective personalized treatment strategies.
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Affiliation(s)
- Lingling Xie
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
- *Correspondence: Lingling Xie,
| | - Rongyang Dai
- Department of Biochemistry and Molecular Biology, Southwest Medical University, Luzhou, China
| | - Xudong Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Guangfei Xie
- Department of Laboratory Medicine, People's Hospital of Sheyang County, Yancheng, China
| | - Zhihua Gao
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xinxin Xu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
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16
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Ma C, Ma RJ, Hu K, Zheng QM, Wang YP, Zhang N, Sun ZG. The molecular mechanism of METTL3 promoting the malignant progression of lung cancer. Cancer Cell Int 2022; 22:133. [PMID: 35331234 PMCID: PMC8944087 DOI: 10.1186/s12935-022-02539-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/01/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer remains one of the major causes of cancer-related death globally. Recent studies have shown that aberrant m6A levels caused by METTL3 are involved in the malignant progression of various tumors, including lung cancer. The m6A modification, the most abundant RNA chemical modification, regulates RNA stabilization, splicing, translation, decay, and nuclear export. The methyltransferase complex plays a key role in the occurrence and development of many tumors by installing m6A modification. In this complex, METTL3 is the first identified methyltransferase, which is also the major catalytic enzyme. Recent findings have revealed that METTL3 is remarkably associated with different aspects of lung cancer progression, influencing the prognosis of patients. In this review, we will focus on the underlying mechanism of METT3 in lung cancer and predict the future work and potential clinical application of targeting METTL3 for lung cancer therapy.
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Affiliation(s)
- Chao Ma
- Department of Thoracic Surgery, Central Hospital Affiliated to Shandong First Medical University, 105 Jiefang Road, Jinan, 250013, Shandong, China.,School of Clinical Medicine, Weifang Medical University, Weifang, 261053, Shangdong, China
| | - Rui-Jie Ma
- Cheeloo College of Medicine, Shandong University, Jinan, 250013, Shangdong, China
| | - Kang Hu
- Department of Thoracic Surgery, Central Hospital Affiliated to Shandong First Medical University, 105 Jiefang Road, Jinan, 250013, Shandong, China.,School of Clinical Medicine, Weifang Medical University, Weifang, 261053, Shangdong, China
| | - Qi-Ming Zheng
- Cheeloo College of Medicine, Shandong University, Jinan, 250013, Shangdong, China
| | - Ye-Peng Wang
- Department of Thoracic Surgery, Central Hospital Affiliated to Shandong First Medical University, 105 Jiefang Road, Jinan, 250013, Shandong, China
| | - Nan Zhang
- Breast Center, Central Hospital Affiliated to Shandong First Medical University, 105 Jiefang Road, Jinan, 250013, Shandong, China.
| | - Zhi-Gang Sun
- Department of Thoracic Surgery, Central Hospital Affiliated to Shandong First Medical University, 105 Jiefang Road, Jinan, 250013, Shandong, China.
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17
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Liu J, Li Z, Cheang I, Li J, Zhou C. RNA-Binding Protein IGF2BP1 Associated With Prognosis and Immunotherapy Response in Lung Adenocarcinoma. Front Genet 2022; 13:777399. [PMID: 35154270 PMCID: PMC8830935 DOI: 10.3389/fgene.2022.777399] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/03/2022] [Indexed: 12/21/2022] Open
Abstract
N6-methyladenosine (m6A) is the most common modification in eukaryotic RNAs and plays a vital role in the tumorigenesis and metastasis of various cancers. However, a comprehensive study of m6A methylation regulators in lung adenocarcinoma (LUAD) is still lacking. The present study aimed to systematically explore the role of m6A methylation regulators in LUAD. RNA sequencing data of 20 m6A methylation regulators and clinical data of LUAD patients were downloaded from The Cancer Genome Atlas (TCGA) database. The prognosis value of m6A methylation regulators in LUAD was evaluated using the Gene Expression Profiling Interactive Analysis (GEPIA) and PrognoScan database. The correlation between IGF2BP1 and immune infiltrates in LUAD was investigated via CIBERSORT and Tumor Immune Estimation Resource (TIMER). A total of 15 m6A modification regulators were significantly abnormally expressed in LUAD tissues. Survival analysis revealed that four genes (HNRNPC, HNRNPA2B1, IGF2BP1, and IGF2BP3) were significantly associated with poor prognosis in LUAD. Multivariate Cox regression analysis showed that only IGF2BP1 was an independent predictor of LUAD after adjusting common clinical parameters. The mutation rates of m6A modification regulators in LUAD were less than 10%. Further analysis revealed that IGF2BP1 expression was significantly correlated with immune infiltration, the expression of immune checkpoints, and tumor mutational burden (TMB) in LUAD. Our findings suggest that IGF2BP1 is an independent predictor and related to immunotherapy response in LUAD, which maybe a potential novel biomarker for LUAD prognosis and the status of tumor immunity.
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Affiliation(s)
- JinFeng Liu
- Department of Immunology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhi Li
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Iokfai Cheang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jinghang Li
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Chunlei Zhou
- Department of Pathology, Children's Hospital of Nanjing Medical University, Nanjing, China
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18
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HNRNPA2B1 inhibited SFRP2 and activated Wnt-β/catenin via m6A-mediated miR-106b-5p processing to aggravate stemness in lung adenocarcinoma. Pathol Res Pract 2022; 233:153794. [DOI: 10.1016/j.prp.2022.153794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 01/24/2022] [Accepted: 02/01/2022] [Indexed: 02/07/2023]
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19
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Tai J, Wang L, Guo H, Yan Z, Liu J. Prognostic implications of N 6-methyladenosine RNA regulators in breast cancer. Sci Rep 2022; 12:1222. [PMID: 35075167 PMCID: PMC8786853 DOI: 10.1038/s41598-022-05125-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 01/07/2022] [Indexed: 11/17/2022] Open
Abstract
The significance of N6-methyladenosine (m6A) RNA modifications in the progression of breast cancer (BC) has been recognised. However, their potential role and mechanism of action in the tumour microenvironment (TME) and immune response has not been demonstrated. Thus, the role of m6A regulators and their downstream target gene components in BC remain to be explored. In this study, we used a series of bioinformatics methods and experiments to conduct exploratory research on the possible role of m6A regulators in BC. First, two regulatory modes of immune activation and inactivation were determined by tumour classification. The TME, immune cell infiltration, and gene set variation analysis results confirmed the reliability of this pattern. The prognostic model of the m6A regulator was established by the least absolute shrinkage and selection operator and univariate and multivariate Cox analyses, with the two regulators most closely related to survival verified by real-time quantitative reverse transcription polymerase chain reaction. Next, the prognostic m6A regulator identified in the model was crossed with the differential copy number of variant genes in invasive BC (IBC), and it was determined that YTHDF1 was a hub regulator. Subsequently, single-cell analysis revealed the expression patterns of m6A regulators in different IBC cell populations and found that YTHDF1 had significantly higher expression in immune-related IBC cells. Therefore, we selected the intersection of the BC differential expression gene set and the differential expression gene set of a cell line with knocked-down YTHDF1 in literature to identify downstream target genes of YTHDF1, in which we found IFI6, EIR, and SPTBN1. A polymerase chain reaction was conducted to verify the results. Finally, we confirmed the role of YTHDF1 as a potential prognostic biomarker through pan-cancer analysis. Furthermore, our findings revealed that YTHDF1 can serve as a new molecular marker for BC immunotherapy.
