101
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Zhou Z, Zhang A, Liu X, Yang Y, Zhao R, Jia Y. m 6A-Mediated PPARA Translational Suppression Contributes to Corticosterone-Induced Visceral Fat Deposition in Chickens. Int J Mol Sci 2022; 23:ijms232415761. [PMID: 36555401 PMCID: PMC9779672 DOI: 10.3390/ijms232415761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Excess fat deposition in broilers leads to great economic losses and is harmful to consumers' health. Chronic stress in the life cycle of chickens could be an important trigger. However, the underlying mechanisms are still unclear. In this study, 30-day-old chickens were subcutaneously injected with 2 mg/kg corticosterone (CORT) twice a day for 14 days to simulate long-term stress. It was shown that chronic CORT exposure significantly increased plasma triglyceride concentrations and enlarged the adipocyte sizes in chickens. Meanwhile, chronic CORT administration significantly enlarged the adipocyte sizes, increased the protein contents of FASN and decreased HSL, ATGL, Beclin1 and PPARA protein levels. Moreover, global m6A methylations were significantly reduced and accompanied by downregulated METTL3 and YTHDF2 protein expression by CORT treatment. Interestingly, the significant differences of site-specific m6A demethylation were observed in exon7 of PPARA mRNA. Additionally, a mutation of the m6A site in the PPARA gene fused GFP and revealed that demethylated RRACH in PPARA CDS impaired protein translation in vitro. In conclusion, these results indicated that m6A-mediated PPARA translational suppression contributes to CORT-induced visceral fat deposition in chickens, which may provide a new target for the treatment of Cushing's syndrome.
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Affiliation(s)
- Zixuan Zhou
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Aijia Zhang
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyi Liu
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Yang
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Ruqian Zhao
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing 210095, China
| | - Yimin Jia
- Key Laboratory of Animal Physiology & Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing 210095, China
- Correspondence: ; Tel.: +86-2584396413; Fax: +86-2584398669
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102
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Alasar AA, Tüncel Ö, Gelmez AB, Sağlam B, Vatansever İE, Akgül B. Genomewide m 6A Mapping Uncovers Dynamic Changes in the m 6A Epitranscriptome of Cisplatin-Treated Apoptotic HeLa Cells. Cells 2022; 11:cells11233905. [PMID: 36497162 PMCID: PMC9738315 DOI: 10.3390/cells11233905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/07/2022] Open
Abstract
Cisplatin (CP), which is a conventional cancer chemotherapeutic drug, induces apoptosis by modulating a diverse array of gene regulatory mechanisms. However, cisplatin-mediated changes in the m6A methylome are unknown. We employed an m6A miCLIP-seq approach to investigate the effect of m6A methylation marks under cisplatin-mediated apoptotic conditions on HeLa cells. Our high-resolution approach revealed numerous m6A marks on 972 target mRNAs with an enrichment on 132 apoptotic mRNAs. We tracked the fate of differentially methylated candidate mRNAs under METTL3 knockdown and cisplatin treatment conditions. Polysome profile analyses revealed perturbations in the translational efficiency of PMAIP1 and PHLDA1 transcripts. Congruently, PMAIP1 amounts were dependent on METTL3. Additionally, cisplatin-mediated apoptosis was sensitized by METTL3 knockdown. These results suggest that apoptotic pathways are modulated by m6A methylation events and that the METTL3-PMAIP1 axis modulates cisplatin-mediated apoptosis in HeLa cells.
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Affiliation(s)
| | | | | | | | | | - Bünyamin Akgül
- Correspondence: ; Tel.: +011-90-232-7507316; Fax: +011-90-232-7507302
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103
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Kleinbielen T, Olasagasti F, Azcarate D, Beristain E, Viguri-Díaz A, Guerra-Merino I, García-Orad Á, de Pancorbo MM. In silico identification and in vitro expression analysis of breast cancer-related m 6A-SNPs. Epigenetics 2022; 17:2144-2156. [PMID: 35971775 PMCID: PMC9665143 DOI: 10.1080/15592294.2022.2111137] [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: 04/05/2022] [Accepted: 08/01/2022] [Indexed: 12/24/2022] Open
Abstract
Research on m6A-associated SNPs (m6A-SNPs) has emerged recently due to their possible critical roles in many key biological processes. In this sense, several investigations have identified m6A-SNPs in different diseases. In order to gain a more complete understanding of the role that m6A-SNPs can play in breast cancer, we performed an in silico analysis to identify the m6A-SNPs associated with breast cancer and to evaluate their possible effects. For this purpose, we downloaded SNPs related to breast cancer and a list of m6A-SNPs from public databases in order to identify which ones appear in both. Subsequently, we assessed the identified m6A-SNPs in silico by expression quantitative trait loci (eQTL) analysis and differential gene expression analysis. We genotyped the m6A-SNPs found in the in silico analysis in 35 patients with breast cancer, and we carried out a gene expression analysis experimentally on those that showed differences. Our results identified 981 m6A-SNPs related to breast cancer. Four m6A-SNPs showed an eQTL effect and only three were in genes that presented an altered gene expression. When the three m6A-SNPs were evaluated in the tissue sample of our breast cancer patients, only the m6A-SNP rs76563149 located in ZNF354A gene presented differences in allele frequencies and a low gene expression in breast cancer tissues, especially in luminal B HER2+ subtype. Future investigations of these m6A-SNPs should expand the study in different ethnic groups and increase the sample sizes to test their association with breast cancer and elucidate their molecular function.
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Affiliation(s)
- Tamara Kleinbielen
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
| | - Felix Olasagasti
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Department of Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
| | - Daniel Azcarate
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
| | - Elena Beristain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Molecular Genetics Laboratory, Araba University Hospital, Osakidetza Basque Health Service. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - Amparo Viguri-Díaz
- Pathology Department, Araba University Hospital. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - Isabel Guerra-Merino
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
- Pathology Department, Araba University Hospital. Postal code: 01009. Vitoria-Gasteiz, Araba, Spain
| | - África García-Orad
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- BioCruces Bizkaia Health Research Institute. Postal code: 48903. Barakaldo, Bizkaia, Spain
| | - Marian M. de Pancorbo
- BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU. Postal code: 01006. Vitoria-Gasteiz, Araba, Spain
- Department of Zoology and Animal Biology. University of the Basque Country (UPV/EHU). Postal code: 48940. Leioa, Bizkaia, Spain
- Bioaraba Health Research Institute. Postal Code: 01009, Vitoria-Gasteiz, Araba, Spain
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104
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Hong J, Xu K, Lee JH. Biological roles of the RNA m 6A modification and its implications in cancer. Exp Mol Med 2022; 54:1822-1832. [PMID: 36446846 PMCID: PMC9722703 DOI: 10.1038/s12276-022-00897-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/06/2022] [Accepted: 10/09/2022] [Indexed: 11/30/2022] Open
Abstract
The N6-Methyladenosine (m6A) modification of RNA transcripts is the most prevalent and abundant internal modification in eukaryotic messenger RNAs (mRNAs) and plays diverse and important roles in normal biological processes. Extensive studies have indicated that dysregulated m6A modification and m6A-associated proteins play critical roles in tumorigenesis and cancer progression. However, m6A-mediated physiological consequences often lead to opposite outcomes in a biological context-dependent manner. Therefore, context-related complexity must be meaningfully considered to obtain a comprehensive understanding of RNA methylation. Recently, it has been reported that m6A-modified RNAs are closely related to the regulation of the DNA damage response and genomic integrity maintenance. Here, we present an overview of the current knowledge on the m6A modification and its function in human cancer, particularly in relation to the DNA damage response and genomic instability.
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Affiliation(s)
- Juyeong Hong
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Kexin Xu
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
| | - Ji Hoon Lee
- grid.267309.90000 0001 0629 5880Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX USA
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105
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Varier RA, Sideri T, Capitanchik C, Manova Z, Calvani E, Rossi A, Edupuganti RR, Ensinck I, Chan VWC, Patel H, Kirkpatrick J, Faull P, Snijders AP, Vermeulen M, Ralser M, Ule J, Luscombe NM, van Werven FJ. N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast. eLife 2022; 11:e84034. [PMID: 36422864 PMCID: PMC9731578 DOI: 10.7554/elife.84034] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/13/2022] [Indexed: 11/25/2022] Open
Abstract
N6- methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here, we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3'end of meiotic mRNAs in both an m6A-dependent and independent manner. Within cells, Pho92 transitions from the nucleus to the cytoplasm, and associates with translating ribosomes. In the nucleus Pho92 associates with target loci through its interaction with transcriptional elongator Paf1C. Functionally, we show that Pho92 promotes and links protein synthesis to mRNA decay. As such, the Pho92-mediated m6A-mRNA decay is contingent on active translation and the CCR4-NOT complex. We propose that the m6A reader Pho92 is loaded co-transcriptionally to facilitate protein synthesis and subsequent decay of m6A modified transcripts, and thereby promotes meiosis.
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Affiliation(s)
| | | | | | | | | | - Alice Rossi
- The Francis Crick InstituteLondonUnited Kingdom
| | - Raghu R Edupuganti
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University NijmegenNijmegenNetherlands
- Department of Human Genetics, University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Biomedical Research BuildingMiamiUnited States
| | | | | | | | | | - Peter Faull
- The Francis Crick InstituteLondonUnited Kingdom
- Biological Mass Spectrometry Facility, The University of Texas at AustinAustinUnited States
| | | | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University NijmegenNijmegenNetherlands
| | - Markus Ralser
- The Francis Crick InstituteLondonUnited Kingdom
- Department of Biochemistry, Charité Universitätsmedizin BerlinBerlinGermany
| | - Jernej Ule
- The Francis Crick InstituteLondonUnited Kingdom
- Dementia Research Institute, King's College LondonLondonUnited Kingdom
| | - Nicholas M Luscombe
- The Francis Crick InstituteLondonUnited Kingdom
- Department of Genetics, Evolution and Environment, UCL Genetics InstituteLondonUnited Kingdom
- Okinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
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106
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Arzumanian VA, Dolgalev GV, Kurbatov IY, Kiseleva OI, Poverennaya EV. Epitranscriptome: Review of Top 25 Most-Studied RNA Modifications. Int J Mol Sci 2022; 23:13851. [PMID: 36430347 PMCID: PMC9695239 DOI: 10.3390/ijms232213851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally and functionally different from their unmodified counterparts. Some of these modifications are constituent and critical for RNA functions, while others serve as dynamic markings to regulate the fate of specific RNA molecules. Together, these modifications form the epitranscriptome, an essential layer of cellular biochemistry. As of the time of writing this review, more than 300 distinct RNA modifications from all three life domains have been identified. However, only a few of the most well-established modifications are included in most reviews on this topic. To provide a complete overview of the current state of research on the epitranscriptome, we analyzed the extent of the available information for all known RNA modifications. We selected 25 modifications to describe in detail. Summarizing our findings, we describe the current status of research on most RNA modifications and identify further developments in this field.
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Affiliation(s)
- Viktoriia A. Arzumanian
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
| | - Georgii V. Dolgalev
- Correspondence: (V.A.A.); (G.V.D.); Tel.: +7-960-889-7117 (V.A.A.); +7-967-236-36-79 (G.V.D.)
