1
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Furze A, Waldron A, Yajima M. Visualizing metabolic regulation using metabolic biosensors during sea urchin embryogenesis. Dev Biol 2024; 516:122-129. [PMID: 39117030 PMCID: PMC11402557 DOI: 10.1016/j.ydbio.2024.08.003] [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: 06/13/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
Growing evidence suggests that metabolic regulation directly influences cellular function and development and thus may be more dynamic than previously expected. In vivo and in real-time analysis of metabolite activities during development is crucial to test this idea directly. In this study, we employ two metabolic biosensors to track the dynamics of pyruvate and oxidative phosphorylation (Oxphos) during the early embryogenesis of the sea urchin. A pyruvate sensor, PyronicSF, shows the signal enrichment on the mitotic apparatus, which is consistent with the localization patterns of the corresponding enzyme, pyruvate kinase (PKM). The addition of pyruvate increases the PyronicSF signal, while PKM knockdown decreases its signal, responding to the pyruvate level in the cell. Similarly, a ratio-metric sensor, Grx-roGFP, that reads the redox potential of the cell responds to DTT and H2O2, the known reducer and inducer of Oxphos. These observations suggest that these metabolic biosensors faithfully reflect the metabolic status in the cell during embryogenesis. The time-lapse imaging of these biosensors suggests that pyruvate and Oxphos levels change both spatially and temporarily during embryonic development. Pyruvate level is increased first in micromeres compared to other blastomeres at the 16-cell stage and remains high in ectoderm while decreasing in endomesoderm during gastrulation. In contrast, the Oxphos signal first decreases in micromeres at the 16-cell stage, while it increases in the endomesoderm during gastrulation, showing the opposite trend of the pyruvate signal. These results suggest that metabolic regulation is indeed both temporally and spatially dynamic during embryogenesis, and these biosensors are a valuable tool to monitor metabolic activities in real-time in developing embryos.
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Affiliation(s)
- Aidan Furze
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA
| | - Ashley Waldron
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA
| | - Mamiko Yajima
- Department of Molecular Biology Cell Biology Biochemistry, Brown University, 185 Meeting Street, BOX-GL277, Providence, RI, 02912, USA.
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2
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Huang F, He Y. Epigenetic control of gene expression by cellular metabolisms in plants. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102572. [PMID: 38875845 DOI: 10.1016/j.pbi.2024.102572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/09/2024] [Accepted: 05/22/2024] [Indexed: 06/16/2024]
Abstract
Covalent modifications on DNA and histones can regulate eukaryotic gene expression and are often referred to as epigenetic modifications. These chemical reactions require various metabolites as donors or co-substrates, such as acetyl coenzyme A, S-adenosyl-l-methionine, and α-ketoglutarate. Metabolic processes that take place in the cytoplasm, nucleus, or other cellular compartments may impact epigenetic modifications in the nucleus. Here, we review recent advances on metabolic control of chromatin modifications and thus gene expression in plants, with a focus on the functions of nuclear compartmentalization of metabolic processes and enzymes in DNA and histone modifications. Furthermore, we discuss the functions of cellular metabolisms in fine-tuning gene expression to facilitate the responses or adaptation to environmental changes in plants.
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Affiliation(s)
- Fei Huang
- Peking-Tsinghua Center for Life Sciences & National Key Laboratory of Wheat Improvement, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yuehui He
- Peking-Tsinghua Center for Life Sciences & National Key Laboratory of Wheat Improvement, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China.
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3
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Kang Z, Hou S, Gao K, Liu Y, Zhang N, Fang Z, Zhang W, Xu X, Xu R, Lü C, Ma C, Xu P, Gao C. An Ultrasensitive Biosensor for Probing Subcellular Distribution and Mitochondrial Transport of l-2-Hydroxyglutarate. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2404119. [PMID: 39005231 DOI: 10.1002/advs.202404119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/02/2024] [Indexed: 07/16/2024]
Abstract
l-2-Hydroxyglutarate (l-2-HG) is a functionally compartmentalized metabolite involved in various physiological processes. However, its subcellular distribution and mitochondrial transport remain unclear owing to technical limitations. In the present study, an ultrasensitive l-2-HG biosensor, sfLHGFRH, composed of circularly permuted yellow fluorescent protein and l-2-HG-specific transcriptional regulator, is developed. The ability of sfLHGFRH to be used for analyzing l-2-HG metabolism is first determined in human embryonic kidney cells (HEK293FT) and macrophages. Then, the subcellular distribution of l-2-HG in HEK293FT cells and the lower abundance of mitochondrial l-2-HG are identified by the sfLHGFRH-supported spatiotemporal l-2-HG monitoring. Finally, the role of the l-glutamate transporter SLC1A1 in mitochondrial l-2-HG uptake is elucidated using sfLHGFRH. Based on the design of sfLHGFRH, another highly sensitive biosensor with a low limit of detection, sfLHGFRL, is developed for the point-of-care diagnosis of l-2-HG-related diseases. The accumulation of l-2-HG in the urine of patients with kidney cancer is determined using the sfLHGFRL biosensor.
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Affiliation(s)
- Zhaoqi Kang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Shuang Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Kaiyu Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Yidong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Ning Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250100, P. R. China
| | - Zhiqing Fang
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250100, P. R. China
| | - Wen Zhang
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250100, P. R. China
| | - Xianzhi Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Rong Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Chuanjuan Lü
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, P. R. China
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4
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Shao Z, Bian L, Ahmadi SK, Daniel TJ, Belmonte MA, Burns JG, Kotla P, Bi Y, Shen Z, Xu SL, Wang ZY, Briggs SP, Qiao H. Nuclear pyruvate dehydrogenase complex regulates histone acetylation and transcriptional regulation in the ethylene response. SCIENCE ADVANCES 2024; 10:eado2825. [PMID: 39058774 PMCID: PMC11277378 DOI: 10.1126/sciadv.ado2825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
Ethylene plays its essential roles in plant development, growth, and defense responses by controlling the transcriptional reprograming, in which EIN2-C-directed regulation of histone acetylation is the first key step for chromatin to perceive ethylene signaling. But how the nuclear acetyl coenzyme A (acetyl CoA) is produced to ensure the ethylene-mediated histone acetylation is unknown. Here we report that ethylene triggers the accumulation of the pyruvate dehydrogenase complex (PDC) in the nucleus to synthesize nuclear acetyl CoA to regulate ethylene response. PDC is identified as an EIN2-C nuclear partner, and ethylene triggers its nuclear accumulation. Mutations in PDC lead to an ethylene hyposensitivity that results from the reduction of histone acetylation and transcription activation. Enzymatically active nuclear PDC synthesizes nuclear acetyl CoA for EIN2-C-directed histone acetylation and transcription regulation. These findings uncover a mechanism by which PDC-EIN2 converges the mitochondrial enzyme-mediated nuclear acetyl CoA synthesis with epigenetic and transcriptional regulation for plant hormone response.
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Affiliation(s)
- Zhengyao Shao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Liangqiao Bian
- Shimadzu Center for Advanced Analytical Chemistry, University of Texas at Arlington, Arlington, TX 76019, USA
| | - Shyon K. Ahmadi
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tyler J. Daniel
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Miguel A. Belmonte
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jackson G. Burns
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Prashanth Kotla
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yang Bi
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Zhouxin Shen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Shou-Ling Xu
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Zhi-Yong Wang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Steven P. Briggs
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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5
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Kancharana B, Dutta H, Jain N. FOXM1 requires IDH1 for late genes expression in mitotic cells. Histochem Cell Biol 2024:10.1007/s00418-024-02307-8. [PMID: 39039166 DOI: 10.1007/s00418-024-02307-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2024] [Indexed: 07/24/2024]
Abstract
Isocitrate dehydrogenase 1 (IDH1) is a metabolic enzyme that converts isocitrate to α-ketoglutarate in cells. However, research on IDH1 is more focused on the metabolite D-2-hydroxyglutarate than the cellular roles of the IDH1 protein. Metabolic enzymes can moonlight by participating in diverse cellular processes in cancer cells. This moonlighting function of the metabolic enzymes can contribute to changes in gene expression. It is unknown whether IDH1 associates with any transcription factor. We asked whether IDH1 coordinates with forkhead box protein M1 (FOXM1) in mitotic cells to regulate late genes expression. We found that depletion of IDH1 reduces canonical FOXM1-target expression in mitotic cells. Also, IDH1 binds to FOXM1 and a subset of MuvB proteins, Lin-9 and Lin-54, in mitotic cells. Based on these observations, we suggest that IDH1 coordinates with FOXM1 in mitotic cells to regulate late genes expression.
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Affiliation(s)
- Balabhaskararao Kancharana
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hashnu Dutta
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Nishant Jain
- Department of Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, 500007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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6
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Stacpoole PW, Dirain CO. The pyruvate dehydrogenase complex at the epigenetic crossroads of acetylation and lactylation. Mol Genet Metab 2024; 143:108540. [PMID: 39067348 DOI: 10.1016/j.ymgme.2024.108540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/25/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024]
Abstract
The pyruvate dehydrogenase complex (PDC) is remarkable for its size and structure as well as for its physiological and pathological importance. Its canonical location is in the mitochondrial matrix, where it primes the tricarboxylic acid (TCA) cycle by decarboxylating glycolytically-derived pyruvate to acetyl-CoA. Less well appreciated is its role in helping to shape the epigenetic landscape, from early development throughout mammalian life by its ability to "moonlight" in the nucleus, with major repercussions for human healthspan and lifespan. The PDC's influence on two crucial modifiers of the epigenome, acetylation and lactylation, is the focus of this brief review.
