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Peng Y, Jia J, Zhang M, Ma W, Cui Y, Yu M. Transcription Factor TFAP2B Exerts Neuroprotective Effects Targeting BNIP3-Mediated Mitophagy in Ischemia/Reperfusion Injury. Mol Neurobiol 2024; 61:7319-7334. [PMID: 38381297 DOI: 10.1007/s12035-024-04004-y] [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: 08/02/2023] [Accepted: 01/30/2024] [Indexed: 02/22/2024]
Abstract
Cerebral ischemia-reperfusion injury (CIRI) leads to malignant brain edema, blood-brain barrier destruction, and neuronal apoptosis. N6-methyladenosine (m6A) RNA modification in CIRI was still limited explored. In this study, MeRIP- and RNA-sequencing were performed of middle cerebral artery occlusion and reperfusion (MCAO/R) rats to find novel potential molecular targets. Transcription factor TFAP2B stood out of which its m6A abundance decreased associated with a marked reduction of its mRNA based on cojoint interactive bioinformatics analysis of the MeRIP- and RNA-sequencing data. It was suggested TFAP2B could have a role in CIRI. Functionally, overexpression of TFAP2B in cultured primary neurons could effectively improve the cell survival and pro-survival autophagy in parallel with reduced cell apoptosis during OGD/R in vitro. Through the RNA-sequencing of TFAP2B overexpressed primary neurons and subsequent validation experiments, it was found that mitophagy receptor BNIP3 was one of the important targets of TFAP2B in OGD/R neurons through which TFAP2B could bind to its promoter region for transcriptional activation of BNIP3, thereby enhancing BNIP3-mediated mitophagy to protect against OGD/R injury of neurons. Lastly, TFAP2B was demonstrated to alleviate the MCAO/R damage to a certain extent in vivo. Although it failed to confirm TFAP2B dysregulation was m6A dependent in current research, this is the first research of TFAP2B in CIRI field with important guiding significance.
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Affiliation(s)
- Yong Peng
- Department of Neurosurgery, The Second Xiangya Hospital of Central South University, No. 139 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Jiaoying Jia
- Department of Neurosurgery, The Second Xiangya Hospital of Central South University, No. 139 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Mingming Zhang
- Department of Neurosurgery, The Second Xiangya Hospital of Central South University, No. 139 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Wenjia Ma
- Department of Neurosurgery, The Second Xiangya Hospital of Central South University, No. 139 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Yan Cui
- Department of Neurosurgery, The Second Xiangya Hospital of Central South University, No. 139 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China
| | - Mengqiang Yu
- Department of Neurosurgery, The Second Xiangya Hospital of Central South University, No. 139 Renmin Middle Road, Changsha, Hunan, 410011, People's Republic of China.
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Wu S, Liu K, Cui Y, Zhou B, Zhao H, Xiao X, Zhou Q, Ma D, Li X. N6-methyladenosine dynamics in placental development and trophoblast functions, and its potential role in placental diseases. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167290. [PMID: 38866113 DOI: 10.1016/j.bbadis.2024.167290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/02/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
N6-methyladenosine (m6A) is the most abundant modification controlling RNA metabolism and cellular functions, but its roles in placental development are still poorly understood. Here, we characterized the synchronization of m6A modifications and placental functions by mapping the m6A methylome in human placentas (n = 3, each trimester), revealing that the dynamic patterns of m6A were associated with gene expression homeostasis and different biological pathways in placental development. Then, we generated trophoblast-specific knockout mice of Wtap, a critical component of methyltransferase complex, and demonstrated that Wtap was essential for trophoblast proliferation, placentation and perinatal growth. Further in vitro experiments which includes cell viability assays and series molecular binding assays demonstrated that WTAP-m6A-IGF2BP3 axis regulated the RNA stability and translation of Anillin (ANLN) and VEGFA, promoting trophoblast proliferation and secretion. Dysregulation of this regulatory axis was observed in placentas from pregnancies with fetal growth restriction (FGR) or preeclampsia, revealing the pathogenic effects of imbalanced m6A modifications. Therefore, our findings provide novel insights into the functions and regulatory mechanisms of m6A modifications in placental development and placental-related gestational diseases.