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Affiliation(s)
- Jiaojiao Tai
- Department of Orthopedics, Honghui Hospital, Xi'an Jiaotong University, No. 555, Youyi Road, Beilin District, Xi'an, 710054, Shaanxi, People's Republic of China
| | - Linbang Wang
- Department of Orthopedic Surgery, The First Affiliated Hospital, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Hao Guo
- Department of Orthopedics, Honghui Hospital, Xi'an Jiaotong University, No. 555, Youyi Road, Beilin District, Xi'an, 710054, Shaanxi, People's Republic of China
| | - Ziqiang Yan
- Department of Orthopedics, Honghui Hospital, Xi'an Jiaotong University, No. 555, Youyi Road, Beilin District, Xi'an, 710054, Shaanxi, People's Republic of China.
| | - Jingkun Liu
- Department of Orthopedics, Honghui Hospital, Xi'an Jiaotong University, No. 555, Youyi Road, Beilin District, Xi'an, 710054, Shaanxi, People's Republic of China.
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20
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Sun N, Chu J, Hu W, Chen X, Yi N, Shen Y. A novel 14-gene signature for overall survival in lung adenocarcinoma based on the Bayesian hierarchical Cox proportional hazards model. Sci Rep 2022; 12:27. [PMID: 34996932 PMCID: PMC8741994 DOI: 10.1038/s41598-021-03645-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/06/2021] [Indexed: 12/14/2022] Open
Abstract
There have been few investigations of cancer prognosis models based on Bayesian hierarchical models. In this study, we used a novel Bayesian method to screen mRNAs and estimate the effects of mRNAs on the prognosis of patients with lung adenocarcinoma. Based on the identified mRNAs, we can build a prognostic model combining mRNAs and clinical features, allowing us to explore new molecules with the potential to predict the prognosis of lung adenocarcinoma. The mRNA data (n = 594) and clinical data (n = 470) for lung adenocarcinoma were obtained from the TCGA database. Gene set enrichment analysis (GSEA), univariate Cox proportional hazards regression, and the Bayesian hierarchical Cox proportional hazards model were used to explore the mRNAs related to the prognosis of lung adenocarcinoma. Multivariate Cox proportional hazard regression was used to identify independent markers. The prediction performance of the prognostic model was evaluated not only by the internal cross-validation but also by the external validation based on the GEO dataset (n = 437). With the Bayesian hierarchical Cox proportional hazards model, a 14-gene signature that included CPS1, CTPS2, DARS2, IGFBP3, MCM5, MCM7, NME4, NT5E, PLK1, POLR3G, PTTG1, SERPINB5, TXNRD1, and TYMS was established to predict overall survival in lung adenocarcinoma. Multivariate analysis demonstrated that the 14-gene signature (HR 3.960, 95% CI 2.710–5.786), T classification (T1, reference; T3, HR 1.925, 95% CI 1.104–3.355) and N classification (N0, reference; N1, HR 2.212, 95% CI 1.520–3.220; N2, HR 2.260, 95% CI 1.499–3.409) were independent predictors. The C-index of the model was 0.733 and 0.735, respectively, after performing cross-validation and external validation, a nomogram was provided for better prediction in clinical application. Bayesian hierarchical Cox proportional hazards models can be used to integrate high-dimensional omics information into a prediction model for lung adenocarcinoma to improve the prognostic prediction and discover potential targets. This approach may be a powerful predictive tool for clinicians treating malignant tumours.
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Affiliation(s)
- Na Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, China
| | - Jiadong Chu
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, China
| | - Wei Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, China
| | - Xuanli Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, China
| | - Nengjun Yi
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Yueping Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, 215123, China.
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21
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Zhang Q, Xu K. The role of regulators of RNA m6A methylation in lung cancer. Genes Dis 2022; 10:495-504. [DOI: 10.1016/j.gendis.2021.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 12/24/2022] Open
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22
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Ma Y, Zhang H. Genomics and Prognosis Analysis of N 6-Methyladenosine Regulators in Lung Adenocarcinoma. Front Genet 2021; 12:746666. [PMID: 34956315 PMCID: PMC8697852 DOI: 10.3389/fgene.2021.746666] [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: 07/24/2021] [Accepted: 10/11/2021] [Indexed: 12/09/2022] Open
Abstract
Objective: N6-methyladenosine (m6A) modification is involved in modulating various biological processes in human cancers. But the implication of m6A modification in lung adenocarcinoma (LUAD) is still unclear. Hence, this study conducted a comprehensive analysis of the expression and clinical implication of m6A regulators in LUAD. Methods: Consensus clustering analysis of 502 LUAD samples in the TCGA dataset was presented based on the expression profiles of 20 m6A regulators using ConsensusClusterPlus package. Overall survival (OS), activation of signaling pathways and tumor immunity (immune/stromal score, tumor purity, expression of HLA and immune checkpoints, and immune cell infiltration) were compared between m6A modification patterns. The m6A-related genes between patterns were identified and prognostic m6A-related genes were imported into LASSO-cox regression analysis. The m6A risk score was developed and its prognostic implication was evaluated and externally verified in the GSE30219 and GSE72094 dataset. Furthermore, a nomogram that contained independent prognostic indicators was established, followed by external verification. Results: Two m6A modification patterns were clustered across LUAD based on the expression similarity of the m6A regulators via consensus clustering analysis, with distinct OS, activation of signaling pathways and tumor immunity. Totally, 213 m6A-related genes that were identified by comparing two patterns were significantly related to LUAD prognosis. By LASSO method, we constructed the m6A risk score that was a reliable and independent prognostic factor for LUAD. Patients with low m6A risk score displayed a prominent survival advantage. After incorporating independent clinical features, we developed the prognostic nomogram that exhibited high predictive accuracy and the best clinical net benefit for OS. Conclusion: Collectively, our study may provide a clinically useful tool for precise prognostic management and optimization of immunotherapeutic strategies for LUAD patients.
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Affiliation(s)
- Yanpin Ma
- Department of Oncology, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Huping Zhang
- Department of Infectious Diseases, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
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23
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Chen Z, Zhong X, Xia M, Zhong J. The roles and mechanisms of the m6A reader protein YTHDF1 in tumor biology and human diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:1270-1279. [PMID: 34853726 PMCID: PMC8609105 DOI: 10.1016/j.omtn.2021.10.023] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
YTHDF1 is the most versatile and powerful reader protein of N6-methyladenosine (m6A)-modified RNA, and it can recognize both G(m6A)C and A(m6A)C RNAs as ligands without sequence selectivity. YTHDF1 regulates target gene expression by different mechanisms, such as promoting translation or regulating the stability of mRNA. Numerous studies have shown that YTHDF1 plays an important role in tumor biology and nontumor lesions by mediating the protein translation of important genes or by affecting the expression of key factors involved in many important cell signaling pathways. Therefore, in this review we focus on some of the roles of YTHDF1 in tumor biology and diseases.
