701
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Zhang C, Guo C, Li Y, Ouyang L, Zhao Q, Liu K. The role of YTH domain containing 2 in epigenetic modification and immune infiltration of pan-cancer. J Cell Mol Med 2021; 25:8615-8627. [PMID: 34312987 PMCID: PMC8435423 DOI: 10.1111/jcmm.16818] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/11/2021] [Accepted: 07/15/2021] [Indexed: 12/17/2022] Open
Abstract
YTH domain containing 2 (YTHDC2) is the largest N6‐Methyladenosine (m6A) binding protein of the YTH protein family and the only member containing ATP‐dependent RNA helicase activity. For further analysing its biological role in epigenetic modification, we comprehensively explored YTHDC2 from gene expression, genetic alteration, protein‐protein interaction (PPI) network, immune infiltration, diagnostic value and prognostic value in pan‐cancer, using a series of databases and bioinformatic tools. We found that YTHDC2 with Missense mutation could cause a different prognosis in uterine corpus endometrial carcinoma (UCEC), and its different methylation level could lead to a totally various prognosis in adrenocortical carcinoma (ACC), cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), lung squamous cell carcinoma (LUSC) and UCEC. The main molecular mechanisms of YTHDC2 focused on catalytic activity, helicase activity, snRNA binding, spliceosome and mRNA surveillance. Additionally, YTHDC2 was notably correlated with tumour immune infiltration. Moreover, YTHDC2 had a high diagnostic value for seven cancer types and a prognostic value for brain lower grade glioma (LGG), rectum adenocarcinoma (READ) and skin cutaneous melanoma (SKCM). Collectively, YTHDC2 plays a significant role in epigenetic modification and immune infiltration and maybe a potential biomarker for diagnosis and prognosis in certain cancers.
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Affiliation(s)
- Chiyuan Zhang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Cuishan Guo
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yan Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ling Ouyang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qi Zhao
- School of Computer Science and Software Engineering, University of Science and Technology Liaoning, Anshan, China
| | - Kuiran Liu
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
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702
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Zeng Y, Huang T, Zuo W, Wang D, Xie Y, Wang X, Xiao Z, Chen Z, Liu Q, Liu N, Xiao Y. Integrated analysis of m 6A mRNA methylation in rats with monocrotaline-induced pulmonary arterial hypertension. Aging (Albany NY) 2021; 13:18238-18256. [PMID: 34310344 PMCID: PMC8351682 DOI: 10.18632/aging.203230] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 06/04/2021] [Indexed: 01/22/2023]
Abstract
Background: N6-methyladenosine (m6A) modification is one of the most common chemical modifications of eukaryotic mRNAs, which play an important role in tumors and cardiovascular disease through regulating mRNA stability, splicing and translation. However, the changes of m6A mRNA and m6A-related enzymes in pulmonary arterial hypertension (PAH) remain largely unexplored. Methods: MeRIP-seq was used to identify m6A methylation in lung tissues from control and MCT-PAH rats. Western blot and immunofluorescence were used to evaluate expression of m6A-related enzymes. Results: Compared with control group, m6A methylation was mainly increased in lung tissues from MCT-PAH rats. The up-methylated coding genes in MCT-PAH rats were primarily enriched in processes associated with inflammation, glycolysis, ECM-receptor interaction and PDGF signal pathway, while genes with down-methylation were enriched in processes associated with TGF-β family receptor members. The expression of FTO and ALKBH5 downregulated, METTL3 and YTHDF1 increased and other methylation modification-related proteins was not significantly changed in MCT-PAH rats lung tissues. Immunofluorescence indicated that expression of FTO decreased and YTHDF1 increased in small pulmonary arteries of MCT-PAH rats. Conclusion: m6A levels and the expression of methylation-related enzymes were altered in PAH rats, in which FTO and YTHDF1 may play a crucial role in m6A modification.
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Affiliation(s)
- Yunhong Zeng
- Academy of Pediatrics, University of South China, Changsha 410007, China.,Department of Cardiology, Hunan Children's Hospital, Changsha 410007, China
| | - Ting Huang
- Academy of Pediatrics, University of South China, Changsha 410007, China.,Department of Utrasound, Hunan Children's Hospital, Changsha 410007, China
| | - Wanyun Zuo
- Department of Cardiovascular Medicine, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Dan Wang
- Department of Cardiology, Hunan Children's Hospital, Changsha 410007, China
| | - Yonghui Xie
- Academy of Pediatrics, University of South China, Changsha 410007, China.,Department of Cardiology, Hunan Children's Hospital, Changsha 410007, China
| | - Xun Wang
- Department of Cardiology, Hunan Children's Hospital, Changsha 410007, China
| | - Zhenghui Xiao
- Department of Intensive Care Unit, Hunan Children's Hospital, Changsha 410007, China
| | - Zhi Chen
- Department of Cardiology, Hunan Children's Hospital, Changsha 410007, China
| | - Qiming Liu
- Department of Cardiovascular Medicine, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Na Liu
- Department of Cardiovascular Medicine, Second Xiangya Hospital, Central South University, Changsha 410011, China
| | - Yunbin Xiao
- Department of Cardiology, Hunan Children's Hospital, Changsha 410007, China
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703
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Ye F, Wang T, Wu X, Liang J, Li J, Sheng W. N6-Methyladenosine RNA modification in cerebrospinal fluid as a novel potential diagnostic biomarker for progressive multiple sclerosis. J Transl Med 2021; 19:316. [PMID: 34294105 PMCID: PMC8296732 DOI: 10.1186/s12967-021-02981-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/11/2021] [Indexed: 01/01/2023] Open
Abstract
Background Progressive multiple sclerosis (PMS) is an uncommon and severe subtype of MS that worsens gradually and leads to irreversible disabilities in young adults. Currently, there are no applicable or reliable biomarkers to distinguish PMS from relapsing–remitting multiple sclerosis (RRMS). Previous studies have demonstrated that dysfunction of N6-methyladenosine (m6A) RNA modification is relevant to many neurological disorders. Thus, the aim of this study was to explore the diagnostic biomarkers for PMS based on m6A regulatory genes in the cerebrospinal fluid (CSF). Methods Gene expression matrices were downloaded from the ArrayExpress database. Then, we identified differentially expressed m6A regulatory genes between MS and non-MS patients. MS clusters were identified by consensus clustering analysis. Next, we analyzed the correlation between clusters and clinical characteristics. The random forest (RF) algorithm was applied to select key m6A-related genes. The support vector machine (SVM) was then used to construct a diagnostic gene signature. Receiver operating characteristic (ROC) curves were plotted to evaluate the accuracy of the diagnostic model. In addition, CSF samples from MS and non-MS patients were collected and used for external validation, as evaluated by an m6A RNA Methylation Quantification Kit and by real-time quantitative polymerase chain reaction. Results The 13 central m6A RNA methylation regulators were all upregulated in MS patients when compared with non-MS patients. Consensus clustering analysis identified two clusters, both of which were significantly associated with MS subtypes. Next, we divided 61 MS patients into a training set (n = 41) and a test set (n = 20). The RF algorithm identified eight feature genes, and the SVM method was successfully applied to construct a diagnostic model. ROC curves revealed good performance. Finally, the analysis of 11 CSF samples demonstrated that RRMS samples exhibited significantly higher levels of m6A RNA methylation and higher gene expression levels of m6A-related genes than PMS samples. Conclusions The dynamic modification of m6A RNA methylation is involved in the progression of MS and could potentially represent a novel CSF biomarker for diagnosing MS and distinguishing PMS from RRMS in the early stages of the disease. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02981-5.
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Affiliation(s)
- Fei Ye
- Department of Neurology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Tianzhu Wang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoxin Wu
- Department of Neurology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jie Liang
- Department of Neurology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Jiaoxing Li
- Department of Neurology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wenli Sheng
- Department of Neurology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China. .,Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
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704
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METTL3-dependent N 6-methyladenosine RNA modification mediates the atherogenic inflammatory cascades in vascular endothelium. Proc Natl Acad Sci U S A 2021; 118:2025070118. [PMID: 33579825 DOI: 10.1073/pnas.2025070118] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Atherosclerosis is characterized by the plaque formation that restricts intraarterial blood flow. The disturbed blood flow with the associated oscillatory stress (OS) at the arterial curvatures and branch points can trigger endothelial activation and is one of the risk factors of atherosclerosis. Many studies reported the mechanotransduction related to OS and atherogenesis; however, the transcriptional and posttranscriptional regulatory mechanisms of atherosclerosis remain unclear. Herein, we investigated the role of N6-methyladenosine (m6A) RNA methylation in mechanotransduction in endothelial cells (ECs) because of its important role in epitranscriptome regulation. We have identified m6A methyltransferase METTL3 as a responsive hub to hemodynamic forces and atherogenic stimuli in ECs. OS led to an up-regulation of METTL3 expression, accompanied by m6A RNA hypermethylation, increased NF-κB p65 Ser536 phosphorylation, and enhanced monocyte adhesion. Knockdown of METTL3 abrogated this OS-induced m6A RNA hypermethylation and other manifestations, while METTL3 overexpression led to changes resembling the OS effects. RNA-sequencing and m6A-enhanced cross-linking and immunoprecipitation (eCLIP) experiments revealed NLRP1 and KLF4 as two hemodynamics-related downstream targets of METTL3-mediated hypermethylation. The METTL3-mediated RNA hypermethylation up-regulated NLRP1 transcript and down-regulated KLF4 transcript through YTHDF1 and YTHDF2 m6A reader proteins, respectively. In the in vivo atherosclerosis model, partial ligation of the carotid artery led to plaque formation and up-regulation of METTL3 and NLRP1, with down-regulation of KLF4; knockdown of METTL3 via repetitive shRNA administration prevented the atherogenic process, NLRP3 up-regulation, and KLF4 down-regulation. Collectively, we have demonstrated that METTL3 serves a central role in the atherogenesis induced by OS and disturbed blood flow.
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705
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Oerum S, Meynier V, Catala M, Tisné C. A comprehensive review of m6A/m6Am RNA methyltransferase structures. Nucleic Acids Res 2021; 49:7239-7255. [PMID: 34023900 PMCID: PMC8287941 DOI: 10.1093/nar/gkab378] [Citation(s) in RCA: 210] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023] Open
Abstract
Gene expression is regulated at many levels including co- or post-transcriptionally, where chemical modifications are added to RNA on riboses and bases. Expression control via RNA modifications has been termed 'epitranscriptomics' to keep with the related 'epigenomics' for DNA modification. One such RNA modification is the N6-methylation found on adenosine (m6A) and 2'-O-methyladenosine (m6Am) in most types of RNA. The N6-methylation can affect the fold, stability, degradation and cellular interaction(s) of the modified RNA, implicating it in processes such as splicing, translation, export and decay. The multiple roles played by this modification explains why m6A misregulation is connected to multiple human cancers. The m6A/m6Am writer enzymes are RNA methyltransferases (MTases). Structures are available for functionally characterized m6A RNA MTases from human (m6A mRNA, m6A snRNA, m6A rRNA and m6Am mRNA MTases), zebrafish (m6Am mRNA MTase) and bacteria (m6A rRNA MTase). For each of these MTases, we describe their overall domain organization, the active site architecture and the substrate binding. We identify areas that remain to be investigated, propose yet unexplored routes for structural characterization of MTase:substrate complexes, and highlight common structural elements that should be described for future m6A/m6Am RNA MTase structures.
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Affiliation(s)
- Stephanie Oerum
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France
| | - Vincent Meynier
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France
| | - Marjorie Catala
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (IBPC), 75005 Paris, France
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706
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Chen H, Guan Q, Guo H, Miao L, Zhuo Z. The Genetic Changes of Hepatoblastoma. Front Oncol 2021; 11:690641. [PMID: 34367972 PMCID: PMC8335155 DOI: 10.3389/fonc.2021.690641] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 07/05/2021] [Indexed: 12/19/2022] Open
Abstract
Hepatoblastoma is the most common malignant liver cancer in childhood. The etiology of hepatoblastoma remains obscure. Hepatoblastoma is closely related to genetic syndromes, hinting that hepatoblastoma is a genetic predisposition disease. However, no precise exposures or genetic events are reported to hepatoblastoma occurrence. During the past decade, significant advances have been made in the understanding of etiology leading to hepatoblastoma, and several important genetic events that appear to be important for the development and progression of this tumor have been identified. Advances in our understanding of the genetic changes that underlie hepatoblastoma may translate into better patient outcomes. Single nucleotide polymorphisms (SNPs) have been generally applied in the research of etiology's exploration, disease treatment, and prognosis assessment. Here, we reviewed and discussed the molecular epidemiology, especially SNPs progresses in hepatoblastoma, to provide references for future studies and promote the study of hepatoblastoma's etiology.