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Affiliation(s)
- Suwen Wu
- Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Ketong Liu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yutong Cui
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Bingyan Zhou
- Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Hubei Clinical Center of Hirschsprung's Disease and Allied Disorders, Wuhan, China
| | - Huanqiang Zhao
- Shenzhen Maternity and Children Health Care Hospital, Shenzhen, China
| | - Xirong Xiao
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Qiongjie Zhou
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China; Shenzhen Maternity and Children Health Care Hospital, Shenzhen, China.
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Wu ZW, Wang L, Mou Q, Wang F, Wang Y, Fang T, Yin Z, Du ZQ, Yang CX. l-valine supplementation disturbs vital molecular pathways and induces apoptosis in mouse testes. Theriogenology 2024; 215:31-42. [PMID: 38000127 DOI: 10.1016/j.theriogenology.2023.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 10/04/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023]
Abstract
The branched-chain amino acids (BCAAs: leucine, isoleucine and valine) are essential for animal growth and metabolic health. However, the effect of valine on male reproduction and its underlying molecular mechanism remain largely unknown. Here, we showed that l-valine supplementation (0.30% or 0.45%, water drinking for 3 weeks) did not change body and testis weights, but significantly altered morphology of sertoli cells and germ cells within seminiferous tubule, and enlarged the space between seminiferous tubules within mouse testis. l-valine treatment (0.45%) increased significantly the Caspase3/9 mRNA levels and CASPASE9 protein levels, therefore induced apoptosis of mouse testis. Moreover, gene expression levels related to autophagy (Atg5 and Lamb3), DNA 5 mC methylation (Dnmt1, Dnmt3a, Tet2 and Tet3), RNA m6A methylation (Mettl14, Alkbh5 and Fto), and m6A methylation binding proteins (Ythdf1/2/3 and Igf2bp1/2) were significantly reduced. Protein abundances of ALKBH5, FTO and YTHDF3 were also significantly reduced, but not for ATG5 and TET2. Testis transcriptome sequencing detected 537 differentially expressed genes (DEGs, 26 up-regulated and 511 down-regulated), involved in multiple important signaling pathways. RT-qPCR validated 8 of 9 DEGs (Cd36, Scd1, Insl3, Anxa5, Lcn2, Hsd17b3, Cyp11a1, Cyp17a1 and Agt) to be decreased significantly, consistent with RNA-seq results. Taken together, l-valine treatment could disturb multiple signaling pathways (autophagy and RNA methylation etc.), and induce apoptosis to destroy the tissue structure of mouse testis.
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Affiliation(s)
- Zi-Wei Wu
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China; Center of Animal Breeding Technology Innovation of Hubei Province, China
| | - Li Wang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China; Center of Animal Breeding Technology Innovation of Hubei Province, China
| | - Qiao Mou
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China
| | - Fang Wang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China; Center of Animal Breeding Technology Innovation of Hubei Province, China
| | - Yi Wang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China; Center of Animal Breeding Technology Innovation of Hubei Province, China
| | - Ting Fang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China; Center of Animal Breeding Technology Innovation of Hubei Province, China
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China; Center of Animal Breeding Technology Innovation of Hubei Province, China.
| | - Cai-Xia Yang
- College of Animal Science, Yangtze University, Jingzhou, 434025, Hubei, China; Center of Animal Breeding Technology Innovation of Hubei Province, China.
