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Liu Y, Koo JS, Zhang H. Chronic intermittent ethanol exposure-induced m6A modifications around mRNA stop codons of opioid receptor genes. Epigenetics 2024; 19:2294515. [PMID: 38118075 PMCID: PMC10761033 DOI: 10.1080/15592294.2023.2294515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Chronic alcohol consumption may alter mRNA methylation and expression levels of genes related to addiction and reward in the brain, potentially contributing to alcohol tolerance and dependence. Neuron-like (SH-SY5Y) and non-neuronal (SW620) cells were utilized as models to examine chronic intermittent ethanol (CIE) exposure-induced global m6A RNA methylation changes, as well as m6A mRNA methylation changes around the stop codon of three opioid receptor genes (OPRM1, OPRD1, and OPRK1), which are known to regulate pain, reward, and addiction behaviours. CIE exposure for three weeks significantly increased global RNA methylation levels in both SH-SY5Y (t = 3.98, P = 0.007) and SW620 (t = 2.24, P = 0.067) cells. However, a 3-week CIE exposure resulted in hypomethylation around mRNA stop codon regions of OPRM1 and OPRD1 in both cell lines [OPRM1(SH-SY5Y): t = -5.05, P = 0.0005; OPRM1(SW620): t = -3.19, P = 0.013; OPRD1(SH-SY5Y): t = -13.43, P < 0.00001; OPRD1(SW620): t = -4.00, P = 0.003]. Additionally, mRNA expression levels of OPRM1, OPRD1, and OPRK1 were downregulated (corresponding to mRNA hypomethylation) in both SH-SY5Y and SW620 cells after a 3-week CIE exposure. The present study demonstrated that chronic ethanol exposure altered global RNA methylation levels, as well as mRNA methylation and expression levels of opioid receptor genes in both neuron-like and non-neuronal cells. Our findings suggest a potential epitranscriptomic mechanism by which chronic alcohol consumption remodels the expression of reward-related and alcohol responsive genes in the brain, thus increasing the risk of alcohol use disorder development.Abbreviations: OPRM1: the μ-opioid receptor; OPRD1: the δ-opioid receptor; OPRK1: the κ-opioid receptor; CIE: chronic intermittent ethanol exposure; CIE+WD: chronic intermittent ethanol exposure followed by a 24-hr withdrawal; SH-SY5Y: human neuroblastoma cell Line; SW620: human colon carcinoma cell line; RT-qPCR: reverse transcription followed by quantitative polymerase reaction; MazF-RT-qPCR: MazF digestion followed by RT-qPCR.
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Affiliation(s)
- Ying Liu
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, USA
| | - Ji Sun Koo
- Department of Biology, Boston University, Boston, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, USA
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2
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Shu W, Huang Q, Chen R, Lan H, Yu L, Cui K, He W, Zhu S, Chen M, Li L, Jiang D, Xu G. Complicated role of ALKBH5 in gastrointestinal cancer: an updated review. Cancer Cell Int 2024; 24:298. [PMID: 39182071 PMCID: PMC11344947 DOI: 10.1186/s12935-024-03480-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 08/13/2024] [Indexed: 08/27/2024] Open
Abstract
Gastrointestinal cancer is the most common malignancy in humans, often accompanied by poor prognosis. N6-methyladenosine (m6A) modification is widely present in eukaryotic cells as the most abundant RNA modification. It plays a crucial role in RNA splicing and processing, nuclear export, translation, and stability. Human AlkB homolog 5 (ALKBH5) is a type of RNA demethylase exhibiting abnormal expression in various gastrointestinal cancers.It is closely related to the tumorigenesis, proliferation, migration, and other biological functions of gastrointestinal cancer. However, recent studies indicated that the role and mechanism of ALKBH5 in gastrointestinal cancer are complicated and even controversial. Thus, this review summarizes recent advances in elucidating the role of ALKBH5 as a tumor suppressor or promoter in gastrointestinal cancer. It examines the biological functions of ALKBH5 and its potential as a therapeutic target, providing new perspectives and insights for gastrointestinal cancer research.
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Affiliation(s)
- Weitong Shu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Qianying Huang
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Rui Chen
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Huatao Lan
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Luxin Yu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Kai Cui
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Wanjun He
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Songshan Zhu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Mei Chen
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Li Li
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China
| | - Dan Jiang
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China.
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China.
| | - Guangxian Xu
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, The First Dongguan Affiliated Hospital, School of Medical Technology, Guangdong Medical University, Dongguan, China.
- Dongguan Key Laboratory of Molecular Immunology and Cell Therapy, Dongguan, China.
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3
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Moon JS, Lee W, Cho YH, Kim Y, Kim GW. The Significance of N6-Methyladenosine RNA Methylation in Regulating the Hepatitis B Virus Life Cycle. J Microbiol Biotechnol 2024; 34:233-239. [PMID: 37942519 PMCID: PMC10940779 DOI: 10.4014/jmb.2309.09013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
N6-methyladenosine (m6A) RNA methylation has recently emerged as a significant co-transcriptional modification involved in regulating various RNA functions. It plays a vital function in numerous biological processes. Enzymes referred to as m6A methyltransferases, such as the methyltransferaselike (METTL) 3-METTL14-Wilms tumor 1 (WT1)-associated protein (WTAP) complex, are responsible for adding m6A modifications, while m6A demethylases, including fat mass and obesity-associated protein (FTO) and alkB homolog 5 (ALKBH5), can remove m6A methylation. The functions of m6A-methylated RNA are regulated through the recognition and interaction of m6A reader proteins. Recent research has shown that m6A methylation takes place at multiple sites within hepatitis B virus (HBV) RNAs, and the location of these modifications can differentially impact the HBV infection. The addition of m6A modifications to HBV RNA can influence its stability and translation, thereby affecting viral replication and pathogenesis. Furthermore, HBV infection can also alter the m6A modification pattern of host RNA, indicating the virus's ability to manipulate host cellular processes, including m6A modification. This manipulation aids in establishing chronic infection, promoting liver disease, and contributing to pathogenesis. A comprehensive understanding of the functional roles of m6A modification during HBV infection is crucial for developing innovative approaches to combat HBV-mediated liver disease. In this review, we explore the functions of m6A modification in HBV replication and its impact on the development of liver disease.
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Affiliation(s)
- Jae-Su Moon
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Wooseong Lee
- Center for Convergent Research of Emerging virus Infection, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Yong-Hee Cho
- Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
- Department of Medical Chemistry and Pharmacology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Yonghyo Kim
- Data Convergence Drug Research Center, Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea
| | - Geon-Woo Kim
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon 34134, Republic of Korea
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4
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Peng Q, Qiao J, Li W, You Q, Hu S, Liu Y, Liu W, Hu K, Sun B. Global m6A methylation and gene expression patterns in human microglial HMC3 cells infected with HIV-1. Heliyon 2023; 9:e21307. [PMID: 38027859 PMCID: PMC10643106 DOI: 10.1016/j.heliyon.2023.e21307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
N6-methyladenosine (m6A) methylation of human immunodeficiency virus type 1 (HIV-1) RNA regulates viral replication, and the m6A of host RNA is affected by HIV-1 infection, but its global pattern and function are still unclear. In this study, we report that the number and position of m6A peaks in huge genes of human microglial HMC3 cells were modulated by a single cycle HIV-1 pseudotyped with VSV-G envelope glycoprotein infection using methylated RNA immunoprecipitation sequencing (MeRIP-seq). A conjoint analysis of MeRIP-seq and high-throughput sequencing for mRNA (RNA-seq) explored four groups of clearly classified genes, including 45 hyper-up (m6A-mRNA), 45 hyper-down, 120 hypo-up, and 54 hypo-down genes, in HIV-1 infected cells compared to uninfected ones. KEGG pathway analysis showed that these genes were mainly enriched in the Wnt and TNF signaling pathway, and cytokine-cytokine receptor interaction, which might be related to the immune response in HMC3 cells. And some of these genes might be associated with the pathway of axon guidance and neuroactive ligan-receptor interaction, which affect the neuronal state. However, the cognitive disorders caused by HIV-1 is associated with inflammatory changes that have not yet been well clarified. Furthermore, we confirmed the expression and m6A levels of four genes using RT-PCR and MeRIP-qPCR. Similar to the sequencing results, the expressions of these genes were significantly upregulated by HIV-1 infection. And the m6A level of IL-6 was downregulated, and those of HLA-B, CFB, and OLR1 were upregulated. These results suggest that HIV-1-induced changes in gene expression may be achieved through the regulation of methylation. Our study revealed the global m6A methylation and gene expression patterns under HIV-1 infection in human microglia, which might provide clues for understanding the interaction between HIV-1 and host cells and the cognitive disorders caused by HIV-1.
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Affiliation(s)
- Qian Peng
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and MolecularPharmaceutics, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education &Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), HubeiUniversity of Technology, Wuhan, China
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Jialu Qiao
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
- Department of Immunology, School of Medicine, Jianghan University, Wuhan, Hubei, 430056, China
| | - Weiling Li
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Qiang You
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Song Hu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Yuchen Liu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Wei Liu
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Kanghong Hu
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and MolecularPharmaceutics, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education &Hubei Province), Key Laboratory of Fermentation Engineering (Ministry of Education), HubeiUniversity of Technology, Wuhan, China
| | - Binlian Sun
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
- Department of Immunology, School of Medicine, Jianghan University, Wuhan, Hubei, 430056, China
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Zhang X, Peng Q, Wang L. N 6-methyladenosine modification-a key player in viral infection. Cell Mol Biol Lett 2023; 28:78. [PMID: 37828480 PMCID: PMC10571408 DOI: 10.1186/s11658-023-00490-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/18/2023] [Indexed: 10/14/2023] Open
Abstract
N6-methyladenosine (m6A) modification is a dynamic, reversible process and is the most prevalent internal modification of RNA. This modification is regulated by three protein groups: methyltransferases ("writers"), demethylases ("erasers"), and m6A-binding proteins ("readers"). m6A modification and related enzymes could represent an optimal strategy to deepen the epigenetic mechanism. Numerous reports have suggested that aberrant modifications of m6A lead to aberrant expression of important viral genes. Here, we review the role of m6A modifications in viral replication and virus-host interactions. In particular, we focus on DNA and RNA viruses associated with human diseases, such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus (HIV)-1, Epstein-Barr virus (EBV), and Kaposi's sarcoma-associated herpesvirus (KSHV). These findings will contribute to the understanding of the mechanisms of virus-host interactions and the design of future therapeutic targets for treatment of tumors associated with viral infections.
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Affiliation(s)
- Xiaoyue Zhang
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013, Hunan, China
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
| | - Qiu Peng
- Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 283 Tongzipo Road, Changsha, 410013, Hunan, China.
| | - Lujuan Wang
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, China.
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China.