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Affiliation(s)
- Huitong Chen
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qian Guan
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Huiqin Guo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Lei Miao
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
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707
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Zhao R, Li B, Zhang S, He Z, Pan Z, Guo Q, Qiu W, Qi Y, Zhao S, Wang S, Chen Z, Zhang P, Guo X, Xue H, Li G. The N 6-Methyladenosine-Modified Pseudogene HSPA7 Correlates With the Tumor Microenvironment and Predicts the Response to Immune Checkpoint Therapy in Glioblastoma. Front Immunol 2021; 12:653711. [PMID: 34354698 PMCID: PMC8329659 DOI: 10.3389/fimmu.2021.653711] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/05/2021] [Indexed: 01/10/2023] Open
Abstract
Background Glioblastoma (GBM), one of the most aggressive tumors of the brain, has no effective or sufficient therapies. Identifying robust biomarkers for the response to immune checkpoint blockade (ICB) therapy, a promising treatment option for GBM patients, is urgently needed. Methods We comprehensively evaluated lncRNA m6A modification patterns in m6A-sequencing (m6A-seq) data for GBM tissues and systematically investigated the immune and stromal regulators of these m6A-regulated lncRNAs. We used the single-sample gene-set enrichment analysis (ssGSEA) algorithm to investigate the difference in enriched tumor microenvironment (TME) infiltrating cells and the functional annotation of HSPA7 in individual GBM samples. Further, we validated that HSPA7 promoted the recruitment of macrophages into GBM TME in vitro, as well as in our GBM tissue section. We also explored its impact on the efficacy of ICB therapy using the patient-derived glioblastoma organoid (GBO) model. Results Here, we depicted the first transcriptome-wide m6A methylation profile of lncRNAs in GBM, revealing highly distinct lncRNA m6A modification patterns compared to those in normal brain tissues. We identified the m6A-modified pseudogene HSPA7 as a novel prognostic risk factor in GBM patients, with crucial roles in immunophenotype determination, stromal activation, and carcinogenic pathway activation. We confirmed that HSPA7 promoted macrophage infiltration and SPP1 expression via upregulating the YAP1 and LOX expression of glioblastoma stem cells (GSCs) in vitro and in our clinical GBM tumor samples. We also confirmed that knockdown of HSPA7 might increase the efficiency of anti-PD1 therapy utilizing the GBO model, highlighting its potential as a novel target for immunotherapy. Conclusions Our results indicated that HSPA7 could be a novel immunotherapy target for GBM patients.
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Affiliation(s)
- Rongrong Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Boyan Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Shouji Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Zheng He
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China.,Department of Neurosurgery, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
| | - Ziwen Pan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Qindong Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Wei Qiu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Yanhua Qi
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Shulin Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Shaobo Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Zihang Chen
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Ping Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Xing Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Hao Xue
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China.,Shandong Key Laboratory of Brain Function Remodeling, Qilu Hospital of Shandong University, Jinan, China
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708
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Yu ZH, Feng ST, Zhang D, Cao XC, Yu Y, Wang X. The functions and prognostic values of m6A RNA methylation regulators in thyroid carcinoma. Cancer Cell Int 2021; 21:385. [PMID: 34281544 PMCID: PMC8287668 DOI: 10.1186/s12935-021-02090-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/13/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND N6-Methyladenosine (m6A) is the most common RNA modification and regulates RNA splicing, translation, translocation, and stability. Aberrant expression of m6A has been reported in various types of human cancers. m6A RNA modification is dynamically and reversibly mediated by different regulators, including methyltransferase, demethylases, and m6A binding proteins. However, the role of m6A RNA methylation regulators in thyroid cancer remains unknown. The aim of this study is to investigate the effect of the 13 main m6A RNA modification regulators in thyroid carcinoma. METHODS We obtained clinical data and RNA sequencing data of 13 m6A RNA methylation regulators from The Cancer Genome Atlas (TCGA) THCA database. We performed consensus clustering to identify the clinical relevance of m6A RNA methylation regulators in thyroid carcinoma. Then we used LASSO Cox regression analysis to generate a prognostic signature based on m6A RNA modification regulator expression. Kyoto Encyclopedia of Genes and Genomes, Gene Ontology and Gene Set Enrichment Analyses were performed to explore differential cellular processes and signaling pathways between the two groups based on risk signature. RESULTS We found that most of the m6A RNA modification regulators are down-regulated in 450 patients with thyroid carcinoma. We derived a three m6A RNA modification regulator genes-based risk signature (FTO, RBM15 and KIAA1429), that is an independent prognostic biomarker in patients with thyroid carcinoma. Moreover, we found that this risk signature could better predict outcome in male than female. Functional research in vitro demonstrated that the m6A RNA methylation regulators involved in the model acted significant role in the proliferation and migration of thyroid cancer cells. CONCLUSIONS Our study revealed the influence of m6A RNA methylation regulators on thyroid carcinoma through biological experiments and three-gene prognostic model.
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Affiliation(s)
- Zhi-Hao Yu
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Huan-Hu-Xi Road, He-Xi District, Tianjin, 300060, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Shao-Ting Feng
- Department of Clinical Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Di Zhang
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Huan-Hu-Xi Road, He-Xi District, Tianjin, 300060, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Xu-Chen Cao
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Huan-Hu-Xi Road, He-Xi District, Tianjin, 300060, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China
| | - Yue Yu
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Huan-Hu-Xi Road, He-Xi District, Tianjin, 300060, China. .,Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China. .,Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China. .,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China.
| | - Xin Wang
- The First Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Huan-Hu-Xi Road, He-Xi District, Tianjin, 300060, China. .,Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China. .,Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China. .,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, China.
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709
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An introduction to the themed issue on RNA biology in China. Essays Biochem 2021; 64:863-866. [PMID: 33284952 DOI: 10.1042/ebc20200031] [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: 09/13/2020] [Revised: 10/25/2020] [Accepted: 11/02/2020] [Indexed: 11/17/2022]
Abstract
The year 2019 marked the fortieth anniversary of the Chinese Society of Biochemistry and Molecular Biology (CSBMB), whose mission is to promote biomolecular research and education in China. The last 40 years have witnessed tremendous growth and achievements in biomolecular research by Chinese scientists and Essays in Biochemistry is delighted to publish this themed issue that focuses on exciting areas within RNA biology, with each review contributed by key experts from China.
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710
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Qian X, Yang J, Qiu Q, Li X, Jiang C, Li J, Dong L, Ying K, Lu B, Chen E, Liu P, Lu Y. LCAT3, a novel m6A-regulated long non-coding RNA, plays an oncogenic role in lung cancer via binding with FUBP1 to activate c-MYC. J Hematol Oncol 2021; 14:112. [PMID: 34274028 PMCID: PMC8285886 DOI: 10.1186/s13045-021-01123-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/02/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are important epigenetic regulators, which play critical roles in diverse physiological and pathological processes. However, the regulatory mechanism of lncRNAs in lung carcinogenesis remains elusive. Here, we characterized a novel oncogenic lncRNA, designated as Lung Cancer Associated Transcript 3 (LCAT3). METHODS We predicted and validated LCAT3 by analyzing RNA-sequencing (RNA-seq) data of lung cancer tissues from TCGA. Methylated RNA immunoprecipitation was performed to assess m6A modification on LCAT3. The LCAT3-FUBP1-MYC axis was assessed by dual-luciferase reporter, RNA immunoprecipitation and Chromatin immunoprecipitation assays. Signaling pathways altered by LCAT3 knockdown were identified using RNA-seq. Furthermore, the mechanism of LCAT3 was investigated using loss-of-function and gain-of-function assays in vivo and in vitro. RESULTS LCAT3 was found to be up-regulated in lung adenocarcinomas (LUAD), and its over-expression was associated with the poor prognosis of LUAD patients. LCAT3 upregulation is attributable to N6-methyladenosine (m6A) modification mediated by methyltransferase like 3 (METTL3), leading to LCAT3 stabilization. Biologically, loss-of-function assays revealed that LCAT3 knockdown significantly suppressed lung cancer cell proliferation, migration and invasion in vitro, and inhibited tumor growth and metastasis in vivo. LCAT3 knockdown induced cell cycle arrest at the G1 phase. Mechanistically, LCAT3 recruited Far Upstream Element Binding Protein 1 (FUBP1) to the MYC far-upstream element (FUSE) sequence, thereby activating MYC transcription to promote proliferation, survival, invasion and metastasis of lung cancer cells. CONCLUSIONS Taken together, we identified and characterized LCAT3 as a novel oncogenic lncRNA in the lung, and validated the LCAT3-FUBP1-MYC axis as a potential therapeutic target for LUAD.
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Affiliation(s)
- Xinyi Qian
- Center for Uterine Cancer Diagnosis and Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Juze Yang
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China
| | - Qiongzi Qiu
- Center for Uterine Cancer Diagnosis and Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Xufan Li
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China
| | - Chengxi Jiang
- Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Jia Li
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China
| | - Liangliang Dong
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China
| | - Kejing Ying
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, 310013, Zhejiang, China
| | - Bingjian Lu
- Center for Uterine Cancer Diagnosis and Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China
| | - Enguo Chen
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China
- Cancer Center, Zhejiang University, Hangzhou, 310013, Zhejiang, China
| | - Pengyuan Liu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310016, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, 310013, Zhejiang, China.
- Department of Physiology and Center of Systems Molecular Medicine, Medical College of Wisconsin, Milwaukee, 53226, WI, USA.
| | - Yan Lu
- Center for Uterine Cancer Diagnosis and Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, 310006, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, 310013, Zhejiang, China.
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711
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Zhang P, Liu G, Lu L. N6-Methylandenosine-Related lncRNA Signature Is a Novel Biomarkers of Prognosis and Immune Response in Colon Adenocarcinoma Patients. Front Cell Dev Biol 2021; 9:703629. [PMID: 34336856 PMCID: PMC8321625 DOI: 10.3389/fcell.2021.703629] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/21/2021] [Indexed: 12/12/2022] Open
Abstract
Background Colon adenocarcinoma (COAD) is the most common type of colon cancer. To date, however, the prognostic values of m6A RNA methylation-related long non-coding RNAs (lncRNAs) in COAD are largely unknown. Materials and Methods The m6A-related lncRNAs were identified from The Cancer Genome Atlas (TCGA) data set. Univariate and multivariate Cox regression analyses were performed to explore the prognostic m6A-related lncRNAs. Consistent clustering analysis was performed to classify the COAD patients into different subgroups based on the expression of m6A-related lncRNAs. The potential biological functions as well as differences in the stemness index and tumor immune microenvironment between different subgroups were analyzed. The prognostic m6A-related lncRNAs were used to establish an m6A-related lncRNA risk model to predict prognosis and survival status. Results We identified 31 m6A-associated lncRNAs with prognostic values from the TCGA data set. Based on the expression of prognostic m6A-associated lncRNAs, TCGA-COAD patients were classified into three clusters using consistent clustering analysis. There was a low correlation of tumor stemness between the three clusters but a significant correlation with the tumor immune microenvironment as well as the tumor mutational load. Thirty-one prognostic-related m6A-associated lncRNAs were used to construct a risk model, which was further determined by survival analysis, receiver operating characteristic (ROC) curve, and univariate and multifactor Cox analysis. The m6A-related risk model demonstrates good performance in predicting prognosis and survival status. The model-based high-risk group exhibited poorer overall survival (OS) compared with the low-risk group. Conclusion In this study, we construct a risk model that consists of 31 m6A-related lncRNAs with independent prognostic values in COAD. Our study shows the critical roles of these 31 m6A-related lncRNAs in the tumor immune microenvironment, indicating the prospect of informing prognostic stratification and the development of immunotherapeutic strategies for COAD patients.
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Affiliation(s)
- Peiling Zhang
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Guolong Liu
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Lin Lu
- Department of Medical Oncology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, China
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712
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Novikov DA, Beletsky AP, Kolosov PM. The Putative Role of m6A-RNA Methylation in Memory Consolidation. NEUROCHEM J+ 2021. [DOI: 10.1134/s1819712421020112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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713
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Chai RC, Chang YZ, Chang X, Pang B, An SY, Zhang KN, Chang YH, Jiang T, Wang YZ. YTHDF2 facilitates UBXN1 mRNA decay by recognizing METTL3-mediated m 6A modification to activate NF-κB and promote the malignant progression of glioma. J Hematol Oncol 2021; 14:109. [PMID: 34246306 PMCID: PMC8272379 DOI: 10.1186/s13045-021-01124-z] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/02/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The prognosis for diffuse gliomas is very poor and the mechanism underlying their malignant progression remains unclear. Here, we aimed to elucidate the role and mechanism of the RNA N6,2'-O-dimethyladenosine (m6A) reader, YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), in regulating the malignant progression of gliomas. METHODS YTHDF2 mRNA levels and functions were assessed using several independent datasets. Western blotting, quantitative polymerase chain reaction, and immunohistochemistry were used to evaluate the expression levels of YTHDF2 and other molecules in human and mouse tumor tissues and cells. Knockdown and overexpression were used to evaluate the effects of YTHDF2, methyltransferase-like 3 (METTL3), and UBX domain protein 1 (UBXN1) on glioma malignancy in cell and orthotopic xenograft models. RNA immunoprecipitation (RIP), methylated RIP, and RNA stability experiments were performed to study the mechanisms underlying the oncogenic role of YTHDF2. RESULTS YTHDF2 expression was positively associated with a higher malignant grade and molecular subtype of glioma and poorer prognosis. YTHDF2 promoted the malignant progression of gliomas in both in vitro and in vivo models. Mechanistically, YTHDF2 accelerated UBXN1 mRNA degradation via METTL3-mediated m6A, which, in turn, promoted NF-κB activation. We further revealed that UBXN1 overexpression attenuated the oncogenic effect of YTHDF2 overexpression and was associated with better survival in patients with elevated YTHDF2 expression. CONCLUSIONS Our findings confirmed that YTHDF2 promotes the malignant progression of gliomas and revealed important insight into the upstream regulatory mechanism of NF-κB activation via UBXN1 with a primary focus on m6A modification.
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Affiliation(s)
- Rui-Chao Chai
- Department of Molecular Neuropathology, Department of Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100050, China.