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Affiliation(s)
- Zuyao Chen
- Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,The First Affiliated Hospital, Institute Center of Clinical Medicine, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,Department of Otorhinolaryngology, The First Affiliated Hospital, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
| | - Xiaolin Zhong
- Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,The First Affiliated Hospital, Institute Center of Clinical Medicine, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
| | - Min Xia
- Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,The First Affiliated Hospital, Institute Center of Clinical Medicine, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
| | - Jing Zhong
- Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,The First Affiliated Hospital, Institute Center of Clinical Medicine, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China.,Hunan Province Key Laboratory of Tumor Cellular and Molecular Pathology, Cancer Research Institute, Hengyang Medical School, University of South China, 421001 Hengyang, Hunan, China
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24
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Qu J, Wang L, Jiang M, Wei Z, Fu G, Zhang X. Survival-associated N 6-adenosine methyltransferase signatures in lung squamous cell carcinoma and clinical verification. BMC Cancer 2021; 21:1265. [PMID: 34814861 PMCID: PMC8611943 DOI: 10.1186/s12885-021-08939-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 10/25/2021] [Indexed: 01/22/2023] Open
Abstract
Background N6-methyladenine (m6A) is the most common modification of mRNA and IncRNA in higher organisms. m6A has been confirmed to be related to the formation and progression of tumors and m6A-related genes can be used as prognostic biomarkers in a variety of tumors. However, there have been no similar studies on lung squamous cell carcinoma. The main purpose of this study was aimed to explore the differential expression of m6A-related genes in lung squamous cell carcinoma tissues and its relationship with patient clinical prognosis. Methods We integrated three m6A writers that catalyze the methylation of adenine on mRNA molecules. The training set including 501 patients with LUSC was collected from The Cancer Genome Atlas (TCGA) database and the test set including 181 patients with LUSC was collected from the Gene Expression Omnibus (GEO) database. Based on the expression level of the m6A methylase gene, we established a tumor subgroup and risk-prognosis model to quantify the risk index and long-term patient prognosis, which were confirmed by principal component analysis (PCA) and receiver operating characteristic (ROC) curve analysis. After lung squamous cell carcinoma tissue specimens were obtained during surgery, immunohistochemistry (IHC) was used to verify the results in vitro. Results The results of the study showed that the expression of the three m6A methylases in tumor tissues and normal tissues was significantly different (P < 0.05). The survival-prognostic model based on METTL3 gene expression showed better predictive performance (AUC: 0.706). Patients in the high-risk and low-risk groups exhibited significant differences in terms of survival time and 5-year and 10-year survival rates. Immunohistochemistry revealed that patients with high METTL3 expression exhibited a longer survival time than those with low METTL3 expression. Conclusions Our study showed that the molecular phenotype based on the expression of METTL3 may be an independent risk factor affecting the prognosis of lung squamous cell carcinoma. These findings not only prove the important role of m6A methylase in lung squamous cell carcinoma, but are also expected to provide more accurate prognostic assessment and individualized treatment for patients with lung squamous cell carcinoma.
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Affiliation(s)
- Jialin Qu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Science, Jinan, 250117, China
| | - Li Wang
- Department of Oncology, Jiujiang University Affiliated Hospital, Jiujiang, 332000, China
| | - Man Jiang
- Cancer Precision Medicine Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
| | - Zhimin Wei
- Pathology Department, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
| | - Guangming Fu
- Pathology Department, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
| | - Xiaochun Zhang
- Cancer Precision Medicine Center, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China.
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25
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Zhang Z, Zhang C, Luo Y, Wu P, Zhang G, Zeng Q, Wang L, Yang Z, Xue L, Zheng B, Zeng H, Tan F, Xue Q, Gao S, Sun N, He J. m 6A regulator expression profile predicts the prognosis, benefit of adjuvant chemotherapy, and response to anti-PD-1 immunotherapy in patients with small-cell lung cancer. BMC Med 2021; 19:284. [PMID: 34802443 PMCID: PMC8607595 DOI: 10.1186/s12916-021-02148-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/29/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Small cell lung cancer (SCLC) is lethal and possesses limited therapeutic options. Platinum-based chemotherapy-with or without immune checkpoint inhibitors (anti-PDs)-is the current first-line therapy for SCLCs; however, its associated outcomes are heterogeneous. N6-methyladenosine (m6A) is a novel and decisive factor in tumour progression, chemotherapy resistance, and immunotherapy response. However, m6A modification in SCLC remains poorly understood. METHODS We systematically explored the molecular features and clinical significance of m6A regulators in SCLC. We then constructed an m6A regulator-based prognostic signature (m6A score) based on our examination of 256 cases with limited-stage SCLC (LS-SCLC) from three different cohorts-including an independent cohort that contained 150 cases with qPCR data. We additionally evaluated the relationships between the m6A score and adjuvant chemotherapy (ACT) benefits and the patients' responses to anti-PD-1 treatment. Immunohistochemical (IHC) staining and the HALO digital pathological platform were used to calculate CD8+ T cell density. RESULTS We observed abnormal somatic mutations and expressions of m6A regulators. Using the LASSO Cox model, a five-regulator-based (G3BP1, METTL5, ALKBH5, IGF2BP3, and RBM15B) m6A score was generated from the significant regulators to classify patients into high- and low-score groups. In the training cohort, patients with high scores had shorter overall survival (HR, 5.19; 2.75-9.77; P < 0.001). The prognostic accuracy of the m6A score was well validated in two independent cohorts (HR 4.6, P = 0.006 and HR 3.07, P < 0.001). Time-dependent ROC and C-index analyses found the m6A score to possess superior predictive power than other clinicopathological parameters. A multicentre multivariate analysis revealed the m6A score to be an independent prognostic indicator. Additionally, patients with low scores received a greater survival benefit from ACT, exhibited more CD8+ T cell infiltration, and were more responsive to cancer immunotherapy. CONCLUSIONS Our results, for the first time, affirm the significance of m6A regulators in LS-SCLC. Our multicentre analysis found that the m6A score was a reliable prognostic tool for guiding chemotherapy and immunotherapy selections for patients with SCLC.