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Affiliation(s)
- Peter W Stacpoole
- University of Florida, College of Medicine Department of Medicine, Department of Biochemistry & Molecular Biology, Gainesville, FL, United States.
| | - Carolyn O Dirain
- University of Florida, College of Medicine Department of Medicine, Gainesville, FL, United States
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7
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Zhao Y, Zhang M, Huang X, Liu J, Sun Y, Zhang F, Zhang N, Lei L. Lactate modulates zygotic genome activation through H3K18 lactylation rather than H3K27 acetylation. Cell Mol Life Sci 2024; 81:298. [PMID: 38992327 PMCID: PMC11335220 DOI: 10.1007/s00018-024-05349-2] [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: 05/23/2024] [Revised: 06/24/2024] [Accepted: 07/03/2024] [Indexed: 07/13/2024]
Abstract
In spite of its essential role in culture media, the precise influence of lactate on early mouse embryonic development remains elusive. Previous studies have implicated lactate accumulation in medium affecting histone acetylation. Recent research has underscored lactate-derived histone lactylation as a novel epigenetic modification in diverse cellular processes and diseases. Our investigation demonstrated that the absence of sodium lactate in the medium resulted in a pronounced 2-cell arrest at the late G2 phase in embryos. RNA-seq analysis revealed that the absence of sodium lactate significantly impaired the maternal-to-zygotic transition (MZT), particularly in zygotic gene activation (ZGA). Investigations were conducted employing Cut&Tag assays targeting the well-studied histone acetylation and lactylation sites, H3K18la and H3K27ac, respectively. The findings revealed a noticeable reduction in H3K18la modification under lactate deficiency, and this alteration showed a significant correlation with changes in gene expression. In contrast, H3K27ac exhibited minimal correlation. These results suggest that lactate may preferentially influence early embryonic development through H3K18la rather than H3K27ac modifications.
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Affiliation(s)
- Yanhua Zhao
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China
| | - Meiting Zhang
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China
| | - Xingwei Huang
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China
| | - Jiqiang Liu
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China
| | - Yuchen Sun
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China
| | - Fan Zhang
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China
| | - Na Zhang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.
| | - Lei Lei
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150081, China.
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8
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Fitzpatrick TB. B Vitamins: An Update on Their Importance for Plant Homeostasis. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:67-93. [PMID: 38424064 DOI: 10.1146/annurev-arplant-060223-025336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
B vitamins are a source of coenzymes for a vast array of enzyme reactions, particularly those of metabolism. As metabolism is the basis of decisions that drive maintenance, growth, and development, B vitamin-derived coenzymes are key components that facilitate these processes. For over a century, we have known about these essential compounds and have elucidated their pathways of biosynthesis, repair, salvage, and degradation in numerous organisms. Only now are we beginning to understand their importance for regulatory processes, which are becoming an important topic in plants. Here, I highlight and discuss emerging evidence on how B vitamins are integrated into vital processes, from energy generation and nutrition to gene expression, and thereby contribute to the coordination of growth and developmental programs, particularly those that concern maintenance of a stable state, which is the foundational tenet of plant homeostasis.
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9
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Dingare C, Cao D, Yang JJ, Sozen B, Steventon B. Mannose controls mesoderm specification and symmetry breaking in mouse gastruloids. Dev Cell 2024; 59:1523-1537.e6. [PMID: 38636516 DOI: 10.1016/j.devcel.2024.03.031] [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: 07/03/2023] [Revised: 01/29/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024]
Abstract
Patterning and growth are fundamental features of embryonic development that must be tightly coordinated. To understand how metabolism impacts early mesoderm development, we used mouse embryonic stem-cell-derived gastruloids, that co-expressed glucose transporters with the mesodermal marker T/Bra. We found that the glucose mimic, 2-deoxy-D-glucose (2-DG), blocked T/Bra expression and abolished axial elongation in gastruloids. However, glucose removal did not phenocopy 2-DG treatment despite a decline in glycolytic intermediates. As 2-DG can also act as a competitive inhibitor of mannose in protein glycosylation, we added mannose together with 2-DG and found that it could rescue the mesoderm specification both in vivo and in vitro. We further showed that blocking production and intracellular recycling of mannose abrogated mesoderm specification. Proteomics analysis demonstrated that mannose reversed glycosylation of the Wnt pathway regulator, secreted frizzled receptor Frzb. Our study showed how mannose controls mesoderm specification in mouse gastruloids.
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Affiliation(s)
- Chaitanya Dingare
- Deptartment of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH, UK.
| | - Dominica Cao
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Jenny Jingni Yang
- Deptartment of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH, UK
| | - Berna Sozen
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA; Yale Stem Cell Centre, Yale University, New Haven, CT, USA; Department of Obstetrics, Gynaecology and Reproductive Sciences, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Benjamin Steventon
- Deptartment of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH, UK.
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10
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Noble M, Chatterjee A, Sekaran T, Schwarzl T, Hentze MW. Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase. RNA (NEW YORK, N.Y.) 2024; 30:839-853. [PMID: 38609156 PMCID: PMC11182015 DOI: 10.1261/rna.079925.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/26/2024] [Indexed: 04/14/2024]
Abstract
Several enzymes of intermediary metabolism have been identified to bind RNA in cells, with potential consequences for the bound RNAs and/or the enzyme. In this study, we investigate the RNA-binding activity of the mitochondrial enzyme malate dehydrogenase 2 (MDH2), which functions in the tricarboxylic acid (TCA) cycle and the malate-aspartate shuttle. We confirmed in cellulo RNA binding of MDH2 using orthogonal biochemical assays and performed enhanced cross-linking and immunoprecipitation (eCLIP) to identify the cellular RNAs associated with endogenous MDH2. Surprisingly, MDH2 preferentially binds cytosolic over mitochondrial RNAs, although the latter are abundant in the milieu of the mature protein. Subcellular fractionation followed by RNA-binding assays revealed that MDH2-RNA interactions occur predominantly outside of mitochondria. We also found that a cytosolically retained N-terminal deletion mutant of MDH2 is competent to bind RNA, indicating that mitochondrial targeting is dispensable for MDH2-RNA interactions. MDH2 RNA binding increased when cellular NAD+ levels (MDH2's cofactor) were pharmacologically diminished, suggesting that the metabolic state of cells affects RNA binding. Taken together, our data implicate an as yet unidentified function of MDH2-binding RNA in the cytosol.
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Affiliation(s)
- Michelle Noble
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | | | - Thileepan Sekaran
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
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11
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Garfinkel AM, Ilker E, Miyazawa H, Schmeisser K, Tennessen JM. Historic obstacles and emerging opportunities in the field of developmental metabolism - lessons from Heidelberg. Development 2024; 151:dev202937. [PMID: 38912552 PMCID: PMC11299503 DOI: 10.1242/dev.202937] [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: 06/25/2024]
Abstract
The field of developmental metabolism is experiencing a technological revolution that is opening entirely new fields of inquiry. Advances in metabolomics, small-molecule sensors, single-cell RNA sequencing and computational modeling present new opportunities for exploring cell-specific and tissue-specific metabolic networks, interorgan metabolic communication, and gene-by-metabolite interactions in time and space. Together, these advances not only present a means by which developmental biologists can tackle questions that have challenged the field for centuries, but also present young scientists with opportunities to define new areas of inquiry. These emerging frontiers of developmental metabolism were at the center of a highly interactive 2023 EMBO workshop 'Developmental metabolism: flows of energy, matter, and information'. Here, we summarize key discussions from this forum, emphasizing modern developmental biology's challenges and opportunities.
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Affiliation(s)
- Alexandra M. Garfinkel
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT 06510, USA
| | - Efe Ilker
- Max Planck Institute for the Physics of Complex Systems, Dresden 01187, Germany
| | - Hidenobu Miyazawa
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Kathrin Schmeisser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
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12
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Ravanelli S, Park JYC, Wicky C, Ewald CY, von Meyenn F. Metabolic enzymes aldo-2 and pdhb-1 as potential epigenetic regulators during C. elegans embryogenesis. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001222. [PMID: 38947245 PMCID: PMC11211921 DOI: 10.17912/micropub.biology.001222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 07/02/2024]
Abstract
The intersection of metabolic processes and epigenetic regulation during embryogenesis is crucial yet not fully understood. Through a candidate RNAi screen in Caenorhabditis elegans , we identified metabolic enzymes ALDO-2 and PDHB-1 as potential epigenetic regulators. Mild alteration of the chromatin remodeler LET-418 /Mi2 activity rescues embryonic lethality induced by suppressing aldo-2 or pdhb-1 , suggesting a critical role for glucose and pyruvate metabolism in chromatin remodeling during embryogenesis. Given the conservation of central metabolic pathways and chromatin modifiers across species, our findings lay the foundation for future mechanistic investigations into the interplay between epigenetics and metabolism during development and upon disease.
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Affiliation(s)
- Sonia Ravanelli
- Laboratory of Nutrition and Metabolic Epigenetics, Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Switzerland
| | - Ji Young Cecilia Park
- Laboratory of Nutrition and Metabolic Epigenetics, Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Switzerland
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Switzerland
| | - Chantal Wicky
- Department of Biology, University of Fribourg, Switzerland
| | - Collin Y. Ewald
- Laboratory of Extracellular Matrix Regeneration, Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Switzerland
| | - Ferdinand von Meyenn
- Laboratory of Nutrition and Metabolic Epigenetics, Institute for Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zurich, Switzerland
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13
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Pines O, Horwitz M, Herrmann JM. Privileged proteins with a second residence: dual targeting and conditional re-routing of mitochondrial proteins. FEBS J 2024. [PMID: 38857249 DOI: 10.1111/febs.17191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/15/2024] [Accepted: 05/22/2024] [Indexed: 06/12/2024]
Abstract
Almost all mitochondrial proteins are encoded by nuclear genes and synthesized in the cytosol as precursor proteins. Signals in the amino acid sequence of these precursors ensure their targeting and translocation into mitochondria. However, in many cases, only a certain fraction of a specific protein is transported into mitochondria, while the rest either remains in the cytosol or undergoes reverse translocation to the cytosol, and can populate other cellular compartments. This phenomenon is called dual localization which can be instigated by different mechanisms. These include alternative start or stop codons, differential transcripts, and ambiguous or competing targeting sequences. In many cases, dual localization might serve as an economic strategy to reduce the number of required genes; for example, when the same groups of enzymes are required both in mitochondria and chloroplasts or both in mitochondria and the nucleus/cytoplasm. Such cases frequently employ ambiguous targeting sequences to distribute proteins between both organelles. However, alternative localizations can also be used for signaling, for example when non-imported precursors serve as mitophagy signals or when they represent transcription factors in the nucleus to induce the mitochondrial unfolded stress response. This review provides an overview regarding the mechanisms and the physiological consequences of dual targeting.
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Affiliation(s)
- Ophry Pines
- Microbiology and Genetics, Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Margalit Horwitz
- Microbiology and Genetics, Faculty of Medicine, Hebrew University of Jerusalem, Israel
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14
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Zhang D, Deng W, Jiang T, Zhao Y, Bai D, Tian Y, Kong S, Zhang L, Wang H, Gao S, Lu Z. Maternal Ezh1/2 deficiency impairs the function of mitochondria in mouse oocytes and early embryos. J Cell Physiol 2024; 239:e31244. [PMID: 38529784 DOI: 10.1002/jcp.31244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/27/2024]
Abstract
Maternal histone methyltransferase is critical for epigenetic regulation and development of mammalian embryos by regulating histone and DNA modifications. Here, we reported a novel mechanism by revealing the critical effects of maternal Ezh1/2 deletion on mitochondria in MII oocytes and early embryos in mice. We found that Ezh1/2 knockout in mouse MII oocytes impaired the structure of mitochondria and decreased its number, but membrane potential and respiratory function of mitochondrion were increased. The similar effects of Ezh1/2 deletion have been observed in 2-cell and morula embryos, indicating that the effects of maternal Ezh1/2 deficiency on mitochondrion extend to early embryos. However, the loss of maternal Ezh1/2 resulted in a severe defect of morula: the number, membrane potential, respiratory function, and ATP production of mitochondrion dropped significantly. Content of reactive oxygen species was raised in both MII oocytes and early embryos, suggesting maternal Ezh1/2 knockout induced oxidative stress. In addition, maternal Ezh1/2 ablation interfered the autophagy in morula and blastocyst embryos. Finally, maternal Ezh1/2 deletion led to cell apoptosis in blastocyst embryos in mice. By analyzing the gene expression profile, we revealed that maternal Ezh1/2 knockout affected the expression of mitochondrial related genes in MII oocytes and early embryos. The chromatin immunoprecipitation-polymerase chain reaction assay demonstrated that Ezh1/2 directly regulated the expression of genes Fxyd6, Adpgk, Aurkb, Zfp521, Ehd3, Sgms2, Pygl, Slc1a1, and Chst12 by H3K27me3 modification. In conclusion, our study revealed the critical effect of maternal Ezh1/2 on the structure and function of mitochondria in oocytes and early embryos, and suggested a novel mechanism underlying maternal epigenetic regulation on early embryonic development through the modulation of mitochondrial status.
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Affiliation(s)
- Dan Zhang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian, China
| | - Wenbo Deng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Ting Jiang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian, China
| | - Yinan Zhao
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian, China
| | - Dandan Bai
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yingpu Tian
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian, China
| | - Shuangbo Kong
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Leilei Zhang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Shaorong Gao
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhongxian Lu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian, China
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
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15
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Bhattacharya S, Tu BP. Histone acylation at a glance. J Cell Sci 2024; 137:jcs261250. [PMID: 38842578 PMCID: PMC11213524 DOI: 10.1242/jcs.261250] [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: 06/07/2024] Open
Abstract
An important mechanism of gene expression regulation is the epigenetic modification of histones. The cofactors and substrates for these modifications are often intermediary metabolites, and it is becoming increasingly clear that the metabolic and nutritional state of cells can influence these marks. These connections between the balance of metabolites, histone modifications and downstream transcriptional changes comprise a metabolic signaling program that can enable cells to adapt to changes in nutrient availability. Beyond acetylation, there is evidence now that histones can be modified by other acyl groups. In this Cell Science at a Glance article and the accompanying poster, we focus on these histone acylation modifications and provide an overview of the players that govern these acylations and their connections with metabolism.
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Affiliation(s)
- Saikat Bhattacharya
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390-9038, USA
| | - Benjamin P. Tu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390-9038, USA
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16
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Aoki S, Inoue Y, Hamazaki M, Hara S, Noguchi T, Shirasuna K, Iwata H. miRNAs in Follicular and Oviductal Fluids Support Global DNA Demethylation in Early-Stage Embryos. Int J Mol Sci 2024; 25:5872. [PMID: 38892059 PMCID: PMC11172648 DOI: 10.3390/ijms25115872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/13/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
Global methylation levels differ in in vitro- and in vivo-developed embryos. Follicular fluid (FF) contains extracellular vesicles (EVs) containing miRNAs that affect embryonic development. Here, we examined our hypothesis that components in FF affect global DNA methylation and embryonic development. Oocytes and FF were collected from bovine ovaries. Treatment of zygotes with a low concentration of FF induced global DNA demethylation, improved embryonic development, and reduced DNMT1/3A levels. We show that embryos take up EVs containing labeled miRNA secreted from granulosa cells and the treatment of zygotes with EVs derived from FF reduces global DNA methylation in embryos. Furthermore, the methylation levels of in vitro-developed blastocysts were higher than those of in their vivo counterparts. Based on small RNA-sequencing and in silico analysis, we predicted miR-29b, -199a-3p, and -148a to target DNMTs and to induce DNA demethylation, thereby improving embryonic development. Moreover, among FF from 30 cows, FF with a high content of these miRNAs demethylated more DNA in the embryos than FF with a lower miRNA content. Thus, miRNAs in FF play a role in early embryonic development.
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Affiliation(s)
| | | | | | | | | | | | - Hisataka Iwata
- Department of Animal Science, Graduate School of Agriculture, Tokyo University of Agriculture, Funako 1737, Atsugi 243-0034, Kanagawa, Japan; (S.A.)
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17
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Shao Z, Bian L, Ahmadi SK, Daniel TJ, Belmonte MA, Burns JG, Kotla P, Bi Y, Shen Z, Xu SL, Wang ZY, Briggs SP, Qiao H. Nuclear Pyruvate Dehydrogenase Complex Regulates Histone Acetylation and Transcriptional Regulation in the Ethylene Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.25.564010. [PMID: 37961310 PMCID: PMC10634830 DOI: 10.1101/2023.10.25.564010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Ethylene plays its essential roles in plant development, growth, and defense responses by controlling the transcriptional reprograming, in which EIN2-C-directed regulation of histone acetylation is the first key-step for chromatin to perceive ethylene signaling. But how the nuclear acetyl coenzyme A (acetyl CoA) is produced to ensure the ethylene-mediated histone acetylation is unknown. Here we report that ethylene triggers the accumulation of the pyruvate dehydrogenase complex (PDC) in the nucleus to synthesize nuclear acetyl CoA to regulate ethylene response. PDC is identified as an EIN2-C nuclear partner, and ethylene triggers its nuclear accumulation. Mutations in PDC lead to an ethylene-hyposensitivity that results from the reduction of histone acetylation and transcription activation. Enzymatically active nuclear PDC synthesize nuclear acetyl CoA for EIN2-C-directed histone acetylation and transcription regulation. These findings uncover a mechanism by which PDC-EIN2 converges the mitochondrial enzyme mediated nuclear acetyl CoA synthesis with epigenetic and transcriptional regulation for plant hormone response.
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18
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Han Q, Ma R, Liu N. Epigenetic reprogramming in the transition from pluripotency to totipotency. J Cell Physiol 2024; 239:e31222. [PMID: 38375873 DOI: 10.1002/jcp.31222] [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: 10/17/2023] [Revised: 01/08/2024] [Accepted: 02/05/2024] [Indexed: 02/21/2024]
Abstract
Mammalian development commences with the zygote, which can differentiate into both embryonic and extraembryonic tissues, a capability known as totipotency. Only the zygote and embryos around zygotic genome activation (ZGA) (two-cell embryo stage in mice and eight-cell embryo in humans) are totipotent cells. Epigenetic modifications undergo extremely extensive changes during the acquisition of totipotency and subsequent development of differentiation. However, the underlying molecular mechanisms remain elusive. Recently, the discovery of mouse two-cell embryo-like cells, human eight-cell embryo-like cells, extended pluripotent stem cells and totipotent-like stem cells with extra-embryonic developmental potential has greatly expanded our understanding of totipotency. Experiments with these in vitro models have led to insights into epigenetic changes in the reprogramming of pluri-to-totipotency, which have informed the exploration of preimplantation development. In this review, we highlight the recent findings in understanding the mechanisms of epigenetic remodeling during totipotency capture, including RNA splicing, DNA methylation, chromatin configuration, histone modifications, and nuclear organization.
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Affiliation(s)
- Qingsheng Han
- School of Medicine, Nankai University, Tianjin, China
| | - Ru Ma
- School of Medicine, Nankai University, Tianjin, China
| | - Na Liu
- School of Medicine, Nankai University, Tianjin, China
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19
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Granath-Panelo M, Kajimura S. Mitochondrial heterogeneity and adaptations to cellular needs. Nat Cell Biol 2024; 26:674-686. [PMID: 38755301 DOI: 10.1038/s41556-024-01410-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/21/2024] [Indexed: 05/18/2024]
Abstract
Although it is well described that mitochondria are at the epicentre of the energy demands of a cell, it is becoming important to consider how each cell tailors its mitochondrial composition and functions to suit its particular needs beyond ATP production. Here we provide insight into mitochondrial heterogeneity throughout development as well as in tissues with specific energy demands and discuss how mitochondrial malleability contributes to cell fate determination and tissue remodelling.
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Affiliation(s)
- Melia Granath-Panelo
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA.
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Shingo Kajimura
- Division of Endocrinology, Beth Israel Deaconess Medical Center, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA.
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20
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García-Giménez JL, Cánovas-Cervera I, Pallardó FV. Oxidative stress and metabolism meet epigenetic modulation in physical exercise. Free Radic Biol Med 2024; 213:123-137. [PMID: 38199289 DOI: 10.1016/j.freeradbiomed.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/12/2024]
Abstract
Physical exercise is established as an important factor of health and generally is recommended for its positive effects on several tissues, organs, and systems. These positive effects come from metabolic adaptations that also include oxidative eustress, in which physical activity increases ROS production and antioxidant mechanisms, although this depends on the intensity of the exercise. Muscle metabolism through mechanisms such as aerobic and anaerobic glycolysis, tricarboxylic acid cycle, and oxidative lipid metabolism can produce metabolites and co-factors which directly impact the epigenetic machinery. In this review, we clearly reinforce the evidence that exercise regulates several epigenetic mechanisms and explain how these mechanisms can be regulated by metabolic products and co-factors produced during exercise. In fact, recent evidence has demonstrated the importance of epigenetics in the gene expression changes implicated in metabolic adaptation after exercise. Importantly, intermediates of the metabolism generated by continuous, acute, moderate, or strenuous exercise control the activity of epigenetic enzymes, therefore turning on or turning off the gene expression of specific programs which can lead to physiological adaptations after exercise.
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Affiliation(s)
- José Luis García-Giménez
- Faculty of Medicine and Dentistry, Department of Physiology, University of Valencia, Av/Blasco Ibañez, 15, Valencia, 46010, Spain; Biomedical Research Institute INCLIVA, Av/Menéndez Pelayo. 4acc, Valencia, 46010, Spain; CIBERER, The Centre for Biomedical Network Research on Rare Diseases, ISCIII, C. de Melchor Fernández Almagro, 3, 28029, Madrid, Spain.
| | - Irene Cánovas-Cervera
- Faculty of Medicine and Dentistry, Department of Physiology, University of Valencia, Av/Blasco Ibañez, 15, Valencia, 46010, Spain; Biomedical Research Institute INCLIVA, Av/Menéndez Pelayo. 4acc, Valencia, 46010, Spain.
| | - Federico V Pallardó
- Faculty of Medicine and Dentistry, Department of Physiology, University of Valencia, Av/Blasco Ibañez, 15, Valencia, 46010, Spain; Biomedical Research Institute INCLIVA, Av/Menéndez Pelayo. 4acc, Valencia, 46010, Spain; CIBERER, The Centre for Biomedical Network Research on Rare Diseases, ISCIII, C. de Melchor Fernández Almagro, 3, 28029, Madrid, Spain.
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21
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Khoa LTP, Yang W, Shan M, Zhang L, Mao F, Zhou B, Li Q, Malcore R, Harris C, Zhao L, Rao RC, Iwase S, Kalantry S, Bielas SL, Lyssiotis CA, Dou Y. Quiescence enables unrestricted cell fate in naive embryonic stem cells. Nat Commun 2024; 15:1721. [PMID: 38409226 PMCID: PMC10897426 DOI: 10.1038/s41467-024-46121-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Quiescence in stem cells is traditionally considered as a state of inactive dormancy or with poised potential. Naive mouse embryonic stem cells (ESCs) can enter quiescence spontaneously or upon inhibition of MYC or fatty acid oxidation, mimicking embryonic diapause in vivo. The molecular underpinning and developmental potential of quiescent ESCs (qESCs) are relatively unexplored. Here we show that qESCs possess an expanded or unrestricted cell fate, capable of generating both embryonic and extraembryonic cell types (e.g., trophoblast stem cells). These cells have a divergent metabolic landscape comparing to the cycling ESCs, with a notable decrease of the one-carbon metabolite S-adenosylmethionine. The metabolic changes are accompanied by a global reduction of H3K27me3, an increase of chromatin accessibility, as well as the de-repression of endogenous retrovirus MERVL and trophoblast master regulators. Depletion of methionine adenosyltransferase Mat2a or deletion of Eed in the polycomb repressive complex 2 results in removal of the developmental constraints towards the extraembryonic lineages. Our findings suggest that quiescent ESCs are not dormant but rather undergo an active transition towards an unrestricted cell fate.
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Affiliation(s)
- Le Tran Phuc Khoa
- Department of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Wentao Yang
- Department of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA
| | - Mengrou Shan
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Li Zhang
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
| | - Bo Zhou
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Qiang Li
- Department of Ophthalmology & Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, 1000 Wall St., Ann Arbor, MI, 48105, USA
| | - Rebecca Malcore
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Clair Harris
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Lili Zhao
- Beaumont Hospital, Wayne, 33155 Annapolis St., Wayne, MI, 48184, USA
| | - Rajesh C Rao
- Department of Ophthalmology & Visual Sciences, W.K. Kellogg Eye Center, University of Michigan, 1000 Wall St., Ann Arbor, MI, 48105, USA
| | - Shigeki Iwase
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Costas A Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yali Dou
- Department of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90033, USA.
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22
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Nakano H, Nakano A. The role of metabolism in cardiac development. Curr Top Dev Biol 2024; 156:201-243. [PMID: 38556424 DOI: 10.1016/bs.ctdb.2024.01.005] [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] [Indexed: 04/02/2024]
Abstract
Metabolism is the fundamental process that sustains life. The heart, in particular, is an organ of high energy demand, and its energy substrates have been studied for more than a century. In recent years, there has been a growing interest in understanding the role of metabolism in the early differentiation of pluripotent stem cells and in cancer research. Studies have revealed that metabolic intermediates from glycolysis and the tricarboxylic acid cycle act as co-factors for intracellular signal transduction, playing crucial roles in regulating cell behaviors. Mitochondria, as the central hub of metabolism, are also under intensive investigation regarding the regulation of their dynamics. The metabolic environment of the fetus is intricately linked to the maternal metabolic status, and the impact of the mother's nutrition and metabolic health on fetal development is significant. For instance, it is well known that maternal diabetes increases the risk of cardiac and nervous system malformations in the fetus. Another notable example is the decrease in the risk of neural tube defects when pregnant women are supplemented with folic acid. These examples highlight the profound influence of the maternal metabolic environment on the fetal organ development program. Therefore, gaining insights into the metabolic environment within developing fetal organs is critical for deepening our understanding of normal organ development. This review aims to summarize recent findings that build upon the historical recognition of the environmental and metabolic factors involved in the developing embryo.
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Affiliation(s)
- Haruko Nakano
- Department of Molecular, Cell, and Developmental Biology, UCLA, Los Angeles, CA, United States
| | - Atsushi Nakano
- Department of Molecular, Cell, and Developmental Biology, UCLA, Los Angeles, CA, United States; Cardiology Division, Department of Medicine, UCLA, Los Angeles, CA, United States; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, United States; Molecular Biology Institute, UCLA, Los Angeles, CA, United States; Department of Cell Physiology, The Jikei University School of Medicine, Tokyo, Japan.
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23
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Li J, Hou W, Zhao Q, Han W, Cui H, Xiao S, Zhu L, Qu J, Liu X, Cong W, Shen J, Zhao Y, Gao S, Huang G, Kong Q. Lactate regulates major zygotic genome activation by H3K18 lactylation in mammals. Natl Sci Rev 2024; 11:nwad295. [PMID: 38327665 PMCID: PMC10849771 DOI: 10.1093/nsr/nwad295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 11/04/2023] [Accepted: 11/13/2023] [Indexed: 02/09/2024] Open
Abstract
Lactate is present at a high level in the microenvironment of mammalian preimplantation embryos in vivo and in vitro. However, its role in preimplantation development is unclear. Here, we report that lactate is highly enriched in the nuclei of early embryos when major zygotic genome activation (ZGA) occurs in humans and mice. The inhibition of its production and uptake results in developmental arrest at the 2-cell stage, major ZGA failure, and loss of lactate-derived H3K18lac, which could be rescued by the addition of Lac-CoA and recapitulated by overexpression of H3K18R mutation. By profiling the landscape of H3K18lac during mouse preimplantation development, we show that H3K18lac is enriched on the promoter regions of most major ZGA genes and correlates with their expressions. In humans, H3K18lac is also enriched in ZGA markers and temporally concomitant with their expressions. Taken together, we profile the landscapes of H3K18lac in mouse and human preimplantation embryos, and demonstrate the important role for H3K18lac in major ZGA, showing that a conserved metabolic mechanism underlies preimplantation development of mammalian embryos.
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Affiliation(s)
- Jingyu Li
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Women and Children's Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Weibo Hou
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Qi Zhao
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Wei Han
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Women and Children's Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Hongdi Cui
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Songling Xiao
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Ling Zhu
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Women and Children's Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Jiadan Qu
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Women and Children's Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Xiaoyu Liu
- Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Weitao Cong
- School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou 325035, China
| | - Jingling Shen
- Institute of Life Sciences, College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325035, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai 2000237, China
| | - Shaorong Gao
- Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Guoning Huang
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Women and Children's Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Qingran Kong
- Oujiang Laboratory, Zhejiang Provincial Key Laboratory of Medical Genetics, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou 325035, China
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24
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Zhang L, Zhao J, Lam SM, Chen L, Gao Y, Wang W, Xu Y, Tan T, Yu H, Zhang M, Liao X, Wu M, Zhang T, Huang J, Li B, Zhou QD, Shen N, Lee HJ, Ye C, Li D, Shui G, Zhang J. Low-input lipidomics reveals lipid metabolism remodelling during early mammalian embryo development. Nat Cell Biol 2024; 26:278-293. [PMID: 38302721 DOI: 10.1038/s41556-023-01341-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/20/2023] [Indexed: 02/03/2024]
Abstract
Lipids are indispensable for energy storage, membrane structure and cell signalling. However, dynamic changes in various categories of endogenous lipids in mammalian early embryonic development have not been systematically characterized. Here we comprehensively investigated the dynamic lipid landscape during mouse and human early embryo development. Lipid signatures of different developmental stages are distinct, particularly for the phospholipid classes. We highlight that the high degree of phospholipid unsaturation is a conserved feature as embryos develop to the blastocyst stage. Moreover, we show that lipid desaturases such as SCD1 are required for in vitro blastocyst development and blastocyst implantation. One of the mechanisms is through the regulation of unsaturated fatty-acid-mediated fluidity of the plasma membrane and apical proteins and the establishment of apical-basal polarity during development of the eight-cell embryo to the blastocyst. Overall, our study provides an invaluable resource about the remodelling of the endogenous lipidome in mammalian preimplantation embryo development and mechanistic insights into the regulation of embryogenesis and implantation by lipid unsaturation.
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Affiliation(s)
- Ling Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Jing Zhao
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- LipidALL Technologies, Changzhou, China
| | - Lang Chen
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingzhuo Gao
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
- NHC Key Laboratory of Advanced Reproductive Medicine and Fertility (China Medical University), National Health Commission, Shenyang, China
| | - Wenjie Wang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuyan Xu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tianyu Tan
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Yu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Min Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xufeng Liao
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Mengchen Wu
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tianyun Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Jie Huang
- College of Biomedical Engineering and Instrument Science, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou, China
| | - Bowen Li
- LipidALL Technologies, Changzhou, China
| | - Quan D Zhou
- Institute of Immunology, Department of Surgical Oncology of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ning Shen
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Hyeon Jeong Lee
- College of Biomedical Engineering and Instrument Science, Key Laboratory for Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou, China
| | - Cunqi Ye
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Da Li
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China.
- NHC Key Laboratory of Advanced Reproductive Medicine and Fertility (China Medical University), National Health Commission, Shenyang, China.
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jin Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- Center of Gene and Cell Therapy and Genome Medicine of Zhejiang Province, Hangzhou, China.
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25
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Ibayashi M, Tsukamoto S. Lipid remodelling in mammalian development. Nat Cell Biol 2024; 26:179-180. [PMID: 38302720 DOI: 10.1038/s41556-023-01327-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Affiliation(s)
- Megumi Ibayashi
- Laboratory Animal and Genome Sciences Section, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Satoshi Tsukamoto
- Laboratory Animal and Genome Sciences Section, National Institutes for Quantum Science and Technology, Chiba, Japan.
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26
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Jackson BT, Finley LWS. Metabolic regulation of the hallmarks of stem cell biology. Cell Stem Cell 2024; 31:161-180. [PMID: 38306993 PMCID: PMC10842269 DOI: 10.1016/j.stem.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Stem cells perform many different functions, each of which requires specific metabolic adaptations. Over the past decades, studies of pluripotent and tissue stem cells have uncovered a range of metabolic preferences and strategies that correlate with or exert control over specific cell states. This review aims to describe the common themes that emerge from the study of stem cell metabolism: (1) metabolic pathways supporting stem cell proliferation, (2) metabolic pathways maintaining stem cell quiescence, (3) metabolic control of cellular stress responses and cell death, (4) metabolic regulation of stem cell identity, and (5) metabolic requirements of the stem cell niche.
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Affiliation(s)
- Benjamin T Jackson
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Lydia W S Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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27
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Szabo E, Nagy B, Czajlik A, Komlodi T, Ozohanics O, Tretter L, Ambrus A. Mitochondrial Alpha-Keto Acid Dehydrogenase Complexes: Recent Developments on Structure and Function in Health and Disease. Subcell Biochem 2024; 104:295-381. [PMID: 38963492 DOI: 10.1007/978-3-031-58843-3_13] [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] [Indexed: 07/05/2024]
Abstract
The present work delves into the enigmatic world of mitochondrial alpha-keto acid dehydrogenase complexes discussing their metabolic significance, enzymatic operation, moonlighting activities, and pathological relevance with links to underlying structural features. This ubiquitous family of related but diverse multienzyme complexes is involved in carbohydrate metabolism (pyruvate dehydrogenase complex), the citric acid cycle (α-ketoglutarate dehydrogenase complex), and amino acid catabolism (branched-chain α-keto acid dehydrogenase complex, α-ketoadipate dehydrogenase complex); the complexes all function at strategic points and also participate in regulation in these metabolic pathways. These systems are among the largest multienzyme complexes with at times more than 100 protein chains and weights ranging up to ~10 million Daltons. Our chapter offers a wealth of up-to-date information on these multienzyme complexes for a comprehensive understanding of their significance in health and disease.
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Affiliation(s)
- Eszter Szabo
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Balint Nagy
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Andras Czajlik
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Timea Komlodi
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Oliver Ozohanics
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Laszlo Tretter
- Department of Biochemistry, Semmelweis University, Budapest, Hungary
| | - Attila Ambrus
- Department of Biochemistry, Semmelweis University, Budapest, Hungary.
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28
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Komatsu M, Takuma H, Imai S, Yamane M, Takahashi M, Ikegawa T, Bai H, Ogawa H, Kawahara M. Dual barrier system against xenomitochondrial contamination in mouse embryos. Sci Rep 2023; 13:23058. [PMID: 38155240 PMCID: PMC10754889 DOI: 10.1038/s41598-023-50444-2] [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: 10/05/2023] [Accepted: 12/20/2023] [Indexed: 12/30/2023] Open
Abstract
Heteroplasmic mammalian embryos between genetically distant species fail to develop to term, preventing transmission of xenomitochondrial DNA to progeny. However, there is no direct evidence indicating the mechanisms by which species specificity of the mitochondrial genome is ensured during mammalian development. Here, we have uncovered a two-step strategy underlying the prevention of xenomitochondrial DNA transmission in mouse embryos harboring bovine mitochondria (mtB-M embryos). First, mtB-M embryos showed metabolic disorder by transient increase of reactive oxygen species at the 4-cell stage, resulting in repressed development. Second, trophoblasts of mtB-M embryos led to implantation failure. Therefore, we tested cell aggregation with tetraploid embryos to compensate for the placentation of mtB-M embryos. The 14 mtB-M embryos harboring bovine mtDNAs developed to term at embryonic day 19.5. Taken together, our results show that contamination of bovine mtDNA is prohibited by embryonic lethality due to metabolic disruption and failure of placentation, suggesting these represent xenomitochondrial elimination mechanisms in mammalian embryos.
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Affiliation(s)
- Masaya Komatsu
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
- Hokkaido Agricultural Research Center, NARO, Sapporo, Hokkaido, 062-8555, Japan
| | - Hikaru Takuma
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Shun Imai
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Maiko Yamane
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Masashi Takahashi
- Graduate School of Global Food Resources/Global Center for Food, Land and Water Resources, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Takuto Ikegawa
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Hanako Bai
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Hidehiko Ogawa
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Manabu Kawahara
- Laboratory of Animal Genetics and Reproduction, Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan.
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29
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Chen A, Jiang Z, Cai L, Tang D. On the road to colorectal cancer development: crosstalk between the gut microbiota, metabolic reprogramming, and epigenetic modifications. Carcinogenesis 2023; 44:631-641. [PMID: 37586059 DOI: 10.1093/carcin/bgad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/21/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023] Open
Abstract
An increasing number of studies have reported the role of gut microbes in colorectal cancer (CRC) development, as they can be influenced by dietary metabolism and mediate alterations in host epigenetics, ultimately affecting CRC. Intake of specific dietary components can affect gut microbial composition and function, and their metabolism regulates important epigenetic functions that may influence CRC risk. Gut microbes can regulate epigenetic modifications through nutrient metabolism, including histone modification, DNA methylation, and noncoding RNAs. Epigenetics, in turn, determines the gut microbial composition and thus influences the risk of developing CRC. This review discusses the complex crosstalk between metabolic reprogramming, gut microbiota, and epigenetics in CRC and highlights the potential applications of the gut microbiota as a biomarker for the prevention, diagnosis, and therapy of CRC.
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Affiliation(s)
- Anqi Chen
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, 225001, China
| | - Zhengting Jiang
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, 225001, China
| | - Lingli Cai
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province, 225001, China
| | - Dong Tang
- Department of General Surgery, Institute of General Surgery, Clinical Medical College, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, 225001, China
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30
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Aizawa E, Ozonov EA, Kawamura YK, Dumeau C, Nagaoka S, Kitajima TS, Saitou M, Peters AHFM, Wutz A. Epigenetic regulation limits competence of pluripotent stem cell-derived oocytes. EMBO J 2023; 42:e113955. [PMID: 37850882 PMCID: PMC10690455 DOI: 10.15252/embj.2023113955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/18/2023] [Accepted: 09/18/2023] [Indexed: 10/19/2023] Open
Abstract
Recent studies have reported the differentiation of pluripotent cells into oocytes in vitro. However, the developmental competence of in vitro-generated oocytes remains low. Here, we perform a comprehensive comparison of mouse germ cell development in vitro over all culture steps versus in vivo with the goal to understand mechanisms underlying poor oocyte quality. We show that the in vitro differentiation of primordial germ cells to growing oocytes and subsequent follicle growth is critical for competence for preimplantation development. Systematic transcriptome analysis of single oocytes that were subjected to different culture steps identifies genes that are normally upregulated during oocyte growth to be susceptible for misregulation during in vitro oogenesis. Many misregulated genes are Polycomb targets. Deregulation of Polycomb repression is therefore a key cause and the earliest defect known in in vitro oocyte differentiation. Conversely, structurally normal in vitro-derived oocytes fail at zygotic genome activation and show abnormal acquisition of 5-hydroxymethylcytosine on maternal chromosomes. Our data identify epigenetic regulation at an early stage of oogenesis limiting developmental competence and suggest opportunities for future improvements.
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Affiliation(s)
- Eishi Aizawa
- Institute of Molecular Health Sciences, Swiss Federal Institute of TechnologyETH ZurichZurichSwitzerland
- RIKEN Center for Biosystems Dynamics ResearchKobeJapan
| | - Evgeniy A Ozonov
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Yumiko K Kawamura
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
| | - Charles‐Etienne Dumeau
- Institute of Molecular Health Sciences, Swiss Federal Institute of TechnologyETH ZurichZurichSwitzerland
| | - So Nagaoka
- Department of EmbryologyNara Medical UniversityNaraJapan
| | | | - Mitinori Saitou
- Institute for the Advanced Study of Human Biology (ASHBi)Kyoto UniversityKyotoJapan
- Department of Anatomy and Cell Biology, Graduate School of MedicineKyoto UniversityKyotoJapan
- Center for iPS Cell Research and Application (CiRA)Kyoto UniversityKyotoJapan
| | - Antoine HFM Peters
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of SciencesUniversity of BaselBaselSwitzerland
| | - Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of TechnologyETH ZurichZurichSwitzerland
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31
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Perera CD, Idrees M, Khan AM, Haider Z, Ullah S, Kang JS, Lee SH, Kang SM, Kong IK. PDGFRβ Activation Induced the Bovine Embryonic Genome Activation via Enhanced NFYA Nuclear Localization. Int J Mol Sci 2023; 24:17047. [PMID: 38069370 PMCID: PMC10707662 DOI: 10.3390/ijms242317047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Embryonic genome activation (EGA) is a critical step during embryonic development. Several transcription factors have been identified that play major roles in initiating EGA; however, this gradual and complex mechanism still needs to be explored. In this study, we investigated the role of nuclear transcription factor Y subunit A (NFYA) in bovine EGA and bovine embryonic development and its relationship with the platelet-derived growth factor receptor-β (PDGFRβ) by using a potent selective activator (PDGF-BB) and inhibitor (CP-673451) of PDGF receptors. Activation and inhibition of PDGFRβ using PDGF-BB and CP-673451 revealed that NFYA expression is significantly (p < 0.05) affected by the PDGFRβ. In addition, PDGFRβ mRNA expression was significantly increased (p < 0.05) in the activator group and significantly decreased (p < 0.05) in the inhibitor group when compared with PDGFRα. Downregulation of NFYA following PDGFRβ inhibition was associated with the expression of critical EGA-related genes, bovine embryo development rate, and implantation potential. Moreover, ROS and mitochondrial apoptosis levels and expression of pluripotency-related markers necessary for inner cell mass development were also significantly (p < 0.05) affected by the downregulation of NFYA while interrupting trophoblast cell (CDX2) differentiation. In conclusion, the PDGFRβ-NFYA axis is critical for bovine embryonic genome activation and embryonic development.
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Affiliation(s)
- Chalani Dilshani Perera
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Muhammad Idrees
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Abdul Majid Khan
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Zaheer Haider
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Safeer Ullah
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Ji-Su Kang
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Seo-Hyun Lee
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Seon-Min Kang
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
| | - Il-Keun Kong
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju 52828, Republic of Korea; (C.D.P.); (M.I.); (A.M.K.); (Z.H.); (S.U.); (J.-S.K.); (S.-H.L.); (S.-M.K.)
- Institute of Agriculture and Life Science (IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
- The King Kong Corp. Ltd., Gyeongsang National University, Jinju 52828, Republic of Korea
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32
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de Lima CB, Martin H, Pecora Milazzotto M, Sirard MA. Genome-wide methylation profile of mitochondrial DNA across bovine preimplantation development. Epigenetics 2023; 18:2241010. [PMID: 37523633 PMCID: PMC10392754 DOI: 10.1080/15592294.2023.2241010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023] Open
Abstract
This study characterized variations in the methylation profile of mitochondrial DNA (mtDNA) during initial bovine embryo development and correlated the presence of methylation with mtDNA transcription. Bovine oocytes were obtained from abattoir ovaries and submitted to in vitro culture procedures. Oocytes and embryos were collected at various stages (immature oocyte, IM; mature oocyte, MII; zygote, ZY; 4-cells, 4C; 16-cells, 16C and blastocysts, BL). Total DNA (including mtDNA) was used for Whole Genome Enzymatic Methyl Sequencing and for quantification of mtDNA copy number. Extracted RNA was used for quantification of mitochondrial transcripts using Droplet Digital PCR. We selected ND6, CYTB, tRNA-Phe and tRNA-Gln based on their location in the mitochondrial genome, functionality and/or previous literature associating these regions with cytosine methylation. The number of mtDNA copies per oocyte/embryo was found to be similar, while methylation levels in mtDNA varied among stages. Higher total methylation levels were found mainly at 4C and 16C. In specific gene regions, higher methylation levels were also observed at 4C and 16C (ND6, CYTB and tRNA-Phe), as well as an inverse correlation with the quantity of transcripts for these regions. This is a first description of epigenetic changes occurring in mtDNA during early embryonic development. Our results indicate that methylation might regulate the mtDNA transcription at a local level, particularly around the time of embryonic genome activation.
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Affiliation(s)
- Camila Bruna de Lima
- Centre de Recherche En Reproduction, Développement Et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Université Laval, Québec, QC, Canada
- Universidade Federal Do ABC, Centro de Ciências Naturais E Humanas, Santo André, SP, Brazil
| | - Hélène Martin
- Centre de Recherche En Reproduction, Développement Et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Université Laval, Québec, QC, Canada
| | - Marcella Pecora Milazzotto
- Centre de Recherche En Reproduction, Développement Et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Université Laval, Québec, QC, Canada
- Universidade Federal Do ABC, Centro de Ciências Naturais E Humanas, Santo André, SP, Brazil
| | - Marc-André Sirard
- Centre de Recherche En Reproduction, Développement Et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Université Laval, Québec, QC, Canada
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33
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MacColl Garfinkel A, Mnatsakanyan N, Patel JH, Wills AE, Shteyman A, Smith PJS, Alavian KN, Jonas EA, Khokha MK. Mitochondrial leak metabolism induces the Spemann-Mangold Organizer via Hif-1α in Xenopus. Dev Cell 2023; 58:2597-2613.e4. [PMID: 37673063 PMCID: PMC10840693 DOI: 10.1016/j.devcel.2023.08.015] [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: 06/23/2022] [Revised: 06/30/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023]
Abstract
An instructive role for metabolism in embryonic patterning is emerging, although a role for mitochondria is poorly defined. We demonstrate that mitochondrial oxidative metabolism establishes the embryonic patterning center, the Spemann-Mangold Organizer, via hypoxia-inducible factor 1α (Hif-1α) in Xenopus. Hypoxia or decoupling ATP production from oxygen consumption expands the Organizer by activating Hif-1α. In addition, oxygen consumption is 20% higher in the Organizer than in the ventral mesoderm, indicating an elevation in mitochondrial respiration. To reconcile increased mitochondrial respiration with activation of Hif-1α, we discovered that the "free" c-subunit ring of the F1Fo ATP synthase creates an inner mitochondrial membrane leak, which decouples ATP production from respiration at the Organizer, driving Hif-1α activation there. Overexpression of either the c-subunit or Hif-1α is sufficient to induce Organizer cell fates even when β-catenin is inhibited. We propose that mitochondrial leak metabolism could be a general mechanism for activating Hif-1α and Wnt signaling.
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Affiliation(s)
- Alexandra MacColl Garfinkel
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT 06510, USA
| | - Nelli Mnatsakanyan
- Department of Cellular and Molecular Physiology, Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Jeet H Patel
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Program in Molecular and Cellular Biology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Andrea E Wills
- Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Amy Shteyman
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT 06510, USA
| | - Peter J S Smith
- Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | | | - Elizabeth Ann Jonas
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT 06510, USA.
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06510, USA.
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34
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Liu WX, Liu HN, Weng ZP, Geng Q, Zhang Y, Li YF, Shen W, Zhou Y, Zhang T. Maternal vitamin B1 is a determinant for the fate of primordial follicle formation in offspring. Nat Commun 2023; 14:7403. [PMID: 37973927 PMCID: PMC10654754 DOI: 10.1038/s41467-023-43261-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
The mediation of maternal-embryonic cross-talk via nutrition and metabolism impacts greatly on offspring health. However, the underlying key interfaces remain elusive. Here, we determined that maternal high-fat diet during pregnancy in mice impaired preservation of the ovarian primordial follicle pool in female offspring, which was concomitant with mitochondrial dysfunction of germ cells. Furthermore, this occurred through a reduction in maternal gut microbiota-related vitamin B1 while the defects were restored via vitamin B1 supplementation. Intriguingly, vitamin B1 promoted acetyl-CoA metabolism in offspring ovaries, contributing to histone acetylation and chromatin accessibility at the promoters of cell cycle-related genes, enhancement of mitochondrial function, and improvement of granulosa cell proliferation. In humans, vitamin B1 is downregulated in the serum of women with gestational diabetes mellitus. In this work, these findings uncover the role of the non-gamete transmission of maternal high-fat diet in influencing offspring oogenic fate. Vitamin B1 could be a promising therapeutic approach for protecting offspring health.
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Affiliation(s)
- Wen-Xiang Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Hai-Ning Liu
- Department of Reproductive Medicine, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, 266011, China
| | - Zhan-Ping Weng
- Department of obstetrical, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao, 266011, China
| | - Qi Geng
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yue Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ya-Feng Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Wei Shen
- College of Life Sciences, Institute of Reproductive Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yang Zhou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Teng Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock (R2BGL), College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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35
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Murnan KM, Horbinski C, Stegh AH. Redox Homeostasis and Beyond: The Role of Wild-Type Isocitrate Dehydrogenases for the Pathogenesis of Glioblastoma. Antioxid Redox Signal 2023; 39:923-941. [PMID: 37132598 PMCID: PMC10654994 DOI: 10.1089/ars.2023.0262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/06/2023] [Indexed: 05/04/2023]
Abstract
Significance: Glioblastoma is an aggressive and devastating brain tumor characterized by a dismal prognosis and resistance to therapeutic intervention. To support catabolic processes critical for unabated cellular growth and defend against harmful reactive oxygen species, glioblastoma tumors upregulate the expression of wild-type isocitrate dehydrogenases (IDHs). IDH enzymes catalyze the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG), NAD(P)H, and CO2. On molecular levels, IDHs epigenetically control gene expression through effects on α-KG-dependent dioxygenases, maintain redox balance, and promote anaplerosis by providing cells with NADPH and precursor substrates for macromolecular synthesis. Recent Advances: While gain-of-function mutations in IDH1 and IDH2 represent one of the most comprehensively studied mechanisms of IDH pathogenic effects, recent studies identified wild-type IDHs as critical regulators of normal organ physiology and, when transcriptionally induced or down regulated, as contributing to glioblastoma progression. Critical Issues: Here, we will discuss molecular mechanisms of how wild-type IDHs control glioma pathogenesis, including the regulation of oxidative stress and de novo lipid biosynthesis, and provide an overview of current and future research directives that aim to fully characterize wild-type IDH-driven metabolic reprogramming and its contribution to the pathogenesis of glioblastoma. Future Directions: Future studies are required to further dissect mechanisms of metabolic and epigenomic reprogramming in tumors and the tumor microenvironment, and to develop pharmacological approaches to inhibit wild-type IDH function. Antioxid. Redox Signal. 39, 923-941.
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Affiliation(s)
- Kevin M. Murnan
- Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, The Robert H. Lurie Comprehensive Cancer Center, Malnati Brain Tumor Institute, Northwestern University, Chicago, Illinois, USA
| | - Craig Horbinski
- Department of Pathology, Feinberg School of Medicine, Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
- Department of Neurological Surgery, Feinberg School of Medicine, Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Alexander H. Stegh
- Department of Neurological Surgery, The Brain Tumor Center, Alvin J. Siteman Comprehensive Cancer Center, Washington University School of Medicine, St. Louis, Missouri, USA
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Zhang J, Chen F, Tian Y, Xu W, Zhu Q, Li Z, Qiu L, Lu X, Peng B, Liu X, Gan H, Liu B, Xu X, Zhu WG. PARylated PDHE1α generates acetyl-CoA for local chromatin acetylation and DNA damage repair. Nat Struct Mol Biol 2023; 30:1719-1734. [PMID: 37735618 DOI: 10.1038/s41594-023-01107-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 08/21/2023] [Indexed: 09/23/2023]
Abstract
Chromatin relaxation is a prerequisite for the DNA repair machinery to access double-strand breaks (DSBs). Local histones around the DSBs then undergo prompt changes in acetylation status, but how the large demands of acetyl-CoA are met is unclear. Here, we report that pyruvate dehydrogenase 1α (PDHE1α) catalyzes pyruvate metabolism to rapidly provide acetyl-CoA in response to DNA damage. We show that PDHE1α is quickly recruited to chromatin in a polyADP-ribosylation-dependent manner, which drives acetyl-CoA generation to support local chromatin acetylation around DSBs. This process increases the formation of relaxed chromatin to facilitate repair-factor loading, genome stability and cancer cell resistance to DNA-damaging treatments in vitro and in vivo. Indeed, we demonstrate that blocking polyADP-ribosylation-based PDHE1α chromatin recruitment attenuates chromatin relaxation and DSB repair efficiency, resulting in genome instability and restored radiosensitivity. These findings support a mechanism in which chromatin-associated PDHE1α locally generates acetyl-CoA to remodel the chromatin environment adjacent to DSBs and promote their repair.
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Affiliation(s)
- Jun Zhang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Feng Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Yuan Tian
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Wenchao Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Qian Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Zhenhai Li
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Lingyu Qiu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Xiaopeng Lu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Bin Peng
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen, China
| | - Xiangyu Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
| | - Haiyun Gan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Baohua Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China
- Shenzhen Key Laboratory for Systemic Aging and Intervention, National Engineering Research Center for Biotechnology (Shenzhen), Shenzhen University Medical School, Shenzhen, China
| | - Xingzhi Xu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen, China
| | - Wei-Guo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen, China.
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37
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Zhao J, Wang W, Zhang L, Zhang J, Sturmey R, Zhang J. Dynamic metabolism during early mammalian embryogenesis. Development 2023; 150:dev202148. [PMID: 37877936 DOI: 10.1242/dev.202148] [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] [Indexed: 10/26/2023]
Abstract
Dynamic metabolism is exhibited by early mammalian embryos to support changing cell fates during development. It is widely acknowledged that metabolic pathways not only satisfy cellular energetic demands, but also play pivotal roles in the process of cell signalling, gene regulation, cell proliferation and differentiation. Recently, various new technological advances have been made in metabolomics and computational analysis, deepening our understanding of the crucial role of dynamic metabolism during early mammalian embryogenesis. In this Review, we summarize recent studies on oocyte and embryo metabolism and its regulation, with a particular focus on its association with key developmental events such as fertilization, zygote genome activation and cell fate determination. In addition, we discuss the mechanisms of certain metabolites that, in addition to serving as energy sources, contribute to epigenetic modifications.
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Affiliation(s)
- Jing Zhao
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Wenjie Wang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
| | - Ling Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Jia Zhang
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
| | - Roger Sturmey
- Biomedical Institute for Multimorbidity, Hull York Medical School, University of Hull, Hull HU6 7RX, UK
| | - Jin Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
- Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University, Hangzhou 310058, China
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Abstract
Metabolic switches are a crucial hallmark of cellular development and regeneration. In response to changes in their environment or physiological state, cells undergo coordinated metabolic switching that is necessary to execute biosynthetic demands of growth and repair. In this Review, we discuss how metabolic switches represent an evolutionarily conserved mechanism that orchestrates tissue development and regeneration, allowing cells to adapt rapidly to changing conditions during development and postnatally. We further explore the dynamic interplay between metabolism and how it is not only an output, but also a driver of cellular functions, such as cell proliferation and maturation. Finally, we underscore the epigenetic and cellular mechanisms by which metabolic switches mediate biosynthetic needs during development and regeneration, and how understanding these mechanisms is important for advancing our knowledge of tissue development and devising new strategies to promote tissue regeneration.
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Affiliation(s)
- Ahmed I. Mahmoud
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
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Russo M, Pileri F, Ghisletti S. Novel insights into the role of acetyl-CoA producing enzymes in epigenetic regulation. Front Endocrinol (Lausanne) 2023; 14:1272646. [PMID: 37842307 PMCID: PMC10570720 DOI: 10.3389/fendo.2023.1272646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023] Open
Abstract
Inflammation-dependent changes in gene expression programs in innate immune cells, such as macrophages, involve extensive reprogramming of metabolism. This reprogramming is essential for the production of metabolites required for chromatin modifications, such as acetyl-CoA, and regulate their usage and availability impacting the macrophage epigenome. One of the most transcriptionally induced proinflammatory mediator is nitric oxide (NO), which has been shown to inhibit key metabolic enzymes involved in the production of these metabolites. Recent evidence indicates that NO inhibits mitochondrial enzymes such as pyruvate dehydrogenase (PDH) in macrophages induced by inflammatory stimulus. PDH is involved in the production of acetyl-CoA, which is essential for chromatin modifications in the nucleus, such as histone acetylation. In addition, acetyl-CoA levels in inflamed macrophages are regulated by ATP citrate lyase (ACLY) and citrate transporter SLC25A1. Interestingly, acetyl-CoA producing enzymes, such as PDH and ACLY, have also been reported to be present in the nucleus and to support the local generation of cofactors such as acetyl-CoA. Here, we will discuss the mechanisms involved in the regulation of acetyl-CoA production by metabolic enzymes, their inhibition by prolonged exposure to inflammation stimuli, their involvement in dynamic inflammatory expression changes and how these emerging findings could have significant implications for the design of novel therapeutic approaches.
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Affiliation(s)
| | | | - Serena Ghisletti
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Milan, Italy
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Huang Z, Wang Q, Khan IA, Li Y, Wang J, Wang J, Liu X, Lin F, Lu J. The Methylcitrate Cycle and Its Crosstalk with the Glyoxylate Cycle and Tricarboxylic Acid Cycle in Pathogenic Fungi. Molecules 2023; 28:6667. [PMID: 37764443 PMCID: PMC10534831 DOI: 10.3390/molecules28186667] [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: 08/01/2023] [Revised: 09/06/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
In fungi, the methylcitrate cycle converts cytotoxic propionyl-coenzyme A (CoA) to pyruvate, which enters gluconeogenesis. The glyoxylate cycle converts acetyl-CoA to succinate, which enters gluconeogenesis. The tricarboxylic acid cycle is a central carbon metabolic pathway that connects the methylcitrate cycle, the glyoxylate cycle, and other metabolisms for lipids, carbohydrates, and amino acids. Fungal citrate synthase and 2-methylcitrate synthase as well as isocitrate lyase and 2-methylisocitrate lyase, each evolved from a common ancestral protein. Impairment of the methylcitrate cycle leads to the accumulation of toxic intermediates such as propionyl-CoA, 2-methylcitrate, and 2-methylisocitrate in fungal cells, which in turn inhibits the activity of many enzymes such as dehydrogenases and remodels cellular carbon metabolic processes. The methylcitrate cycle and the glyoxylate cycle synergistically regulate carbon source utilization as well as fungal growth, development, and pathogenic process in pathogenic fungi.
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Affiliation(s)
- Zhicheng Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (Z.H.); (Q.W.); (Y.L.)
| | - Qing Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (Z.H.); (Q.W.); (Y.L.)
| | - Irshad Ali Khan
- Department of Agriculture, The University of Swabi, Khyber 29380, Pakistan;
| | - Yan Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (Z.H.); (Q.W.); (Y.L.)
| | - Jing Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.W.); (J.W.); (F.L.)
| | - Jiaoyu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.W.); (J.W.); (F.L.)
| | - Xiaohong Liu
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Fucheng Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (J.W.); (J.W.); (F.L.)
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Jianping Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (Z.H.); (Q.W.); (Y.L.)
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41
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Cho UH, Hetzer MW. Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. eLife 2023; 12:RP89066. [PMID: 37665327 PMCID: PMC10476967 DOI: 10.7554/elife.89066] [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: 09/05/2023] Open
Abstract
During apoptosis, caspases degrade 8 out of ~30 nucleoporins to irreversibly demolish the nuclear pore complex. However, for poorly understood reasons, caspases are also activated during cell differentiation. Here, we show that sublethal activation of caspases during myogenesis results in the transient proteolysis of four peripheral Nups and one transmembrane Nup. 'Trimmed' NPCs become nuclear export-defective, and we identified in an unbiased manner several classes of cytoplasmic, plasma membrane, and mitochondrial proteins that rapidly accumulate in the nucleus. NPC trimming by non-apoptotic caspases was also observed in neurogenesis and endoplasmic reticulum stress. Our results suggest that caspases can reversibly modulate nuclear transport activity, which allows them to function as agents of cell differentiation and adaptation at sublethal levels.
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Affiliation(s)
- Ukrae H Cho
- Molecular and Cell Biology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, Salk Institute for Biological StudiesLa JollaUnited States
- Institute of Science and Technology Austria (IST Austria)KlosterneuburgAustria
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42
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Sun H, Zhang Z, Li T, Li T, Chen W, Pan T, Fang S, Liu C, Zhang Y, Wang L, Feng G, Li W, Zhou Q, Zhao Y. Live-cell imaging reveals redox metabolic reprogramming during zygotic genome activation. J Cell Physiol 2023; 238:2039-2049. [PMID: 37334430 DOI: 10.1002/jcp.31054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/13/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023]
Abstract
Metabolic programming is deeply intertwined with early embryonic development including zygotic genome activation (ZGA), the polarization of zygotic cells, and cell fate commitment. It is crucial to establish a noninvasive imaging technology that spatiotemporally illuminates the cellular metabolism pathways in embryos to track developmental metabolism in situ. In this study, we used two high-quality genetically encoded fluorescent biosensors, SoNar for NADH/NAD+ and iNap1 for NADPH, to characterize the dynamic regulation of energy metabolism and redox homeostasis during early zygotic cleavage. Our imaging results showed that NADH/NAD+ levels decreased from the early to the late two-cell stage, whereas the levels of the reducing equivalent NADPH increased. Mechanistically, transcriptome profiling suggested that during the two-cell stage, zygotic cells downregulated the expression of genes involved in glucose uptake and glycolysis, and upregulated the expression of genes for pyruvate metabolism in mitochondria and oxidative phosphorylation, with a decline in the expression of two peroxiredoxin genes, Prdx1 and Prdx2. Collectively, with the establishment of in situ metabolic monitoring technology, our study revealed the programming of redox metabolism during ZGA.
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Affiliation(s)
- Hao Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Zhuo Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Research Unit of New Techniques for Live-Cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China
| | - Tianda Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Ting Li
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Research Unit of New Techniques for Live-Cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China
| | - Weicai Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Research Unit of New Techniques for Live-Cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China
| | - Tianshi Pan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Sen Fang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Leyun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Yuzheng Zhao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science and Technology, Shanghai, China
- Research Unit of New Techniques for Live-Cell Metabolic Imaging, Chinese Academy of Medical Sciences, Beijing, China
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Zhang KY, Guo J, Zhan CL, Yuan CS, Min CG, Li ZQ, Liu HY, Wang J, Zhao J, Lu WF, Ma X. β-hydroxybutyrate impairs bovine oocyte maturation via pyruvate dehydrogenase (PDH) associated energy metabolism abnormality. Front Pharmacol 2023; 14:1243243. [PMID: 37637420 PMCID: PMC10450765 DOI: 10.3389/fphar.2023.1243243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
Background: Ketosis is one of the most frequent and costly metabolic disorders in high-producing dairy cows, and negatively associated with the health and reproductive performance of bovine. Ketosis is mainly caused by the accumulation of ketone body β-hydroxybutyric acid and its diagnosis is based on β-hydroxybutyrate (βHB) concentration in blood. Methods: In this study, we investigated the effects of βHB on bovine oocyte maturation in the concentration of subclinical (1.2 mM) βHB and clinical (3.6 mM). Results: The results showed βHB disrupted bovine oocyte maturation and development capacity. Further analysis showed that βHB induced oxidative stress and mitochondrial dysfunction, as indicated by the increased level of reactive oxygen species (ROS), disrupted mitochondrial structure and distribution, and depolarized membrane potential. Furthermore, oxidative stress triggered early apoptosis, as shown by the enhanced levels of Caspase-3 and Annexin-V. Moreover, 3.6 mM βHB induced the disruption of the pyruvate dehydrogenase (PDH) activity, showing with the decrease of the global acetylation modification and the increase of the abnormal spindle rate. Conclusion: Our study showed that βHB in subclinical/clinical concentration had toxic effects on mitochondrial function and PDH activity, which might affect energy metabolism and epigenetic modification of bovine oocytes and embryos.
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Affiliation(s)
- Kai-Yan Zhang
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Jing Guo
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Cheng-Lin Zhan
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Chong-Shan Yuan
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Chang-Guo Min
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Zhi-Qiang Li
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Hong-Yu Liu
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Jun Wang
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Jing Zhao
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Wen-Fa Lu
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Xin Ma
- Key Laboratory of the Animal Production, Product Quality and Security, Ministry of Education, Jilin Agricultural University, Changchun, Jilin, China
- Jilin Provincial International Joint Research Center of Animal Breeding and Reproduction Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
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Menezes AP, Murillo AM, de Castro CG, Bellini NK, Tosi LRO, Thiemann OH, Elias MC, Silber AM, da Cunha JPC. Navigating the boundaries between metabolism and epigenetics in trypanosomes. Trends Parasitol 2023; 39:682-695. [PMID: 37349193 DOI: 10.1016/j.pt.2023.05.010] [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: 02/15/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023]
Abstract
Epigenetic marks enable cells to acquire new biological features that favor their adaptation to environmental changes. These marks are chemical modifications on chromatin-associated proteins and nucleic acids that lead to changes in the chromatin landscape and may eventually affect gene expression. The chemical tags of these epigenetic marks are comprised of intermediate cellular metabolites. The number of discovered associations between metabolism and epigenetics has increased, revealing how environment influences gene regulation and phenotype diversity. This connection is relevant to all organisms but underappreciated in digenetic parasites, which must adapt to different environments as they progress through their life cycles. This review speculates and proposes associations between epigenetics and metabolism in trypanosomes, which are protozoan parasites that cause human and livestock diseases.
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Affiliation(s)
- Ana Paula Menezes
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Ana Milena Murillo
- Laboratório de Bioquímica de Tryps - LabTryps, Departamento de Parasitologia, Universidade de São Paulo, São Paulo-SP, Brazil
| | - Camila Gachet de Castro
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Natalia Karla Bellini
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | | | | | - Maria Carolina Elias
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Ariel Mariano Silber
- Laboratório de Bioquímica de Tryps - LabTryps, Departamento de Parasitologia, Universidade de São Paulo, São Paulo-SP, Brazil.
| | - Julia Pinheiro Chagas da Cunha
- Laboratório de Ciclo Celular - Instituto Butantan, São Paulo-SP, Brazil; Centro de Toxinas, Resposta Imune e Sinalização Celular (CeTICS), Instituto Butantan, São Paulo, Brazil.
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Wu J, Liang C, Wang X, Huang Y, Liu W, Wang R, Cao J, Su X, Yin T, Wang X, Zhang Z, Shen L, Li D, Zou W, Wu J, Qiu L, Di W, Cao Y, Ji D, Qian K. Efficient Metabolic Fingerprinting of Follicular Fluid Encodes Ovarian Reserve and Fertility. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2302023. [PMID: 37311196 PMCID: PMC10427401 DOI: 10.1002/advs.202302023] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/30/2023] [Indexed: 06/15/2023]
Abstract
Ovarian reserve (OR) and fertility are critical in women's healthcare. Clinical methods for encoding OR and fertility rely on the combination of tests, which cannot serve as a multi-functional platform with limited information from specific biofluids. Herein, metabolic fingerprinting of follicular fluid (MFFF) from follicles is performed, using particle-assisted laser desorption/ionization mass spectrometry (PALDI-MS) to encode OR and fertility. PALDI-MS allows efficient MFFF, showing fast speed (≈30 s), high sensitivity (≈60 fmol), and desirable reproducibility (coefficients of variation <15%). Further, machine learning of MFFF is applied to diagnose diminished OR (area under the curve of 0.929) and identify high-quality oocytes/embryos (p < 0.05) by a single PALDI-MS test. Meanwhile, metabolic biomarkers from MFFF are identified, which also determine oocyte/embryo quality (p < 0.05) from the sampling follicles toward fertility prediction in clinics. This approach offers a powerful platform in women's healthcare, not limited to OR and fertility.
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Srivastava S, Gajwani P, Jousma J, Miyamoto H, Kwon Y, Jana A, Toth PT, Yan G, Ong SG, Rehman J. Nuclear translocation of mitochondrial dehydrogenases as an adaptive cardioprotective mechanism. Nat Commun 2023; 14:4360. [PMID: 37468519 DOI: 10.1038/s41467-023-40084-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 07/12/2023] [Indexed: 07/21/2023] Open
Abstract
Chemotherapy-induced cardiac damage remains a leading cause of death amongst cancer survivors. Anthracycline-induced cardiotoxicity is mediated by severe mitochondrial injury, but little is known about the mechanisms by which cardiomyocytes adaptively respond to the injury. We observed the translocation of selected mitochondrial tricarboxylic acid (TCA) cycle dehydrogenases to the nucleus as an adaptive stress response to anthracycline-cardiotoxicity in human induced pluripotent stem cell-derived cardiomyocytes and in vivo. The expression of nuclear-targeted mitochondrial dehydrogenases shifts the nuclear metabolic milieu to maintain their function both in vitro and in vivo. This protective effect is mediated by two parallel pathways: metabolite-induced chromatin accessibility and AMP-kinase (AMPK) signaling. The extent of chemotherapy-induced cardiac damage thus reflects a balance between mitochondrial injury and the protective response initiated by the nuclear pool of mitochondrial dehydrogenases. Our study identifies nuclear translocation of mitochondrial dehydrogenases as an endogenous adaptive mechanism that can be leveraged to attenuate cardiomyocyte injury.
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Affiliation(s)
- Shubhi Srivastava
- Department of Biochemistry and Molecular Genetics, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Priyanka Gajwani
- Department of Biochemistry and Molecular Genetics, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Jordan Jousma
- Department of Pharmacology and Regenerative Medicine, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Hiroe Miyamoto
- Department of Pharmacology and Regenerative Medicine, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Youjeong Kwon
- Department of Pharmacology and Regenerative Medicine, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Arundhati Jana
- Division of Cardiology, Department of Medicine, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Peter T Toth
- Department of Pharmacology and Regenerative Medicine, The University of Illinois College of Medicine, Chicago, IL, USA
- Research Resources Center, University of Illinois, Chicago, IL, USA
| | - