1
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Chen Z, Yang J, Zhang W, Qian Y, Zhang N, Chen Z, Lu M, Ge L, Liu C, Tian X, Jia G, Ma L, Li B. Understanding m6A changes in chromophobe renal cell carcinoma and predicting patient outcomes survival. BMC Cancer 2024; 24:1187. [PMID: 39334021 PMCID: PMC11438101 DOI: 10.1186/s12885-024-12956-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 09/17/2024] [Indexed: 09/30/2024] Open
Abstract
N6-methyladenosine (m6A) is a prevalent mRNA modification known for its implications in various cancer types, yet its role in chromophobe renal cell carcinoma (chRCC) remains largely unexplored. In this study, we performed m6A-SEAL-seq and RNA-seq analyses on tissues from three chRCC subjects, aiming to uncover m6A alterations in chRCC. Our findings revealed reduced expression levels of four m6A regulators in chRCC tissues and highlighted differences in m6A levels compared to normal tissues. Furthermore, we identified specific genes and cancer-related pathways affected by these differences, including notable candidates like NOTCH1 and FGFR1, implicated in chRCC development. Additionally, we developed a predictive model based on the expression level of m6A associated genes, demonstrating promising prognostic capabilities for patient survival prediction. Overall, our study provides valuable insights into the role of m6A in chRCC and its potential as a prognostic indicator.
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Affiliation(s)
- Zhigang Chen
- Department of Urology, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, 100080, China
| | - Junbo Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Wei Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yang Qian
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Nan Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Zixin Chen
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Min Lu
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
- Department of Pathology, Peking University Third Hospital, Beijing, 100191, China
| | - Liyuan Ge
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Cheng Liu
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Xiaojun Tian
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
| | - Lulin Ma
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China.
| | - Baoguo Li
- Department of Urology, Beijing Haidian Hospital (Haidian Section of Peking University Third Hospital), Beijing, 100080, China.
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2
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Zhu M, Huang F, Sun H, Liu K, Chen Z, Yu B, Hao H, Liu H, Ding S, Zhang X, Liu L, Zhang K, Ren J, Liu Y, Liu H, Shan C, Guan W. Characterization of ACTN4 as a novel antiviral target against SARS-CoV-2. Signal Transduct Target Ther 2024; 9:243. [PMID: 39289355 PMCID: PMC11408661 DOI: 10.1038/s41392-024-01956-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 08/13/2024] [Accepted: 08/27/2024] [Indexed: 09/19/2024] Open
Abstract
The various mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pose a substantial challenge in mitigating the viral infectivity. The identification of novel host factors influencing SARS-CoV-2 replication holds potential for discovering new targets for broad-spectrum antiviral drugs that can combat future viral mutations. In this study, potential host factors regulated by SARS-CoV-2 infection were screened through different high-throughput sequencing techniques and further identified in cells. Subsequent analysis and experiments showed that the reduction of m6A modification level on ACTN4 (Alpha-actinin-4) mRNA leads to a decrease in mRNA stability and translation efficiency, ultimately inhibiting ACTN4 expression. In addition, ACTN4 was demonstrated to target nsp12 for binding and characterized as a competitor for SARS-CoV-2 RNA and the RNA-dependent RNA polymerase complex, thereby impeding viral replication. Furthermore, two ACTN4 agonists, YS-49 and demethyl-coclaurine, were found to dose-dependently inhibit SARS-CoV-2 infection in both Huh7 cells and K18-hACE2 transgenic mice. Collectively, this study unveils the pivotal role of ACTN4 in SARS-CoV-2 infection, offering novel insights into the intricate interplay between the virus and host cells, and reveals two potential candidates for future anti-SARS-CoV-2 drug development.
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Affiliation(s)
- Miao Zhu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Huang
- Hubei Jiangxia Laboratory, Wuhan, Hubei, 430200, China
| | - Huize Sun
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kunpeng Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Chen
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Baocheng Yu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haojie Hao
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Haizhou Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Shuang Ding
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Xueyan Zhang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
| | - Lishi Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kui Zhang
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jierao Ren
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yi Liu
- Hubei Jiangxia Laboratory, Wuhan, Hubei, 430200, China
| | - Haibin Liu
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- Hubei Jiangxia Laboratory, Wuhan, Hubei, 430200, China
| | - Chao Shan
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China
- Hubei Jiangxia Laboratory, Wuhan, Hubei, 430200, China
| | - Wuxiang Guan
- Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, China.
- Hubei Jiangxia Laboratory, Wuhan, Hubei, 430200, China.
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3
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Liu ZY, You QY, Liu ZY, Lin LC, Yang JJ, Tao H. m6A control programmed cell death in cardiac fibrosis. Life Sci 2024; 353:122922. [PMID: 39032691 DOI: 10.1016/j.lfs.2024.122922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/29/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
N6-methyladenosine (m6A) modification is closely related to cardiac fibrosis. As the most common and abundant form of mRNA modification in eukaryotes, m6A is deposited by methylases ("writers"), recognized and effected by RNA-binding proteins ("readers"), and removed by demethylases ("erasers"), achieving highly dynamic reversibility. m6A modification is involved in regulating the entire biological process of target RNA, including transcription, processing and splicing, export from the nucleus to the cytoplasm, and enhancement or reduction of stability and translation. Programmed cell death (PCD) comprises many forms and pathways, with apoptosis and autophagy being the most common. Other forms include pyroptosis, ferroptosis, necroptosis, mitochondrial permeability transition (MPT)-dependent necrosis, and parthanatos. In recent years, increasing evidence suggests that m6A modification can mediate PCD, affecting cardiac fibrosis. Since the correlation between some PCD types and m6A modification is not yet clear, this article mainly introduces the relationship between four common PCD types (apoptosis, autophagy, pyroptosis, and ferroptosis) and m6A modification, as well as their role and influence in cardiac fibrosis.
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Affiliation(s)
- Zhen-Yu Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Qing-Ye You
- Anhui Women and Children's Medical Center, Hefei 230001, PR China
| | - Zhi-Yan Liu
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Li-Chan Lin
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China
| | - Jing-Jing Yang
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China.
| | - Hui Tao
- Department of Anesthesiology and Perioperative Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China; Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, PR China.
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4
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Zhu C, Cheng Y, Yu Y, Zhang Y, Ren G. VIRMA promotes the progression of head and neck squamous cell carcinoma by regulating UBR5 mRNA and m6A levels. BIOMOLECULES & BIOMEDICINE 2024; 24:1244-1257. [PMID: 38577917 PMCID: PMC11379021 DOI: 10.17305/bb.2024.10358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/23/2024] [Accepted: 03/23/2024] [Indexed: 04/06/2024]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a globally prevalent and lethal cancer form which precise mechanisms remain incompletely understood. Increasing evidence suggests that N6-methyladenosine (m6A) plays a crucial role in cancer progression. This study aimed to explore the biological function of m6A modification and vir-like m6A methyltransferase associated (VIRMA) in HNSCC. We conducted an analysis of VIRMA expression in HNSCC cells using The Cancer Genome Atlas (TCGA) database and employed reverse transcription quantitative polymerase chain reaction (RT-qPCR) and western blotting to assess its expression levels in HNSCC cell lines. Additionally, m6A levels in HNSCC cells were quantified, and the correlation between VIRMA expression levels and the clinical and pathological features of other genes was analyzed. Upon knocking down VIRMA levels, we assessed HNSCC cell proliferation, migration, and invasion and validated downstream genes using RT-qPCR and western blot. Our findings suggested that VIRMA, as an m6A-related regulator, may significantly influence HNSCC progression by regulating ubiquitin protein ligase E3 component N-recognin 5 (UBR5) through m6A modification. Therefore, VIRMA may serve as a prognostic biomarker.
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Affiliation(s)
- Chunyu Zhu
- Department of Oral and Maxillofacial Surgery, School of Stomatology and Stomatological Hospital, Hebei Medical University, Shijiazhuang, China
| | - Yameng Cheng
- The Key Laboratory of Oral Medicine in Hebei Province, School of Stomatology and Stomatological Hospital, Hebei Medical University, Shijiazhuang, China
| | - Yao Yu
- Hebei Provincial Clinical Research Center for Oral Diseases, Shijiazhuang, China
| | - Yanning Zhang
- The Key Laboratory of Oral Medicine in Hebei Province, School of Stomatology and Stomatological Hospital, Hebei Medical University, Shijiazhuang, China
| | - Guiyun Ren
- Department of Oral and Maxillofacial Surgery, School of Stomatology and Stomatological Hospital, Hebei Medical University, Shijiazhuang, China
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5
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Deng T, Ma J. Structures and mechanisms of the RNA m 6A writer. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 39238441 DOI: 10.3724/abbs.2024152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024] Open
Abstract
N 6-methyladenosine (m 6A) is the most prevalent epigenetic modification found in eukaryotic mRNAs and plays a crucial role in regulating gene expression by influencing numerous aspects of mRNA metabolism. The m 6A writer for mRNAs and long non-coding RNAs consists of the catalytic subunit m 6A-METTL complex (MTC) (including METTL3/METTL14) and the regulatory subunit m 6A-METTL-associated complex (MACOM) (including HAKAI, WTAP, VIRMA, ZC3H13, and RBM15/15B). In this review, we focus on recent advances in our understanding of the structural and functional properties of m 6A writers and the possible mechanism by which they recognize RNA substrates and perform selective m 6A modifications.
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6
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Xu GE, Zhao X, Li G, Gokulnath P, Wang L, Xiao J. The landscape of epigenetic regulation and therapeutic application of N 6-methyladenosine modifications in non-coding RNAs. Genes Dis 2024; 11:101045. [PMID: 38988321 PMCID: PMC11233902 DOI: 10.1016/j.gendis.2023.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/18/2023] [Accepted: 06/04/2023] [Indexed: 07/12/2024] Open
Abstract
RNA N6-methyladenosine (m6A) methylation is the most abundant and conserved RNA modification in eukaryotes. It participates in the regulation of RNA metabolism and various pathophysiological processes. Non-coding RNAs (ncRNAs) are defined as small or long transcripts which do not encode proteins and display numerous biological regulatory functions. Similar to mRNAs, m6A deposition is observed in ncRNAs. Studying RNA m6A modifications on ncRNAs is of great importance specifically to deepen our understanding of their biological roles and clinical implications. In this review, we summarized the recent research findings regarding the mutual regulation between RNA m6A modification and ncRNAs (with a specific focus on microRNAs, long non-coding RNAs, and circular RNAs) and their functions. We also discussed the challenges of m6A-containing ncRNAs and RNA m6A as therapeutic targets in human diseases and their future perspective in translational roles.