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Zhang F, Ignatova VV, Ming GL, Song H. Advances in brain epitranscriptomics research and translational opportunities. Mol Psychiatry 2024; 29:449-463. [PMID: 38123727 PMCID: PMC11116067 DOI: 10.1038/s41380-023-02339-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Various chemical modifications of all RNA transcripts, or epitranscriptomics, have emerged as crucial regulators of RNA metabolism, attracting significant interest from both basic and clinical researchers due to their diverse functions in biological processes and immense clinical potential as highlighted by the recent profound success of RNA modifications in improving COVID-19 mRNA vaccines. Rapid accumulation of evidence underscores the critical involvement of various RNA modifications in governing normal neural development and brain functions as well as pathogenesis of brain disorders. Here we provide an overview of RNA modifications and recent advancements in epitranscriptomic studies utilizing animal models to elucidate important roles of RNA modifications in regulating mammalian neurogenesis, gliogenesis, synaptic formation, and brain function. Moreover, we emphasize the pivotal involvement of RNA modifications and their regulators in the pathogenesis of various human brain disorders, encompassing neurodevelopmental disorders, brain tumors, psychiatric and neurodegenerative disorders. Furthermore, we discuss potential translational opportunities afforded by RNA modifications in combatting brain disorders, including their use as biomarkers, in the development of drugs or gene therapies targeting epitranscriptomic pathways, and in applications for mRNA-based vaccines and therapies. We also address current limitations and challenges hindering the widespread clinical application of epitranscriptomic research, along with the improvements necessary for future progress.
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Affiliation(s)
- Feng Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Valentina V Ignatova
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Wan C, Pei J, Wang D, Hu J, Tang Z, Zhao W. Identification of m 6A methylation-related genes in cerebral ischaemia‒reperfusion of Breviscapus therapy based on bioinformatics methods. BMC Med Genomics 2023; 16:210. [PMID: 37670341 PMCID: PMC10478429 DOI: 10.1186/s12920-023-01651-3] [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: 05/05/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Cerebral ischaemia‒reperfusion (I/R) frequently causes late-onset neuronal damage. Breviscapine promotes autophagy in microvascular endothelial cells in I/R and can inhibit oxidative damage and apoptosis. However, the mediation mechanism of breviscapine on neuronal cell death is unclear. METHODS First, transcriptome sequencing was performed on three groups of mice: the neuronal normal group (Control group), the oxygen-glucose deprivation/ reoxygenation group (OGD/R group) and the breviscapine administration group (Therapy group). Differentially expressed genes (DEGs) between the OGD/R and control groups and between the Therapy and OGD/R groups were obtained by the limma package. N6-methyladenosine (m6A) methylation-related DEGs were selected by Pearson correlation analysis. Then, prediction and confirmation of drug targets were performed by Swiss Target Prediction and UniProt Knowledgebase (UniProtKB) database, and key genes were obtained by Pearson correlation analysis between m6A-related DEGs and drug target genes. Next, gene set enrichment analysis (GSEA) and Ingenuity pathway analysis (IPA) were used to obtain the pathways of key genes. Finally, a circRNA-miRNA‒mRNA network was constructed based on the mRNAs, circRNAs and miRNAs. RESULTS A total of 2250 DEGs between the OGD/R and control groups and 757 DEGs between the Therapy and OGD/R groups were selected by differential analysis. A total of 7 m6A-related DEGs, including Arl4d, Gm10653, Gm1113, Kcns3, Olfml2a, Stk26 and Tfcp2l1, were obtained by Pearson correlation analysis. Four key genes (Tfcp2l1, Kcns3, Olfml2a and Arl4d) were acquired, and GSEA showed that these key genes significantly participated in DNA repair, e2f targets and the g2m checkpoint. IPA revealed that Tfcp2l1 played a significant role in human embryonic stem cell pluripotency. The circRNA-miRNA‒mRNA network showed that mmu_circ_0001258 regulated Tfcp2l1 by mmu-miR-301b-3p. CONCLUSIONS In conclusion, four key genes, Tfcp2l1, Kcns3, Olfml2a and Arl4d, significantly associated with the treatment of OGD/R by breviscapine were identified, which provides a theoretical basis for clinical trials.
