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Wen Y, Chen X, Li R, Xie H, Zhi S, Wang K, Yi S, Liang W, Hu H, Rao S, Gao X. A novel prognostic risk-scoring system based on m 5C methylation regulator-mediated patterns for glioma patients. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200790. [PMID: 38595980 PMCID: PMC10965830 DOI: 10.1016/j.omton.2024.200790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/01/2024] [Indexed: 04/11/2024]
Abstract
N5-methylcytosine (m5C) methylation modification plays a crucial role in the epigenetic mechanisms underlying tumorigenesis, aggressiveness, and malignancy in diffuse glioma. Our study aimed to develop a novel prognostic risk-scoring system to assess the impact of m5C modification in glioma patients. Initially, we identified two distinct m5C clusters based on the expression level of m5C regulators in The Cancer Genome Atlas glioblastoma (TCGA-GBM) dataset. Differentially expressed genes (DEGs) between the two m5C cluster groups were determined. Utilizing these m5C regulation-related DEGs, we classified glioma patients into three gene cluster groups: A, B, and C. Subsequently, an m5C scoring system was developed through a univariate Cox regression model, quantifying the m5C modification patterns utilizing six DEGs associated with disease prognosis. The resulting scoring system allowed us to categorize patients into high- or low-risk groups based on their m5C scores. In test (TCGA-GBM) and validation (Chinese Glioma Genome Atlas [CGGA]-1018 and CGGA-301) datasets, glioma patients with a higher m5C score consistently exhibited shorter survival durations, fewer isocitrate dehydrogenase (IDH) mutations, less 1p/19q codeletion and higher World Health Organization (WHO) grades. Additionally, distinct immune cell infiltration characteristics were observed among different m5C cluster groups and risk groups. Our study developed a novel prognostic scoring system based on m5C modification patterns for glioma patients, complementing existing molecular classifications and providing valuable insights into prognosis for glioma patients.
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Affiliation(s)
- Yutong Wen
- Department of Neurology, Zhujiang Hospital of Southern Medical University, 253 Gongye Avenue, Guangzhou, Guangdong 510282, P.R. China
| | - Xiaotong Chen
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Runtong Li
- Department of Neurology, Zhujiang Hospital of Southern Medical University, 253 Gongye Avenue, Guangzhou, Guangdong 510282, P.R. China
| | - Haiting Xie
- Department of Neurology, Zhujiang Hospital of Southern Medical University, 253 Gongye Avenue, Guangzhou, Guangdong 510282, P.R. China
| | - Shuai Zhi
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Kaitao Wang
- Department of Neurology, Zhujiang Hospital of Southern Medical University, 253 Gongye Avenue, Guangzhou, Guangdong 510282, P.R. China
| | - Shang Yi
- Department of Neurology, Zhujiang Hospital of Southern Medical University, 253 Gongye Avenue, Guangzhou, Guangdong 510282, P.R. China
| | - Wen Liang
- Department of Radiology, Zhujiang Hospital of Southern Medical University, 253 Gongye Avenue, Guangzhou, Guangdong 510282, P.R. China
| | - Haiyan Hu
- Department of Oncology, Shanghai Jiao Tong University Affiliated Sixth People’s Hospital, Shanghai 200233, P.R. China
| | - Shitao Rao
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350122, China
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China
| | - Xiaoya Gao
- Department of Neurology, Zhujiang Hospital of Southern Medical University, 253 Gongye Avenue, Guangzhou, Guangdong 510282, P.R. China
- Department of Pediatric Neurology, Zhujiang Hospital of Southern Medical University, 253 Gongye Avenue, Guangzhou, Guangdong 510282, P.R. China
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Qin H, Yang S, Feng Z, Wu S, Cai T, Xie Z, Hu H. RNA modification-related EIF4G2 is an immunotherapy determinant in osteosarcoma: A single-cell sequencing analysis. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 38578024 DOI: 10.1002/tox.24261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/08/2024] [Accepted: 03/23/2024] [Indexed: 04/06/2024]
Abstract
The clinical outcomes of osteosarcoma are relatively dismal. As immunotherapy has revolutionized treatment for solid tumors, exploring novel immunotherapy-related therapeutic targets for osteosarcoma is important. In this study, we aimed to establish the connection between RNA modification and immunotherapy in osteosarcoma to identify novel therapeutic targets. An RNA modification-related signature was first developed using weight gene correlation network analysis and a machine-learning algorithm, random forest. The signature's prognostic value, drug prediction, and immune characteristics were analyzed. EIF4G2 from the signature was next identified as a critical immunotherapy determinant. EIF4G2 could also promote tumor proliferation, migration, and M2 macrophage migration by single-cell sequencing analysis and in vitro validation. Our signature and EIF4G2 are expected to provide valuable insights into the clinical management of osteosarcoma.
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Affiliation(s)
- Haocheng Qin
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Shu Yang
- Respiratory Intensive Care Unit, The First Affiliated Hospital, Hunan Normal University Hunan Provincial People's Hospital, Changsha, China
| | - Zhennan Feng
- Department of Orthopedics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Song Wu
- Department of Orthopedics, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ting Cai
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Changsha Medical University, Changsha, China
| | - Zijing Xie
- Hunan Provincial Key Laboratory of the Traditional Chinese Medicine Agricultural Biogenomics, Changsha Medical University, Changsha, China
| | - Hai Hu
- Department of Orthopedics, The Third Xiangya Hospital, Central South University, Changsha, China
- Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Changsha Medical University, Changsha, China
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3
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Perlegos AE, Byrns CN, Bonini NM. Cell type-specific regulation of m 6 A modified RNAs in the aging Drosophila brain. Aging Cell 2024; 23:e14076. [PMID: 38205931 DOI: 10.1111/acel.14076] [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: 08/15/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
The aging brain is highly vulnerable to cellular stress, and neurons employ numerous mechanisms to combat neurotoxic proteins and promote healthy brain aging. The RNA modification m6 A is highly enriched in the Drosophila brain and is critical for the acute heat stress response of the brain. Here we examine m6 A in the fly brain with the chronic stresses of aging and degenerative disease. m6 A levels dynamically increased with both age and disease in the brain, marking integral neuronal identity and signaling pathway transcripts that decline in level with age and disease. Unexpectedly, there is opposing impact of m6 A transcripts in neurons versus glia, which conferred different outcomes on animal health span upon Mettl3 knockdown to reduce m6 A: whereas Mettl3 function is normally beneficial to neurons, it is deleterious to glia. Moreover, knockdown of Mettl3 in glial tauopathy reduced tau pathology and increased animal survival. These findings provide mechanistic insight into regulation of m6 A modified transcripts with age and disease, highlighting an overall beneficial function of Mettl3 in neurons in response to chronic stresses, versus a deleterious impact in glia.
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Affiliation(s)
- Alexandra E Perlegos
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - China N Byrns
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nancy M Bonini
- Neuroscience Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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4
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Zheng P, Zhang X, Ren D, Bai Q. Classification of Glioblastoma Associated with Immune Checkpoints and Tumor Microenvironment based on Immunogenomic Profiling. Neurol India 2024; 72:297-303. [PMID: 38691473 DOI: 10.4103/ni.ni_1070_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 08/01/2022] [Indexed: 05/03/2024]
Abstract
BACKGROUND Immune microenvironment is involved in tumor initiation and progression, and its effect on glioblastoma (GBM) is still unknown. OBJECT We sought to investigate the association between immune status and GBM. METHODS Transcriptome data and the relevant clinical data were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus (GEO) databases, and we identified two immune subtypes based on 29 immune-associated gene sets. RESULTS Through single-sample gene set enrichment analysis (ssGSEA), we found that the high-immunity subtype had the most tumor-infiltrating immune cells and immune checkpoint molecules in GBM patients. Furthermore, we could more effectively identify immune signature pathways in GBM. CONCLUSION After validation with the GEO dataset, we conclude that the identified GBM high-immune subtypes may be amenable to the application of novel immune therapy for GBM.
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Affiliation(s)
- Ping Zheng
- Department of Neurosurgery, Shanghai Pudong New Area People's Hospital, Shanghai, China
- Department of Key Molecular Lab, Shanghai Pudong New Area People's Hospital, Shanghai, China
| | - Xiaoxue Zhang
- Department of Key Molecular Lab, Shanghai Pudong New Area People's Hospital, Shanghai, China
| | - Dabin Ren
- Department of Neurosurgery, Shanghai Pudong New Area People's Hospital, Shanghai, China
| | - Qingke Bai
- Department of Neurology, Shanghai Pudong New Area People's Hospital, Shanghai, China
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5
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Li Y, Liu H, He C, Ma L. Comparison of transcriptome-wide N6-methyladenosine profiles from healthy trio families reveals regulator-mediated methylation alterations. Genetics 2024; 226:iyad206. [PMID: 38001375 DOI: 10.1093/genetics/iyad206] [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: 09/19/2023] [Revised: 09/19/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
The N6-methyladenosine (m6A) modification is a highly conserved RNA modification found in eukaryotic messenger RNAs (mRNAs). It plays a vital role in regulating various biological processes. Dysregulation of m6A modifications has been linked to a range of complex genetic diseases in humans. However, there has been a lack of comprehensive characterization and comparison of m6A modifications at the transcriptome-wide level within families. To address this gap, we profiled transcriptome-wide m6A methylation in 18 individuals across 6 Yoruba trio families. The m6A methylomes of these 18 individuals revealed that m6A modifications in children showed greater similarity to each other than to their parents. This suggests that m6A modifications are influenced by multiple factors rather than solely determined by genetic factors. Additionally, we found that mRNAs exhibiting m6A modifications specific to children were enriched in cell cycle control processes, while those with m6A modifications specific to parents were associated with chromatin modifications. Furthermore, our analysis on the interactions between differentially expressed m6A-related regulatory genes and age-related genes suggested that age might be one of the factors influencing m6A modifications. In summary, our study provided a valuable dataset that highlighted the differences and functional diversity of m6A modifications within and between trio families.
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Affiliation(s)
- Yini Li
- School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 201100, China
- Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou 310024, Zhejiang, China
| | - Hang Liu
- Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou 310024, Zhejiang, China
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
- Medical Scientist Training Program/Committee on Cancer Biology, The University of Chicago, Chicago, IL 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Lijia Ma
- Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
- School of Life Sciences, Westlake University, 600 Dunyu Road, Hangzhou 310024, Zhejiang, China
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6
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Xin Z, Lv R, Liu W, Wang S, Gao Q, Zhang B, Sun G. An ensemble learning-based feature selection algorithm for identification of biomarkers of renal cell carcinoma. PeerJ Comput Sci 2024; 10:e1768. [PMID: 38196962 PMCID: PMC10773758 DOI: 10.7717/peerj-cs.1768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/30/2023] [Indexed: 01/11/2024]
Abstract
Feature selection plays a crucial role in classification tasks as part of the data preprocessing process. Effective feature selection can improve the robustness and interpretability of learning algorithms, and accelerate model learning. However, traditional statistical methods for feature selection are no longer practical in the context of high-dimensional data due to the computationally complex. Ensemble learning, a prominent learning method in machine learning, has demonstrated exceptional performance, particularly in classification problems. To address the issue, we propose a three-stage feature selection algorithm framework for high-dimensional data based on ensemble learning (EFS-GINI). Firstly, highly linearly correlated features are eliminated using the Spearman coefficient. Then, a feature selector based on the F-test is employed for the first stage selection. For the second stage, four feature subsets are formed using mutual information (MI), ReliefF, SURF, and SURF* filters in parallel. The third stage involves feature selection using a combinator based on GINI coefficient. Finally, a soft voting approach is proposed to employ for classification, including decision tree, naive Bayes, support vector machine (SVM), k-nearest neighbors (KNN) and random forest classifiers. To demonstrate the effectiveness and efficiency of the proposed algorithm, eight high-dimensional datasets are used and five feature selection methods are employed to compare with our proposed algorithm. Experimental results show that our method effectively enhances the accuracy and speed of feature selection. Moreover, to explore the biological significance of the proposed algorithm, we apply it on the renal cell carcinoma dataset GSE40435 from the Gene Expression Omnibus database. Two feature genes, NOP2 and NSUN5, are selected by our proposed algorithm. They are directly involved in regulating m5c RNA modification, which reveals the biological importance of EFS-GINI. Through bioinformatics analysis, we shows that m5C-related genes play an important role in the occurrence and progression of renal cell carcinoma, and are expected to become an important marker to predict the prognosis of patients.