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Affiliation(s)
- Zhihui Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chaoqi Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yuejun Luo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Peng Wu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Guochao Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Qingpeng Zeng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lide Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Zhaoyang Yang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Liyan Xue
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Bo Zheng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hua Zeng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fengwei Tan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Qi Xue
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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26
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Zhang K, Han Z, Zhao H, Liu S, Zeng F. An integrated model of FTO and METTL3 expression that predicts prognosis in lung squamous cell carcinoma patients. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1523. [PMID: 34790729 PMCID: PMC8576700 DOI: 10.21037/atm-21-4470] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/02/2021] [Indexed: 12/13/2022]
Abstract
Background Lung squamous cell carcinoma (LUSC) approximately accounts for a third of lung cancers. However, the role of N6-methyladenosine (m6A) in LUSC remains largely unknown according to previous studies. Methods In this study, we investigated the mutations, copy number variants (CNVs), expression of 20 m6A RNA methylation regulators, and clinical data from The Cancer Genome Atlas-LUSC (TCGA-LUSC). These data were used for the training cohort of screening potential biomarkers. The prognostic model of m6A RNA methylation regulators was constructed. A receiver operating characteristic (ROC) analysis was undertaken to determine the area under the curves (AUCs) (for 3- and 5-year survival) for the model. Additionally, the accuracy of the two-gene model was confirmed with external data verifications. Combined two-gene model and clinincal information were performed to construct a nomogram to predict patient’s prognostic risk assessment. Results Fat mass- and obesity-associated protein (FTO) and methyltransferase-like 3 (METTL3) were identified as potential prognostic biomarkers to evaluate benign and malignant tumors and prognosticate. The following prognostic model of m6A RNA methylation regulators was constructed: risk score = 0.162 × FTO − 0.069 × METTL3. Patients in low-risk group [median overall survival (mOS), 43.4 months] had longer survival than those with high-risk (mOS, 67.3 months) with P=0.0023. The smoking grade and risk score could be independent prognostic factors (P=0.00098 and P=0.0014, respectively). Ultimately, a nomogram was developed to assist clinicians to predict clinical outcomes. Conclusions FTO and METTL3 are potential prognostic biomarkers of LUSC. The two-gene model’s use of prognostic risk scores may provide guidance in the selection of therapeutic strategies.
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Affiliation(s)
- Kun Zhang
- Department of Thoracic Surgery, Sichuan Provincial People's Hospital, Chengdu, China
| | - Zhaojie Han
- Department of Thoracic Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Hongmei Zhao
- Chosen Med Technology (Beijing) Co., Ltd., Beijing, China
| | - Siyao Liu
- Chosen Med Technology (Beijing) Co., Ltd., Beijing, China
| | - Fuchun Zeng
- Department of Thoracic Surgery, Sichuan Provincial People's Hospital, Chengdu, China
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27
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Zhang RN, Wu DM, Wu LP, Gao GW. LncRNA LINC00337 sponges mir-1285-3p to promote proliferation and metastasis of lung adenocarcinoma cells by upregulating YTHDF1. Cancer Cell Int 2021; 21:550. [PMID: 34663343 PMCID: PMC8524958 DOI: 10.1186/s12935-021-02253-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 10/07/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Emerging studies have shown that long noncoding RNAs (lncRNAs) predominantly function in the carcinogenesis of multiple developing human tumors. The current study aimed to investigate the underlying mechanisms of LINC00337 in lung adenocarcinoma. METHODS We analyzed TCGA and GTEx datasets and chose LINC00337 as the research object. Cell proliferation, cell apoptosis, cell cycle, migration, and invasion were detected in the gain and loss experiments of LINC00337 both in vitro and in vivo. Moreover, RNA pull-down, luciferase reporter assays, western blotting analysis, and rescue experiments were performed to investigate the underlying molecular mechanisms of LINC00337 function. RESULTS LINC00337 expression was remarkably upregulated in lung adenocarcinoma. In addition, LINC00337 knockdown was shown to repress cell migration, invasion, and proliferation, as well as the cell cycle, and gear up apoptosis in lung adenocarcinoma in vitro and in vivo. With respect to the mechanism, LINC00337 knockdown boosted miR-1285-3p expression and then restrained YTHDF1 expression post-transcriptionally. Crucially, both miR-1285-3p decrement and YTHDF1 overexpression successfully reversed the influence on cell proliferation, migration, invasion, and apoptosis caused by LINC00337 shRNA. CONCLUSIONS These results suggest that LINC00337 acts as an oncogenic lncRNA, targeting miR-1285-3p and regulating YTHDF1 expression, to promote the progression of lung adenocarcinoma.
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Affiliation(s)
- Ru-Nan Zhang
- Department of Radiation Oncology, Xinxiang Central Hospital, No.56 Jinsui Road, Xinxiang, 453000, Henan, People's Republic of China.
| | - Dong-Mei Wu
- Department of Radiation Oncology, Xinxiang Central Hospital, No.56 Jinsui Road, Xinxiang, 453000, Henan, People's Republic of China
| | - Li-Ping Wu
- Department of Radiation Oncology, Xinxiang Central Hospital, No.56 Jinsui Road, Xinxiang, 453000, Henan, People's Republic of China
| | - Guo-Wei Gao
- Department of Radiation Oncology, Xinxiang Central Hospital, No.56 Jinsui Road, Xinxiang, 453000, Henan, People's Republic of China
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28
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Yuan Q, Ren J, Li L, Li S, Xiang K, Shang D. Development and validation of a novel N6-methyladenosine (m6A)-related multi- long non-coding RNA (lncRNA) prognostic signature in pancreatic adenocarcinoma. Bioengineered 2021; 12:2432-2448. [PMID: 34233576 PMCID: PMC8806915 DOI: 10.1080/21655979.2021.1933868] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Accumulating evidence has unveiled the pivotal roles of N6-methyladenosine (m6A) in pancreatic adenocarcinoma (PAAD). However, there are not many researches to predict the prognosis of PAAD using m6A-related long non-coding RNAs (lncRNAs). Raw data from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and the Genotype-Tissue Expression project (GTEx) were utilized to comprehensively analyze the expression and prognostic performances of 145 m6A-related lncRNAs in PAAD and to develop and validate a novel m6A-related multi-lncRNA prognostic signature (m6A-LPS) for PAAD patients. In total, 57 differentially expressed m6A-related lncRNAs with prognostic values were identified. Based on LASSO-Cox regression analysis, m6A-LPS was constructed and verified by using five-lncRNA expression profiles for TCGA and ICGC cohorts. PAAD patients were then divided into high- and low-risKBIE_A_1933868k subgroups with different clinical outcomes according to the median risk score; this was further verified by time-dependent receiver operating characteristic curves. Risk scores were significantly associated with clinical parameters such as histological grade and cancer status among PAAD patients. A nomogram consisting of risk score, grade, and cancer status was generated to predict the survival probability of PAAD patients, as also demonstrated by calibration curves. Discrepancies in cellular processes, signaling pathways, and immune status between the high- and low-risk subgroups were investigated by functional and single-sample gene set enrichment analyses. In conclusion, the novel m6A-LPS for PAAD patients was developed and validated, which might provide new insight into clinical decision-making and precision medicine.