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Affiliation(s)
- Cheng Wan
- Department of Interventional Radiology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Jingchun Pei
- Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Dan Wang
- Department of Organ Transplantation Centre, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Jihong Hu
- Department of Interventional Radiology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China
| | - Zhiwei Tang
- Department of Neurosurgery, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China.
| | - Wei Zhao
- Department of Interventional Radiology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, 650032, China.
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Wu S, Liu K, Zhou B, Wu S. N6-methyladenosine modifications in maternal-fetal crosstalk and gestational diseases. Front Cell Dev Biol 2023; 11:1164706. [PMID: 37009476 PMCID: PMC10060529 DOI: 10.3389/fcell.2023.1164706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
As a medium among pregnant women, environment and fetus, placenta owns powerful and delicate epigenetic processes to regulate gene expression and maintain cellular homeostasis. N6-methyladenosine (m6A) is the most prevalent modification that determines the fate of RNA, and its dynamic reversibility indicates that m6A may serve as a sensitive responder to environmental stimuli. Emerging evidence suggests that m6A modifications play an essential role in placental development and maternal-fetal crosstalk, and are closely related to gestational diseases. Herein, we summarized the latest techniques for m6A sequencing and highlighted current advances of m6A modifications in maternal-fetal crosstalk and the underlying mechanisms in gestational diseases. Therefore, proper m6A modifications are important in placental development, but its disturbance mainly caused by various environmental factors can lead to abnormal placentation and function with possible consequences of gestational diseases, fetal growth and disease susceptibility in adulthood.
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Affiliation(s)
- Suqi Wu
- First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ketong Liu
- Department of Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Bingyan Zhou
- Hubei Clinical Center of Hirschsprung’s Disease and Allied Disorders, Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Bingyan Zhou, ; Suwen Wu,
| | - Suwen Wu
- Department of Obstetrics, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- *Correspondence: Bingyan Zhou, ; Suwen Wu,
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Zhang F, Yoon K, Zhang DY, Kim NS, Ming GL, Song H. Epitranscriptomic regulation of cortical neurogenesis via Mettl8-dependent mitochondrial tRNA m 3C modification. Cell Stem Cell 2023; 30:300-311.e11. [PMID: 36764294 PMCID: PMC10031801 DOI: 10.1016/j.stem.2023.01.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/07/2022] [Accepted: 01/17/2023] [Indexed: 02/11/2023]
Abstract
Increasing evidence implicates the critical roles of various epitranscriptomic RNA modifications in different biological processes. Methyltransferase METTL8 installs 3-methylcytosine (m3C) modification of mitochondrial tRNAs in vitro; however, its role in intact biological systems is unknown. Here, we show that Mettl8 is localized in mitochondria and installs m3C specifically on mitochondrial tRNAThr/Ser(UCN) in mouse embryonic cortical neural stem cells. At molecular and cellular levels, Mettl8 deletion in cortical neural stem cells leads to reduced mitochondrial protein translation and attenuated respiration activity. At the functional level, conditional Mettl8 deletion in mice results in impaired embryonic cortical neural stem cell maintenance in vivo, which can be rescued by pharmacologically enhancing mitochondrial functions. Similarly, METTL8 promotes mitochondrial protein expression and neural stem cell maintenance in human forebrain cortical organoids. Together, our study reveals a conserved epitranscriptomic mechanism of Mettl8 and mitochondrial tRNA m3C modification in maintaining embryonic cortical neural stem cells in mice and humans.