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Affiliation(s)
- Zekun Xin
- Department of Urology, Aerospace Center Hospital, Beijing, China
| | - Ruhong Lv
- School of Computer and Information Technology, Beijing Jiaotong University, Beijing, China
| | - Wei Liu
- Department of Urology, Aerospace Center Hospital, Beijing, China
| | - Shenghan Wang
- Department of Urology, Aerospace Center Hospital, Beijing, China
| | - Qiang Gao
- Department of Urology, Aerospace Center Hospital, Beijing, China
| | - Bao Zhang
- Department of Urology, Aerospace Center Hospital, Beijing, China
| | - Guangyu Sun
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
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7
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Wei H, Xu Y, Lin L, Li Y, Zhu X. A review on the role of RNA methylation in aging-related diseases. Int J Biol Macromol 2024; 254:127769. [PMID: 38287578 DOI: 10.1016/j.ijbiomac.2023.127769] [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: 09/18/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024]
Abstract
Senescence is the underlying mechanism of organism aging and is robustly regulated at the post-transcriptional level. This regulation involves the chemical modifications, of which the RNA methylation is the most common. Recently, a rapidly growing number of studies have demonstrated that methylation is relevant to aging and aging-associated diseases. Owing to the rapid development of detection methods, the understanding on RNA methylation has gone deeper. In this review, we summarize the current understanding on the influence of RNA modification on cellular senescence, with a focus on mRNA methylation in aging-related diseases, and discuss the emerging potential of RNA modification in diagnosis and therapy.
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Affiliation(s)
- Hong Wei
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Department of Neurology, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuhao Xu
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Li Lin
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Yuefeng Li
- Medical School, Jiangsu University, Zhenjiang, Jiangsu 212001, China.
| | - Xiaolan Zhu
- Reproductive Center, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China; Central Laboratory of the Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China.
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8
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Shao D, Liu C, Wang Y, Lin J, Cheng X, Han P, Li Z, Jian D, Nie J, Jiang M, Wei Y, Xing J, Guo Z, Wang W, Yi X, Tang H. DNMT1 determines osteosarcoma cell resistance to apoptosis by associatively modulating DNA and mRNA cytosine-5 methylation. FASEB J 2023; 37:e23284. [PMID: 37905981 DOI: 10.1096/fj.202301306r] [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: 06/28/2023] [Revised: 09/17/2023] [Accepted: 10/17/2023] [Indexed: 11/02/2023]
Abstract
Cellular apoptosis is a central mechanism leveraged by chemotherapy to treat human cancers. 5-Methylcytosine (m5C) modifications installed on both DNA and mRNA are documented to regulate apoptosis independently. However, the interplay or crosstalk between them in cellular apoptosis has not yet been explored. Here, we reported that promoter methylation by DNMT1 coordinated with mRNA methylation by NSun2 to regulate osteosarcoma cell apoptosis. DNMT1 was induced during osteosarcoma cell apoptosis triggered by chemotherapeutic drugs, whereas NSun2 expression was suppressed. DNMT1 was found to repress NSun2 expression by methylating the NSun2 promoter. Moreover, DNMT1 and NSun2 regulate the anti-apoptotic genes AXL, NOTCH2, and YAP1 through DNA and mRNA methylation, respectively. Upon exposure to cisplatin or doxorubicin, DNMT1 elevation drastically reduced the expression of these anti-apoptotic genes via enhanced promoter methylation coupled with NSun2 ablation-mediated attenuation of mRNA methylation, thus rendering osteosarcoma cells to apoptosis. Collectively, our findings establish crosstalk of importance between DNA and RNA cytosine methylations in determining osteosarcoma resistance to apoptosis during chemotherapy, shedding new light on future treatment of osteosarcoma, and adding additional layers to the control of gene expression at different epigenetic levels.
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Affiliation(s)
- Dongxing Shao
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
| | - Cihang Liu
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
| | - Yingying Wang
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
| | - Jing Lin
- Department of Laboratory Medicine, the Fourth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaolei Cheng
- Department of Anesthesiology, Affiliated Drum Tower Hospital of Medical School of Nanjing University, Nanjing, China
| | - Pei Han
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Zhen Li
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
| | - Dongdong Jian
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Junwei Nie
- R&D Department, Vazyme Biotech Co., Ltd, Nanjing, China
| | | | - Yuanzhi Wei
- R&D Department, Vazyme Biotech Co., Ltd, Nanjing, China
| | - Junyue Xing
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
- Henan Key Laboratory of Chronic Disease Management, Department of Health Management Center, Henan Provincial People's Hospital, Department of Health Management Center of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhiping Guo
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
- Henan Key Laboratory of Chronic Disease Management, Department of Health Management Center, Henan Provincial People's Hospital, Department of Health Management Center of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China
| | - Wengong Wang
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xia Yi
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hao Tang
- National Health Commission Key Laboratory of Cardiovascular Regenerative Medicine, Heart Center of Henan Provincial People's Hospital, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases, Zhengzhou, China
- Henan Key Laboratory of Chronic Disease Management, Department of Health Management Center, Henan Provincial People's Hospital, Department of Health Management Center of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China
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Yang Y, Wang F, Teng H, Zhang C, Zhang Y, Chen P, Li Q, Kan X, Chen Z, Wang Z, Yu Y. Integrative analysis of multi-omics data reveals a pseudouridine-related lncRNA signature for prediction of glioma prognosis and chemoradiotherapy sensitivity. Comput Biol Med 2023; 166:107428. [PMID: 37748218 DOI: 10.1016/j.compbiomed.2023.107428] [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: 05/06/2023] [Revised: 07/12/2023] [Accepted: 08/28/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Glioblastoma is the most common type of glioma with a high incidence and poor prognosis, and effective medical treatment remains challenging. Pseudouridine (Ψ) is the first post-transcriptional modification discovered and one of the most abundant modifications to RNA. However, the prognostic value of Ψ-related lncRNAs (ΨrLs) for glioma patients has never been systematically evaluated. This study aims to construct a risk model based on ΨrLs signature and to validate the predictive efficiency of the model. METHOD Transcriptomic data, genomic data, and relevant clinical data of glioma patients were extracted from the Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). ΨrLs with significant correlation with Ψ-related genes were identified, and univariate Cox regression, least absolute shrinkage and selection operator (LASSO) regression, and multivariate Cox regression were used to further select biomarkers and construct a ΨrLs signature risk model. Then, the expression of lncRNAs of ΨrLs signature in multiple glioma cell lines was detected by qPCR. Further, ROC analysis, stratification analysis, correlation analysis, survival analysis, nomogram, enrichment analysis, immune infiltration analysis, chemoradiotherapy sensitivity analysis, somatic mutation, and recurrent copy number variation (CNV) analysis were used to validate the predictive efficiency of ΨrLs signature in TCGA and CGGA datasets. RESULTS A four-lncRNA ΨrLs signature (DNAJC27-AS1, GDNF-AS1, ZBTB20-AS4, and DNMBP-AS1) risk model was constructed. By ROC analysis, stratified analysis, correlation analysis, survival analysis, and nomogram, the signature showed satisfactory predictive efficiency. Functional enrichment analysis revealed the differences in immune-related biological processes between high- and low-risk groups. Immune infiltration analysis showed that the high-risk group had lower tumor purity and higher stromal, immune and ESTIMATE scores. Mitoxantrone was identified as effective drug for low-risk group of glioma patients. Key genes in glioma development, including IDH1, EGFR, PTEN, etc., were differentially mutated between risk groups. The main recurrent CNVs in low-risk groups were 19q13.42 deletion and 7q34 amplification; 10q23.31 deletion and 12q14.1 in the high-risk group. CONCLUSIONS Our study identified a four-lncRNA ΨrLs signature that effectively predicts the prognosis of glioma patients and may serve as a diagnostic tool. Risk scores of glioma patients generated by the signature is associated with immune-related biological processes and chemoradiotherapy sensitivity. These findings may inform the development of more targeted and effective therapies for glioma patients.
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Affiliation(s)
- Yanbo Yang
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100000, China.
| | - Fei Wang
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215400, China; Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, 215127, China.
| | - Haiying Teng
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215400, China.
| | - Chuanpeng Zhang
- Department of Neurosurgery, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China.
| | - Yulian Zhang
- Department of Neurosurgery, China-Japan Friendship Hospital, Beijing, China.
| | - Pengyu Chen
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100000, China.
| | - Quan Li
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215400, China; Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, 215127, China.
| | - Xiuji Kan
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215400, China; Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, 215127, China.
| | - Zhouqing Chen
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215400, China.
| | - Zhong Wang
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, 215400, China.
| | - Yanbing Yu
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100000, China.
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10
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Zheng P, Zhang X, Ren D, Bai Q, Jiang P. Novel Immune-Related LncRNA Pairs are Associated with Immunol Infiltration and Survival Status in Glioblastoma. Neurol India 2023; 71:1226-1234. [PMID: 38174463 DOI: 10.4103/0028-3886.391381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Background Immune-related lncRNA is involved in tumor initiation and progression, while its effect in glioblastoma (GBM) is still unknown. Objective We sought to investigate the association between immune-related lncRNA (ir-lncRNA) and GBM. Methods Transcriptomic and clinical data were obtained from the TCGA dataset, and we found 2008 ir-lncRNA differentially expressed between GBM and adjacent brain tissues. Results Appling the univariate Cox and Lasso regression model, we found 30 prognosis-related ir-lncRNA pairs to construct a Cox regression risk model to associate the outcome of GBM patients. Furthermore, with this risk model, we can identify the tumor immune infiltration status, the expression of immunosuppressive biomarkers, and chemical sensitivity in GBM patients. Conclusions We constructed an immunologic risk model with lncRNA to associate the survival outcome of GBM patients, which can provide useful biomarkers.
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Affiliation(s)
- Ping Zheng
- Department of Neurosurgery, Shanghai Pudong New Area People's Hospital; Key Molecular Lab, Shanghai Pudong New Area People's Hospital, Shanghai, China
| | - Xiaoxue Zhang
- Key Molecular Lab, Shanghai Pudong New Area People's Hospital, Shanghai, China
| | - Dabin Ren
- Department of Neurosurgery, Shanghai Pudong New Area People's Hospital, Shanghai, China
| | - Qingke Bai
- Department of Neurology, Shanghai Pudong New Area People's Hospital, Shanghai, China
| | - Ping Jiang
- Department of Nursing, Shanghai Pudong New Area People's Hospital, Shanghai, China
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11
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Zhou J, Kong YS, Vincent KM, Dieters‐Castator D, Bukhari AB, Glubrecht D, Liu R, Quilty D, Findlay SD, Huang X, Xu Z, Yang RZ, Zhang L, Tang E, Lajoie G, Eisenstat DD, Gamper AM, Fahlman R, Godbout R, Postovit L, Fu Y. RNA cytosine methyltransferase NSUN5 promotes protein synthesis and tumorigenic phenotypes in glioblastoma. Mol Oncol 2023; 17:1763-1783. [PMID: 37057706 PMCID: PMC10483612 DOI: 10.1002/1878-0261.13434] [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: 07/15/2022] [Revised: 02/28/2023] [Accepted: 04/13/2023] [Indexed: 04/15/2023] Open
Abstract
Glioblastoma (GBM) is the most common and aggressive malignant primary brain tumor in adults. The standard treatment achieves a median overall survival for GBM patients of only 15 months. Hence, novel therapies based on an increased understanding of the mechanistic underpinnings of GBM are desperately needed. In this study, we show that elevated expression of 28S rRNA (cytosine-C(5))-methyltransferase NSUN5, which methylates cytosine 3782 of 28S rRNA in GBM cells, is strongly associated with the poor survival of GBM patients. Moreover, we demonstrate that overexpression of NSUN5 increases protein synthesis in GBM cells. NSUN5 knockdown decreased protein synthesis, cell proliferation, sphere formation, migration, and resistance to temozolomide in GBM cell lines. NSUN5 knockdown also decreased the number and size of GBM neurospheres in vitro. As a corollary, mice harboring U251 tumors wherein NSUN5 was knocked down survived longer than mice harboring control tumors. Taken together, our results suggest that NSUN5 plays a protumorigenic role in GBM by enabling the enhanced protein synthesis requisite for tumor progression. Accordingly, NSUN5 may be a hitherto unappreciated target for the treatment of GBM.
