1
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Li Y, Wang Y, Vera-Rodriguez M, Lindeman LC, Skuggen LE, Rasmussen EMK, Jermstad I, Khan S, Fosslie M, Skuland T, Indahl M, Khodeer S, Klemsdal EK, Jin KX, Dalen KT, Fedorcsak P, Greggains GD, Lerdrup M, Klungland A, Au KF, Dahl JA. Single-cell m 6A mapping in vivo using picoMeRIP-seq. Nat Biotechnol 2024; 42:591-596. [PMID: 37349523 PMCID: PMC10739642 DOI: 10.1038/s41587-023-01831-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 05/17/2023] [Indexed: 06/24/2023]
Abstract
Current N6-methyladenosine (m6A) mapping methods need large amounts of RNA or are limited to cultured cells. Through optimized sample recovery and signal-to-noise ratio, we developed picogram-scale m6A RNA immunoprecipitation and sequencing (picoMeRIP-seq) for studying m6A in vivo in single cells and scarce cell types using standard laboratory equipment. We benchmark m6A mapping on titrations of poly(A) RNA and embryonic stem cells and in single zebrafish zygotes, mouse oocytes and embryos.
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Affiliation(s)
- Yanjiao Li
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Maria Vera-Rodriguez
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Reproductive Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | | | | | - Erik M K Rasmussen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Aas, Norway
| | - Ingunn Jermstad
- Norwegian Transgenic Centre, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Shaista Khan
- Norwegian Transgenic Centre, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Madeleine Fosslie
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Trine Skuland
- Department of Reproductive Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Division of Gynaecology and Obstetrics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Marie Indahl
- Department of Reproductive Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Division of Gynaecology and Obstetrics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sherif Khodeer
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Institute for Single-Cell Omics (LISCO), Leuven Stem Cell Institute, Leuven, Belgium
| | | | - Kang-Xuan Jin
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Knut Tomas Dalen
- Norwegian Transgenic Centre, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Peter Fedorcsak
- Department of Reproductive Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Division of Gynaecology and Obstetrics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gareth D Greggains
- Department of Reproductive Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Mads Lerdrup
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Department of Microbiology, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA.
| | - John Arne Dahl
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
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2
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Zhang J, Liu X, Gao Y. FTO protein regulates the TGF-β signalling pathway through RNA N6-methyladenosine modification to induce unexplained recurrent spontaneous abortion. FEBS J 2024; 291:1545-1559. [PMID: 38245815 DOI: 10.1111/febs.17053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/26/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024]
Abstract
Recent studies have revealed the involvement of RNA m6A modification in embryonic development; however, the relationship between aberrant RNA m6A modification and unexplained recurrent spontaneous abortion (URSA) remains unclear. In this study, we analysed the level of RNA m6A modification in trophoblasts using dot blot, RNA m6A quantification, and MeRIP assays. By integrating data from the GEO database, RNA-Seq, and MeRIP-Seq, we examined the aberrant expression of m6A methyltransferases and their downstream molecules in chorionic villus (placental) tissues. RNA pull-down, RIP, and electrophoretic mobility shift assay were used to analyse the binding relationship between the YTHDC1 protein and MEG3. Additionally, RNA stability and BrU immunoprecipitation chase assays were utilised to elucidate the regulation of MEG3 stability by YTHDC1. ChIP and DNA pull-down RNA experiments were performed to elucidate the mechanism by which MEG3 targets EZH2 to the TGF-β1 promoter. The results showed that the expression of the m6A demethylase FTO protein was significantly increased in URSA trophoblasts, leading to inhibition of the MEG3 m6A modification and weakening of the stabilising effect of the m6A binding protein YTHDC1 on MEG3. Furthermore, MEG3 was found to bind simultaneously with the EZH2 protein and the TGF-β1 gene promoter, enabling the localisation of EZH2 protein to the TGF-β1 gene promoter and subsequent inhibition of TGF-β1 gene expression. In summary, our findings elucidate the mechanism by which FTO protein regulates the MEG3-TGF-β signalling pathway, thereby suppressing trophoblast invasion and proliferation in URSA trophoblast cells. These findings provide new insights for the treatment of URSA.