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Affiliation(s)
- Gui-E Xu
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong) and School of Life Sciences, Shanghai University, Nantong, Jiangsu 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Xuan Zhao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong) and School of Life Sciences, Shanghai University, Nantong, Jiangsu 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Priyanka Gokulnath
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Lijun Wang
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong) and School of Life Sciences, Shanghai University, Nantong, Jiangsu 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People's Hospital of Nantong) and School of Life Sciences, Shanghai University, Nantong, Jiangsu 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
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7
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Cun Y, Guo W, Ma B, Okuno Y, Wang J. Decoding the specificity of m 6A RNA methylation and its implication in cancer therapy. Mol Ther 2024; 32:2461-2469. [PMID: 38796701 PMCID: PMC11405154 DOI: 10.1016/j.ymthe.2024.05.035] [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: 03/19/2024] [Revised: 05/14/2024] [Accepted: 05/23/2024] [Indexed: 05/28/2024] Open
Abstract
N6-methyladenosine (m6A) is the most abundant endogenous modification in eukaryotic RNAs. It plays important roles in various biological processes and diseases, including cancers. More and more studies have revealed that the deposition of m6A is specifically regulated in a context-dependent manner. Here, we review the diverse mechanisms that determine the topology of m6A along RNAs and the cell-type-specific m6A methylomes. The exon junction complex (EJC) as well as histone modifications play important roles in determining the topological distribution of m6A along nascent RNAs, while the transcription factors and RNA-binding proteins, which usually bind specific DNAs and RNAs in a cell-type-specific manner, largely account for the cell-type-specific m6A methylomes. Due to the lack of specificity of m6A writers and readers, there are still challenges to target the core m6A machinery for cancer therapies. Therefore, understanding the mechanisms underlying the specificity of m6A modifications in cancers would be important for future cancer therapies through m6A intervention.
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Affiliation(s)
- Yixian Cun
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangdong 510080, China
| | - Wenbing Guo
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangdong 510080, China
| | - Biao Ma
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Yasushi Okuno
- RIKEN Center for Computational Science, 7-1-26 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Jinkai Wang
- Department of Medical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-Sen University), Ministry of Education, Guangdong 510080, China; Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangdong 510080, China.
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8
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Liu X, Wei X, Wu J, Xu Y, Hu J, Qin C, Chen C, Lin Y. CBLL1 promotes endometrial stromal cell senescence via inhibiting PTEN in recurrent spontaneous abortion. FASEB J 2024; 38:e23833. [PMID: 39012313 DOI: 10.1096/fj.202400972r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024]
Abstract
Recurrent spontaneous abortion (RSA) is a common pregnancy-related disorder. Cbl proto-oncogene like 1 (CBLL1) is an E3 ubiquitin ligase, which has been reported to vary with the menstrual cycle in the endometrium. However, whether CBLL1 is involved in the occurrence and development of RSA remains unclear. This study aimed to investigate the effects of CBLL1 on RSA. We analyzed the expression of CBLL1 in the decidua of RSA patients, as well as its functional effects on cellular senescence, oxidative stress, and proliferation of human endometrial stromal cells (HESCs). RNA sequencing was employed to identify a key downstream target gene regulated by CBLL1. We found that CBLL1 was upregulated in the decidua of RSA patients. Additionally, overexpression of CBLL1 promoted HESC senescence, increased oxidative stress levels, and inhibited proliferation. Phosphatase and tensin homolog located on chromosome 10 (PTEN) was identified as one of the important downstream target genes of CBLL1. In vivo experiments demonstrated that CBLL1 overexpression in the endometrium caused higher embryo absorption rate in mice. Consequently, elevated CBLL1 expression is a potential cause of RSA, representing a novel therapeutic target for RSA.
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Affiliation(s)
- Xueqing Liu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowei Wei
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiayi Wu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yichi Xu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianing Hu
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chuanmei Qin
- Department of Obstetrics and Gynecology, the Sixth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Cailian Chen
- Department of Automation, Shanghai Jiao Tong University, Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai, China
| | - Yi Lin
- Department of Obstetrics and Gynecology, the Sixth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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9
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Xiang Y, Zhang D, Li L, Xue YX, Zhang CY, Meng QF, Wang J, Tan XL, Li YL. Detection, distribution, and functions of RNA N 6-methyladenosine (m 6A) in plant development and environmental signal responses. FRONTIERS IN PLANT SCIENCE 2024; 15:1429011. [PMID: 39081522 PMCID: PMC11286456 DOI: 10.3389/fpls.2024.1429011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/24/2024] [Indexed: 08/02/2024]
Abstract
The epitranscriptomic mark N 6-methyladenosine (m6A) is the most common type of messenger RNA (mRNA) post-transcriptional modification in eukaryotes. With the discovery of the demethylase FTO (FAT MASS AND OBESITY-ASSOCIATED PROTEIN) in Homo Sapiens, this modification has been proven to be dynamically reversible. With technological advances, research on m6A modification in plants also rapidly developed. m6A modification is widely distributed in plants, which is usually enriched near the stop codons and 3'-UTRs, and has conserved modification sequences. The related proteins of m6A modification mainly consist of three components: methyltransferases (writers), demethylases (erasers), and reading proteins (readers). m6A modification mainly regulates the growth and development of plants by modulating the RNA metabolic processes and playing an important role in their responses to environmental signals. In this review, we briefly outline the development of m6A modification detection techniques; comparatively analyze the distribution characteristics of m6A in plants; summarize the methyltransferases, demethylases, and binding proteins related to m6A; elaborate on how m6A modification functions in plant growth, development, and response to environmental signals; and provide a summary and outlook on the research of m6A in plants.
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10
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Yang Y, Lu Y, Wang Y, Wen X, Qi C, Piao W, Jin H. Current progress in strategies to profile transcriptomic m 6A modifications. Front Cell Dev Biol 2024; 12:1392159. [PMID: 39055651 PMCID: PMC11269109 DOI: 10.3389/fcell.2024.1392159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
Various methods have been developed so far for detecting N 6-methyladenosine (m6A). The total m6A level or the m6A status at individual positions on mRNA can be detected and quantified through some sequencing-independent biochemical methods, such as LC/MS, SCARLET, SELECT, and m6A-ELISA. However, the m6A-detection techniques relying on high-throughput sequencing have more effectively advanced the understanding about biological significance of m6A-containing mRNA and m6A pathway at a transcriptomic level over the past decade. Various SGS-based (Second Generation Sequencing-based) methods with different detection principles have been widely employed for this purpose. These principles include m6A-enrichment using antibodies, discrimination of m6A from unmodified A-base by nucleases, a fusion protein strategy relying on RNA-editing enzymes, and marking m6A with chemical/biochemical reactions. Recently, TGS-based (Third Generation Sequencing-based) methods have brought a new trend by direct m6A-detection. This review first gives a brief introduction of current knowledge about m6A biogenesis and function, and then comprehensively describes m6A-profiling strategies including their principles, procedures, and features. This will guide users to pick appropriate methods according to research goals, give insights for developing novel techniques in varying areas, and continue to expand our boundary of knowledge on m6A.
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Affiliation(s)
- Yuening Yang
- Laboratory of Genetics and Disorders, Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yanming Lu
- Laboratory of Genetics and Disorders, Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Yan Wang
- Laboratory of Genetics and Disorders, Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Xianghui Wen
- Laboratory of Genetics and Disorders, Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Changhai Qi
- Department of Pathology, Aerospace Center Hospital, Beijing, China
| | - Weilan Piao
- Laboratory of Genetics and Disorders, Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, China
- Advanced Technology Research Institute, Beijing Institute of Technology, Jinan, China
| | - Hua Jin
- Laboratory of Genetics and Disorders, Key Laboratory of Molecular Medicine and Biotherapy, Aerospace Center Hospital, School of Life Science, Beijing Institute of Technology, Beijing, China
- Advanced Technology Research Institute, Beijing Institute of Technology, Jinan, China
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11
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Bove G, Crepaldi M, Amin S, Megchelenbrink WL, Nebbioso A, Carafa V, Altucci L, Del Gaudio N. The m 6A-independent role of epitranscriptomic factors in cancer. Int J Cancer 2024. [PMID: 38935523 DOI: 10.1002/ijc.35067] [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: 04/09/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/29/2024]
Abstract
Protein function alteration and protein mislocalization are cancer hallmarks that drive oncogenesis. N6-methyladenosine (m6A) deposition mediated by METTL3, METTL16, and METTL5 together with the contribution of additional subunits of the m6A system, has shown a dramatic impact on cancer development. However, the cellular localization of m6A proteins inside tumor cells has been little studied so far. Interestingly, recent evidence indicates that m6A methyltransferases are not always confined to the nucleus, suggesting that epitranscriptomic factors may also have multiple oncogenic roles beyond m6A that still represent an unexplored field. To date novel epigenetic drugs targeting m6A modifiers, such as METTL3 inhibitors, are entering into clinical trials, therefore, the study of the potential onco-properties of m6A effectors beyond m6A is required. Here we will provide an overview of methylation-independent functions of the m6A players in cancer, describing the molecular mechanisms involved and the future implications for therapeutics.
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Affiliation(s)
- Guglielmo Bove
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Marco Crepaldi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Sajid Amin
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Wouter Leonard Megchelenbrink
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- Prinses Máxima Centrum, Utrecht, The Netherlands
| | - Angela Nebbioso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- Program of Medical Epigenetics, Vanvitelli Hospital, Naples, Italy
| | - Vincenzo Carafa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- BIOGEM, Via Camporeale, Ariano Irpino, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- Prinses Máxima Centrum, Utrecht, The Netherlands
- BIOGEM, Via Camporeale, Ariano Irpino, Italy
- IEOS-CNR Institute for Endocrinology and Oncology "Gaetano Salvatore", Naples, Italy
| | - Nunzio Del Gaudio
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
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12
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Dragonetti M, Turco C, Benedetti A, Goeman F, Forcato M, Scalera S, Allegretti M, Esposito G, Fazi F, Blandino G, Donzelli S, Fontemaggi G. The lncRNAMALAT1-WTAP axis: a novel layer of EMT regulation in hypoxic triple-negative breast cancer. Cell Death Discov 2024; 10:276. [PMID: 38862471 PMCID: PMC11166650 DOI: 10.1038/s41420-024-02058-4] [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: 02/22/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Early metastatic disease development is one characteristic that defines triple-negative breast cancer (TNBC) as the most aggressive breast cancer (BC) subtype. Numerous studies have identified long non-coding RNAs (lncRNA) as critical players in regulating tumor progression and metastasis formation. Here, we show that MALAT1, a long non-coding RNA known to promote various features of BC malignancy, such as migration and neo angiogenesis, regulates TNBC cell response to hypoxia. By profiling MALAT1-associated transcripts, we discovered that lncRNA MALAT1 interacts with the mRNA encoding WTAP protein, previously reported as a component of the N6-methyladenosine (m6A) modification writer complex. In hypoxic conditions, MALAT1 positively regulates WTAP protein expression, which influences the response to hypoxia by favoring the transcription of the master regulators HIF1α and HIF1β. Furthermore, WTAP stimulates BC cell migratory ability and the expression of N-Cadherin and Vimentin, hallmarks of epithelial-to-mesenchymal transition (EMT). In conclusion, this study highlights the functional axis comprising MALAT1 and WTAP as a novel prognostic marker of TNBC progression and as a potential target for the development of therapeutic approaches for TNBC treatment.
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Affiliation(s)
- Martina Dragonetti
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Chiara Turco
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Anna Benedetti
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Frauke Goeman
- SAFU Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Scalera
- Biostatistics and Bioinformatics Unit, Clinical Trial Center, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Matteo Allegretti
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Gabriella Esposito
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopaedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Via A. Scarpa, 16, 00161, Rome, Italy
| | - Giovanni Blandino
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy
| | - Sara Donzelli
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
| | - Giulia Fontemaggi
- Translational Oncology Research Unit, IRCCS Regina Elena National Cancer Institute, Via Elio Chianesi 53, 00144, Rome, Italy.