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107
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Liu H, Zheng YL, Wang XQ. The emerging roles of N 6-methyladenosine in osteoarthritis. Front Mol Neurosci 2022; 15:1040699. [PMID: 36466802 PMCID: PMC9710225 DOI: 10.3389/fnmol.2022.1040699] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/19/2022] [Indexed: 08/30/2023] Open
Abstract
Finding new biomarkers and molecular targets to guide OA treatment remains a significant challenge. One of the most frequent forms of RNA methylation, N6-methyladenosine (m6A), can affect gene expression and RNA transcription, processing, translation, and metabolism. Osteoarthritis (OA) can cause disability and pain degenerative disease, reduce the quality of life of the elderly, and increase the social and economic burden. Changes in m6A levels are crucial in OA progress. In this review, the discussion will concentrate on the role that m6A plays in OA occurrence and progression. The m6A involved in the OA process mainly includes METTL3 and FTO. Current studies on m6A and OA primarily focus on four signaling pathways, namely, NF-κB, LNCRNAs, ATG7, and Bcl2. m6A participates in these signaling pathways and affects cellular inflammation, apoptosis, senescence, and autophagy, thus controlling the OA process. The modification of m6A affects so many signaling pathways. For the treatment of OA, it may represent a viable new therapeutic target.
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Affiliation(s)
- Hui Liu
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai, China
| | - Yi-Li Zheng
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai, China
- Department of Rehabilitation Medicine, Shanghai Shangti Orthopaedic Hospital, Shanghai, China
| | - Xue-Qiang Wang
- Department of Sport Rehabilitation, Shanghai University of Sport, Shanghai, China
- Department of Rehabilitation Medicine, Shanghai Shangti Orthopaedic Hospital, Shanghai, China
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108
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Ye J, Li P, Zhang H, Wu Q, Yang D. Identifying Prognostic Biomarkers Related to m6A Modification and Immune Infiltration in Renal Cell Carcinoma. Genes (Basel) 2022; 13:2059. [PMID: 36360294 PMCID: PMC9690957 DOI: 10.3390/genes13112059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) is the largest category of kidney tumors and usually does not have a good prognosis. N6-methyladenosine(m6A) and immune infiltration have received increased attention because of their great influence on the clinical outcome and prognosis of cancer patients. METHODS We identified hub genes through multi-dimensional screening, including DEGs, PPI analysis, LASSO regression, and random forest. Meanwhile, GO/KEGG enrichment, cMAP analysis, prognostic analysis, m6A prediction, and immune infiltration analysis were performed to understand the potential mechanism and screen therapeutic drugs. RESULTS We screened 275 downregulated and 185 upregulated genes using three GEO datasets and the TCGA dataset. In total, 82 candidate hub genes were selected using STRING and Cytoscape. Enrichment analysis illustrated that the top 3 biological process terms and top 1 KEGG term were related to immunity. cMAP analysis showed some antagonistic molecules can be candidate drugs for the treatment of RCC. Then, six hub genes (ERBB2, CASR, P2RY8, CAT, PLAUR, and TIMP1) with strong predictive values for prognosis and clinicopathological features were selected. Meanwhile, P2RY8, ERBB2, CAT, and TIMP1 may obtain m6A modification by binding METTL3 or METTL14. On the other hand, differential expression of CAT, ERBB2, P2RY8, PLAUR, and TIMP1 affects the infiltration of the majority of immune cells. CONCLUSIONS We identified six hub genes through multi-dimensional screening. They all possess strong predictive value for prognosis and clinicopathological features. Meanwhile, hub genes may regulate the progression of RCC via an m6A- and immunity-dependent mechanism.
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Affiliation(s)
- Junjie Ye
- The Second Affiliated Hospital of Soochow University, Suzhou 215000, China
- Lishui City People’s Hospital, Lishui 323000, China
| | - Peng Li
- Lishui City People’s Hospital, Lishui 323000, China
| | | | - Qi Wu
- Lishui City People’s Hospital, Lishui 323000, China
| | - Dongrong Yang
- The Second Affiliated Hospital of Soochow University, Suzhou 215000, China
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109
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Li P, Wang Y, Sun Y, Jiang S, Li J. N 6-methyladenosine RNA methylation: From regulatory mechanisms to potential clinical applications. Front Cell Dev Biol 2022; 10:1055808. [PMID: 36407103 PMCID: PMC9669580 DOI: 10.3389/fcell.2022.1055808] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/24/2022] [Indexed: 10/20/2023] Open
Abstract
Epitranscriptomics has emerged as another level of epigenetic regulation similar to DNA and histone modifications. N 6-methyladenosine (m6A) is one of the most prevalent and abundant posttranscriptional modifications, widely distributed in many biological species. The level of N 6-methyladenosine RNA methylation is dynamically and reversibly regulated by distinct effectors including methyltransferases, demethylases, histone modification and metabolites. In addition, N 6-methyladenosine RNA methylation is involved in multiple RNA metabolism pathways, such as splicing, localization, translation efficiency, stability and degradation, ultimately affecting various pathological processes, especially the oncogenic and tumor-suppressing activities. Recent studies also reveal that N 6-methyladenosine modification exerts the function in immune cells and tumor immunity. In this review, we mainly focus on the regulatory mechanisms of N 6-methyladenosine RNA methylation, the techniques for detecting N 6-methyladenosine methylation, the role of N 6-methyladenosine modification in cancer and other diseases, and the potential clinical applications.
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Affiliation(s)
- Peipei Li
- Department of Oncology, Weifang Medical University, Weifang, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Yuntao Wang
- Department of Oncology, Weifang Medical University, Weifang, China
| | - Yiwen Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | | | - Jingjing Li
- Department of Oncology, Weifang Medical University, Weifang, China
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110
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Wan L, Liu J, Huang C, Zhu Z, Wang K, Sun G, Zhu L, Hu Z. Comprehensive Analysis and Functional Characteristics of Differential Expression of N6-Methyladenosine Methylation Modification in the Whole Transcriptome of Rheumatoid Arthritis. Mediators Inflamm 2022; 2022:4766992. [PMID: 36330380 PMCID: PMC9626244 DOI: 10.1155/2022/4766992] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/22/2022] [Indexed: 08/04/2023] Open
Abstract
N6-methyladenosine (m6A) modification is the most prevalent chemical modification in eukaryotic mRNA and is associated with the development of various immune diseases. However, the role of m6A methylation in rheumatoid arthritis (RA) development is unclear. We preliminarily explored the role of m6A methylation-related mRNAs in RA for its clinical application. The discovery of m6A methylation-modifying genes in this study may provide a fresh perspective on the development of drugs for RA treatment. High-throughput sequencing combined with methylated RNA immunoprecipitation (MeRIP-seq) and RNA sequencing were used to assess whole-transcriptome m6A modifications in the synovium of patients with RA. The relationship between m6A-modified target genes and RA inflammation and macrophages was determined. The expression of the m6A-modified significant transcript-enriched inflammatory signaling pathway was assessed through animal experiments. Differentially expressed m6A genes were correlated with macrophage activation involved in immune response, vascular endothelium, MAPK signaling pathway, PI3K - Akt signaling pathway, and other inflammatory processes. Furthermore, combined analysis with m6A-seq and RNA-seq revealed 120 genes with significant changes in both m6A modification and mRNA expression. We selected the top 3 candidate mRNAs that were upregulated and downregulated simultaneously. The expression of phosphatase and tensin homolog deleted on chromosome ten (PTEN) mRNA and protein in RA patients was lower than that in healthy control (HC). SHC-binding protein 1 (SHCBP1) and neurexophilin-3 (NXPH3) mRNA expressions were increased in RA patients. The expression of M1 macrophages was increased in RA patients. RA markers are such as rheumatoid factor (RF) and peptide containing citrulline (CCP). Further animal experiments showed that the expression of synovial MAPK, PI3K, and Akt1 proteins in the RA model was increased, and the PTEN, p-PTEN protein expression was decreased. PI3K, Akt1, PTEN, and p-PTEN were correlated to RA joint inflammation. This study revealed a unique pattern of differential m6A methylation modifications in RA and concluded that m6A modification is related to the occurrence of RA synovial inflammation.
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Affiliation(s)
- Lei Wan
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230038, China
- Key Laboratory of Xin'an Medical Education Ministry, Hefei 230038, China
| | - Jian Liu
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230038, China
- Key Laboratory of Xin'an Medical Education Ministry, Hefei 230038, China
| | - Chuanbing Huang
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230038, China
| | - Ziheng Zhu
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230038, China
| | - Kun Wang
- Key Laboratory of Xin'an Medical Education Ministry, Hefei 230038, China
- College of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Guanghan Sun
- College of Traditional Chinese Medicine, Anhui University of Chinese Medicine, Hefei 230012, China
| | - Lei Zhu
- The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei 230038, China
| | - Zhongxiang Hu
- The First Affiliated Hospital of University of Science and Technology of China, Hefei 230000, China
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111
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YTHDC2 Promotes Malignant Phenotypes of Breast Cancer Cells. JOURNAL OF ONCOLOGY 2022; 2022:9188920. [PMID: 36245989 PMCID: PMC9568362 DOI: 10.1155/2022/9188920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/30/2022] [Accepted: 09/19/2022] [Indexed: 12/03/2022]
Abstract
YTH domain-containing 2 (YTHDC2) is known to be an important regulator for RNA metabolism. Here, we show that YTHDC2 is essential for breast cancer tumorigenesis and metastasis. We examined YTHDC2 expression levels by immunohistochemistry in human breast tumor tissues from 99 patients and found a significantly positive correlation between the YTHDC2 expression level and the tumor stage. We established YTHDC2-knocked-down cell lines using four breast cancer cell lines with different subtypes. Knockdown of YTHDC2 attenuated the sphere-forming and the metastatic ability of breast cancer cells. Although stemness and EMT markers, such as SOX2, c-MYC, and NANOG, were downregulated in several YTHDC2-knocked-down breast cancer cells, a common target gene of YTHDC2 in breast cancer cells was not identified. These findings suggest that while YTHDC2 is involved in malignant progression of breast cancers, the mechanism by which YTHDC2 regulates those phenotypes is different between subtypes of breast cancers.
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112
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Ma W, Wu T. RNA m6A modification in liver biology and its implication in hepatic diseases and carcinogenesis. Am J Physiol Cell Physiol 2022; 323:C1190-C1205. [PMID: 36036444 PMCID: PMC9576175 DOI: 10.1152/ajpcell.00214.2022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/22/2022]
Abstract
N6-methyladenosine (m6A) is the most prevalent internal modification in eukaryotic RNAs. This modification is regulated by three different factors (writers, erasers, and readers) and affects multiple aspects of RNA metabolism, including RNA splicing, nuclear export, translation, stability and decay. The m6A-mediated modification plays important roles in posttranscriptional regulation of gene expression and mediates a variety of cellular and biological processes. Accordingly, deregulation in m6A modification is closely related to the occurrence and development of human diseases. The liver is the largest digestive and metabolic organ in human and recent studies have shown that m6A modification is importantly implicated in liver cellular and physiological functions and in the pathogenesis of hepatic diseases and cancers. In the current review, we summarize the functions of m6A in RNA metabolism and its roles in liver cell biology and discuss its implication in hepatic diseases and carcinogenesis.
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Affiliation(s)
- Wenbo Ma
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Tong Wu
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, Louisiana
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113
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RNA modifications: importance in immune cell biology and related diseases. Signal Transduct Target Ther 2022; 7:334. [PMID: 36138023 PMCID: PMC9499983 DOI: 10.1038/s41392-022-01175-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
RNA modifications have become hot topics recently. By influencing RNA processes, including generation, transportation, function, and metabolization, they act as critical regulators of cell biology. The immune cell abnormality in human diseases is also a research focus and progressing rapidly these years. Studies have demonstrated that RNA modifications participate in the multiple biological processes of immune cells, including development, differentiation, activation, migration, and polarization, thereby modulating the immune responses and are involved in some immune related diseases. In this review, we present existing knowledge of the biological functions and underlying mechanisms of RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, and adenosine-to-inosine (A-to-I) RNA editing, and summarize their critical roles in immune cell biology. Via regulating the biological processes of immune cells, RNA modifications can participate in the pathogenesis of immune related diseases, such as cancers, infection, inflammatory and autoimmune diseases. We further highlight the challenges and future directions based on the existing knowledge. All in all, this review will provide helpful knowledge as well as novel ideas for the researchers in this area.