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Affiliation(s)
- Feng Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kijun Yoon
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel Y Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nam-Shik Kim
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; The Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Liu P, Yan X, Ma C, Gu J, Tian F, Qu J. Prognostic value of m6A regulators and the nomogram construction in glioma patients. Medicine (Baltimore) 2022; 101:e30643. [PMID: 36123877 PMCID: PMC9478228 DOI: 10.1097/md.0000000000030643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Although N6-methyladenosine (m6A) has been implicated in various biological functions in human cancers, its role in predicting the prognosis of glioma remains unclear. In this study, the transcriptome expression profiles and the clinical data of 961 patients were derived from the Chinese Glioma Genome Atlas (CGGA). We comprehensively evaluated the association between the expression of m6A regulators and the prognosis of glioma and established a 3-gene (YTHDF2, FTO, and ALKBH5) risk signature using least absolute shrinkage and selection operator (LASSO) analysis. Patients with a high-risk signature had significantly adverse prognoses. Gene set enrichment analysis (GSEA) analysis revealed that the G2M checkpoint, MTORC1 signaling, epithelial mesenchymal transition, and PI3K-AKT-mTOR signaling were significantly enriched in the high-risk group. Univariate and multivariate Cox regression analyses confirmed the independent prognostic value of this risk signature. We then constructed a nomogram for individualized prediction of overall survival (OS) by integrating clinicopathological features (age, World Health Organization [WHO] grade), treatment information (radiotherapy, temozolomide therapy), and m6A risk signature. The calibration curves showed excellent agreement between the predicted and actual probabilities for the 1-, 3-, and 5-year OS, with a C-index of 0.780 in the training cohort and 0.717 in the validation cohort. Altogether, our study elucidated the important role of m6A regulators in glioma prognosis, which is valuable for the selection of therapeutic methods and clinical management of patients with glioma.
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Affiliation(s)
- Pengdi Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Shaanxi Province, China
| | - Xianxia Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Shaanxi Province, China
| | - Chengwen Ma
- Department of Neurosurgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Shaanxi Province, China
| | - Junxiang Gu
- Department of Neurosurgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Shaanxi Province, China
| | - Fuyu Tian
- Department of Neurosurgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Shaanxi Province, China
| | - Jianqiang Qu
- Department of Neurosurgery, The Second Affiliated Hospital of Xi’an Jiaotong University, Shaanxi Province, China
- *Correspondence: Jianqiang Qu, Department of Neurosurgery, The Second Affiliated Hospital of Xi’an Jiaotong University, No. 157 Xiwu road, Xi’an 710004, shaanxi Province, China (e-mail: )
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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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10
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Shen WB, Yang JJ, Yang P. RNA Hypomethylation and Unchanged DNA Methylation Levels in the Cortex of ApoE4 Carriers and Alzheimer's Disease Subjects. Curr Alzheimer Res 2022; 19:530-540. [PMID: 36045519 DOI: 10.2174/1567205019666220831125142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/07/2022] [Accepted: 07/22/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is a progressive neurodegenerative disorder, and ApoE4 variants are significant risk factors for AD. Epigenetic modifications are involved in AD pathology. However, it is unclear whether DNA/RNA methylation plays a role in AD pathology, and dysregulation of DNA/RNA methylation occurs in ApoE4 carriers. OBJECTIVE The present study aimed to determine whether dysregulation of DNA/RNA methylation is present in the brains of ApoE4 carriers and AD patients. METHODS In this study, postmortem brain tissues from carriers of ApoE4 and ApoE3, from AD and non- AD controls, were used in the analysis of DNA/RNA methylation, methyltransferases, and their demethylases. RESULTS Immunofluorescence staining indicates that RNA methylation is suppressed in ApoE4 carriers. Further analysis shows that the expression of RNA methyltransferases and an RNA methylation reader is suppressed in ApoE4 carriers, whereas RNA demethylase expression is increased. RNA hypomethylation occurs in NeuN+ neurons in ApoE4 carriers and AD patients. Furthermore, in ApoE4 carriers, both DNA methyltransferases and demethylases are downregulated, and overall DNA methylation levels are unchanged. CONCLUSION Our finding indicates that RNA methylation decreased in ApoE4 carriers before AD pathology and AD individuals. The expression of RNA methyltransferases and RNA methylation reader is inhibited, and RNA demethylase is upregulated in ApoE4 carriers, which leads to suppression of RNA methylation, and the suppression precedes the AD pathogenesis and persists through AD pathology.
