51
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Selberg S, Seli N, Kankuri E, Karelson M. Rational Design of Novel Anticancer Small-Molecule RNA m6A Demethylase ALKBH5 Inhibitors. ACS OMEGA 2021; 6:13310-13320. [PMID: 34056479 PMCID: PMC8158789 DOI: 10.1021/acsomega.1c01289] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/05/2021] [Indexed: 05/05/2023]
Abstract
The RNA 6-N-methyladenosine (m6A) demethylase ALKBH5 has been shown to be oncogenic in several cancer types, including leukemia and glioblastoma. We present here the target-tailored development and first evaluation of the antiproliferative effects of new ALKBH5 inhibitors. Two compounds, 2-[(1-hydroxy-2-oxo-2-phenylethyl)sulfanyl]acetic acid (3) and 4-{[(furan-2-yl)methyl]amino}-1,2-diazinane-3,6-dione (6), with IC50 values of 0.84 μM and 1.79 μM, respectively, were identified in high-throughput virtual screening of the library of 144 000 preselected compounds and subsequent verification of hits in an m6A antibody-based enzyme-linked immunosorbent assay (ELISA) enzyme inhibition assay. The effect of these compounds on the proliferation of selected target cancer cell lines was then measured. In the case of three leukemia cell lines (HL-60, CCRF-CEM, and K562) the cell proliferation was suppressed at low micromolar concentrations of inhibitors, with IC50 ranging from 1.38 to 16.5 μM. However, the effect was low or negligible in the case of another leukemia cell line, Jurkat, and the glioblastoma cell line A-172. These results demonstrate the potential of ALKBH5 inhibition as a cancer-cell-type-selective antiproliferative strategy.
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Affiliation(s)
- Simona Selberg
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
| | - Neinar Seli
- Chemestmed, Ltd., Riia tn 130b/2, Tartu 50411, Estonia
| | - Esko Kankuri
- Faculty of Medicine, Department of Pharmacology, University of Helsinki, Helsinki 00014, Finland
| | - Mati Karelson
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu 50411, Estonia
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52
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Mathoux J, Henshall DC, Brennan GP. Regulatory Mechanisms of the RNA Modification m 6A and Significance in Brain Function in Health and Disease. Front Cell Neurosci 2021; 15:671932. [PMID: 34093133 PMCID: PMC8170084 DOI: 10.3389/fncel.2021.671932] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/19/2021] [Indexed: 12/11/2022] Open
Abstract
RNA modifications have emerged as an additional layer of regulatory complexity governing the function of almost all species of RNA. N6-methyladenosine (m6A), the addition of methyl groups to adenine residues, is the most abundant and well understood RNA modification. The current review discusses the regulatory mechanisms governing m6A, how this influences neuronal development and function and how aberrant m6A signaling may contribute to neurological disease. M6A is known to regulate the stability of mRNA, the processing of microRNAs and function/processing of tRNAs among other roles. The development of antibodies against m6A has facilitated the application of next generation sequencing to profile methylated RNAs in both health and disease contexts, revealing the extent of this transcriptomic modification. The mechanisms by which m6A is deposited, processed, and potentially removed are increasingly understood. Writer enzymes include METTL3 and METTL14 while YTHDC1 and YTHDF1 are key reader proteins, which recognize and bind the m6A mark. Finally, FTO and ALKBH5 have been identified as potential erasers of m6A, although there in vivo activity and the dynamic nature of this modification requires further study. M6A is enriched in the brain and has emerged as a key regulator of neuronal activity and function in processes including neurodevelopment, learning and memory, synaptic plasticity, and the stress response. Changes to m6A have recently been linked with Schizophrenia and Alzheimer disease. Elucidating the functional consequences of m6A changes in these and other brain diseases may lead to novel insight into disease pathomechanisms, molecular biomarkers and novel therapeutic targets.
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Affiliation(s)
- Justine Mathoux
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin, Ireland.,FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - David C Henshall
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin, Ireland.,FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin, Ireland
| | - Gary P Brennan
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin, Ireland.,UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
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53
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Lan Y, Liu B, Guo H. The role of M 6A modification in the regulation of tumor-related lncRNAs. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 24:768-779. [PMID: 33996258 PMCID: PMC8094576 DOI: 10.1016/j.omtn.2021.04.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
N6-methyladenosine (m6A) is the most abundant modification in eukaryotic cells, and it regulates RNA transcription, processing, splicing, degradation, and translation. Long non-coding RNAs (lncRNAs), as transcriptional products with no or limited protein coding ability more than 200 nt in length, play an important role in epigenetic modification, mRNA transcription, splicing, stability, translation, and other biological functions. Extensive studies have shown that both m6A modification and lncRNAs are involved in the pathogenesis of various diseases, such as kinds of cancers, heart failure, Alzheimer’s disease, periodontitis, human abdominal aortic aneurysm, and obesity. To date, m6A modification has been identified as an important biological function in enrichment and regulation of lncRNAs. In this review, we summarize the role of m6A modification in the regulation and function of tumor-related lncRNAs. Moreover, we discuss the potential applications and possible future directions in the field.
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Affiliation(s)
- Yufei Lan
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Boyang Liu
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Hongbo Guo
- Neurosurgery Center, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China on Diagnosis and Treatment of Cerebrovascular Disease, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
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54
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Fang F, Wang X, Li Z, Ni K, Xiong C. Epigenetic regulation of mRNA N6-methyladenosine modifications in mammalian gametogenesis. Mol Hum Reprod 2021; 27:6212059. [PMID: 33823008 DOI: 10.1093/molehr/gaab025] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/12/2021] [Indexed: 12/20/2022] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent epigenetic modification of mRNAs and broadly influences various biological processes by regulating post-transcriptional gene expression in eukaryotes. The reversible m6A modification is catalyzed by methyltransferases, METTL3 and METTL14 (writers), removed by the demethylases FTO and ALKBH5 (erasers) and recognized by m6A-binding proteins, namely the YTH domain-containing family of proteins (readers). Both m6A modification and the related enzymes are involved in the regulation of normal gametogenesis and embryonic development in many species. Recent studies showed that loss of m6A compromises gamete maturation, sex hormone synthesis, fertility and early embryonic development. In this review, we have summarized the most recent findings on the role of mRNA m6A modification in mammalian gametogenesis to emphasize the epigenetic regulation of mRNA in the reproductive system.