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Affiliation(s)
- Qihang Yuan
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, China.,Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Jie Ren
- Department of Oncology, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Lunxu Li
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, China.,Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Shuang Li
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, China.,Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Kailai Xiang
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, China.,Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Dong Shang
- Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, China.,Clinical Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, China
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29
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Guo B, Zhang H, Wang J, Wu R, Zhang J, Zhang Q, Xu L, Shen M, Zhang Z, Gu F, Zeng W, Jia X, Yin C. Identification of the Signature Associated With m 6A RNA Methylation Regulators and m 6A-Related Genes and Construction of the Risk Score for Prognostication in Early-Stage Lung Adenocarcinoma. Front Genet 2021; 12:656114. [PMID: 34178026 PMCID: PMC8226131 DOI: 10.3389/fgene.2021.656114] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/21/2021] [Indexed: 12/22/2022] Open
Abstract
Background N6-methyladenosine (m6A) RNA modification is vital for cancers because methylation can alter gene expression and even affect some functional modification. Our study aimed to analyze m6A RNA methylation regulators and m6A-related genes to understand the prognosis of early lung adenocarcinoma. Methods The relevant datasets were utilized to analyze 21 m6A RNA methylation regulators and 5,486 m6A-related genes in m6Avar. Univariate Cox regression analysis, random survival forest analysis, Kaplan-Meier analysis, Chi-square analysis, and multivariate cox analysis were carried out on the datasets, and a risk prognostic model based on three feature genes was constructed. Results Respectively, we treated GSE31210 (n = 226) as the training set, GSE50081 (n = 128) and TCGA data (n = 400) as the test set. By performing univariable cox regression analysis and random survival forest algorithm in the training group, 218 genes were significant and three prognosis-related genes (ZCRB1, ADH1C, and YTHDC2) were screened out, which could divide LUAD patients into low and high-risk group (P < 0.0001). The predictive efficacy of the model was confirmed in the test group GSE50081 (P = 0.0018) and the TCGA datasets (P = 0.014). Multivariable cox manifested that the three-gene signature was an independent risk factor in LUAD. Furthermore, genes in the signature were also externally validated using the online database. Moreover, YTHDC2 was the important gene in the risk score model and played a vital role in readers of m6A methylation. Conclusion The findings of this study suggested that associated with m6A RNA methylation regulators and m6A-related genes, the three-gene signature was a reliable prognostic indicator for LUAD patients, indicating a clinical application prospect to serve as a potential therapeutic target.
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Affiliation(s)
- Bingzhou Guo
- School of Mathematical Sciences, Harbin Normal University, Harbin, China
| | - Hongliang Zhang
- Department of Emergency, The First Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jinliang Wang
- Department of Oncology, The Second Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Rilige Wu
- National Engineering Laboratory for Medical Big Data Application Technology, Chinese PLA General Hospital, Beijing, China.,Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Junyan Zhang
- National Engineering Laboratory for Medical Big Data Application Technology, Chinese PLA General Hospital, Beijing, China.,Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Qiqin Zhang
- Department of Orthopedics, Weifang Traditional Chinese Hospital, Weifang, China
| | - Lu Xu
- Laboratory of Translational Medicine, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Ming Shen
- Laboratory of Translational Medicine, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Zhibo Zhang
- The 78th Group Army Hospital of Chinese PLA, Mudanjiang, China
| | - Fangyan Gu
- Clinical Biobank Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, China
| | - Weiliang Zeng
- School of Mathematical Sciences, Harbin Normal University, Harbin, China
| | - Xiaodong Jia
- Department of Liver Disease, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chengliang Yin
- Faculty of Medicine, Macau University of Science and Technology, Macau, China
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30
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Li R, Yin YH, Ji XL, Liu X, Li JP, Qu YQ. Pan-Cancer Prognostic, Immunity, Stemness, and Anticancer Drug Sensitivity Characterization of N6-Methyladenosine RNA Modification Regulators in Human Cancers. Front Mol Biosci 2021; 8:644620. [PMID: 34150845 PMCID: PMC8211991 DOI: 10.3389/fmolb.2021.644620] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine RNA modification plays a significant role in the progression of multiple tumorigenesis. Our study identified the imperative role of m6A regulators in the tumor immune microenvironment, survival, stemness score, and anticancer drug sensitivity of pan-cancer. The Wilcox test was to identify the differential expression between 17 m6A regulators across 33 TCGA cancer types and their normal tissues from UCSC Xena GDC pan-cancer. Survival analysis of m6A-related regulators in 33 TCGA cancer types was identified using the "survival" and "survminer" package. The Spearman correlation test and Pearson correlation test were used to identify the correlation relationship between m6A regulators expression and tumor microenvironment, tumor stem cell score, and drug sensitivity of anticancer drugs. ConsensusPathDB was used for exploring m6A regulators functional enrichment. The 17 (METTL3, WTAP, METTL14, RBM15, RBM15B, VIRMA, HNRNPC, HNRNPA2B1, YTHDC1, ZC3H13, YTHDF1, YTHDC2, YTHDF2, IGF2BP3, IGF2BP1, FTO, and ALKBH5) m6A regulators were differentially expressed in 18 TCGA cancer types and adjacent normal tissues. Correlation analysis indicated that the relationship between the expression of 17 m6A regulators and tumor microenvironment indicated that the higher expression of m6A regulators, the higher the degree of tumor stem cells. The anticancer drug sensitivity analysis indicated that ZC3H13 expression had a positive relationship with anticancer drugs such as selumetinib, dabrafenib, cobimetinib, trametinib, and hypothemycin (p < 0.001). YTHDF2 expression was significantly negatively correlated with the anticancer drug dasatinib (p < 0.001). The pan-cancer immune subtype analysis showed that the 17 m6A regulators were significantly different in immune subtype C1 (wound healing), C3 (inflammatory), C2 (IFN-gamma dominant), C5 (immunological quiet), C4 (lymphocyte depleted), and C6 (TGF-beta dominant) (p < 0.001). Our study provides a comprehensive insight for revealing the significant role of m6A regulators in the tumor immune microenvironment, stemness score, and anticancer drug sensitivity of human cancers.
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Affiliation(s)
- Rui Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yun-Hong Yin
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xiu-Li Ji
- Department of Pulmonary Disease, Traditional Chinese Medicine Hospital of Jinan, Jinan, China
| | - Xiao Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jian-Ping Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
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31
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Wang Y, Su X, Zhao M, Xu M, Chen Y, Li Z, Zhuang W. Importance of N 6-methyladenosine RNA modification in lung cancer (Review). Mol Clin Oncol 2021; 14:128. [PMID: 33981432 PMCID: PMC8108057 DOI: 10.3892/mco.2021.2290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
The N6-methyladenosine (m6A) modification is the most common mRNA modification in eukaryotes and exerts biological functions by affecting RNA metabolism. The m6A modification is installed by m6A methyltransferases, removed by demethylases and recognized by m6A-binding proteins. The interaction between these three elements maintains the dynamic equilibrium of m6A in cells. Accumulating evidence indicates that m6A RNA methylation has a significant impact on RNA metabolism and is involved in the pathogenesis of cancer. Lung cancer is the leading cause of cancer-related deaths worldwide. The treatment options for lung cancer have developed considerably over the past few years; however, the survival rate of patients with lung cancer still remains very low. Although diagnostic methods and targeted therapies have been rapidly developed in recent years, the underlying mechanism and importance of m6A RNA methylation in the pathogenesis of lung cancer remains ambiguous. The current review summarized the biological functions of m6A modification and considers the potential roles of m6A regulators in the occurrence and development of lung cancer.