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Affiliation(s)
- Jun Zhang
- Department of Reproductive Medicine, Obstetrics and Gynecology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University), China
| | - Xinqiong Liu
- Department of Reproductive Medicine, Obstetrics and Gynecology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University), China
| | - Yali Gao
- Department of Ophthalmology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University), China
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3
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Ma L, Zhou X, Yao S, Zhang X, Mao J, Vona B, Fan L, Lou S, Li D, Wang L, Pan Y. METTL3-dependent m 6A modification of PSEN1 mRNA regulates craniofacial development through the Wnt/β-catenin signaling pathway. Cell Death Dis 2024; 15:229. [PMID: 38509077 PMCID: PMC10954657 DOI: 10.1038/s41419-024-06606-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/22/2024]
Abstract
Craniofacial malformations, often associated with syndromes, are prevalent birth defects. Emerging evidence underscores the importance of m6A modifications in various bioprocesses such as stem cell differentiation, tissue development, and tumorigenesis. Here, in vivo, experiments with zebrafish models revealed that mettl3-knockdown embryos at 144 h postfertilization exhibited aberrant craniofacial features, including altered mouth opening, jaw dimensions, ethmoid plate, tooth formation and hypoactive behavior. Similarly, low METTL3 expression inhibited the proliferation and migration of BMSCs, HEPM cells, and DPSCs. Loss of METTL3 led to reduced mRNA m6A methylation and PSEN1 expression, impacting craniofacial phenotypes. Co-injection of mettl3 or psen1 mRNA rescued the level of Sox10 fusion protein, promoted voluntary movement, and mitigated abnormal craniofacial phenotypes induced by mettl3 knockdown in zebrafish. Mechanistically, YTHDF1 enhanced the mRNA stability of m6A-modified PSEN1, while decreased METTL3-mediated m6A methylation hindered β-catenin binding to PSEN1, suppressing Wnt/β-catenin signaling. Pharmacological activation of the Wnt/β-catenin pathway partially alleviated the phenotypes of mettl3 morphant and reversed the decreases in cell proliferation and migration induced by METTL3 silencing. This study elucidates the pivotal role of METTL3 in craniofacial development via the METTL3/YTHDF1/PSEN1/β-catenin signaling axis.
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Affiliation(s)
- Lan Ma
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Xi Zhou
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
| | - Siyue Yao
- The Affiliated Stomatology Hospital of Suzhou Vocational Health College, Suzhou, China
| | - Xinyu Zhang
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
| | - Ji Mao
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
| | - Barbara Vona
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- Institute for Auditory Neuroscience and Inner Ear Lab, University Medical Center Göttingen, Göttingen, Germany
| | - Liwen Fan
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
| | - Shu Lou
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
| | - Dandan Li
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
| | - Lin Wang
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.
- Department of Orthodontics, The Affiliated Stomatology Hospital of Nanjing Medical University, Nanjing, China.
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.
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4
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Westbrook ER, Ford HZ, Antolović V, Chubb JR. Clearing the slate: RNA turnover to enable cell state switching? Development 2023; 150:dev202084. [PMID: 37831057 PMCID: PMC10617622 DOI: 10.1242/dev.202084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The distribution of mRNA in tissue is determined by the balance between transcription and decay. Understanding the control of RNA decay during development has been somewhat neglected compared with transcriptional control. Here, we explore the potential for mRNA decay to trigger rapid cell state transitions during development, comparing a bistable switch model of cell state conversion with experimental evidence from different developmental systems. We also consider another potential role for large-scale RNA decay that has emerged from studies of stress-induced cell state transitions, in which removal of mRNA unblocks the translation machinery to prioritise the synthesis of proteins that establish the new cell state.
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Affiliation(s)
- Elizabeth R. Westbrook
- UCL Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Hugh Z. Ford
- UCL Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Vlatka Antolović
- UCL Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Jonathan R. Chubb
- UCL Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
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5
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Xie L, Zhang X, Xie J, Xu Y, Li XJ, Lin L. Emerging Roles for DNA 6mA and RNA m6A Methylation in Mammalian Genome. Int J Mol Sci 2023; 24:13897. [PMID: 37762200 PMCID: PMC10531503 DOI: 10.3390/ijms241813897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/25/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Epigenetic methylation has been shown to play an important role in transcriptional regulation and disease pathogenesis. Recent advancements in detection techniques have identified DNA N6-methyldeoxyadenosine (6mA) and RNA N6-methyladenosine (m6A) as methylation modifications at the sixth position of adenine in DNA and RNA, respectively. While the distributions and functions of 6mA and m6A have been extensively studied in prokaryotes, their roles in the mammalian brain, where they are enriched, are still not fully understood. In this review, we provide a comprehensive summary of the current research progress on 6mA and m6A, as well as their associated writers, erasers, and readers at both DNA and RNA levels. Specifically, we focus on the potential roles of 6mA and m6A in the fundamental biological pathways of the mammalian genome and highlight the significant regulatory functions of 6mA in neurodegenerative diseases.