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13
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Cao Y, Qiu G, Dong Y, Zhao W, Wang Y. Exploring the role of m 6 A writer RBM15 in cancer: a systematic review. Front Oncol 2024; 14:1375942. [PMID: 38915367 PMCID: PMC11194397 DOI: 10.3389/fonc.2024.1375942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
In the contemporary epoch, cancer stands as the predominant cause of premature global mortality, necessitating a focused exploration of molecular markers and advanced therapeutic strategies. N6-methyladenosine (m6A), the most prevalent mRNA modification, undergoes dynamic regulation by enzymes referred to as methyltransferases (writers), demethylases (erasers), and effective proteins (readers). Despite lacking methylation activity, RNA-binding motif protein 15 (RBM15), a member of the m6A writer family, assumes a crucial role in recruiting the methyltransferase complex (MTC) and binding to mRNA. Although the impact of m6A modifications on cancer has garnered widespread attention, RBM15 has been relatively overlooked. This review briefly outlines the structure and operational mechanism, and delineates the unique role of RBM15 in various cancers, shedding light on its molecular basis and providing a groundwork for potential tumor-targeted therapies.
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Affiliation(s)
- Yuan Cao
- Fourth Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning, China
| | - Guanzhen Qiu
- Fourth Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning, China
- Shenyang 242 Hospital, Shenyang, Liaoning, China
| | - Yu Dong
- Fourth Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning, China
| | - Wei Zhao
- Fourth Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning, China
| | - Yong Wang
- Fourth Department of Orthopedic Surgery, Central Hospital Affiliated to Shenyang Medical College, Shenyang, Liaoning, China
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14
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Yin H, Ju Z, Zhang X, Zuo W, Yang Y, Zheng M, Zhang X, Liu Y, Peng Y, Xing Y, Yang A, Zhang R. Inhibition of METTL3 in macrophages provides protection against intestinal inflammation. Cell Mol Immunol 2024; 21:589-603. [PMID: 38649449 PMCID: PMC11143309 DOI: 10.1038/s41423-024-01156-8] [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: 11/14/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Inflammatory bowel disease (IBD) is prevalent, and no satisfactory therapeutic options are available because the mechanisms underlying its development are poorly understood. In this study, we discovered that increased expression of methyltransferase-like 3 (METTL3) in macrophages was correlated with the development of colitis and that depletion of METTL3 in macrophages protected mice against dextran sodium sulfate (DSS)-induced colitis. Mechanistic characterization indicated that METTL3 depletion increased the YTHDF3-mediated expression of phosphoglycolate phosphatase (PGP), which resulted in glucose metabolism reprogramming and the suppression of CD4+ T helper 1 (Th1) cell differentiation. Further analysis revealed that glucose metabolism contributed to the ability of METTL3 depletion to ameliorate colitis symptoms. In addition, we developed two potent small molecule METTL3 inhibitors, namely, F039-0002 and 7460-0250, that strongly ameliorated DSS-induced colitis. Overall, our study suggests that METTL3 plays crucial roles in the progression of colitis and highlights the potential of targeting METTL3 to attenuate intestinal inflammation for the treatment of colitis.
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Affiliation(s)
- Huilong Yin
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Molecular Immunology and Immunotherapy Laboratory, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
| | - Zhuan Ju
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Xiang Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Wenjie Zuo
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Molecular Immunology and Immunotherapy Laboratory, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
| | - Yuhang Yang
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Molecular Immunology and Immunotherapy Laboratory, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
| | - Minhua Zheng
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Xiaofang Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Yuning Liu
- Henan Key Laboratory of Immunology and Targeted Therapy, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Molecular Immunology and Immunotherapy Laboratory, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
- Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, Henan, 453003, China
| | - Yingran Peng
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China
| | - Ying Xing
- Department of Endocrinology, Xi'an Daxing Hospital, Xi'an, Shaanxi, 710000, China
| | - Angang Yang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
| | - Rui Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Immunology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers and Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, Shaanxi, 710032, China.
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15
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Zhong X, Zhou Z, Yang G. The Functions of N-methyladenosine (m6A) Modification on HIV-1 mRNA. Cell Biochem Biophys 2024; 82:561-574. [PMID: 38753251 DOI: 10.1007/s12013-024-01280-2] [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] [Accepted: 04/17/2024] [Indexed: 08/25/2024]
Abstract
In recent years, there has been a growing interest in the study of RNA modifications, with some researchers focusing specifically on the connection between these modifications and viruses, as well as the impact they have on viral mRNA and its functionality. The most common type of RNA chemical modification is m6A, which involves the addition of a methyl group covalently to the N6 position of adenosine. It is a widely observed and evolutionarily conserved RNA modification. The regulation of m6A modification primarily involves methyltransferases (writers) and demethylases (erasers) and is mediated by m6A-binding proteins (readers). In HIV-1, m6A sites are predominantly located in the 5' untranslated region (5'UTR) and 3' untranslated region (3'UTR). Additionally, m6A modifications are also present in the RRE RNA of HIV-1. This review provides a detailed account of the effects of these m6A modifications on HIV-1 functionality.
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Affiliation(s)
- XinYu Zhong
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, 310013, China
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, 310013, China
| | - ZhuJiao Zhou
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, 310013, China
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, 310013, China
| | - Geng Yang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, 310013, China.
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, 310013, China.
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16
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Ni Z, Ahmed N, Nabeel-Shah S, Guo X, Pu S, Song J, Marcon E, Burke G, Tong AH, Chan K, Ha KH, Blencowe B, Moffat J, Greenblatt J. Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter. Nucleic Acids Res 2024; 52:4483-4501. [PMID: 38587191 PMCID: PMC11077057 DOI: 10.1093/nar/gkae240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024] Open
Abstract
Messenger RNA precursors (pre-mRNA) generally undergo 3' end processing by cleavage and polyadenylation (CPA), which is specified by a polyadenylation site (PAS) and adjacent RNA sequences and regulated by a large variety of core and auxiliary CPA factors. To date, most of the human CPA factors have been discovered through biochemical and proteomic studies. However, genetic identification of the human CPA factors has been hampered by the lack of a reliable genome-wide screening method. We describe here a dual fluorescence readthrough reporter system with a PAS inserted between two fluorescent reporters. This system enables measurement of the efficiency of 3' end processing in living cells. Using this system in combination with a human genome-wide CRISPR/Cas9 library, we conducted a screen for CPA factors. The screens identified most components of the known core CPA complexes and other known CPA factors. The screens also identified CCNK/CDK12 as a potential core CPA factor, and RPRD1B as a CPA factor that binds RNA and regulates the release of RNA polymerase II at the 3' ends of genes. Thus, this dual fluorescence reporter coupled with CRISPR/Cas9 screens reliably identifies bona fide CPA factors and provides a platform for investigating the requirements for CPA in various contexts.
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Affiliation(s)
- Zuyao Ni
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Nujhat Ahmed
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Syed Nabeel-Shah
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Xinghua Guo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Shuye Pu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jingwen Song
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Edyta Marcon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Giovanni L Burke
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Amy Hin Yan Tong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Katherine Chan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Kevin C H Ha
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Benjamin J Blencowe
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, ON Canada
| | - Jack F Greenblatt
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5A 1A8, Canada
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17
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Liu X, Wu L, Wang L, Li Y. Identification and classification of glioma subtypes based on RNA-binding proteins. Comput Biol Med 2024; 174:108404. [PMID: 38582000 DOI: 10.1016/j.compbiomed.2024.108404] [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: 12/04/2023] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
BACKGROUND Glioma is a common and aggressive primary malignant cancer known for its high morbidity, mortality, and recurrence rates. Despite this, treatment options for glioma are currently restricted. The dysregulation of RBPs has been linked to the advancement of several types of cancer, but their precise role in glioma evolution is still not fully understood. This study sought to investigate how RBPs may impact the development and prognosis of glioma, with potential implications for prognosis and therapy. METHODS RNA-seq profiles of glioma and corresponding clinical data from the CGGA database were initially collected for analysis. Unsupervised clustering was utilized to identify crucial tumor subtypes in glioma development. Subsequent time-series analysis and MS model were employed to track the progression of these identified subtypes. RBPs playing a significant role in glioma progression were then pinpointed using WGCNA and Lasso Cox regression models. Functional analysis of these key RBP-related genes was conducted through GSEA. Additionally, the CIBERSORT algorithm was utilized to estimate immune infiltrating cells, while the STRING database was consulted to uncover potential mechanisms of the identified biomarkers. RESULTS Six tumor subgroups were identified and found to be highly homogeneous within each subgroup. The progression stages of these tumor subgroups were determined using time-series analysis and a MS model. Through WGCNA, Lasso Cox, and multivariate Cox regression analysis, it was confirmed that BCLAF1 is correlated with survival in glioma patients and is closely linked to glioma progression. Functional annotation suggests that BCLAF1 may impact glioma progression by influencing RNA splicing, which in turn affects the cell cycle, Wnt signaling pathway, and other cancer development pathways. CONCLUSIONS The study initially identified six subtypes of glioma progression and assessed their malignancy ranking. Furthermore, it was determined that BCLAF1 could serve as an RBP-related prognostic marker, offering significant implications for the clinical diagnosis and personalized treatment of glioma.
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Affiliation(s)
- Xudong Liu
- School of Medicine, Chongqing University, Chongqing, 400044, China; Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Lei Wu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Lei Wang
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China.
| | - Yongsheng Li
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China.
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18
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Hu J, Wang S, Li X. A comprehensive review of m 6A research in cervical cancer. Epigenomics 2024; 16:753-773. [PMID: 38639713 PMCID: PMC11318741 DOI: 10.2217/epi-2024-0002] [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: 01/03/2024] [Accepted: 03/27/2024] [Indexed: 04/20/2024] Open
Abstract
Cervical cancer (CC) remains one of the most common malignancies among women worldwide, posing a serious threat to women's health. N6-methyladenosine (m6A) modification, as the most abundant type of RNA methylation modification, and has been found to play a crucial role in various cancers. Current research suggests a close association between RNA m6A modification and the occurrence and progression of CC, encompassing disruptions in m6A levels and its regulatory machinery. This review summarizes the current status of m6A modification research in CC, explores the mechanisms underlying m6A levels and regulators (methyltransferases, demethylases, reader proteins) in CC and examines the application of small-molecule inhibitors of m6A regulators in disease treatment. The findings provide new insights into the future treatment of CC.
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Affiliation(s)
- Jing Hu
- Key Laboratory of Environmental Medicine & Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine & Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Xiuting Li
- Department of Public Health, Jiangsu Health Vocational College, Nanjing, 210000, China
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19
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Li R, Zhu C, Wang Y, Wang X, Wang Y, Wang J, Wang K. The relationship between the network of non-coding RNAs-molecular targets and N6-methyladenosine modification in tumors of urinary system. Cell Death Dis 2024; 15:275. [PMID: 38632251 PMCID: PMC11024199 DOI: 10.1038/s41419-024-06664-z] [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: 11/02/2023] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
N6-methyladenosine (m6A) methylation, a prevalent eukaryotic post-transcriptional modification, is involved in multiple biological functions, including mediating variable splicing, RNA maturation, transcription, and nuclear export, and also is vital for regulating RNA translation, stability, and cytoplasmic degradation. For example, m6A methylation can regulate pre-miRNA expression by affecting both splicing and maturation. Non-coding RNA (ncRNA), which includes microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), does not encode proteins but has powerful impacts on transcription and translation. Conversely, ncRNAs may impact m6A methylation by affecting the expression of m6A regulators, including miRNAs targeting mRNA of m6A regulators, or lncRNAs, and circRNAs, acting as scaffolds to regulate transcription of m6A regulatory factors. Dysregulation of m6A methylation is common in urinary tumors, and the regulatory role of ncRNAs is also important for these malignancies. This article provides a systematic review of the role and mechanisms of action of m6A methylation and ncRNAs in urinary tumors.