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, China.
| | - Yu-Zhou Chang
- Department of Molecular Neuropathology, Department of Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100050, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100050, China
| | - Xin Chang
- Department of Molecular Neuropathology, Department of Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100050, China
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Bo Pang
- Department of Molecular Neuropathology, Department of Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100050, China
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Song Yuan An
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100050, China
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Ke-Nan Zhang
- Department of Molecular Neuropathology, Department of Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100050, China
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Yuan-Hao Chang
- Department of Molecular Neuropathology, Department of Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100050, China
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, China
| | - Tao Jiang
- Department of Molecular Neuropathology, Department of Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100050, China.
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100050, China.
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, China.
| | - Yong-Zhi Wang
- Department of Molecular Neuropathology, Department of Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100050, China.
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, No. 119 Nan Si Huan Xi Road, Fengtai District, Beijing, 100050, China.
- Chinese Glioma Genome Atlas Network (CGGA), Beijing, China.
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714
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Cheng Q, Wang P, Wu G, Wang Y, Tan J, Li C, Zhang X, Liu S, Huang S, Huang T, Yang M, He H, Bian J. Coordination of m 6A mRNA methylation and gene transcriptome in rice response to cadmium stress. RICE (NEW YORK, N.Y.) 2021; 14:62. [PMID: 34224034 PMCID: PMC8257850 DOI: 10.1186/s12284-021-00502-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/08/2021] [Indexed: 05/19/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification present in the mRNAs of all higher eukaryotes. However, the role of the m6A methylomes in rice is still poorly understood. With the development of the MeRIP-seq technique, the in-depth identification of mRNAs with m6A modification has become feasible. A study suggested that m6A modification is crucial for posttranscriptional regulation related to Cd2+-induced malignant transformation, but the association between m6A modification in plants and Cd tolerance has not been reported. We investigated the m6A methylomes in the roots of a cadmium (Cd)-treated group and compared them with the roots in the control (CK) group by m6A sequencing of cv. 9311 and cv. Nipponbare (NIP) plants. The results indicated that Cd leads to an altered modification profile in 3,406 differential m6A peaks in cv. 9311 and 2,065 differential m6A peaks in cv. NIP. KEGG pathway analysis of the genes with differentially modified m6A peaks indicated that the "phenylalanine", "tyrosine and tryptophan biosynthesis", "glycine", "adherens junctions", "glycerophospholipid metabolism" and "threonine metabolism" signalling pathways may be associated with the abnormal root development of cv. 9311 rice due to exposure to Cd. The "arginine", "proline metabolism", "glycerolipid", and "protein processing in endoplasmic reticulum" metabolism pathways were significantly enriched in genes with differentially modified m6A peaks in cv. NIP. Unlike that in Arabidopsis, the m6A-modified nucleotide position on mRNAs (m6A peak) distribution in rice exhibited a preference towards both the stop codon and 3' untranslated regions (3' UTRs). These findings provide a resource for plant RNA epitranscriptomic studies and further increase our knowledge on the function of m6A modification in RNA in plants.
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Affiliation(s)
- Qin Cheng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Peng Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Guangliang Wu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Yanning Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Jingai Tan
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Caijing Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Xiangyu Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Shilei Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Shiying Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Tao Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Mengmeng Yang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Jianmin Bian
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, 330045 Nanchang, China
- College of Agronomy, Jiangxi Agricultural University, 330045 Nanchang, China
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715
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Albik S, Tao YX. Emerging role of RNA m6A modification in chronic pain. Pain 2021; 162:1897-1898. [PMID: 33675633 PMCID: PMC8205953 DOI: 10.1097/j.pain.0000000000002219] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/04/2021] [Indexed: 01/25/2023]
Affiliation(s)
- Sfian Albik
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Yuan-Xiang Tao
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
- Department of Physiology, Pharmacology & Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
- Department of Cell Biology & Molecular Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
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716
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Genetic drivers of m 6A methylation in human brain, lung, heart and muscle. Nat Genet 2021; 53:1156-1165. [PMID: 34211177 DOI: 10.1038/s41588-021-00890-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 05/18/2021] [Indexed: 01/22/2023]
Abstract
The most prevalent post-transcriptional mRNA modification, N6-methyladenosine (m6A), plays diverse RNA-regulatory roles, but its genetic control in human tissues remains uncharted. Here we report 129 transcriptome-wide m6A profiles, covering 91 individuals and 4 tissues (brain, lung, muscle and heart) from GTEx/eGTEx. We integrate these with interindividual genetic and expression variation, revealing 8,843 tissue-specific and 469 tissue-shared m6A quantitative trait loci (QTLs), which are modestly enriched in, but mostly orthogonal to, expression QTLs. We integrate m6A QTLs with disease genetics, identifying 184 GWAS-colocalized m6A QTL, including brain m6A QTLs underlying neuroticism, depression, schizophrenia and anxiety; lung m6A QTLs underlying expiratory flow and asthma; and muscle/heart m6A QTLs underlying coronary artery disease. Last, we predict novel m6A regulators that show preferential binding in m6A QTLs, protein interactions with known m6A regulators and expression correlation with the m6A levels of their targets. Our results provide important insights and resources for understanding both cis and trans regulation of epitranscriptomic modifications, their interindividual variation and their roles in human disease.
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717
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Ninomiya K, Iwakiri J, Aly MK, Sakaguchi Y, Adachi S, Natsume T, Terai G, Asai K, Suzuki T, Hirose T. m 6 A modification of HSATIII lncRNAs regulates temperature-dependent splicing. EMBO J 2021; 40:e107976. [PMID: 34184765 DOI: 10.15252/embj.2021107976] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 12/21/2022] Open
Abstract
Nuclear stress bodies (nSBs) are nuclear membraneless organelles formed around stress-inducible HSATIII architectural long noncoding RNAs (lncRNAs). nSBs repress splicing of hundreds of introns during thermal stress recovery, which are partly regulated by CLK1 kinase phosphorylation of temperature-dependent Ser/Arg-rich splicing factors (SRSFs). Here, we report a distinct mechanism for this splicing repression through protein sequestration by nSBs. Comprehensive identification of RNA-binding proteins revealed HSATIII association with proteins related to N6 -methyladenosine (m6 A) RNA modification. 11% of the first adenosine in the repetitive HSATIII sequence were m6 A-modified. nSBs sequester the m6 A writer complex to methylate HSATIII, leading to subsequent sequestration of the nuclear m6 A reader, YTHDC1. Sequestration of these factors from the nucleoplasm represses m6 A modification of pre-mRNAs, leading to repression of m6 A-dependent splicing during stress recovery phase. Thus, nSBs serve as a common platform for regulation of temperature-dependent splicing through dual mechanisms employing two distinct ribonucleoprotein modules with partially m6 A-modified architectural lncRNAs.
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Affiliation(s)
- Kensuke Ninomiya
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Junichi Iwakiri
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Mahmoud Khamis Aly
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.,Faculty of Biotechnology, Modern Sciences and Arts University, Giza, Egypt
| | - Yuriko Sakaguchi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Shungo Adachi
- Cellular and Molecular Biotechnology Research Institute, National Institute for Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Tohru Natsume
- Cellular and Molecular Biotechnology Research Institute, National Institute for Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Goro Terai
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Kiyoshi Asai
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Tsutomu Suzuki
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
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718
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Mapping single-nucleotide m 6A by m 6A-REF-seq. Methods 2021; 203:392-398. [PMID: 34174388 DOI: 10.1016/j.ymeth.2021.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/20/2021] [Accepted: 06/21/2021] [Indexed: 11/23/2022] Open
Abstract
The past few years have witnessed rapid progress in the field of RNA modifications. As the most prevailing modification on eukaryotic mRNA, m6A is characterized to play a vital role in various cellular activities. However, limitations of the detection method impede functional studies of m6A. Here we introduce m6A-REF-seq, a powerful and straightforward method to identify m6A at single-nucleotide resolution. m6A-REF-seq relies on the recognition of RNA endonuclease MazF towards m6A at the ACA motif, providing an orthogonal method independent of the m6A antibody being adopted by most of current methods. We describe a detailed protocol to perform m6A-REF-seq, including NGS library construction and sequencing data analysis. In particular, we describe an optimized assay to validate individual m6A sites identified by m6A-REF-seq, which can also be applied to detect any candidate m6A sites.
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719
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Du Y, Ma Y, Zhu Q, Liu T, Jiao Y, Yuan P, Wang X. An m6A-Related Prognostic Biomarker Associated With the Hepatocellular Carcinoma Immune Microenvironment. Front Pharmacol 2021; 12:707930. [PMID: 34248650 PMCID: PMC8263919 DOI: 10.3389/fphar.2021.707930] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/14/2021] [Indexed: 12/24/2022] Open
Abstract
Background: N6-methyladenosine (m6A) is related to the progression of multiple cancers. However, the underlying influences of m6A-associated genes on the tumor immune microenvironment in hepatocellular carcinoma (HCC) remain poorly understood. Therefore, we sought to construct a survival prediction model using m6A-associated genes to clarify the molecular and immune characteristics of HCC. Methods: HCC case data were downloaded from The Cancer Genome Atlas (TCGA). Then, by applying consensus clustering, we identified two distinct HCC clusters. Next, four m6A-related genes were identified to construct a prognostic model, which we validated with Gene Expression Omnibus (GEO) and International Cancer Genome Consortium (ICGC) datasets. Additionally, the molecular and immune characteristics in different subgroups were analyzed. Results: m6A RNA methylation regulators were differentially expressed between HCC and normal samples and linked with immune checkpoint expression. Using consensus clustering, we divided HCC samples into two subtypes with distinct clinical features. Cluster 2 was associated with unfavorable prognosis, higher immune checkpoint expression and immune cell infiltration levels. In addition, the immune and carcinogenic signaling pathways were enriched in cluster 2. Furthermore, we constructed a risk model using four m6A-associated genes. Patients with different risk scores had distinct survival times, expression levels of immunotherapy biomarkers, TP53 mutation rates, and sensitivities to chemotherapy and targeted therapy. Similarly, the model exhibited an identical impact on overall survival in the validation cohorts. Conclusion: The constructed m6A-based signature may be promising as a biomarker for prognostics and to distinguish immune characteristics in HCC.
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Affiliation(s)
- Yingxi Du
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yarui Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qing Zhu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tongzheng Liu
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Yuchen Jiao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peng Yuan
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobing Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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720
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Wang W, Shao F, Yang X, Wang J, Zhu R, Yang Y, Zhao G, Guo D, Sun Y, Wang J, Xue Q, Gao S, Gao Y, He J, Lu Z. METTL3 promotes tumour development by decreasing APC expression mediated by APC mRNA N 6-methyladenosine-dependent YTHDF binding. Nat Commun 2021; 12:3803. [PMID: 34155197 PMCID: PMC8217513 DOI: 10.1038/s41467-021-23501-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 04/23/2021] [Indexed: 12/24/2022] Open
Abstract
The adenomatous polyposis coli (APC) is a frequently mutated tumour suppressor gene in cancers. However, whether APC is regulated at the epitranscriptomic level remains elusive. In this study, we analysed TCGA data and separated 200 paired oesophageal squamous cell carcinoma (ESCC) specimens and their adjacent normal tissues and demonstrated that methyltransferase-like 3 (METTL3) is highly expressed in tumour tissues. m6A-RNA immunoprecipitation sequencing revealed that METTL3 upregulates the m6A modification of APC, which recruits YTHDF for APC mRNA degradation. Reduced APC expression increases the expression of β-catenin and β-catenin-mediated cyclin D1, c-Myc, and PKM2 expression, thereby leading to enhanced aerobic glycolysis, ESCC cell proliferation, and tumour formation in mice. In addition, downregulated APC expression correlates with upregulated METTL3 expression in human ESCC specimens and poor prognosis in ESCC patients. Our findings reveal a mechanism by which the Wnt/β-catenin pathway is upregulated in ESCC via METTL3/YTHDF-coupled epitranscriptomal downregulation of APC. The epitranscriptomic regulation of adenomatous polyposis coli (APC) tumour suppressor gene in cancers is unclear. Here the authors show that N6-methyladenosine methylation writer METTL3 downregulates APC by recruiting YTHDF2 for APC mRNA degradation, and that this promotes glycolysis and tumour growth in oesophageal cancers.
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Affiliation(s)
- Wei Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Shao
- Affiliated Hospital of Qingdao University and Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Xueying Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Juhong Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rongxuan Zhu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yannan Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Gaoxiang Zhao
- Affiliated Hospital of Qingdao University and Qingdao Cancer Institute, Qingdao, Shandong, China
| | - Dong Guo
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingli Sun
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Jie Wang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qi Xue
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yibo Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. .,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. .,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Zhimin Lu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. .,Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China. .,Zhejiang University Cancer Center, Hangzhou, China.
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721
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The m 6A RNA Modification Quantity and mRNA Expression Level of RNA Methylation-Related Genes in Head and Neck Squamous Cell Carcinoma Cell Lines and Patients. Biomolecules 2021; 11:biom11060908. [PMID: 34207099 PMCID: PMC8235215 DOI: 10.3390/biom11060908] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 12/14/2022] Open
Abstract
RNA methylation at the nitrogen sixth of adenosine (m6A, N6-methyladenosine) is the most abundant RNA modification which plays a crucial role in all RNA metabolic aspects. Recently, m6A modification has been assigned to mediate the biological processes of cancer cells, but their significance in HNSCC development is still poorly described. Thus, the main aim of this study was to globally quantify m6A modification by the mass spectrometry approach and determine the mRNA expression level of selected m6A RNA methyltransferase (METTL3), demethylase (FTO), and m6A readers (YTHDF2, YTHDC2) in 45 HNSCC patients and 4 cell lines (FaDu, Detroit 562, A-253 and SCC-15) using qPCR. In the results, we have not observed differences in the global amount of m6A modification and the mRNA level of the selected genes between the cancerous and paired-matched histopathologically unchanged tissues from 45 HNSCC patients. However, we have found a positive correlation between selected RNA methylation machinery genes expression and m6A abundance on total RNA and characterized the transcript level of those genes in the HNSCC cell lines. Moreover, the lack of global m6A differences between cancerous and histopathologically unchanged tissues suggests that m6A alterations in specific RNA sites may specifically influence HNSCC tumorigenesis.