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Affiliation(s)
- Wei-Bin Shen
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, Maryland, MD 21201, USA
| | - James Jiao Yang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, Maryland, MD 21201, USA
| | - Peixin Yang
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Maryland School of Medicine, Baltimore, Maryland, MD 21201, USA.,Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, MD 21201, USA
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11
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Liu J, Jiang K. METTL3‐mediated maturation of miR‐589‐5p promotes the malignant development of liver cancer. J Cell Mol Med 2022; 26:2505-2519. [PMID: 35348293 PMCID: PMC9077310 DOI: 10.1111/jcmm.16845] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
MiR‐589‐5p could promote liver cancer, but the specific mechanisms are largely unknown. This study examined the role and mechanisms of miR‐589‐5p in liver cancer. The expressions of miR‐589‐5p, METTL3 and m6A in liver cancers were determined by RT‐qPCR. The relationship between miR‐589‐5p and METTL3‐mediated m6A methylation was examined by m6A RNA immunoprecipitation. After transfection, the viability, migration, invasion and expressions of METTL3 and miR‐589‐5p in liver cancer cells were detected by CCK‐8, wound‐healing, transwell and RT‐qPCR. After the xenograft tumour was established in mice, the tumour volume was determined and the expressions of METTL3, miR‐589‐5p, MMP‐2, TIMP‐2, E‐cadherin, N‐cadherin and Vimentin in tumour tissue were detected by RT‐qPCR and Western blotting. In vitro study showed that miR‐589‐5p and METTL3 were highly expressed in liver cancer. METTL3 was positively correlated with miR‐589‐5p. METTL3 up‐regulated the expression of miR‐589‐5p and promoted the maturation of miR‐589‐5p. Overexpressed miR‐589‐5p and METTL3 promoted the viability, migration and invasion of liver cancer cells, while the effects of silencing miR‐589‐5p and METTL3 on the cells were the opposite. The effects of METTL3 overexpression and silencing were reversed by miR‐589‐5p inhibitor and mimic, respectively. In vivo study showed that METLL3 silencing inhibited the growth of xenograft tumour and the expressions of METTL3, MMP‐2, N‐cadherin and Vimentin, promoted the expressions of TIMP‐2 and E‐cadherin, while miR‐589‐5p mimic caused the opposite results and further reversed the effects of METLL3 silencing. In summary, this study found that METTL3‐mediated maturation of miR‐589‐5p promoted the malignant development of liver cancer.
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Affiliation(s)
- Jie Liu
- Hepatobiliary and Pancreatic Surgery Department Zhejiang Provincial People’s Hospital People’s Hospital of Hangzhou Medical College Hangzhou China
| | - Kai Jiang
- Hepatobiliary and Pancreatic Surgery Department Zhejiang Provincial People’s Hospital People’s Hospital of Hangzhou Medical College Hangzhou China
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12
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Mubarak G, Zahir FR. Recent Major Transcriptomics and Epitranscriptomics Contributions toward Personalized and Precision Medicine. J Pers Med 2022; 12:199. [PMID: 35207687 PMCID: PMC8877836 DOI: 10.3390/jpm12020199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 12/07/2022] Open
Abstract
With the advent of genome-wide screening methods-beginning with microarray technologies and moving onto next generation sequencing methods-the era of precision and personalized medicine was born. Genomics led the way, and its contributions are well recognized. However, "other-omics" fields have rapidly emerged and are becoming as important toward defining disease causes and exploring therapeutic benefits. In this review, we focus on the impacts of transcriptomics, and its extension-epitranscriptomics-on personalized and precision medicine efforts. There has been an explosion of transcriptomic studies particularly in the last decade, along with a growing number of recent epitranscriptomic studies in several disease areas. Here, we summarize and overview major efforts for cancer, cardiovascular disease, and neurodevelopmental disorders (including autism spectrum disorder and intellectual disability) for transcriptomics/epitranscriptomics in precision and personalized medicine. We show that leading advances are being made in both diagnostics, and in investigative and landscaping disease pathophysiological studies. As transcriptomics/epitranscriptomics screens become more widespread, it is certain that they will yield vital and transformative precision and personalized medicine contributions in ways that will significantly further genomics gains.