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Affiliation(s)
| | | | | | | | | | - Li Lin
- Guangdong Key Laboratory of Non-Human Primate Research, Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou 510632, China; (L.X.); (X.Z.); (J.X.); (Y.X.); (X.-J.L.)
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6
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Song YP, Lv JW, Zhang ZC, Qian QH, Fan YJ, Chen DZ, Zhang H, Xu FX, Zhang C, Huang Y, Wang H, Wei W, Xu DX. Effects of Gestational Arsenic Exposures on Placental and Fetal Development in Mice: The Role of Cyr61 m6A. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:97004. [PMID: 37682722 PMCID: PMC10489955 DOI: 10.1289/ehp12207] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 06/13/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
BACKGROUND Several epidemiological investigations demonstrated that maternal arsenic (As) exposure elevated risk of fetal growth restriction (FGR), but the mechanism remains unclear. OBJECTIVES This study aimed to investigate the effects of gestational As exposure on placental and fetal development and its underlying mechanism. METHODS Dams were exposed to 0.15, 1.5, and 15 mg / L NaAsO 2 throughout pregnancy via drinking water. Sizes of fetuses and placentas, placental histopathology, and glycogen content were measured. Placental RNA sequencing was conducted. Human trophoblasts were exposed to NaAsO 2 (2 μ M ) to establish an in vitro model of As exposure. The mRNA stability and protein level of genes identified through RNA sequencing were measured. N 6 -Methyladenosine (m 6 A ) modification was detected by methylated RNA immunoprecipitation-quantitative real-time polymerase chain reason (qPCR). The binding ability of insulin-like growth factor 2 binding protein 2 to the gene of interest was detected by RNA-binding protein immunoprecipitation-qPCR. Intracellular S-adenosylmethionine (SAM) and methyltransferase activity were determined by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and colorimetry, respectively. In vitro As + 3 methyltransferase (As3MT) knockdown or SAM supplementation and in vivo folic acid (FA) supplementation were used to evaluate the protective effect. A case-control study verified the findings. RESULTS Sizes of fetuses (exposed to 1.5 and 15 mg / L NaAsO 2 ) and placentas (exposed to 15 mg / L NaAsO 2 ) were lower in As-exposed mice. More glycogen + trophoblasts accumulated and the expression of markers of interstitial invasion was lower in the 15 mg / L NaAsO 2 -exposed mouse group in comparison with control. Placental RNA sequencing identified cysteine-rich angiogenic inducer 61 (Cyr61) as a candidate gene of interest. Mechanistically, mice and cells exposed to As had lower protein expression of CYR61, and this was attributed to a lower incidence of Cyr61 m 6 A . Furthermore, cells exposed to As had lower methyltransferase activity, suggesting that this could be the mechanism by which Cyr61 m 6 A was affected. Depletion of intracellular SAM, a cofactor for m 6 A methyltransferase catalytic domain, partially contributed to As-induced methyltransferase activity reduction. Either As3MT knockdown or SAM supplementation attenuated As-induced Cyr61 m 6 A down-regulation. In mice, FA supplementation rescued As-induced defective trophoblastic invasion and FGR. In humans, a negative correlation between maternal urinary As and plasma CYR61 was observed in infants who were small for gestational age. DISCUSSION Using in vitro and in vivo models, we found that intracellular SAM depletion-mediated Cyr61 m 6 A down-regulation partially contributed to As-induced defective trophoblastic invasion and FGR. https://doi.org/10.1289/EHP12207.