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722
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Zhang TY, Wang ZQ, Hu HC, Chen ZQ, Liu P, Gao SQ, Zhang F, He L, Jin P, Xu MZ, Chen JP, Yang J. Transcriptome-Wide N 6-Methyladenosine (m 6A) Profiling of Susceptible and Resistant Wheat Varieties Reveals the Involvement of Variety-Specific m 6A Modification Involved in Virus-Host Interaction Pathways. Front Microbiol 2021; 12:656302. [PMID: 34122371 PMCID: PMC8187603 DOI: 10.3389/fmicb.2021.656302] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/29/2021] [Indexed: 11/17/2022] Open
Abstract
N6-methyladenosine (m6A) methylation is the most prevalent internal modification of post-transcriptional modifications in mRNA, tRNA, miRNA, and long non-coding RNA in eukaryotes. m6A methylation has been proven to be involved in plant resistance to pathogens. However, there are no reports on wheat (Triticum aestivum) m6A transcriptome-wide map and its potential biological function in wheat resistance to wheat yellow mosaic virus (WYMV). To the best of our knowledge, this study is the first to determine the transcriptome-wide m6A profile of two wheat varieties with different resistances to WYMV. By analyzing m6A-sequencing (m6A-seq) data, we identified 25,752 common m6A peaks and 30,582 common m6A genes in two groups [WYMV-infected resistant wheat variety (WRV) and WYMV-infected sensitive wheat variety (WSV)], and all these peaks were mainly enriched in 3′ untranslated regions and stop codons of coding sequences. Gene Ontology analysis of m6A-seq and RNA-sequencing data revealed that genes that showed significant changes in both m6A and mRNA levels were associated with plant defense responses. Kyoto Encyclopedia of Genes and Genomes analysis revealed that these selected genes were enriched in the plant–pathogen interaction pathway. We further verified these changes in m6A and mRNA levels through gene-specific m6A real-time quantitative PCR (RT-qPCR) and normal RT-qPCR. This study highlights the role of m6A methylation in wheat resistance to WYMV, providing a solid basis for the potential functional role of m6A RNA methylation in wheat resistance to infection by RNA viruses.
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Affiliation(s)
- Tian-Ye Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Zi-Qiong Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hai-Chao Hu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Zhi-Qing Chen
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Peng Liu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Shi-Qi Gao
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Fan Zhang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Long He
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Peng Jin
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Miao-Ze Xu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian-Ping Chen
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China.,State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo, China
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723
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Identification of an m6A-Related Signature as Biomarker for Hepatocellular Carcinoma Prognosis and Correlates with Sorafenib and Anti-PD-1 Immunotherapy Treatment Response. DISEASE MARKERS 2021; 2021:5576683. [PMID: 34221187 PMCID: PMC8213471 DOI: 10.1155/2021/5576683] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/26/2021] [Indexed: 12/13/2022]
Abstract
Background N6-methyladenosine (m6A) modification plays an essential role in diverse key biological processes and may take part in the development and progression of hepatocellular carcinoma (HCC). Here, we systematically analyzed the expression profiles and prognostic values of 13 widely reported m6A modification-related genes in HCC. Methods The mRNA expression of 13 m6A modification-related genes and clinical parameters of HCC patients were downloaded from TCGA, ICGC, GSE109211, and GSE78220. Univariate and LASSO analyses were used to develop risk signature. Time-dependent ROC was performed to assess the predictive accuracy and sensitivity of risk signature. Results FTO, YTHDC1, YTHDC2, ALKBH5, KIAA1429, HNRNPC, METTL3, RBM15, YTHDF2, YTHDF1, and WTAP were significantly overexpressed in HCC patients. YTHDF1, HNRNPC, RBM15, METTL3, and YTHDF2 were independent prognostic factors for OS and DFS in HCC patients. Next, a risk signature was also developed and validated with five m6A modification-related genes in TCGA and ICGC HCC cohort. It could effectively stratify HCC patients into high-risk patients with shorter OS and DFS and low-risk patients with longer OS and DFS and showed good predictive efficiency in predicting OS and DFS. Moreover, significantly higher proportions of macrophages M0 cells, neutrophils, and Tregs were found to be enriched in HCC patients with high risk scores, while significantly higher proportions of memory CD4 T cells, gamma delta T cells, and naive B cells were found to be enriched in HCC patients with low scores. Finally, significantly lower risk scores were found at sorafenib treatment responders and anti-PD-1 immunotherapy responders compared to that in nonresponders, and anti-PD-1 immunotherapy-treated patients with lower risk scores had better OS than patients with higher risk scores. Conclusion A risk signature developed with the expression of 5 m6A-related genes could improve the prediction of prognosis of HCC and correlated with sorafenib treatment and anti-PD-1 immunotherapy response.
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724
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Fu G, Du S, Huang T, Cao M, Feng X, Wu S, Albik S, Bekker A, Tao YX. FTO (Fat-Mass and Obesity-Associated Protein) Participates in Hemorrhage-Induced Thalamic Pain by Stabilizing Toll-Like Receptor 4 Expression in Thalamic Neurons. Stroke 2021; 52:2393-2403. [PMID: 34102854 DOI: 10.1161/strokeaha.121.034173] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Ganglan Fu
- Department of Anesthesiology (G.F., S.D., T.H., M.C., X.F., S.W., S.A., A.B., Y.X.T.), New Jersey Medical School, Rutgers, The State University of New Jersey, Newark.,Now with Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China (G.F., M.C.)
| | - Shibin Du
- Department of Anesthesiology (G.F., S.D., T.H., M.C., X.F., S.W., S.A., A.B., Y.X.T.), New Jersey Medical School, Rutgers, The State University of New Jersey, Newark
| | - Tianfeng Huang
- Department of Anesthesiology (G.F., S.D., T.H., M.C., X.F., S.W., S.A., A.B., Y.X.T.), New Jersey Medical School, Rutgers, The State University of New Jersey, Newark
| | - Minghui Cao
- Department of Anesthesiology (G.F., S.D., T.H., M.C., X.F., S.W., S.A., A.B., Y.X.T.), New Jersey Medical School, Rutgers, The State University of New Jersey, Newark.,Now with Department of Anesthesiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China (G.F., M.C.)
| | - Xiaozhou Feng
- Department of Anesthesiology (G.F., S.D., T.H., M.C., X.F., S.W., S.A., A.B., Y.X.T.), New Jersey Medical School, Rutgers, The State University of New Jersey, Newark
| | - Shaogen Wu
- Department of Anesthesiology (G.F., S.D., T.H., M.C., X.F., S.W., S.A., A.B., Y.X.T.), New Jersey Medical School, Rutgers, The State University of New Jersey, Newark
| | - Sfian Albik
- Department of Anesthesiology (G.F., S.D., T.H., M.C., X.F., S.W., S.A., A.B., Y.X.T.), New Jersey Medical School, Rutgers, The State University of New Jersey, Newark
| | - Alex Bekker
- Department of Anesthesiology (G.F., S.D., T.H., M.C., X.F., S.W., S.A., A.B., Y.X.T.), New Jersey Medical School, Rutgers, The State University of New Jersey, Newark
| | - Yuan-Xiang Tao
- Department of Anesthesiology (G.F., S.D., T.H., M.C., X.F., S.W., S.A., A.B., Y.X.T.), New Jersey Medical School, Rutgers, The State University of New Jersey, Newark.,Department of Physiology, Pharmacology and Neuroscience (Y.X.T.), New Jersey Medical School, Rutgers, The State University of New Jersey, Newark.,Department of Cell Biology and Molecular Medicine (Y.X.T.), New Jersey Medical School, Rutgers, The State University of New Jersey, Newark
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725
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Kou T, Chai R, Jin L, Bai Z, Yang Y, Zhao Y, Wu D, Zhang Z, Yang Y. Systematic analysis of molecular characterization and clinical relevance of m6A regulators in digestive system pan-cancers. Exp Biol Med (Maywood) 2021; 246:2007-2018. [PMID: 34102905 DOI: 10.1177/15353702211019681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Digestive system tumors, which mainly include esophagus, stomach, colorectum, liver, pancreas, bile duct, and some other tumors, often have a poor prognosis. N6-methyladenosine (m6A) has critical functions in development and tumorigenesis and may help improve the molecular mechanisms of digestive system tumors. However, current understanding of the reconstitution of m6A in digestive system tumors is far from comprehensive. Herein, this study systematically analyzed multi-layered genomic characteristics and clinical relevance of m6A regulators in 1906 patients involving seven digestive system tumor types. We discovered that m6A regulators showed extensive genetic changes and highly consistent expression regulation. The m6A expression was closely related to the activity of cancer pathways. At the same time, we also identified m6A regulators significantly related to the common cancer pathways of digestive system tumors and specific cancer pathways of digestive tract and digestive glands. These cancer pathways may explain the prognostic differences of patients with digestive tract tumors. In addition, m6A regulators demonstrated strong potential in prognostic stratification and drug development, especially in multiple research cohorts on pancreatic cancer, pointing to a strong prognostic stratification capability of m6A regulators. Finally, a m6A scoring model significantly related to highly active ubiquitin-mediated proteolysis, mismatch repair, cell cycle, ebasal transcription factors was constructed and had a strong prognostic stratification ability in digestive gland tumors. The score showed a significant negative correlation with the tumor immune microenvironment. This study demonstrated that the similarities and difference of the action mechanism m6A regulators in the digestive tract and digestive gland tumor progression could guide potential drug development.
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Affiliation(s)
- Tiankuo Kou
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing 100032, China
| | - Ruizhi Chai
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing 100032, China
| | - Lan Jin
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing 100032, China
| | - Zhigang Bai
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing 100032, China
| | - Yun Yang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing 100032, China
| | - Yongtian Zhao
- YuceBio Technology Co., Ltd., Shenzhen, Guangdong 518000, China
| | - Dongfang Wu
- YuceBio Technology Co., Ltd., Shenzhen, Guangdong 518000, China
| | - Zhongtao Zhang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing 100032, China
| | - Yingchi Yang
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Beijing 100032, China
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726
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Kazimierczyk M, Wrzesinski J. Long Non-Coding RNA Epigenetics. Int J Mol Sci 2021; 22:6166. [PMID: 34200507 PMCID: PMC8201194 DOI: 10.3390/ijms22116166] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs exceeding a length of 200 nucleotides play an important role in ensuring cell functions and proper organism development by interacting with cellular compounds such as miRNA, mRNA, DNA and proteins. However, there is an additional level of lncRNA regulation, called lncRNA epigenetics, in gene expression control. In this review, we describe the most common modified nucleosides found in lncRNA, 6-methyladenosine, 5-methylcytidine, pseudouridine and inosine. The biosynthetic pathways of these nucleosides modified by the writer, eraser and reader enzymes are important to understanding these processes. The characteristics of the individual methylases, pseudouridine synthases and adenine-inosine editing enzymes and the methods of lncRNA epigenetics for the detection of modified nucleosides, as well as the advantages and disadvantages of these methods, are discussed in detail. The final sections are devoted to the role of modifications in the most abundant lncRNAs and their functions in pathogenic processes.
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Affiliation(s)
| | - Jan Wrzesinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland;
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727
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Zhang JX, Huang PJ, Wang DP, Yang WY, Lu J, Zhu Y, Meng XX, Wu X, Lin QH, Lv H, Xie H, Wang RL. m 6A modification regulates lung fibroblast-to-myofibroblast transition through modulating KCNH6 mRNA translation. Mol Ther 2021; 29:3436-3448. [PMID: 34111558 DOI: 10.1016/j.ymthe.2021.06.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/02/2021] [Accepted: 06/01/2021] [Indexed: 11/30/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, fatal lung disease characterized by progressive and non-reversible abnormal matrix deposition in lung parenchyma. Myofibroblasts origin mainly from resident fibroblasts via fibroblast-to-myofibroblast transition (FMT) are the dominant collagen-producing cells in pulmonary fibrosis. N6-methyladenosine (m6A) modification has been implicated in various biological process. However, the role of m6A modification in pulmonary fibrosis remains elusive. In this study, we reveal that m6A modification is up-regulated in bleomycin induced pulmonary fibrosis mice model, FMT-derived myofibroblasts and idiopathic pulmonary fibrosis patient lung samples. Lowering m6A level through silencing METTL3 inhibits FMT process in vitro and vivo. Mechanistically, KCNH6 is involved in m6A-regulated FMT process. m6A modification regulates the expression of KCNH6 by modulating its translation in a YTHDF1 dependent manner. Together, our study highlights the critical role of m6A modification in pulmonary fibrosis. Manipulation of m6A modification through targeting METTL3 may become a promising strategy for the treatment of pulmonary fibrosis.