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Wang X, Li S, Song H, Ding Y, Gao R, Shi X, Li R, Ge X. METTL14-upregulated miR-6858 triggers cell apoptosis in keratinocytes of oral lichen planus through decreasing GSDMC. Commun Biol 2023; 6:976. [PMID: 37741915 PMCID: PMC10517968 DOI: 10.1038/s42003-023-05360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023] Open
Abstract
Oral lichen planus (OLP), a chronic inflammatory disorder, is characterized by the massive cell apoptosis in the keratinocytes of oral mucosa. However, the mechanism responsible for triggering oral keratinocyte apoptosis is not fully explained. Here, we identify that Gasdermin C (GSDMC) downregulation contributes to apoptosis in human oral keratinocytes. Mechanistically, we describe that activated nuclear factor kappa B (NF-κB) pathway induces overexpression of methyltransferase-like 14 (METTL14), which increases N6-adenosine methylation (m6A) levels in the epithelial layer of OLP. m6A modification is capable of regulating primary miR-6858 processing and alternative splicing, leading to miR-6858 increases. miR-6858 can bind and promote GSDMC mRNA degradation. Forced expression of GSDMC is able to rescue cell apoptosis in human oral keratinocyte models resembling OLP. Collectively, our data unveil that m6A modification regulates miR-6858 production to decrease GSDMC expression and to trigger keratinocyte apoptosis in the context of OLP.
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Affiliation(s)
- Xiangyu Wang
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
- Department of Child Dental and Preventive Dentistry, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
- Department of Oral Medicine, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Shuangting Li
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Huimin Song
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
- Department of Child Dental and Preventive Dentistry, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
- Department of Oral Medicine, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Yan Ding
- Department of Dermatology, Hainan Provincial Hospital of Skin Disease, Haikou, Hainan, China
- Department of Dermatology, Skin Disease Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Ruifang Gao
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Xiaotong Shi
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
- Department of Child Dental and Preventive Dentistry, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
- Department of Oral Medicine, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Ran Li
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China
| | - Xuejun Ge
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New Materials, Shanxi Medical University School and Hospital of Stomatology, Taiyuan, Shanxi, China.
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Ahmadi Ghezeldasht S, Bidkhori HR, Miri R, Baghban A, Mosavat A, Rezaee SA. Momordica charantia phytoconstituents can inhibit human T-lymphotropic virus type-1 (HTLV-1) infectivity in vitro and in vivo. J Neurovirol 2023:10.1007/s13365-023-01160-0. [PMID: 37531001 DOI: 10.1007/s13365-023-01160-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/04/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023]
Abstract
There is an urgent need to find an effective therapy for life-threatening HTLV-1-associated diseases. Bitter melon (Momordica charantia) is considered a traditional herb with antiviral and anticancer properties and was tested in this study on HTLV-1 infectivity. GC-MS analyzed the alcoholic extract. In vitro assay was carried out using transfection of HUVEC cells by HTLV-1-MT2 cell line. The cells were exposed to alcoholic and aqueous extracts at 5,10, and 20 µg/mL concentrations. In vivo, mice were divided into four groups. Three groups were treated with HTLV-1-MT-2 cells as test groups and positive control, and PBS as the negative control group in the presence and absence of M. charantia extracts. Peripheral blood mononuclear cells (PBMCs), mesenteric lymph nodes (MLNs), and splenocytes were collected for HTLV-1-proviral load (PVL) assessment, TaqMan-qPCR. The GC-MS analysis revealed 36 components in M. charantia. The studies showed significant reductions in HTLV-1-PVL in the presence of extract in the HUVEC-treated groups (P = 0.001). Furthermore, the inhibitory effects of extracts on HTLV-1 infected mice showed significant differences in HTLV-1-PVL among M. charantia treated groups with untreated (P = 0.001). The T-cells in MLNs were significantly more susceptible to HTLV-1 than others (P = 0.001). There were significant differences among HTLV-1-infected cells in MLNs and splenocytes (P = 0.001 and 0.046, respectively). Also, aqueous and alcoholic extract-treated groups significantly affected HTLV-1-infected PBMCs (P = 0.002 and 0.009, respectively). M. charantia may have effective antiviral properties. The substantial compound of M. charantia could have inhibitory effects on the proliferation and transmission of HTLV-1 oncovirus.
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Affiliation(s)
- Sanaz Ahmadi Ghezeldasht
- Blood Borne Infections Research Center, Academic Center for Education, Culture and Research (ACECR), Azadi-Square, Ferdowsi University Campus, Razavi Khorasan, Mashhad, 9177949367, Iran
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hamid Reza Bidkhori
- Stem Cells and Regenerative Medicine Department, Academic Center for Education, Culture and Research (ACECR), Razavi Khorasan, Mashhad, Iran
| | - Raheleh Miri
- Blood Borne Infections Research Center, Academic Center for Education, Culture and Research (ACECR), Azadi-Square, Ferdowsi University Campus, Razavi Khorasan, Mashhad, 9177949367, Iran
| | - Arezoo Baghban
- Department of Chemistry, Faculty of Science, Azad University of Mashhad, Mashhad, Iran
| | - Arman Mosavat
- Blood Borne Infections Research Center, Academic Center for Education, Culture and Research (ACECR), Azadi-Square, Ferdowsi University Campus, Razavi Khorasan, Mashhad, 9177949367, Iran.
| | - Seyed Abdolrahim Rezaee
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Mashhad University of Medical Sciences, Mashhad, Iran.
- Immunology Research Center, Inflammation and Inflammatory Diseases Division, Faculty of Medicine, Mashhad University of Medical Sciences, Azadi-Square, Medical Campus, 9177948564, Mashhad, Iran.
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Verghese M, Wilkinson E, He Y. Role of RNA modifications in carcinogenesis and carcinogen damage response. Mol Carcinog 2023; 62:24-37. [PMID: 35560957 PMCID: PMC9653521 DOI: 10.1002/mc.23418] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/26/2022] [Indexed: 02/03/2023]
Abstract
The field of epitranscriptomics encompasses the study of post-transcriptional RNA modifications and their regulatory enzymes. Among the numerous RNA modifications, N6 -methyladenosine (m6 A) has been identified as the most common internal modification of messenger RNA (mRNA). Although m6 A modifications were first discovered in the 1970s, advances in technology have revived interest in this field, driving an abundance of research into the role of RNA modifications in various biological processes, including cancer. As analogs to epigenetic modifications, RNA modifications also play an important role in carcinogenesis by regulating gene expression post-transcriptionally. A growing body of evidence suggests that carcinogens can modulate RNA modifications to alter the expression of oncogenes or tumor suppressors during cellular transformation. Additionally, the expression and activity of the enzymes that regulate RNA modifications can be dysregulated and contribute to carcinogenesis, making these enzymes promising targets of drug discovery. Here we summarize the roles of RNA modifications during carcinogenesis induced by exposure to various environmental carcinogens, with a main focus on the roles of the most widely studied m6 A mRNA methylation.
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Affiliation(s)
- Michelle Verghese
- Department of Medicine, Section of DermatologyUniversity of ChicagoChicagoIllinoisUSA
- Pritzker School of MedicineUniversity of ChicagoChicagoIllinoisUSA
| | - Emma Wilkinson
- Department of Medicine, Section of DermatologyUniversity of ChicagoChicagoIllinoisUSA
- Committee on Cancer BiologyUniversity of ChicagoChicagoIllinoisUSA
| | - Yu‐Ying He
- Department of Medicine, Section of DermatologyUniversity of ChicagoChicagoIllinoisUSA
- Committee on Cancer BiologyUniversity of ChicagoChicagoIllinoisUSA
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9
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Yin H, Xie Y, Gu P, Li W, Zhang Y, Yao Y, Chen W, Ma J. The emerging role of epigenetic regulation in the progression of silicosis. Clin Epigenetics 2022; 14:169. [PMID: 36494831 PMCID: PMC9737765 DOI: 10.1186/s13148-022-01391-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Silicosis is one of the most severe occupational diseases worldwide and is characterized by silicon nodules and diffuse pulmonary fibrosis. However, specific treatments for silicosis are still lacking at present. Therefore, elucidating the pathogenesis of silicosis plays a significant guiding role for its treatment and prevention. The occurrence and development of silicosis are accompanied by many regulatory mechanisms, including epigenetic regulation. The main epigenetic regulatory mechanisms of silicosis include DNA methylation, non-coding RNA (ncRNA), and histone modifications. In recent years, the expression and regulation of genes related to silicosis have been explored at epigenetic level to reveal its pathogenesis further, and the identification of aberrant epigenetic markers provides new biomarkers for prediction and diagnosis of silicosis. Here, we summarize the studies on the role of epigenetic changes in the pathogenesis of silicosis to give some clues for finding specific therapeutic targets for silicosis.
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Affiliation(s)
- Haoyu Yin
- grid.33199.310000 0004 0368 7223Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China ,grid.33199.310000 0004 0368 7223Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China
| | - Yujia Xie
- grid.33199.310000 0004 0368 7223Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China ,grid.33199.310000 0004 0368 7223Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China
| | - Pei Gu
- grid.33199.310000 0004 0368 7223Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China ,grid.33199.310000 0004 0368 7223Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China
| | - Wei Li
- grid.417303.20000 0000 9927 0537Key Lab of Environment and Health, School of Public Health, Xuzhou Medical University, Xuzhou, 221004 Jiangsu China
| | - Yingdie Zhang
- grid.33199.310000 0004 0368 7223Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China ,grid.33199.310000 0004 0368 7223Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China
| | - Yuxin Yao
- grid.33199.310000 0004 0368 7223Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China ,grid.33199.310000 0004 0368 7223Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China
| | - Weihong Chen
- grid.33199.310000 0004 0368 7223Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China ,grid.33199.310000 0004 0368 7223Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China
| | - Jixuan Ma
- grid.33199.310000 0004 0368 7223Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China ,grid.33199.310000 0004 0368 7223Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 Hubei China
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10
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Lu L, Li Y, Ao X, Huang J, Liu B, Wu L, Li D. The risk of COVID-19 can be predicted by a nomogram based on m6A-related genes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 106:105389. [PMID: 36460278 PMCID: PMC9707050 DOI: 10.1016/j.meegid.2022.105389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/24/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
BACKGROUND The expression of m6A-related genes and their significance in COVID-19 patients are still unknown. METHODS The GSE177477 and GSE157103 datasets of the Gene Expression Omnibus were used to extract RNA-seq data. The expression of 26 m6A-related genes and immune cell infiltration in COVID-19 patients were analyzed. Finally, we built and validated a nomogram model to predict the risk of COVID-19 infection. RESULTS There were significant differences in 11 m6A regulatory factors between patients with COVID-19 and healthy individuals. The classification of disease subtypes based on m6A-related gene levels can be distinguished. COVID-19 patients in GSE177477 were classified into two categories based on m6A-related genes. The patients in cluster A were all symptomatic, while those in cluster B were asymptomatic. A significant correlation was also found between immune cells and m6A-related genes. Finally, seven m6A-related disease-characteristic genes, HNRNPA2B1, ELAVL1, RBM15, RBM15B, YTHDC1, HNRNPC, and WTAP, were screened to construct a nomogram model for predicting risk. The calibration curve, decision curve analysis, and clinical impact curve analysis were used to show that the nomogram model was effective and had a high net efficacy for risk prediction. CONCLUSIONS m6A-related genes were correlated with immune cells. The nomogram model effectively predicted COVID-19 risk. Moreover, m6A-related genes may be associated with the presence or absence of symptoms in COVID-19 patients.