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Affiliation(s)
- Ya-Ping Song
- Department of Toxicology, Anhui Medical University, Hefei, Anhui, China
| | - Jin-Wei Lv
- Department of Toxicology, Anhui Medical University, Hefei, Anhui, China
| | - Zhi-Cheng Zhang
- Department of Toxicology, Anhui Medical University, Hefei, Anhui, China
| | - Qing-Hua Qian
- Department of Toxicology, Anhui Medical University, Hefei, Anhui, China
| | - Yi-Jun Fan
- Department of Toxicology, Anhui Medical University, Hefei, Anhui, China
- Second Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Dao-Zhen Chen
- Wuxi Maternity and Child Health Care Hospital, Wuxi, Jiangsu, China
| | - Heng Zhang
- Wuxi Maternity and Child Health Care Hospital, Wuxi, Jiangsu, China
| | - Fei-Xiang Xu
- Department of Toxicology, Anhui Medical University, Hefei, Anhui, China
| | - Cheng Zhang
- Department of Toxicology, Anhui Medical University, Hefei, Anhui, China
| | - Yichao Huang
- Department of Toxicology, Anhui Medical University, Hefei, Anhui, China
| | - Hua Wang
- Department of Toxicology, Anhui Medical University, Hefei, Anhui, China
| | - Wei Wei
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Education Ministry of China, Anhui Medical University, Hefei, Anhui, China
| | - De-Xiang Xu
- Department of Toxicology, Anhui Medical University, Hefei, Anhui, China
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7
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Arekatla G, Trenzinger C, Reimann A, Loeffler D, Kull T, Schroeder T. Optogenetic manipulation identifies the roles of ERK and AKT dynamics in controlling mouse embryonic stem cell exit from pluripotency. Dev Cell 2023:S1534-5807(23)00183-1. [PMID: 37207652 DOI: 10.1016/j.devcel.2023.04.013] [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: 05/30/2022] [Revised: 03/08/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023]
Abstract
ERK and AKT signaling control pluripotent cell self-renewal versus differentiation. ERK pathway activity over time (i.e., dynamics) is heterogeneous between individual pluripotent cells, even in response to the same stimuli. To analyze potential functions of ERK and AKT dynamics in controlling mouse embryonic stem cell (ESC) fates, we developed ESC lines and experimental pipelines for the simultaneous long-term manipulation and quantification of ERK or AKT dynamics and cell fates. We show that ERK activity duration or amplitude or the type of ERK dynamics (e.g., transient, sustained, or oscillatory) alone does not influence exit from pluripotency, but the sum of activity over time does. Interestingly, cells retain memory of previous ERK pulses, with duration of memory retention dependent on duration of previous pulse length. FGF receptor/AKT dynamics counteract ERK-induced pluripotency exit. These findings improve our understanding of how cells integrate dynamics from multiple signaling pathways and translate them into cell fate cues.
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Affiliation(s)
- Geethika Arekatla
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Christoph Trenzinger
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Andreas Reimann
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Dirk Loeffler
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Tobias Kull
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
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8
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Wu Y, Li J, Li C, Lu S, Wei X, Li Y, Xia W, Qian C, Wang Z, Liu M, Gu Y, Huang B, Tan Y, Hu Z. Fat mass and obesity-associated factor (FTO)-mediated N6-methyladenosine regulates spermatogenesis in an age-dependent manner. J Biol Chem 2023:104783. [PMID: 37146971 DOI: 10.1016/j.jbc.2023.104783] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/07/2023] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent reversible RNA modification in the mammalian transcriptome. It has recently been demonstrated that m6A is crucial for male germline development. Fat mass and obesity-associated factor (FTO), a known m6A demethylase, is widely expressed in human and mouse tissues and is involved in manifold biological processes and human diseases. However, the function of FTO in spermatogenesis and male fertility remains poorly understood. Here, we generated an Fto knockout mouse model using CRISPR/Cas9-mediated genome editing techniques to address this knowledge gap. Remarkably, we found that loss of Fto in mice caused spermatogenesis defects in an age-dependent manner, resulting from the attenuated proliferation ability of undifferentiated spermatogonia and increased male germ cell apoptosis. Further research showed that FTO plays a vital role in the modulation of spermatogenesis and Leydig cell maturation by regulating the translation of the androgen receptor in an m6A-dependent manner. In addition, we identified two functional mutations of FTO in male infertility patients, resulting in truncated FTO protein and increased m6A modification in vitro. Our results highlight the crucial effects of FTO on spermatogonia and Leydig cells for the long-term maintenance of spermatogenesis and expand our understanding of the function of m6A in male fertility.
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Affiliation(s)
- Yifei Wu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jincheng Li
- State Key Laboratory of Reproductive Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, China; Suzhou Municipal Hospital, Suzhou 215002, China
| | - Chenmeijie Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Shuai Lu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiaoyu Wei
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yang Li
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Wenjuan Xia
- State Key Laboratory of Reproductive Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, China; Suzhou Municipal Hospital, Suzhou 215002, China
| | - Chunfeng Qian
- State Key Laboratory of Reproductive Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, China; Suzhou Municipal Hospital, Suzhou 215002, China
| | - Zihang Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Mingxi Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yayun Gu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Boxian Huang
- State Key Laboratory of Reproductive Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, China; Suzhou Municipal Hospital, Suzhou 215002, China.
| | - Yueqiu Tan
- Institute of Reproductive and Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha 410000, China; Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha 410000, China.
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.