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Affiliation(s)
- Ruiming Li
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Chunming Zhu
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Yuan Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xia Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Yibing Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
| | - Jiahe Wang
- Department of Family Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
| | - Kefeng Wang
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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20
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Sudhakar SRN, Khan SN, Clark A, Hendrickson-Rebizant T, Patel S, Lakowski TM, Davie JR. Protein arginine methyltransferase 1, a major regulator of biological processes. Biochem Cell Biol 2024; 102:106-126. [PMID: 37922507 DOI: 10.1139/bcb-2023-0212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023] Open
Abstract
Protein arginine methyltransferase 1 (PRMT1) is a major type I arginine methyltransferase that catalyzes the formation of monomethyl and asymmetric dimethylarginine in protein substrates. It was first identified to asymmetrically methylate histone H4 at the third arginine residue forming the H4R3me2a active histone mark. However, several protein substrates are now identified as being methylated by PRMT1. As a result of its association with diverse classes of substrates, PRMT1 regulates several biological processes like chromatin dynamics, transcription, RNA processing, and signal transduction. The review provides an overview of PRMT1 structure, biochemical features, specificity, regulation, and role in cellular functions. We discuss the genomic distribution of PRMT1 and its association with tRNA genes. Further, we explore the different substrates of PRMT1 involved in splicing. In the end, we discuss the proteins that interact with PRMT1 and their downstream effects in diseased states.
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Affiliation(s)
- Sadhana R N Sudhakar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Shahper N Khan
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ariel Clark
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | | | - Shrinal Patel
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ted M Lakowski
- College of Pharmacy Pharmaceutical Analysis Laboratory, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
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21
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Migale R, Neumann M, Mitter R, Rafiee MR, Wood S, Olsen J, Lovell-Badge R. FOXL2 interaction with different binding partners regulates the dynamics of ovarian development. SCIENCE ADVANCES 2024; 10:eadl0788. [PMID: 38517962 PMCID: PMC10959415 DOI: 10.1126/sciadv.adl0788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
The transcription factor FOXL2 is required in ovarian somatic cells for female fertility. Differential timing of Foxl2 deletion, in embryonic versus adult mouse ovary, leads to distinctive outcomes, suggesting different roles across development. Here, we comprehensively investigated FOXL2's role through a multi-omics approach to characterize gene expression dynamics and chromatin accessibility changes, coupled with genome-wide identification of FOXL2 targets and on-chromatin interacting partners in somatic cells across ovarian development. We found that FOXL2 regulates more targets postnatally, through interaction with factors regulating primordial follicle formation and steroidogenesis. Deletion of one interactor, ubiquitin-specific protease 7 (Usp7), results in impairment of somatic cell differentiation, germ cell nest breakdown, and ovarian development, leading to sterility. Our datasets constitute a comprehensive resource for exploration of the molecular mechanisms of ovarian development and causes of female infertility.
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Affiliation(s)
- Roberta Migale
- Laboratory of Stem Cell Biology and Developmental Genetics, The Francis Crick Institute, London NW1 1AT, UK
| | - Michelle Neumann
- Laboratory of Stem Cell Biology and Developmental Genetics, The Francis Crick Institute, London NW1 1AT, UK
| | - Richard Mitter
- Bioinformatics core, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mahmoud-Reza Rafiee
- RNA Networks Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sophie Wood
- Genetic Modification Service, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jessica Olsen
- Genetic Modification Service, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Robin Lovell-Badge
- Laboratory of Stem Cell Biology and Developmental Genetics, The Francis Crick Institute, London NW1 1AT, UK
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22
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Hobble HV, Schaner Tooley CE. Intrafamily heterooligomerization as an emerging mechanism of methyltransferase regulation. Epigenetics Chromatin 2024; 17:5. [PMID: 38429855 PMCID: PMC10908127 DOI: 10.1186/s13072-024-00530-0] [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: 12/15/2023] [Accepted: 02/10/2024] [Indexed: 03/03/2024] Open
Abstract
Protein and nucleic acid methylation are important biochemical modifications. In addition to their well-established roles in gene regulation, they also regulate cell signaling, metabolism, and translation. Despite this high biological relevance, little is known about the general regulation of methyltransferase function. Methyltransferases are divided into superfamilies based on structural similarities and further classified into smaller families based on sequence/domain/target similarity. While members within superfamilies differ in substrate specificity, their structurally similar active sites indicate a potential for shared modes of regulation. Growing evidence from one superfamily suggests a common regulatory mode may be through heterooligomerization with other family members. Here, we describe examples of methyltransferase regulation through intrafamily heterooligomerization and discuss how this can be exploited for therapeutic use.
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Affiliation(s)
- Haley V Hobble
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, 14203, USA
| | - Christine E Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, 14203, USA.
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23
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Alfonsín G, Berral-González A, Rodríguez-Alonso A, Quiroga M, De Las Rivas J, Figueroa A. Stratification of Colorectal Patients Based on Survival Analysis Shows the Value of Consensus Molecular Subtypes and Reveals the CBLL1 Gene as a Biomarker of CMS2 Tumours. Int J Mol Sci 2024; 25:1919. [PMID: 38339195 PMCID: PMC10856263 DOI: 10.3390/ijms25031919] [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: 12/11/2023] [Revised: 01/17/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
The consensus molecular subtypes (CMSs) classification of colorectal cancer (CRC) is a system for patient stratification that can be potentially applied to therapeutic decisions. Hakai (CBLL1) is an E3 ubiquitin-ligase that induces the ubiquitination and degradation of E-cadherin, inducing epithelial-to-mesenchymal transition (EMT), tumour progression and metastasis. Using bioinformatic methods, we have analysed CBLL1 expression on a large integrated cohort of primary tumour samples from CRC patients. The cohort included survival data and was divided into consensus molecular subtypes. Colon cancer tumourspheres were used to analyse the expression of stem cancer cells markers via RT-PCR and Western blotting. We show that CBLL1 gene expression is specifically associated with canonical subtype CMS2. WNT target genes LGR5 and c-MYC show a similar association with CMS2 as CBLL1. These mRNA levels are highly upregulated in cancer tumourspheres, while CBLL1 silencing shows a clear reduction in tumoursphere size and in stem cell biomarkers. Importantly, CMS2 patients with high CBLL1 expression displayed worse overall survival (OS), which is similar to that associated with CMS4 tumours. Our findings reveal CBLL1 as a specific biomarker for CMS2 and the potential of using CMS2 with high CBLL1 expression to stratify patients with poor OS.
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Affiliation(s)
- Gloria Alfonsín
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), 15006 A Coruña, Spain; (G.A.); (A.R.-A.); (M.Q.)
| | - Alberto Berral-González
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL & IBSAL), Consejo Superior de Investigaciones Cientificas (CSIC), University of Salamanca (USAL) and Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain;
| | - Andrea Rodríguez-Alonso
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), 15006 A Coruña, Spain; (G.A.); (A.R.-A.); (M.Q.)
| | - Macarena Quiroga
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), 15006 A Coruña, Spain; (G.A.); (A.R.-A.); (M.Q.)
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC, CSIC/USAL & IBSAL), Consejo Superior de Investigaciones Cientificas (CSIC), University of Salamanca (USAL) and Instituto de Investigación Biomédica de Salamanca (IBSAL), 37007 Salamanca, Spain;
| | - Angélica Figueroa
- Epithelial Plasticity and Metastasis Group, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), 15006 A Coruña, Spain; (G.A.); (A.R.-A.); (M.Q.)
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24
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Kim H, Hu J, Kang H, Kim W. Phylogenetic and functional analyses of N6-methyladenosine RNA methylation factors in the wheat scab fungus Fusarium graminearum. mSphere 2024; 9:e0055223. [PMID: 38085094 PMCID: PMC10826363 DOI: 10.1128/msphere.00552-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/31/2023] [Indexed: 01/31/2024] Open
Abstract
In eukaryotes, N6-methyladenosine (m6A) RNA modification plays a crucial role in governing the fate of RNA molecules and has been linked to various developmental processes. However, the phyletic distribution and functions of genetic factors responsible for m6A modification remain largely unexplored in fungi. To get insights into the evolution of m6A machineries, we reconstructed global phylogenies of potential m6A writers, readers, and erasers in fungi. Substantial copy number variations were observed, ranging from up to five m6A writers in early-diverging fungi to a single copy in the subphylum Pezizomycotina, which primarily comprises filamentous fungi. To characterize m6A factors in a phytopathogenic fungus Fusarium graminearum, we generated knockout mutants lacking potential m6A factors including the sole m6A writer MTA1. However, the resulting knockouts did not exhibit any noticeable phenotypic changes during vegetative and sexual growth stages. As obtaining a homozygous knockout lacking MTA1 was likely hindered by its essential role, we generated MTA1-overexpressing strains (MTA1-OE). The MTA1-OE5 strain showed delayed conidial germination and reduced hyphal branching, suggesting its involvement during vegetative growth. Consistent with these findings, the expression levels of MTA1 and a potential m6A reader YTH1 were dramatically induced in germinating conidia, followed by the expression of potential m6A erasers at later vegetative stages. Several genes including transcription factors, transporters, and various enzymes were found to be significantly upregulated and downregulated in the MTA1-OE5 strain. Overall, our study highlights the functional importance of the m6A methylation during conidial germination in F. graminearum and provides a foundation for future investigations into m6A modification sites in filamentous fungi.IMPORTANCEN6-methyladenosine (m6A) RNA methylation is a reversible posttranscriptional modification that regulates RNA function and plays a crucial role in diverse developmental processes. This study addresses the knowledge gap regarding phyletic distribution and functions of m6A factors in fungi. The identification of copy number variations among fungal groups enriches our knowledge regarding the evolution of m6A machinery in fungi. Functional characterization of m6A factors in a phytopathogenic filamentous fungus Fusarium graminearum provides insights into the essential role of the m6A writer MTA1 in conidial germination and hyphal branching. The observed effects of overexpressing MTA1 on fungal growth and gene expression patterns of m6A factors throughout the life cycle of F. graminearum further underscore the importance of m6A modification in conidial germination. Overall, this study significantly advances our understanding of m6A modification in fungi, paving the way for future research into its roles in filamentous growth and potential applications in disease control.
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Affiliation(s)
- Hyeonjae Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
| | - Jianzhong Hu
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Wonyong Kim
- Korean Lichen Research Institute, Sunchon National University, Suncheon, South Korea
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
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25
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Zhou X, Chai K, Zhu H, Luo C, Zou X, Zou J, Zhang G. The role of the methyltransferase METTL3 in prostate cancer: a potential therapeutic target. BMC Cancer 2024; 24:8. [PMID: 38166703 PMCID: PMC10762986 DOI: 10.1186/s12885-023-11741-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
The incidence of prostate cancer (PCa), the most prevalent malignancy, is currently at the forefront. RNA modification is a subfield of the booming field of epigenetics. To date, more than 170 types of RNA modifications have been described, and N6-methyladenosine (m6A) is the most abundant and well-characterized internal modification of mRNAs involved in various aspects of cancer progression. METTL3, the first identified key methyltransferase, regulates human mRNA and non-coding RNA expression in an m6A-dependent manner. This review elucidates the biological function and role of METTL3 in PCa and discusses the implications of METTL3 as a potential therapeutic target for future research directions and clinical applications.
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Affiliation(s)
- Xuming Zhou
- First Clinical College, Gannan Medical University, Ganzhou, 341000, China
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Keqiang Chai
- Department of Urology, Third Affiliated Hospital of Gansu University of Chinese Medicine, Baiyin, 730900, China
| | - Hezhen Zhu
- First Clinical College, Gannan Medical University, Ganzhou, 341000, China
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Cong Luo
- First Clinical College, Gannan Medical University, Ganzhou, 341000, China
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
| | - Xiaofeng Zou
- Department of Urology, Third Affiliated Hospital of Gansu University of Chinese Medicine, Baiyin, 730900, China
- Institute of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
- Jiangxi Engineering Technology Research Center of Calculi Prevention, Ganzhou, 341000, China
| | - Junrong Zou
- Department of Urology, Third Affiliated Hospital of Gansu University of Chinese Medicine, Baiyin, 730900, China
- Institute of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China
- Jiangxi Engineering Technology Research Center of Calculi Prevention, Ganzhou, 341000, China
| | - Guoxi Zhang
- Department of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China.
- Institute of Urology, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, China.
- Jiangxi Engineering Technology Research Center of Calculi Prevention, Ganzhou, 341000, China.
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26
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Sun YH, Zhao TJ, Li LH, Wang Z, Li HB. Emerging role of N6-methyladenosine in the homeostasis of glucose metabolism. Am J Physiol Endocrinol Metab 2024; 326:E1-E13. [PMID: 37938178 DOI: 10.1152/ajpendo.00225.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/21/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent post-transcriptional internal RNA modification, which is involved in the regulation of diverse physiological processes. Dynamic and reversible m6A modification has been shown to regulate glucose metabolism, and dysregulation of m6A modification contributes to glucose metabolic disorders in multiple organs and tissues including the pancreas, liver, adipose tissue, skeletal muscle, kidney, blood vessels, and so forth. In this review, the role and molecular mechanism of m6A modification in the regulation of glucose metabolism were summarized, the potential therapeutic strategies that improve glucose metabolism by targeting m6A modifiers were outlined, and feasible directions of future research in this field were discussed as well, providing clues for translational research on combating metabolic diseases based on m6A modification in the future.
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Affiliation(s)
- Yuan-Hai Sun
- Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Teng-Jiao Zhao
- Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Ling-Huan Li
- Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, People's Republic of China
- College of Chemistry and Materials Science, Zhejiang Normal University, Jinhua, People's Republic of China
| | - Zhen Wang
- Center for Laboratory Medicine, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Han-Bing Li
- Institute of Pharmacology, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, People's Republic of China
- Section of Endocrinology, School of Medicine, Yale University, New Haven, Connecticut, United States
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27
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Höfler S, Duss O. Interconnections between m 6A RNA modification, RNA structure, and protein-RNA complex assembly. Life Sci Alliance 2024; 7:e202302240. [PMID: 37935465 PMCID: PMC10629537 DOI: 10.26508/lsa.202302240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
Protein-RNA complexes exist in many forms within the cell, from stable machines such as the ribosome to transient assemblies like the spliceosome. All protein-RNA assemblies rely on spatially and temporally coordinated interactions between specific proteins and RNAs to achieve a functional form. RNA folding and structure are often critical for successful protein binding and protein-RNA complex formation. RNA modifications change the chemical nature of a given RNA and often alter its folding kinetics. Both these alterations can affect how and if proteins or other RNAs can interact with the modified RNA and assemble into complexes. N6-methyladenosine (m6A) is the most common base modification on mRNAs and regulatory noncoding RNAs and has been shown to impact RNA structure and directly modulate protein-RNA interactions. In this review, focusing on the mechanisms and available quantitative information, we discuss first how the METTL3/14 m6A writer complex is specifically targeted to RNA assisted by protein-RNA and other interactions to enable site-specific and co-transcriptional RNA modification and, once introduced, how the m6A modification affects RNA folding and protein-RNA interactions.
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Affiliation(s)
- Simone Höfler
- https://ror.org/03mstc592 Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Olivier Duss
- https://ror.org/03mstc592 Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
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28
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He H, Ge L, Chen Y, Zhao S, Li Z, Zhou X, Li F. m 6A modification of plant virus enables host recognition by NMD factors in plants. SCIENCE CHINA. LIFE SCIENCES 2024; 67:161-174. [PMID: 37837530 DOI: 10.1007/s11427-022-2377-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 05/26/2023] [Indexed: 10/16/2023]
Abstract
N6-methyladenosine (m6A) is the most abundant eukaryotic mRNA modification and is involved in various biological processes. Increasing evidence has implicated that m6A modification is an important anti-viral defense mechanism in mammals and plants, but it is largely unknown how m6A regulates viral infection in plants. Here we report the dynamic changes and functional anatomy of m6A in Nicotiana benthamiana and Solanum lycopersicum during Pepino mosaic virus (PepMV) infection. m6A modification in the PepMV RNA genome is conserved in these two species. Overexpression of the m6A writers, mRNA adenosine methylase A (MTA), and HAKAI inhibit the PepMV RNA accumulation accompanied by increased viral m6A modifications, whereas deficiency of these writers decreases the viral RNA m6A levels but enhances virus infection. Further study reveals that the cytoplasmic YTH-domain family protein NbECT2A/2B/2C as m6A readers are involved in anti-viral immunity. Protein-protein interactions indicate that NbECT2A/2B/2C interact with nonsense-mediated mRNA decay (NMD)-related proteins, including NbUPF3 and NbSMG7, but not with NbUPF1. m6A modification-mediated restriction to PepMV infection is dependent on NMD-related factors. These findings provide new insights into the functionality of m6A anti-viral activity and reveal a distinct immune response that NMD factors recognize the m6A readers-viral m6A RNA complex for viral RNA degradation to limit virus infection in plants.
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Affiliation(s)
- Hao He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Linhao Ge
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yalin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Siwen Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhaolei Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310029, China.
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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29
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Chen Y, Jiang Z, Yang Y, Zhang C, Liu H, Wan J. The functions and mechanisms of post-translational modification in protein regulators of RNA methylation: Current status and future perspectives. Int J Biol Macromol 2023; 253:126773. [PMID: 37690652 DOI: 10.1016/j.ijbiomac.2023.126773] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
RNA methylation, an epigenetic modification that does not alter gene sequence, may be important to diverse biological processes. Protein regulators of RNA methylation include "writers," "erasers," and "readers," which respectively deposit, remove, and recognize methylated RNA. RNA methylation, particularly N6-methyladenosine (m6A), 5-methylcytosine (m5C), N3-methylcytosine (m3C), N1-methyladenosine (m1A) and N7-methylguanosine (m7G), has been suggested as disease therapeutic targets. Despite advances in the structure and pharmacology of RNA methylation regulators that have improved drug discovery, regulating these proteins by various post-translational modifications (PTMs) has received little attention. PTM modifies protein structure and function, affecting all aspects of normal biology and pathogenesis, including immunology, cell differentiation, DNA damage repair, and tumors. It is becoming evident that RNA methylation regulators are also regulated by diverse PTMs. PTM of RNA methylation regulators induces their covalent linkage to new functional groups, hence modifying their activity and function. Mass spectrometry has identified many PTMs on protein regulators of RNA methylation. In this review, we describe the functions and PTM of protein regulators of RNA methylation and summarize the recent advances in the regulatory mode of human disease and its underlying mechanisms.
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Affiliation(s)
- Youming Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zuli Jiang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ying Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Chenxing Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Hongyang Liu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Junhu Wan
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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30
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Zhou J, Han Y, Hou R. Potential role of N6-methyladenosine modification in the development of Parkinson's disease. Front Cell Dev Biol 2023; 11:1321995. [PMID: 38155838 PMCID: PMC10753761 DOI: 10.3389/fcell.2023.1321995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/04/2023] [Indexed: 12/30/2023] Open
Abstract
N6-methyladenosine (m6A) represents the most abundant modification of messenger RNA (mRNA) and is regulated by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers). A dynamic modification process is implicated in nearly every critical stage of RNA metabolism, including mRNA stability, transcription, translation, splicing, nuclear export, and decay. Notably, m6A methylation is significantly enriched in the brain and has recently been shown to be associated with neurodevelopmental disorders and the development of Parkinson's disease (PD). In this review, we summarize the proteins involved in the process of m6A modification and elucidate the emerging role of m6A modification in PD, which could illuminate alternative strategies for the prevention and treatment of PD.
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Affiliation(s)
- Jiale Zhou
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yang Han
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
- Laboratory Animal Center, College of Animal Science, Jilin University, Changchun, China
| | - Ruizhe Hou
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun, China
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31
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Sun Y, Jin D, Zhang Z, Ji H, An X, Zhang Y, Yang C, Sun W, Zhang Y, Duan Y, Kang X, Jiang L, Zhao X, Lian F. N6-methyladenosine (m6A) methylation in kidney diseases: Mechanisms and therapeutic potential. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194967. [PMID: 37553065 DOI: 10.1016/j.bbagrm.2023.194967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023]
Abstract
The N6-methyladenosine (m6A) modification is regulated by methylases, commonly referred to as "writers," and demethylases, known as "erasers," leading to a dynamic and reversible process. Changes in m6A levels have been implicated in a wide range of cellular processes, including nuclear RNA export, mRNA metabolism, protein translation, and RNA splicing, establishing a strong correlation with various diseases. Both physiologically and pathologically, m6A methylation plays a critical role in the initiation and progression of kidney disease. The methylation of m6A may also facilitate the early diagnosis and treatment of kidney diseases, according to accumulating research. This review aims to provide a comprehensive overview of the potential role and mechanism of m6A methylation in kidney diseases, as well as its potential application in the treatment of such diseases. There will be a thorough examination of m6A methylation mechanisms, paying particular attention to the interplay between m6A writers, m6A erasers, and m6A readers. Furthermore, this paper will elucidate the interplay between various kidney diseases and m6A methylation, summarize the expression patterns of m6A in pathological kidney tissues, and discuss the potential therapeutic benefits of targeting m6A in the context of kidney diseases.
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Affiliation(s)
- Yuting Sun
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - De Jin
- Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, China
| | - Ziwei Zhang
- College of Traditional Chinese Medicine, Changchun University of Chinese Medicine, Changchun, China
| | - Hangyu Ji
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuedong An
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuehong Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Cunqing Yang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenjie Sun
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuqing Zhang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yingying Duan
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaomin Kang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Linlin Jiang
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xuefei Zhao
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fengmei Lian
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
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Yu Y, Lu S, Jin H, Zhu H, Wei X, Zhou T, Zhao M. RNA N6-methyladenosine methylation and skin diseases. Autoimmunity 2023; 56:2167983. [PMID: 36708146 DOI: 10.1080/08916934.2023.2167983] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Skin diseases are global health issues caused by multiple pathogenic factors, in which epigenetics plays an invaluable role. Post-transcriptional RNA modifications are important epigenetic mechanism that regulate gene expression at the genome-wide level. N6-methyladenosine (m6A) is the most prevalent modification that occurs in the messenger RNAs (mRNA) of most eukaryotes, which is installed by methyltransferases called "writers", removed by demethylases called "erasers", and recognised by RNA-binding proteins called "readers". To date, m6A is emerging to play essential part in both physiological processes and pathological progression, including skin diseases. However, a systematic summary of m6A in skin disease has not yet been reported. This review starts by illustrating each m6A-related modifier specifically and their roles in RNA processing, and then focus on the existing research advances of m6A in immune homeostasis and skin diseases.