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Affiliation(s)
- Jiesi Zhou
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Yan Shu Kong
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Krista M. Vincent
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | | | - Amirali B. Bukhari
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Darryl Glubrecht
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Rong‐Zong Liu
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Douglas Quilty
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
- Department of Biomedical and Molecular SciencesQueen's UniversityKingstonONCanada
| | - Scott D. Findlay
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Xiaowei Huang
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Zhihua Xu
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Rui Zhe Yang
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Lanyue Zhang
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Emily Tang
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Gilles Lajoie
- Department of BiochemistryWestern UniversityLondonONCanada
| | - David D. Eisenstat
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
- Department of PaediatricsUniversity of MelbourneParkvilleVic.Australia
| | - Armin M. Gamper
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Richard Fahlman
- Department of Biochemistry, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Roseline Godbout
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
| | - Lynne‐Marie Postovit
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
- Department of Biomedical and Molecular SciencesQueen's UniversityKingstonONCanada
| | - YangXin Fu
- Department of Oncology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonABCanada
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12
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Mekala JR, Adusumilli K, Chamarthy S, Angirekula HSR. Novel sights on therapeutic, prognostic, and diagnostics aspects of non-coding RNAs in glioblastoma multiforme. Metab Brain Dis 2023; 38:1801-1829. [PMID: 37249862 PMCID: PMC10227410 DOI: 10.1007/s11011-023-01234-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/09/2023] [Indexed: 05/31/2023]
Abstract
Glioblastoma Multiforme (GBM) is the primary brain tumor and accounts for 200,000 deaths each year worldwide. The standard therapy includes surgical resection followed by temozolomide (TMZ)-based chemotherapy and radiotherapy. The survival period of GBM patients is only 12-15 months. Therefore, novel treatment modalities for GBM treatment are urgently needed. Mounting evidence reveals that non-coding RNAs (ncRNAs) were involved in regulating gene expression, the pathophysiology of GBM, and enhancing therapeutic outcomes. The combinatory use of ncRNAs, chemotherapeutic drugs, and tumor suppressor gene expression induction might provide an innovative, alternative therapeutic approach for managing GBM. Studies have highlighted the role of Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in prognosis and diagnosis. Dysregulation of ncRNAs is observed in virtually all tumor types, including GBMs. Studies have also indicated the blood-brain barrier (BBB) as a crucial factor that hinders chemotherapy. Although several nanoparticle-mediated drug deliveries were degrading effectively against GBM in vitro conditions. However, the potential to cross the BBB and optimum delivery of oligonucleotide RNA into GBM cells in the brain is currently under intense clinical trials. Despite several advances in molecular pathogenesis, GBM remains resistant to chemo and radiotherapy. Targeted therapies have less clinical benefit due to high genetic heterogeneity and activation of alternative pathways. Thus, identifying GBM-specific prognostic pathways, essential genes, and genomic aberrations provide several potential benefits as subtypes of GBM. Also, these approaches will provide insights into new strategies to overcome the heterogenous nature of GBM, which will eventually lead to successful therapeutic interventions toward precision medicine and precision oncology.
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Affiliation(s)
- Janaki Ramaiah Mekala
- Department of Bio-Technology, Koneru Lakshmaiah Education Foundation (KLEF), Vaddeswaram, Guntur, 522302, Andhra Pradesh, India.
| | - Kowsalya Adusumilli
- Department of Bio-Technology, Koneru Lakshmaiah Education Foundation (KLEF), Vaddeswaram, Guntur, 522302, Andhra Pradesh, India
| | - Sahiti Chamarthy
- Department of Bio-Technology, Koneru Lakshmaiah Education Foundation (KLEF), Vaddeswaram, Guntur, 522302, Andhra Pradesh, India
| | - Hari Sai Ram Angirekula
- Department of Bio-Technology, Koneru Lakshmaiah Education Foundation (KLEF), Vaddeswaram, Guntur, 522302, Andhra Pradesh, India
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13
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Kumari S, Singh M, Kumar S, Muthuswamy S. SETD2 controls m6A modification of transcriptome and regulates the molecular oncogenesis of glioma. Med Oncol 2023; 40:249. [PMID: 37490181 DOI: 10.1007/s12032-023-02121-7] [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: 05/25/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023]
Abstract
SETD2 is known for its epigenetic regulatory function and a frequently mutated gene in multiple cancers. Recently, it has been inferred that SETD2 regulates m6A mRNA methylation (epitranscriptome) via H3K36me3. The m6A RNA methylation is vital for tumor maintenance, self-renewal, and tumorigenesis. RNA modifications are executed by writers, readers, and erasers. m6A modifiers work along with the molecular cues, H3K36me3, laid down by SETD2. A positive correlation observed between SETD2 and RNA modifiers signifies their direct role in epitranscriptomics. Hence, understanding the epitranscriptomics will provide a new facet for molecular oncogenesis. Glioma is a common, malignant grade IV tumor with limited therapeutic alternatives and a poor prognosis. Yet, its function in glioma is not fully defined. In the present study, thorough investigations were done in the m6A RNA methylation regulators expression, the molecular pathways leading to tumor progression, and their respective outcomes in SETD2-mediated RNA methylation. In vitro analysis reveals that SETD2 knockdown positively affected the oncogenic properties of the glioma cell line and a global reduction in m6A levels in the transcriptome. The reduction of m6A in the transcriptome can be attributed to the decreased expression of METTL3 and METTL14. Therefore, we conclude that SETD2-mediated m6A modifications are crucial for glioma oncogenesis.
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Affiliation(s)
- Subhadra Kumari
- Human Molecular Genetics (HMG) Lab., Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Mandakini Singh
- RNA Biology Lab., Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Santosh Kumar
- RNA Biology Lab., Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Srinivasan Muthuswamy
- Human Molecular Genetics (HMG) Lab., Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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14
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Deacon S, Walker L, Radhi M, Smith S. The Regulation of m6A Modification in Glioblastoma: Functional Mechanisms and Therapeutic Approaches. Cancers (Basel) 2023; 15:3307. [PMID: 37444417 DOI: 10.3390/cancers15133307] [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: 05/30/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Glioblastoma is the most prevalent primary brain tumour and invariably confers a poor prognosis. The immense intra-tumoral heterogeneity of glioblastoma and its ability to rapidly develop treatment resistance are key barriers to successful therapy. As such, there is an urgent need for the greater understanding of the tumour biology in order to guide the development of novel therapeutics in this field. N6-methyladenosine (m6A) is the most abundant of the RNA modifications in eukaryotes. Studies have demonstrated that the regulation of this RNA modification is altered in glioblastoma and may serve to regulate diverse mechanisms including glioma stem-cell self-renewal, tumorigenesis, invasion and treatment evasion. However, the precise mechanisms by which m6A modifications exert their functional effects are poorly understood. This review summarises the evidence for the disordered regulation of m6A in glioblastoma and discusses the downstream functional effects of m6A modification on RNA fate. The wide-ranging biological consequences of m6A modification raises the hope that novel cancer therapies can be targeted against this mechanism.
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Affiliation(s)
- Simon Deacon
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK
| | - Lauryn Walker
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham NG7 2RD, UK
| | - Masar Radhi
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham NG7 2RD, UK
| | - Stuart Smith
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham NG7 2RD, UK
- Nottingham University Hospitals NHS Trust, Nottingham NG7 2UH, UK
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15
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Piperi C, Markouli M, Gargalionis AN, Papavassiliou KA, Papavassiliou AG. Deciphering glioma epitranscriptome: focus on RNA modifications. Oncogene 2023:10.1038/s41388-023-02746-y. [PMID: 37322070 DOI: 10.1038/s41388-023-02746-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023]
Abstract
Gliomas are highly malignant tumors accounting for the majority of brain neoplasms. They are characterized by nuclear atypia, high mitotic rate and cellular polymorphism that often contributes to aggressiveness and resistance to standard therapy. They often associate with challenging treatment approaches and poor outcomes. New treatment strategies or regimens to improve the efficacy of glioma treatment require a deeper understanding of glioma occurrence and development as well as elucidation of their molecular biological characteristics. Recent studies have revealed RNA modifications as a key regulatory mechanism involved in tumorigenesis, tumor progression, immune regulation, and response to therapy. The present review discusses research advances on several RNA modifications involved in glioma progression and tumor microenvironment (TME) immunoregulation as well as in the development of adaptive drug resistance, summarizing current progress on major RNA modification targeting strategies.
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Affiliation(s)
- Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
| | - Mariam Markouli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Antonios N Gargalionis
- Department of Biopathology, 'Eginition' Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Kostas A Papavassiliou
- First University Department of Respiratory Medicine, 'Sotiria' Hospital, Medical School, National and Kapodistrian University of Athens, 11527, Athens, Greece
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, Athens, Greece.
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16
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Song T, Hu Z, Zeng C, Luo H, Liu J. FLOT1, stabilized by WTAP/IGF2BP2 mediated N6-methyladenosine modification, predicts poor prognosis and promotes growth and invasion in gliomas. Heliyon 2023; 9:e16280. [PMID: 37260902 PMCID: PMC10227343 DOI: 10.1016/j.heliyon.2023.e16280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/06/2023] [Accepted: 05/11/2023] [Indexed: 06/02/2023] Open
Abstract
The expression, function, and mechanism of FLOT1 (flotillin-1) remains unknown in gliomas. Here, the expression and clinical value of FLOT1 in gliomas was bioinformatically and experimentally analyzed via online omics data and local tissues. Moreover, the effects of FLOT1 depletion on cell proliferation and invasion were also detected. Besides, the underlying roles of N6-methyladenosine modification (m6A) in FLOT1 upregulation was further explored. The results demonstrated that FLOT1 was significantly upregulated in gliomas and positively correlated with advanced progression and poor prognosis of patients. FLOT1 silencing notably suppressed the cell proliferation and invasion in gliomas. The expression of WTAP and IGF2BP2was positively correlated with FLOT1 expression and served as the writer and reader of FLOT1 m6A, respectively, which stabilized FLOT1 mRNA and maintained its upregulation in gliomas. Lastly, ectopic expression of FLOT1 could notably restore the inhibitory effects caused by WTAP and IGF2BP2 depletion in glioma cells. Collectively, our results originally confirmed the upregulation and oncogenic roles of FLOT1, and revealed that WTAP/IGF2BP2 mediated m6A contributed to the upregulation of FLOT1 in gliomas, highlighting the promising application of WTAP/IGF2BP2/FLOT1 axis in target treatment of gliomas.
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Affiliation(s)
- Tao Song
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Neurosurgery, Xiangya Jiangxi Hospital, Central South University, Nanchang, China
- National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhongxu Hu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center of Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Chong Zeng
- Department of Medicine, The Seventh Affiliated Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Haijun Luo
- Department of Pathology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, China
| | - Jie Liu
- Department of Pathology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, Hunan, China
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17
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Li L, Yang M, Pu X, Tang Y, Fei F, Li Z, Hou H, Chen Q, Wang Q, Wu Y, Zhang Y, Ren C, Gong A. ALKBH5-PYCR2 Positive Feedback Loop Promotes Proneural-Mesenchymal Transition Via Proline Synthesis In GBM. J Cancer 2023; 14:1579-1591. [PMID: 37325047 PMCID: PMC10266253 DOI: 10.7150/jca.84213] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 04/19/2023] [Indexed: 06/17/2023] Open
Abstract
AlkB homolog 5, RNA demethylase (ALKBH5) is abnormally highly expressed in glioblastoma multiforme (GBM) and is negatively correlated with overall survival in GBM patients. In this study, we found a new mechanism that ALKBH5 and pyrroline-5-carboxylate reductase 2 (PYCR2) formed a positive feedback loop involved in proline synthesis in GBM. ALKBH5 promoted PYCR2 expression and PYCR2-mediated proline synthesis; while PYCR2 promoted ALKBH5 expression through the AMPK/mTOR pathway in GBM cells. In addition, ALKBH5 and PYCR2 promoted GBM cell proliferation, migration, and invasion, as well as proneural-mesenchymal transition (PMT). Furthermore, proline rescued AMPK/mTOR activation and PMT after silencing PYCR2 expression. Our findings reveal an ALKBH5-PYCR2 axis linked to proline metabolism, which plays an important role in promoting PMT in GBM cells and may be a promising therapeutic pathway for GBM.