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Affiliation(s)
- Yueyang Wang
- Department of Molecular Biology Test Technique, College of Medical Technology, Beihua University, Jilin 132000, P.R. China
| | - Xiaoming Su
- Department of Molecular Biology Test Technique, College of Medical Technology, Beihua University, Jilin 132000, P.R. China
| | - Mingyao Zhao
- Department of Molecular Biology Test Technique, College of Medical Technology, Beihua University, Jilin 132000, P.R. China
| | - Mingchen Xu
- Department of Molecular Biology Test Technique, College of Medical Technology, Beihua University, Jilin 132000, P.R. China
| | - Yueqi Chen
- Department of Molecular Biology Test Technique, College of Medical Technology, Beihua University, Jilin 132000, P.R. China
| | - Zhengyi Li
- Department of Clinical Examination Basis, Laboratory Academy, Jilin Medical University, Jilin 132000, P.R. China
| | - Wenyue Zhuang
- Department of Molecular Biology Test Technique, College of Medical Technology, Beihua University, Jilin 132000, P.R. China
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32
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Wood S, Willbanks A, Cheng JX. The Role of RNA Modifications and RNA-modifying Proteins in Cancer Therapy and Drug Resistance. Curr Cancer Drug Targets 2021; 21:326-352. [PMID: 33504307 DOI: 10.2174/1568009621666210127092828] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
The advent of new genome-wide sequencing technologies has uncovered abnormal RNA modifications and RNA editing in a variety of human cancers. The discovery of reversible RNA N6-methyladenosine (RNA: m6A) by fat mass and obesity-associated protein (FTO) demethylase has led to exponential publications on the pathophysiological functions of m6A and its corresponding RNA modifying proteins (RMPs) in the past decade. Some excellent reviews have summarized the recent progress in this field. Compared to the extent of research into RNA: m6A and DNA 5-methylcytosine (DNA: m5C), much less is known about other RNA modifications and their associated RMPs, such as the role of RNA: m5C and its RNA cytosine methyltransferases (RCMTs) in cancer therapy and drug resistance. In this review, we will summarize the recent progress surrounding the function, intramolecular distribution and subcellular localization of several major RNA modifications, including 5' cap N7-methylguanosine (m7G) and 2'-O-methylation (Nm), m6A, m5C, A-to-I editing, and the associated RMPs. We will then discuss dysregulation of those RNA modifications and RMPs in cancer and their role in cancer therapy and drug resistance.
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Affiliation(s)
- Shaun Wood
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Amber Willbanks
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Jason X Cheng
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
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33
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Hu J, Cai D, Zhao Z, Zhong GC, Gong J. Suppression of Heterogeneous Nuclear Ribonucleoprotein C Inhibit Hepatocellular Carcinoma Proliferation, Migration, and Invasion via Ras/MAPK Signaling Pathway. Front Oncol 2021; 11:659676. [PMID: 33937074 PMCID: PMC8087488 DOI: 10.3389/fonc.2021.659676] [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: 01/28/2021] [Accepted: 03/30/2021] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC), the most common malignant tumor, has high fatality and recurrence rates. Accumulating evidence shows that heterogeneous nuclear ribonucleoprotein C (HNRNPC), which is mainly involved in RNA splicing, export, and translation, promotes progression and metastasis of multiple tumor types; however, the effects of HNRNPC in HCC are unknown. In the present study, high levels of HNRNPC were detected in tumor tissues compared with para-tumor tissues by immunohistochemical and western blot assays. Furthermore, Cox proportional hazards regression models, the Kaplan–Meier method, and clinicopathologic features analysis showed that HNRNPC was not only an independent prognostic factor for both overall and disease-free survival in HCC but also a predictor of large tumor size and advanced tumor stage. Functional experiments revealed that silencing of HNRNPC not only led to arrest of more HCC cells at G0/G1 phase to inhibit their proliferation, but also suppressed EMT process to block their invasion, and migration in vitro; this was related to the Ras/MAPK signaling pathway. In addition, blocking of HCC cell proliferation regulated by HNRNPC silencing was observed in vivo. Finally, rescue tests showed that after recovery of Ras/MAPK signaling pathway activity by treatment with Ras agonists, the proliferation, migration, and invasion suppression of Huh-7 and Hep 3B cell lines caused by HNRNPC knockdown was partially reversed. Taken together, these results indicate that HNRNPC knockdown inhibits HCC cell proliferation, migration and invasion, in part via the Ras/MAPK signaling pathway. Thus, HNRNPC may have an important role in the progression of HCC and represents a promising biomarker for evaluation of prognosis and a potential therapeutic target in HCC patients.
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Affiliation(s)
- Jiejun Hu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dong Cai
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhibo Zhao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guo-Chao Zhong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jianping Gong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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34
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Wu X, Sheng H, Wang L, Xia P, Wang Y, Yu L, Lv W, Hu J. A five-m6A regulatory gene signature is a prognostic biomarker in lung adenocarcinoma patients. Aging (Albany NY) 2021; 13:10034-10057. [PMID: 33795529 PMCID: PMC8064222 DOI: 10.18632/aging.202761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/13/2021] [Indexed: 12/15/2022]
Abstract
We analyzed the prognostic value of N6-methyladenosine (m6A) regulatory genes in lung adenocarcinoma (LADC) and their association with tumor immunity and immunotherapy response. Seventeen of 20 m6A regulatory genes were differentially expressed in LDAC tissue samples from the TCGA and GEO databases. We developed a five-m6A regulatory gene prognostic signature based on univariate and Lasso Cox regression analysis. Western blot analysis confirmed that the five prognostic m6A regulatory proteins were highly expressed in LADC tissues. We constructed a nomogram with five-m6A regulatory gene prognostic risk signature and AJCC stages. ROC curves and calibration curves showed that the nomogram was well calibrated and accurately distinguished high-risk and low-risk LADC patients. Weighted gene co-expression analysis showed significant correlation between prognostic risk signature genes and the turquoise module enriched with cell cycle genes. The high-risk LADC patients showed significantly higher PD-L1 levels, increased tumor mutational burden, and a lower proportion of CD8+ T cells in the tumor tissues and improved response to immune checkpoint blockade therapy. These findings show that this five-m6A regulatory gene signature is a prognostic biomarker in LADC and that immune checkpoint blockade is a potential therapeutic option for high-risk LADC patients.
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Affiliation(s)
- Xiao Wu
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Hongxu Sheng
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Luming Wang
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Pinghui Xia
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Yiqing Wang
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Li Yu
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Wang Lv
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
| | - Jian Hu
- Department of Thoracic Surgery, First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
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35
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Cheng Y, Wang M, Zhou J, Dong H, Wang S, Xu H. The Important Role of N6-methyladenosine RNA Modification in Non-Small Cell Lung Cancer. Genes (Basel) 2021; 12:genes12030440. [PMID: 33808751 PMCID: PMC8003501 DOI: 10.3390/genes12030440] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
N6-methyladenosine (m6A) is one of the most prevalent epigenetic modifications of eukaryotic RNA. The m6A modification is a dynamic and reversible process, regulated by three kinds of regulator, including m6A methyltransferases, demethylases and m6A-binding proteins, and this modification plays a vital role in many diseases, especially in cancers. Accumulated evidence has proven that this modification has a significant effect on cellular biological functions and cancer progression; however, little is known about the effects of the m6A modification in non-small cell lung cancer (NSCLC). In this review, we summarized how various m6A regulators modulate m6A RNA metabolism and demonstrated the effect of m6A modification on the progression and cellular biological functions of NSCLC. We also discussed how m6A modification affects the treatment, drug resistance, diagnosis and prognosis of NSCLC patients.