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Affiliation(s)
- Yaqin Yu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China.,Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Shuang Lu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China.,Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Hui Jin
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China.,Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Huan Zhu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China.,Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Xingyu Wei
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China.,Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Tian Zhou
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China.,Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China.,Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
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Hosseiniyan Khatibi SM, Rahbar Saadat Y, Hejazian SM, Sharifi S, Ardalan M, Teshnehlab M, Zununi Vahed S, Pirmoradi S. Decoding the Possible Molecular Mechanisms in Pediatric Wilms Tumor and Rhabdoid Tumor of the Kidney through Machine Learning Approaches. Fetal Pediatr Pathol 2023; 42:825-844. [PMID: 37548233 DOI: 10.1080/15513815.2023.2242979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
Objective: Wilms tumor (WT) and Rhabdoid tumor (RT) are pediatric renal tumors and their differentiation is based on histopathological and molecular analysis. The present study aimed to introduce the panels of mRNAs and microRNAs involved in the pathogenesis of these cancers using deep learning algorithms. Methods: Filter, graph, and association rule mining algorithms were applied to the mRNAs/microRNAs data. Results: Candidate miRNAs and mRNAs with high accuracy (AUC: 97%/93% and 94%/97%, respectively) could differentiate the WT and RT classes in training and test data. Let-7a-2 and C19orf24 were identified in the WT, while miR-199b and RP1-3E10.2 were detected in the RT by analysis of Association Rule Mining. Conclusion: The application of the machine learning methods could identify mRNA/miRNA patterns to discriminate WT from RT. The identified miRNAs/mRNAs panels could offer novel insights into the underlying molecular mechanisms that are responsible for the initiation and development of these cancers. They may provide further insight into the pathogenesis, prognosis, diagnosis, and molecular-targeted therapy in pediatric renal tumors.
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Affiliation(s)
- Seyed Mahdi Hosseiniyan Khatibi
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Simin Sharifi
- Dental and Periodontal Research Center, Tabriz University of Medical Sciences, Tabriz Iran
| | | | - Mohammad Teshnehlab
- Department of Electrical and Computer Engineering, K.N. Toosi University of Technology, Tehran, Iran
| | | | - Saeed Pirmoradi
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
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Shao N, Ye T, Xuan W, Zhang M, Chen Q, Liu J, Zhou P, Song H, Cai B. The effects of N 6-methyladenosine RNA methylation on the nervous system. Mol Cell Biochem 2023; 478:2657-2669. [PMID: 36899139 DOI: 10.1007/s11010-023-04691-6] [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: 03/19/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023]
Abstract
Epitranscriptomics, also known as "RNA epigenetics", is a type of chemical modification that regulates RNA. RNA methylation is a significant discovery after DNA and histone methylation. The dynamic reversible process of m6A involves methyltransferases (writers), m6A binding proteins (readers), as well as demethylases (erasers). We summarized the current research status of m6A RNA methylation in the neural stem cells' growth, synaptic and axonal function, brain development, learning and memory, neurodegenerative diseases, and glioblastoma. This review aims to provide a theoretical basis for studying the mechanism of m6A methylation and finding its potential therapeutic targets in nervous system diseases.
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Affiliation(s)
- Nan Shao
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Ting Ye
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Weiting Xuan
- Department of Neurosurgery (Rehabilitation), Anhui Hospital of Integrated Chinese and Western Medicine, Hefei, 230031, China
| | - Meng Zhang
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Qian Chen
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China
| | - Juan Liu
- Department of Chinese Internal Medicine, Taihe County People's Hospital, Fuyang, 236699, China
| | - Peng Zhou
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China.
- Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, 230012, China.
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230012, China.
- Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China.
| | - Hang Song
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China.
- Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, 230012, China.
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230012, China.
- Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China.
| | - Biao Cai
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, 230012, China.
- Institute of Integrated Chinese and Western Medicine, Anhui Academy of Chinese Medicine, Hefei, 230012, China.
- Key Laboratory of Xin'an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei, 230012, China.
- Anhui Province Key Laboratory of Chinese Medicinal Formula, Hefei, 230012, China.
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35
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Huang C, Zhang K, Guo Y, Shen C, Liu X, Huang H, Dou X, Yu B. The crucial roles of m 6A RNA modifications in cutaneous cancers: Implications in pathogenesis, metastasis, drug resistance, and targeted therapies. Genes Dis 2023; 10:2320-2330. [PMID: 37554186 PMCID: PMC10404882 DOI: 10.1016/j.gendis.2022.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/11/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification on RNA. It is a dynamical and reversible process, which is regulated by m6A methyltransferase and m6A demethylase. The m6A modified RNA can be specifically recognized by the m6A reader, leading to RNA splicing, maturation, degradation or translation. The abnormality of m6A RNA modification is closely related to a variety of biological processes, especially the occurrence and development of tumors. Recent studies have shown that m6A RNA modification is involved in the pathogenesis of skin cancers. However, the precise molecular mechanisms of m6A-mediated cutaneous tumorigenesis have not been fully elucidated. Therefore, this review will summarize the biological characteristics of m6A modification, its regulatory role and mechanism in skin cancers, and the recent research progress of m6A-related molecular drugs, aiming to provide new ideas for clinical diagnosis and targeted therapy of cutaneous cancers.
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Affiliation(s)
- Cong Huang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, China
| | - Kaoyuan Zhang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China
| | - Yang Guo
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, China
| | - Changbing Shen
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China
| | - Xiaoming Liu
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China
| | - Haiyan Huang
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China
| | - Xia Dou
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China
| | - Bo Yu
- Department of Dermatology, Skin Research Institute of Peking University Shenzhen Hospital, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong 518036, China
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36
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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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Wu L, Niu L, Yang Z, Xia Q, Xu J, Lu X. RNA N6‑methyladenosine methyltransferase WTAP promotes the differentiation of endothelial progenitor cells. Exp Ther Med 2023; 26:420. [PMID: 37602313 PMCID: PMC10433437 DOI: 10.3892/etm.2023.12119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/23/2023] [Indexed: 08/22/2023] Open
Abstract
N6-methyladenosine (m6A) serves a critical role in regulating gene expression and has been associated with various diseases; however, its role in the differentiation of endothelial progenitor cells (EPCs) remains unclear. The present study used liquid chromatography with tandem mass spectrometry and immunofluorescence assays to quantify the levels of m6A in human peripheral blood-derived EPCs (HPB-EPCs) before and after differentiation into mature cells. The present study performed Cell Counting Kit 8, Transwell, and tube formation assays to determine the effects of overexpression and knockdown of Wilms' tumor 1-associated protein (WTAP) on HPB-EPCs. The results revealed that the level of m6A modification was significantly increased during HPB-EPCs differentiation, and WTAP exhibited the most significant alteration among the enzymes involved in m6A regulation. When WTAP was overexpressed in HPB-EPCs, cell proliferation, invasion, and the formation of tubes were improved, whereas WTAP knockdown yielded the opposite effects. In conclusion, the present study highlighted the involvement of m6A in regulating EPC differentiation, with WTAP acting as a promoter of EPC differentiation.
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Affiliation(s)
- Longyun Wu
- Department of Gastroenterology, Fudan University Pudong Medical Center, Shanghai 201399, P.R. China
| | - Lili Niu
- Department of Gastroenterology, Fudan University Pudong Medical Center, Shanghai 201399, P.R. China
- Central Laboratory, First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116021, P.R. China
- Institute of Integrative Medicine, Dalian Medical University, Dalian, Liaoning 116021, P.R. China
| | - Zhou Yang
- Department of Gastroenterology, Fudan University Pudong Medical Center, Shanghai 201399, P.R. China
- Department of Cardiovascular Surgery, Fudan University Shanghai Cancer Center, Shanghai 200120, P.R. China
| | - Qiaoyun Xia
- Department of Gastroenterology, Fudan University Pudong Medical Center, Shanghai 201399, P.R. China
| | - Jingyuan Xu
- Department of Gastroenterology, Fudan University Pudong Medical Center, Shanghai 201399, P.R. China
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Xiaolan Lu
- Department of Gastroenterology, Fudan University Pudong Medical Center, Shanghai 201399, P.R. China
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
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Zhang H, Yang Y, Liu Z, Xu H, Zhu H, Wang P, Liang G. Significance of methylation-related genes in diagnosis and subtype classification of renal interstitial fibrosis. Hereditas 2023; 160:32. [PMID: 37496082 PMCID: PMC10373342 DOI: 10.1186/s41065-023-00295-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/16/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND RNA methylation modifications, such as N1-methyladenosine/N6-methyladenosine /N5-methylcytosine (m1A/m6A/m5C), are the most common RNA modifications and are crucial for a number of biological processes. Nonetheless, the role of RNA methylation modifications of m1A/m6A/m5C in the pathogenesis of renal interstitial fibrosis (RIF) remains incompletely understood. METHODS Firstly, we downloaded 2 expression datasets from the GEO database, namely GSE22459 and GSE76882. In a differential analysis of these datasets between patients with and without RIF, we selected 33 methylation-related genes (MRGs). We then applied a PPI network, LASSO analysis, SVM-RFE algorithm, and RF algorithm to identify key MRGs. RESULTS We eventually obtained five candidate MRGs (WTAP, ALKBH5, YTHDF2, RBMX, and ELAVL1) to forecast the risk of RIF. We created a nomogram model derived from five key MRGs, which revealed that the nomogram model may be advantageous to patients. Based on the selected five significant MRGs, patients with RIF were classified into two MRG patterns using consensus clustering, and the correlation between the five MRGs, the two MRG patterns, and the genetic pattern with immune cell infiltration was shown. Moreover, we conducted GO and KEGG analyses on 768 DEGs between MRG clusters A and B to look into their different involvement in RIF. To measure the MRG patterns, a PCA algorithm was developed to determine MRG scores for each sample. The MRG scores of the patients in cluster B were higher than those in cluster A. CONCLUSIONS Ultimately, we concluded that cluster A in the two MRG patterns identified on these five key m1A/m6A/m5C regulators may be associated with RIF.
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Affiliation(s)
- Hanchao Zhang
- Department of Urology, The Affilated Hospital and Clinical Medical College of Chengdu University, Chengdu, Sichuan, China
- Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Yue Yang
- Department of Urology, The Affilated Hospital and Clinical Medical College of Chengdu University, Chengdu, Sichuan, China
- Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Zhengdao Liu
- Medical College of Soochow University, Suzhou, Jiangsu, China
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Hong Xu
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Han Zhu
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Peirui Wang
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Guobiao Liang
- Medical College of Soochow University, Suzhou, Jiangsu, China.
- Department of Urology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou, China.
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Li X, Ma J, Sun Z, Li N, Jiao G, Zhang T, Cao H. Development and validation of a N6 methylation regulator-related gene signature for prognostic and immune response prediction in non-small cell lung cancer. Am J Cancer Res 2023; 13:2984-2997. [PMID: 37560004 PMCID: PMC10408494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/20/2023] [Indexed: 08/11/2023] Open
Abstract
N6 methylation (m6A) has been reported to play an important role in tumor progression. Non-small cell lung cancer (NSCLC) is the predominant pathological type of lung cancer with a high mortality rate. The purpose of this study was to develop and validate a N6 methylation regulator-related gene signature for assessing prognosis and response to immunotherapy in NSCLC. Data from The Cancer Genome Atlas was used as the training cohort. Data from Gene Expression Omnibus and Xena served as the two validation cohorts. We performed Cox regression, last absolute shrinkage and selection operator, receiver operating characteristic curves and Kaplan-Meier survival analysis to generate and validate a prognostic signature based on m6A regulator-related genes. We explored the association between the signature and tumor microenvironment including genomic mutation, immune cell infiltration and tumor mutation burden. We also analyzed the association between the signature and immunotherapy. Finally, among the genes that constituted the signature, GGA2 was the only favorable factor for NSCLC prognosis. Molecular experiments were used to explore GGA2 function in NSCLC. We generated a prognostic signature based on seven m6A regulator-related genes (GGA2, CD70, BMP2, GPX8, YWHAZ, NOG and TEAD4). And the data from three cohorts showed that the signature could effectively assess prognosis in NSCLC. Patients with high risk scores had the higher mutational load and lower immune infiltration levels and were more likely to not respond to immunotherapy. The experiments revealed overexpression of GGA2 inhibited proliferation and motility of NSCLC cells. Mechanically, GGA2 downregulated METTL3 expression and thus reduced m6A abundance in NSCLC. This study developed and validated a prognostic signature based on m6A regulator-related genes, providing useful insights for the management of NSCLC. And GGA2 may be a target of m6A regulation.
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Affiliation(s)
- Xiang Li
- Qilu Hospital of Shandong UniversityJinan 250000, Shandong, China
- Cheeloo College of Medicine, Shandong UniversityJinan 250000, Shandong, China
| | - Jinlong Ma
- Qilu Hospital of Shandong UniversityJinan 250000, Shandong, China
- Cheeloo College of Medicine, Shandong UniversityJinan 250000, Shandong, China
| | - Zhenqian Sun
- Qilu Hospital of Shandong UniversityJinan 250000, Shandong, China
- Cheeloo College of Medicine, Shandong UniversityJinan 250000, Shandong, China
| | - Na Li
- Mechanics Laboratory, Binzhou Medical UniversityYantai 250000, Shandong, China
| | - Guangjun Jiao
- Qilu Hospital of Shandong UniversityJinan 250000, Shandong, China
- Cheeloo College of Medicine, Shandong UniversityJinan 250000, Shandong, China
| | - Tianqi Zhang
- Qilu Medical UniversityZibo 250000, Shandong, China
| | - Hongxin Cao
- Department of Medical Oncology, Qilu Hospital of Shandong UniversityJinan 250000, Shandong, China
- Key Laboratory of Chemical Biology (Ministry of Education), Institute of Biochemical and Biotechnological Drug, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong UniversityJinan 250000, Shandong, China
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40
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Wang Y, Wang Y, Patel H, Chen J, Wang J, Chen ZS, Wang H. Epigenetic modification of m 6A regulator proteins in cancer. Mol Cancer 2023; 22:102. [PMID: 37391814 PMCID: PMC10311752 DOI: 10.1186/s12943-023-01810-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/19/2023] [Indexed: 07/02/2023] Open
Abstract
Divergent N6-methyladenosine (m6A) modifications are dynamic and reversible posttranscriptional RNA modifications that are mediated by m6A regulators or m6A RNA methylation regulators, i.e., methyltransferases ("writers"), demethylases ("erasers"), and m6A-binding proteins ("readers"). Aberrant m6A modifications are associated with cancer occurrence, development, progression, and prognosis. Numerous studies have established that aberrant m6A regulators function as either tumor suppressors or oncogenes in multiple tumor types. However, the functions and mechanisms of m6A regulators in cancer remain largely elusive and should be explored. Emerging studies suggest that m6A regulators can be modulated by epigenetic modifications, namely, ubiquitination, SUMOylation, acetylation, methylation, phosphorylation, O-GlcNAcylation, ISGylation, and lactylation or via noncoding RNA action, in cancer. This review summarizes the current roles of m6A regulators in cancer. The roles and mechanisms for epigenetic modification of m6A regulators in cancer genesis are segregated. The review will improve the understanding of the epigenetic regulatory mechanisms of m6A regulators.
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Affiliation(s)
- Yumin Wang
- Department of Respiratory and Critical Care Medicine, Aerospace Center Hospital, Peking University Aerospace School of Clinical Medicine, Beijing, 100049, China
| | - Yan Wang
- Hunan Provincial Key Laboratory of Hepatobiliary Disease Research, Division of Hepato-Biliary-Pancreatic Surgery, Department of Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410008, China
| | - Harsh Patel
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Jichao Chen
- Department of Respiratory and Critical Care Medicine, Aerospace Center Hospital, Peking University Aerospace School of Clinical Medicine, Beijing, 100049, China
| | - Jinhua Wang
- Beijing Key Laboratory of Drug Target and Screening Research, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA.
| | - Hongquan Wang
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
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41
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Abstract
Over the past decade, mRNA modifications have emerged as important regulators of gene expression control in cells. Fueled in large part by the development of tools for detecting RNA modifications transcriptome wide, researchers have uncovered a diverse epitranscriptome that serves as an additional layer of gene regulation beyond simple RNA sequence. Here, we review the proteins that write, read, and erase these marks, with a particular focus on the most abundant internal modification, N6-methyladenosine (m6A). We first describe the discovery of the key enzymes that deposit and remove m6A and other modifications and discuss how our understanding of these proteins has shaped our views of modification dynamics. We then review current models for the function of m6A reader proteins and how our knowledge of these proteins has evolved. Finally, we highlight important future directions for the field and discuss key questions that remain unanswered.
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Affiliation(s)
- Mathieu N Flamand
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Matthew Tegowski
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kate D Meyer
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, USA;
- Department of Neurobiology, Duke University School of Medicine, Durham, North Carolina, USA
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42
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Lv J, Xing L, Zhong X, Li K, Liu M, Du K. Role of N6-methyladenosine modification in central nervous system diseases and related therapeutic agents. Biomed Pharmacother 2023; 162:114583. [PMID: 36989722 DOI: 10.1016/j.biopha.2023.114583] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
N6-methyladenosine (m6A) is a ubiquitous mRNA modification in eukaryotes. m6A occurs through the action of methyltransferases, demethylases, and methylation-binding proteins. m6A methylation of RNA is associated with various neurological disorders, including Alzheimer's disease (AD), Parkinson's disease (PD), depression, cerebral apoplexy, brain injury, epilepsy, cerebral arteriovenous malformations, and glioma. Furthermore, recent studies report that m6A-related drugs have attracted considerable concerns in the therapeutic areas of neurological disorders. Here, we mainly summarized the role of m6A modification in neurological diseases and the therapeutic potential of m6A-related drugs. The aim of this review is expected to be useful to systematically assess m6A as a new potential biomarker and develop innovative modulators of m6A for the amelioration and treatment of neurological disorders.
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Affiliation(s)
- Junya Lv
- School of Pharmacy, Department of Pharmacology, China Medical University, Shenyang 110122, China
| | - Lijuan Xing
- Precision Laboratory of Panjin Central Hospital, Panjin 124000, China
| | - Xin Zhong
- School of Pharmacy, Department of Pharmacology, China Medical University, Shenyang 110122, China
| | - Kai Li
- Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, the First Affiliated Hospital of China Medical University, Shenyang 110001, China.
| | - Mingyan Liu
- School of Pharmacy, Department of Pharmacology, China Medical University, Shenyang 110122, China; Liaoning Medical Diagnosis and Treatment Center, Shenyang 110179, China.
| | - Ke Du
- School of Pharmacy, Department of Pharmacology, China Medical University, Shenyang 110122, China; Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, the First Affiliated Hospital of China Medical University, Shenyang 110001, China; Liaoning Medical Diagnosis and Treatment Center, Shenyang 110179, China.
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43
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Lv Z, Ran R, Yang Y, Xiang M, Su H, Huang J. The interplay between N6-methyladenosine and precancerous liver disease: molecular functions and mechanisms. Discov Oncol 2023; 14:78. [PMID: 37227534 DOI: 10.1007/s12672-023-00695-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/19/2023] [Indexed: 05/26/2023] Open
Abstract
N6-methyladenosine(m6A) is one of the most abundant modifications of mammalian cellular RNAs. m6A regulates various biological functions in epitranscriptomic ways, including RNA stability, decay, splicing, translation and nuclear export. Recent studies have indicated the growing importance of m6A modification in precancerous disease, influencing viral replication, immune escape, and carcinogenesis. Here, we review the role of m6A modification in HBV/HCV infection, NAFLD and liver fibrosis, and its function in liver disease pathogenesis. Our review will provide a new sight for the innovative treatment strategy for precancerous liver disease.
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Affiliation(s)
- Zhihua Lv
- Department of Clinical Laboratory, Institute of Translational Medcine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Ruoxi Ran
- Department of Clinical Laboratory, Institute of Translational Medcine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Yuting Yang
- Department of General Office, School of Stomatology, Wuhan University, Wuhan, China
| | - Meixian Xiang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China
| | - Hanwen Su
- Department of Clinical Laboratory, Institute of Translational Medcine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China
| | - Jingtao Huang
- Department of Clinical Laboratory, Institute of Translational Medcine, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei, China.
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44
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Park ZM, Belnap E, Remillard M, Rose MD. Vir1p, the yeast homolog of virilizer, is required for mRNA m6A methylation and meiosis. Genetics 2023; 224:iyad043. [PMID: 36930734 PMCID: PMC10474941 DOI: 10.1093/genetics/iyad043] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/19/2023] Open
Abstract
N6-Methyladenosine (m6A) is among the most abundant modifications of eukaryotic mRNAs. mRNA methylation regulates many biological processes including playing an essential role in meiosis. During meiosis in the budding yeast, Saccharomyces cerevisiae, m6A levels peak early, before the initiation of the meiotic divisions. High-throughput studies suggested, and this work confirms that the uncharacterized protein Ygl036wp interacts with Kar4p, a component of the mRNA m6A-methyltransferase complex. Protein structure programs predict that Ygl036wp folds like VIRMA/Virilizer/VIR, which is involved in mRNA m6A-methylation in higher eukaryotes. In addition, Ygl036wp contains conserved motifs shared with VIRMA/Virilizer/VIR. Accordingly, we propose the name VIR1 for budding yeast ortholog of VIRMA/Virilizer/VIR 1. Vir1p interacts with all other members of the yeast methyltransferase complex and is itself required for mRNA m6A methylation and meiosis. In the absence of Vir1p proteins comprising the methyltransferase complex become unstable, suggesting that Vir1p acts as a scaffold for the complex. The vir1Δ/Δ mutant is defective for the premeiotic S-phase, which is suppressed by overexpression of the early meiotic transcription factor IME1; additional overexpression of the translational regulator RIM4 is required for sporulation. The vir1Δ/Δ mutant exhibits reduced levels of IME1 mRNA, as well as transcripts within Ime1p's regulon. Suppression by IME1 revealed an additional defect in the expression of the middle meiotic transcription factor, Ndt80p (and genes in its regulon), which is rescued by overexpression of RIM4. Together, these data suggest that Vir1p is required for cells to initiate the meiotic program and for progression through the meiotic divisions and spore formation.