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Affiliation(s)
- Lingling Lu
- Fuzong Clinical Medical College of Fujian Medical University, The 900th hospital. No.156 Xierhuan Road, Fuzhou, Fujian 350025, China,Department of Hepatobiliary Disease, 900th Hospital of Joint Logistics Support Force, No.156 Xierhuan Road, Fuzhou, Fujian 350025, China
| | - Yijing Li
- Fuzhou First Hospital Affiliated to Fujian Medical University, Fuzhou, Fujian, China
| | - Xiulan Ao
- Department of Hepatobiliary Disease, 900th Hospital of Joint Logistics Support Force, No.156 Xierhuan Road, Fuzhou, Fujian 350025, China
| | - Jiaofeng Huang
- Fuzong Clinical Medical College of Fujian Medical University, The 900th hospital. No.156 Xierhuan Road, Fuzhou, Fujian 350025, China
| | - Bang Liu
- Fuzong Clinical Medical College of Fujian Medical University, The 900th hospital. No.156 Xierhuan Road, Fuzhou, Fujian 350025, China,Department of Hepatobiliary Disease, 900th Hospital of Joint Logistics Support Force, No.156 Xierhuan Road, Fuzhou, Fujian 350025, China
| | - Liqing Wu
- Department of Hepatobiliary Disease, 900th Hospital of Joint Logistics Support Force, No.156 Xierhuan Road, Fuzhou, Fujian 350025, China
| | - Dongliang Li
- Fuzong Clinical Medical College of Fujian Medical University, The 900th hospital. No.156 Xierhuan Road, Fuzhou, Fujian 350025, China,Department of Hepatobiliary Disease, 900th Hospital of Joint Logistics Support Force, No.156 Xierhuan Road, Fuzhou, Fujian 350025, China,Corresponding author at: Fuzong Clinical Medical College of Fujian Medical University, The 900th hospital of Joint Logistics Support Force. No.156 Xierhuan Road, Fuzhou, Fujian 350025, China
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Sacco MT, Bland KM, Horner SM. WTAP targets the METTL3 m 6 A-methyltransferase complex to cytoplasmic hepatitis C virus RNA to regulate infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.27.497872. [PMID: 35794896 PMCID: PMC9258289 DOI: 10.1101/2022.06.27.497872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
UNLABELLED Modification of the hepatitis C virus (HCV) positive-strand RNA genome by N6-methyladenosine (m 6 A) regulates the viral lifecycle. This lifecycle takes place solely in the cytoplasm, while m 6 A addition on cellular mRNA takes place in the nucleus. Thus, the mechanisms by which m 6 A is deposited on the viral RNA have been unclear. In this work, we find that m 6 A modification of HCV RNA by the m 6 A-methyltransferase proteins METTL3 and METTL14 is regulated by WTAP. WTAP, a predominantly nuclear protein, is an essential member of the cellular mRNA m 6 A-methyltransferase complex and known to target METTL3 to mRNA. We found that HCV infection induces localization of WTAP to the cytoplasm. Importantly, we found that WTAP is required for both METTL3 interaction with HCV RNA and for m 6 A modification across the viral RNA genome. Further, we found that WTAP, like METTL3 and METTL14, negatively regulates the production of infectious HCV virions, a process that we have previously shown is regulated by m 6 A. Excitingly, WTAP regulation of both HCV RNA m 6 A modification and virion production were independent of its ability to localize to the nucleus. Together, these results reveal that WTAP is critical for HCV RNA m 6 A modification by METTL3 and METTL14 in the cytoplasm. IMPORTANCE Positive-strand RNA viruses such as HCV represent a significant global health burden. Previous work has described how HCV RNA contains the RNA modification m 6 A and how this modification regulates viral infection. Yet, how this modification is targeted to HCV RNA has remained unclear due to the incompatibility of the nuclear cellular processes that drive m 6 A modification with the cytoplasmic HCV lifecycle. In this study, we present evidence for how m 6 A modification is targeted to HCV RNA in the cytoplasm by a mechanism in which WTAP recruits the m 6 A-methyltransferase METTL3 to HCV RNA. This targeting strategy for m 6 A modification of cytoplasmic RNA viruses is likely relevant for other m 6 A-modified positive-strand RNA viruses with cytoplasmic lifecycles such as enterovirus 71 and SARS-CoV-2 and provides an exciting new target for potential antiviral therapies.
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12
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Liu Y, Li K, Xu YP, Zhu Z, Zhao H, Li XF, Ye Q, Yi C, Qin CF. Characterization of m 6 A modifications in the contemporary Zika virus genome and host cellular transcripts. J Med Virol 2022; 94:4309-4318. [PMID: 35587571 DOI: 10.1002/jmv.27869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 11/07/2022]
Abstract
Zika virus (ZIKV) suddenly evolved from a neglected arthropod-borne flavivirus into a pandemic pathogen during 2015-2016. A panel of amino acid mutations have been shown to be responsible for the enhanced neurovirulence and transmissibility of ZIKV. Recent studies have demonstrated that ZIKV genomic RNA is modified by host N6-methyladenosine (m6 A) machinery during viral replication in host cells, and the m6 A profiles vary among different isolates and different host cells. In the present study, using a contemporary Asian ZIKV strain isolated in 2019 (SZ1901) as a model, we profiled m6 A modifications on both the viral genome RNA and cellular transcripts from the ZIKV-infected human hepatocarcinoma cell line Huh7. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) identified a unique m6 A map in the genome of ZIKV strain SZ1901 that is different from all previous isolates. Meanwhile, ZIKV infection induced m6 A upregulation in the CDS regions but downregulation in the 3' UTR of host RNA transcripts. The m6 A peak intensity in the majority of host genes was downregulated, include including ISG-related genes. Overall, our study describes unique viral and host m6 A profiles in contemporary ZIKV-infected Huh7 cells, highlighting the complexity and importance of m6 A modification during viral infection. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yu Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Kai Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yan-Peng Xu
- Laboratory of Virology, Beijing Key Laboratory of Etiology of Viral Diseases in Children, Capital Institute of Pediatrics, Beijing, China
| | - Zhu Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Hui Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Xiao-Feng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Qing Ye
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, China
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13
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Mohammed Salih M, Carpenter S. What sequencing technologies can teach us about innate immunity. Immunol Rev 2022; 305:9-28. [PMID: 34747035 PMCID: PMC8865538 DOI: 10.1111/imr.13033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/22/2021] [Accepted: 10/16/2021] [Indexed: 01/03/2023]
Abstract
For years, we have taken a reductionist approach to understanding gene regulation through the study of one gene in one cell at a time. While this approach has been fruitful it is laborious and fails to provide a global picture of what is occurring in complex situations involving tightly coordinated immune responses. The emergence of whole-genome techniques provides a system-level view of a response and can provide a plethora of information on events occurring in a cell from gene expression changes to splicing changes and chemical modifications. As with any technology, this often results in more questions than answers, but this wealth of knowledge is providing us with an unprecedented view of what occurs inside our cells during an immune response. In this review, we will discuss the current RNA-sequencing technologies and what they are helping us learn about the innate immune system.
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Affiliation(s)
- Mays Mohammed Salih
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, USA
| | - Susan Carpenter
- Department of Molecular Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, USA
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14
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Xu W, Tian X, Liu W, Anwaier A, Su J, Zhu W, Wan F, Shi G, Wei G, Qu Y, Zhang H, Ye D. m 6A Regulator-Mediated Methylation Modification Model Predicts Prognosis, Tumor Microenvironment Characterizations and Response to Immunotherapies of Clear Cell Renal Cell Carcinoma. Front Oncol 2021; 11:709579. [PMID: 34295828 PMCID: PMC8290143 DOI: 10.3389/fonc.2021.709579] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/21/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND This study aims to establish an N6-methyladenosine (m6A) RNA methylation regulators-mediated methylation model and explore its role in predicting prognostic accuracy of immune contexture and characterizations of clear cell renal cell carcinoma (ccRCC). METHODS The m6A modification subclasses (m6AMS) were identified by unsupervised cluster analysis and three clusters were determined by consensus clustering algorithm in a discovering cohort. Testing and real-world validation cohorts were used to identify predictive responses for immune checkpoint therapies (ICTs) of m6AMS. RESULTS Prognostic implications landscape of m6A regulators in cancers and its differential expression levels in ccRCC patients were identified. Based on discovering cohort, ccRCC were automatically divided into three m6AMS, and cluster 3 showed significant worse survival than cluster 1/2. Importantly, it was found that the immune checkpoint molecules expression was significantly elevated in cluster 3. Besides, m6A scoreLow group (cluster 1&2) have significantly elevated TIDE score compared with m6A scoreHigh group (cluster 3). There was conspicuous tertiary lymphoid tissue, aggressive phenotype, elevated glycolysis, expression of PD-L1, abundance of CD8+ T cells, CD4+ FOXP3+ Treg cells and TCRn immune cells infiltration in the high m6A score group. Interestingly, there are significantly increased patients with clinical benefit in m6A scoreHigh group in 368 patients receiving ICTs from testing IMvigor210 (n = 292) and validation FUSCC (n = 55) cohorts. CONCLUSION Our discovery highlights the relationship between tumor epigenetic heterogeneity and immune contexture. Immune-rejection cluster 3 has pro-tumorigenic immune infiltration, and shows significant clinical benefits for ccRCC patients receiving ICTs, enabling patient selection for future clinical treatment.
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Affiliation(s)
- Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi Tian
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wangrui Liu
- Department of Urology, Affiliated Hospital of Youjiang Medical College for Nationalities, Baise, China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaqi Su
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenkai Zhu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fangning Wan
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Guohai Shi
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gaomeng Wei
- Department of Urology, Affiliated Hospital of Youjiang Medical College for Nationalities, Baise, China
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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15
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Kumar S, Nagpal R, Kumar A, Ashraf MU, Bae YS. Immunotherapeutic Potential of m6A-Modifiers and MicroRNAs in Controlling Acute Myeloid Leukaemia. Biomedicines 2021; 9:690. [PMID: 34207299 PMCID: PMC8234128 DOI: 10.3390/biomedicines9060690] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 05/30/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
Epigenetic alterations have contributed greatly to human carcinogenesis. Conventional epigenetic studies have been predominantly focused on DNA methylation, histone modifications, and chromatin remodelling. Epitranscriptomics is an emerging field that encompasses the study of RNA modifications that do not affect the RNA sequence but affect functionality via a series of RNA binding proteins called writer, reader and eraser. Several kinds of epi-RNA modifications are known, such as 6-methyladenosine (m6A), 5-methylcytidine (m5C), and 1-methyladenosine. M6A modification is the most studied and has large therapeutic implications. In this review, we have summarised the therapeutic potential of m6A-modifiers in controlling haematological disorders, especially acute myeloid leukaemia (AML). AML is a type of blood cancer affecting specific subsets of blood-forming hematopoietic stem/progenitor cells (HSPCs), which proliferate rapidly and acquire self-renewal capacities with impaired terminal cell-differentiation and apoptosis leading to abnormal accumulation of white blood cells, and thus, an alternative therapeutic approach is required urgently. Here, we have described how RNA m6A-modification machineries EEE (Editor/writer: Mettl3, Mettl14; Eraser/remover: FTO, ALKBH5, and Effector/reader: YTHDF-1/2) could be reformed into potential druggable candidates or as RNA-modifying drugs (RMD) to treat leukaemia. Moreover, we have shed light on the role of microRNAs and suppressors of cytokine signalling (SOCS/CISH) in increasing anti-tumour immunity towards leukaemia. We anticipate, our investigation will provide fundamental knowledge in nurturing the potential of RNA modifiers in discovering novel therapeutics or immunotherapeutic procedures.