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Affiliation(s)
- Li Li
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiang Su Province, China
| | - Mengting Yang
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiang Su Province, China
| | - Xufeng Pu
- Department of Medical Imaging, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiang Su Province, China
| | - Yu Tang
- Department of Pathology, The Affiliated Hospital of Jiangsu University, Zhenjiang, Jiang Su Province, China
| | - Fei Fei
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiang Su Province, China
| | - Zhangzuo Li
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiang Su Province, China
| | - Hanjin Hou
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiang Su Province, China
| | - Qian Chen
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiang Su Province, China
| | - Qiaowei Wang
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiang Su Province, China
| | - Yuqing Wu
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiang Su Province, China
| | - Ying Zhang
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiang Su Province, China
| | - Caifang Ren
- Department of Pathology, School of Medicine, Jiangsu University, Zhenjiang, Jiang Su Province, China
| | - Aihua Gong
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, Jiang Su Province, China
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18
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Zhang L, Xu X, Su X. Modifications of noncoding RNAs in cancer and their therapeutic implications. Cell Signal 2023:110726. [PMID: 37230201 DOI: 10.1016/j.cellsig.2023.110726] [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: 03/10/2023] [Revised: 05/06/2023] [Accepted: 05/18/2023] [Indexed: 05/27/2023]
Abstract
In the last 50 years, over 150 various chemical modifications on RNA molecules, including mRNAs, rRNAs, tRNAs, and other noncoding RNAs (ncRNAs), have been identified and characterized. These RNA modifications regulate RNA biogenesis and biological functions and are widely involved in various physiological processes and diseases, including cancer. In recent decades, broad interest has arisen in the epigenetic modification of ncRNAs due to the increased knowledge of the critical roles of ncRNAs in cancer. In this review, we summarize the various modifications of ncRNAs and highlight their roles in cancer initiation and progression. In particular, we discuss the potential of RNA modifications as novel biomarkers and therapeutic targets in cancer.
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Affiliation(s)
- Le Zhang
- Center for Reproductive Medicine, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China
| | - Xiaonan Xu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612-9497, USA
| | - Xiulan Su
- Clinical Medical Research Center, the Affiliated Hospital of Inner Mongolia Medical University, Hohhot 010050, Inner Mongolia, China.
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19
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Kumari S, Kumar S, Muthuswamy S. RNA N6-methyladenosine modification in regulating cancer stem cells and tumor immune microenvironment and its implication for cancer therapy. J Cancer Res Clin Oncol 2023; 149:1621-1633. [PMID: 35796777 DOI: 10.1007/s00432-022-04158-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022]
Abstract
Therapy resistance is a well-known phenomenon in cancer treatment. It can be intrinsic or acquired, accountable for frequent tumor relapse and death worldwide. The interplay between cancer cells and their neighboring environment can activate complex signaling mechanisms influencing epigenetic changes and maintain cancer cell survival leading to the malignant phenotype. Cancer stem cells (CSCs) are tumor-initiating cells (TICs) and constitute the primary source of drug resistance and tumor recurrence. Studies have shown that cancer cells exhibit dysregulated RNA N6-methyladenosine (m6A) "writers," "erasers," and "readers" levels after acquiring drug resistance. The present review provides novel insight into the role of m6A modifiers involved in CSC generation, cancer cell proliferation, and therapy resistance. m6A RNA modifications in the cross-talk between CSC and the tumor immune microenvironment (TIME) have also been highlighted. Further, we have discussed the therapeutic potential of targeting m6A machinery for cancer diagnosis and the development of new therapies for cancer treatment.
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Affiliation(s)
- Subhadra Kumari
- Department of Life Science, National Institute of Technology, Rourkela, India
| | - Santosh Kumar
- Department of Life Science, National Institute of Technology, Rourkela, India
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20
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Single-Cell Sequencing Reveals Necroptosis-Related Prognostic Genes of Glioblastoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:2926655. [PMID: 36860730 PMCID: PMC9970716 DOI: 10.1155/2023/2926655] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/18/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023]
Abstract
Background Glioblastoma (GBM) is one of the most malignant forms of brain cancer, with the extremely lower survival rate. Necroptosis (NCPS) is also one of the most wide types of cell death, and its clinical importance in GBM is not clear. Methods We first identified necroptotic genes in GBM by single-cell RNA sequencing analysis of our surgical samples and weighted coexpression network analysis (WGNCA) from TCGA GBM data. The cox regression model with least absolute shrinkage and selection operator (LASSO) was used to construct the risk model. Then, KM plot and reactive operation curve (ROC) analysis were used to assess the prediction ability of the model. At last, the infiltrated immune cells and gene mutation profiling were investigated between the high- and low-NCPS groups as well. Result The risk model including ten necroptosis-related genes was identified as an independent risk factor for the outcome. In addition, we found that the risk model is correlated with the infiltrated immune cells and tumor mutation burden in GBM. NDUFB2 is identified to be a risk gene in GBM with bioinformatical analysis and in vitro experiment validation. Conclusion This risk model of necroptosis-related genes might provide clinical evidence for GBM interventions.
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21
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Tűzesi Á, Hallal S, Satgunaseelan L, Buckland ME, Alexander KL. Understanding the Epitranscriptome for Avant-Garde Brain Tumour Diagnostics. Cancers (Basel) 2023; 15:cancers15041232. [PMID: 36831575 PMCID: PMC9954771 DOI: 10.3390/cancers15041232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
RNA modifications are diverse, dynamic, and reversible transcript alterations rapidly gaining attention due to their newly defined RNA regulatory roles in cellular pathways and pathogenic mechanisms. The exciting emerging field of 'epitranscriptomics' is predominantly centred on studying the most abundant mRNA modification, N6-methyladenine (m6A). The m6A mark, similar to many other RNA modifications, is strictly regulated by so-called 'writer', 'reader', and 'eraser' protein species. The abundance of genes coding for the expression of these regulator proteins and m6A levels shows great potential as diagnostic and predictive tools across several cancer fields. This review explores our current understanding of RNA modifications in glioma biology and the potential of epitranscriptomics to develop new diagnostic and predictive classification tools that can stratify these highly complex and heterogeneous brain tumours.
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Affiliation(s)
- Ágota Tűzesi
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Susannah Hallal
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Department of Neurosurgery, Chris O’Brien Lifehouse, Camperdown, NSW 2050, Australia
| | - Laveniya Satgunaseelan
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- Sydney Medical School, Faculty of Medicine and Health Sciences, The University of Sydney, Sydney, NSW 2050, Australia
| | - Michael E. Buckland
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
| | - Kimberley L. Alexander
- Department of Neuropathology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2050, Australia
- Department of Neurosurgery, Chris O’Brien Lifehouse, Camperdown, NSW 2050, Australia
- Correspondence:
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Progress in targeting PTEN/PI3K/Akt axis in glioblastoma therapy: Revisiting molecular interactions. Biomed Pharmacother 2023; 158:114204. [PMID: 36916430 DOI: 10.1016/j.biopha.2022.114204] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/30/2022] [Indexed: 01/05/2023] Open
Abstract
Glioblastoma (GBM) is one of the most malignant cancers of central nervous system and due to its sensitive location, surgical resection has high risk and therefore, chemotherapy and radiotherapy are utilized for its treatment. However, chemoresistance and radio-resistance are other problems in GBM treatment. Hence, new therapies based on genes are recommended for treatment of GBM. PTEN is a tumor-suppressor operator in cancer that inhibits PI3K/Akt/mTOR axis in diminishing growth, metastasis and drug resistance. In the current review, the function of PTEN/PI3K/Akt axis in GBM progression is evaluated. Mutation or depletion of PTEN leads to increase in GBM progression. Low expression level of PTEN mediates poor prognosis in GBM and by increasing proliferation and invasion, promotes malignancy of tumor cells. Moreover, loss of PTEN signaling can result in therapy resistance in GBM. Activation of PTEN signaling impairs GBM metabolism via glycolysis inhibition. In contrast to PTEN, PI3K/Akt signaling has oncogenic function and during tumor progression, expression level of PI3K/Akt enhances. PI3K/Akt signaling shows positive association with oncogenic pathways and its expression similar to PTEN signaling, is regulated by non-coding RNAs. PTEN upregulation and PI3K/Akt signaling inhibition by anti-cancer agents can be beneficial in interfering GBM progression. This review emphasizes on the signaling networks related to PTEN/PI3K/Akt and provides new insights for targeting this axis in effective GBM treatment.
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Non-Association of Driver Alterations in PTEN with Differential Gene Expression and Gene Methylation in IDH1 Wildtype Glioblastomas. Brain Sci 2023; 13:brainsci13020186. [PMID: 36831729 PMCID: PMC9953940 DOI: 10.3390/brainsci13020186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
During oncogenesis, alterations in driver genes called driver alterations (DAs) modulate the transcriptome, methylome and proteome through oncogenic signaling pathways. These modulatory effects of any DA may be analyzed by examining differentially expressed mRNAs (DEMs), differentially methylated genes (DMGs) and differentially expressed proteins (DEPs) between tumor samples with and without that DA. We aimed to analyze these modulations with 12 common driver genes in Isocitrate Dehydrogenase 1 wildtype glioblastomas (IDH1-W-GBs). Using Cbioportal, groups of tumor samples with and without DAs in these 12 genes were generated from the IDH1-W-GBs available from "The Cancer Genomics Atlas Firehose Legacy Study Group" (TCGA-FL-SG) on Glioblastomas (GBs). For all 12 genes, samples with and without DAs were compared for DEMs, DMGs and DEPs. We found that DAs in PTEN were unassociated with any DEM or DMG in contrast to DAs in all other drivers, which were associated with several DEMs and DMGs. This contrasting PTEN-related property of being unassociated with differential gene expression or methylation in IDH1-W-GBs was unaffected by concurrent DAs in other common drivers or by the types of DAs affecting PTEN. From the lists of DEMs and DMGs associated with some common drivers other than PTEN, enriched gene ontology terms and insights into the co-regulatory effects of these drivers on the transcriptome were obtained. The findings from this study can improve our understanding of the molecular mechanisms underlying gliomagenesis with potential therapeutic benefits.
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Tang L, Li Y, Shen L, Li N, Shen L, Li Z. Integrative analyses reveal prognostic and immunogenic characteristics of m7G methylation regulators in patients with glioma. Am J Transl Res 2023; 15:288-309. [PMID: 36777864 PMCID: PMC9908444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 12/03/2022] [Indexed: 02/14/2023]
Abstract
OBJECTIVES The expression profiles, biological mechanisms, and clinical relevance of m7G regulators in glioma were studied in this research. METHODS Based on the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) datasets, glioma patients, can be categorized into three groups according to 29 m7G regulators, and different subtypes of glioma show different immune cell infiltration characteristics, function enrichment, and clinical prognosis. Three gene clusters were confirmed by utilizing the differentially expressed genes (DEGs) across the three m7G clusters. RESULTS A prognostic signature based on 12 m7G regulators was established and validated, producing an effective tool for predicting overall survival (OS) in glioma patients. High m7G scores indicated elevated tumor mutation burden and activation of immunity, suggesting an inflamed tumor microenvironment phenotype with poor overall survival. Low m7G scores characterized by a lack of immune infiltration and low mutation burden indicated a non-inflamed phenotype with a favorable clinical prognosis. It was also found that the m7G risk scores can affect chemotherapy sensitivity and prognosis of patients who received immunotherapy. The hub gene EIF4E1B of m7G regulators can inhibit the in vitro progression of glioma cells by regulating PD-L1 expression through p53 signaling pathway-related inactivation. CONCLUSIONS The m7G prognostic signature can be a biomarker of the overall survival of patients with glioma. An initial in-vitro experiment suggested the potential biological mechanisms of immune regulation, with m7G regulators affecting glioma progression by modulating immune responses. The present research provides a better understanding of how m7G regulators function in glioma progression as well as the impact on clinical outcomes, which can provide new insights that might be beneficial for precision therapy of glioma.