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114
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Isono M, Nakano M, Fukami T, Nakajima M. Adenosine N 6-methylation upregulates the expression of human CYP2B6 by altering the chromatin status. Biochem Pharmacol 2022; 205:115247. [PMID: 36113565 DOI: 10.1016/j.bcp.2022.115247] [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: 06/07/2022] [Revised: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 11/02/2022]
Abstract
N6-Methyladenosine (m6A) modification is the most prevalent RNA modification in mammals. We have recently demonstrated that inhibition of m6A modification by 3-deazaadenosine results in an increase in the expression of the cytochrome P450 (CYP) isoforms CYP1A2, CYP2B6, and CYP2C8 in human liver-derived cells. In the present study, we aimed to clarify the mechanism of m6A-mediated regulation of CYP2B6 expression. RNA immunoprecipitation using an anti-m6A antibody revealed that CYP2B6 mRNA in human liver and hepatocarcinoma-derived HepaRG cells was m6A-modified around the stop codon. In contrast to the treatment with 3-deazaadenosine, double knockdown of methyltransferase like (METTL) 3 and METTL14 (METTL3/14) resulted in a decrease in the levels of CYP2B6 mRNA in Huh-7 and HepaRG cells and a decrease in bupropion hydroxylase activity, a marker activity of CYP2B6, in HepaRG cells. The stability of CYP2B6 mRNA was not influenced by siMETTL3/14. Reporter assays using the plasmids containing the last exon or 5'-flanking region of CYP2B6 indicated that reporter activities were not influenced by knockdown of METTL3/14. The expression levels of the constitutive androstane receptor, pregnane X receptor, and retinoid X receptor, which are the nuclear receptors regulating the transcription of CYP2B6, were not influenced by siMETTL3/14. The chromatin immunoprecipitation and formaldehyde-assisted enrichment of regulatory elements assays revealed that H3K9me2, a repressive histone marker, was enriched in the vicinity of the upstream region of CYP2B6, and knockdown of METTL3/14 induced the condensation of the chromatin structure in this region. In conclusion, we demonstrated that METTL3/14 upregulated CYP2B6 expression by altering the chromatin status.
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Affiliation(s)
- Motoki Isono
- DrugMetabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Masataka Nakano
- DrugMetabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPINano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Tatsuki Fukami
- DrugMetabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPINano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Miki Nakajima
- DrugMetabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPINano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
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115
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Chen S, Ren H, Zhang X, Chang L, Wang Z, Wu H, Zhang J, Ren J, Zhou L. Research advances of N6-methyladenosine in diagnosis and therapy of pancreatic cancer. J Clin Lab Anal 2022; 36:e24611. [PMID: 35837987 PMCID: PMC9459282 DOI: 10.1002/jcla.24611] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND N6-methyladenosine (m6A) is the addition of a methyl group on the N6 position of adenosine and is the most prevalent and abundant epigenetic modification in eukaryote mRNA. m6A marks are added to mRNA by the m6A methyltransferase complex ("writers"), removed by m6A demethylases ("erasers"), and recognized by m6A-binding proteins ("readers"). Recent evidence has shown that the m6A modification plays a crucial role in the pathogenic mechanism and malignant progression of pancreatic cancer, with roles in cell survival, proliferation, migration, invasion, tumor metastasis, and drug resistance. METHODS Literature was searched in Pubmed and Web of Science for the following keywords: "N6-methyladenosine", "pancreatic cancer", "epigenetic modification", "immunotherapy". RESULTS Among classical m6A regulators, while METTL3, METTL14, WTAP, FTO, YTHDF2, IGF2BP1-3, hnRNPC, and NKAP are upregulated in pancreatic cancer, METTL16 and ALKBH5 are downregulated in pancreatic cancer. m6A modification has been investigated in pancreatic cancer therapy. CONCLUSION Dysregulated m6A and its related factors in pancreatic cancer cells and patients indicate their potential values as novel biomarkers in pancreatic cancer diagnosis and targeted therapy.
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Affiliation(s)
- Sai Chen
- Department of Laboratory Medicine, Shanghai Changzheng HospitalNaval Medical UniversityShanghaiChina
| | - Hefei Ren
- Department of Laboratory Medicine, Shanghai Changzheng HospitalNaval Medical UniversityShanghaiChina
| | - Xiaomin Zhang
- Department of Laboratory Medicine, Shanghai Changzheng HospitalNaval Medical UniversityShanghaiChina
| | - Liu Chang
- Department of Laboratory Medicine, Shanghai Changzheng HospitalNaval Medical UniversityShanghaiChina
| | - Zhenhua Wang
- Department of Laboratory Medicine, Shanghai Changzheng HospitalNaval Medical UniversityShanghaiChina
| | - Hongkun Wu
- Department of Laboratory Medicine, Shanghai Changzheng HospitalNaval Medical UniversityShanghaiChina
| | - Jiafeng Zhang
- Department of Laboratory Medicine, Shanghai Changzheng HospitalNaval Medical UniversityShanghaiChina
| | - Jigang Ren
- Department of Laboratory Medicine, Shanghai Changzheng HospitalNaval Medical UniversityShanghaiChina
| | - Lin Zhou
- Department of Laboratory Medicine, Shanghai Changzheng HospitalNaval Medical UniversityShanghaiChina
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Shafik AM, Allen EG, Jin P. Epitranscriptomic dynamics in brain development and disease. Mol Psychiatry 2022; 27:3633-3646. [PMID: 35474104 PMCID: PMC9596619 DOI: 10.1038/s41380-022-01570-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 02/08/2023]
Abstract
Distinct cell types are generated at specific times during brain development and are regulated by epigenetic, transcriptional, and newly emerging epitranscriptomic mechanisms. RNA modifications are known to affect many aspects of RNA metabolism and have been implicated in the regulation of various biological processes and in disease. Recent studies imply that dysregulation of the epitranscriptome may be significantly associated with neuropsychiatric, neurodevelopmental, and neurodegenerative disorders. Here we review the current knowledge surrounding the role of the RNA modifications N6-methyladenosine, 5-methylcytidine, pseudouridine, A-to-I RNA editing, 2'O-methylation, and their associated machinery, in brain development and human diseases. We also highlight the need for the development of new technologies in the pursuit of directly mapping RNA modifications in both genome- and single-molecule-level approach.
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Affiliation(s)
- Andrew M Shafik
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, 30322, USA.
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Campos JHC, Alves GV, Maricato JT, Braconi CT, Antoneli FM, Janini LMR, Briones MRS. The epitranscriptome of Vero cells infected with SARS-CoV-2 assessed by direct RNA sequencing reveals m6A pattern changes and DRACH motif biases in viral and cellular RNAs. Front Cell Infect Microbiol 2022; 12:906578. [PMID: 36051243 PMCID: PMC9425070 DOI: 10.3389/fcimb.2022.906578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/25/2022] [Indexed: 11/18/2022] Open
Abstract
The epitranscriptomics of the SARS-CoV-2 infected cell reveals its response to viral replication. Among various types of RNA nucleotide modifications, the m6A is the most common and is involved in several crucial processes of RNA intracellular location, maturation, half-life and translatability. This epitranscriptome contains a mixture of viral RNAs and cellular transcripts. In a previous study we presented the analysis of the SARS-CoV-2 RNA m6A methylation based on direct RNA sequencing and characterized DRACH motif mutations in different viral lineages. Here we present the analysis of the m6A transcript methylation of Vero cells (derived from African Green Monkeys) and Calu-3 cells (human) upon infection by SARS-CoV-2 using direct RNA sequencing data. Analysis of these data by nonparametric statistics and two computational methods (m6anet and EpiNano) show that m6A levels are higher in RNAs of infected cells. Functional enrichment analysis reveals increased m6A methylation of transcripts involved in translation, peptide and amine metabolism. This analysis allowed the identification of differentially methylated transcripts and m6A unique sites in the infected cell transcripts. Results here presented indicate that the cell response to viral infection not only changes the levels of mRNAs, as previously shown, but also its epitranscriptional pattern. Also, transcriptome-wide analysis shows strong nucleotide biases in DRACH motifs of cellular transcripts, both in Vero and Calu-3 cells, which use the signature GGACU whereas in viral RNAs the signature is GAACU. We hypothesize that the differences of DRACH motif biases, might force the convergent evolution of the viral genome resulting in better adaptation to target sequence preferences of writer, reader and eraser enzymes. To our knowledge, this is the first report on m6A epitranscriptome of the SARS-CoV-2 infected Vero cells by direct RNA sequencing, which is the sensu stricto RNA-seq.
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Affiliation(s)
- João H. C. Campos
- Center for Medical Bioinformatics, Escola Paulista de Medicina, UNIFESP, São Paulo, Brazil
| | - Gustavo V. Alves
- Center for Medical Bioinformatics, Escola Paulista de Medicina, UNIFESP, São Paulo, Brazil
| | - Juliana T. Maricato
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, UNIFESP, São Paulo, Brazil
| | - Carla T. Braconi
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, UNIFESP, São Paulo, Brazil
| | - Fernando M. Antoneli
- Center for Medical Bioinformatics, Escola Paulista de Medicina, UNIFESP, São Paulo, Brazil
| | - Luiz Mario R. Janini
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina, UNIFESP, São Paulo, Brazil
| | - Marcelo R. S. Briones
- Center for Medical Bioinformatics, Escola Paulista de Medicina, UNIFESP, São Paulo, Brazil
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118
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Multiple Roles of m6A RNA Modification in Translational Regulation in Cancer. Int J Mol Sci 2022; 23:ijms23168971. [PMID: 36012237 PMCID: PMC9408962 DOI: 10.3390/ijms23168971] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022] Open
Abstract
Despite its discovery in the early 1970s, m6A modification within mRNA molecules has only powerfully entered the oncology field in recent years. This chemical modification can control all aspects of the maturation of mRNAs, both in the nucleus and in the cytoplasm. Thus, the alteration in expression levels of writers, erasers, and readers may significantly contribute to the alteration of gene expression observed in cancer. In particular, the activation of oncogenic pathways can lead to an alteration of the global rate of mRNA translation or the selective translation of specific mRNAs. In both cases, m6A can play an important role. In this review, we highlight the role of m6A in the regulation of translation by focusing on regulatory mechanisms and cancer-related functions of this novel but still controversial field.
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119
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The Potential Role of m6A in the Regulation of TBI-Induced BGA Dysfunction. Antioxidants (Basel) 2022; 11:antiox11081521. [PMID: 36009239 PMCID: PMC9405408 DOI: 10.3390/antiox11081521] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023] Open
Abstract
The brain–gut axis (BGA) is an important bidirectional communication pathway for the development, progress and interaction of many diseases between the brain and gut, but the mechanisms remain unclear, especially the post-transcriptional regulation of BGA after traumatic brain injury (TBI). RNA methylation is one of the most important modifications in post-transcriptional regulation. N6-methyladenosine (m6A), as the most abundant post-transcriptional modification of mRNA in eukaryotes, has recently been identified and characterized in both the brain and gut. The purpose of this review is to describe the pathophysiological changes in BGA after TBI, and then investigate the post-transcriptional bidirectional regulation mechanisms of TBI-induced BGA dysfunction. Here, we mainly focus on the characteristics of m6A RNA methylation in the post-TBI BGA, highlight the possible regulatory mechanisms of m6A modification in TBI-induced BGA dysfunction, and finally discuss the outcome of considering m6A as a therapeutic target to improve the recovery of the brain and gut dysfunction caused by TBI.