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Affiliation(s)
- Jia-Xiang Zhang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Pei-Jie Huang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Da-Peng Wang
- Department of Intensive Medicine,Wuxi People's Hospital Affiliated to Nanjing Medical University,Wuxi,Jiangsu, 214021,China
| | - Wen-Yu Yang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Jian Lu
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Yong Zhu
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Xiao-Xiao Meng
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Xin Wu
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Qiu-Hai Lin
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Hui Lv
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China
| | - Hui Xie
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China.
| | - Rui-Lan Wang
- Department of Critical Care Medicine, Shanghai General Hospital, Shanghai Jiaotong University, School of Medicine, 650 Xinsongjiang Rd, Shanghai, 201620, China.
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728
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Qi Y, Yao R, Zhang W, Cui Q. KAT1 triggers YTHDF2-mediated ITGB1 mRNA instability to alleviate the progression of diabetic retinopathy. Pharmacol Res 2021; 170:105713. [PMID: 34098071 DOI: 10.1016/j.phrs.2021.105713] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 01/17/2023]
Abstract
Diabetic retinopathy (DR) is a major complication of diabetes and a leading cause of blindness and visual impairment. This study focuses on the function of lysine acetyltransferase 1 (KAT1) in the progression of DR and the epigenetic mechanism. A mouse model with DR was induced by streptozotocin (STZ). Abundantly expressed genes in STZ-induced mice were analyzed. KAT1 was found to be significantly downregulated in the retinal tissues of model mice. Retinal microvascular endothelial cells (RMECs) and retinal Müller cells (rMCs) were cultured in high-glucose medium for in vitro studies. Upregulation of KAT1 suppressed inflammation, neovascularization, and vascular leakage in mouse retinal tissues, and it reduced the activity and inflammatory responses in rMCs, as well as the proliferation and metastatic potential of RMECs. KAT1 activated the transcription activity of YTHDF2 through histone acetylation of the promoter, and YTHDF2 triggered the instability of ITGB1 mRNA to induce mRNA degradation in an m6A manner. The activities of rMCs and RMECs were increased by sh-YTHDF2 but suppressed by sh-ITGB1. The FAK/PI3K/AKT signaling pathway was suppressed upon ITGB1 silencing. Collectively, this study demonstrated that KAT1 triggers YTHDF2-mediated ITGB1 mRNA instability to alleviate the progression of DR.
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Affiliation(s)
- Ying Qi
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, the Laboratory for Ophthalmology and Vision Science, Henan Eye Hospital, Zhengzhou 450052, Henan, PR China.
| | - Renjie Yao
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, the Laboratory for Ophthalmology and Vision Science, Henan Eye Hospital, Zhengzhou 450052, Henan, PR China
| | - Wenjing Zhang
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, the Laboratory for Ophthalmology and Vision Science, Henan Eye Hospital, Zhengzhou 450052, Henan, PR China
| | - Qingqing Cui
- Department of Ophthalmology, the First Affiliated Hospital of Zhengzhou University, the Laboratory for Ophthalmology and Vision Science, Henan Eye Hospital, Zhengzhou 450052, Henan, PR China
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729
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Zhong S, Lin Z, Chen H, Mao L, Feng J, Zhou S. The m 6A-related gene signature for predicting the prognosis of breast cancer. PeerJ 2021; 9:e11561. [PMID: 34141492 PMCID: PMC8183431 DOI: 10.7717/peerj.11561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/13/2021] [Indexed: 11/20/2022] Open
Abstract
N6-methyladenosine (m6A) modification has been shown to participate in tumorigenesis and metastasis of human cancers. The present study aimed to investigate the roles of m6A RNA methylation regulators in breast cancer. We used LASSO regression to identify m6A-related gene signature predicting breast cancer survival with the datasets downloaded from Gene Expression Omnibus and The Cancer Genome Atlas (TCGA). RNA-Seq data of 3409 breast cancer patients from GSE96058 and 1097 from TCGA were used in present study. A 10 m6A-related gene signature associated with prognosis was identified from 22 m6A RNA methylation regulators. The signature divided patients into low- and high-risk group. High-risk patients had a worse prognosis than the low-risk group. Further analyses indicated that IGF2BP1 may be a key m6A RNA methylation regulator in breast cancer. Survival analysis showed that IGF2BP1 is an independent prognostic factor of breast cancer, and higher expression level of IGF2BP1 is associated with shorter overall survival of breast cancer patients. In conclusion, we identified a 10 m6A-related gene signature associated with overall survival of breast cancer. IGF2BP1 may be a key m6A RNA methylation regulator in breast cancer.
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Affiliation(s)
- Shanliang Zhong
- Center of Clinical Laboratory Science, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Zhenzhong Lin
- Department of Pathology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Huanwen Chen
- Xinglin laboratory, The First Affiliated Hospital of Xiamen University, Nanjing, China
| | - Ling Mao
- Department of Thyroid Breast Surgery, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Jifeng Feng
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing, China
| | - Siying Zhou
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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730
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Li R, Yin YH, Ji XL, Liu X, Li JP, Qu YQ. Pan-Cancer Prognostic, Immunity, Stemness, and Anticancer Drug Sensitivity Characterization of N6-Methyladenosine RNA Modification Regulators in Human Cancers. Front Mol Biosci 2021; 8:644620. [PMID: 34150845 PMCID: PMC8211991 DOI: 10.3389/fmolb.2021.644620] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine RNA modification plays a significant role in the progression of multiple tumorigenesis. Our study identified the imperative role of m6A regulators in the tumor immune microenvironment, survival, stemness score, and anticancer drug sensitivity of pan-cancer. The Wilcox test was to identify the differential expression between 17 m6A regulators across 33 TCGA cancer types and their normal tissues from UCSC Xena GDC pan-cancer. Survival analysis of m6A-related regulators in 33 TCGA cancer types was identified using the "survival" and "survminer" package. The Spearman correlation test and Pearson correlation test were used to identify the correlation relationship between m6A regulators expression and tumor microenvironment, tumor stem cell score, and drug sensitivity of anticancer drugs. ConsensusPathDB was used for exploring m6A regulators functional enrichment. The 17 (METTL3, WTAP, METTL14, RBM15, RBM15B, VIRMA, HNRNPC, HNRNPA2B1, YTHDC1, ZC3H13, YTHDF1, YTHDC2, YTHDF2, IGF2BP3, IGF2BP1, FTO, and ALKBH5) m6A regulators were differentially expressed in 18 TCGA cancer types and adjacent normal tissues. Correlation analysis indicated that the relationship between the expression of 17 m6A regulators and tumor microenvironment indicated that the higher expression of m6A regulators, the higher the degree of tumor stem cells. The anticancer drug sensitivity analysis indicated that ZC3H13 expression had a positive relationship with anticancer drugs such as selumetinib, dabrafenib, cobimetinib, trametinib, and hypothemycin (p < 0.001). YTHDF2 expression was significantly negatively correlated with the anticancer drug dasatinib (p < 0.001). The pan-cancer immune subtype analysis showed that the 17 m6A regulators were significantly different in immune subtype C1 (wound healing), C3 (inflammatory), C2 (IFN-gamma dominant), C5 (immunological quiet), C4 (lymphocyte depleted), and C6 (TGF-beta dominant) (p < 0.001). Our study provides a comprehensive insight for revealing the significant role of m6A regulators in the tumor immune microenvironment, stemness score, and anticancer drug sensitivity of human cancers.
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Affiliation(s)
- Rui Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yun-Hong Yin
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Xiu-Li Ji
- Department of Pulmonary Disease, Traditional Chinese Medicine Hospital of Jinan, Jinan, China
| | - Xiao Liu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jian-Ping Li
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yi-Qing Qu
- Department of Pulmonary and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
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731
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YTHDF2 mediates LPS-induced osteoclastogenesis and inflammatory response via the NF-κB and MAPK signaling pathways. Cell Signal 2021; 85:110060. [PMID: 34089814 DOI: 10.1016/j.cellsig.2021.110060] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 05/14/2021] [Accepted: 05/30/2021] [Indexed: 12/26/2022]
Abstract
Aberrant elevation of osteoclast differentiation and function is responsible for disrupting bone homeostasis in various inflammatory bone diseases. YTH domain family 2 (YTHDF2) is a well-known m6A-binding protein that plays an essential role in regulating cell differentiation and inflammatory processes by mediating mRNA degradation. However, the regulatory role of YTHDF2 in inflammatory osteoclast differentiation remains unelucidated. Here, we detected the expression of m6A-related genes and found that YTHDF2 was upregulated in RANKL-primed osteoclast precursors stimulated with lipopolysaccharide (LPS). Ythdf2 knockdown in RAW264.7 cells and primary bone marrow-derived macrophages (BMMs) enhanced osteoclast formation and bone resorption, which was assessed by TRAP staining assay and pit formation assay. Ythdf2 depletion upregulated osteoclast-related gene expression and proinflammatory cytokine secretion. In contrast, overexpression of Ythdf2 produced the reverse effect. Furthermore, Ythdf2 knockdown enhanced the phosphorylation of IKKα/β, IκBα, ERK, P38 and JNK. NF-κB and MAPK signaling pathway inhibitors effectively abrogated the enhanced expression of Nfact1, c-Fos, IL-1β and TNF-α caused by Ythdf2 knockdown. Mechanistically, the mRNA stability assay revealed that Ythdf2 depletion led to stabilization of Tnfrsf11a, Traf6, Map4k4, Map2k3, Map2k4 and Nfatc1 mRNA. In summary, our findings demonstrated that YTHDF2 has a negative regulatory role in LPS-induced osteoclast differentiation and the inflammatory response via the NF-κB and MAPK signaling pathways.
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732
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Lang C, Yin C, Lin K, Li Y, Yang Q, Wu Z, Du H, Ren D, Dai Y, Peng X. m 6 A modification of lncRNA PCAT6 promotes bone metastasis in prostate cancer through IGF2BP2-mediated IGF1R mRNA stabilization. Clin Transl Med 2021; 11:e426. [PMID: 34185427 PMCID: PMC8181202 DOI: 10.1002/ctm2.426] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Bone metastasis is the leading cause of tumor-related death in prostate cancer (PCa) patients. Long noncoding RNAs (lncRNAs) have been well documented to be involved in the progression of multiple cancers. Nevertheless, the role of lncRNAs in PCa bone metastasis remains largely unclear. METHODS The expression of prostate cancer-associated transcripts was analyzed in published datasets and further verified in clinical samples and cell lines by RT-qPCR and in situ hybridization assays. Colony formation assay, MTT assay, cell cycle analysis, EdU assay, Transwell migration and invasion assays, wound healing assay, and in vivo experiments were carried out to investigate the function of prostate cancer-associated transcript 6 (PCAT6) in bone metastasis and tumor growth of PCa. Bioinformatic analysis, RNA pull-down, and RIP assays were conducted to identify the proteins binding to PCAT6 and the potential targets of PCAT6. The therapeutic potential of targeting PCAT6 by antisense oligonucleotides (ASO) was further explored in vivo. RESULTS PCAT6 was upregulated in PCa tissues with bone metastasis and increased PCAT6 expression predicted poor prognosis in PCa patients. Functional experiments found that PCAT6 knockdown significantly inhibited PCa cell invasion, migration, and proliferation in vitro, as well as bone metastasis and tumor growth in vivo. Mechanistically, METTL3-mediated m6 A modification contributed to PCAT6 upregulation in an IGF2BP2-dependent manner. Furthermore, PCAT6 upregulated IGF1R expression by enhancing IGF1R mRNA stability through the PCAT6/IGF2BP2/IGF1R RNA-protein three-dimensional complex. Importantly, PCAT6 inhibition by ASO in vivo showed therapeutic potential against bone metastasis in PCa. Finally, the clinical correlation of METTL3, IGF2BP2, IGF1R, and PCAT6 was further demonstrated in PCa tissues and cells. CONCLUSIONS Our study uncovers a novel molecular mechanism by which the m6 A-induced PCAT6/IGF2BP2/IGF1R axis promotes PCa bone metastasis and tumor growth, suggesting that PCAT6 may serve as a promising prognostic marker and therapeutic target against bone-metastatic PCa.
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MESH Headings
- Adenosine/analogs & derivatives
- Adenosine/chemistry
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Bone Neoplasms/genetics
- Bone Neoplasms/metabolism
- Bone Neoplasms/secondary
- Cell Cycle
- Cell Movement
- Cell Proliferation
- Gene Expression Regulation, Neoplastic
- Humans
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Prognosis
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- RNA Stability
- RNA, Long Noncoding/chemistry
- RNA, Long Noncoding/genetics
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptor, IGF Type 1/genetics
- Receptor, IGF Type 1/metabolism
- Survival Rate
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Chuandong Lang
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Chi Yin
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Kaiyuan Lin
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Yue Li
- Department of Experimental ResearchState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Qing Yang
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Zhengquan Wu
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Hong Du
- Department of Pathologythe First People's Hospital of Guangzhou CityGuangzhouChina
| | - Dong Ren
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Yuhu Dai
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Xinsheng Peng
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
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733
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Wang Y, Su X, Zhao M, Xu M, Chen Y, Li Z, Zhuang W. Importance of N 6-methyladenosine RNA modification in lung cancer (Review). Mol Clin Oncol 2021; 14:128. [PMID: 33981432 PMCID: PMC8108057 DOI: 10.3892/mco.2021.2290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
The N6-methyladenosine (m6A) modification is the most common mRNA modification in eukaryotes and exerts biological functions by affecting RNA metabolism. The m6A modification is installed by m6A methyltransferases, removed by demethylases and recognized by m6A-binding proteins. The interaction between these three elements maintains the dynamic equilibrium of m6A in cells. Accumulating evidence indicates that m6A RNA methylation has a significant impact on RNA metabolism and is involved in the pathogenesis of cancer. Lung cancer is the leading cause of cancer-related deaths worldwide. The treatment options for lung cancer have developed considerably over the past few years; however, the survival rate of patients with lung cancer still remains very low. Although diagnostic methods and targeted therapies have been rapidly developed in recent years, the underlying mechanism and importance of m6A RNA methylation in the pathogenesis of lung cancer remains ambiguous. The current review summarized the biological functions of m6A modification and considers the potential roles of m6A regulators in the occurrence and development of lung cancer.