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Affiliation(s)
- Sunil Kumar
- Department of Biological Sciences, Sungkyunkwan University, Jangan-gu, Suwon 16419, Gyeonggi-do, Korea;
- Science Research Center (SRC) for Immune Research on Non-lymphoid Organ (CIRNO), Sungkyunkwan University, Jangan-gu, Suwon 16419, Gyeonggi-do, Korea
| | - Ravinder Nagpal
- Department of Nutrition & Integrative Physiology, Florida State University, Tallahassee, FL 32306, USA;
| | - Amit Kumar
- Medical Writer, Quebec City, QC G1X 3E1, Canada;
| | - Muhammad Umer Ashraf
- Department of Biological Sciences, Sungkyunkwan University, Jangan-gu, Suwon 16419, Gyeonggi-do, Korea;
- Science Research Center (SRC) for Immune Research on Non-lymphoid Organ (CIRNO), Sungkyunkwan University, Jangan-gu, Suwon 16419, Gyeonggi-do, Korea
| | - Yong-Soo Bae
- Department of Biological Sciences, Sungkyunkwan University, Jangan-gu, Suwon 16419, Gyeonggi-do, Korea;
- Science Research Center (SRC) for Immune Research on Non-lymphoid Organ (CIRNO), Sungkyunkwan University, Jangan-gu, Suwon 16419, Gyeonggi-do, Korea
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Luo J, Xu T, Sun K. N6-Methyladenosine RNA Modification in Inflammation: Roles, Mechanisms, and Applications. Front Cell Dev Biol 2021; 9:670711. [PMID: 34150765 PMCID: PMC8213350 DOI: 10.3389/fcell.2021.670711] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/10/2021] [Indexed: 12/21/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent internal mRNA modification. m6A can be installed by the methyltransferase complex and removed by demethylases, which are involved in regulating post-transcriptional expression of target genes. RNA methylation is linked to various inflammatory states, including autoimmunity, infection, metabolic disease, cancer, neurodegenerative diseases, heart diseases, and bone diseases. However, systematic knowledge of the relationship between m6A modification and inflammation in human diseases remains unclear. In this review, we will discuss the association between m6A modification and inflammatory response in diseases, especially the role, mechanisms, and potential clinical application of m6A as a biomarker and therapeutic target for inflammatory diseases.
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Affiliation(s)
- Jiahui Luo
- The Center for Biomedical Research, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Xu
- Department of Rehabilitation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Sun
- Department of Orthopedics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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17
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From A to m 6A: The Emerging Viral Epitranscriptome. Viruses 2021; 13:v13061049. [PMID: 34205979 PMCID: PMC8227502 DOI: 10.3390/v13061049] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 12/18/2022] Open
Abstract
There are over 100 different chemical RNA modifications, collectively known as the epitranscriptome. N6-methyladenosine (m6A) is the most commonly found internal RNA modification in cellular mRNAs where it plays important roles in the regulation of the mRNA structure, stability, translation and nuclear export. This modification is also found in viral RNA genomes and in viral mRNAs derived from both RNA and DNA viruses. A growing body of evidence indicates that m6A modifications play important roles in regulating viral replication by interacting with the cellular m6A machinery. In this review, we will exhaustively detail the current knowledge on m6A modification, with an emphasis on its function in virus biology.
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18
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EDLm 6APred: ensemble deep learning approach for mRNA m 6A site prediction. BMC Bioinformatics 2021; 22:288. [PMID: 34051729 PMCID: PMC8164815 DOI: 10.1186/s12859-021-04206-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As a common and abundant RNA methylation modification, N6-methyladenosine (m6A) is widely spread in various species' transcriptomes, and it is closely related to the occurrence and development of various life processes and diseases. Thus, accurate identification of m6A methylation sites has become a hot topic. Most biological methods rely on high-throughput sequencing technology, which places great demands on the sequencing library preparation and data analysis. Thus, various machine learning methods have been proposed to extract various types of features based on sequences, then occupied conventional classifiers, such as SVM, RF, etc., for m6A methylation site identification. However, the identification performance relies heavily on the extracted features, which still need to be improved. RESULTS This paper mainly studies feature extraction and classification of m6A methylation sites in a natural language processing way, which manages to organically integrate the feature extraction and classification simultaneously, with consideration of upstream and downstream information of m6A sites. One-hot, RNA word embedding, and Word2vec are adopted to depict sites from the perspectives of the base as well as its upstream and downstream sequence. The BiLSTM model, a well-known sequence model, was then constructed to discriminate the sequences with potential m6A sites. Since the above-mentioned three feature extraction methods focus on different perspectives of m6A sites, an ensemble deep learning predictor (EDLm6APred) was finally constructed for m6A site prediction. Experimental results on human and mouse data sets show that EDLm6APred outperforms the other single ones, indicating that base, upstream, and downstream information are all essential for m6A site detection. Compared with the existing m6A methylation site prediction models without genomic features, EDLm6APred obtains 86.6% of the area under receiver operating curve on the human data sets, indicating the effectiveness of sequential modeling on RNA. To maximize user convenience, a webserver was developed as an implementation of EDLm6APred and made publicly available at www.xjtlu.edu.cn/biologicalsciences/EDLm6APred . CONCLUSIONS Our proposed EDLm6APred method is a reliable predictor for m6A methylation sites.
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Wood S, Willbanks A, Cheng JX. The Role of RNA Modifications and RNA-modifying Proteins in Cancer Therapy and Drug Resistance. Curr Cancer Drug Targets 2021; 21:326-352. [PMID: 33504307 DOI: 10.2174/1568009621666210127092828] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022]
Abstract
The advent of new genome-wide sequencing technologies has uncovered abnormal RNA modifications and RNA editing in a variety of human cancers. The discovery of reversible RNA N6-methyladenosine (RNA: m6A) by fat mass and obesity-associated protein (FTO) demethylase has led to exponential publications on the pathophysiological functions of m6A and its corresponding RNA modifying proteins (RMPs) in the past decade. Some excellent reviews have summarized the recent progress in this field. Compared to the extent of research into RNA: m6A and DNA 5-methylcytosine (DNA: m5C), much less is known about other RNA modifications and their associated RMPs, such as the role of RNA: m5C and its RNA cytosine methyltransferases (RCMTs) in cancer therapy and drug resistance. In this review, we will summarize the recent progress surrounding the function, intramolecular distribution and subcellular localization of several major RNA modifications, including 5' cap N7-methylguanosine (m7G) and 2'-O-methylation (Nm), m6A, m5C, A-to-I editing, and the associated RMPs. We will then discuss dysregulation of those RNA modifications and RMPs in cancer and their role in cancer therapy and drug resistance.
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Affiliation(s)
- Shaun Wood
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Amber Willbanks
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
| | - Jason X Cheng
- Department of Pathology, Hematopathology Section, University of Chicago, Chicago, IL60637, United States
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20
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Netzband R, Pager CT. Viral Epitranscriptomics. Virology 2021. [DOI: 10.1002/9781119818526.ch4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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21
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Liu J, Xu YP, Li K, Ye Q, Zhou HY, Sun H, Li X, Yu L, Deng YQ, Li RT, Cheng ML, He B, Zhou J, Li XF, Wu A, Yi C, Qin CF. The m 6A methylome of SARS-CoV-2 in host cells. Cell Res 2021; 31:404-414. [PMID: 33510385 PMCID: PMC8115241 DOI: 10.1038/s41422-020-00465-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
The newly identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a global health emergency because of its rapid spread and high mortality. The molecular mechanism of interaction between host and viral genomic RNA is yet unclear. We demonstrate herein that SARS-CoV-2 genomic RNA, as well as the negative-sense RNA, is dynamically N6-methyladenosine (m6A)-modified in human and monkey cells. Combined RIP-seq and miCLIP analyses identified a total of 8 m6A sites at single-base resolution in the genome. Especially, epidemic strains with mutations at these identified m6A sites have emerged worldwide, and formed a unique cluster in the US as indicated by phylogenetic analysis. Further functional experiments showed that m6A methylation negatively regulates SARS-CoV-2 infection. SARS-CoV-2 infection also triggered a global increase in host m6A methylome, exhibiting altered localization and motifs of m6A methylation in mRNAs. Altogether, our results identify m6A as a dynamic epitranscriptomic mark mediating the virus-host interaction.
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Affiliation(s)
- Jun'e Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China
- Biomedical Pioneering Innovation Center, Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, 100871, China
| | - Yan-Peng Xu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Kai Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Qing Ye
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Hang-Yu Zhou
- Suzhou Institute of System Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, Jiangsu, 215000, China
| | - Hanxiao Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaoyu Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Liu Yu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Yong-Qiang Deng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Rui-Ting Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Meng-Li Cheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Bo He
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Jia Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Xiao-Feng Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Aiping Wu
- Suzhou Institute of System Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, Jiangsu, 215000, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences, Beijing, 100071, China.
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22
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Tang L, Wei X, Li T, Chen Y, Dai Z, Lu C, Zheng G. Emerging Perspectives of RNA N 6-methyladenosine (m 6A) Modification on Immunity and Autoimmune Diseases. Front Immunol 2021; 12:630358. [PMID: 33746967 PMCID: PMC7973041 DOI: 10.3389/fimmu.2021.630358] [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: 11/17/2020] [Accepted: 02/16/2021] [Indexed: 12/21/2022] Open
Abstract
N 6-methyladenosine (m6A) modification, the addition of a methylation decoration at the position of N6 of adenosine, is one of the most prevalent modifications among the over 100 known chemical modifications of RNA. Numerous studies have recently characterized that RNA m6A modification functions as a critical post-transcriptional regulator of gene expression through modulating various aspects of RNA metabolism. In this review, we will illustrate the current perspectives on the biological process of m6A methylation. Then we will further summarize the vital modulatory effects of m6A modification on immunity, viral infection, and autoinflammatory disorders. Recent studies suggest that m6A decoration plays an important role in immunity, viral infection, and autoimmune diseases, thereby providing promising biomarkers and therapeutic targets for viral infection and autoimmune disorders.
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Affiliation(s)
- Lipeng Tang
- Department of Pharmacology of Traditional Chinese Medicine, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xingyan Wei
- Department of Pathogen Biology, The Chinses Center for Disease Control and Prevention, Beijing, China
| | - Tong Li
- Department of Pharmacology of Traditional Chinese Medicine, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Pharmacy, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yi Chen
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhenhua Dai
- Section of Immunology, Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | - Chuanjian Lu
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guangjuan Zheng
- Department of Pharmacology of Traditional Chinese Medicine, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Pathology, The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
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23
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Kim GW, Siddiqui A. The role of N6-methyladenosine modification in the life cycle and disease pathogenesis of hepatitis B and C viruses. Exp Mol Med 2021; 53:339-345. [PMID: 33742132 PMCID: PMC8080661 DOI: 10.1038/s12276-021-00581-3] [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: 09/14/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/11/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent modification of mammalian cellular RNAs. m6A methylation is linked to epigenetic regulation of several aspects of gene expression, including RNA stability, splicing, nuclear export, RNA folding, and translational activity. m6A modification is reversibly catalyzed by methyltransferases (m6A writers) and demethylases (m6A erasers), and the dynamics of m6A-modified RNA are regulated by m6A-binding proteins (m6A readers). Recently, several studies have shown that m6A methylation sites have been identified in hepatitis B virus (HBV) transcripts and the hepatitis C virus (HCV) RNA genome. Here, we review the role of m6A modification in HBV/HCV replication and its contribution to liver disease pathogenesis. A better understanding of the functions of m6A methylation in the life cycles of HBV and HCV is required to establish the role of these modifications in liver diseases associated with these viral infections.
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Affiliation(s)
- Geon-Woo Kim
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Aleem Siddiqui
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
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24
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Wang Y, Zheng J, Duan C, Jiao J, Gong Y, Shi H, Xiang Y. Detection of locus-specific N6-methyladenosine modification based on Ag +-assisted ligation and supersandwich signal amplification. Analyst 2021; 146:1355-1360. [PMID: 33393556 DOI: 10.1039/d0an02214d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Emerging evidence reveals that the epitranscriptomic mark N6-methyladenosine (m6A) plays vital roles in organisms, including gene regulation and disease progression. However, developing sensitive methods to detect m6A modification, especially the identification of m6A marks at the single-site level, remains a challenge. Therefore, based on target-specific triggered signal amplification, we developed a highly sensitive electrochemical method to detect site-specific m6A modifications in DNA. In this work, the m6A site in DNA can restrict the ligation assisted by Ag+, and this restriction effect can activate the subsequent strand displacement reaction and hybridization chain reaction (HCR), thus achieving signal amplification from the m6A site, and finally realizing high sensitivity analysis of m6A methylation. Benefiting from the high specificity of base pairs and the extremely weak binding affinity between Ag+ and m6A, the proposed method was used for not only detecting the target DNA with a putative m6A site, but also identifying m6A marks at the single-site level in DNA. In addition, this study does not rely on antibodies and radiolabeling, so it has the advantage of cost-effectiveness. Therefore, we believe that the proposed strategy may provide a new perspective for methylation research, which can be used to test more clinical samples in further research.
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Affiliation(s)
- Yanxia Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Ji Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Chengjie Duan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Jin Jiao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Youjing Gong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Hai Shi
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
| | - Yang Xiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China.
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25
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Xia TL, Li X, Wang X, Zhu YJ, Zhang H, Cheng W, Chen ML, Ye Y, Li Y, Zhang A, Dai DL, Zhu QY, Yuan L, Zheng J, Huang H, Chen SQ, Xiao ZW, Wang HB, Roy G, Zhong Q, Lin D, Zeng YX, Wang J, Zhao B, Gewurz BE, Chen J, Zuo Z, Zeng MS. N(6)-methyladenosine-binding protein YTHDF1 suppresses EBV replication and promotes EBV RNA decay. EMBO Rep 2021; 22:e50128. [PMID: 33605073 PMCID: PMC8025027 DOI: 10.15252/embr.202050128] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 01/10/2021] [Accepted: 01/15/2021] [Indexed: 12/14/2022] Open
Abstract
N6‐methyladenosine (m6A) modification of mRNA mediates diverse cellular and viral functions. Infection with Epstein–Barr virus (EBV) is causally associated with nasopharyngeal carcinoma (NPC), 10% of gastric carcinoma, and various B‐cell lymphomas, in which the viral latent and lytic phases both play vital roles. Here, we show that EBV transcripts exhibit differential m6A modification in human NPC biopsies, patient‐derived xenograft tissues, and cells at different EBV infection stages. m6A‐modified EBV transcripts are recognized and destabilized by the YTHDF1 protein, which leads to the m6A‐dependent suppression of EBV infection and replication. Mechanistically, YTHDF1 hastens viral RNA decapping and mediates RNA decay by recruiting RNA degradation complexes, including ZAP, DDX17, and DCP2, thereby post‐transcriptionally downregulating the expression of EBV genes. Taken together, our results reveal the critical roles of m6A modifications and their reader YTHDF1 in EBV replication. These findings contribute novel targets for the treatment of EBV‐associated cancers.
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Affiliation(s)
- Tian-Liang Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xingyang Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xueping Wang
- Department of Laboratory Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yun-Jia Zhu
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hua Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Weisheng Cheng
- Key Laboratory of Stem Cells and Tissue Engineering (Sun Yat-sen University), Department of Medical Bioinformatics, Zhongshan School of Medicine, Ministry of Education, Guangzhou, China
| | - Mei-Ling Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ying Ye
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan Li
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ao Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dan-Ling Dai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qian-Ying Zhu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Li Yuan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jian Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Huilin Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Si-Qi Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhi-Wen Xiao
- Department of Otolaryngology-Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Guangzhou, China.,Department of Otorhinolaryngology-Head and Neck Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hong-Bo Wang
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Gaurab Roy
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qian Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dongxin Lin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yi-Xin Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jinkai Wang
- Key Laboratory of Stem Cells and Tissue Engineering (Sun Yat-sen University), Department of Medical Bioinformatics, Zhongshan School of Medicine, Ministry of Education, Guangzhou, China.,RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bo Zhao
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin E Gewurz
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Monrovia, CA, USA
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
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26
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Wang H, Zhao X, Lu Z. m 6A RNA Methylation Regulators Act as Potential Prognostic Biomarkers in Lung Adenocarcinoma. Front Genet 2021; 12:622233. [PMID: 33643384 PMCID: PMC7902930 DOI: 10.3389/fgene.2021.622233] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/15/2021] [Indexed: 12/16/2022] Open
Abstract
N6-methyladenosine [m(6)A/m6A] methylation is one of the most common RNA modifications in eukaryotic cell mRNA and plays an important regulatory role in mRNA metabolism, splicing, translocation, stability, and translation. Previous studies have demonstrated that the m6A modification is highly associated with tumor cell proliferation, migration, and invasion. In the present study, five m6A regulatory factors have been revealed, namely heterogeneous nuclear ribonucleoprotein A2/B1(HNRNPA2B1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), Vir like m6A methyltransferase associated protein (KIAA1429/VIRMA), RNA binding motif protein 15 (RBM15) and methyltransferase like 3 (METTL3), which are closely related to the overall survival (OS) of patients with lung adenocarcinoma (LUAD). These five m6A regulatory factors exhibited potential prognostic value for the 1, 3, and 5-years survival outcomes of LUAD patients. Our findings revealed that several signaling pathways, such as cell cycle, DNA replication, RNA degradation, RNA polymerase, nucleotide excision repair and basal transcription factors, are activated in the high-risk group of LUAD patients.
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Affiliation(s)
- Hongbo Wang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiangxuan Zhao
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zaiming Lu
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
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27
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Ruggieri A, Helm M, Chatel-Chaix L. An epigenetic 'extreme makeover': the methylation of flaviviral RNA (and beyond). RNA Biol 2021; 18:696-708. [PMID: 33356825 DOI: 10.1080/15476286.2020.1868150] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Beyond their high clinical relevance worldwide, flaviviruses (comprising dengue and Zika viruses) are of particular interest to understand the spatiotemporal control of RNA metabolism. Indeed, their positive single-stranded viral RNA genome (vRNA) undergoes in the cytoplasm replication, translation and encapsidation, three steps of the flavivirus life cycle that are coordinated through a fine-tuned equilibrium. Over the last years, RNA methylation has emerged as a powerful mechanism to regulate messenger RNA metabolism at the posttranscriptional level. Not surprisingly, flaviviruses exploit RNA epigenetic strategies to control crucial steps of their replication cycle as well as to evade sensing by the innate immune system. This review summarizes the current knowledge about vRNA methylation events and their impacts on flavivirus replication and pathogenesis. We also address the important challenges that the field of epitranscriptomics faces in reliably and accurately identifying RNA methylation sites, which should be considered in future studies on viral RNA modifications.
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Affiliation(s)
- Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Centre for Integrative Infectious Disease Research University of Heidelberg, Heidelberg, Germany
| | - Mark Helm
- Johannes Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Sciences, Mainz, Germany
| | - Laurent Chatel-Chaix
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
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28
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Bayoumi M, Munir M. Structural Insights Into m6A-Erasers: A Step Toward Understanding Molecule Specificity and Potential Antiviral Targeting. Front Cell Dev Biol 2021; 8:587108. [PMID: 33511112 PMCID: PMC7835257 DOI: 10.3389/fcell.2020.587108] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 11/26/2020] [Indexed: 12/13/2022] Open
Abstract
The cellular RNA can acquire a variety of chemical modifications during the cell cycle, and compelling pieces of evidence highlight the importance of these modifications in determining the metabolism of RNA and, subsequently, cell physiology. Among myriads of modifications, methylation at the N6-position of adenosine (m6A) is the most important and abundant internal modification in the messenger RNA. The m6A marks are installed by methyltransferase complex proteins (writers) in the majority of eukaryotes and dynamically reversed by demethylases such as FTO and ALKBH5 (erasers). The incorporated m6A marks on the RNA transcripts are recognized by m6A-binding proteins collectively called readers. Recent epigenetic studies have unequivocally highlighted the association of m6A demethylases with a range of biomedical aspects, including human diseases, cancers, and metabolic disorders. Moreover, the mechanisms of demethylation by m6A erasers represent a new frontier in the future basic research on RNA biology. In this review, we focused on recent advances describing various physiological, pathological, and viral regulatory roles of m6A erasers. Additionally, we aim to analyze structural insights into well-known m6A-demethylases in assessing their substrate binding-specificity, efficiency, and selectivity. Knowledge on cellular and viral RNA metabolism will shed light on m6A-specific recognition by demethylases and will provide foundations for the future development of efficacious therapeutic agents to various cancerous conditions and open new avenues for the development of antivirals.
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Affiliation(s)
- Mahmoud Bayoumi
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom.,Virology Department, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Muhammad Munir
- Division of Biomedical and Life Sciences, Lancaster University, Lancaster, United Kingdom
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29
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Liu XM, Zhou J. Multifaceted regulation of translation by the epitranscriptomic modification N 6-methyladenosine. Crit Rev Biochem Mol Biol 2021; 56:137-148. [PMID: 33412937 DOI: 10.1080/10409238.2020.1869174] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Translation occurring on cytoplasmic mRNA is precisely governed at three consecutive stages, including initiation, elongation and termination. A growing body of evidence has revealed that an emerging epitranscriptomic code N6-methyladenosine (m6A), asymmetrically present in a large subset of coding and non-coding transcripts, is crucially required for mediating the translatomic stability. Through recruiting translation machinery proteins, serving as a physical barrier, or directing RNA structural rearrangement and mRNA looping formation, m6A has been decoded to modulate translational dynamics through potentially influencing the progress of different stages, thereby forming an additional layer of complexity to the regulation of translation. In this review, we summarize the current understanding of how m6A guides mRNA translation under normal and stress conditions, highlighting the divergent molecular mechanisms of multifarious regulation of m6A-mediated translation.