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Affiliation(s)
- Fang Fang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Xiao Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zili Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ke Ni
- Department of Gynecology and Obstetrics, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Chengliang Xiong
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.,Center of Reproductive Medicine, Wuhan Tongji Reproductive Medicine Hospital, Wuhan 430013, China
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55
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Destefanis E, Avşar G, Groza P, Romitelli A, Torrini S, Pir P, Conticello SG, Aguilo F, Dassi E. A mark of disease: how mRNA modifications shape genetic and acquired pathologies. RNA (NEW YORK, N.Y.) 2021; 27:367-389. [PMID: 33376192 PMCID: PMC7962492 DOI: 10.1261/rna.077271.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
RNA modifications have recently emerged as a widespread and complex facet of gene expression regulation. Counting more than 170 distinct chemical modifications with far-reaching implications for RNA fate, they are collectively referred to as the epitranscriptome. These modifications can occur in all RNA species, including messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). In mRNAs the deposition, removal, and recognition of chemical marks by writers, erasers and readers influence their structure, localization, stability, and translation. In turn, this modulates key molecular and cellular processes such as RNA metabolism, cell cycle, apoptosis, and others. Unsurprisingly, given their relevance for cellular and organismal functions, alterations of epitranscriptomic marks have been observed in a broad range of human diseases, including cancer, neurological and metabolic disorders. Here, we will review the major types of mRNA modifications and editing processes in conjunction with the enzymes involved in their metabolism and describe their impact on human diseases. We present the current knowledge in an updated catalog. We will also discuss the emerging evidence on the crosstalk of epitranscriptomic marks and what this interplay could imply for the dynamics of mRNA modifications. Understanding how this complex regulatory layer can affect the course of human pathologies will ultimately lead to its exploitation toward novel epitranscriptomic therapeutic strategies.
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Affiliation(s)
- Eliana Destefanis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- The EPITRAN COST Action Consortium, COST Action CA16120
| | - Gülben Avşar
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Bioengineering, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Paula Groza
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Medical Biosciences, Umeå University, 901 87 Umeå, Sweden
- Wallenberg Center for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Antonia Romitelli
- The EPITRAN COST Action Consortium, COST Action CA16120
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy
- Department of Medical Biotechnologies, Università di Siena, 53100 Siena, Italy
| | - Serena Torrini
- The EPITRAN COST Action Consortium, COST Action CA16120
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy
- Department of Medical Biotechnologies, Università di Siena, 53100 Siena, Italy
| | - Pınar Pir
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Bioengineering, Gebze Technical University, 41400 Kocaeli, Turkey
| | - Silvestro G Conticello
- The EPITRAN COST Action Consortium, COST Action CA16120
- Core Research Laboratory, ISPRO-Institute for Cancer Research, Prevention and Clinical Network, 50139 Firenze, Italy
- Institute of Clinical Physiology, National Research Council, 56124 Pisa, Italy
| | - Francesca Aguilo
- The EPITRAN COST Action Consortium, COST Action CA16120
- Department of Medical Biosciences, Umeå University, 901 87 Umeå, Sweden
- Wallenberg Center for Molecular Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Erik Dassi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
- The EPITRAN COST Action Consortium, COST Action CA16120
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56
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Ma X, Long C, Wang F, Lou B, Yuan M, Duan F, Yang Y, Li J, Qian X, Zeng J, Lin S, Shen H, Lin X. METTL3 attenuates proliferative vitreoretinopathy and epithelial-mesenchymal transition of retinal pigment epithelial cells via wnt/β-catenin pathway. J Cell Mol Med 2021; 25:4220-4234. [PMID: 33759344 PMCID: PMC8093987 DOI: 10.1111/jcmm.16476] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/28/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Proliferative vitreoretinopathy (PVR) is a refractory vitreoretinal fibrosis disease, and epithelial-mesenchymal transition (EMT) of retinal pigment epithelial (RPE) cells is the key pathological mechanism of PVR. However, few studies focused on the role of METTL3, the dominating methyltransferase for m6A RNA modification in PVR pathogenesis. Immunofluorescence staining and qRT-PCR were used to determine the expression of METTL3 in human tissues. Lentiviral transfection was used to stably overexpress and knockdown METTL3 in ARPE-19 cells. MTT assay was employed to study the effects of METTL3 on cell proliferation. The impact of METTL3 on the EMT of ARPE-19 cells was assessed by migratory assay, morphological observation and expression of EMT markers. Intravitreal injection of cells overexpressing METTL3 was used to assess the impact of METTL3 on the establishment of the PVR model. We found that METTL3 expression was less in human PVR membranes than in the normal RPE layers. In ARPE-19 cells, total m6A abundance and the METTL3 expression were down-regulated after EMT. Additionally, METTL3 overexpression inhibited cell proliferation through inducing cell cycle arrest at G0/G1 phase. Furthermore, METTL3 overexpression weakened the capacity of TGFβ1 to trigger EMT by regulating wnt/β -catenin pathway. Oppositely, knockdown of METTL3 facilitated proliferation and EMT of ARPE-19 cells. In vivo, intravitreal injection of METTL3-overexpressing cells delayed the development of PVR compared with injection of control cells. In summary, this study suggested that METTL3 is involved in the PVR process, and METTL3 overexpression inhibits the EMT of ARPE-19 cells in vitro and suppresses the PVR process in vivo.
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Affiliation(s)
- Xinqi Ma
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Chongde Long
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Fangyu Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Bingsheng Lou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Miner Yuan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Fang Duan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yao Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jiaqing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaobing Qian
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jieting Zeng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shuibin Lin
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Huangxuan Shen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Biobank of Eye, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaofeng Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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57
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Abstract
PURPOSE OF REVIEW In recent years, the N6-methyladenosine (m6A) modification of RNA has been shown to play an important role in the development of acute myeloid leukemia (AML) and the maintenance of leukemic stem cells (LSCs). In this review we summarise the recent findings in the field of epitranscriptomics related to m6A and its relevance in AML. RECENT FINDINGS Recent studies have focused on the role of m6A regulators in the development of AML and their potential as translational targets. The writer Methyltransferase Like 3 and its binding partner Methyltransferase Like 14, as well as the reader YTH domain-containing family protein 2, were shown to be vital for LSC survival, and their loss has detrimental effects on AML cells. Similar observations were made with the demethylases fat mass and obesity-associated protein and AlkB homologue 5 RNA demethylase. Of importance, loss of any of these genes has little to no effect on normal hemopoietic stem cells, suggesting therapeutic potential. SUMMARY The field of epitranscriptomics is still in its infancy and the importance of m6A and other RNA-modifications in AML will only come into sharper focus. The development of therapeutics targeting RNA-modifying enzymes may open up new avenues for treatment of such malignancies.
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Affiliation(s)
- Eliza Yankova
- Milner Therapeutics Institute, University of Cambridge, Puddicombe Way
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Demetrios Aspris
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
- The Center for the Study of Hematological Malignancies, Nicandrou Papamina Avenue, Nicosia, Cyprus
| | - Konstantinos Tzelepis
- Milner Therapeutics Institute, University of Cambridge, Puddicombe Way
- Haematological Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
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58
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Schaefer MR. The Regulation of RNA Modification Systems: The Next Frontier in Epitranscriptomics? Genes (Basel) 2021; 12:genes12030345. [PMID: 33652758 PMCID: PMC7996938 DOI: 10.3390/genes12030345] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/12/2022] Open
Abstract
RNA modifications, long considered to be molecular curiosities embellishing just abundant and non-coding RNAs, have now moved into the focus of both academic and applied research. Dedicated research efforts (epitranscriptomics) aim at deciphering the underlying principles by determining RNA modification landscapes and investigating the molecular mechanisms that establish, interpret and modulate the information potential of RNA beyond the combination of four canonical nucleotides. This has resulted in mapping various epitranscriptomes at high resolution and in cataloguing the effects caused by aberrant RNA modification circuitry. While the scope of the obtained insights has been complex and exciting, most of current epitranscriptomics appears to be stuck in the process of producing data, with very few efforts to disentangle cause from consequence when studying a specific RNA modification system. This article discusses various knowledge gaps in this field with the aim to raise one specific question: how are the enzymes regulated that dynamically install and modify RNA modifications? Furthermore, various technologies will be highlighted whose development and use might allow identifying specific and context-dependent regulators of epitranscriptomic mechanisms. Given the complexity of individual epitranscriptomes, determining their regulatory principles will become crucially important, especially when aiming at modifying specific aspects of an epitranscriptome both for experimental and, potentially, therapeutic purposes.