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Affiliation(s)
- Zachory M Park
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Ethan Belnap
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Matthew Remillard
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Mark D Rose
- Department of Biology, Georgetown University, Washington, DC 20057, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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Zhu X, Zhou C, Zhao S, Zheng Z. Role of m6A methylation in retinal diseases. Exp Eye Res 2023; 231:109489. [PMID: 37084873 DOI: 10.1016/j.exer.2023.109489] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 03/06/2023] [Accepted: 04/19/2023] [Indexed: 04/23/2023]
Abstract
Retinal diseases remain among the leading causes of visual impairment in developed countries, despite great efforts in prevention and early intervention. Due to the limited efficacy of current retinal therapies, novel therapeutic methods are urgently required. Over the past two decades, advances in next-generation sequencing technology have facilitated research on RNA modifications, which can elucidate the relevance of epigenetic mechanisms to disease. N6-methyladenosine (m6A), formed by methylation of adenosine at the N6-position, is the most widely studied RNA modification and plays an important role in RNA metabolism. It is dynamically regulated by writers (methyltransferases) and erasers (demethylases), and recognized by readers (m6A binding proteins). Although the discovery of m6A methylation can be traced back to the 1970s, its regulatory roles in retinal diseases are rarely appreciated. Here, we provide an overview of m6A methylation, and discuss its effects and possible mechanisms on retinal diseases, including diabetic retinopathy, age-related macular degeneration, retinoblastoma, retinitis pigmentosa, and proliferative vitreoretinopathy. Furthermore, we highlight potential agents targeting m6A methylation for retinal disease treatment and discuss the limitations and challenges of research in the field of m6A methylation.
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Affiliation(s)
- Xinyu Zhu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, 200080, China
| | - Chuandi Zhou
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, 200080, China
| | - Shuzhi Zhao
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, 200080, China.
| | - Zhi Zheng
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China; National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, 200080, China.
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Shen LT, Che LR, He Z, Lu Q, Chen DF, Qin ZY, Wang B. Aberrant RNA m 6A modification in gastrointestinal malignancies: versatile regulators of cancer hallmarks and novel therapeutic opportunities. Cell Death Dis 2023; 14:236. [PMID: 37015927 PMCID: PMC10072051 DOI: 10.1038/s41419-023-05736-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/02/2023] [Accepted: 03/13/2023] [Indexed: 04/06/2023]
Abstract
Gastrointestinal (GI) cancer is one of the most common malignancies, and a leading cause of cancer-related death worldwide. However, molecular targeted therapies are still lacking, leading to poor treatment efficacies. As an important layer of epigenetic regulation, RNA N6-Methyladenosine (m6A) modification is recently linked to various biological hallmarks of cancer by orchestrating RNA metabolism, including RNA splicing, export, translation, and decay, which is partially involved in a novel biological process termed phase separation. Through these regulatory mechanisms, m6A dictates gene expression in a dynamic and reversible manner and may play oncogenic, tumor suppressive or context-dependent roles in GI tumorigenesis. Therefore, regulators and effectors of m6A, as well as their modified substrates, represent a novel class of molecular targets for cancer treatments. In this review, we comprehensively summarize recent advances in this field and highlight research findings that documented key roles of RNA m6A modification in governing hallmarks of GI cancers. From a historical perspective, milestone findings in m6A machinery are integrated with a timeline of developing m6A targeting compounds. These available chemical compounds, as well as other approaches that target core components of the RNA m6A pathway hold promises for clinical translational to treat human GI cancers. Further investigation on several outstanding issues, e.g. how oncogenic insults may disrupt m6A homeostasis, and how m6A modification impacts on the tumor microenvironment, may dissect novel mechanisms underlying human tumorigenesis and identifies next-generation anti-cancer therapeutics. In this review, we discuss advances in our understanding of m6A RNA modification since its discovery in the 1970s to the latest progress in defining its potential clinic relevance. We summarize the molecular basis and roles of m6A regulators in the hallmarks of GI cancer and discuss their context-dependent functions. Furthermore, the identification and characterization of inhibitors or activators of m6A regulators and their potential anti-cancer effects are discussed. With the rapid growth in this field there is significant potential for developing m6A targeted therapy in GI cancers.
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Affiliation(s)
- Li-Ting Shen
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, China
- Department of Internal Medicine, Hospital of Zhejiang Armed Police (PAP), Hangzhou, 310051, China
| | - Lin-Rong Che
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, China
| | - Zongsheng He
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, China
| | - Qian Lu
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, China
| | - Dong-Feng Chen
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, China
| | - Zhong-Yi Qin
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, China
- Institute of Pathology and Southwest Cancer Center, and Key Laboratory of Tumor Immunopathology of Ministry of Education of China, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China
- Jinfeng Laboratory, Chongqing, 401329, China
| | - Bin Wang
- Department of Gastroenterology & Chongqing Key Laboratory of Digestive Malignancies, Daping Hospital, Army Medical University (Third Military Medical University), Chongqing, 400042, China.
- Institute of Pathology and Southwest Cancer Center, and Key Laboratory of Tumor Immunopathology of Ministry of Education of China, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing, 400038, China.
- Jinfeng Laboratory, Chongqing, 401329, China.
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47
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Hong W, Zhao Y, Weng YL, Cheng C. Random Forest model reveals the interaction between N6-methyladenosine modifications and RNA-binding proteins. iScience 2023; 26:106250. [PMID: 36922995 PMCID: PMC10009289 DOI: 10.1016/j.isci.2023.106250] [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: 07/11/2022] [Revised: 12/16/2022] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
RNA-binding proteins (RBPs) have critical roles in N6-methyladenosine (m6A) modification process. We designed a Random Forest (RF) model to systematically analyze the interaction among RBPs and m6A modifications by integrating the binding signals from hundreds of RBPs. Accurate prediction of m6A sites demonstrated significant connections between RBP bindings and m6A modifications. The relative importance of different RBPs from the model provided a quantitative metric to evaluate their interactions with m6A modifications. Redundancy analysis showed that several RBPs may have similar binding patterns with m6A sites. The RF model exhibited fairly high prediction accuracy across cell lines, suggesting a conservative RBP interaction network regulates m6A occupancy. Specific RBPs can engage to the corresponding regional m6A sites and deploy distinct regulatory processes, such as cleavage site selection of the alternative polyadenylation (APA). We also integrated histone modifications into our RF model, which demonstrated H3K36me3 and H3K27me3 as determining features for m6A distribution.
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Affiliation(s)
- Wei Hong
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yanding Zhao
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi-Lan Weng
- Center for Neuroregeneration, Department of Neurosurgery, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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Li S, Liu H, Ruan Z, Guo R, Sun C, Tang Y, Huang X, Gao T, Hao S, Li H, Song N, Su Y, Ning F, Li Z, Chang T. Landscape analysis of m6A modification regulators related biological functions and immune characteristics in myasthenia gravis. J Transl Med 2023; 21:166. [PMID: 36864526 PMCID: PMC9983271 DOI: 10.1186/s12967-023-03947-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/01/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) modification has been recognized to play fundamental roles in the development of autoimmune diseases. However, the implication of m6A modification in myasthenia gravis (MG) remains largely unknown. Thus, we aimed to systematically explore the potential functions and related immune characteristics of m6A regulators in MG. METHODS The GSE85452 dataset with MG and healthy samples was downloaded from Gene Expression Omnibus (GEO) database. m6A modification regulators were manually curated. The targets of m6A regulators were obtained from m6A2Target database. The differential expressed m6A regulators in GSE85452 dataset were identified by "limma" package and were validated by RT-PCR. Function enrichment analysis of dysregulated m6A regulators was performed using "clusterProfiler" package. Correlation analysis was applied for analyzing the relationships between m6A regulators and immune characteristics. Unsupervised clustering analysis was used to identify distinct m6A modification subtypes. The differences between subtypes were analyzed, including the expression level of all genes and the enrichment degree of immune characteristics. Weighted gene co-expression network analysis (WGCNA) was conducted to obtain modules associated with m6A modification subtypes. RESULTS We found that CBLL1, RBM15 and YTHDF1 were upregulated in MG samples of GSE85452 dataset, and the results were verified by RT-PCR in blood samples from19 MG patients and 19 controls. The targeted genes common modified by CBLL1, RBM15, and YTHDF1 were mainly enriched in histone modification and Wnt signaling pathway. Correlation analysis showed that three dysregulated m6A regulators were closely associated with immune characteristics. Among them, RBM15 possessed the strongest correlation with immune characteristics, including CD56dim natural killer cell (r = 0.77, P = 0.0023), T follicular helper cell (r = - 0.86, P = 0.0002), Interferon Receptor (r = 0.78, P = 0.0017), and HLA-DOA (r = 0.64, P = 0.0200). Further two distinct m6A modification patterns mediated by three dysregulated m6A regulators was identified. Bioinformatics analysis found that there were 3029 differentially expressed genes and different immune characteristics between two m6A modification patterns. Finally, WGCNA analysis obtained a total of 12 modules and yellow module was the most positively correlated to subtype-2. CONCLUSION Our findings suggested that m6A RNA modification had an important effect on immunity molecular mechanism of MG and provided a new perspective into understanding the pathogenesis of MG.
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Affiliation(s)
- Shuang Li
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Hui Liu
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China.,Xi'an Medical University, Xi'an, 710021, Shaanxi, China
| | - Zhe Ruan
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Rongjing Guo
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Chao Sun
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yonglan Tang
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Xiaoxi Huang
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Ting Gao
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Sijia Hao
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Huanhuan Li
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Na Song
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yue Su
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Fan Ning
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Zhuyi Li
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Ting Chang
- Department of Neurology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, 710038, Shaanxi, China.
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49
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Appel LM, Benedum J, Engl M, Platzer S, Schleiffer A, Strobl X, Slade D. SPOC domain proteins in health and disease. Genes Dev 2023; 37:140-170. [PMID: 36927757 PMCID: PMC10111866 DOI: 10.1101/gad.350314.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Since it was first described >20 yr ago, the SPOC domain (Spen paralog and ortholog C-terminal domain) has been identified in many proteins all across eukaryotic species. SPOC-containing proteins regulate gene expression on various levels ranging from transcription to RNA processing, modification, export, and stability, as well as X-chromosome inactivation. Their manifold roles in controlling transcriptional output implicate them in a plethora of developmental processes, and their misregulation is often associated with cancer. Here, we provide an overview of the biophysical properties of the SPOC domain and its interaction with phosphorylated binding partners, the phylogenetic origin of SPOC domain proteins, the diverse functions of mammalian SPOC proteins and their homologs, the mechanisms by which they regulate differentiation and development, and their roles in cancer.
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Affiliation(s)
- Lisa-Marie Appel
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Johannes Benedum
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Magdalena Engl
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sebastian Platzer
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), 1030 Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Xué Strobl
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Dea Slade
- Department of Radiation Oncology, Medical University of Vienna, 1090 Vienna, Austria;
- Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
- Department of Medical Biochemistry, Medical University of Vienna, Max Perutz Laboratories, Vienna Biocenter, 1030 Vienna, Austria
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50
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Wang S, Li H, Lian Z, Deng S. The Role of m 6A Modifications in B-Cell Development and B-Cell-Related Diseases. Int J Mol Sci 2023; 24:4721. [PMID: 36902149 PMCID: PMC10003095 DOI: 10.3390/ijms24054721] [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: 12/10/2022] [Revised: 01/17/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023] Open
Abstract
B cells are a class of professional antigen-presenting cells that produce antibodies to mediate humoral immune response and participate in immune regulation. m6A modification is the most common RNA modification in mRNA; it involves almost all aspects of RNA metabolism and can affect RNA splicing, translation, stability, etc. This review focuses on the B-cell maturation process as well as the role of three m6A modification-related regulators-writer, eraser, and reader-in B-cell development and B-cell-related diseases. The identification of genes and modifiers that contribute to immune deficiency may shed light on regulatory requirements for normal B-cell development and the underlying mechanism of some common diseases.
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Affiliation(s)
- Shuqi Wang
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huanxiang Li
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhengxing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shoulong Deng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing 100021, China
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