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9
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Wang Y, Li Y, Skuland T, Zhou C, Li A, Hashim A, Jermstad I, Khan S, Dalen KT, Greggains GD, Klungland A, Dahl JA, Au KF. The RNA m 6A landscape of mouse oocytes and preimplantation embryos. Nat Struct Mol Biol 2023; 30:703-709. [PMID: 37081317 DOI: 10.1038/s41594-023-00969-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/16/2023] [Indexed: 04/22/2023]
Abstract
Despite the significance of N6-methyladenosine (m6A) in gene regulation, the requirement for large amounts of RNA has hindered m6A profiling in mammalian early embryos. Here we apply low-input methyl RNA immunoprecipitation and sequencing to map m6A in mouse oocytes and preimplantation embryos. We define the landscape of m6A during the maternal-to-zygotic transition, including stage-specifically expressed transcription factors essential for cell fate determination. Both the maternally inherited transcripts to be degraded post fertilization and the zygotically activated genes during zygotic genome activation are widely marked by m6A. In contrast to m6A-marked zygotic ally-activated genes, m6A-marked maternally inherited transcripts have a higher tendency to be targeted by microRNAs. Moreover, RNAs derived from retrotransposons, such as MTA that is maternally expressed and MERVL that is transcriptionally activated at the two-cell stage, are largely marked by m6A. Our results provide a foundation for future studies exploring the regulatory roles of m6A in mammalian early embryonic development.
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Affiliation(s)
- Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yanjiao Li
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Trine Skuland
- Department of Reproductive Medicine, Oslo University Hospital, Oslo, Norway
- Division of Gynaecology and Obstetrics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Chengjie Zhou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Aifu Li
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Adnan Hashim
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Ingunn Jermstad
- Norwegian Transgenic Centre, Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Shaista Khan
- Norwegian Transgenic Centre, Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Knut Tomas Dalen
- Norwegian Transgenic Centre, Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Gareth D Greggains
- Department of Reproductive Medicine, Oslo University Hospital, Oslo, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
| | - John Arne Dahl
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA.
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10
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Kumari S, Kumar S, Muthuswamy S. RNA N6-methyladenosine modification in regulating cancer stem cells and tumor immune microenvironment and its implication for cancer therapy. J Cancer Res Clin Oncol 2023; 149:1621-1633. [PMID: 35796777 DOI: 10.1007/s00432-022-04158-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/15/2022] [Indexed: 11/28/2022]
Abstract
Therapy resistance is a well-known phenomenon in cancer treatment. It can be intrinsic or acquired, accountable for frequent tumor relapse and death worldwide. The interplay between cancer cells and their neighboring environment can activate complex signaling mechanisms influencing epigenetic changes and maintain cancer cell survival leading to the malignant phenotype. Cancer stem cells (CSCs) are tumor-initiating cells (TICs) and constitute the primary source of drug resistance and tumor recurrence. Studies have shown that cancer cells exhibit dysregulated RNA N6-methyladenosine (m6A) "writers," "erasers," and "readers" levels after acquiring drug resistance. The present review provides novel insight into the role of m6A modifiers involved in CSC generation, cancer cell proliferation, and therapy resistance. m6A RNA modifications in the cross-talk between CSC and the tumor immune microenvironment (TIME) have also been highlighted. Further, we have discussed the therapeutic potential of targeting m6A machinery for cancer diagnosis and the development of new therapies for cancer treatment.
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Affiliation(s)
- Subhadra Kumari
- Department of Life Science, National Institute of Technology, Rourkela, India
| | - Santosh Kumar
- Department of Life Science, National Institute of Technology, Rourkela, India
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11
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Abstract
The methyltransferase-like (METTL) family is a diverse group of methyltransferases that can methylate nucleotides, proteins, and small molecules. Despite this diverse array of substrates, they all share a characteristic seven-beta-strand catalytic domain, and recent evidence suggests many also share an important role in stem cell biology. The most well characterized family members METTL3 and METTL14 dimerize to form an N6-methyladenosine (m6A) RNA methyltransferase with established roles in cancer progression. However, new mouse models indicate that METTL3/METTL14 are also important for embryonic stem cell (ESC) development and postnatal hematopoietic and neural stem cell self-renewal and differentiation. METTL1, METTL5, METTL6, METTL8, and METTL17 also have recently identified roles in ESC pluripotency and differentiation, while METTL11A/11B, METTL4, METTL7A, and METTL22 have been shown to play roles in neural, mesenchymal, bone, and hematopoietic stem cell development, respectively. Additionally, a variety of other METTL family members are translational regulators, a role that could place them as important players in the transition from stem cell quiescence to differentiation. Here we will summarize what is known about the role of METTL proteins in stem cell differentiation and highlight the connection between their growing importance in development and their established roles in oncogenesis.