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Affiliation(s)
- Matthias R Schaefer
- Centre for Anatomy & Cell Biology, Division of Cell-and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Haus C, 1st Floor, 1090 Vienna, Austria
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59
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Tassinari V, Cesarini V, Tomaselli S, Ianniello Z, Silvestris DA, Ginistrelli LC, Martini M, De Angelis B, De Luca G, Vitiani LR, Fatica A, Locatelli F, Gallo A. ADAR1 is a new target of METTL3 and plays a pro-oncogenic role in glioblastoma by an editing-independent mechanism. Genome Biol 2021; 22:51. [PMID: 33509238 PMCID: PMC7842030 DOI: 10.1186/s13059-021-02271-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/14/2021] [Indexed: 01/15/2023] Open
Abstract
Background N6-methyladenosine (m6A) and adenosine-to-inosine (A-to-I) RNA editing are two of the most abundant RNA modification events affecting adenosines in mammals. Both these RNA modifications determine mRNA fate and play a pivotal role in tumor development and progression. Results Here, we show that METTL3, upregulated in glioblastoma, methylates ADAR1 mRNA and increases its protein level leading to a pro-tumorigenic mechanism connecting METTL3, YTHDF1, and ADAR1. We show that ADAR1 plays a cancer-promoting role independently of its deaminase activity by binding CDK2 mRNA, underlining the importance of ADARs as essential RNA-binding proteins for cell homeostasis as well as cancer progression. Additionally, we show that ADAR1 knockdown is sufficient to strongly inhibit glioblastoma growth in vivo. Conclusions Hence, our findings underscore METTL3/ADAR1 axis as a novel crucial pathway in cancer progression that connects m6A and A-to-I editing post-transcriptional events. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02271-9.
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Affiliation(s)
- Valentina Tassinari
- Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesu, Viale di San Paolo 15, 00146, Rome, Italy.,Present address: Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Valeriana Cesarini
- Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesu, Viale di San Paolo 15, 00146, Rome, Italy.,Present address: Department of Biomedical Sciences, Institute of Translational Pharmacology, National Research Council of Italy (CNR), Rome, Italy
| | - Sara Tomaselli
- Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesu, Viale di San Paolo 15, 00146, Rome, Italy
| | - Zaira Ianniello
- Department of Biology and Biotechnology "Charles Darwin", La Sapienza University of Rome, Rome, Italy
| | | | - Lavinia Ceci Ginistrelli
- Department of Biology and Biotechnology "Charles Darwin", La Sapienza University of Rome, Rome, Italy
| | - Maurizio Martini
- Department of Women's, Children's and Public Health Studies, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy.,Department of Health Science and Public Health, Institute of Pathology, Largo F. vito 1, 00168, Rome, Italy
| | - Biagio De Angelis
- Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesu, Viale di San Paolo 15, 00146, Rome, Italy
| | - Gabriele De Luca
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Lucia Ricci Vitiani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology "Charles Darwin", La Sapienza University of Rome, Rome, Italy
| | - Franco Locatelli
- Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesu, Viale di San Paolo 15, 00146, Rome, Italy.,Department of Pediatrics, La Sapienza University of Rome, Rome, Italy
| | - Angela Gallo
- Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesu, Viale di San Paolo 15, 00146, Rome, Italy.
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60
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Worpenberg L, Paolantoni C, Longhi S, Mulorz MM, Lence T, Wessels HH, Dassi E, Aiello G, Sutandy FXR, Scheibe M, Edupuganti RR, Busch A, Möckel MM, Vermeulen M, Butter F, König J, Notarangelo M, Ohler U, Dieterich C, Quattrone A, Soldano A, Roignant JY. Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila. EMBO J 2021; 40:e104975. [PMID: 33428246 PMCID: PMC7883056 DOI: 10.15252/embj.2020104975] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022] Open
Abstract
N6‐methyladenosine (m6A) regulates a variety of physiological processes through modulation of RNA metabolism. This modification is particularly enriched in the nervous system of several species, and its dysregulation has been associated with neurodevelopmental defects and neural dysfunctions. In Drosophila, loss of m6A alters fly behavior, albeit the underlying molecular mechanism and the role of m6A during nervous system development have remained elusive. Here we find that impairment of the m6A pathway leads to axonal overgrowth and misguidance at larval neuromuscular junctions as well as in the adult mushroom bodies. We identify Ythdf as the main m6A reader in the nervous system, being required to limit axonal growth. Mechanistically, we show that the m6A reader Ythdf directly interacts with Fmr1, the fly homolog of Fragile X mental retardation RNA binding protein (FMRP), to inhibit the translation of key transcripts involved in axonal growth regulation. Altogether, this study demonstrates that the m6A pathway controls development of the nervous system and modulates Fmr1 target transcript selection.
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Affiliation(s)
- Lina Worpenberg
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Chiara Paolantoni
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Sara Longhi
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | | | - Tina Lence
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Hans-Hermann Wessels
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department CIBIO, University of Trento, Trento, Italy
| | - Giuseppe Aiello
- Armenise-Harvard Laboratory of Brain Disorders and Cancer, Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Raghu R Edupuganti
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anke Busch
- Bioinformatics Core Facility, IMB, Mainz, Germany
| | | | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Michela Notarangelo
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Uwe Ohler
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.,Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner site Heidelberg-Mannheim, Heidelberg, Germany
| | - Alessandro Quattrone
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Alessia Soldano
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Génopode Building, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.,Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
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61
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Yin L, Zhu X, Novák P, Zhou L, Gao L, Yang M, Zhao G, Yin K. The epitranscriptome of long noncoding RNAs in metabolic diseases. Clin Chim Acta 2021; 515:80-89. [PMID: 33422492 DOI: 10.1016/j.cca.2021.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) have abundant content and extensive functions that regulate the expression of genes at multiple levels. Recently, transcriptome-wide analysis confirmed that RNA can undergo various chemical modifications in response to stimulation by the environment that further determine the action mechanisms of RNAs and expand the diversity of the transcriptome. Modifications that occur in lncRNAs can affect their expression and the regulation of downstream molecules by changing the secondary structure, splicing, degradation or molecular stability of lncRNAs. During the development of metabolic diseases, reversible RNA modifications show a complex transcriptional landscape. Although a wide quantity and variety of lncRNA modifications have been identified, the knowledge regarding their underlying actions in alcohol use disorders (AUDs), osteoporosis, obesity, and cardiovascular disease (CVD) is still in its infancy. Herein, we will focus on the epitranscriptomic modifications that occur on lncRNAs and the crosstalk between them that affect metabolic diseases.
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Affiliation(s)
- Linjie Yin
- Research Lab for Clinical & Translational Medicine, Medical School, University of South China, Hengyang 421001, China; The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Xiao Zhu
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Petr Novák
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Le Zhou
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - Ling Gao
- Research Lab for Clinical & Translational Medicine, Medical School, University of South China, Hengyang 421001, China
| | - Min Yang
- Research Lab for Clinical & Translational Medicine, Medical School, University of South China, Hengyang 421001, China; The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China
| | - GuoJun Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan City People's Hospital, Qingyuan 511518, China.
| | - Kai Yin
- The Second Affiliated Hospital of Guilin Medical University, Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin, Guangxi 541100, China.
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Huang J, Chen Z, Chen X, Chen J, Cheng Z, Wang Z. The role of RNA N 6-methyladenosine methyltransferase in cancers. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:887-896. [PMID: 33614237 PMCID: PMC7868687 DOI: 10.1016/j.omtn.2020.12.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Modification of eukaryotic RNA by methylation of adenosine residues to generate N6-methyladenosine (m6A) is a highly prevalent process. m6A is dynamically regulated during cell metabolism and embryo development, and it is mainly involved in various aspects of RNA metabolism, including RNA splicing, processing, transport from the nucleus, translation, and degradation. Accumulating evidence shows that dynamic changes to m6A are closely related to the occurrence and development of cancer and that methyltransferases, as key elements in the dynamic regulation of m6A, play a crucial role in these processes. Therefore, in this review, we describe the role of methyltransferases as m6A writers in cancer and summarize their potential molecular mechanisms of action.
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Affiliation(s)
- Jiali Huang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Zhenyao Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Xin Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Jun Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China.,Department of Oncology, Suzhou Ninth People's Hospital, Suzhou, China
| | - Zhixiang Cheng
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
| | - Zhaoxia Wang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, China
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63
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Lunger JC, Batista PJ. You Get a Modification, and You Get a Modification… Everyone Gets a Modification! Mol Cell 2020; 80:557-559. [PMID: 33217314 DOI: 10.1016/j.molcel.2020.10.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In this issue of Molecular Cell,Sun et al. (2020) identify ERK-mediated phosphorylation of the m6A methyltransferase complex as a regulatory mechanism for m6A and pluripotency and highlight the potential of this interaction as a target for cancer therapy.
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Affiliation(s)
- Judith C Lunger
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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64
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Pei Y, Lou X, Li K, Xu X, Guo Y, Xu D, Yang Z, Xu D, Cui W, Zhang D. Peripheral Blood Leukocyte N6-methyladenosine is a Noninvasive Biomarker for Non-small-cell Lung Carcinoma. Onco Targets Ther 2020; 13:11913-11921. [PMID: 33239892 PMCID: PMC7682600 DOI: 10.2147/ott.s267344] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Background N6-methyladenosine (m6A) triggers a new layer of epi-transcription. However, the potential noninvasive screening and diagnostic value of peripheral blood m6A for cancer are still unknown. Here, we intend to investigate whether leukocyte m6A can be a novel biomarker for non-small-cell lung cancer (NSCLC). Materials and Methods Peripheral blood was collected from 119 NSCLC patients and 74 age-matched healthy controls. Total RNA was isolated from leukocytes for m6A measurement, and clinical information of participants was reviewed. The sensitivity, specificity, and area under the curve (AUC) of m6A for cancer diagnosis were evaluated by the receiver-operating characteristic (ROC) curve analysis. Flow cytometry and the Human Protein Atlas (HPA) database were used to characterize m6A in leukocyte differentials. Pearson's correlation was applied to indicate the relationship between m6A level and hematology variables. qPCR and bioinformatic analysis were used to identity the expression of m6A regulators in leukocyte. Results Leukocyte m6A was significantly elevated in 119 NSCLC patients compared with 74 healthy controls (P<0.001). We did not find significant association between m6A and age or gender. Elevated m6A level in NSCLC was associated with tumor stage (P<0.05) and tumor differentiation (P<0.05), and was significantly reduced after surgery (P<0.01). ROC curve analysis revealed that leukocyte m6A could significantly discriminate patients with lung adenocarcinoma (LUAD) (AUC=0.736, P<0.001) and lung squamous cell carcinoma (LUSC) (AUC=0.963, P<0.001) from healthy individuals. m6A displayed superior sensitivity (100%) and specificity (85.7%) for LUSC than squamous cell carcinoma (SCC) antigen and cytokeratin fragment 211 (Cyfra211). Flow cytometry analysis showed m6A modification was mainly localized on T cells and monocytes among leukocyte differentials. Leukocyte m6A was positively correlated with the number of lymphocytes and negatively correlated with monocytes in NSCLC but not in healthy controls. qPCR and bioinformatic analysis showed that elevated leukocyte m6A in NSCLC was caused by upregulated methyltransferase complex and downregulated FTO and ALKBH5. Conclusion Leukocyte m6A represents a potential noninvasive biomarker for NSCLC screening, monitoring and diagnosis.
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Affiliation(s)
- Yuqing Pei
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Xiaoying Lou
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Kexin Li
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Xiaotian Xu
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Ye Guo
- Department of Laboratory Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, People's Republic of China
| | - Danfei Xu
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Zhenxi Yang
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Dongsheng Xu
- Hematopathology Program, CBL Path, Inc, Rye Brook, NY 10753, USA
| | - Wei Cui
- State Key Laboratory of Molecular Oncology, Department of Clinical Laboratory, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
| | - Donghong Zhang
- Center for Molecular and Translational Medicine, Georgia State University, Research Science Center, Atlanta, GA 30303, USA
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65
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Sun D, Zhao T, Zhang Q, Wu M, Zhang Z. Fat mass and obesity-associated protein regulates lipogenesis via m 6 A modification in fatty acid synthase mRNA. Cell Biol Int 2020; 45:334-344. [PMID: 33079435 DOI: 10.1002/cbin.11490] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/01/2020] [Accepted: 10/18/2020] [Indexed: 12/13/2022]
Abstract
As the first identified N6 -methyladenosine (m6 A) demethylase, fat mass and obesity-associated (FTO) protein is associated with fatty acid synthase (FASN) and lipid accumulation. However, little is known about the regulatory role of FTO in the expression of FASN and de novo lipogenesis through m6 A modification. In this study, we used FTO small interfering RNA to explore the effects of FTO knockdown on hepatic lipogenesis and its underlying epigenetic mechanism in HepG2 cells. We found that knockdown of FTO increased m6 A levels in total RNA and enhanced the expression of YTH domain family member 2 which serves as the m6 A-binding protein. The de novo lipogenic enzymes and intracellular lipid content were significantly decreased under FTO knockdown. Mechanistically, knockdown of FTO dramatically enhanced m6 A levels in FASN messenger RNA (mRNA), leading to the reduced expression of FASN mRNA through m6 A-mediated mRNA decay. The protein expressions of FASN along with acetyl CoA carboxylase and ATP-citrate lyase were further decreased, which inhibited de novo lipogenesis, thereby resulting in the deficiency of lipid accumulation in HepG2 cells and the induction of cellular apoptosis. The results reveal that FTO regulates hepatic lipogenesis via FTO-dependent m6 A demethylation in FASN mRNA and indicate the critical role of FTO-mediated lipid metabolism in the survival of HepG2 cells. This study provides novel insights into a unique RNA epigenetic mechanism by which FTO mediates hepatic lipid accumulation through m6 A modification and indicates that FTO could be a potential target for obesity-related diseases and cancer.
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Affiliation(s)
- Donglei Sun
- Department of Environmental and Occupational Health, West China School of Public Health, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Tianhe Zhao
- Department of Environmental and Occupational Health, West China School of Public Health, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qian Zhang
- Department of Environmental and Occupational Health, West China School of Public Health, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mei Wu
- Department of Environmental and Occupational Health, West China School of Public Health, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zunzhen Zhang
- Department of Environmental and Occupational Health, West China School of Public Health, West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
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66
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Hao L, Wang JM, Liu BQ, Yan J, Li C, Jiang JY, Zhao FY, Qiao HY, Wang HQ. m6A-YTHDF1-mediated TRIM29 upregulation facilitates the stem cell-like phenotype of cisplatin-resistant ovarian cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118878. [PMID: 33011193 DOI: 10.1016/j.bbamcr.2020.118878] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/05/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023]
Abstract
Ovarian cancer is the deadliest gynaecologic malignancy, and the five-year survival rate of patients is less than 35% worldwide. Cancer stem cells (CSCs) are a population of cells with stem-like characteristics that are thought to cause chemoresistance and recurrence. TRIM29 is aberrantly expressed in various cancers and associated with cancer development and progression. Previous studies showed that the upregulation of TRIM29 expression in pancreatic cancer is related to stem-like characteristics. However, the role of TRIM29 in ovarian cancer is poorly understood. In this study, we found that TRIM29 expression was increased at the translational level in both the cisplatin-resistant ovarian cancer cells and clinical tissues. Increased TRIM29 expression was associated with a poor prognosis of patients with ovarian cancer. In addition, TRIM29 could enhance the CSC-like characteristics of the cisplatin-resistant ovarian cancer cells. Recruitment of YTHDF1 to m6A-modified TRIM29 was involved in promoting TRIM29 translation in the cisplatin-resistant ovarian cancer cells. Knockdown of YTHDF1 suppressed the CSC-like characteristics of the cisplatin-resistant ovarian cancer cells, which could be rescued by ectopic expression of TRIM29. This study suggests TRIM29 may act as an oncogene to promote the CSC-like features of cisplatin-resistant ovarian cancer in an m6A-YTHDF1-dependent manner. Due to the roles of TRIM29 and YTHDF1 in the promotion of CSC-like features, they may become potential therapeutic targets to combat the recurrence of ovarian cancer.
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Affiliation(s)
- Liang Hao
- Department of Biochemistry & Molecular Biology, China Medical University, Shenyang 110122, China; Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China; Department of Chemistry, China Medical University, Shenyang 110122, China
| | - Jia-Mei Wang
- Department of Biochemistry & Molecular Biology, China Medical University, Shenyang 110122, China
| | - Bao-Qin Liu
- Department of Biochemistry & Molecular Biology, China Medical University, Shenyang 110122, China
| | - Jing Yan
- Department of Biochemistry & Molecular Biology, China Medical University, Shenyang 110122, China
| | - Chao Li
- Department of Biochemistry & Molecular Biology, China Medical University, Shenyang 110122, China
| | - Jing-Yi Jiang
- Department of Biochemistry & Molecular Biology, China Medical University, Shenyang 110122, China
| | - Fu-Ying Zhao
- Department of Biochemistry & Molecular Biology, China Medical University, Shenyang 110122, China
| | - Huai-Yu Qiao
- Department of Biochemistry & Molecular Biology, China Medical University, Shenyang 110122, China
| | - Hua-Qin Wang
- Department of Biochemistry & Molecular Biology, China Medical University, Shenyang 110122, China; Key Laboratory of Cell Biology, Ministry of Public Health, Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110122, China.
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67
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Ru W, Zhang X, Yue B, Qi A, Shen X, Huang Y, Lan X, Lei C, Chen H. Insight into m 6A methylation from occurrence to functions. Open Biol 2020; 10:200091. [PMID: 32898471 PMCID: PMC7536083 DOI: 10.1098/rsob.200091] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 08/11/2020] [Indexed: 01/01/2023] Open
Abstract
RNA m6A methylation is a post-transcriptional modification that occurs at the nitrogen-6 position of adenine. This dynamically reversible modification is installed, removed and recognized by methyltransferases, demethylases and readers, respectively. This modification has been found in most eukaryotic mRNA, tRNA, rRNA and other non-coding RNA. Recent studies have revealed important regulatory functions of the m6A including effects on gene expression regulation, organism development and cancer development. In this review, we summarize the discovery and features of m6A, and briefly introduce the mammalian m6A writers, erasers and readers. Finally, we discuss progress in identifying additional functions of m6A and the outstanding questions about the regulatory effect of this widespread modification.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hong Chen
- Key laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
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68
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Le Franc L, Bernay B, Petton B, Since M, Favrel P, Rivière G. A functional m 6 A-RNA methylation pathway in the oyster Crassostrea gigas assumes epitranscriptomic regulation of lophotrochozoan development. FEBS J 2020; 288:1696-1711. [PMID: 32743927 DOI: 10.1111/febs.15500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/13/2020] [Accepted: 07/28/2020] [Indexed: 11/30/2022]
Abstract
N6 -methyladenosine (m6 A) is a prevalent epitranscriptomic mark in eukaryotic RNA, with crucial roles for mammalian and ecdysozoan development. Indeed, m6 A-RNA and the related protein machinery are important for splicing, translation, maternal-to-zygotic transition and cell differentiation. However, to date, the presence of an m6 A-RNA pathway remains unknown in more distant animals, questioning the evolution and significance of the epitranscriptomic regulation. Therefore, we investigated the m6 A-RNA pathway in the oyster Crassostrea gigas, a lophotrochozoan model whose development was demonstrated under strong epigenetic influence. Using mass spectrometry and dot blot assays, we demonstrated that m6 A-RNA is actually present in the oyster and displays variations throughout early oyster development, with the lowest levels at the end of cleavage. In parallel, by in silico analyses, we were able to characterize at the molecular level a complete and conserved putative m6 A machinery. The expression levels of the identified putative m6 A writers, erasers and readers were strongly regulated across oyster development. Finally, RNA pull-down coupled to LC-MS/MS allowed us to prove the actual presence of readers able to bind m6 A-RNA and exhibiting specific developmental patterns. Altogether, our results demonstrate the conservation of a complete m6 A-RNA pathway in the oyster and strongly suggest its implication in early developmental processes including MZT. This first demonstration and characterization of an epitranscriptomic regulation in a lophotrochozoan model, potentially involved in the embryogenesis, bring new insights into our understanding of developmental epigenetic processes and their evolution.
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Affiliation(s)
- Lorane Le Franc
- UNICAEN, CNRS, BOREA, Normandie Univ, Caen, France.,Laboratoire Biologie des organismes et Ecosystèmes aquatiques (BOREA), Muséum d'Histoire naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, Caen, France
| | - Benoit Bernay
- UNICAEN, ICORE, PROTEOGEN Core Facility, Caen, SF, France
| | - Bruno Petton
- Ifremer, Laboratoire des Sciences de l'Environnement Marin, UMR 6539 CNRS/UBO/IRD/Ifremer, Centre Bretagne, Normandie Univ, Plouzané, France
| | - Marc Since
- UNICAEN, Comprehensive Cancer Center F. Baclesse, SF ICORE, PRISMM Core Facility, Normandie Univ, Caen, France
| | - Pascal Favrel
- UNICAEN, CNRS, BOREA, Normandie Univ, Caen, France.,Laboratoire Biologie des organismes et Ecosystèmes aquatiques (BOREA), Muséum d'Histoire naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, Caen, France
| | - Guillaume Rivière
- UNICAEN, CNRS, BOREA, Normandie Univ, Caen, France.,Laboratoire Biologie des organismes et Ecosystèmes aquatiques (BOREA), Muséum d'Histoire naturelle, CNRS, IRD, Sorbonne Université, Université de Caen Normandie, Université des Antilles, Caen, France
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69
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Chellamuthu A, Gray SG. The RNA Methyltransferase NSUN2 and Its Potential Roles in Cancer. Cells 2020; 9:cells9081758. [PMID: 32708015 PMCID: PMC7463552 DOI: 10.3390/cells9081758] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 12/12/2022] Open
Abstract
5-methylcytosine is often associated as an epigenetic modifier in DNA. However, it is also found increasingly in a plethora of RNA species, predominantly transfer RNAs, but increasingly found in cytoplasmic and mitochondrial ribosomal RNAs, enhancer RNAs, and a number of long noncoding RNAs. Moreover, this modification can also be found in messenger RNAs and has led to an increasing appreciation that RNA methylation can functionally regulate gene expression and cellular activities. In mammalian cells, the addition of m5C to RNA cytosines is carried out by enzymes of the NOL1/NOP2/SUN domain (NSUN) family as well as the DNA methyltransferase homologue DNMT2. In this regard, NSUN2 is a critical RNA methyltransferase for adding m5C to mRNA. In this review, using non-small cell lung cancer and other cancers as primary examples, we discuss the recent developments in the known functions of this RNA methyltransferase and its potential critical role in cancer.
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Affiliation(s)
- Anitha Chellamuthu
- Department of Clinical Medicine, Trinity College Dublin, Dublin D08 W9RT, Ireland;
| | - Steven G. Gray
- Department of Clinical Medicine, Trinity College Dublin, Dublin D08 W9RT, Ireland;
- Thoracic Oncology Research Group, St. James’s Hospital, Dublin D08 RX0X, Ireland
- Correspondence:
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70
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Leismann J, Spagnuolo M, Pradhan M, Wacheul L, Vu MA, Musheev M, Mier P, Andrade-Navarro MA, Graille M, Niehrs C, Lafontaine DL, Roignant JY. The 18S ribosomal RNA m 6 A methyltransferase Mettl5 is required for normal walking behavior in Drosophila. EMBO Rep 2020; 21:e49443. [PMID: 32350990 DOI: 10.15252/embr.201949443] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 04/02/2020] [Accepted: 04/07/2020] [Indexed: 11/09/2022] Open
Abstract
RNA modifications have recently emerged as an important layer of gene regulation. N6-methyladenosine (m6 A) is the most prominent modification on eukaryotic messenger RNA and has also been found on noncoding RNA, including ribosomal and small nuclear RNA. Recently, several m6 A methyltransferases were identified, uncovering the specificity of m6 A deposition by structurally distinct enzymes. In order to discover additional m6 A enzymes, we performed an RNAi screen to deplete annotated orthologs of human methyltransferase-like proteins (METTLs) in Drosophila cells and identified CG9666, the ortholog of human METTL5. We show that CG9666 is required for specific deposition of m6 A on 18S ribosomal RNA via direct interaction with the Drosophila ortholog of human TRMT112, CG12975. Depletion of CG9666 yields a subsequent loss of the 18S rRNA m6 A modification, which lies in the vicinity of the ribosome decoding center; however, this does not compromise rRNA maturation. Instead, a loss of CG9666-mediated m6 A impacts fly behavior, providing an underlying molecular mechanism for the reported human phenotype in intellectual disability. Thus, our work expands the repertoire of m6 A methyltransferases, demonstrates the specialization of these enzymes, and further addresses the significance of ribosomal RNA modifications in gene expression and animal behavior.
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Affiliation(s)
| | | | | | - Ludivine Wacheul
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Centre for Microscopy and Molecular Imaging (CMMI), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Minh Anh Vu
- Institute of Molecular Biology (IMB), Mainz, Germany
| | | | - Pablo Mier
- Faculty of Biology, Johannes-Gutenberg Universität Mainz, Mainz, Germany
| | | | - Marc Graille
- BIOC, CNRS, Ecole Polytechnique, IP Paris, Palaiseau, France
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany.,Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Denis Lj Lafontaine
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Centre for Microscopy and Molecular Imaging (CMMI), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), Charleroi-Gosselies, Belgium
| | - Jean-Yves Roignant
- Institute of Molecular Biology (IMB), Mainz, Germany.,Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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71
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Dong Z, Cui H. The Emerging Roles of RNA Modifications in Glioblastoma. Cancers (Basel) 2020; 12:E736. [PMID: 32244981 PMCID: PMC7140112 DOI: 10.3390/cancers12030736] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 12/11/2022] Open
Abstract
Glioblastoma (GBM) is a grade IV glioma that is the most malignant brain tumor type. Currently, there are no effective and sufficient therapeutic strategies for its treatment because its pathological mechanism is not fully characterized. With the fast development of the Next Generation Sequencing (NGS) technology, more than 170 kinds of covalent ribonucleic acid (RNA) modifications are found to be extensively present in almost all living organisms and all kinds of RNAs, including ribosomal RNAs (rRNAs), transfer RNAs (tRNAs) and messenger RNAs (mRNAs). RNA modifications are also emerging as important modulators in the regulation of biological processes and pathological progression, and study of the epi-transcriptome has been a new area for researchers to explore their connections with the initiation and progression of cancers. Recently, RNA modifications, especially m6A, and their RNA-modifying proteins (RMPs) such as methyltransferase like 3 (METTL3) and α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5), have also emerged as important epigenetic mechanisms for the aggressiveness and malignancy of GBM, especially the pluripotency of glioma stem-like cells (GSCs). Although the current study is just the tip of an iceberg, these new evidences will provide new insights for possible GBM treatments. In this review, we summarize the recent studies about RNA modifications, such as N6-methyladenosine (m6A), N6,2'O-dimethyladenosine (m6Am), 5-methylcytosine (m5C), N1-methyladenosine (m1A), inosine (I) and pseudouridine (ψ) as well as the corresponding RMPs including the writers, erasers and readers that participate in the tumorigenesis and development of GBM, so as to provide some clues for GBM treatment.