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120
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Hu L, Liu S, Peng Y, Ge R, Su R, Senevirathne C, Harada BT, Dai Q, Wei J, Zhang L, Hao Z, Luo L, Wang H, Wang Y, Luo M, Chen M, Chen J, He C. m 6A RNA modifications are measured at single-base resolution across the mammalian transcriptome. Nat Biotechnol 2022; 40:1210-1219. [PMID: 35288668 PMCID: PMC9378555 DOI: 10.1038/s41587-022-01243-z] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/28/2022] [Indexed: 01/28/2023]
Abstract
Functional studies of the RNA N6-methyladenosine (m6A) modification have been limited by an inability to map individual m6A-modified sites in whole transcriptomes. To enable such studies, here, we introduce m6A-selective allyl chemical labeling and sequencing (m6A-SAC-seq), a method for quantitative, whole-transcriptome mapping of m6A at single-nucleotide resolution. The method requires only ~30 ng of poly(A) or rRNA-depleted RNA. We mapped m6A modification stoichiometries in RNA from cell lines and during in vitro monocytopoiesis from human hematopoietic stem and progenitor cells (HSPCs). We identified numerous cell-state-specific m6A sites whose methylation status was highly dynamic during cell differentiation. We observed changes of m6A stoichiometry as well as expression levels of transcripts encoding or regulated by key transcriptional factors (TFs) critical for HSPC differentiation. m6A-SAC-seq is a quantitative method to dissect the dynamics and functional roles of m6A sites in diverse biological processes using limited input RNA.
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Affiliation(s)
- Lulu Hu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
- Fudan University Institutes of Biomedical Sciences, Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai, China.
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Yong Peng
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Ruiqi Ge
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Chamara Senevirathne
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bryan T Harada
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Lisheng Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Ziyang Hao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Liangzhi Luo
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Huanyu Wang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yuru Wang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Program of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Mengjie Chen
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA.
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA.
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
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Govindan G, Sharma B, Li Y, Armstrong CD, Merum P, Rohila JS, Gregory BD, Sunkar R. mRNA N 6 -methyladenosine is critical for cold tolerance in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1052-1068. [PMID: 35710867 PMCID: PMC9543165 DOI: 10.1111/tpj.15872] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 05/28/2022] [Accepted: 06/13/2022] [Indexed: 05/16/2023]
Abstract
Plants respond to low temperatures by altering the mRNA abundance of thousands of genes contributing to numerous physiological and metabolic processes that allow them to adapt. At the post-transcriptional level, these cold stress-responsive transcripts undergo alternative splicing, microRNA-mediated regulation and alternative polyadenylation, amongst others. Recently, m6 A, m5 C and other mRNA modifications that can affect the regulation and stability of RNA were discovered, thus revealing another layer of post-transcriptional regulation that plays an important role in modulating gene expression. The importance of m6 A in plant growth and development has been appreciated, although its significance under stress conditions is still underexplored. To assess the role of m6 A modifications during cold stress responses, methylated RNA immunoprecipitation sequencing was performed in Arabidopsis seedlings esposed to low temperature stress (4°C) for 24 h. This transcriptome-wide m6 A analysis revealed large-scale shifts in this modification in response to low temperature stress. Because m6 A is known to affect transcript stability/degradation and translation, we investigated these possibilities. Interestingly, we found that cold-enriched m6 A-containing transcripts demonstrated the largest increases in transcript abundance coupled with increased ribosome occupancy under cold stress. The significance of the m6 A epitranscriptome on plant cold tolerance was further assessed using the mta mutant in which the major m6 A methyltransferase gene was mutated. Compared to the wild-type, along with the differences in CBFs and COR gene expression levels, the mta mutant exhibited hypersensitivity to cold treatment as determined by primary root growth, biomass, and reactive oxygen species accumulation. Furthermore, and most importantly, both non-acclimated and cold-acclimated mta mutant demonstrated hypersensitivity to freezing tolerance. Taken together, these findings suggest a critical role for the epitranscriptome in cold tolerance of Arabidopsis.
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Affiliation(s)
- Ganesan Govindan
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
| | - Bishwas Sharma
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Yong‐Fang Li
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
| | | | - Pandrangaiah Merum
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
| | - Jai S. Rohila
- Dale Bumpers National Rice Research CenterUnited States Department of Agriculture‐Agricultural Research ServicesStuttgartAR72160USA
| | - Brian D. Gregory
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPA19104USA
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOK74078USA
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Jang KH, Heras CR, Lee G. m 6A in the Signal Transduction Network. Mol Cells 2022; 45:435-443. [PMID: 35748227 PMCID: PMC9260138 DOI: 10.14348/molcells.2022.0017] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/14/2022] [Accepted: 03/23/2022] [Indexed: 11/27/2022] Open
Abstract
In response to environmental changes, signaling pathways rewire gene expression programs through transcription factors. Epigenetic modification of the transcribed RNA can be another layer of gene expression regulation. N6-adenosine methylation (m6A) is one of the most common modifications on mRNA. It is a reversible chemical mark catalyzed by the enzymes that deposit and remove methyl groups. m6A recruits effector proteins that determine the fate of mRNAs through changes in splicing, cellular localization, stability, and translation efficiency. Emerging evidence shows that key signal transduction pathways including TGFβ (transforming growth factor-β), ERK (extracellular signal-regulated kinase), and mTORC1 (mechanistic target of rapamycin complex 1) regulate downstream gene expression through m6A processing. Conversely, m6A can modulate the activity of signal transduction networks via m6A modification of signaling pathway genes or by acting as a ligand for receptors. In this review, we discuss the current understanding of the crosstalk between m6A and signaling pathways and its implication for biological systems.
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Affiliation(s)
- Ki-Hong Jang
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA 92617, USA
| | - Chloe R. Heras
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA 92617, USA
- School of Biological Sciences, University of California Irvine, Irvine, CA 92697, USA
| | - Gina Lee
- Department of Microbiology and Molecular Genetics, Chao Family Comprehensive Cancer Center, School of Medicine, University of California Irvine, Irvine, CA 92617, USA
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123
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Hu X, Lei X, Guo J, Fu W, Sun W, Lu Q, Su W, Xu Q, Tu K. The Emerging Role of RNA N6-Methyladenosine Modification in Pancreatic Cancer. Front Oncol 2022; 12:927640. [PMID: 35936737 PMCID: PMC9354683 DOI: 10.3389/fonc.2022.927640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/15/2022] [Indexed: 12/04/2022] Open
Abstract
Pancreatic cancer (PC) is one of the most common malignant cancers, ranking the seventh highest causes of cancer-related deaths globally. Recently, RNA N6-methyladenosine (m6A) is emerging as one of the most abundant RNA modifications in eukaryote cells, involved in multiple RNA processes including RNA translocation, alternative splicing, maturation, stability, and degradation. As reported, m6A was dynamically and reversibly regulated by its “writers”, “erasers”, and “readers”, Increasing evidence has revealed the vital role of m6A modification in the development of multiple types of cancers including PC. Currently, aberrant m6A modification level has been found in both PC tissues and cell lines. Moreover, abnormal expressions of m6A regulators and m6A-modified genes have been reported to contribute to the malignant development of PC. Here in this review, we will focus on the function and molecular mechanism of m6A-modulated RNAs including coding RNAs as well as non-coding RNAs. Then the m6A regulators will be summarized to reveal their potential applications in the clinical diagnosis, prognosis, and therapeutics of PC.
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Affiliation(s)
- Xiaoge Hu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Xiangxiang Lei
- Institute of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Jinhui Guo
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Wen Fu
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Wen Sun
- The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qiliang Lu
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Wei Su
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine; Zhejiang Provincial Key Laboratory of Pancreatic Disease; Innovation Center for the Study of Pancreatic Diseases, Hangzhou, China
- *Correspondence: Wei Su, ; Qiuran Xu, ; Kangsheng Tu,
| | - Qiuran Xu
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Wei Su, ; Qiuran Xu, ; Kangsheng Tu,
| | - Kangsheng Tu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Wei Su, ; Qiuran Xu, ; Kangsheng Tu,
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124
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del Valle-Morales D, Le P, Saviana M, Romano G, Nigita G, Nana-Sinkam P, Acunzo M. The Epitranscriptome in miRNAs: Crosstalk, Detection, and Function in Cancer. Genes (Basel) 2022; 13:1289. [PMID: 35886072 PMCID: PMC9316458 DOI: 10.3390/genes13071289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/09/2022] [Accepted: 07/19/2022] [Indexed: 02/06/2023] Open
Abstract
The epitranscriptome encompasses all post-transcriptional modifications that occur on RNAs. These modifications can alter the function and regulation of their RNA targets, which, if dysregulated, result in various diseases and cancers. As with other RNAs, miRNAs are highly modified by epitranscriptomic modifications such as m6A methylation, 2'-O-methylation, m5C methylation, m7G methylation, polyuridine, and A-to-I editing. miRNAs are a class of small non-coding RNAs that regulates gene expression at the post-transcriptional level. miRNAs have gathered high clinical interest due to their role in disease, development, and cancer progression. Epitranscriptomic modifications alter the targeting, regulation, and biogenesis of miRNAs, increasing the complexity of miRNA regulation. In addition, emerging studies have revealed crosstalk between these modifications. In this review, we will summarize the epitranscriptomic modifications-focusing on those relevant to miRNAs-examine the recent crosstalk between these modifications, and give a perspective on how this crosstalk expands the complexity of miRNA biology.
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Affiliation(s)
- Daniel del Valle-Morales
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Patricia Le
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Michela Saviana
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Giovanni Nigita
- Comprehensive Cancer Center, Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH 43210, USA;
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (D.d.V.-M.); (P.L.); (M.S.); (G.R.); (P.N.-S.)
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125
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Sevoflurane Inhibits lncRNA HOTAIR-Modulated Stability of HK2 mRNA in a m6A-Dependent Manner to Dampen Aerobic Glycolysis and Proliferation in Lung Cancer. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4668774. [PMID: 35845960 PMCID: PMC9279057 DOI: 10.1155/2022/4668774] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/16/2022] [Accepted: 05/26/2022] [Indexed: 12/13/2022]
Abstract
Previous studies have shown that sevoflurane has an inhibitory effect on tumor cells. So far, the effect of sevoflurane on hepatocellular carcinoma needs to be confirmed by more studies. HOX transcript antisense intergenic RNA (HOTAIR), a long noncoding RNA (lncRNA), has been shown to enhance cancer cell proliferation and medication resistance. The inherent importance and biological function of HOTAIR in the course of lung cancer (LC) is, however, poorly unclear. HOTAIR was shown to be highly elevated in LC cells in this investigation. Impairment of function trials with sevoflurane indicated that it has anticancer effects on LC cell growth, apoptosis, and aerobic glycolysis. In a mechanistic manner, HOTAIR was related to HK2 mRNA and promoted expression and constancy. Additional research revealed that HOTAIR coupled with hexokinase 2 (HK2) mRNA and favorably controlled its stabilization in a traditional-component way. By HK2, the LC enhancement role was mediated. In summary, our data show that HOTAIR promotes the synthesis and proliferation of LC glycogen by increasing the transcription of HK2, and HOTAIR is likely to be a potential treatment for LC patients.
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Krokowski D, Jobava R, Szkop KJ, Chen CW, Fu X, Venus S, Guan BJ, Wu J, Gao Z, Banaszuk W, Tchorzewski M, Mu T, Ropelewski P, Merrick WC, Mao Y, Sevval AI, Miranda H, Qian SB, Manifava M, Ktistakis NT, Vourekas A, Jankowsky E, Topisirovic I, Larsson O, Hatzoglou M. Stress-induced perturbations in intracellular amino acids reprogram mRNA translation in osmoadaptation independently of the ISR. Cell Rep 2022; 40:111092. [PMID: 35858571 PMCID: PMC9491157 DOI: 10.1016/j.celrep.2022.111092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 04/26/2022] [Accepted: 06/22/2022] [Indexed: 12/23/2022] Open
Abstract
The integrated stress response (ISR) plays a pivotal role in adaptation of translation machinery to cellular stress. Here, we demonstrate an ISR-independent osmoadaptation mechanism involving reprogramming of translation via coordinated but independent actions of mTOR and plasma membrane amino acid transporter SNAT2. This biphasic response entails reduced global protein synthesis and mTOR signaling followed by translation of SNAT2. Induction of SNAT2 leads to accumulation of amino acids and reactivation of mTOR and global protein synthesis, paralleled by partial reversal of the early-phase, stress-induced translatome. We propose SNAT2 functions as a molecular switch between inhibition of protein synthesis and establishment of an osmoadaptive translation program involving the formation of cytoplasmic condensates of SNAT2-regulated RNA-binding proteins DDX3X and FUS. In summary, we define key roles of SNAT2 in osmotolerance.
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Affiliation(s)
- Dawid Krokowski
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland.
| | - Raul Jobava
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA; Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Krzysztof J Szkop
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden
| | - Chien-Wen Chen
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Xu Fu
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Sarah Venus
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Bo-Jhih Guan
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jing Wu
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Zhaofeng Gao
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Wioleta Banaszuk
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Marek Tchorzewski
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland; EcoTech-Complex Centre, Maria Curie-Skłodowska University, Lublin, Poland
| | - Tingwei Mu
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Phil Ropelewski
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - William C Merrick
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Yuanhui Mao
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Aksoylu Inci Sevval
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden
| | - Helen Miranda
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Shu-Bing Qian
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
| | | | | | - Anastasios Vourekas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Eckhard Jankowsky
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Ivan Topisirovic
- The Lady Davis Institute, Jewish General Hospital, Montréal, QC, Canada; Gerald Bronfman Department of Oncology, McGill University, Montréal, QC, Canada; Department of Biochemistry and Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden.
| | - Maria Hatzoglou
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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127
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Zhang T, Zhang SW, Feng J, Zhang B. m 6 Aexpress-BHM: predicting m6A regulation of gene expression in multiple-groups context by a Bayesian hierarchical mixture model. Brief Bioinform 2022; 23:6644383. [PMID: 35848879 DOI: 10.1093/bib/bbac295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/16/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022] Open
Abstract
As the most abundant RNA modification, N6-methyladenosine (m6A) plays an important role in various RNA activities including gene expression and translation. With the rapid application of MeRIP-seq technology, samples of multiple groups, such as the involved multiple viral/ bacterial infection or distinct cell differentiation stages, are extracted from same experimental unit. However, our current knowledge about how the dynamic m6A regulating gene expression and the role in certain biological processes (e.g. immune response in this complex context) is largely elusive due to lack of effective tools. To address this issue, we proposed a Bayesian hierarchical mixture model (called m6Aexpress-BHM) to predict m6A regulation of gene expression (m6A-reg-exp) in multiple groups of MeRIP-seq experiment with limited samples. Comprehensive evaluations of m6Aexpress-BHM on the simulated data demonstrate its high predicting precision and robustness. Applying m6Aexpress-BHM on three real-world datasets (i.e. Flaviviridae infection, infected time-points of bacteria and differentiation stages of dendritic cells), we predicted more m6A-reg-exp genes with positive regulatory mode that significantly participate in innate immune or adaptive immune pathways, revealing the underlying mechanism of the regulatory function of m6A during immune response. In addition, we also found that m6A may influence the expression of PD-1/PD-L1 via regulating its interacted genes. These results demonstrate the power of m6Aexpress-BHM, helping us understand the m6A regulatory function in immune system.
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Affiliation(s)
- Teng Zhang
- School of Automation from the Northwestern Polytechnical University, China
| | - Shao-Wu Zhang
- Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, China
| | - Jian Feng
- department of microbiology and molecular genetics, University of Pittsburgh
| | - Bei Zhang
- Henan University of Science and Technology Affiliated First Hospital
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128
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Qin S, Zhang Q, Xu Y, Ma S, Wang T, Huang Y, Ju S. m 6A-modified circRNAs: detections, mechanisms, and prospects in cancers. Mol Med 2022; 28:79. [PMID: 35836125 PMCID: PMC9284916 DOI: 10.1186/s10020-022-00505-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/30/2022] [Indexed: 12/15/2022] Open
Abstract
Circular RNAs (circRNAs) have become a research hotspot in recent years with their universality, diversity, stability, conservativeness, and spatiotemporal specificity. N6-methyladenosine (m6A), the most abundant modification in the eukaryotic cells, is engaged in the pathophysiological processes of various diseases. An increasing amount of evidence has suggested that m6A modification is common in circRNAs and is associated with their biological functions. This review summarizes the effects of m6A modification on circRNAs and their regulation mechanisms in cancers, providing some suggestions of m6A-modified circRNAs in cancer therapy.
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Affiliation(s)
- Shiyi Qin
- Medical School of Nantong University, Nantong University, No. 19, Qixiu Road, Nantong, 226001, Jiangsu, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Qi Zhang
- Medical School of Nantong University, Nantong University, No. 19, Qixiu Road, Nantong, 226001, Jiangsu, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Yanhua Xu
- Medical School of Nantong University, Nantong University, No. 19, Qixiu Road, Nantong, 226001, Jiangsu, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Shuo Ma
- Medical School of Nantong University, Nantong University, No. 19, Qixiu Road, Nantong, 226001, Jiangsu, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Tianyi Wang
- Medical School of Nantong University, Nantong University, No. 19, Qixiu Road, Nantong, 226001, Jiangsu, China.,Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, No. 19, Qixiu Road, Nantong, 226001, Jiangsu, China. .,Department of Medical Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, 226001, Jiangsu, China. .,Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, China.
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.
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129
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Li L, Xu N, Liu J, Chen Z, Liu X, Wang J. m6A Methylation in Cardiovascular Diseases: From Mechanisms to Therapeutic Potential. Front Genet 2022; 13:908976. [PMID: 35836571 PMCID: PMC9274458 DOI: 10.3389/fgene.2022.908976] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/07/2022] [Indexed: 01/12/2023] Open
Abstract
Cardiovascular disease (CVD) is a leading cause of morbidity and mortality worldwide. Recent studies have shown that n6-methyladenosine (m6A) plays a major role in cardiovascular homeostasis and pathophysiology. These studies have confirmed that m6A methylation affects the pathophysiology of cardiovascular diseases by regulating cellular processes such as differentiation, proliferation, inflammation, autophagy, and apoptosis. Moreover, plenty of research has confirmed that m6A modification can delay the progression of CVD via the post-transcriptional regulation of RNA. However, there are few available summaries of m6A modification regarding CVD. In this review, we highlight advances in CVD-specific research concerning m6A modification, summarize the mechanisms underlying the involvement of m6A modification during the development of CVD, and discuss the potential of m6A modification as a therapeutic target of CVD.
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Affiliation(s)
| | | | | | | | | | - Junnan Wang
- Department of Cardiology, Second Hospital of Jilin University, Changchun, China
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130
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Ouyang X, Gong Y. One Stone, Two Birds: N6-Methyladenosine RNA Modification in Leukemia Stem Cells and the Tumor Immune Microenvironment in Acute Myeloid Leukemia. Front Immunol 2022; 13:912526. [PMID: 35720276 PMCID: PMC9201081 DOI: 10.3389/fimmu.2022.912526] [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: 04/04/2022] [Accepted: 05/09/2022] [Indexed: 02/05/2023] Open
Abstract
Acute myeloid leukemia is the most common acute leukemia in adults, with accumulation of abundant blasts and impairment of hematogenic function. Despite great advances in diagnosis and therapy, the overall survival of patients with acute myeloid leukemia remains poor. Leukemia stem cells are the root cause of relapse and chemoresistance in acute myeloid leukemia. The tumor immune microenvironment is another trigger to induce recurrence and drug resistance. Understanding the underlying factors influencing leukemia stem cells and the tumor immune microenvironment is an urgent and unmet need. Intriguingly, N6-methyladenosine, the most widespread internal mRNA modification in eukaryotes, is found to regulate both leukemia stem cells and the tumor immune microenvironment. Methyltransferases and demethylases cooperatively make N6-methyladenosine modification reversible and dynamic. Increasing evidence demonstrates that N6-methyladenosine modification extensively participates in tumorigenesis and progression in various cancers, including acute myeloid leukemia. In this review, we summarize the current progress in studies on the functions of N6-methyladenosine modification in acute myeloid leukemia, especially in leukemia stem cells and the tumor immune microenvironment. We generalize the landscape of N6-methyladenosine modification in self-renewal of leukemia stem cells and immune microenvironment regulation, as well as in the initiation, growth, proliferation, differentiation, and apoptosis of leukemia cells. In addition, we further explore the clinical application of N6-methyladenosine modification in diagnosis, prognostic stratification, and effect evaluation. Considering the roles of N6-methyladenosine modification in leukemia stem cells and the tumor immune microenvironment, we propose targeting N6-methyladenosine regulators as one stone to kill two birds for acute myeloid leukemia treatment.
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Affiliation(s)
- Xianfeng Ouyang
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China.,Department of Hematology, Jiujiang First People's Hospital, Jiujiang, China
| | - Yuping Gong
- Department of Hematology, West China Hospital, Sichuan University, Chengdu, China
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131
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Xu Z, Xie T, Sui X, Xu Y, Ji L, Zhang Y, Zhang A, Chen J. Crosstalk Between Histone and m6A Modifications and Emerging Roles of m6A RNA Methylation. Front Genet 2022; 13:908289. [PMID: 35783260 PMCID: PMC9240596 DOI: 10.3389/fgene.2022.908289] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/27/2022] [Indexed: 12/15/2022] Open
Abstract
RNA, like DNA and proteins, has been discovered to undergo dynamic and reversible chemical alterations, increasing the diversity and functional complexity of the molecule. N-6-methyladenosine (m6A) RNA methylation serves as a bridge between transcription and translation and is critical for many diseases’ progression. There is a complex interrelationship between m6A modifications and other epigenetic modifications. Their crosstalk significantly affects transcriptional outputs, translation, recruitment of chromatin modifiers, as well as the deployment of the m6A methyltransferase complex at target sites. This article outlines the potential function of m6A RNA methylation in epigenetics and summarizes its interactions with histone modifications.
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Affiliation(s)
- Zibin Xu
- Department of Nephrology, Affiliated Bao’an Hospital of Shenzhen, The Second School of Clinical Medicine, Southern Medical University, Shenzhen, China
| | - Tingfei Xie
- Department of Nephrology, Affiliated Bao’an Hospital of Shenzhen, The Second School of Clinical Medicine, Southern Medical University, Shenzhen, China
| | - Xiaolu Sui
- Department of Nephrology, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yunpeng Xu
- Department of Nephrology, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Lecai Ji
- Department of Nephrology, Affiliated Bao’an Hospital of Shenzhen, The Second School of Clinical Medicine, Southern Medical University, Shenzhen, China
| | - Yanzi Zhang
- Department of Nephrology, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Aisha Zhang
- Department of Nephrology, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Jihong Chen
- Department of Nephrology, Affiliated Bao’an Hospital of Shenzhen, The Second School of Clinical Medicine, Southern Medical University, Shenzhen, China
- Department of Nephrology, The Second Affiliated Hospital of Shenzhen University, Shenzhen, China
- *Correspondence: Jihong Chen,
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132
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Xu J, Li T, Zhang Y, Qiu D, Chen N, Chai X, PengLi, Li J. C-myc/TSPEAR-AS2 Axis Facilitates Breast Cancer Growth and Metastasis in a GLUT1-Dependent Glycolysis Manner. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4239500. [PMID: 35692593 PMCID: PMC9187470 DOI: 10.1155/2022/4239500] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/22/2022] [Accepted: 04/22/2022] [Indexed: 11/17/2022]
Abstract
A large number of facts have shown that epigenetic modification and metabolic reprogramming represented by noncoding RNA play an important role in the invasion and metastasis of breast cancer, but the mechanism is not clear. The purpose of our study is to find a new biomarker of breast cancer and to provide a new perspective for regulating glucose metabolism and aerobic glycolysis of BC. In this paper, by downregulating C-myc protein, our team found that the expression of long-chain noncoding RNATSPAR-AS2 was significantly downregulated. However, the expression of long-chain noncoding RNASPAR-AS2 in BC is relatively high, and the prognosis is poor. TSPEAR-AS2 can promote the malignant phenotype of BC cells, including proliferation, apoptosis, invasion and metastasis, and glycolysis. At the same time, TSPEAR-AS2 can also upregulate the expression of GLUT1, an important regulator of glycolysis, thus promoting the metabolic reprogramming of BC. Molecular mechanism experiments show that TSPEAR-AS2 may promote the expression of GLUT1 by participating in IGF2BP2 modified by the GLUT1 gene. Our results suggest that the C-myc/TSPEAR-AS2/GLUT1 axis promotes the invasion and metastasis of BC by inducing glucose metabolism reprogramming. However, more phenotypic and molecular mechanism results need to be further verified.
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Affiliation(s)
- Jian Xu
- SAN Biomedical Center-Zhejiang SAN Biomedical Technology Co., Ltd., China
| | - Tao Li
- Sino-American Cells Biotechnology Co., Ltd., China
| | - Yang Zhang
- SAN Biomedical Center-Zhejiang SAN Biomedical Technology Co., Ltd., China
| | - Donghai Qiu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, China
| | - Nan Chen
- Department of Cardiac Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xupeng Chai
- Institute of Orthopedic Research, Zhejiang University, Hangzhou, Zhejiang 310000, China
| | - PengLi
- Department of Anesthesia, The Sixth Medical Center of Chinese PLA General Hospital, Beijing 100048, China
| | - Jia Li
- Department of Nutrition, Jinhua People's Hospital, China
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133
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Abe N, Imaeda A, Inagaki M, Li Z, Kawaguchi D, Onda K, Nakashima Y, Uchida S, Hashiya F, Kimura Y, Abe H. Complete Chemical Synthesis of Minimal Messenger RNA by Efficient Chemical Capping Reaction. ACS Chem Biol 2022; 17:1308-1314. [PMID: 35608277 DOI: 10.1021/acschembio.1c00996] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Site-specific chemical modification of mRNA can improve its translational efficiency and stability. For this purpose, it is desirable to develop a complete chemical synthesis method for chemically modified mRNA. The key is a chemical reaction that introduces a cap structure into the chemically synthesized RNA. In this study, we developed a fast and quantitative chemical capping reaction between 5'-phosphorylated RNA and N7-methylated GDP imidazolide in the presence of 1-methylimidazole in the organic solvent dimethyl sulfoxide. It enabled quantitative preparation of capping RNA within 3 h. We prepared chemically modified 107-nucleotide mRNAs, including N6-methyladenosine, insertion of non-nucleotide linkers, and 2'-O-methylated nucleotides at the 5' end and evaluated their effects on translational activity in cultured HeLa cells. The results showed that mRNAs with non-nucleotide linkers in the untranslated regions were sufficiently tolerant to translation and that mRNAs with the Cap_2 structure had higher translational activity than those with the Cap_0 structure.
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Affiliation(s)
- Naoko Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Akihiro Imaeda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Masahito Inagaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Zhenmin Li
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Daisuke Kawaguchi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Kaoru Onda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yuko Nakashima
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Satoshi Uchida
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Fumitaka Hashiya
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- CREST, Japan Science and Technology Agency, 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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Li J, Zhang X, Wang X, Sun C, Zheng J, Li J, Yi G, Yang N. The m6A methylation regulates gonadal sex differentiation in chicken embryo. J Anim Sci Biotechnol 2022; 13:52. [PMID: 35581635 PMCID: PMC9115958 DOI: 10.1186/s40104-022-00710-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/16/2022] [Indexed: 01/06/2023] Open
Abstract
Background As a ubiquitous reversible epigenetic RNA modification, N6-methyladenosine (m6A) plays crucial regulatory roles in multiple biological pathways. However, its functional mechanisms in sex determination and differentiation during gonadal development of chicken embryos are not clear. Therefore, we established a transcriptome-wide m6A map in the female and male chicken left gonads of embryonic day 7 (E7) by methylated RNA immunoprecipitation sequencing (MeRIP-seq) to offer insight into the landscape of m6A methylation and investigate the post-transcriptional modification underlying gonadal differentiation. Results The chicken embryonic gonadal transcriptome was extensively methylated. We found 15,191 and 16,111 m6A peaks in the female and male left gonads, respectively, which were mainly enriched in the coding sequence (CDS) and stop codon. Among these m6A peaks, we identified that 1013 and 751 were hypermethylated in females and males, respectively. These differential peaks covered 281 and 327 genes, such as BMP2, SMAD2, SOX9 and CYP19A1, which were primarily associated with development, morphogenesis and sex differentiation by functional enrichment. Further analysis revealed that the m6A methylation level was positively correlated with gene expression abundance. Furthermore, we found that YTHDC2 could regulate the expression of sex-related genes, especially HEMGN and SOX9, in male mesonephros/gonad mingle cells, which was verified by in vitro experiments, suggesting a regulatory role of m6A methylation in chicken gonad differentiation. Conclusions This work provided a comprehensive m6A methylation profile of chicken embryonic gonads and revealed YTHDC2 as a key regulator responsible for sex differentiation. Our results contribute to a better understanding of epigenetic factors involved in chicken sex determination and differentiation and to promoting the future development of sex manipulation in poultry industry. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00710-6.
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Affiliation(s)
- Jianbo Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Xiuan Zhang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Xiqiong Wang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Jiangxia Zheng
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Junying Li
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China
| | - Guoqiang Yi
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing, China.
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135
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Rajendren S, Karijolich J. The Impact of RNA modifications on the Biology of DNA Virus Infection. Eur J Cell Biol 2022; 101:151239. [PMID: 35623231 PMCID: PMC9549750 DOI: 10.1016/j.ejcb.2022.151239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/15/2022] [Accepted: 05/16/2022] [Indexed: 11/26/2022] Open
Abstract
Approximately 170 RNA modifications have been identified and these are critical for determining the fate and function of cellular RNAs. Similar to human transcripts, viral RNAs possess an extensive RNA modification landscape. While initial efforts largely focused on investigating the RNA modification landscape in the context of RNA virus infection, a growing body of work has explored the impact of RNA modifications on DNA virus biology. These studies have revealed roles for RNA modifications in DNA virus infection, including gene regulation and viral pathogenesis. In this review, we will discuss the current knowledge on how RNA modifications impact DNA virus biology.
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136
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Hou N, Li C, He J, Liu Y, Yu S, Malnoy M, Mobeen Tahir M, Xu L, Ma F, Guan Q. MdMTA-mediated m 6 A modification enhances drought tolerance by promoting mRNA stability and translation efficiency of genes involved in lignin deposition and oxidative stress. THE NEW PHYTOLOGIST 2022; 234:1294-1314. [PMID: 35246985 DOI: 10.1111/nph.18069] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Although the N6 -methyladenosine (m6 A) modification is the most prevalent RNA modification in eukaryotes, the global m6 A modification landscape and its molecular regulatory mechanism in response to drought stress remain unclear. Transcriptome-wide m6 A methylome profiling revealed that m6 A is mainly enriched in the coding sequence and 3' untranslated region in response to drought stress in apple, by recognizing the plant-specific sequence motif UGUAH (H=A, U or C). We identified a catalytically active component of the m6 A methyltransferase complex, MdMTA. An in vitro methyl transfer assay, dot blot, LC-MS/MS and m6 A-sequencing (m6 A-seq) suggested that MdMTA is an m6 A writer and essential for m6 A mRNA modification. Further studies revealed that MdMTA is required for apple drought tolerance. m6 A-seq and RNA-seq analyses under drought conditions showed that MdMTA mediates m6 A modification and transcripts of mRNAs involved in oxidative stress and lignin deposition. Moreover, m6 A modification promotes mRNA stability and the translation efficiency of these genes in response to drought stress. Consistently, MdMTA enhances lignin deposition and scavenging of reactive oxygen species under drought conditions. Our results reveal the global involvement of m6 A modification in the drought response of perennial apple trees and illustrate its molecular mechanisms, thereby providing candidate genes for the breeding of stress-tolerant apple cultivars.
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Affiliation(s)
- Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Chaoshuo Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Yu Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Sisi Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Mickael Malnoy
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach, San Michele all'Adige, 38010, Italy
| | - Muhammad Mobeen Tahir
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Lingfei Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, No. 3 Taicheng Road, Yangling, Shaanxi, 712100, China
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137
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Wu M, Chen G, Liao X, Xiao L, Zheng J. YTHDF2 interference suppresses the EMT of cervical cancer cells and enhances cisplatin chemosensitivity by regulating AXIN1. Drug Dev Res 2022; 83:1190-1200. [PMID: 35489084 DOI: 10.1002/ddr.21942] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 02/02/2023]
Abstract
M6A reader YTH structural domain family 2 (YTHDF2) has been recognized to play an oncogenic role in numerous tumors, but its role in cervical cancer has not been extensively discussed yet. This paper was designed to explore the role of YTHDF2 in cervical cancer and identify its underlying mechanism. The expression of YTHDF2 was first determined in cervical cancer cells by quantitative reverse-transcription polymerase chain reaction and western blot. Then, the migration, invasion, and epithelial-mesenchymal transition (EMT) process were observed in YTHDF2-knockdown Hela cells using wound healing, transwell and immunofluorescence assays. The cisplatin chemosensitivity of Hela cells was also investigated by assessing cell activity with cell counting kit-8 and TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling). After MeRIP-Seq assay and actinomycin D treatment to confirm the binding relationship between YTHDF2 and AXIN1, the migration, invasion, EMT process, and cisplatin chemosensitivity were assessed again in Hela cells silenced by YTHDF2 and AXIN1 or treated with Wnt agonist. YTHDF2 was increased in cervical cancer cells, and depletion of YTHDF2 led to reduced migration, invasion and EMT process but enhanced chemosensitivity of cisplatin in Hela cells. Furthermore, YTHDF2 could bind to and stabilize the expression of AXIN1. When the YTHDF2-knockdown Hela cells were further transfected with AXIN1 knockdown or treated with Wnt agonist, the effects of YTHDF2 knockdown on the migration, invasion and EMT process were partially abolished, together with reduced cisplatin chemosensitivity. To sum up, we reported that YTHDF2 interference could suppress the EMT of cervical cancer cells and enhance cisplatin chemosensitivity by regulating AXIN1.
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Affiliation(s)
- Min Wu
- Radiation Oncology Department, The Second Affiliated Hospital of Fujian Medical University, Quanzhou City, Fujian Province, China
| | - Guozhong Chen
- Radiation Oncology Department, The Second Affiliated Hospital of Fujian Medical University, Quanzhou City, Fujian Province, China
| | - Xiaowen Liao
- Radiation Oncology Department, The Second Affiliated Hospital of Fujian Medical University, Quanzhou City, Fujian Province, China
| | - Lihua Xiao
- Radiation Oncology Department, The Second Affiliated Hospital of Fujian Medical University, Quanzhou City, Fujian Province, China
| | - Jianqing Zheng
- Radiation Oncology Department, The Second Affiliated Hospital of Fujian Medical University, Quanzhou City, Fujian Province, China
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138
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Liu C, Gu L, Deng W, Meng Q, Li N, Dai G, Yu S, Fang H. N6-Methyladenosine RNA Methylation in Cardiovascular Diseases. Front Cardiovasc Med 2022; 9:887838. [PMID: 35571209 PMCID: PMC9098837 DOI: 10.3389/fcvm.2022.887838] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/12/2022] [Indexed: 12/18/2022] Open
Abstract
N6-methyladenosine (m6A) modification is the most universal and abundant post-transcriptional modification of eukaryotic RNA and occurs mainly at the consensus motif RR (m6A) CH (R = A or G, H = A, C, or U) in long internal exons, near stop codons, or in the 3' untranslated region (UTR). "Writers," "erasers," and "readers" are responsible for the occurrence, removal, and recognition of m6A modification, respectively. Substantial evidence has shown that m6A RNA modification can exert important functions in physiological and pathological processes. Cardiovascular diseases (CVDs) are a wide array of disorders affecting heart or vessels, including atherosclerosis (AS), hypertension (HT), ischemia/reperfusion (I/R) injury, myocardial infarction (MI), stroke, cardiac hypertrophy, heart failure (HF), and so on. Despite the advances in lipid-lowering drugs, antihypertensives, antiplatelet agents, and anticoagulation therapy, CVDs are still the leading cause of death worldwide. Recent studies have suggested that m6A modification of RNA may contribute to the pathogenesis of CVDs, providing a novel research insight for CVDs. Herein, we provide an up-of-date summarization of the molecular mechanism of m6A and the roles of m6A in different types of CVDs. At last, we propose that m6A might be a potiential biomarker or therapeutic target for CVDs.
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Affiliation(s)
- Chi Liu
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Geriatrics Center, National Clinical Research Center for Aging and Medicine, Jing’an District Central Hospital of Shanghai, Fudan University, Shanghai, China
| | - Lei Gu
- Department of Internal Medicine, Shanghai Shende Hospital, Shanghai, China
| | - Wenjuan Deng
- Department of Geriatrics Center, National Clinical Research Center for Aging and Medicine, Jing’an District Central Hospital of Shanghai, Fudan University, Shanghai, China
| | - Qianchao Meng
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Nan Li
- Department of Geriatrics Center, National Clinical Research Center for Aging and Medicine, Jing’an District Central Hospital of Shanghai, Fudan University, Shanghai, China
| | - Guifeng Dai
- Department of Geriatrics Center, National Clinical Research Center for Aging and Medicine, Jing’an District Central Hospital of Shanghai, Fudan University, Shanghai, China
| | - Suli Yu
- Department of Hand and Upper Extremity Surgery and Limb Function Reconstruction Center, Jing’an District Central Hospital, Shanghai, China
| | - Hong Fang
- Department of Cardiology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
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139
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Fang S, Peng B, Wen Y, Yang J, Wang H, Wang Z, Qian K, Wei Y, Jiao Y, Gao C, Dou L. Transcriptome-Wide Analysis of RNA N6-Methyladenosine Modification in Adriamycin-Resistant Acute Myeloid Leukemia Cells. Front Genet 2022; 13:833694. [PMID: 35571033 PMCID: PMC9100953 DOI: 10.3389/fgene.2022.833694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 03/18/2022] [Indexed: 11/28/2022] Open
Abstract
Acute myeloid leukemia (AML) is one of the most aggressive hematopoietic malignancies. Patients still suffer from refractory/relapsed disease after anthracycline-based therapy, which leads to a poor prognosis. N6-Methyladenosine (m6A) is the most abundant post-transcriptional modification in eukaryotes, the imbalance of which is reported to be associated with various pathological processes, including drug resistance. However, the relationship between m6A modification and drug resistance has not been well defined in AML. In this study, we analyzed the sequencing data of HL60 and its Adriamycin-resistant cell line HL60/ADR. We found a total of 40,550 m6A-methylated peaks, representing 15,640 genes in HL60, and 38,834 m6A-methylated peaks, representing 15,285 genes in HL60/ADR. KEGG pathway analysis showed that pathways were enriched in the FoxO signaling pathway, p53 signaling pathway, and Notch signaling pathway. MeRIP-seq results showed that the fold enrichment of the global m6A level in HL60/ADR was higher than that in HL60, and dot blot assay results indicated that the global m6A level was elevated in HL60/ADR cells compared with that in HL60 cells. Further analysis revealed that the expression level of METTL3 was elevated in HL60/ADR cells compared with that in HL60 cells. After a combined treatment of STM2457 (an inhibitor of METTL3) and Adriamycin, the proliferation of HL60/ADR was inhibited. Thus, we hypothesized that the abnormality of m6A modification played an important role in Adriamycin-resistant AML.
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Affiliation(s)
- Shu Fang
- School of Medicine, Nankai University, Tianjin, China
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Bo Peng
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yanan Wen
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Jingjing Yang
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Hao Wang
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Ziwei Wang
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Kun Qian
- School of Medicine, Nankai University, Tianjin, China
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yan Wei
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Yifan Jiao
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
- Medical School of Chinese PLA, Beijing, China
| | - Chunji Gao
- School of Medicine, Nankai University, Tianjin, China
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
- *Correspondence: Chunji Gao, ; Liping Dou,
| | - Liping Dou
- Department of Hematology, the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
- *Correspondence: Chunji Gao, ; Liping Dou,
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Li P, Richard HT, Zhu K, Li L, Huang S. The Roles and Regulation of m 6A Modification in Glioblastoma Stem Cells and Tumorigenesis. Biomedicines 2022; 10:969. [PMID: 35625706 PMCID: PMC9138636 DOI: 10.3390/biomedicines10050969] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 12/15/2022] Open
Abstract
Glioblastoma is the most common and most lethal primary malignant brain tumor. N6-methyladenosine (m6A) is a widespread and abundant internal messenger RNA (mRNA) modification found in eukaryotes. Accumulated evidence demonstrates that m6A modification is aberrantly activated in human cancers and is critical for tumorigenesis and metastasis. m6A modification is also strongly involved in key signaling pathways and is associated with prognosis in glioblastoma. Here, we briefly outline the functions of m6A and its regulatory proteins, including m6A writers, erasers, and readers of the fate of RNA. We also summarize the latest breakthroughs in this field, describe the underlying molecular mechanisms that contribute to the tumorigenesis and progression, and highlight the inhibitors targeting the factors in m6A modification in glioblastoma. Further studies focusing on the specific pathways of m6A modification could help identify biomarkers and therapeutic targets that might prevent and treat glioblastoma.
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Affiliation(s)
- Peng Li
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (K.Z.); (L.L.)
| | - Hope T. Richard
- Department of Pathology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Kezhou Zhu
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (K.Z.); (L.L.)
| | - Linlin Li
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (K.Z.); (L.L.)
| | - Suyun Huang
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (P.L.); (K.Z.); (L.L.)
- Institute of Molecular Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
- VCU Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
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141
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Shi H, Xu Y, Tian N, Yang M, Liang FS. Inducible and reversible RNA N 6-methyladenosine editing. Nat Commun 2022; 13:1958. [PMID: 35414049 PMCID: PMC9005610 DOI: 10.1038/s41467-022-29665-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/18/2022] [Indexed: 12/26/2022] Open
Abstract
RNA modifications, including N6-methyladenosine (m6A), have been reported to regulate fundamental RNA processes and properties, and directly linked to various human diseases. Methods enabling temporal and transcript/locus-specific editing of specific RNA modifications are essential, but still limited, to dissect the dynamic and context-dependent functions of these epigenetic modifications. Here, we develop a chemically inducible and reversible RNA m6A modification editing platform integrating chemically induced proximity (CIP) and CRISPR methods. We show that m6A editing can be temporally controlled at specific sites of individual RNA transcripts by the addition or removal of the CIP inducer, abscisic acid (ABA), in the system. By incorporating a photo-caged ABA, a light-controlled version of m6A editing platform can be developed. We expect that this platform and strategy can be generally applied to edit other RNA modifications in addition to m6A. RNA modifications, including N6-methyladenosine (m6A), have been reported to regulate fundamental RNA processes and properties, and directly linked to various human diseases. Here, the authors develop a chemically inducible and reversible RNA m6A modification editing platform integrating chemically induced proximity (CIP) and CRISPR methods.
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Affiliation(s)
- Huaxia Shi
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH, 44106, USA
| | - Ying Xu
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH, 44106, USA
| | - Na Tian
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH, 44106, USA
| | - Ming Yang
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH, 44106, USA
| | - Fu-Sen Liang
- Department of Chemistry, Case Western Reserve University, 2080 Adelbert Road, Cleveland, OH, 44106, USA.
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142
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Song D, Shyh-Chang N. An RNA methylation code to regulate protein translation and cell fate. Cell Prolif 2022; 55:e13224. [PMID: 35355346 PMCID: PMC9136488 DOI: 10.1111/cpr.13224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/28/2022] [Accepted: 03/06/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Dan Song
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Ng Shyh-Chang
- State Key Laboratory of Stem Cell and Reproductive Biology, Chinese Academy of Sciences, Beijing, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
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143
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Liao J, Wei Y, Liang J, Wen J, Chen X, Zhang B, Chu L. Insight into the structure, physiological function, and role in cancer of m6A readers—YTH domain-containing proteins. Cell Death Dis 2022; 8:137. [PMID: 35351856 PMCID: PMC8964710 DOI: 10.1038/s41420-022-00947-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/24/2022] [Accepted: 03/15/2022] [Indexed: 12/14/2022]
Abstract
YT521-B homology (YTH) domain-containing proteins (YTHDF1-3, YTHDC1-2) are the most crucial part of N6-methyladenosine (m6A) readers and play a regulatory role in almost all stages of methylated RNA metabolism and the progression of various cancers. Since m6A is identified as an essential post-transcriptional type, YTH domain-containing proteins have played a key role in the m6A sites of RNA. Hence, it is of great significance to study the interaction between YTH family proteins and m6A-modified RNA metabolism and tumor. In this review, their basic structure and physical functions in RNA transcription, splicing, exporting, stability, and degradation as well as protein translation are introduced. Then we discussed the expression regulation of YTH domain-containing proteins in cancers. Furthermore, we introduced the role of the YTH family in cancer biology and systematically demonstrated their functions in various aspects of tumorigenesis and development. To provide a more institute understanding of the role of YTH family proteins in cancers, we summarized their functions and specific mechanisms in various cancer types and presented their involvement in cancer-related signaling pathways.
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144
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Sun CY, Cao D, Du BB, Chen CW, Liu D. The role of Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) as m 6A readers in cancer. Int J Biol Sci 2022; 18:2744-2758. [PMID: 35541906 PMCID: PMC9066119 DOI: 10.7150/ijbs.70458] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
RNA can be modified by over 170 types of distinct chemical modifications, and the most abundant internal modification of mRNA in eukaryotes is N6-methyladenosine (m6A). The m6A modification accelerates mRNA process, including mRNA splicing, translation, transcript stability, export and decay. m6A RNA modification is installed by methyltransferase-like proteins (writers), and potentially removed by demethylases (erasers), and this process is recognized by m6A-binding proteins (readers). Notably, alterations of m6A-modified proteins (writers, erasers and readers) are involved in the tumorigenesis, progression and metastasis. Importantly, the fate of m6A-methylated mRNA is mediated mostly through m6A readers, and among these readers, insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs) are unique RNA-binding proteins (RBPs) that stabilize their targets mRNA via m6A modification. In this review, we update the writers, erasers and readers, and their cross-talks in m6A modification, and briefly discuss the oncogenic role of IGF2BPs in cancer. Most importantly, we mainly review the up-to-date knowledges of IGF2BPs (IGF2BP1/2/3) as m6A readers in an m6A-modified manner in cancer progression.