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Affiliation(s)
- Lingwei Tang
- Department of Oncology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China
| | - Yanyan Li
- Department of Nursing, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China
| | - Lin Shen
- Department of Oncology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China
| | - Na Li
- Department of Oncology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China
| | - Liangfang Shen
- Department of Oncology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China
| | - Zhanzhan Li
- Department of Oncology, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South UniversityChangsha 410008, Hunan, P. R. China
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25
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Zhang Z, Chen P, Yun J. Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer. Front Genet 2023; 14:1156095. [PMID: 37124622 PMCID: PMC10131083 DOI: 10.3389/fgene.2023.1156095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/31/2023] [Indexed: 05/02/2023] Open
Abstract
Background: Bladder cancer (BCa) is the leading reason for death among genitourinary malignancies. RNA modifications in tumors closely link to the immune microenvironment. Our study aimed to propose a promising model associated with the "writer" enzymes of five primary RNA adenosine modifications (including m6A, m6Am, m1A, APA, and A-to-I editing), thus characterizing the clinical outcome, immune landscape and therapeutic efficacy of BCa. Methods: Unsupervised clustering was employed to categorize BCa into different RNA modification patterns based on gene expression profiles of 34 RNA modification "writers". The RNA modification "writers" score (RMS) signature composed of RNA phenotype-associated differentially expressed genes (DEGs) was established using the least absolute shrinkage and selection operator (LASSO), which was evaluated in meta-GEO (including eight independent GEO datasets) training cohort and the TCGA-BLCA validation cohort. The hub genes in the RMS model were determined via weighted gene co-expression network analysis (WGCNA) and were further validated using human specimen. The potential applicability of the RMS model in predicting the therapeutic responsiveness was assessed through the Genomics of Drug Sensitivity in Cancer database and multiple immunotherapy datasets. Results: Two distinct RNA modification patterns were determined among 1,410 BCa samples from a meta-GEO cohort, showing radically varying clinical outcomes and biological characteristics. The RMS model comprising 14 RNA modification phenotype-associated prognostic DEGs positively correlated with the unsatisfactory outcome of BCa patients in meta-GEO training cohort (HR = 3.00, 95% CI = 2.19-4.12) and TCGA-BLCA validation cohort (HR = 1.53, 95% CI = 1.13-2.09). The infiltration of immunosuppressive cells and the activation of EMT, angiogenesis, IL-6/JAK/STAT3 signaling were markedly enriched in RMS-high group. A nomogram exhibited high prognostic prediction accuracy, with a concordance index of 0.785. The therapeutic effect of chemotherapeutic agents and antibody-drug conjugates was significantly different between RMS-low and -high groups. The combination of the RMS model and conventional characteristics (TMB, TNB and PD-L1) achieved an optimal AUC value of 0.828 in differentiating responders from non-responders to immunotherapy. Conclusion: We conferred the first landscape of five forms of RNA modifications in BCa and emphasized the excellent power of an RNA modifications-related model in evaluating BCa prognosis and immune landscape.
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Affiliation(s)
- Ziying Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Peng Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jingping Yun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
- *Correspondence: Jingping Yun,
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Transcription factor YY1 mediates self-renewal of glioblastoma stem cells through regulation of the SENP1/METTL3/MYC axis. Cancer Gene Ther 2022; 30:683-693. [PMID: 36575317 DOI: 10.1038/s41417-022-00580-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/10/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022]
Abstract
Glioma is a primary brain tumor with limited treatment approaches and glioblastoma stem cells (GSCs) are manifested with the self-renewal capability and high tumorigenic capacity. This study was performed to investigate the regulatory effect of the SUMO-specific protease 1 (SENP1)/methyltransferase-like 3 (METTL3)/MYC axis on the self-renewal of GSCs mediated by transcription factor Yin Yang 1 (YY1). Following bioinformatics analysis and clinical and cellular experiments, we found that YY1 was highly expressed in GBM tissues and cells, while silencing its expression reduced the self-renewal ability of GSCs. Functionally, YY1 promoted the transcriptional expression of SENP1 by binding to the promoter region of SENP1, while the deSUMOase SENP1 facilitated the methylase activity of m6A through deSUMOylation of the methylase METTL3, thereby promoting the m6A modification of MYC mRNA via METL3 and promoting the expression of MYC. A nude mouse xenograft model of GBM was also constructed to examine the tumorigenicity of GSCs. The obtained findings demonstrated that YY1 promoted tumorigenicity of GSCs by promoting the expression of MYC in vivo. Conclusively, YY1 can transcriptionally upregulate the SUMOylase SENP1 and enhance the methylase activity of METTL3, resulting in the increased m6A modification level of MYC mRNA, thereby promoting the self-renewal of GSCs.
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27
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Liu Z, Zou H, Dang Q, Xu H, Liu L, Zhang Y, Lv J, Li H, Zhou Z, Han X. Biological and pharmacological roles of m 6A modifications in cancer drug resistance. Mol Cancer 2022; 21:220. [PMID: 36517820 PMCID: PMC9749187 DOI: 10.1186/s12943-022-01680-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/11/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer drug resistance represents the main obstacle in cancer treatment. Drug-resistant cancers exhibit complex molecular mechanisms to hit back therapy under pharmacological pressure. As a reversible epigenetic modification, N6-methyladenosine (m6A) RNA modification was regarded to be the most common epigenetic RNA modification. RNA methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers) are frequently disordered in several tumors, thus regulating the expression of oncoproteins, enhancing tumorigenesis, cancer proliferation, development, and metastasis. The review elucidated the underlying role of m6A in therapy resistance. Alteration of the m6A modification affected drug efficacy by restructuring multidrug efflux transporters, drug-metabolizing enzymes, and anticancer drug targets. Furthermore, the variation resulted in resistance by regulating DNA damage repair, downstream adaptive response (apoptosis, autophagy, and oncogenic bypass signaling), cell stemness, tumor immune microenvironment, and exosomal non-coding RNA. It is highlighted that several small molecules targeting m6A regulators have shown significant potential for overcoming drug resistance in different cancer categories. Further inhibitors and activators of RNA m6A-modified proteins are expected to provide novel anticancer drugs, delivering the therapeutic potential for addressing the challenge of resistance in clinical resistance.
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Affiliation(s)
- Zaoqu Liu
- grid.412633.10000 0004 1799 0733Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China ,grid.207374.50000 0001 2189 3846Interventional Institute of Zhengzhou University, Zhengzhou, 450052 Henan China ,grid.412633.10000 0004 1799 0733Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, 450052 Henan China
| | - Haijiao Zou
- grid.412633.10000 0004 1799 0733Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Qin Dang
- grid.412633.10000 0004 1799 0733Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Hui Xu
- grid.412633.10000 0004 1799 0733Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Long Liu
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Yuyuan Zhang
- grid.412633.10000 0004 1799 0733Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Jinxiang Lv
- grid.412633.10000 0004 1799 0733Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Huanyun Li
- grid.412633.10000 0004 1799 0733Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Zhaokai Zhou
- grid.412633.10000 0004 1799 0733Department of Pediatric Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Xinwei Han
- grid.412633.10000 0004 1799 0733Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China ,grid.207374.50000 0001 2189 3846Interventional Institute of Zhengzhou University, Zhengzhou, 450052 Henan China ,grid.412633.10000 0004 1799 0733Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, 450052 Henan China
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28
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Yan Y, Wei W, Long S, Ye S, Yang B, Jiang J, Li X, Chen J. The role of RNA modification in the generation of acquired drug resistance in glioma. Front Genet 2022; 13:1032286. [DOI: 10.3389/fgene.2022.1032286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/25/2022] [Indexed: 11/13/2022] Open
Abstract
Glioma is the most common malignant tumor in the central nervous system. The clinical treatment strategy is mainly surgery combined with concurrent temozolomide chemotherapy, but patients can develop drug resistance during treatment, which severely limits its therapeutic efficacy. Epigenetic regulation at the RNA level is plastic and adaptable, and it can induce a variety of tumor responses to drugs. The regulators of RNA modification include methyltransferases, demethylases, and methylation binding proteins; these are also considered to play an important role in the development, prognosis, and therapeutic response of gliomas, which provides a basis for finding new targets of epigenetic drugs and resetting the sensitivity of tumor cells to temozolomide. This review discusses the relationship between the development of adaptive drug resistance and RNA modification in glioma and summarizes the progress of several major RNA modification strategies in this field, especially RNA m6A modification, m5C modification, and adenosine-to-inosine editing.
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29
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Guan S, He Y, Su Y, Zhou L. A Risk Signature Consisting of Eight m 6A Methylation Regulators Predicts the Prognosis of Glioma. Cell Mol Neurobiol 2022; 42:2733-2743. [PMID: 34432221 DOI: 10.1007/s10571-021-01135-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/27/2021] [Indexed: 01/05/2023]
Abstract
Glioma progression seriously correlates to the epigenetic context. This study aims to identify glioma subtypes by clustering analysis of patients using the multi-omics data of N6-methyladenosine (m6A) methylation regulators and to construct a risk signature for investigating the role of m6A methylation regulators in the prognosis of glioma. Multi-omics data of glioma and normal control tissues were obtained through The Cancer Genome Atlas (TCGA) database. The clustering analysis of multi-omics data of patients was conducted using the R package iClusterPlus software. The risk model was constructed by univariate and multivariate Cox analysis, and the glioma expression data and related clinical data were obtained by Chinese Glioma Genome Atlas (CGGA) datasets to verify the risk model. By analyzing the glioma data in TCGA, we found that the risk signature could be constructed according to the eight genes with m6A methylation modification function, including ALKBH5, HNRNPA2B1, IGF2BP2, IGF2BP3, RBM15, WTAP, YTHDF1, and YTHDF2. Meanwhile, we found that IGF2BP2 and IGF2BP3 were highly expressed in glioma subtypes with high-risk scores and closely related to the prognosis of glioma patients. m6A methylation regulators, especially IGF2BP2 and IGF2BP3, play important roles in the malignant progression of glioma. The risk signature constructed by eight m6A methylation regulators can predict the prognosis of glioma. IGF2BP2 and IGF2BP3 may be the key regulatory factors of m6A methylation regulators involved in the occurrence and development of glioma, and can serve as molecular markers for the prognosis of glioma.
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Affiliation(s)
- Sizhong Guan
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Ye He
- Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Yanna Su
- Department of Laboratory Medicine, The First Hospital of China Medical University, Shenyang, 110001, People's Republic of China
| | - Liping Zhou
- Post Graduation Training Department, The First Hospital of China Medical University, No. 155, Northern Nanjing Road, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China.