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Affiliation(s)
- Zhen Dong
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Biotechnology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, College of Biotechnology, Southwest University, Beibei, Chongqing 400716, China
- Cancer Center, Medical Research Institute, Southwest University, Beibei, Chongqing 400716, China
- Engineering Research Center for Cancer Biomedical and Translational Medicine, Southwest University, Beibei, Chongqing 400716, China
- Chongqing Engineering and Technology Research Center for Silk Biomaterials and Regenerative Medicine, Southwest University, Beibei, Chongqing 400716, China
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72
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Liu L, Wang Y, Wu J, Liu J, Qin Z, Fan H. N 6-Methyladenosine: A Potential Breakthrough for Human Cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:804-813. [PMID: 31958696 PMCID: PMC7005339 DOI: 10.1016/j.omtn.2019.12.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/15/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023]
Abstract
Among more than 100 types of identified RNA modification, N6-methyladenosine (m6A) modification is the predominant mRNA modification, which regulates RNA splicing, translocation, stability, and translation. m6A modification plays critical roles in the growth, differentiation, and metabolism of cells. As a dynamic and reversible modification, m6A is catalyzed by "writers" (RNA methyltransferases), removed by "erasers" (demethylases), and interacts with "readers" (m6A-binding proteins). With more advanced technology applied to research, the molecular mechanisms of RNA methyltransferase, demethylase, and m6A-binding protein have been revealed. An increasing number of studies have implicated the correlation between m6A modification and human cancers. In this review, we summarize that the occurrence and development of various human cancers are associated with aberrant m6A modification. We also discuss the progress in research related to m6A modification, providing novel therapeutic insight and potential breakthrough in anticancer therapy.
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Affiliation(s)
- Lina Liu
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, P.R. China
| | - Yuwei Wang
- School of Stomatology, Qingdao University, Qingdao 266071, P.R. China
| | - Jie Wu
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, P.R. China
| | - Jingwen Liu
- The School and Hospital of Stomatology, Tianjin Medical University, Tianjin 300070, P.R. China.
| | - Zongchang Qin
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, P.R. China.
| | - Hong Fan
- Department of Prosthodontics, Tianjin Stomatological Hospital, Hospital of Stomatology, NanKai University, Tianjin 300041, P.R. China.
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73
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Gu X, Zhang Y, Li D, Cai H, Cai L, Xu Q. N6-methyladenosine demethylase FTO promotes M1 and M2 macrophage activation. Cell Signal 2020; 69:109553. [PMID: 32018056 DOI: 10.1016/j.cellsig.2020.109553] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/31/2020] [Accepted: 01/31/2020] [Indexed: 11/29/2022]
Abstract
Macrophage polarization is the driving force of various inflammatory diseases, especially those involved in M1/M2 imbalance. N6-methyladenosine (m6A) is the most prevalent internal mRNA modification in eukaryotes that affects multiple biological processes, including those involved developmental arrest and immune response. However, the role of m6A in macrophage polarization remains unclear. This study found that FTO silencing significantly suppressed both M1 and M2 polarization. FTO depletion decreased the phosphorylation levels of IKKα/β, IκBα and p65 in the NF-κB signaling pathway. The expression of STAT1 was downregulated in M1-polarized macrophages while the expression of STAT6 and PPAR-γ decreased in M2 polarization after FTO knockdown. The actinomycin D experiments showed that FTO knockdown accelerated mRNA decay of STAT1 and PPAR-γ. Furthermore, the stability and expression of STAT1 and PPAR-γ mRNAs increased when the m6A reader YTHDF2 was silenced. In conclusion, our results suggest that FTO knockdown inhibits the NF-κB signaling pathway and reduces the mRNA stability of STAT1 and PPAR-γ via YTHDF2 involvement, thereby impeding macrophage activation. These findings indicated a previously unrecognized link between FTO and macrophage polarization and might open new avenues for research into the molecular mechanisms of macrophage polarization-related diseases.
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Affiliation(s)
- Xiaofei Gu
- Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China.
| | - Yiwen Zhang
- Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China
| | - Di Li
- Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China.
| | - Hongshi Cai
- Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China.
| | - Luhui Cai
- Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China.
| | - Qiong Xu
- Guanghua School of Stomatology & Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou 510055, China.
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74
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Molecular Mechanisms Driving mRNA Degradation by m 6A Modification. Trends Genet 2020; 36:177-188. [PMID: 31964509 DOI: 10.1016/j.tig.2019.12.007] [Citation(s) in RCA: 224] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/05/2019] [Accepted: 12/10/2019] [Indexed: 02/08/2023]
Abstract
N6-Methyladenosine (m6A), the most prevalent internal modification associated with eukaryotic mRNAs, influences many steps of mRNA metabolism, including splicing, export, and translation, as well as stability. Recent studies have revealed that m6A-containing mRNAs undergo one of two distinct pathways of rapid degradation: deadenylation via the YT521-B homology (YTH) domain-containing family protein 2 (YTHDF2; an m6A reader protein)-CCR4/NOT (deadenylase) complex or endoribonucleolytic cleavage by the YTHDF2-HRSP12-ribonuclease (RNase) P/mitochondrial RNA-processing (MRP) (endoribonuclease) complex. Some m6A-containing circular RNAs (circRNAs) are also subject to endoribonucleolytic cleavage by YTHDF2-HRSP12-RNase P/MRP. Here, we highlight recent progress on the molecular mechanisms underlying rapid mRNA degradation via m6A and describe our current understanding of the dynamic regulation of m6A-mediated mRNA decay through the crosstalk between m6A (or YTHDF2) and other cellular factors.
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75
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Zheng W, Dong X, Zhao Y, Wang S, Jiang H, Zhang M, Zheng X, Gu M. Multiple Functions and Mechanisms Underlying the Role of METTL3 in Human Cancers. Front Oncol 2019; 9:1403. [PMID: 31921660 PMCID: PMC6920212 DOI: 10.3389/fonc.2019.01403] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/27/2019] [Indexed: 12/13/2022] Open
Abstract
Methyltransferase-like 3 (METTL3), a predominantly catalytic enzyme in the N6-methyladenosine (m6A) methyltransferase system, is dysregulated and plays a dual role (oncogene or tumor suppressor) in different human cancers. The expression and pro- or anticancer role of METTL3 in different cancers remain controversial. METTL3 is implicated in many aspects of tumor progression, including tumorigenesis, proliferation, invasion, migration, cell cycle, differentiation, and viability. Most underlying mechanisms involve multiple signaling pathways that rely on m6A-dependent modification. However, METTL3 can also modulate the cancer process by directly promoting the translation of oncogenes via interaction with the translation initiation machinery through recruitment of eukaryotic translation initiation factor 3 subunit h (eIF3h). In this review, we summarized the current evidence on METTL3 in diverse human malignancies and its potential as a prognostic/ therapeutic target.
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Affiliation(s)
- Wenhui Zheng
- Department of Anesthesiology, The Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaoshen Dong
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yan Zhao
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Shuo Wang
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Haiyang Jiang
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Mingdi Zhang
- Department of Breast Surgery, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xinyu Zheng
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China.,Lab 1, Cancer Institute, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ming Gu
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
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76
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Heck AM, Wilusz CJ. Small changes, big implications: The impact of m 6A RNA methylation on gene expression in pluripotency and development. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:194402. [PMID: 31325527 PMCID: PMC6742438 DOI: 10.1016/j.bbagrm.2019.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/21/2019] [Accepted: 07/12/2019] [Indexed: 12/20/2022]
Abstract
In order to maintain a state of self-renewal, yet retain the ability to rapidly differentiate in response to external signals, pluripotent cells exert tight control over gene expression at many levels. Recent studies have suggested that N6-methyladenosine (m6A) RNA methylation, one of the most abundant post-transcriptional modifications, is important for both pluripotency and differentiation. In this review, we summarize the current state of the m6A field, with emphasis on the impact of writers, erasers and readers of m6A on RNA metabolism and stem cell biology.