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Affiliation(s)
- John G Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main St., Buffalo, NY, 14203, USA
| | - James P Catlin
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main St., Buffalo, NY, 14203, USA
| | - Christine E Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, 955 Main St., Buffalo, NY, 14203, USA.
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12
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New insights into the epitranscriptomic control of pluripotent stem cell fate. Exp Mol Med 2022; 54:1643-1651. [PMID: 36266446 PMCID: PMC9636187 DOI: 10.1038/s12276-022-00824-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/26/2022] [Accepted: 06/01/2022] [Indexed: 12/29/2022] Open
Abstract
Each cell in the human body has a distinguishable fate. Pluripotent stem cells are challenged with a myriad of lineage differentiation options. Defects are more likely to be fatal to stem cells than to somatic cells due to the broad impact of the former on early development. Hence, a detailed understanding of the mechanisms that determine the fate of stem cells is needed. The mechanisms by which human pluripotent stem cells, although not fully equipped with complex chromatin structures or epigenetic regulatory mechanisms, accurately control gene expression and are important to the stem cell field. In this review, we examine the events driving pluripotent stem cell fate and the underlying changes in gene expression during early development. In addition, we highlight the role played by the epitranscriptome in the regulation of gene expression that is necessary for each fate-related event.
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13
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Shen X, Li M, Wang C, Liu Z, Wu K, Wang A, Bi C, Lu S, Long H, Zhu G. Hypoxia is fine-tuned by Hif-1α and regulates mesendoderm differentiation through the Wnt/β-Catenin pathway. BMC Biol 2022; 20:219. [PMID: 36199093 PMCID: PMC9536055 DOI: 10.1186/s12915-022-01423-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/28/2022] [Indexed: 11/10/2022] Open
Abstract
Background Hypoxia naturally happens in embryogenesis and thus serves as an important environmental factor affecting embryo development. Hif-1α, an essential hypoxia response factor, was mostly considered to mediate or synergistically regulate the effect of hypoxia on stem cells. However, the function and relationship of hypoxia and Hif-1α in regulating mesendoderm differentiation remains controversial. Results We here discovered that hypoxia dramatically suppressed the mesendoderm differentiation and promoted the ectoderm differentiation of mouse embryonic stem cells (mESCs). However, hypoxia treatment after mesendoderm was established promoted the downstream differentiation of mesendoderm-derived lineages. These effects of hypoxia were mediated by the repression of the Wnt/β-Catenin pathway and the Wnt/β-Catenin pathway was at least partially regulated by the Akt/Gsk3β axis. Blocking the Wnt/β-Catenin pathway under normoxia using IWP2 mimicked the effects of hypoxia while activating the Wnt/β-Catenin pathway with CHIR99021 fully rescued the mesendoderm differentiation suppression caused by hypoxia. Unexpectedly, Hif-1α overexpression, in contrast to hypoxia, promoted mesendoderm differentiation and suppressed ectoderm differentiation. Knockdown of Hif-1α under normoxia and hypoxia both inhibited the mesendoderm differentiation. Moreover, hypoxia even suppressed the mesendoderm differentiation of Hif-1α knockdown mESCs, further implying that the effects of hypoxia on the mesendoderm differentiation were Hif-1α independent. Consistently, the Wnt/β-Catenin pathway was enhanced by Hif-1α overexpression and inhibited by Hif-1α knockdown. As shown by RNA-seq, unlike hypoxia, the effect of Hif-1α was relatively mild and selectively regulated part of hypoxia response genes, which fine-tuned the effect of hypoxia on mESC differentiation. Conclusions This study revealed that hypoxia is fine-tuned by Hif-1α and regulates the mesendoderm and ectoderm differentiation by manipulating the Wnt/β-Catenin pathway, which contributed to the understanding of hypoxia-mediated regulation of development. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01423-y.
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Affiliation(s)
- Xiaopeng Shen
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China. .,Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China. .,Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.
| | - Meng Li
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Chunguang Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Zhongxian Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Kun Wu
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Ao Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Chao Bi
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Shan Lu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, 266003, Shandong, China
| | - Guoping Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China.,Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, 241000, Anhui, China
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14
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Chen H, Wang Y, Su H, Zhang X, Chen H, Yu J. RNA N6-Methyladenine Modification, Cellular Reprogramming, and Cancer Stemness. Front Cell Dev Biol 2022; 10:935224. [PMID: 35859892 PMCID: PMC9289108 DOI: 10.3389/fcell.2022.935224] [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: 05/03/2022] [Accepted: 05/26/2022] [Indexed: 11/13/2022] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant modification on eukaryote messenger RNA and plays a key role in posttranscriptional regulation of RNA metabolism including splicing, intracellular transport, degradation, and translation. m6A is dynamically regulated by methyltransferases (writers), RNA-binding proteins (readers), and demethylases (erasers). Recent studies demonstrate that perturbation of m6A regulators remarkably influences cell fate transitions through rewiring various biological processes, such as growth, differentiation, and survival. Moreover, aberrant m6A modification is implicated in a variety of diseases, in particular cancer. In this review, we describe the functional linkage of m6A modifications to cellular reprogramming and cancer stemness properties.
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Affiliation(s)
- Huarong Chen
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- *Correspondence: Huarong Chen, ; Jun Yu,
| | - Yifei Wang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Hao Su
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoting Zhang
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Hongyan Chen
- Department of Anaesthesia and Intensive Care and Peter Hung Pain Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
- *Correspondence: Huarong Chen, ; Jun Yu,
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15
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Alagia A, Gullerova M. The Methylation Game: Epigenetic and Epitranscriptomic Dynamics of 5-Methylcytosine. Front Cell Dev Biol 2022; 10:915685. [PMID: 35721489 PMCID: PMC9204050 DOI: 10.3389/fcell.2022.915685] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
DNA and RNA methylation dynamics have been linked to a variety of cellular processes such as development, differentiation, and the maintenance of genome integrity. The correct deposition and removal of methylated cytosine and its oxidized analogues is pivotal for cellular homeostasis, rapid responses to exogenous stimuli, and regulated gene expression. Uncoordinated expression of DNA/RNA methyltransferases and demethylase enzymes has been linked to genome instability and consequently to cancer progression. Furthermore, accumulating evidence indicates that post-transcriptional DNA/RNA modifications are important features in DNA/RNA function, regulating the timely recruitment of modification-specific reader proteins. Understanding the biological processes that lead to tumorigenesis or somatic reprogramming has attracted a lot of attention from the scientific community. This work has revealed extensive crosstalk between epigenetic and epitranscriptomic pathways, adding a new layer of complexity to our understanding of cellular programming and responses to environmental cues. One of the key modifications, m5C, has been identified as a contributor to regulation of the DNA damage response (DDR). However, the various mechanisms of dynamic m5C deposition and removal, and the role m5C plays within the cell, remains to be fully understood.
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Affiliation(s)
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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16
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Applications of machine learning in pine nuts classification. Sci Rep 2022; 12:8799. [PMID: 35614118 PMCID: PMC9132955 DOI: 10.1038/s41598-022-12754-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/16/2022] [Indexed: 11/09/2022] Open
Abstract
Pine nuts are not only the important agent of pine reproduction and afforestation, but also the commonly consumed nut with high nutritive values. However, it is difficult to distinguish among pine nuts due to the morphological similarity among species. Therefore, it is important to improve the quality of pine nuts and solve the adulteration problem quickly and non-destructively. In this study, seven pine nuts (Pinus bungeana, Pinus yunnanensis, Pinus thunbergii, Pinus armandii, Pinus massoniana, Pinus elliottii and Pinus taiwanensis) were used as study species. 210 near-infrared (NIR) spectra were collected from the seven species of pine nuts, five machine learning methods (Decision Tree (DT), Random Forest (RF), Multilayer Perceptron (MLP), Support Vector Machine (SVM) and Naive Bayes (NB)) were used to identify species of pine nuts. 303 images were used to collect morphological data to construct a classification model based on five convolutional neural network (CNN) models (VGG16, VGG19, Xception, InceptionV3 and ResNet50). The experimental results of NIR spectroscopy show the best classification model is MLP and the accuracy is closed to 0.99. Another experimental result of images shows the best classification model is InceptionV3 and the accuracy is closed to 0.964. Four important range of wavebands, 951–957 nm, 1,147–1,154 nm, 1,907–1,927 nm, 2,227–2,254 nm, were found to be highly related to the classification of pine nuts. This study shows that machine learning is effective for the classification of pine nuts, providing solutions and scientific methods for rapid, non-destructive and accurate classification of different species of pine nuts.
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17
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Fisher JL, Jones EF, Flanary VL, Williams AS, Ramsey EJ, Lasseigne BN. Considerations and challenges for sex-aware drug repurposing. Biol Sex Differ 2022; 13:13. [PMID: 35337371 PMCID: PMC8949654 DOI: 10.1186/s13293-022-00420-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/06/2022] [Indexed: 01/09/2023] Open
Abstract
Sex differences are essential factors in disease etiology and manifestation in many diseases such as cardiovascular disease, cancer, and neurodegeneration [33]. The biological influence of sex differences (including genomic, epigenetic, hormonal, immunological, and metabolic differences between males and females) and the lack of biomedical studies considering sex differences in their study design has led to several policies. For example, the National Institute of Health's (NIH) sex as a biological variable (SABV) and Sex and Gender Equity in Research (SAGER) policies to motivate researchers to consider sex differences [204]. However, drug repurposing, a promising alternative to traditional drug discovery by identifying novel uses for FDA-approved drugs, lacks sex-aware methods that can improve the identification of drugs that have sex-specific responses [7, 11, 14, 33]. Sex-aware drug repurposing methods either select drug candidates that are more efficacious in one sex or deprioritize drug candidates based on if they are predicted to cause a sex-bias adverse event (SBAE), unintended therapeutic effects that are more likely to occur in one sex. Computational drug repurposing methods are encouraging approaches to develop for sex-aware drug repurposing because they can prioritize sex-specific drug candidates or SBAEs at lower cost and time than traditional drug discovery. Sex-aware methods currently exist for clinical, genomic, and transcriptomic information [1, 7, 155]. They have not expanded to other data types, such as DNA variation, which has been beneficial in other drug repurposing methods that do not consider sex [114]. Additionally, some sex-aware methods suffer from poorer performance because a disproportionate number of male and female samples are available to train computational methods [7]. However, there is development potential for several different categories (i.e., data mining, ligand binding predictions, molecular associations, and networks). Low-dimensional representations of molecular association and network approaches are also especially promising candidates for future sex-aware drug repurposing methodologies because they reduce the multiple hypothesis testing burden and capture sex-specific variation better than the other methods [151, 159]. Here we review how sex influences drug response, the current state of drug repurposing including with respect to sex-bias drug response, and how model organism study design choices influence drug repurposing validation.
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Affiliation(s)
- Jennifer L. Fisher
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Emma F. Jones
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Victoria L. Flanary
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Avery S. Williams
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Elizabeth J. Ramsey
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Brittany N. Lasseigne
- Department of Cell, Developmental and Integrative Biology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294 USA
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18
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Vo TTL, Nguyen TN, Nguyen TT, Pham ATD, Vuong DL, Ta VT, Ho VS. SHOX2 methylation in Vietnamese patients with lung cancer. Mol Biol Rep 2022; 49:3413-3421. [PMID: 35088378 DOI: 10.1007/s11033-022-07172-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/19/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND DNA methylation on cytosine in the CpG dinucleotides is one of the most common epigenetic perturbations taking place during cancer initiation, progression, occurrence and resistance therapy. DNA methylation seems to be sufficiently stable epigenetic modification to be utilized as a cancer biomarker in in vitro diagnostic (IVD) settings. Nowadays, the SHOX2 methylation (mSHOX2) is one of the most valuable DNA methylation biomarkers of lung cancer that is the leading cause of cancer death. It is being continuously validated across ethnicities, lifestyles and lifespan. This study focused on characteristics of mSHOX2 in Vietnamese patients with lung cancer since a lack of investigation and evidence of its utility in this country. METHODS The probe and primer sets were designed according to the MethyLight method for quantitative assessment of the mSHOX2 in 214 formalin-fixed paraffin-embedded (FFPE) lung tissues and 57 plasma samples. RESULTS mSHOX2 in FFPE tissues allowed discriminating benign and malignant lung diseases with 60% (95% CI 50.7-68.8%) sensitivity and 90.4% (95% CI 82.6-95.5%) specificity. Importantly, based on mSHOX2 in plasma, lung cancer could be detected with 83.3% (95% CI 65.3-94.4%) sensitivity and 92.6% (95% CI 75.7-99.1%) specificity, respectively. There were insignificant associations between mSHOX2 with age, cancer stage, EGFR mutation and serum CEA, CYFRA21-1 concentrations except for that gender. CONCLUSION Our study indicated that mSHOX2 was satisfactory for distinguishing malignant from benign lung tissue and noninvasively detecting lung cancer.
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Affiliation(s)
- Thi Thuong Lan Vo
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam.
| | - Thuy Ngan Nguyen
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Thu Trang Nguyen
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Anh Thuy Duong Pham
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Dieu Linh Vuong
- Pathology and Molecular Biology Center, Vietnam National Cancer Hospital, Hanoi, Vietnam
| | - Van To Ta
- Pathology and Molecular Biology Center, Vietnam National Cancer Hospital, Hanoi, Vietnam
| | - Van Son Ho
- Department of Chemistry, 175 Hospital, Ho Chi Minh City, Vietnam
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