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Affiliation(s)
| | - Farah R. Zahir
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
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13
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Yi D, Wang Q, Zhao Y, Song Y, You H, Wang J, Liu R, Shi Z, Chen X, Luo Q. Alteration of N 6 -Methyladenosine mRNA Methylation in a Rat Model of Cerebral Ischemia-Reperfusion Injury. Front Neurosci 2021; 15:605654. [PMID: 33796004 PMCID: PMC8009187 DOI: 10.3389/fnins.2021.605654] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/03/2021] [Indexed: 01/11/2023] Open
Abstract
Aim This study was conducted in order to reveal the alterations in the N6-methyladenosine (m6A) modification profile of cerebral ischemia–reperfusion injury model rats. Materials and Methods Rats were used to establish the middle cerebral artery occlusion and reperfusion (MCAO/R) model. MeRIP-seq and RNA-seq were performed to identify differences in m6A methylation and gene expression. The expression of m6A methylation regulators was analyzed in three datasets and detected by quantitative real-time polymerase chain reaction, western blot, and immunofluorescence. Results We identified 1,160 differentially expressed genes with hypermethylated or hypomethylated m6A modifications. The differentially expressed genes with hypermethylated m6A modifications were involved in the pathways associated with inflammation, while hypomethylated differentially expressed genes were related to neurons and nerve synapses. Among the m6A regulators, FTO was specifically localized in neurons and significantly downregulated after MCAO/R. Conclusion Our study provided an m6A transcriptome-wide map of the MACO/R rat samples, which might provide new insights into the mechanisms of cerebral ischemia–reperfusion injury.
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Affiliation(s)
- Dazhuang Yi
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Qunhui Wang
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Yuhao Zhao
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Yu Song
- Department of Neurosurgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hong You
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Jian Wang
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Renjie Liu
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Zhongqiang Shi
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Xuan Chen
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
| | - Qi Luo
- Department of Neurosurgery, The First Hospital of Jilin University, Changchun, China
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14
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Ruggieri A, Helm M, Chatel-Chaix L. An epigenetic 'extreme makeover': the methylation of flaviviral RNA (and beyond). RNA Biol 2021; 18:696-708. [PMID: 33356825 DOI: 10.1080/15476286.2020.1868150] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Beyond their high clinical relevance worldwide, flaviviruses (comprising dengue and Zika viruses) are of particular interest to understand the spatiotemporal control of RNA metabolism. Indeed, their positive single-stranded viral RNA genome (vRNA) undergoes in the cytoplasm replication, translation and encapsidation, three steps of the flavivirus life cycle that are coordinated through a fine-tuned equilibrium. Over the last years, RNA methylation has emerged as a powerful mechanism to regulate messenger RNA metabolism at the posttranscriptional level. Not surprisingly, flaviviruses exploit RNA epigenetic strategies to control crucial steps of their replication cycle as well as to evade sensing by the innate immune system. This review summarizes the current knowledge about vRNA methylation events and their impacts on flavivirus replication and pathogenesis. We also address the important challenges that the field of epitranscriptomics faces in reliably and accurately identifying RNA methylation sites, which should be considered in future studies on viral RNA modifications.