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Affiliation(s)
- Adam M Heck
- Program in Cell & Molecular Biology, and Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80525, United States of America
| | - Carol J Wilusz
- Program in Cell & Molecular Biology, and Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO 80525, United States of America.
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77
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Liu Y, Liu Z, Tang H, Shen Y, Gong Z, Xie N, Zhang X, Wang W, Kong W, Zhou Y, Fu Y. The N6-methyladenosine (m 6A)-forming enzyme METTL3 facilitates M1 macrophage polarization through the methylation of STAT1 mRNA. Am J Physiol Cell Physiol 2019; 317:C762-C775. [PMID: 31365297 DOI: 10.1152/ajpcell.00212.2019] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Compelling evidence indicates that epigenetic regulations orchestrate dynamic macrophage polarization. N6-methyladenosine (m6A) methylation is the most abundant epigenetic modification of mammalian mRNA, but its role in macrophage polarization is still completely unknown. Here, we show that the m6A-catalytic enzyme methyltransferase like 3 (METTL3) is specifically upregulated following the M1 polarization of mouse macrophages. Furthermore, METTL3 knockdown through siRNA transfection markedly inhibited M1, but enhanced M2, macrophage polarization. Conversely, its overexpression via plasmid transfection greatly facilitated M1, but attenuated M2, macrophage polarization. Further methylated RNA immunoprecipitation and in vitro m6A methylation assays suggested that METTL3 directly methylates mRNA encoding signal transducer and activator of transcription 1 (STAT1), a master transcription factor controlling M1 macrophage polarization, at its coding sequence and 3'-untranslated regions. In addition, METTL3-mediated STAT1 mRNA methylation significantly increased mRNA stability and subsequently upregulated STAT1 expression. In conclusion, METTL3 drives M1 macrophage polarization by directly methylating STAT1 mRNA, potentially serving as an anti-inflammatory target.
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Affiliation(s)
- Yihan Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, People's Republic of China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, People's Republic of China
| | - Zhujiang Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, People's Republic of China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, People's Republic of China
| | - Hao Tang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University, Beijing, People's Republic of China
| | - Yicong Shen
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, People's Republic of China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, People's Republic of China
| | - Ze Gong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, People's Republic of China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, People's Republic of China
| | - Nan Xie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, People's Republic of China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, People's Republic of China
| | - Xu Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, People's Republic of China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, People's Republic of China
| | - Wengong Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University, Beijing, People's Republic of China
| | - Wei Kong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, People's Republic of China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, People's Republic of China
| | - Yuan Zhou
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing, People's Republic of China
| | - Yi Fu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, People's Republic of China.,Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, People's Republic of China
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78
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Fazi F, Fatica A. Interplay Between N 6-Methyladenosine (m 6A) and Non-coding RNAs in Cell Development and Cancer. Front Cell Dev Biol 2019; 7:116. [PMID: 31316981 PMCID: PMC6611489 DOI: 10.3389/fcell.2019.00116] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
RNA chemical modifications in coding and non-coding RNAs have been known for decades. They are generally installed by specific enzymes and, in some cases, can be read and erased by other specific proteins. The impact of RNA chemical modifications on gene expression regulation and the reversible nature of some of these modifications led to the birth of the word epitranscriptomics, in analogy with the changes that occur on DNA and histones. Among more than 100 different modifications identified so far, most of the epitranscriptomics studies focused on the N6-methyladenosine (m6A), which is the more abundant internal modification in protein coding RNAs. m6A can control several pathways of gene expression, including spicing, export, stability, and translation. In this review, we describe the interplay between m6A and non-coding RNAs, in particular microRNAs and lncRNAs, with examples of its role in gene expression regulation. Finally, we discuss its relevance in cell development and disease.
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Affiliation(s)
- Francesco Fazi
- Department of Anatomical, Histological, Forensic and Orthopedic Sciences, Section of Histology and Medical Embryology, Sapienza University of Rome, Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
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79
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Li Z, Zhao P, Xia Q. Epigenetic Methylations on N6-Adenine and N6-Adenosine with the same Input but Different Output. Int J Mol Sci 2019; 20:ijms20122931. [PMID: 31208067 PMCID: PMC6627651 DOI: 10.3390/ijms20122931] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetic modifications on individual bases in DNA and RNA can encode inheritable genetic information beyond the canonical bases. Among the nucleic acid modifications, DNA N6-methadenine (6mA) and RNA N6-methyladenosine (m6A) have recently been well-studied due to the technological development of detection strategies and the functional identification of modification enzymes. The current findings demonstrate a wide spectrum of 6mA and m6A distributions from prokaryotes to eukaryotes and critical roles in multiple cellular processes. It is interesting that the processes of modification in which the methyl group is added to adenine and adenosine are the same, but the outcomes of these modifications in terms of their physiological impacts in organisms are quite different. In this review, we summarize the latest progress in the study of enzymes involved in the 6mA and m6A methylation machinery, including methyltransferases and demethylases, and their functions in various biological pathways. In particular, we focus on the mechanisms by which 6mA and m6A regulate the expression of target genes, and we highlight the future challenges in epigenetic regulation.
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Affiliation(s)
- Zhiqing Li
- Biological Science Research Center, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China.
| | - Ping Zhao
- Biological Science Research Center, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China.
| | - Qingyou Xia
- Biological Science Research Center, Southwest University, Chongqing 400715, China.
- Chongqing Key Laboratory of Sericultural Science, Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China.
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80
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Ianniello Z, Paiardini A, Fatica A. N 6-Methyladenosine (m 6A): A Promising New Molecular Target in Acute Myeloid Leukemia. Front Oncol 2019; 9:251. [PMID: 31024852 PMCID: PMC6465620 DOI: 10.3389/fonc.2019.00251] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 03/19/2019] [Indexed: 12/25/2022] Open
Abstract
Recent studies have uncovered an important role for RNA modifications in gene expression regulation, which led to the birth of the epitranscriptomics field. It is now acknowledged that RNA modifiers play a crucial role in the control of differentiation of stem and progenitor cells and that changes in their levels are a relevant feature of different types of cancer. To date, among more than 160 different RNA chemical modifications, the more relevant in cancer biology is the reversible and dynamic N6-methylation of adenosine, yielding N6-methyladenosine (m6A). m6A is the more abundant internal modification in mRNA, regulating the expression of the latter at different levels, from maturation to translation. Here, we will describe the emerging role of m6A modification in acute myeloid leukemia (AML), which, among first, has demonstrated how mis-regulation of the m6A modifying system can contribute to the development and progression of cancer. Moreover, we will discuss how AML is paving the way to the development of new therapeutic options based on the inhibition of m6A deposition.
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Affiliation(s)
- Zaira Ianniello
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli," Sapienza University of Rome, Rome, Italy
| | - Alessandro Fatica
- Department of Biology and Biotechnology "Charles Darwin," Sapienza University of Rome, Rome, Italy
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