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Affiliation(s)
- Yueyang Wang
- Department of Molecular Biology Test Technique, College of Medical Technology, Beihua University, Jilin 132000, P.R. China
| | - Xiaoming Su
- Department of Molecular Biology Test Technique, College of Medical Technology, Beihua University, Jilin 132000, P.R. China
| | - Mingyao Zhao
- Department of Molecular Biology Test Technique, College of Medical Technology, Beihua University, Jilin 132000, P.R. China
| | - Mingchen Xu
- Department of Molecular Biology Test Technique, College of Medical Technology, Beihua University, Jilin 132000, P.R. China
| | - Yueqi Chen
- Department of Molecular Biology Test Technique, College of Medical Technology, Beihua University, Jilin 132000, P.R. China
| | - Zhengyi Li
- Department of Clinical Examination Basis, Laboratory Academy, Jilin Medical University, Jilin 132000, P.R. China
| | - Wenyue Zhuang
- Department of Molecular Biology Test Technique, College of Medical Technology, Beihua University, Jilin 132000, P.R. China
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734
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Tang M, Lv Y. The Role of N6 -Methyladenosine Modified Circular RNA in Pathophysiological Processes. Int J Biol Sci 2021; 17:2262-2277. [PMID: 34239354 PMCID: PMC8241720 DOI: 10.7150/ijbs.60131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/21/2021] [Indexed: 12/14/2022] Open
Abstract
Circular RNA (circRNA) is a type of covalently closed and endogenous non-coding RNA (ncRNA) with tissue- and cell-specific expression patterns generated by a non-canonical splicing event. Previous reports have indicated that circRNAs exert their functions in different ways, thereby participating in various pathophysiological processes. N6 -methyladenosine (m6A) methylation occurs in the N6-position, which is the most abundant and conserved internal transcriptional modification in eukaryotes, including mRNA and ncRNAs. Accumulating evidences confirm that m6A modification also exists in the circRNA and greatly affects the biological functions of circRNA. Their dysregulated expression can be a cause of various pathophysiological processes, such as spermatogenesis, myoblast differentiation, cancer, cardiovascular disease, mental illness and so on. Understanding the role of m6A-modified circRNAs in pathophysiological processes may contribute to better understanding the physiological mechanisms and develop new biomarkers. This review summarizes the regulatory mechanism of m6A modification on circRNA metabolism and the role of m6A-modified circRNAs in pathophysiological processes. This article may pave the way for a better understanding of the role of epigenetically modified circRNAs in pathophysiological process.
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Affiliation(s)
| | - Yonggang Lv
- Mechanobiology and Regenerative Medicine Laboratory, Bioengineering College, Chongqing University, Chongqing, 400044, China
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735
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Li C, Tian C, Liu Y, Liang J, Zeng Y, Yang Q, Liu Y, Wu D, Wu J, Wang J, Zhang K, Gu F, Hu Y, Liu L. Comprehensive Profiling Reveals Distinct Microenvironment and Metabolism Characterization of Lung Adenocarcinoma. Front Genet 2021; 12:619821. [PMID: 34122500 PMCID: PMC8193848 DOI: 10.3389/fgene.2021.619821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 04/15/2021] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma has entered into an era of immunotherapy with the development of immune checkpoint inhibitors (ICIs). The identification of immune subtype is crucial to prolonging survival in patients. The tumor microenvironment (TME) and metabolism have a profound impact on prognosis and therapy. The majority of previous studies focused on only one aspect, while both of them are essential to the understanding of tumorigenesis and development. We hypothesized that lung adenocarcinoma can be stratified into immune subgroups with alterations in the TME infiltration. We aimed to explore the "TME-Metabolism-Risk" patterns in each subtypes and the mechanism behind. Glycolysis and cholesterol were selected for the analysis of metabolic states based on the first half of the study. Bioinformatic analysis was performed to investigate the transcriptomic and clinical data integrated by three lung adenocarcinoma cohorts (GSE30219, GSE31210, GSE37745, N = 415). The results were validated in an independent cohort (GSE50081, N = 127). In total, 415 lung adenocarcinoma samples were integrated and analyzed. Four major immune subtypes were indentified using bioinformatic analysis. Subtype NC1, characterized by a high level of glycolysis, with extremely low microenvironment cell infiltration. Subtype NC2, characterized by the "Silence" and "Cholesterol biosynthesis Predominant" metabolic states, with a middle degree infiltration of microenvironment cell. Subtype NC3, characterized by the lack of "Cholesterol biosynthesis Predominant" metabolic state, with abundant microenvironment cell infiltration. Subtype NC4, characterized by "Mixed" metabolic state, with a relatively low microenvironment cell infiltration. Least absolute shrinkage and selection operator (LASSO) regression and multivariate analyses were performed to calculate the risk of each sample, and we attempted to find out the potential immune escape mechanism in different subtypes. The result revealed that the lack of immune cells infiltration might contribute to the immune escape in subtypes NC1 and NC4. NC3 was characterized by the high expression of immune checkpoint molecules and fibroblasts. NC2 had defects in activation of innate immune cells. There existed an obviously survival advantage in subtype NC2. Gene set enrichment analysis (GSEA) and Gene Ontology analysis indicated that the PI3K-AKT-mTOR, TGF-β, MYC-related pathways might be correlated with this phenomenon. In addition, some differentially expressed genes (DEGs) were indentified in subtype NC3, which might be potential targets for survival phenotype transformation.
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Affiliation(s)
- Chang Li
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chen Tian
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yangyang Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinyan Liang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yulan Zeng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qifan Yang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuting Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Di Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jingjing Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Juanjuan Wang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feifei Gu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yue Hu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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736
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Selberg S, Seli N, Kankuri E, Karelson M. Rational Design of Novel Anticancer Small-Molecule RNA m6A Demethylase ALKBH5 Inhibitors. ACS OMEGA 2021; 6:13310-13320. [PMID: 34056479 PMCID: PMC8158789 DOI: 10.1021/acsomega.1c01289] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/05/2021] [Indexed: 05/05/2023]
Abstract
The RNA 6-N-methyladenosine (m6A) demethylase ALKBH5 has been shown to be oncogenic in several cancer types, including leukemia and glioblastoma. We present here the target-tailored development and first evaluation of the antiproliferative effects of new ALKBH5 inhibitors. Two compounds, 2-[(1-hydroxy-2-oxo-2-phenylethyl)sulfanyl]acetic acid (3) and 4-{[(furan-2-yl)methyl]amino}-1,2-diazinane-3,6-dione (6), with IC50 values of 0.84 μM and 1.79 μM, respectively, were identified in high-throughput virtual screening of the library of 144 000 preselected compounds and subsequent verification of hits in an m6A antibody-based enzyme-linked immunosorbent assay (ELISA) enzyme inhibition assay. The effect of these compounds on the proliferation of selected target cancer cell lines was then measured. In the case of three leukemia cell lines (HL-60, CCRF-CEM, and K562) the cell proliferation was suppressed at low micromolar concentrations of inhibitors, with IC50 ranging from 1.38 to 16.5 μM. However, the effect was low or negligible in the case of another leukemia cell line, Jurkat, and the glioblastoma cell line A-172. These results demonstrate the potential of ALKBH5 inhibition as a cancer-cell-type-selective antiproliferative strategy.
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Affiliation(s)
- Simona Selberg
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
| | - Neinar Seli
- Chemestmed, Ltd., Riia tn 130b/2, Tartu 50411, Estonia
| | - Esko Kankuri
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Helsinki 00014, Finland
| | - Mati Karelson
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
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737
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Identification of m6A methyltransferase-related lncRNA signature for predicting immunotherapy and prognosis in patients with hepatocellular carcinoma. Biosci Rep 2021; 41:228714. [PMID: 34027555 PMCID: PMC8188173 DOI: 10.1042/bsr20210760] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 12/16/2022] Open
Abstract
N6-methyladenosine (m6A) methyltransferase has been shown to be an oncogene in a variety of cancers. Nevertheless, the relationship between the long non-coding RNAs (lncRNAs) and hepatocellular carcinoma (HCC) remains elusive. We integrated the gene expression data of 371 HCC and 50 normal tissues from The Cancer Genome Atlas (TCGA) database. Differentially expressed protein-coding genes (DE-PCGs)/lncRNAs (DE-lncRs) analysis and univariate regression and Kaplan–Meier (K–M) analysis were performed to identify m6A methyltransferase-related lncRNAs. Three prognostic lncRNAs were selected by univariate and LASSO Cox regression analyses to construct the m6A methyltransferase-related lncRNA signature. Multivariate Cox regression analyses illustrated that this signature was an independent prognostic factor for overall survival (OS) prediction. The Gene Set Enrichment Analysis (GSEA) suggested that the m6A methyltransferase-related lncRNAs were involved in the immune-related biological processes (BPs) and pathways. Besides, we discovered that the lncRNAs signature was correlated with the tumor microenvironment (TME) and the expression of critical immune checkpoints. Tumor Immune Dysfunction and Exclusion (TIDE) analysis revealed that the lncRNAs could predict the clinical response to immunotherapy. Our study had originated a prognostic signature for HCC based on the potential prognostic m6A methyltransferase-related lncRNAs. The present study had deepened the understanding of the TME status of HCC patients and laid a theoretical foundation for the choice of immunotherapy.
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738
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Pan ZP, Wang B, Hou DY, You RL, Wang XT, Xie WH, Huang HF. METTL3 mediates bone marrow mesenchymal stem cell adipogenesis to promote chemoresistance in acute myeloid leukaemia. FEBS Open Bio 2021; 11:1659-1672. [PMID: 33932138 PMCID: PMC8167861 DOI: 10.1002/2211-5463.13165] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 03/13/2021] [Accepted: 04/12/2021] [Indexed: 02/02/2023] Open
Abstract
Adipogenesis of bone marrow mesenchymal stem cells (MSCs) promotes chemoresistance of acute myeloid leukaemia (AML) cells. MSCs from AML patients (AML‐MSCs) display enhanced adipogenesis compared with bone marrow MSCs from healthy donors. However, the precise molecular mechanism by which adipogenesis of MSCs from AML marrow differs from normal counterparts remains obscure. We found that METTL3 significantly inhibits MSC adipogenesis. Here, we aimed to identify the molecular mechanism linking METTL3 and MSC adipogenesis. Analysis of m6A epigenetic changes in MSCs determined via RIP‐qPCR and MeRIP‐qPCR indicated that METTL3 affects AKT protein expression in MSCs by mediating m6A modification of AKT1‐mRNA. Downregulated METTL3 expression in AML‐MSCs induced an increase in AKT protein, resulting in enhanced MSC adipogenesis, thereby contributing to chemoresistance in AML cells. Therefore, targeting AKT regulation by mRNA modification in MSC adipogenesis might provide a novel therapeutic strategy to overcome AML chemoresistance.
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Affiliation(s)
- Zhi-Peng Pan
- Central Laboratory, Fujian Medical University Union Hospital, China
| | - Bin Wang
- Central Laboratory, Fujian Medical University Union Hospital, China.,Clinical Laboratory, Fujian Maternal and Child Health Hospital, Fujian Children's Hospital, China
| | - Di-Yu Hou
- Central Laboratory, Fujian Medical University Union Hospital, China
| | - Ruo-Lan You
- Central Laboratory, Fujian Medical University Union Hospital, China
| | - Xiao-Ting Wang
- Central Laboratory, Fujian Medical University Union Hospital, China
| | - Wen-Hui Xie
- Graduate School, Fujian Medical University, Fujian Medical University Union Hospital, China
| | - Hui-Fang Huang
- Central Laboratory, Fujian Medical University Union Hospital, China
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739
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Villa E, Sahu U, O'Hara BP, Ali ES, Helmin KA, Asara JM, Gao P, Singer BD, Ben-Sahra I. mTORC1 stimulates cell growth through SAM synthesis and m 6A mRNA-dependent control of protein synthesis. Mol Cell 2021; 81:2076-2093.e9. [PMID: 33756106 PMCID: PMC8141029 DOI: 10.1016/j.molcel.2021.03.009] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 01/21/2021] [Accepted: 03/08/2021] [Indexed: 12/13/2022]
Abstract
The mechanistic target of rapamycin complex 1 (mTORC1) regulates metabolism and cell growth in response to nutrient, growth, and oncogenic signals. We found that mTORC1 stimulates the synthesis of the major methyl donor, S-adenosylmethionine (SAM), through the control of methionine adenosyltransferase 2 alpha (MAT2A) expression. The transcription factor c-MYC, downstream of mTORC1, directly binds to intron 1 of MAT2A and promotes its expression. Furthermore, mTORC1 increases the protein abundance of Wilms' tumor 1-associating protein (WTAP), the positive regulatory subunit of the human N6-methyladenosine (m6A) RNA methyltransferase complex. Through the control of MAT2A and WTAP levels, mTORC1 signaling stimulates m6A RNA modification to promote protein synthesis and cell growth. A decline in intracellular SAM levels upon MAT2A inhibition decreases m6A RNA modification, protein synthesis rate, and tumor growth. Thus, mTORC1 adjusts m6A RNA modification through the control of SAM and WTAP levels to prime the translation machinery for anabolic cell growth.