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36
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Wang H, Zhao X, Lu Z. m 6A RNA Methylation Regulators Act as Potential Prognostic Biomarkers in Lung Adenocarcinoma. Front Genet 2021; 12:622233. [PMID: 33643384 PMCID: PMC7902930 DOI: 10.3389/fgene.2021.622233] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/15/2021] [Indexed: 12/16/2022] Open
Abstract
N6-methyladenosine [m(6)A/m6A] methylation is one of the most common RNA modifications in eukaryotic cell mRNA and plays an important regulatory role in mRNA metabolism, splicing, translocation, stability, and translation. Previous studies have demonstrated that the m6A modification is highly associated with tumor cell proliferation, migration, and invasion. In the present study, five m6A regulatory factors have been revealed, namely heterogeneous nuclear ribonucleoprotein A2/B1(HNRNPA2B1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), Vir like m6A methyltransferase associated protein (KIAA1429/VIRMA), RNA binding motif protein 15 (RBM15) and methyltransferase like 3 (METTL3), which are closely related to the overall survival (OS) of patients with lung adenocarcinoma (LUAD). These five m6A regulatory factors exhibited potential prognostic value for the 1, 3, and 5-years survival outcomes of LUAD patients. Our findings revealed that several signaling pathways, such as cell cycle, DNA replication, RNA degradation, RNA polymerase, nucleotide excision repair and basal transcription factors, are activated in the high-risk group of LUAD patients.
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Affiliation(s)
- Hongbo Wang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiangxuan Zhao
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zaiming Lu
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
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37
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Gao C, Zhuang J, Li H, Liu C, Zhou C, Liu L, Feng F, Sun C. Gene signatures of 6-methyladenine regulators in women with lung adenocarcinoma and development of a risk scoring system: a retrospective study using the cancer genome atlas database. Aging (Albany NY) 2021; 13:3957-3968. [PMID: 33428597 PMCID: PMC7906130 DOI: 10.18632/aging.202364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/23/2020] [Indexed: 01/22/2023]
Abstract
Although the emergence of new treatments has improved the prognosis of women with lung adenocarcinoma (LUAD), the emergence of drug resistance limits their clinical efficacy. Therefore, there is an urgent need to identify new targets and develop a risk scoring system to evaluate the prognosis of patients. 6-methyladenine (M6A), as the most common methyl modification in RNA modification, its clinicopathological features, diagnosis and prognostic value in lung cancer, especially in LUAD remain to be discussed. We analyzed the clinical and sequencing data of the female LUAD cohort from The Cancer Genome Atlas (TCGA), evaluated the expression profiles of 16 M6A regulation-related genes in the cohort and the relationships between genetic changes and clinical characteristics, developed an M6A-related risk scoring system using Cox analysis. Finally, the copy number variations (CNVs) of the related genes in the samples were analyzed and verified using the cBioPortal platform. Compared with other clinical factors, this risk scoring system showed a higher predictive sensitivity and specificity. The M6A-related risk scoring system developed in this study may help to improve the screening of female patients at high risk of LUAD and provides important theoretical bioinformatics support for evaluating the prognosis of such patients.
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Affiliation(s)
- Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, Shandong, PR China
| | - Jing Zhuang
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, Shandong, PR China
| | - Huayao Li
- College of Basic Medical Sciences, Shandong University of Traditional Chinese Medicine, Jinan 250014, Shandong, PR China
| | - Cun Liu
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, Shandong, PR China
| | - Chao Zhou
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, Shandong, PR China
| | - Lijuan Liu
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, Shandong, PR China
| | - Fubin Feng
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, Shandong, PR China
| | - Changgang Sun
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, Shandong, PR China.,Cancer and Immunology Institute, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, PR China
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38
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Huang Y, Chen S, Qin W, Wang Y, Li L, Li Q, Yuan X. A Novel RNA Binding Protein-Related Prognostic Signature for Hepatocellular Carcinoma. Front Oncol 2020; 10:580513. [PMID: 33251144 PMCID: PMC7673432 DOI: 10.3389/fonc.2020.580513] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/24/2020] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a highly malignant and aggressive cancer with high recurrence rates and mortality. Some studies have illustrated that RNA binding proteins (RBPs) were involved in the carcinogenesis and development of multiple cancers, but the roles in HCC were still unclear. We downloaded the RNA-seq and corresponding clinical information of HCC from The Cancer Genome Atlas (TCGA) database, and 330 differentially expressed RBPs were identified between normal and HCC tissues. Through series of the univariate, the least absolute shrinkage selection operator (LASSO), and the stepwise multivariate Cox regression analyses, six prognosis-related key RBPs (CNOT6, UPF3B, MRPL54, ZC3H13, IFIT5, and PPARGC1A) were screened out from DE RBPs, and a six-RBP gene risk score signature was constructed in training set. Survival analysis indicated that HCC patients with high-risk scores had significantly worse overall survival than low-risk patients, and furthermore, the signature can be used as an independent prognostic indicator. The good accuracy of this prognostic signature was confirmed by the ROC curve analysis and was further validated in the International Cancer Genome Consortium (ICGC) HCC cohort. Besides, a nomogram based on six RBP genes was established and internally validated in the TCGA cohort. Gene set enrichment analysis demonstrated some cancer-related phenotypes were significantly gathered in the high-risk group. Overall, our study first identified an RBP-related six-gene prognostic signature, which could serve as a promising prognostic biomarker and provide some potential therapeutic targets for HCC.
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Affiliation(s)
- Yongbiao Huang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Chen
- Department of Hepatobiliary Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Wan Qin
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Yali Wang
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Long Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Qianxia Li
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
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39
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Li Y, Gu J, Xu F, Zhu Q, Chen Y, Ge D, Lu C. Molecular characterization, biological function, tumor microenvironment association and clinical significance of m6A regulators in lung adenocarcinoma. Brief Bioinform 2020; 22:5916941. [PMID: 33003204 DOI: 10.1093/bib/bbaa225] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/03/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022] Open
Abstract
N6-methyladenosine (m6A) modification can regulate a variety of biological processes. However, the implications of m6A modification in lung adenocarcinoma (LUAD) remain largely unknown. Here, we systematically evaluated the m6A modification features in more than 2400 LUAD samples by analyzing the multi-omics features of 23 m6A regulators. We depicted the genetic variation features of m6A regulators, and found mutations of FTO and YTHDF3 were linked to worse overall survival. Many m6A regulators were aberrantly expressed in tumors, among which FTO, IGF2BP3, YTHDF1 and RBM15 showed consistent alteration features across 11 independent cohorts. Besides, the regulator-pathway interaction network demonstrated that m6A modification was associated with various biological pathways, including immune-related pathways. The correlation between m6A regulators and tumor microenvironment was also assessed. We found that LRPPRC was negatively correlated with most tumor-infiltrating immune cells. On the other hand, we established a scoring tool named m6Sig, which was positively correlated with PD-L1 expression and could reflect both the tumor microenvironment characterization and prognosis of LUAD patients. Comparison of CNV between high and low m6Sig groups revealed differences on chromosome 7. Application of m6Sig on an anti-PD-L1 immunotherapy cohort confirmed that the high m6Sig group demonstrated therapeutic advantages and clinical benefits. Our study indicated that m6A modification is involved in many aspects of LUAD and contributes to tumor microenvironment formation. A better understanding of m6A modification will provide more insights into the molecular mechanisms of LUAD and facilitate developing more effective personalized treatment strategies. A web application was built along with this study (http://www.bioinfo-zs.com/luadexpress/).