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30
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Wu H, Xu H, Huang S, Tang Y, Tang J, Zhou H, Xie L, Qiao G. m 6A-binding protein IGF2BP1 promotes the malignant phenotypes of lung adenocarcinoma. Front Oncol 2022; 12:989817. [PMID: 36249006 PMCID: PMC9554348 DOI: 10.3389/fonc.2022.989817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/06/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD), the most common type of lung cancer, poses a significant threat to the life of patients. N6-methyladenosine modification is the most abundant epigenetic modification and may play an important role in the lung carcinogenesis. IGF2BP1 is a newly discovered m6A-binding protein, but little is known about its role in LUAD. METHODS Data from TCGA, GEO, Kaplan-Meier Plotter, and GEPIA databases were systematically analyzed to access the expression and prognostic value of IGF2BP1 on LUAD. Real-time polymerase chain reaction, Western blot, and immunohistochemistry were performed to detect the mRNA and protein level of IGF2BP1 in LUAD tissues and para-carcinoma tissues. Functional cell experiments, including Cell Counting Kit-8 assay, Transwell invasion assay, wound healing assay, Annexin V-FITC/PI double-staining assay, and TUNEL assay, were used to investigate the functions of IGF2BP1 on LUAD cell proliferation, invasion, migration, and apoptosis, respectively. The top 50 genes that were positively or negatively related to the expression of IGF2BP1 were identified, and pathway enrichment analysis was performed. m6A modification sites within IGF2BP1-related genes were predicted by SRAMP. RESULT 16 m6A regulators were significantly differentially expressed in LUAD tissues. IGF2BP1 was upregulated in LUAD tissues compared with para-carcinoma tissues. High expression of IGF2PB1 was significantly associated with higher clinical stages and poor prognosis of LUAD patients. Furthermore, our functional experiments indicated that IGF2BP1 facilitated cell proliferation, invasion, and migration and suppressed apoptosis in LUAD. Functional enrichment analysis of IGF2BP1-related genes indicated enrichment in several pathways related to oncogenesis. Additionally, m6A modification sites were detected within IGF2BP1-related genes. CONCLUSIONS Our findings demonstrate that IGF2BP1 plays a contributory role in the development and progression of LUAD. IGF2BP1 has the potential to become a prognostic predictor and therapeutic target for LUAD.
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Affiliation(s)
- Hansheng Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Haijie Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Shantou University Medical College, Shantou, China
| | - Shujie Huang
- Shantou University Medical College, Shantou, China
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yong Tang
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jiming Tang
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Haiyu Zhou
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Liang Xie
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Guibin Qiao
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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The Critical Role of RNA m6A Methylation in Gliomas: Targeting the Hallmarks of Cancer. Cell Mol Neurobiol 2022:10.1007/s10571-022-01283-8. [DOI: 10.1007/s10571-022-01283-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/04/2022] [Indexed: 11/03/2022]
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Determination of adenosine and its modifications in urine and plasma from breast cancer patients by hydrophilic interaction liquid chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1209:123428. [PMID: 36041348 DOI: 10.1016/j.jchromb.2022.123428] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/04/2022] [Accepted: 08/14/2022] [Indexed: 01/15/2023]
Abstract
RNA modifications have been revealed to be essential in many biological activities, and their disorders are associated with various human diseases, including cancers. 2'-O-methyladenosine (Am), N1-methyladenosine (m1A), N6-methyladenosine (m6A), N6,2'-O-dimethyladenosine (m6Am) and N6,N6-dimethyladenosine (m62A) are important adenosine (A) modifications. The noninvasive collection of urine samples and the diverse contents of metabolites in plasma make them favored biofluids for biomarkers discovery. In this work, we established a hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) method to quantify these six nucleosides in urine and plasma of healthy controls and breast cancer (BC) patients. The limit of detection (LOD) for A, Am, m1A, m6A, m6Am, and m62A were 0.0025, 0.01, 0.05, 0.005, 0.005, and 0.005 nM. The results showed that the concentrations of Am, m6A, and m6Am were increased, whereas m1A was decreased in the urine of BC patients compared with the healthy controls. We also found that the level ratios of m1A/A, m6A/A, and m6Am/A were all reduced in plasma from BC patients, compared with healthy controls. Interestingly, these ratios of methylated adenosine nucleosides to adenosine in plasma could better discriminate BC patients from healthy controls, compared to the levels of these nucleosides. The present study not only suggests these modified adenosines can act as noninvasive biomarkers of BC but also will contribute to investigating the impacts of RNA methylation on the occurrence and development of BC.
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Dou X, Wang Z, Lu W, Miao L, Zhao Y. METTL3 promotes non-small cell lung cancer (NSCLC) cell proliferation and colony formation in a m6A-YTHDF1 dependent way. BMC Pulm Med 2022; 22:324. [PMID: 36008805 PMCID: PMC9413890 DOI: 10.1186/s12890-022-02119-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
Background N6-methyladenosine (m6A) is the most common RNA modification, which plays a pivotal role in tumor development and progression. In this study, we assessed the role of m6A methyltransferase METTL3 in FRAS1-involved cell proliferation and colony formation of non-small cell lung cancer (NSCLC) cell lines. Methods Cell viability was analyzed by Cell Counting Kit (CCK-8) and colony formation. M6A RNA immunoprecipitation (IP), Ribosomal immunoprecipitation, RNA immunoprecipitation (RIP) were performed to verify the relationship between METTL3, FRAS1 and YTHDF1. Rescue experiments to confirm the regulatory mechanism of METTL3-FRAS1 promoted NSCLC cell proliferation through CDON by cooperating YTHDF1. Results We found that FRAS1 was correlated with poor prognosis in NSCLC patients, of which the transcript undergoes m6A modification regulated by METTL3. METTL3 silence reduced cell viability of NSCLC cells HCC827 and NCI-H1975, which could be restored by FRAS1 overexpression. The m6A modification of FRAS1 could be recognized by YTHDF1. FRAS1 silence or YTHDF1 silence could rescue the elevated NSCLC cell proliferation, colony formation, and tumor growth induced by METTL3 overexpression in vitro and in vivo. Conclusions Our study reveals that METTL3-FRAS1 plays a crucial role in NSCLC cell proliferation, colony formation, and tumor growth through the regulation of CDON by cooperating YTHDF1. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-022-02119-3.
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Affiliation(s)
- Xuejun Dou
- Department of Thoracic Surgery, Space Central Hospital, Beijing, China.
| | - Zhiyuan Wang
- Department of Thoracic Surgery, Space Central Hospital, Beijing, China
| | - Weiqiang Lu
- Department of Thoracic Surgery, Space Central Hospital, Beijing, China
| | - Libin Miao
- Department of Thoracic Surgery, Space Central Hospital, Beijing, China
| | - Yuefeng Zhao
- Department of Thoracic Surgery, Space Central Hospital, Beijing, China
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Relier S, Amalric A, Attina A, Koumare IB, Rigau V, Burel Vandenbos F, Fontaine D, Baroncini M, Hugnot JP, Duffau H, Bauchet L, Hirtz C, Rivals E, David A. Multivariate Analysis of RNA Chemistry Marks Uncovers Epitranscriptomics-Based Biomarker Signature for Adult Diffuse Glioma Diagnostics. Anal Chem 2022; 94:11967-11972. [PMID: 35998076 PMCID: PMC9453740 DOI: 10.1021/acs.analchem.2c01526] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
One of the main challenges in cancer management relates
to the
discovery of reliable biomarkers, which could guide decision-making
and predict treatment outcome. In particular, the rise and democratization
of high-throughput molecular profiling technologies bolstered the
discovery of “biomarker signatures” that could maximize
the prediction performance. Such an approach was largely employed
from diverse OMICs data (i.e., genomics, transcriptomics, proteomics,
metabolomics) but not from epitranscriptomics, which encompasses more
than 100 biochemical modifications driving the post-transcriptional
fate of RNA: stability, splicing, storage, and translation. We and
others have studied chemical marks in isolation and associated them
with cancer evolution, adaptation, as well as the response to conventional
therapy. In this study, we have designed a unique pipeline combining
multiplex analysis of the epitranscriptomic landscape by high-performance
liquid chromatography coupled to tandem mass spectrometry with statistical
multivariate analysis and machine learning approaches in order to
identify biomarker signatures that could guide precision medicine
and improve disease diagnosis. We applied this approach to analyze
a cohort of adult diffuse glioma patients and demonstrate the existence
of an “epitranscriptomics-based signature” that permits
glioma grades to be discriminated and predicted with unmet accuracy.
This study demonstrates that epitranscriptomics (co)evolves along
cancer progression and opens new prospects in the field of omics molecular
profiling and personalized medicine.
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Affiliation(s)
- S Relier
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France
| | - A Amalric
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France.,IRMB-PPC, INM, Univ Montpellier, CHU Montpellier, INSERM CNRS, Montpellier 34295, France
| | - A Attina
- IRMB-PPC, INM, Univ Montpellier, CHU Montpellier, INSERM CNRS, Montpellier 34295, France
| | - I B Koumare
- Neurosurgery Department, Montpellier University Medical Center, Montpellier, Hérault 34295, France.,Neurosurgery Department, CHU Gabriel Toure, Bamako, Mali
| | - V Rigau
- Department of Pathology and Oncobiology, Montpellier University Medical Center, Montpellier, Hérault 34295, France
| | - F Burel Vandenbos
- Central Laboratory of Pathology, Univ. Côte d'Azur, CHU Nice, CNRS, INSERM, Nice, Alpes-Maritimes 06000, France
| | - D Fontaine
- Neurosurgery Department, Univ. Côte d'Azur, CHU Nice, Nice, Alpes-Maritimes 06000, France
| | - M Baroncini
- Neurosurgery Department, CHU Lille, Univ. of Lille, Lille, Nord 59037, France
| | - J P Hugnot
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France
| | - H Duffau
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France.,Neurosurgery Department, Montpellier University Medical Center, Montpellier, Hérault 34295, France
| | - L Bauchet
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France.,Neurosurgery Department, Montpellier University Medical Center, Montpellier, Hérault 34295, France
| | - C Hirtz
- IRMB-PPC, INM, Univ Montpellier, CHU Montpellier, INSERM CNRS, Montpellier 34295, France
| | - E Rivals
- LIRMM, Univ. Montpellier, CNRS, Montpellier, Hérault 34095, France
| | - A David
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France.,IRMB-PPC, INM, Univ Montpellier, CHU Montpellier, INSERM CNRS, Montpellier 34295, France
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35
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Post-Transcriptional Modifications of RNA as Regulators of Apoptosis in Glioblastoma. Int J Mol Sci 2022; 23:ijms23169272. [PMID: 36012529 PMCID: PMC9408889 DOI: 10.3390/ijms23169272] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
This review is devoted to changes in the post-transcriptional maturation of RNA in human glioblastoma cells, which leads to disruption of the normal course of apoptosis in them. The review thoroughly highlights the latest information on both post-transcriptional modifications of certain regulatory RNAs, associated with the process of apoptosis, presents data on the features of apoptosis in glioblastoma cells, and shows the relationship between regulatory RNAs and the apoptosis in tumor cells. In conclusion, potential target candidates are presented that are necessary for the development of new drugs for the treatment of glioblastoma.
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miRNome and Proteome Profiling of Small Extracellular Vesicles Secreted by Human Glioblastoma Cell Lines and Primary Cancer Stem Cells. Biomedicines 2022; 10:biomedicines10081886. [PMID: 36009432 PMCID: PMC9405730 DOI: 10.3390/biomedicines10081886] [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: 07/01/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
Glioblastoma (GBM) is the most common and aggressive brain tumor in adults. Despite available therapeutic interventions, it is very difficult to treat, and a cure is not yet available. The intra-tumoral GBM heterogeneity is a crucial factor contributing to poor clinical outcomes. GBM derives from a small heterogeneous population of cancer stem cells (CSCs). In cancer tissue, CSCs are concentrated within the so-called niches, where they progress from a slowly proliferating phase. CSCs, as most tumor cells, release extracellular vesicles (EVs) into the surrounding microenvironment. To explore the role of EVs in CSCs and GBM tumor cells, we investigated the miRNA and protein content of the small EVs (sEVs) secreted by two GBM-established cell lines and by GBM primary CSCs using omics analysis. Our data indicate that GBM-sEVs are selectively enriched for miRNAs that are known to display tumor suppressor activity, while their protein cargo is enriched for oncoproteins and tumor-associated proteins. Conversely, among the most up-regulated miRNAs in CSC-sEVs, we also found pro-tumor miRNAs and proteins related to stemness, cell proliferation, and apoptosis. Collectively, our findings support the hypothesis that sEVs selectively incorporate different miRNAs and proteins belonging both to fundamental processes (e.g., cell proliferation, cell death, stemness) as well as to more specialized ones (e.g., EMT, membrane docking, cell junction organization, ncRNA processing).