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Affiliation(s)
- Elodie Villa
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Umakant Sahu
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Brendan P O'Hara
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Eunus S Ali
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Kathryn A Helmin
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - John M Asara
- Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Gao
- Metabolomics Core Facility, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA
| | - Benjamin D Singer
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Issam Ben-Sahra
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA.
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740
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Zhang Y, Wang Y, Ying L, Tao S, Shi M, Lin P, Wang Y, Han B. Regulatory Role of N6-methyladenosine (m 6A) Modification in Osteosarcoma. Front Oncol 2021; 11:683768. [PMID: 34094986 PMCID: PMC8170137 DOI: 10.3389/fonc.2021.683768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/30/2021] [Indexed: 12/30/2022] Open
Abstract
Osteosarcoma is the most common primary bone malignancy, typically occurring in childhood or adolescence. Unfortunately, the clinical outcomes of patients with osteosarcoma are usually poor because of the aggressive nature of this disease and few treatment advances in the past four decades. N6-methyladenosine (m6A) is one of the most extensive forms of RNA modification in eukaryotes found both in coding and non-coding RNAs. Accumulating evidence suggests that m6A-related factors are dysregulated in multiple osteosarcoma processes. In this review, we highlight m6A modification implicated in osteosarcoma, describing its pathophysiological role and molecular mechanism, as well as future research trends and potential clinical application in osteosarcoma.
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Affiliation(s)
- Yujie Zhang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yanyan Wang
- Department of Oncology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liwei Ying
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Sifeng Tao
- Department of Oncology Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mingmin Shi
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Peng Lin
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yangxin Wang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bin Han
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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741
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Mo P, Xie S, Cai W, Ruan J, Du Q, Ye J, Mao J. N6-methyladenosine (m 6A) RNA methylation signature as a predictor of stomach adenocarcinoma outcomes and its association with immune checkpoint molecules. J Int Med Res 2021; 48:300060520951405. [PMID: 32972288 PMCID: PMC7522833 DOI: 10.1177/0300060520951405] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE Although N6-methyladenosine (m6A) RNA methylation is the most common mRNA modification process, few studies have examined the role of m6A in stomach adenocarcinomas (STADs). METHODS In this retrospective study, we analyzed 293 STAD samples from The Cancer Genome Atlas with complete clinicopathological feature profiles. The m6A methylation risk signature was derived from LASSO-Cox regression analyses with 15 m6A regulators. Statistical analysis was performed and figures were prepared using R software (https://www.R-project.org/). RESULTS The m6A signature was established as follows: risk score = FTO × 0.127 + YTHDF1 × 0.004 + KIAA1429 × 0.044 + YTHDC2 × 0.112 - RBM15 × 0.135 - ALKBH5 × 0.019 - YTHDF2 × 0.028, which was confirmed as an independent prognostic indicator to predict overall survival of patients with STAD. Risk scores and tumor grades were closely associated. Cell cycle, p53 signaling pathways, DNA mismatch repair, and RNA degradation were enriched in the low-risk subgroup. This subgroup showed significantly higher expression of immune checkpoint molecules including PD-1 (programmed death 1), PD-L1 (programmed death-ligand 1), and CTLA-4 (cytotoxic T-lymphocyte-associated antigen 4), suggesting that the signature may be a useful immunotherapy predictor. CONCLUSIONS We established an m6A methylation signature as an independent prognostic tool to predict overall survival, which may also be useful as an immunotherapy predictor.
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Affiliation(s)
- Pingfan Mo
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Siyuan Xie
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Wen Cai
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jingjing Ruan
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Qin Du
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jun Ye
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
| | - Jianshan Mao
- Department of Gastroenterology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province, China
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742
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Yang X, Shao F, Guo D, Wang W, Wang J, Zhu R, Gao Y, He J, Lu Z. WNT/β-catenin-suppressed FTO expression increases m 6A of c-Myc mRNA to promote tumor cell glycolysis and tumorigenesis. Cell Death Dis 2021; 12:462. [PMID: 33966037 PMCID: PMC8106678 DOI: 10.1038/s41419-021-03739-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 02/03/2023]
Abstract
FTO removes the N6-methyladenosine (m6A) modification from genes and plays a critical role in cancer development. However, the mechanisms underlying the regulation of FTO and its subsequent impact on the regulation of the epitranscriptome remain to be further elucidated. Here, we demonstrate that FTO expression is downregulated and inversely correlated with poor survival of lung adenocarcinoma patients. Mechanistically, Wnt signaling induces the binding of EZH2 to β-catenin. This protein complex binds to the LEF/TCF-binding elements at the promoter region of FTO, where EZH2 enhances H3K27me3 and inhibits FTO expression. Downregulated FTO expression substantially enhances the m6A levels in the mRNAs of a large number of genes in critical pathways, particularly metabolic pathway genes, such as MYC. Enhanced m6A levels on MYC mRNA recruit YTHDF1 binding, which promotes MYC mRNA translation and a subsequent increase in glycolysis and proliferation of tumor cells and tumorigenesis. Our findings uncovered a critical mechanism of epitranscriptome regulation by Wnt/β-catenin-mediated FTO downregulation and underscored the role of m6A modifications of MYC mRNA in regulating tumor cell glycolysis and growth.
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Affiliation(s)
- Xueying Yang
- grid.506261.60000 0001 0706 7839Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021 Beijing, China
| | - Fei Shao
- grid.412521.1The Affiliated Hospital of Qingdao University and Qingdao Cancer Institute, 266071 Qingdao, Shandong China
| | - Dong Guo
- grid.13402.340000 0004 1759 700XZhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, 310029 Hangzhou, China
| | - Wei Wang
- grid.506261.60000 0001 0706 7839Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021 Beijing, China
| | - Juhong Wang
- grid.506261.60000 0001 0706 7839Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021 Beijing, China
| | - Rongxuan Zhu
- grid.506261.60000 0001 0706 7839Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021 Beijing, China
| | - Yibo Gao
- grid.506261.60000 0001 0706 7839Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021 Beijing, China ,grid.506261.60000 0001 0706 7839State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021 Beijing, China
| | - Jie He
- grid.506261.60000 0001 0706 7839Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021 Beijing, China ,grid.506261.60000 0001 0706 7839State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021 Beijing, China
| | - Zhimin Lu
- grid.13402.340000 0004 1759 700XZhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, 310029 Hangzhou, China ,grid.13402.340000 0004 1759 700XZhejiang University Cancer Center, 310029 Hangzhou, China
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743
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Diao LT, Xie SJ, Lei H, Qiu XS, Huang MC, Tao S, Hou YR, Hu YX, Sun YJ, Zhang Q, Xiao ZD. METTL3 regulates skeletal muscle specific miRNAs at both transcriptional and post-transcriptional levels. Biochem Biophys Res Commun 2021; 552:52-58. [PMID: 33740664 DOI: 10.1016/j.bbrc.2021.03.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/07/2021] [Indexed: 12/31/2022]
Abstract
METTL3 increasing the mature miRNA levels via N6-Methyladenosine (m6A) modification of primary miRNA (pri-miRNA) transcripts has emerged as an important post-transcriptional regulation of miRNA biogenesis. Our previous studies and others have showed that muscle specific miRNAs are essential for skeletal muscle differentiation. Whether these miRNAs are also regulated by METTL3 is still unclear. Here, we found that m6A motifs were present around most of these miRNAs, which were indeed m6A modified as confirmed by m6A-modified RNA immunoprecipitation (m6A RIP). However, we surprisingly found that these muscle specific miRNAs were repressed instead of increased by METTL3 in C2C12 in vitro differentiation and mouse skeletal muscle regeneration after injury in vivo model. To elucidate the underlined mechanism, we performed reporter assays in 293T cells and validated METTL3 increasing these miRNAs at post-transcriptional level as expected. Furthermore, in myogenic C2C12 cells, we found that METTL3 not only repressed the expression of myogenic transcription factors (TFs) which can enhance the muscle specific miRNAs, but also increased the expression of epigenetic regulators which can repress these miRNAs. Thus, METTL3 could repress the muscle specific miRNAs at transcriptional level indirectly. Taken together, our results demonstrated that skeletal muscle specific miRNAs were repressed by METTL3 and such repression is likely synthesized transcriptional and post-transcriptional regulations.
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Affiliation(s)
- Li-Ting Diao
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Shu-Juan Xie
- Vaccine Research Institute of Sun Yat-sen University, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Hang Lei
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Xiu-Sheng Qiu
- Vaccine Research Institute of Sun Yat-sen University, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Meng-Chun Huang
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Shuang Tao
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Ya-Rui Hou
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Yan-Xia Hu
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Yu-Jia Sun
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China
| | - Qi Zhang
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China; Vaccine Research Institute of Sun Yat-sen University, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
| | - Zhen-Dong Xiao
- Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
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744
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Dong S, Wu Y, Liu Y, Weng H, Huang H. N 6 -methyladenosine Steers RNA Metabolism and Regulation in Cancer. Cancer Commun (Lond) 2021; 41:538-559. [PMID: 33955720 PMCID: PMC8286143 DOI: 10.1002/cac2.12161] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 12/24/2022] Open
Abstract
As one of the most studied ribonucleic acid (RNA) modifications in eukaryotes, N6 -methyladenosine (m6 A) has been shown to play a predominant role in controlling gene expression and influence physiological and pathological processes such as oncogenesis and tumor progression. Writer and eraser proteins, acting opposite to deposit and remove m6 A epigenetic marks, respectively, shape the cellular m6 A landscape, while reader proteins preferentially recognize m6 A modifications and mediate fate decision of the methylated RNAs, including RNA synthesis, splicing, exportation, translation, and stability. Therefore, RNA metabolism in cells is greatly influenced by these three classes of m6 A regulators. Aberrant expression of m6 A regulators has been widely reported in various types of cancer, leading to cancer initiation, progression, and drug resistance. The close links between m6 A and cancer shed light on the potential use of m6 A methylation and its regulators as prognostic biomarkers and drug targets for cancer therapy. Given the notable effects of m6 A in reversing chemoresistance and enhancing immune therapy, it is a promising target for combined therapy. Herein, we summarize the recent discoveries on m6 A and its regulators, emphasizing their influences on RNA metabolism, their dysregulation and impacts in diverse malignancies, and discuss the clinical implications of m6 A modification in cancer.
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Affiliation(s)
- Shenghua Dong
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Yutong Wu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Yadi Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
| | - Hengyou Weng
- Bioland Laboratory, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, P. R. China
| | - Huilin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, 510060, P. R. China
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745
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Wu Y, Zhan S, Xu Y, Gao X. RNA modifications in cardiovascular diseases, the potential therapeutic targets. Life Sci 2021; 278:119565. [PMID: 33965380 DOI: 10.1016/j.lfs.2021.119565] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/10/2021] [Accepted: 04/18/2021] [Indexed: 02/08/2023]
Abstract
More than one hundred RNA modifications decorate the chemical and topological properties of these ribose nucleotides, thereby executing their biological functions through post-transcriptional regulation. In cardiovascular diseases, a wide range of RNA modifications including m6A (N6-adenosine methylation), m5C (5-methylcytidin), Nm (2'-O-ribose-methylation), Ψ (pseudouridine), m7G (N7-methylguanosine), and m1A (N1-adenosine methylation) have been found in tRNA, rRNA, mRNA and other noncoding RNA, which can function as a novel mechanism in metabolic syndrome, heart failure, coronary heart disease, and hypertension. In this review, we will summarize the current understanding of the regulatory roles and significance of several types of RNA modifications in CVDs (cardiovascular diseases) and the interplay between RNA modifications and noncoding RNA, epigenetics. Finally, we will focus on the potential therapeutic strategies by using RNA modifications.
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Affiliation(s)
- Yirong Wu
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 310006 Zhejiang, China
| | - Siyao Zhan
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 310006 Zhejiang, China
| | - Yizhou Xu
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 310006 Zhejiang, China.
| | - Xiangwei Gao
- Institute of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, China
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746
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Gundert L, Strick A, Hagen F, Schmidt D, Klümper N, Tolkach Y, Toma M, Kristiansen G, Ritter M, Ellinger J. Systematic expression analysis of m
6
A RNA methyltransferases in clear cell renal cell carcinoma. BJUI COMPASS 2021; 2:402-411. [PMID: 35474700 PMCID: PMC8988738 DOI: 10.1002/bco2.89] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/12/2021] [Accepted: 04/12/2021] [Indexed: 01/17/2023] Open
Abstract
Objectives To investigate the regulation of the N‐6‐methyladenosine (m6A) methyltransferases METTL3, METTL14, WTAP, KIAA1429, and METTL4, referred to as “m6A writers,” in clear cell renal cell carcinoma (ccRCC), and other RCC subtypes in respect of the potential prognostic value. Patients and methods Tissue samples were collected within the framework of the Biobank at the Center for Integrated Oncology Bonn. The expression of the methyltransferases was systematically determined in clear cell renal carcinoma (ccRCC) on the RNA (real‐time PCR) and protein level (immunohistochemistry). Additionally, protein expression of the m6A writers was further investigated in papillary RCC, chromophobe RCC, sarcomatoid RCC, oncocytoma, and normal renal tissue (immunohistochemistry). Results The expression of all m6A‐methyltransferases was significantly downregulated in ccRCC compared to benign renal tissue. Low m6A‐methyltransferase levels were correlated with higher histological grade, advanced pT‐stage, pN‐stage, and metastatic disease. Reduced m6A‐methyltransferase expression was associated with shorter overall survival. Conclusion In conclusion, m6A‐methyltransferases are dysregulated in ccRCC and might act as tumor suppressor genes, which could be of particular importance for future diagnostic and therapeutic options.