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Affiliation(s)
- Yin Li
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
| | - Jie Gu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
| | - Fengkai Xu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
| | - Qiaoliang Zhu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
| | - Yiwei Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
| | - Di Ge
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
| | - Chunlai Lu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University
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40
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Ma Z, Ji J. N6-methyladenosine (m6A) RNA modification in cancer stem cells. Stem Cells 2020; 38:1511-1519. [PMID: 32985068 DOI: 10.1002/stem.3279] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/11/2020] [Indexed: 11/08/2022]
Abstract
Cancer stem cells (CSCs), a unique subset of undifferentiated cells with stem cell-like properties, have emerged as driving forces in mediating tumor growth, metastasis, and therapeutic resistance. Recent advances have highlighted that N6-methyladenosine (m6A) RNA modification plays an important role in cancer biology and CSCs. Dynamic m6A decoration has been demonstrated to be involved in CSC generation and maintenance, governing cancer progression and therapeutic resistance. In this review, we provide the first overview of the current knowledge of m6A modification implicated in CSCs and their impact on CSC properties, tumor progression, and responses to treatment. Finally, we also highlight the potential of m6A machinery as novel targets for cancer therapeutics. The involvement of m6A modification in CSCs provides a new direction for exploring cancer pathogenesis and inspires the development of effective strategies to fully eliminate both cancer cells and CSCs.
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Affiliation(s)
- Zhonghua Ma
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital and Institute, Beijing People's Republic of, China
| | - Jiafu Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Division of Gastrointestinal Cancer Translational Research Laboratory, Peking University Cancer Hospital and Institute, Beijing People's Republic of, China
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41
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Sun S, Han Q, Liang M, Zhang Q, Zhang J, Cao J. Downregulation of m 6 A reader YTHDC2 promotes tumor progression and predicts poor prognosis in non-small cell lung cancer. Thorac Cancer 2020; 11:3269-3279. [PMID: 32956555 PMCID: PMC7606000 DOI: 10.1111/1759-7714.13667] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/03/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
Background m6A modification affects the pathological progress of many diseases by affecting RNA stability and translocation. YTHDC2, a m6A reader, is associated with multiple cancers; however, little is known of its role in non‐small cell lung cancer (NSCLC). Methods The GEPIA, Oncomine and GEO databases were analyzed to assess expression of YTHDC2 in NSCLC patients. Quantitative polymerase chain reaction, western blot and immunohistochemistry were used to detect YTHDC2 expression in different NSCLC cell lines (H1299, H460, H292 and A549) and patients. The effects of YTHDC2 on NSCLC cell lines (A549 and H1299) proliferation and migration were employed using CCK8 and transwell assays. The potential target RNAs of YTHDC2 were obtained from the POSTAR database. Functional enrichment analysis of YTHDC2 targeted RNAs was performed using the Metascape database. Results GEPIA, Oncomine and GEO databases showed low expression of YTHDC2 in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) patients. YTHDC2 expression was significantly decreased in different NSCLC cell lines and our clinical samples. Moreover, low expression of YTHDC2 was significantly associated with poor differentiation, lymph node metastasis, tumor size and stage. In addition, YTHDC2 could suppress the proliferation and migration ability of A549 and H1299 cell lines. Kaplan‐Meier Plotter database analysis revealed that patients with low level of YTHDC2 had a significantly poor prognosis. Finally, functional enrichment analysis of YTHDC2 targeted RNAs indicated several enriched pathways related to cancer. Conclusions These findings elucidate that YTHDC2 suppresses tumorigenesis in NSCLC, indicating that YTHDC2 may be a promising therapeutic target for NSCLC. Key points Significant findings of the study This study demonstrated that the downregulation of YTHDC2 promotes tumor progression and predicts poor prognosis in non‐small cell lung cancer (NSCLC). What this study adds YTHDC2 might be a promising therapeutic target for non‐small cell lung cancer (NSCLC).
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Affiliation(s)
- Shulei Sun
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Qiang Han
- Department of Pathology, College of Basic Medical Sciences and First Affiliated Hospital of China Medical University, Shenyang, China
| | - Maoli Liang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Qian Zhang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Jing Zhang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Jie Cao
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University General Hospital, Tianjin, China
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Dai F, Wu Y, Lu Y, An C, Zheng X, Dai L, Guo Y, Zhang L, Li H, Xu W, Gao W. Crosstalk between RNA m 6A Modification and Non-coding RNA Contributes to Cancer Growth and Progression. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 22:62-71. [PMID: 32911345 PMCID: PMC7486578 DOI: 10.1016/j.omtn.2020.08.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 06/04/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022]
Abstract
N6-methyladenosine (m6A) is the most common RNA modification and has an important role in normal development and tumorigenesis. The abnormal expression of m6A regulators can lead to an imbalance in m6A levels in cancer cells, leading to the dysregulated expression of oncogenes and tumor suppressor genes that may contribute to cancer development, patient response to chemoradiotherapy, and clinical prognosis. Recent studies demonstrate that non-coding RNAs are involved in epigenetic modification of both DNA and RNA in tumor cells, and may also affect the development and progression of cancer by targeting m6A regulators. In this review, we describe the functional crosstalk between m6A and non-coding RNAs, particularly microRNA, long non-coding RNA, and circular RNA, and illustrate their roles in tumor regulation. Finally, we discuss the significance of non-coding RNA and m6A modification in the diagnosis, treatment, and prognosis of cancer patients, as well as potential future research directions.
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Affiliation(s)
- Fengsheng Dai
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Yongyan Wu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, P. R. China.
| | - Yan Lu
- Department of Otolaryngology Head & Neck Surgery, The First Hospital of Jinzhou Medical University, Jinzhou 121001, P. R. China
| | - Changming An
- Department of Head and Neck Surgery, Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P. R. China
| | - Xiwang Zheng
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Li Dai
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Yujia Guo
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China
| | - Linshi Zhang
- Department of Thyroid Surgery, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, P. R. China
| | - Huizheng Li
- Department of Otolaryngology Head & Neck Surgery, Dalian Municipal Friendship Hospital of Dalian Medical University, Dalian 116100, P. R. China
| | - Wei Xu
- Department of Head & Neck Surgery, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan 250022, P. R. China; Shandong Provincial Institute of Otolaryngology, Jinan 250022, P. R. China; Key Laboratory of Otolaryngology, Ministry of Health, Shandong University, Jinan 250022, P. R. China.
| | - Wei Gao
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Shanxi Province Clinical Medical Research Center for Precision Medicine of Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, P. R. China; Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan 030001, P. R. China.
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