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Chen HM, Li H, Lin MX, Fan WJ, Zhang Y, Lin YT, Wu SX. Research Progress for RNA Modifications in Physiological and Pathological Angiogenesis. Front Genet 2022; 13:952667. [PMID: 35937999 PMCID: PMC9354963 DOI: 10.3389/fgene.2022.952667] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022] Open
Abstract
As a critical layer of epigenetics, RNA modifications demonstrate various molecular functions and participate in numerous biological processes. RNA modifications have been shown to be essential for embryogenesis and stem cell fate. As high-throughput sequencing and antibody technologies advanced by leaps and bounds, the association of RNA modifications with multiple human diseases sparked research enthusiasm; in addition, aberrant RNA modification leads to tumor angiogenesis by regulating angiogenesis-related factors. This review collected recent cutting-edge studies focused on RNA modifications (N6-methyladenosine (m6A), N5-methylcytosine (m5C), N7-methylguanosine (m7G), N1-methyladenosine (m1A), and pseudopuridine (Ψ)), and their related regulators in tumor angiogenesis to emphasize the role and impact of RNA modifications.
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Affiliation(s)
- Hui-Ming Chen
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
| | - Hang Li
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Meng-Xian Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Wei-Jie Fan
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yi Zhang
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yan-Ting Lin
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
- *Correspondence: Shu-Xiang Wu, ; Yan-Ting Lin,
| | - Shu-Xiang Wu
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumor Microbiology, Department of Medical Microbiology, Fujian Medical University, Fuzhou, China
- *Correspondence: Shu-Xiang Wu, ; Yan-Ting Lin,
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38
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Zheng P, Zhang X, Ren D, Zhang Y. RP11-552D4.1: a novel m6a-related LncRNA associated with immune status in glioblastoma. Aging (Albany NY) 2022; 14:7348-7363. [PMID: 35852867 PMCID: PMC9550243 DOI: 10.18632/aging.204177] [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: 01/22/2022] [Accepted: 07/05/2022] [Indexed: 11/25/2022]
Abstract
Glioblastoma (GBM) is the most malignant form of brain cancer in the world. Nevertheless, the survival rate of patients with GBM is extremely low. N6-methyladenosine (m6A) and long noncoding RNAs (lncRNAs) conduct important biological functions in patients’ survival status and the immunotherapeutic response. Here, m6A-related lncRNAs were identified by a co-expression method. Univariate and multivariate Cox regression together with LASSO were applied to establish the risk model. Kaplan-Meier and ROC analysis were applied to evaluate the prediction power of this risk model. Finally, the related immune profiling and chemical sensitivity targets were also investigated. The risk model holding three m6A-related lncRNAs was confirmed as an independent predictor for the prognosis. Furthermore, we found the risk model based on m6A-related lncRNAs is associated with the immune status, immunosuppressive biomarkers, and chemo-sensitivity in GBM patients. The RP11-552D4.1 is found to facilitate neuronal proliferation. This risk model consisted of m6A-related lncRNAs may be available for the clinical interventions in GBM patients.
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Affiliation(s)
- Ping Zheng
- Department of Neurosurgery, Shanghai Pudong New Area People’s Hospital, Shanghai, China
- Key Molecular Lab, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Xiaoxue Zhang
- Key Molecular Lab, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Dabin Ren
- Department of Neurosurgery, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Yisong Zhang
- Department of Neurosurgery, Shanghai Pudong New Area People’s Hospital, Shanghai, China
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Xie P, Yan H, Gao Y, Li X, Zhou DB, Liu ZQ. Construction of m6A-Related lncRNA Prognostic Signature Model and Immunomodulatory Effect in Glioblastoma Multiforme. Front Oncol 2022; 12:920926. [PMID: 35719945 PMCID: PMC9201336 DOI: 10.3389/fonc.2022.920926] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/11/2022] [Indexed: 12/15/2022] Open
Abstract
Background Glioblastoma multiforme (GBM), the most prevalent and aggressive of primary malignant central nervous system tumors (grade IV), has a poor clinical prognosis. This study aimed to assess and predict the survival of GBM patients by establishing an m6A-related lncRNA signaling model and to validate its validity, accuracy and applicability. Methods RNA sequencing data and clinical data of GBM patients were obtained from TCGA data. First, m6A-associated lncRNAs were screened and lncRNAs associated with overall survival in GBM patients were obtained. Subsequently, the signal model was established using LASSO regression analysis, and its accuracy and validity are further verified. Finally, GO enrichment analysis was performed, and the influence of this signature on the immune regulation response and anticancer drug sensitivity of GBM patients was discussed. Results The signature constructed by four lncRNAs AC005229.3, SOX21-AS1, AL133523.1, and AC004847.1 is obtained. Furthermore, the signature proved to be effective and accurate in predicting and assessing the survival of GBM patients and could function independently of other clinical characteristics (Age, Gender and IDH1 mutation). Finally, Immunosuppression-related factors, including APC co-inhibition, T-cell co-inhibition, CCR and Check-point, were found to be significantly up-regulated in GBM patients in the high-risk group. Some chemotherapeutic drugs (Doxorubicin and Methotrexate) and targeted drugs (AZD8055, BI.2536, GW843682X and Vorinostat) were shown to have higher IC50 values in patients in the high-risk group. Conclusion We constructed an m6A-associated lncRNA risk model to predict the prognosis of GBM patients and provide new ideas for the treatment of GBM. Further biological experiments can be conducted on this basis to validate the clinical value of the model.
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Affiliation(s)
- Pan Xie
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Han Yan
- Department of Pharmacy, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Ying Gao
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Gerontology, Xiangya Hospital, Central South University, Changsha, China
| | - Xi Li
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Dong-Bo Zhou
- Department of Gerontology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhao-Qian Liu
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Institute of Clinical Pharmacology, Central South University, Changsha, China
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40
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Gupta T, Malkin MG, Huang S. tRNA Function and Dysregulation in Cancer. Front Cell Dev Biol 2022; 10:886642. [PMID: 35721477 PMCID: PMC9198291 DOI: 10.3389/fcell.2022.886642] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/05/2022] [Indexed: 11/24/2022] Open
Abstract
Transfer RNA (tRNA) is a central component of protein synthesis and plays important roles in epigenetic regulation of gene expression in tumors. tRNAs are also involved in many cell processes including cell proliferation, cell signaling pathways and stress response, implicating a role in tumorigenesis and cancer progression. The complex role of tRNA in cell regulation implies that an understanding of tRNA function and dysregulation can be used to develop treatments for many cancers including breast cancer, colon cancer, and glioblastoma. Moreover, tRNA modifications including methylation are necessary for tRNA folding, stability, and function. In response to certain stress conditions, tRNAs can be cleaved in half to form tiRNAs, or even shorter tRNA fragments (tRF). tRNA structure and modifications, tiRNA induction of stress granule formation, and tRF regulation of gene expression through the repression of translation can all impact a cell’s fate. This review focuses on how these functions of tRNAs, tiRNA, and tRFs can lead to tumor development and progression. Further studies focusing on the specific pathways of tRNA regulation could help identify tRNA biomarkers and therapeutic targets, which might prevent and treat cancers.
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Affiliation(s)
- Tania Gupta
- Virginia Commonwealth University, Richmond, VA, United States
| | - Mark G. Malkin
- Department of Neurology, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Suyun Huang
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- Institute of Molecular Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
- *Correspondence: Suyun Huang,
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Shao D, Li Y, Wu J, Zhang B, Xie S, Zheng X, Jiang Z. An m6A/m5C/m1A/m7G-Related Long Non-coding RNA Signature to Predict Prognosis and Immune Features of Glioma. Front Genet 2022; 13:903117. [PMID: 35692827 PMCID: PMC9178125 DOI: 10.3389/fgene.2022.903117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/03/2022] [Indexed: 01/14/2023] Open
Abstract
Background: Gliomas are the most common and fatal malignant type of tumor of the central nervous system. RNA post-transcriptional modifications, as a frontier and hotspot in the field of epigenetics, have attracted increased attention in recent years. Among such modifications, methylation is most abundant, and encompasses N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1 methyladenosine (m1A), and 7-methylguanosine (m7G) methylation.Methods: RNA-sequencing data from healthy tissue and low-grade glioma samples were downloaded from of The Cancer Genome Atlas database along with clinical information and mutation data from glioblastoma tumor samples. Forty-nine m6A/m5C/m1A/m7G-related genes were identified and an m6A/m5C/m1A/m7G-lncRNA signature of co-expressed long non-coding RNAs selected. Least absolute shrinkage and selection operator Cox regression analysis was used to identify 12 m6A/m5C/m1A/m7G-related lncRNAs associated with the prognostic characteristics of glioma and their correlation with immune function and drug sensitivity analyzed. Furthermore, the Chinese Glioma Genome Atlas dataset was used for model validation.Results: A total of 12 m6A/m5C/m1A/m7G-related genes (AL080276.2, AC092111.1, SOX21-AS1, DNAJC9-AS1, AC025171.1, AL356019.2, AC017104.1, AC099850.3, UNC5B-AS1, AC006064.2, AC010319.4, and AC016822.1) were used to construct a survival and prognosis model, which had good independent prediction ability for patients with glioma. Patients were divided into low and high m6A/m5C/m1A/m7G-LS groups, the latter of which had poor prognosis. In addition, the m6A/m5C/m1A/m7G-LS enabled improved interpretation of the results of enrichment analysis, as well as informing immunotherapy response and drug sensitivity of patients with glioma in different subgroups.Conclusion: In this study we constructed an m6A/m5C/m1A/m7G-LS and established a nomogram model, which can accurately predict the prognosis of patients with glioma and provides direction toward promising immunotherapy strategies for the future.
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Ezra Manicum AL, Sargazi S, Razzaq S, Kumar GV, Rahdar A, Er S, Ain QU, Bilal M, Aboudzadeh MA. Nano-immunotherapeutic strategies for targeted RNA delivery: Emphasizing the role of monocyte/macrophages as nanovehicles to treat glioblastoma multiforme. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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43
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Zhang G, Zheng P, Lv Y, Shi Z, Shi F. m6A Regulatory Gene-Mediated Methylation Modification in Glioma Survival Prediction. Front Genet 2022; 13:873764. [PMID: 35559019 PMCID: PMC9086406 DOI: 10.3389/fgene.2022.873764] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/11/2022] [Indexed: 01/11/2023] Open
Abstract
The median survival of patients with gliomas is relatively short. To investigate the epigenetic mechanisms associated with poor survival, we analyzed publicly available datasets from patients with glioma. This analysis revealed 12 prognosis-related m6A regulatory genes that may be responsible for poor prognosis. These genes may be involved in genomic changes inherent to oxidative phosphorylation, adipogenesis, hedgehog signaling, and Myc signaling. We reconstructed a risk model with univariate and multivariate Cox analyses and identified older age and the m6A risk score as independent risk factors for predicting the prognosis of glioma patients, which is associated with glioma immune infiltration. In conclusion, m6A regulatory genes may serve as both reliable biomarkers and potential targets to increase the chance of survival of patients with glioma.