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Affiliation(s)
- Chao-Yue Sun
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
| | - Di Cao
- Department of Radiology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, P.R. China
| | - Bin-Bin Du
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
| | - Cun-Wu Chen
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
| | - Dong Liu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, China
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145
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Li L, Krasnykov K, Homolka D, Gos P, Mendel M, Fish RJ, Pandey RR, Pillai RS. The XRN1-regulated RNA helicase activity of YTHDC2 ensures mouse fertility independently of m 6A recognition. Mol Cell 2022; 82:1678-1690.e12. [PMID: 35305312 DOI: 10.1016/j.molcel.2022.02.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/11/2022]
Abstract
The functional consequence of N6-methyladenosine (m6A) RNA modification is mediated by "reader" proteins of the YTH family. YTH domain-containing 2 (YTHDC2) is essential for mammalian fertility, but its molecular function is poorly understood. Here, we identify U-rich motifs as binding sites of YTHDC2 on 3' UTRs of mouse testicular RNA targets. Although its YTH domain is an m6A-binder in vitro, the YTH point mutant mice are fertile. Significantly, the loss of its 3'→5' RNA helicase activity causes mouse infertility, with the catalytic-dead mutation being dominant negative. Biochemical studies reveal that the weak helicase activity of YTHDC2 is enhanced by its interaction with the 5'→3' exoribonuclease XRN1. Single-cell transcriptomics indicate that Ythdc2 mutant mitotic germ cells transition into meiosis but accumulate a transcriptome with mixed mitotic/meiotic identity that fail to progress further into meiosis. Finally, our demonstration that ythdc2 mutant zebrafish are infertile highlights its conserved role in animal germ cell development.
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Affiliation(s)
- Lingyun Li
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Kyrylo Krasnykov
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - David Homolka
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Pascal Gos
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Mateusz Mendel
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Richard J Fish
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
| | - Radha Raman Pandey
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.
| | - Ramesh S Pillai
- Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.
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146
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Xu T, He B, Sun H, Xiong M, Nie J, Wang S, Pan Y. Novel insights into the interaction between N6-methyladenosine modification and circular RNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:824-837. [PMID: 35141044 PMCID: PMC8807973 DOI: 10.1016/j.omtn.2022.01.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
As the most prevalent type of RNA modification in eukaryotes, N6-methyladenosine (m6A) can modulate RNA fates such as processing, splicing, maturation, export, stability, translation, and degradation. Circular RNAs (circRNAs), a novel type of non-coding RNA (ncRNAs) characterized by a covalently closed loop structure, play an essential role in various physiological and pathological processes. Extensive studies have revealed that m6A modification is widespread in circRNAs and influences their biogenesis and functions. Intriguingly, circRNAs can affect m6A modification by regulating m6A regulatory proteins. In this review, we summarize the characteristics and biological functions of m6A and circRNAs and focus on recent advances in the interaction of m6A modification and circRNAs. In addition, the potential clinical applications of m6A modification and circRNAs in diagnosis and therapeutic targets are discussed.
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Affiliation(s)
- Tao Xu
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Bangshun He
- Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Huiling Sun
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Mengqiu Xiong
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Junjie Nie
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Shukui Wang
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
| | - Yuqin Pan
- General Clinical Research Center, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, China
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147
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Zhao T, Wang M, Zhao X, Weng S, Qian K, Shi K, Gu Y, Ying W, Qian X, Zhang Y. YTHDF2 Inhibits the Migration and Invasion of Lung Adenocarcinoma by Negatively Regulating the FAM83D-TGFβ1-SMAD2/3 Pathway. Front Oncol 2022; 12:763341. [PMID: 35186724 PMCID: PMC8847186 DOI: 10.3389/fonc.2022.763341] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/17/2022] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVE YTH domain family 2 (YTHDF2) is an important N6-methyladenosine (m6A) reader, but its role in lung adenocarcinoma remains elusive. This study assessed its function in lung adenocarcinoma. METHODS YTHDF2 expression in lung adenocarcinoma was explored using public databases, such as The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumour Analysis Consortium (CPTAC). The effect of YTHDF2 on a lung adenocarcinoma cell line was explored by performing cytological and molecular experiments. Molecules downstream of YTHDF2 were identified using proteomics, and the related pathways were verified through cytological and molecular biology experiments. RESULTS YTHDF2 expression was upregulated in lung adenocarcinoma, and patients with high YTHDF2 expression experienced prolonged overall survival. In two lung cancer cell lines, YTHDF2 knockdown inhibited proliferation but promoted migration, invasion, and the epithelial-mesenchymal transition. The proteomic analysis identified 142 molecules downstream of YTHDF2, and 11 were closely related to survival. Further experiments revealed that YTHDF2 inhibited expression of the family with sequence similarity 83D (FAM83D)-TGFβ1-SMAD2/3 pathway components. This study is the first to show that YTHDF2 regulated the downstream TGFβ1-SMAD2/3 pathway through FAM83D in lung adenocarcinoma. CONCLUSION YTHDF2 inhibits the migration and invasion of lung adenocarcinoma cells by regulating the FAM83D-TGFβ1-pSMAD2/3 pathway, which may play an important role in lung cancer metastasis.
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Affiliation(s)
- Teng Zhao
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Mingchao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xin Zhao
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Shuang Weng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Kun Qian
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Kejian Shi
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yanfei Gu
- Department of Oncology, United Family New Hope Oncology Center, Beijing, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yi Zhang
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
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148
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Macveigh-Fierro D, Cicerchia A, Cadorette A, Sharma V, Muller M. The m 6A reader YTHDC2 is essential for escape from KSHV SOX-induced RNA decay. Proc Natl Acad Sci U S A 2022; 119:e2116662119. [PMID: 35177478 PMCID: PMC8872733 DOI: 10.1073/pnas.2116662119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/13/2022] [Indexed: 11/18/2022] Open
Abstract
The role of N6-methyladenosine (m6A) modifications has increasingly been associated with a diverse set of roles in modulating viruses and influencing the outcomes of viral infection. Here, we report that the landscape of m6A deposition is drastically shifted during Kaposi's sarcoma-associated herpesvirus (KSHV) lytic infection for both viral and host transcripts. In line with previous reports, we also saw an overall decrease in host methylation in favor of viral messenger RNA (mRNA), along with 5' hypomethylation and 3' hypermethylation. During KSHV lytic infection, a major shift in overall mRNA abundance is driven by the viral endoribonuclease SOX, which induces the decay of greater than 70% of transcripts. Here, we reveal that interlukin-6 (IL-6) mRNA, a well-characterized, SOX-resistant transcript, is m6A modified during lytic infection. Furthermore, we show that this modification falls within the IL-6 SOX resistance element, an RNA element in the IL-6 3' untranslated region (UTR) that was previously shown to be sufficient for protection from SOX cleavage. We show that the presence of this m6A modification is essential to confer SOX resistance to the IL-6 mRNA. We next show that this modification recruits the m6A reader YTHDC2 and found that YTHDC2 is necessary for the escape of the IL-6 transcript. These results shed light on how the host cell has evolved to use RNA modifications to circumvent viral manipulation of RNA fate during KSHV infection.
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Affiliation(s)
- Daniel Macveigh-Fierro
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003
| | - Angelina Cicerchia
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003
| | - Ashley Cadorette
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003
| | - Vasudha Sharma
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003
| | - Mandy Muller
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003;
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003
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149
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Lawrence M, Shahsavari A, Bornelöv S, Moreau T, McDonald R, Vallance TM, Kania K, Paramor M, Baye J, Perrin M, Steindel M, Jimenez-Gomez P, Penfold C, Mohorianu I, Ghevaert C. Mapping the biogenesis of forward programmed megakaryocytes from induced pluripotent stem cells. SCIENCE ADVANCES 2022; 8:eabj8618. [PMID: 35171685 PMCID: PMC8849335 DOI: 10.1126/sciadv.abj8618] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Platelet deficiency, known as thrombocytopenia, can cause hemorrhage and is treated with platelet transfusions. We developed a system for the production of platelet precursor cells, megakaryocytes, from pluripotent stem cells. These cultures can be maintained for >100 days, implying culture renewal by megakaryocyte progenitors (MKPs). However, it is unclear whether the MKP state in vitro mirrors the state in vivo, and MKPs cannot be purified using conventional surface markers. We performed single-cell RNA sequencing throughout in vitro differentiation and mapped each state to its equivalent in vivo. This enabled the identification of five surface markers that reproducibly purify MKPs, allowing us insight into their transcriptional and epigenetic profiles. Last, we performed culture optimization, increasing MKP production. Together, this study has mapped parallels between the MKP states in vivo and in vitro and allowed the purification of MKPs, accelerating the progress of in vitro-derived transfusion products toward the clinic.
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Affiliation(s)
- Moyra Lawrence
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
- Department of Haematology and NHS Blood and Transplant, University of Cambridge, Cambridge, UK
| | - Arash Shahsavari
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Susanne Bornelöv
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Thomas Moreau
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
- Department of Haematology and NHS Blood and Transplant, University of Cambridge, Cambridge, UK
- Bit Bio, Discovery Drive, Cambridge Biomedical Campus, Cambridge CB2 0AX, UK
| | - Rebecca McDonald
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Thomas M. Vallance
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Katarzyna Kania
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Maike Paramor
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - James Baye
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Marion Perrin
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Maike Steindel
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Paula Jimenez-Gomez
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Christopher Penfold
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Irina Mohorianu
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Cedric Ghevaert
- Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
- Department of Haematology and NHS Blood and Transplant, University of Cambridge, Cambridge, UK
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150
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N6-methyladenosine modification of the 5' epsilon structure of the HBV pregenome RNA regulates its encapsidation by the viral core protein. Proc Natl Acad Sci U S A 2022; 119:2120485119. [PMID: 35135882 PMCID: PMC8851549 DOI: 10.1073/pnas.2120485119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2022] [Indexed: 12/19/2022] Open
Abstract
HBV infections are the leading cause of chronic hepatitis and carry the risk of liver cirrhosis and cancer. The HBV life cycle is perpetuated by an RNA intermediate termed pregenomic RNA (pgRNA), which is encapsidated by the viral core protein. The pgRNA packaging process is an essential step in viral replication. Here, we investigated the role of N6-methyladenosine (m6A) modification in the recognition of pgRNA by the core protein during encapsidation. m6A modification of 5′ epsilon structural motifs serves as the recognition signal for the core protein interaction, as evidenced by the failure of 5′ epsilon m6A mutant to encapsidate pgRNA. This study identifies the structural role of m6A modification in pgRNA encapsidation and provides an avenue in RNA–protein complex interactions. Hepatitis B virus (HBV) contains a partially double-stranded DNA genome. During infection, its replication is mediated by reverse transcription (RT) of an RNA intermediate termed pregenomic RNA (pgRNA) within core particles in the cytoplasm. An epsilon structural element located in the 5′ end of the pgRNA primes the RT activity. We have previously identified the N6-methyladenosine (m6A)–modified DRACH motif at 1905 to 1909 nucleotides in the epsilon structure that affects myriad functions of the viral life cycle. In this study, we investigated the functional role of m6A modification of the 5′ ε (epsilon) structural element of the HBV pgRNA in the nucleocapsid assembly. Using the m6A site mutant in the HBV 5′ epsilon, we present evidence that m6A methylation of 5′ epsilon is necessary for its encapsidation. The m6A modification of 5′ epsilon increased the efficiency of viral RNA packaging, whereas the m6A of 3′ epsilon is dispensable for encapsidation. Similarly, depletion of methyltransferases (METTL3/14) decreased pgRNA and viral DNA levels within the core particles. Furthermore, the m6A modification at 5′ epsilon of HBV pgRNA promoted the interaction with core proteins, whereas the 5′ epsilon m6A site–mutated pgRNA failed to interact. HBV polymerase interaction with 5′ epsilon was independent of m6A modification of 5′ epsilon. This study highlights yet another pivotal role of m6A modification in dictating the key events of the HBV life cycle and provides avenues for investigating RNA–protein interactions in various biological processes, including viral RNA genome encapsidation in the context of m6A modification.
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