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Affiliation(s)
- Xiao-Min Liu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Jun Zhou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China.,State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
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30
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Price AM, Hayer KE, McIntyre ABR, Gokhale NS, Abebe JS, Della Fera AN, Mason CE, Horner SM, Wilson AC, Depledge DP, Weitzman MD. Direct RNA sequencing reveals m 6A modifications on adenovirus RNA are necessary for efficient splicing. Nat Commun 2020; 11:6016. [PMID: 33243990 PMCID: PMC7691994 DOI: 10.1038/s41467-020-19787-6] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/09/2020] [Indexed: 12/20/2022] Open
Abstract
Adenovirus is a nuclear replicating DNA virus reliant on host RNA processing machinery. Processing and metabolism of cellular RNAs can be regulated by METTL3, which catalyzes the addition of N6-methyladenosine (m6A) to mRNAs. While m6A-modified adenoviral RNAs have been previously detected, the location and function of this mark within the infectious cycle is unknown. Since the complex adenovirus transcriptome includes overlapping spliced units that would impede accurate m6A mapping using short-read sequencing, here we profile m6A within the adenovirus transcriptome using a combination of meRIP-seq and direct RNA long-read sequencing to yield both nucleotide and transcript-resolved m6A detection. Although both early and late viral transcripts contain m6A, depletion of m6A writer METTL3 specifically impacts viral late transcripts by reducing their splicing efficiency. These data showcase a new technique for m6A discovery within individual transcripts at nucleotide resolution, and highlight the role of m6A in regulating splicing of a viral pathogen.
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Affiliation(s)
- Alexander M Price
- Division of Protective Immunity and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Katharina E Hayer
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Alexa B R McIntyre
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, 10065, USA
- Department of Molecular Life Sciences, University of Zurich, 8006, Zurich, Switzerland
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Immunology, University of Washington, Seattle, WA, 98115, USA
| | - Jonathan S Abebe
- Department of Medicine, New York University School of Medicine, New York, NY, 10017, USA
| | - Ashley N Della Fera
- Division of Protective Immunity and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Biological Sciences Graduate Group, University of Maryland, College Park, MD, 20742, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- The HRH Prince Alwaleed Bin Talal Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
- The World Quant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10065, USA
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Angus C Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY, 10017, USA
| | - Daniel P Depledge
- Department of Medicine, New York University School of Medicine, New York, NY, 10017, USA.
| | - Matthew D Weitzman
- Division of Protective Immunity and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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31
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Imam H, Kim GW, Siddiqui A. Epitranscriptomic(N6-methyladenosine) Modification of Viral RNA and Virus-Host Interactions. Front Cell Infect Microbiol 2020; 10:584283. [PMID: 33330128 PMCID: PMC7732492 DOI: 10.3389/fcimb.2020.584283] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/27/2020] [Indexed: 12/18/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent and internal modification of eukaryotic mRNA. Multiple m6A methylation sites have been identified in the viral RNA genome and transcripts of DNA viruses in recent years. m6A modification is involved in all the phases of RNA metabolism, including RNA stability, splicing, nuclear exporting, RNA folding, translational modulation, and RNA degradation. Three protein groups, methyltransferases (m6A-writers), demethylases (m6A-erasers), and m6A-binding proteins (m6A-readers) regulate this dynamic reversible process. Here, we have reviewed the role of m6A modification dictating viral replication, morphogenesis, life cycle, and its contribution to disease progression. A better understanding of the m6A methylation process during viral pathogenesis is required to reveal novel approaches to combat the virus-associated diseases.
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Affiliation(s)
- Hasan Imam
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Geon-Woo Kim
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Aleem Siddiqui
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA, United States
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32
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Abstract
Chemical modifications of viral RNA are an integral part of the viral life cycle and are present in most classes of viruses. To date, more than 170 RNA modifications have been discovered in all types of cellular RNA. Only a few, however, have been found in viral RNA, and the function of most of these has yet to be elucidated. Those few we have discovered and whose functions we understand have a varied effect on each virus. They facilitate RNA export from the nucleus, aid in viral protein synthesis, recruit host enzymes, and even interact with the host immune machinery. The most common methods for their study are mass spectrometry and antibody assays linked to next-generation sequencing. However, given that the actual amount of modified RNA can be very small, it is important to pair meticulous scientific methodology with the appropriate detection methods and to interpret the results with a grain of salt. Once discovered, RNA modifications enhance our understanding of viruses and present a potential target in combating them. This review provides a summary of the currently known chemical modifications of viral RNA, the effects they have on viral machinery, and the methods used to detect them.
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Affiliation(s)
- Jiří František Potužník
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Cahová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
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33
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Hoang HD, Neault S, Pelin A, Alain T. Emerging translation strategies during virus-host interaction. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1619. [PMID: 32757266 PMCID: PMC7435527 DOI: 10.1002/wrna.1619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 01/02/2023]
Abstract
Translation control is crucial during virus-host interaction. On one hand, viruses completely rely on the protein synthesis machinery of host cells to propagate and have evolved various mechanisms to redirect the host's ribosomes toward their viral mRNAs. On the other hand, the host rewires its translation program in an attempt to contain and suppress the virus early on during infection; the antiviral program includes specific control on protein synthesis to translate several antiviral mRNAs involved in quenching the infection. As the infection progresses, host translation is in turn inhibited in order to limit viral propagation. We have learnt of very diverse strategies that both parties utilize to gain or retain control over the protein synthesis machinery. Yet novel strategies continue to be discovered, attesting for the importance of mRNA translation in virus-host interaction. This review focuses on recently described translation strategies employed by both hosts and viruses. These discoveries provide additional pieces in the understanding of the complex virus-host translation landscape. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation.
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Affiliation(s)
- Huy-Dung Hoang
- Children's Hospital of Eastern Ontario Research Institute, Apoptosis Research Centre, Ottawa, Ontario, K1H8L1, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Serge Neault
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.,Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Adrian Pelin
- Centre for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Tommy Alain
- Children's Hospital of Eastern Ontario Research Institute, Apoptosis Research Centre, Ottawa, Ontario, K1H8L1, Canada.,Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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34
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Asada K, Bolatkan A, Takasawa K, Komatsu M, Kaneko S, Hamamoto R. Critical Roles of N6-Methyladenosine (m 6A) in Cancer and Virus Infection. Biomolecules 2020; 10:biom10071071. [PMID: 32709063 PMCID: PMC7408378 DOI: 10.3390/biom10071071] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/05/2020] [Accepted: 07/15/2020] [Indexed: 12/12/2022] Open
Abstract
Studies have shown that epigenetic abnormalities are involved in various diseases, including cancer. In particular, in order to realize precision medicine, the integrated analysis of genetics and epigenetics is considered to be important; detailed epigenetic analysis in the medical field has been becoming increasingly important. In the epigenetics analysis, DNA methylation and histone modification analyses have been actively studied for a long time, and many important findings were accumulated. On the other hand, recently, attention has also been focused on RNA modification in the field of epigenetics; now it is known that RNA modification is associated with various biological functions, such as regulation of gene expression. Among RNA modifications, functional analysis of N6-methyladenosine (m6A), the most abundant RNA modification found from humans to plants is actively progressing, and it has also been known that m6A abnormality is involved in cancer and other diseases. Importantly, recent studies have shown that m6A is related to viral infections. Considering the current world situation under threat of viral infections, it is important to deepen knowledge of RNA modification from the viewpoint of viral diseases. Hence, in this review, we have summarized the recent findings regarding the roles of RNA modifications in biological functions, cancer biology, and virus infection, particularly focusing on m6A in mRNA.
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Affiliation(s)
- Ken Asada
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
- Correspondence: (K.A.); (R.H.); Tel.: +81-3-3547-5271 (R.H.)
| | - Amina Bolatkan
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Ken Takasawa
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Masaaki Komatsu
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Syuzo Kaneko
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
| | - Ryuji Hamamoto
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; (A.B.); (K.T.); (M.K.)
- Division of Molecular Modification and Cancer Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan;
- Correspondence: (K.A.); (R.H.); Tel.: +81-3-3547-5271 (R.H.)
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Shi H, Chai P, Jia R, Fan X. Novel insight into the regulatory roles of diverse RNA modifications: Re-defining the bridge between transcription and translation. Mol Cancer 2020; 19:78. [PMID: 32303268 PMCID: PMC7164178 DOI: 10.1186/s12943-020-01194-6] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/27/2020] [Indexed: 12/31/2022] Open
Abstract
RNA modifications can be added or removed by a variety of enzymes that catalyse the necessary reactions, and these modifications play roles in essential molecular mechanisms. The prevalent modifications on mRNA include N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), 5-hydroxymethylcytosine (hm5C), pseudouridine (Ψ), inosine (I), uridine (U) and ribosemethylation (2’-O-Me). Most of these modifications contribute to pre-mRNA splicing, nuclear export, transcript stability and translation initiation in eukaryotic cells. By participating in various physiological processes, RNA modifications also have regulatory roles in the pathogenesis of tumour and non-tumour diseases. We discussed the physiological roles of RNA modifications and associated these roles with disease pathogenesis. Functioning as the bridge between transcription and translation, RNA modifications are vital for the progression of numerous diseases and can even regulate the fate of cancer cells.
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Affiliation(s)
- Hanhan Shi
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P.R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China
| | - Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P.R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P.R. China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China.
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P.R. China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China.
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36
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Multiple m 6A RNA methylation modulators promote the malignant progression of hepatocellular carcinoma and affect its clinical prognosis. BMC Cancer 2020; 20:165. [PMID: 32111180 PMCID: PMC7047390 DOI: 10.1186/s12885-020-6638-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/17/2020] [Indexed: 12/13/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the second most common cause of cancer-related death in the world. N6-methyladenosine (m6A) RNA methylation is dynamically regulated by m6A RNA methylation modulators (“writer,” “eraser,” and “reader” proteins), which are associated with cancer occurrence and development. The purpose of this study was to explore the relationships between m6A RNA methylation modulators and HCC. Methods First, using data from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases, we compared the expression levels of 13 major m6A RNA methylation modulators between HCC and normal tissues. Second, we applied consensus clustering to the expression data on the m6A RNA methylation modulators to divide the HCC tissues into two subgroups (clusters 1 and 2), and we compared the clusters in terms of overall survival (OS), World Health Organization (WHO) stage, and pathological grade. Third, using least absolute shrinkage and selection operator (LASSO) regression, we constructed a risk signature involving the m6A RNA methylation modulators that affected OS in TCGA and ICGC analyses. Results We found that the expression levels of 12 major m6A RNA methylation modulators were significantly different between HCC and normal tissues. After dividing the HCC tissues into clusters 1 and 2, we found that cluster 2 had poorer OS, higher WHO stage, and higher pathological grade. Four m6A RNA methylation modulators (YTHDF1, YTHDF2, METTL3, and KIAA1429) affecting OS in the TCGA and ICGC analyses were selected to construct a risk signature, which was significantly associated with WHO stage and was also an independent prognostic marker of OS. Conclusions In summary, m6A RNA methylation modulators are key participants in the malignant progression of HCC and have potential value in prognostication and treatment decisions.