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Affiliation(s)
- Guiyun Zhang
- Department of Neurovascular Intervention, Clinical Center of Neuroscience, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Zheng
- Department of Neurosurgery, Shanghai Pudong New Area People’s Hospital, Shanghai, China
| | - Yisong Lv
- School of Continuing Education, Shanghai Jiao Tong University, Shanghai, China
| | - Zhonghua Shi
- Department of Neurosurgery, 904th Hospital of PLA, Wuxi, China,*Correspondence: Zhonghua Shi, ; Fei Shi,
| | - Fei Shi
- Department of Neurovascular Intervention, Clinical Center of Neuroscience, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Zhonghua Shi, ; Fei Shi,
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Ma Q, Zhang SW, Zhang SY. m6Acancer-Net: Identification of m6A-mediated cancer driver genes from gene-site heterogeneous network. Methods 2022; 203:125-138. [DOI: 10.1016/j.ymeth.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/21/2022] [Accepted: 04/11/2022] [Indexed: 02/08/2023] Open
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Xiong W, Li C, Wan B, Zheng Z, Zhang Y, Wang S, Fan J. N6-Methyladenosine Regulator-Mediated Immue Patterns and Tumor Microenvironment Infiltration Characterization in Glioblastoma. Front Immunol 2022; 13:819080. [PMID: 35359993 PMCID: PMC8961865 DOI: 10.3389/fimmu.2022.819080] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/22/2022] [Indexed: 12/12/2022] Open
Abstract
Background Epigenetic modifications, according to emerging evidence, perform a critical role for cellular immune response and tumorigenesis. Nonetheless, the role of N6-methyladenosine modification in shaping of the glioblastoma tumor microenvironment is unknown. Methods N6-methyladenosine(m6A) methylation patterns in GBM patients were evaluated via multiple omics analysis of 15 m6A regulators and systematically correlated with tumor immune features. For quantification of N6-methyladenosine methylation patterns of individual patients, GM-score was developed and correlated with clinical and immunological characteristics. Results Glioblastoma has two different m6A methylation patterns that are strongly associated with TME characteristics, tumor subtype, immunotherapy response, and patient prognosis. High-GM-score is associated with an immune tolerance phenotype dominated by the IDH1 wild molecular subtype and the Mesenchymal tissue subtype, as well as a high infiltration of immune cells and stromal cells and a poor prognosis. Furthermore, despite higher immune checkpoint expression, individuals with a high-GM-score have a poorer response to anti-CTLA4 immunotherapy regimens due to T-cells dysfunctional. Low-GM-score individuals had an immunodeficient phenotype dominated by IDH mutant molecular subtypes and Proneural tissue subtypes, with less immune cell infiltration and a better prognosis. Furthermore, patients with low-GM-scores had higher microsatellite instability (MSI) and t-cell exclusion scores, as well as a better response to anti-CTLA4 immunotherapy regimens. Conclusion This study demonstrated that m6A modification patterns play an important role in the shaping of TME complexity and diversity. The GM-score could identify m6A modification patterns in individual patients, resulting in a more personalization and efficacious anti-tumor immunotherapy strategy.
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Affiliation(s)
- Wu Xiong
- Department of Orthopaedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Cong Li
- Department of Orthopaedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Bowen Wan
- Department of Orthopaedics, Subei People’s Hospital of Jiangsu, Clinical Medical College of Yangzhou University, Yangzhou, China
| | - Ziyang Zheng
- Department of Orthopaedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Yingfei Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Siming Wang
- Department of Orthopaedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Medical University, Nanjing, China
| | - Jin Fan
- Department of Orthopaedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Nanjing Medical University, Nanjing, China
- *Correspondence: Jin Fan,
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Wang L, Cao H, Zhong Y, Ji P, Chen F. The Role of m6A Regulator-Mediated Methylation Modification and Tumor Microenvironment Infiltration in Glioblastoma Multiforme. Front Cell Dev Biol 2022; 10:842835. [PMID: 35265626 PMCID: PMC8898963 DOI: 10.3389/fcell.2022.842835] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/01/2022] [Indexed: 01/12/2023] Open
Abstract
N6-methyladenosine (m6A) RNA methylation is an emerging epigenetic modification in recent years and epigenetic regulation of the immune response has been demonstrated, but the potential role of m6A modification in GBM tumor microenvironment (TME) cell infiltration and stemness remain unknown. The m6A modification patterns of 310 GBM samples were comprehensively evaluated based on 21 m6A regulators, and we systematically correlated these modification patterns with TME cell infiltration characteristics and stemness characteristics. Construction of m6Ascore to quantify the m6A modification patterns of individual GBM samples using a principal component analysis algorithm. We identified two distinct patterns of m6A modification. The infiltration characteristics of TME cells in these two patterns were highly consistent with the immunophenotype of the GBM, including the immune activation differentiation pattern and the immune desert dedifferentiation pattern. We also identified two modes of regulation of immunity and stemness by m6A methylation. Stromal activation and lack of effective immune infiltration were observed in the high m6Ascore subtype. Pan-cancer analysis results illustrate a significant correlation between m6AScore and tumor clinical outcome, immune infiltration, and stemness. Our work reveals that m6A modifications play an important role in the development of TME and stemness diversity and complexity. Patients with a low m6AScore showed significant therapeutic advantages and clinical benefits. Assessing the m6A modification pattern of individual tumors will help enhance our knowledge of TME infiltration and stemness characteristics, contribute to the development of immunotherapeutic strategies.
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Affiliation(s)
- Liang Wang
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China
| | - Haiyan Cao
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China
| | - Ying Zhong
- Department of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Peigang Ji
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China
| | - Fan Chen
- Department of Neurosurgery, Tangdu Hospital of Fourth Military Medical University, Xi'an, China
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Yang Z, He Y, Wang Y, Huang L, Tang Y, He Y, Chen Y, Han Z. Genome-Wide Analysis for the Regulation of Gene Alternative Splicing by DNA Methylation Level in Glioma and its Prognostic Implications. Front Genet 2022; 13:799913. [PMID: 35309147 PMCID: PMC8931337 DOI: 10.3389/fgene.2022.799913] [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: 10/22/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Glioma is a primary high malignant intracranial tumor with poorly understood molecular mechanisms. Previous studies found that both DNA methylation modification and gene alternative splicing (AS) play a key role in tumorigenesis of glioma, and there is an obvious regulatory relationship between them. However, to date, no comprehensive study has been performed to analyze the influence of DNA methylation level on gene AS in glioma on a genome-wide scale. Here, we performed this study by integrating DNA methylation, gene expression, AS, disease risk methylation at position, and clinical data from 537 low-grade glioma (LGG) and glioblastoma (GBM) individuals. We first conducted a differential analysis of AS events and DNA methylation positions between LGG and GBM subjects, respectively. Then, we evaluated the influence of differential methylation positions on differential AS events. Further, Fisher’s exact test was used to verify our findings and identify potential key genes in glioma. Finally, we performed a series of analyses to investigate influence of these genes on the clinical prognosis of glioma. In total, we identified 130 glioma-related genes whose AS significantly affected by DNA methylation level. Eleven of them play an important role in glioma prognosis. In short, these results will help to better understand the pathogenesis of glioma.
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Affiliation(s)
- Zeyuan Yang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Yijie He
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Yongheng Wang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Lin Huang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Yaqin Tang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Yue He
- Group of Mathematics Education Teaching and Research, Chongqing Fudan Secondary School, Chongqing, China
| | - Yihan Chen
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Zhijie Han
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- *Correspondence: Zhijie Han,
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48
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Chokkalla AK, Mehta SL, Vemuganti R. Epitranscriptomic Modifications Modulate Normal and Pathological Functions in CNS. Transl Stroke Res 2022; 13:1-11. [PMID: 34224107 PMCID: PMC8727632 DOI: 10.1007/s12975-021-00927-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 05/28/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022]
Abstract
RNA is more than just a combination of four genetically encoded nucleobases as it carries extra information in the form of epitranscriptomic modifications. Diverse chemical groups attach covalently to RNA to enhance the plasticity of cellular transcriptome. The reversible and dynamic nature of epitranscriptomic modifications allows RNAs to achieve rapid and context-specific gene regulation. Dedicated cellular machinery comprising of writers, erasers, and readers drives the epitranscriptomic signaling. Epitranscriptomic modifications control crucial steps of mRNA metabolism such as splicing, export, localization, stability, degradation, and translation. The majority of the epitranscriptomic modifications are highly abundant in the brain and contribute to activity-dependent gene expression. Thus, they regulate the vital physiological processes of the brain, such as synaptic plasticity, neurogenesis, and stress response. Furthermore, epitranscriptomic alterations influence the progression of several neurologic disorders. This review discussed the molecular mechanisms of epitranscriptomic regulation in neurodevelopmental and neuropathological conditions with the goal to identify novel therapeutic targets.
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Affiliation(s)
- Anil K Chokkalla
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA
- Department of Neurological Surgery, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA
| | - Suresh L Mehta
- Department of Neurological Surgery, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA
| | - Raghu Vemuganti
- Cellular and Molecular Pathology Graduate Program, University of Wisconsin, Madison, WI, USA.
- Department of Neurological Surgery, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA.
- William S. Middleton Memorial Veteran Administration Hospital, Madison, WI, USA.
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49
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Zhang N, Ding C, Zuo Y, Peng Y, Zuo L. N6-methyladenosine and Neurological Diseases. Mol Neurobiol 2022; 59:1925-1937. [PMID: 35032318 DOI: 10.1007/s12035-022-02739-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/08/2022] [Indexed: 12/14/2022]
Abstract
N6-methyladenosine (m6A) is a dynamic reversible methylation modification of the adenosine N6 position and is the most common chemical epigenetic modification among mRNA post-transcriptional modifications, including methylation, demethylation, and recognition. Post-transcriptional modification involves multiple protein molecules, including METTL3, METTL14, WTAP, KIAA1429, ALKBH5, YTHDF1/2/3, and YTHDC1/2. m6A-related proteins are expressed in almost all cells. However, the abnormal expression of m6A-related proteins may occur in the nervous system, thereby affecting neuritogenesis, brain volume, learning and memory, memory formation and consolidation, etc., and is implicated in the development of diseases, such as Parkinson's disease, Alzheimer's disease, multiple sclerosis, depression, epilepsy, and brain tumors. This review focuses on the functions of m6A in the development of central nervous system diseases, thus contributing to a deeper understanding of disease pathogenesis and providing potential clinical therapeutic targets for neurological diseases.
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Affiliation(s)
- Nan Zhang
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Chunhong Ding
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Yuxin Zuo
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Yu Peng
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China
| | - Lielian Zuo
- Department of Physiology, Institute of Neuroscience Research, Hengyang Key Laboratory of Neurodegeneration and Cognitive Impairment, Hengyang Medical College, University of South China, 28 West Changsheng Road, Hengyang, 421001, Hunan, China.
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50
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Chen J, Sun S, Ren L, Hua L, Wang D, Xie Q, Wirsching HG, Deng J, Weller M, Gong Y. m 6A Regulator Expression Segregates Meningiomas Into Biologically Distinct Subtypes. Front Oncol 2022; 11:760892. [PMID: 35004283 PMCID: PMC8727752 DOI: 10.3389/fonc.2021.760892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/29/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Meningiomas are the most common primary intracranial tumors in adults. According to the 2021 World Health Organization (WHO) classification of central nervous system tumors, approximately 80% of meningiomas are WHO grade 1, that is, histopathologically benign, whereas about 20% are WHO grade 2 or grade 3, showing signs of atypia or malignancy. The dysregulation of N6-methylation (m6A) regulators is associated with disorders of diverse critical biological processes in human cancer. This study aimed to explore whether m6A regulator expression was associated with meningioma molecular subtypes and immune infiltration. METHODS We evaluated the m6A modification patterns of 160 meningioma samples based on 19 m6A regulators and correlated them with immune infiltration characteristics. Novel molecular subtypes were defined based on prognostic hub gene expression. RESULTS Two meningioma clusters were identified based on the expression of 19 m6A regulators. In cluster 1, 607 differentially expressed genes (DEGs) were upregulated and 519 were downregulated. A total of 1,126 DEGs comprised three gene expression modules characterized by turquoise, blue, and gray. Functional annotation suggested that the turquoise module was involved in Wnt-related and other important cancer-related pathways. We identified 32 hub genes in this module by constructing a protein-protein interaction network. The meningioma samples were divided into two molecular subtypes. EPN1, EXOSC4, H2AX, and MZT2B not only showed significant differences between meningioma molecular subtypes but also had the potential to be the marker genes of specific meningioma subtypes. CONCLUSION m6A regulator gene expression may be a novel prognostic marker in meningioma.
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Affiliation(s)
- Jiawei Chen
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Shuchen Sun
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Leihao Ren
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Lingyang Hua
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Daijun Wang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Qing Xie
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Hans-Georg Wirsching
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Jiaojiao Deng
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Ye Gong
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China.,Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
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