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Affiliation(s)
- Alessia Ruggieri
- Department of Infectious Diseases, Molecular Virology, Centre for Integrative Infectious Disease Research University of Heidelberg, Heidelberg, Germany
| | - Mark Helm
- Johannes Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Sciences, Mainz, Germany
| | - Laurent Chatel-Chaix
- Institut National de la Recherche Scientifique, Centre Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
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15
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Rockwell AL, Hongay CF. Dm Ime4 depletion affects permeability barrier and Chic function in Drosophila spermatogenesis. Mech Dev 2020; 164:103650. [PMID: 33038528 DOI: 10.1016/j.mod.2020.103650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/27/2020] [Accepted: 09/29/2020] [Indexed: 12/01/2022]
Abstract
Adenosine methylation of messenger RNA at the N6 position (m6A) is a non-editing modification that can affect several aspects of mRNA metabolism. Dm Ime4, also known as METTL3, MTA, and MTA-70 in other organisms, is the catalytic subunit of the methyltransferase complex that adds this modification. Dm ime4 is evolutionarily conserved and essential for development in metazoans and plants. Because of its pleiotropic effects, it has been difficult to establish the main reason why embryonic arrest occurs in plants, mice, and zebrafish. Using a strategy that depletes Dm Ime4 specifically in the somatic cyst cells of Drosophila testes without affecting essential functions in development, our lab has found that Dm Ime4 may potentially regulate splicing of profilin (chic) mRNA, the message for an essential and evolutionarily conserved protein mainly known for its function in actin polymerization. One of the lesser known roles for Chic is its requirement for establishment and maintenance of the somatic cyst-cell permeability barrier in Drosophila spermatogenesis. Chic and Dm Ime4 colocalize and are abundant in somatic cyst cells throughout spermatogenesis. Upon selective depletion of Dm Ime4, we observe significant reduction of Chic protein levels and malfunction of the permeability barrier. We have found that chic mRNA contains intronic Dm Ime4 binding sites that can form the hairpin structures required for recognition by the methyltransferase complex. Our data show that the reduced levels of Chic protein observed in Dm ime4 somatic cyst-cell knockdowns could be the result of aberrant splicing of its mRNA. In turn, low levels of Chic are known to affect the function of the somatic permeability barrier, leading to germline death and the reduced fertility observed in Dm ime4 knockdown males. We propose that Dm Ime4 may regulate chic in other developmental contexts and in other organisms, including mice and humans. Chic is an essential protein that is evolutionarily conserved, and establishment and maintenance of cell barriers and domains are important strategies used in metazoan development. Taken together, our findings define a framework to investigate specific functions of Dm Ime4 and its homologs in multicellular organisms by bypassing its pleiotropic requirement in early developmental stages.
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Affiliation(s)
- Antonio L Rockwell
- Susquehanna University, Department of Biology, 514 University Avenue, Selinsgrove, PA 17870, USA.
| | - Cintia F Hongay
- Susquehanna University, Department of Biology, 514 University Avenue, Selinsgrove, PA 17870, USA.
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Dermentzaki G, Lotti F. New Insights on the Role of N 6-Methyladenosine RNA Methylation in the Physiology and Pathology of the Nervous System. Front Mol Biosci 2020; 7:555372. [PMID: 32984403 PMCID: PMC7492240 DOI: 10.3389/fmolb.2020.555372] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/12/2020] [Indexed: 12/21/2022] Open
Abstract
RNA modifications termed epitranscriptomics represent an additional layer of gene regulation similar to epigenetic mechanisms operating on DNA. The dynamic nature and the increasing number of RNA modifications offer new opportunities for a rapid fine-tuning of gene expression in response to specific environmental cues. In cooperation with a diverse and versatile set of effector proteins that "recognize" them, these RNA modifications have the ability to mediate and control diverse fundamental cellular functions, such as pre-mRNA splicing, nuclear export, stability, and translation. N 6-methyladenosine (m6A) is the most abundant of these RNA modifications, particularly in the nervous system, where recent studies have highlighted it as an important post-transcriptional regulator of physiological functions from development to synaptic plasticity, learning and memory. Here we review recent findings surrounding the role of m6A modification in regulating physiological responses of the mammalian nervous system and we discuss its emerging role in pathological conditions such as neuropsychiatric and neurodegenerative disorders.
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Affiliation(s)
- Georgia Dermentzaki
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York City, NY, United States
- Department of Neurology, Columbia University, New York City, NY, United States
| | - Francesco Lotti
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York City, NY, United States
- Department of Neurology, Columbia University, New York City, NY, United States
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