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37
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Chen M, Wong CM. The emerging roles of N6-methyladenosine (m6A) deregulation in liver carcinogenesis. Mol Cancer 2020; 19:44. [PMID: 32111216 PMCID: PMC7047367 DOI: 10.1186/s12943-020-01172-y] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is a common cancer worldwide. Although the etiological factors of liver carcinogenesis are well defined, the underlying molecular mechanisms remain largely elusive. Epigenetic deregulations, such as aberrant DNA methylation and histone modifications, play a critical role in liver carcinogenesis. Analogous to DNA and core histone proteins, reversible chemical modifications on mRNA have recently been recognized as important regulatory mechanisms to control gene expression. N6-methyladenosine (m6A) is the most prevalent internal mRNA modification in mammalian cells. m6A modification is important for controlling many cellular and biological processes. Deregulation of m6A modification has been recently implicated in human carcinogenesis, including liver cancer. In this review, we summarize the recent findings on m6A regulation and its biological impacts in normal and cancer cells. We will focus on the deregulation of m6A modification and m6A regulators in liver diseases and liver cancers. We will highlight the clinical relevance of m6A deregulation in liver cancer. We will also discuss the potential of exploiting m6A modification for cancer diagnosis and therapeutics.
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Affiliation(s)
- Mengnuo Chen
- State Key Laboratory of Liver Research, the University of Hong Kong, Hong Kong, China
| | - Chun-Ming Wong
- Department of Pathology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong, China.
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38
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Oncogenic Role of an Epigenetic Reader of m 6A RNA Modification: YTHDF1 in Merkel Cell Carcinoma. Cancers (Basel) 2020; 12:cancers12010202. [PMID: 31947544 PMCID: PMC7016651 DOI: 10.3390/cancers12010202] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/05/2020] [Accepted: 01/10/2020] [Indexed: 12/14/2022] Open
Abstract
Merkel cell carcinoma is a deadly skin cancer, which in the majority of cases is caused by the Merkel cell polyomavirus (MCPyV). The viral small T antigen is regarded as the dominant oncoprotein expressed in the tumor cells. We used genomic screening of copy number aberrations along with transcriptomic analysis to investigate regions with amplification that harbor differentially expressed genes. We identified YTHDF1, a protein that is a reader of N6-methyladenosine (m6A) RNA modifications, to have high copy gains and to be highly expressed in Merkel cell carcinoma. Importantly, we identified the presence of m6A on small T antigen mRNA suggesting a relation between YTHDF1 amplification and MCPyV gene expression. Interestingly, knockdown of YTHDF1 in Merkel cell carcinoma (MCC) cell lines negatively affected the translation initiation factor eIF3 and reduced proliferation and clonogenic capacity in vitro. Furthermore, analysis of survival data revealed worse overall survival in YTHDF1high MCC patients compared to YTHDF1low patients. Our findings indicate a novel oncogenic role of YTHDF1 through m6A machinery in the tumorigenesis of MCC.
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39
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Sherpa C, Grice SFJL. Structural Fluidity of the Human Immunodeficiency Virus Rev Response Element. Viruses 2020; 12:v12010086. [PMID: 31940828 PMCID: PMC7019801 DOI: 10.3390/v12010086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 01/22/2023] Open
Abstract
Nucleocytoplasmic transport of unspliced and partially spliced human immunodeficiency virus (HIV) RNA is mediated in part by the Rev response element (RRE), a ~350 nt cis-acting element located in the envelope coding region of the viral genome. Understanding the interaction of the RRE with the viral Rev protein, cellular co-factors, and its therapeutic potential has been the subject of almost three decades of structural studies, throughout which a recurring discussion theme has been RRE topology, i.e., whether it comprises 4 or 5 stem-loops (SLs) and whether this has biological significance. Moreover, while in vitro mutagenesis allows the construction of 4 SL and 5 SL RRE conformers and testing of their roles in cell culture, it has not been immediately clear if such findings can be translated to a clinical setting. Herein, we review several articles demonstrating remarkable flexibility of the HIV-1 and HIV-2 RREs following initial observations that HIV-1 resistance to trans-dominant Rev therapy was founded in structural rearrangement of its RRE. These observations can be extended not only to cell culture studies demonstrating a growth advantage for the 5 SL RRE conformer but also to evolution in RRE topology in patient isolates. Finally, RRE conformational flexibility provides a target for therapeutic intervention, and we describe high throughput screening approaches to exploit this property.
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40
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Wu F, Cheng W, Zhao F, Tang M, Diao Y, Xu R. Association of N6-methyladenosine with viruses and related diseases. Virol J 2019; 16:133. [PMID: 31711514 PMCID: PMC6849232 DOI: 10.1186/s12985-019-1236-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/03/2019] [Indexed: 02/07/2023] Open
Abstract
Background N6-methyladenosine (m6A) modification is the most prevalent internal modification of eukaryotic mRNA modulating gene expression. m6A modification is a dynamic reversible process regulated by three protein groups: methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers). m6A modification is involved in all phases of RNA metabolism, including RNA folding, stability, splicing, nuclear exporting, translational modulation and degradation. Main body In recent years, numerous studies have reported that abnormal m6A modification causes aberrant expression of important viral genes. Herein, we review the role of m6A in viral lifecycle and its contribution to the pathogenesis of human diseases. Particularly, we focus on the viruses associated with human diseases such as HIV-1, IAV, HBV, HCV, EBV and many others. Conclusions A better understanding of m6A-virus relationship would provide new insights into the viral replication process and pathogenesis of human diseases caused by viruses. In addition, exploration of the role of m6A in disease-causing viruses will reveal novel approaches for the treatment of such diseases.
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Affiliation(s)
- Fang Wu
- Engineering Research Center of Molecular Medicine, Ministry of Education, Huaqiao University, Xiamen, China.,School of Medicine, Huaqiao University, Xiamen, China
| | - Wenzhao Cheng
- Engineering Research Center of Molecular Medicine, Ministry of Education, Huaqiao University, Xiamen, China. .,Stem Cell Laboratory, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China.
| | - Feiyuan Zhao
- Engineering Research Center of Molecular Medicine, Ministry of Education, Huaqiao University, Xiamen, China.,School of Medicine, Huaqiao University, Xiamen, China
| | - Mingqing Tang
- Engineering Research Center of Molecular Medicine, Ministry of Education, Huaqiao University, Xiamen, China.,School of Medicine, Huaqiao University, Xiamen, China.,Fujian Provincial Key Laboratory of Molecular Medicine & Fujian Provincial Key Laboratory of Precision Medicine and Molecular Detection in Universities, Xiamen, China
| | - Yong Diao
- School of Medicine, Huaqiao University, Xiamen, China
| | - Ruian Xu
- Engineering Research Center of Molecular Medicine, Ministry of Education, Huaqiao University, Xiamen, China. .,School of Medicine, Huaqiao University, Xiamen, China. .,Fujian Provincial Key Laboratory of Molecular Medicine & Fujian Provincial Key Laboratory of Precision Medicine and Molecular Detection in Universities, Xiamen, China.
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41
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Netzband R, Pager CT. Epitranscriptomic marks: Emerging modulators of RNA virus gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1576. [PMID: 31694072 PMCID: PMC7169815 DOI: 10.1002/wrna.1576] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/27/2022]
Abstract
Epitranscriptomics, the study of posttranscriptional chemical moieties placed on RNA, has blossomed in recent years. This is due in part to the emergence of high‐throughput detection methods as well as the burst of discoveries showing biological function of select chemical marks. RNA modifications have been shown to affect RNA structure, localization, and functions such as alternative splicing, stabilizing transcripts, nuclear export, cap‐dependent and cap‐independent translation, microRNA biogenesis and binding, RNA degradation, and immune regulation. As such, the deposition of chemical marks on RNA has the unique capability to spatially and temporally regulate gene expression. The goal of this article is to present the exciting convergence of the epitranscriptomic and virology fields, specifically the deposition and biological impact of N7‐methylguanosine, ribose 2′‐O‐methylation, pseudouridine, inosine, N6‐methyladenosine, and 5‐methylcytosine epitranscriptomic marks on gene expression of RNA viruses. This article is categorized under:RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
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Affiliation(s)
- Rachel Netzband
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, New York
| | - Cara T Pager
- Department of Biological Sciences, The RNA Institute, University at Albany-SUNY, Albany, New York
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Xue M, Zhao BS, Zhang Z, Lu M, Harder O, Chen P, Lu Z, Li A, Ma Y, Xu Y, Liang X, Zhou J, Niewiesk S, Peeples ME, He C, Li J. Viral N 6-methyladenosine upregulates replication and pathogenesis of human respiratory syncytial virus. Nat Commun 2019; 10:4595. [PMID: 31597913 PMCID: PMC6785563 DOI: 10.1038/s41467-019-12504-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/11/2019] [Indexed: 12/02/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification of mRNAs in most eukaryotes. Here we show that RNAs of human respiratory syncytial virus (RSV) are modified by m6A within discreet regions and that these modifications enhance viral replication and pathogenesis. Knockdown of m6A methyltransferases decreases RSV replication and gene expression whereas knockdown of m6A demethylases has the opposite effect. The G gene transcript contains the most m6A modifications. Recombinant RSV variants expressing G transcripts that lack particular clusters of m6A display reduced replication in A549 cells, primary well differentiated human airway epithelial cultures, and respiratory tracts of cotton rats. One of the m6A-deficient variants is highly attenuated yet retains high immunogenicity in cotton rats. Collectively, our results demonstrate that viral m6A methylation upregulates RSV replication and pathogenesis and identify viral m6A methylation as a target for rational design of live attenuated vaccine candidates for RSV and perhaps other pneumoviruses.
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Affiliation(s)
- Miaoge Xue
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Boxuan Simen Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Zijie Zhang
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Mijia Lu
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Olivia Harder
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Phylip Chen
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Zhike Lu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
| | - Anzhong Li
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Yuanmei Ma
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Yunsheng Xu
- Institute of Translational Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325015, Zhejiang, P.R. China
| | - Xueya Liang
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Jiyong Zhou
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, P. R. China
| | - Stefan Niewiesk
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Mark E Peeples
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, 60637, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Jianrong Li
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, 43210, USA.