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Affiliation(s)
| | | | - Felix Hagen
- Department of Urology University Hospital Bonn Bonn Germany
| | - Doris Schmidt
- Department of Urology University Hospital Bonn Bonn Germany
| | - Niklas Klümper
- Department of Urology University Hospital Bonn Bonn Germany
| | - Yuri Tolkach
- Department of Pathology University Hospital Bonn Bonn Germany
- Department of Pathology University Hospital Cologne Cologne Germany
| | - Marieta Toma
- Department of Pathology University Hospital Bonn Bonn Germany
| | | | - Manuel Ritter
- Department of Urology University Hospital Bonn Bonn Germany
| | - Jörg Ellinger
- Department of Urology University Hospital Bonn Bonn Germany
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747
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Zhao Y, Hu J, Sun X, Yang K, Yang L, Kong L, Zhang B, Li F, Li C, Shi B, Hu K, Sun A, Ge J. Loss of m6A demethylase ALKBH5 promotes post-ischemic angiogenesis via post-transcriptional stabilization of WNT5A. Clin Transl Med 2021; 11:e402. [PMID: 34047466 PMCID: PMC8087997 DOI: 10.1002/ctm2.402] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/11/2021] [Accepted: 04/18/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Post-ischemic angiogenesis is critical for blood flow recovery and ischemic tissue repair. N6-methyladenosine (m6A) plays essential roles in numerous biological processes. However, the impact and connected mechanism of m6A on post-ischemic angiogenesis are not fully understood. METHODS AlkB homolog 5 (ALKBH5) was screened out among several methyltransferases and demethylases involved in dynamic m6A regulation. Cardiac microvascular endothelial cells (CMECs) angiogenesis and WNT family member 5A (WNT5A) stability were analyzed upon ALKBH5 overexpression with adenovirus or knockdown with small interfering RNAs in vitro. The blood flow recovery, capillary, and small artery densities were evaluated in adeno-associated virus (AAV)-ALKBH5 overexpression or ALKBH5 knockout (KO) mice in a hind-limb ischemia model. The same experiments were conducted to explore the translational value of transient silencing of ALKBH5 with adenovirus. RESULTS ALKBH5 was significantly upregulated in hypoxic CMECs and led to a global decrease of m6A level. ALKBH5 overexpression further reduced m6A level in normoxic and hypoxic CMECs, impaired proliferation, migration, and tube formation only in hypoxic CMECs. Conversely, ALKBH5 knockdown preserved m6A levels and promoted angiogenic phenotypes in hypoxic but not in normoxic CMECs. Mechanistically, ALKBH5 regulated WNT5A expression through post-transcriptional mRNA modulation in an m6A-dependent manner, which decreased its stability and subsequently impeded angiogenesis in hypoxic CMECs. Furthermore, ALKBH5 overexpression hindered blood flow recovery and reduced CD31 and alpha-smooth muscle actin expression in hind-limb ischemia mice. As expected, ALKBH5-KO mice exhibited improved blood flow recovery, increased capillary, and small artery densities after hind-limb ischemia, and similar beneficial effects were observed in mice with transient adenoviral ALKBH5 gene silencing. CONCLUSION We demonstrate that ALKBH5 is a negative regulator of post-ischemic angiogenesis via post-transcriptional modulation and destabilization of WNT5A mRNA in an m6A-dependent manner. Targeting ALKBH5 may be a potential therapeutic option for ischemic diseases, including peripheral artery disease.
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Affiliation(s)
- Yongchao Zhao
- Department of CardiologyZhongshan HospitalFudan UniversityShanghai Institute of Cardiovascular DiseasesShanghaiChina
- Institute of Biomedical SciencesFudan UniversityShanghaiChina
- NHC Key Laboratory of Viral Heart DiseasesShanghaiChina
- Key Laboratory of Viral Heart DiseasesChinese Academy of Medical SciencesShanghaiChina
- Department of CardiologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Jingjing Hu
- Department of CardiologyZhongshan HospitalFudan UniversityShanghai Institute of Cardiovascular DiseasesShanghaiChina
- Institute of Biomedical SciencesFudan UniversityShanghaiChina
- NHC Key Laboratory of Viral Heart DiseasesShanghaiChina
- Key Laboratory of Viral Heart DiseasesChinese Academy of Medical SciencesShanghaiChina
| | - Xiaolei Sun
- Department of CardiologyZhongshan HospitalFudan UniversityShanghai Institute of Cardiovascular DiseasesShanghaiChina
- Institute of Biomedical SciencesFudan UniversityShanghaiChina
- NHC Key Laboratory of Viral Heart DiseasesShanghaiChina
- Key Laboratory of Viral Heart DiseasesChinese Academy of Medical SciencesShanghaiChina
| | - Kun Yang
- Department of CardiologyZhongshan HospitalFudan UniversityShanghai Institute of Cardiovascular DiseasesShanghaiChina
- Institute of Biomedical SciencesFudan UniversityShanghaiChina
- NHC Key Laboratory of Viral Heart DiseasesShanghaiChina
- Key Laboratory of Viral Heart DiseasesChinese Academy of Medical SciencesShanghaiChina
| | - Lebing Yang
- Department of CardiologyWenzhou Medicial UniversityWenzhouChina
| | - Lingqiu Kong
- Department of CardiologyZhongshan HospitalFudan UniversityShanghai Institute of Cardiovascular DiseasesShanghaiChina
- Institute of Biomedical SciencesFudan UniversityShanghaiChina
- NHC Key Laboratory of Viral Heart DiseasesShanghaiChina
- Key Laboratory of Viral Heart DiseasesChinese Academy of Medical SciencesShanghaiChina
| | - Beijian Zhang
- Department of CardiologyZhongshan HospitalFudan UniversityShanghai Institute of Cardiovascular DiseasesShanghaiChina
- Institute of Biomedical SciencesFudan UniversityShanghaiChina
- NHC Key Laboratory of Viral Heart DiseasesShanghaiChina
- Key Laboratory of Viral Heart DiseasesChinese Academy of Medical SciencesShanghaiChina
| | - Fuhai Li
- Department of CardiologyZhongshan HospitalFudan UniversityShanghai Institute of Cardiovascular DiseasesShanghaiChina
- Institute of Biomedical SciencesFudan UniversityShanghaiChina
| | - Chaofu Li
- Department of CardiologyZhongshan HospitalFudan UniversityShanghai Institute of Cardiovascular DiseasesShanghaiChina
- Institute of Biomedical SciencesFudan UniversityShanghaiChina
| | - Bei Shi
- Department of CardiologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Kai Hu
- Department of CardiologyZhongshan HospitalFudan UniversityShanghai Institute of Cardiovascular DiseasesShanghaiChina
- Institute of Biomedical SciencesFudan UniversityShanghaiChina
| | - Aijun Sun
- Department of CardiologyZhongshan HospitalFudan UniversityShanghai Institute of Cardiovascular DiseasesShanghaiChina
- Institute of Biomedical SciencesFudan UniversityShanghaiChina
- NHC Key Laboratory of Viral Heart DiseasesShanghaiChina
- Key Laboratory of Viral Heart DiseasesChinese Academy of Medical SciencesShanghaiChina
| | - Junbo Ge
- Department of CardiologyZhongshan HospitalFudan UniversityShanghai Institute of Cardiovascular DiseasesShanghaiChina
- Institute of Biomedical SciencesFudan UniversityShanghaiChina
- NHC Key Laboratory of Viral Heart DiseasesShanghaiChina
- Key Laboratory of Viral Heart DiseasesChinese Academy of Medical SciencesShanghaiChina
- Department of CardiologyAffiliated Hospital of Zunyi Medical UniversityZunyiChina
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748
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Yang X, Wei X, Yang J, Du T, Yin C, Fu B, Huang M, Liang J, Gong P, Liu S, Xie W, Guo Z, Wang S, Wu Q, Nauen R, Zhou X, Bass C, Zhang Y. Epitranscriptomic regulation of insecticide resistance. SCIENCE ADVANCES 2021; 7:eabe5903. [PMID: 33952517 PMCID: PMC8099183 DOI: 10.1126/sciadv.abe5903] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 03/16/2021] [Indexed: 05/07/2023]
Abstract
N 6-methyladenosine (m6A) is the most prevalent messenger RNA modification in eukaryotes and an important posttranscriptional regulator of gene expression. However, the biological roles of m6A in most insects remain largely unknown. Here, we show that m6A regulates a cytochrome P450 gene (CYP4C64) in the global whitefly pest, Bemisia tabaci, leading to insecticide resistance. Investigation of the regulation of CYP4C64, which confers resistance to the insecticide thiamethoxam, revealed a mutation in the 5' untranslated region of this gene in resistant B. tabaci strains that introduces a predicted m6A site. We provide several lines of evidence that mRNA methylation of the adenine at this position, in combination with modified expression of m6A writers, acts to increase expression of CYP4C64 and resistance. Collectively, these results provide an example of the epitranscriptomic regulation of the xenobiotic response in insects and implicate the m6A regulatory axis in the development of insecticide resistance.
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Affiliation(s)
- Xin Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuegao Wei
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jing Yang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tianhua Du
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cheng Yin
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Buli Fu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mingjiao Huang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinjin Liang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Peipan Gong
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaonan Liu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wen Xie
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaoli Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingjun Wu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ralf Nauen
- Bayer AG, Crop Science Division, R&D, Alfred Nobel-Strasse 50, 40789 Monheim, Germany
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, KY 40546-0091, USA
| | - Chris Bass
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall, UK.
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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749
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Ma L, Huang Y, Zhang F, Gao DS, Sun N, Ren J, Xia S, Li J, Peng X, Yu L, Jiang BC, Yan M. MMP24 Contributes to Neuropathic Pain in an FTO-Dependent Manner in the Spinal Cord Neurons. Front Pharmacol 2021; 12:673831. [PMID: 33995105 PMCID: PMC8118694 DOI: 10.3389/fphar.2021.673831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/06/2021] [Indexed: 12/04/2022] Open
Abstract
Nerve injury-induced gene expression change in the spinal cord is critical for neuropathic pain genesis. RNA N6-methyladenosine (m6A) modification represents an additional layer of gene regulation. We showed that spinal nerve ligation (SNL) upregulated the expression of matrix metallopeptidase 24 (MMP24) protein, but not Mmp24 mRNA, in the spinal cord neurons. Blocking the SNL-induced upregulation of spinal MMP24 attenuated local neuron sensitization, neuropathic pain development and maintenance. Conversely, mimicking MMP24 increase promoted the spinal ERK activation and produced evoked nociceptive hypersensitivity. Methylated RNA Immunoprecipitation Sequencing (MeRIP-seq) and RNA Immunoprecipitation (RIP) assay indicated the decreased m6A enrichment in the Mmp24 mRNA under neuropathic pain condition. Moreover, fat-mass and obesity-associated protein (FTO) was colocalized with MMP24 in spinal neurons and shown increased binding to the Mmp24 mRNA in the spinal cord after SNL. Overexpression or suppression of FTO correlates with promotion or inhibition of MMP24 expression in cultured spinal cord neurons. In conclusion, SNL promoted the m6A eraser FTO binding to the Mmp24 mRNA, which subsequently facilitated the translation of MMP24 in the spinal cord, and ultimately contributed to neuropathic pain genesis.
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Affiliation(s)
- Longfei Ma
- Department of Anesthesiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yangyuxin Huang
- Department of Anesthesiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Fengjiang Zhang
- Department of Anesthesiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Dave Schwinn Gao
- Department of Anesthesiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Na Sun
- Department of Anesthesiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Jinxuan Ren
- Department of Anesthesiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Suyun Xia
- Department of Anesthesiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Jia Li
- Department of Anesthesiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyi Peng
- Department of Anesthesiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Lina Yu
- Department of Anesthesiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Bao-Chun Jiang
- Institute of Pain Medicine and Special Environmental Medicine, Nantong University, Nantong, China
| | - Min Yan
- Department of Anesthesiology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
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750
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METTL3 enhances the stability of MALAT1 with the assistance of HuR via m6A modification and activates NF-κB to promote the malignant progression of IDH-wildtype glioma. Cancer Lett 2021; 511:36-46. [PMID: 33933553 DOI: 10.1016/j.canlet.2021.04.020] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/18/2021] [Accepted: 04/25/2021] [Indexed: 02/06/2023]
Abstract
Understanding the role of N6-methyladenosine (m6A) in tumorigenesis and stem cell maintenance is an emerging field in glioma research. However, it is necessary to study the function of m6A in IDH-mutation and IDH-wildtype gliomas separately. Here, we aimed to elucidate the role and mechanism of the m6A writer METTL3 in regulating the malignant progression of IDH-wildtype gliomas. We demonstrated that METTL3 expression is positively associated with a higher malignant grade and poorer prognosis of IDH-wildtype gliomas but not IDH-mutant gliomas. METTL3 could also promote the malignant progression of gliomas in both in vitro and in vivo models. Mechanistically, METTL3 upregulated MALAT1 expression by enhancing its stability via m6A modification. We further revealed that HuR was essential for METTL3-mediated MALAT1 stabilization, and upregulated MALAT1 subsequently activated NF-κB. Taken together, our findings confirmed that METTL3 promoted the malignant progression of IDH-wildtype gliomas and revealed important insight into the upstream regulatory mechanism of MALAT1 and NF-κB with a primary focus on m6A modification.
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