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43
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Chen Y, Peng C, Chen J, Chen D, Yang B, He B, Hu W, Zhang Y, Liu H, Dai L, Xie H, Zhou L, Wu J, Zheng S. WTAP facilitates progression of hepatocellular carcinoma via m6A-HuR-dependent epigenetic silencing of ETS1. Mol Cancer 2019; 18:127. [PMID: 31438961 PMCID: PMC6704583 DOI: 10.1186/s12943-019-1053-8] [Citation(s) in RCA: 383] [Impact Index Per Article: 76.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 08/14/2019] [Indexed: 02/08/2023] Open
Abstract
Background N6-methyladenosine (m6A) methylation, a well-known modification with new epigenetic functions, has been reported to participate in the tumorigenesis of hepatocellular carcinoma (HCC), providing novel insights into the molecular pathogenesis of this disease. However, as the key component of m6A methylation, Wilms tumor 1-associated protein (WTAP) has not been well studied in HCC. Here we investigated the biological role and underlying mechanism of WTAP in liver cancer. Methods We determined the expression of WTAP and its correlation with clinicopathological features using tissue microarrays and the Cancer Genome Atlas (TCGA) dataset. And we clarified the effects of WTAP on HCC cells using cell proliferation assay, colony formation, Edu assay and subcutaneous xenograft experiments. We then applied RNA sequencing combined with gene expression omnibus (GEO) data to screen candidate targets of WTAP. Finally, we investigated the regulatory mechanism of WTAP in HCC by m6A dot blot assay, methylated RNA immunoprecipitation (MeRIP) assay, dual luciferase reporter assay, RNA immunoprecipitation (RIP) assay and Chromatin immunoprecipitation (ChIP) assay. Results We demonstrated that WTAP was highly expressed in HCC which indicated the poor prognosis, and that WTAP expression served as an independent predictor of HCC survival. Functionally, WTAP promoted the proliferation capability and tumor growth of HCC cells in vitro and in vivo. Furthermore, ETS proto-oncogene 1 (ETS1) was identified as the downstream effector of WTAP. The m6A modification regulated by WTAP led to post-transcriptional suppression of ETS1, with the implication of Hu-Antigen R (HuR) as an RNA stabilizer. Then ETS1 was found to inhibit the progression of HCC and could rescue the phenotype induced by WTAP deficiency. Moreover, WTAP modulated the G2/M phase of HCC cells through a p21/p27-dependent pattern mediated by ETS1. Conclusion We have identified that WTAP is significantly up-regulated in HCC and promotes liver cancer development. WTAP-guided m6A modification contributes to the progression of HCC via the HuR-ETS1-p21/p27 axis. Our study is the first to report that WTAP-mediated m6A methylation has a crucial role in HCC oncogenesis, and highlights WTAP as a potential therapeutic target of HCC treatment. Electronic supplementary material The online version of this article (10.1186/s12943-019-1053-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunhao Chen
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China
| | - Chuanhui Peng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China
| | - Junru Chen
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Diyu Chen
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Beng Yang
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Bin He
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Wendi Hu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Yanpeng Zhang
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Hua Liu
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Longfei Dai
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China
| | - Haiyang Xie
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China
| | - Lin Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China.,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China.,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China
| | - Jian Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China. .,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China. .,Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Hangzhou, China. .,Key Laboratory of Organ Transplantation, Hangzhou, Zhejiang Province, China. .,Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, CAMS, Hangzhou, China.
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McIntyre W, Netzband R, Bonenfant G, Biegel JM, Miller C, Fuchs G, Henderson E, Arra M, Canki M, Fabris D, Pager CT. Positive-sense RNA viruses reveal the complexity and dynamics of the cellular and viral epitranscriptomes during infection. Nucleic Acids Res 2019; 46:5776-5791. [PMID: 29373715 PMCID: PMC6009648 DOI: 10.1093/nar/gky029] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/15/2018] [Indexed: 12/26/2022] Open
Abstract
More than 140 post-transcriptional modifications (PTMs) are known to decorate cellular RNAs, but their incidence, identity and significance in viral RNA are still largely unknown. We have developed an agnostic analytical approach to comprehensively survey PTMs on viral and cellular RNAs. Specifically, we used mass spectrometry to analyze PTMs on total RNA isolated from cells infected with Zika virus, Dengue virus, hepatitis C virus (HCV), poliovirus and human immunodeficiency virus type 1. All five RNA viruses significantly altered global PTM landscapes. Examination of PTM profiles of individual viral genomes isolated by affinity capture revealed a plethora of PTMs on viral RNAs, which far exceeds the handful of well-characterized modifications. Direct comparison of viral epitranscriptomes identified common and virus-specific PTMs. In particular, specific dimethylcytosine modifications were only present in total RNA from virus-infected cells, and in intracellular HCV RNA, and viral RNA from Zika and HCV virions. Moreover, dimethylcytosine abundance during viral infection was modulated by the cellular DEAD-box RNA helicase DDX6. By opening the Pandora's box on viral PTMs, this report presents numerous questions and hypotheses on PTM function and strongly supports PTMs as a new tier of regulation by which RNA viruses subvert the host and evade cellular surveillance systems.
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Affiliation(s)
- Will McIntyre
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Rachel Netzband
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Gaston Bonenfant
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Jason M Biegel
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Clare Miller
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Gabriele Fuchs
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Eric Henderson
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Manoj Arra
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208, USA
| | - Mario Canki
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY 12208, USA
| | - Daniele Fabris
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
| | - Cara T Pager
- The RNA Institute, University at Albany-SUNY, Albany, NY 12222, USA
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45
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Williams GD, Gokhale NS, Horner SM. Regulation of Viral Infection by the RNA Modification N6-Methyladenosine. Annu Rev Virol 2019; 6:235-253. [PMID: 31283446 DOI: 10.1146/annurev-virology-092818-015559] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In recent years, the RNA modification N6-methyladenosine (m6A) has been found to play a role in the life cycles of numerous viruses and also in the cellular response to viral infection. m6A has emerged as a regulator of many fundamental aspects of RNA biology. Here, we highlight recent advances in techniques for the study of m6A, as well as advances in our understanding of the cellular machinery that controls the addition, removal, recognition, and functions of m6A. We then summarize the many newly discovered roles of m6A during viral infection, including how it regulates innate and adaptive immune responses to infection. Overall, the goals of this review are to summarize the roles of m6A on both cellular and viral RNAs and to describe future directions for uncovering new functions of m6A during infection.
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Affiliation(s)
- Graham D Williams
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA; , ,
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA; , ,
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA; , , .,Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA
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46
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Ianniello Z, Paiardini A, Fatica A. N 6-Methyladenosine (m 6A): A Promising New Molecular Target in Acute Myeloid Leukemia. Front Oncol 2019; 9:251. [PMID: 31024852 PMCID: PMC6465620 DOI: 10.3389/fonc.2019.00251] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/19/2019] [Indexed: 12/25/2022] Open
Abstract
Recent studies have uncovered an important role for RNA modifications in gene expression regulation, which led to the birth of the epitranscriptomics field. It is now acknowledged that RNA modifiers play a crucial role in the control of differentiation of stem and progenitor cells and that changes in their levels are a relevant feature of different types of cancer. To date, among more than 160 different RNA chemical modifications, the more relevant in cancer biology is the reversible and dynamic N6-methylation of adenosine, yielding N6-methyladenosine (m6A). m6A is the more abundant internal modification in mRNA, regulating the expression of the latter at different levels, from maturation to translation. Here, we will describe the emerging role of m6A modification in acute myeloid leukemia (AML), which, among first, has demonstrated how mis-regulation of the m6A modifying system can contribute to the development and progression of cancer. Moreover, we will discuss how AML is paving the way to the development of new therapeutic options based on the inhibition of m6A deposition.
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Affiliation(s)
- Zaira Ianniello
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome, Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
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47
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Dang W, Xie Y, Cao P, Xin S, Wang J, Li S, Li Y, Lu J. N 6-Methyladenosine and Viral Infection. Front Microbiol 2019; 10:417. [PMID: 30891023 PMCID: PMC6413633 DOI: 10.3389/fmicb.2019.00417] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/18/2019] [Indexed: 12/12/2022] Open
Abstract
N6-methyladenosine (m6A), as a dynamic posttranscriptional RNA modification, recently gave rise to the field of viral epitranscriptomics. The interaction between virus and host is affected by m6A. Multiple m6A-modified viral RNAs have been observed. The epitranscriptome of m6A in host cells are altered after viral infection. The expression of viral genes, the replication of virus and the generation of progeny virions are influenced by m6A modifications in viral RNAs during virus infection. Meanwhile, the decorations of m6A in host mRNAs can make viral infections more likely to happen or can enhance the resistance of host to virus infection. However, the mechanism of m6A regulation in viral infection and host immune response has not been thoroughly elucidated to date. With the development of sequencing-based biotechnologies, transcriptome-wide mapping of m6A in viruses has been achieved, laying the foundation for expanding its functions and corresponding mechanisms. In this report, we summarize the positive and negative effects of m6A in distinct viral infection. Given the increasingly important roles of m6A in diverse viruses, m6A represents a novel potential target for antiviral therapy.
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Affiliation(s)
- Wei Dang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Yan Xie
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Pengfei Cao
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China
| | - Shuyu Xin
- Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Jia Wang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Shen Li
- Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Yanling Li
- Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
| | - Jianhong Lu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
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48
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Manners O, Baquero-Perez B, Whitehouse A. m 6A: Widespread regulatory control in virus replication. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:370-381. [PMID: 30412798 PMCID: PMC6414752 DOI: 10.1016/j.bbagrm.2018.10.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/25/2018] [Accepted: 10/30/2018] [Indexed: 12/20/2022]
Abstract
N6-methyladenosine (m6A) is a highly pervasive and dynamic modification found on eukaryotic RNA. Despite the failure to comprehend the true regulatory potential of this epitranscriptomic mark for decades, our knowledge of m6A has rapidly expanded in recent years. The modification has now been functionally linked to all stages of mRNA metabolism and demonstrated to regulate a variety of biological processes. Furthermore, m6A has been identified on transcripts encoded by a wide range of viruses. Studies to investigate m6A function in viral-host interactions have highlighted distinct roles indicating widespread regulatory control over viral life cycles. As a result, unveiling the true influence of m6A modification could revolutionise our comprehension of the regulatory mechanisms controlling viral replication. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.
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Affiliation(s)
- Oliver Manners
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Belinda Baquero-Perez
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom; Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
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49
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Sun T, Wu R, Ming L. The role of m6A RNA methylation in cancer. Biomed Pharmacother 2019; 112:108613. [PMID: 30784918 DOI: 10.1016/j.biopha.2019.108613] [Citation(s) in RCA: 503] [Impact Index Per Article: 100.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/09/2023] Open
Abstract
N6-methyladenosine (m6A), the most abundant internal modification of RNA in eukaryotic cells, has gained increasing attention in recent years. The m6A modification affects multiple aspects of RNA metabolism, ranging from RNA processing, nuclear export, RNA translation to decay. Emerging evidence suggests that m6A methylation plays a critical role in cancer through various mechanisms. Moreover, m6A methylation has provided more possibilities for the early diagnosis and treatment of cancers. In this review, we focus on m6A-associated mechanisms and functions in several major malignancies and summarize the dual role of m6A methylation as well as its prospects in cancer.
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Affiliation(s)
- Ting Sun
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| | - Ruiyan Wu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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50
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Yang J, Wang H, Zhang W. Regulation of Virus Replication and T Cell Homeostasis by N 6-Methyladenosine. Virol Sin 2019; 34:22-29. [PMID: 30671921 DOI: 10.1007/s12250-018-0075-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 11/26/2018] [Indexed: 01/04/2023] Open
Abstract
RNA modifications are abundant in eukaryotes, bacteria, and archaea. N6-methyladenosine (m6A), a type of RNA modification mainly found in messenger RNA (mRNA), has significant effects on the metabolism and function of mRNAs. This modification is governed by three types of proteins, namely methyltransferases as "writers", demethylases as "erasers", and specific m6A-binding proteins (YTHDF1-3) as "readers". Further, it is important for the regulation of cell fate and has a critical function in many biological processes including virus replication, stem cell differentiation, and cancer development, and exerts its effect by controlling gene expression. Herein, we summarize recent advances in research on m6A in virus replication and T cell regulation, which is a rapidly emerging field that will facilitate the development of antiviral therapies and the study of innate immunity.
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Affiliation(s)
- Jing Yang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, China
| | - Hong Wang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, China.
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, 130021, China.
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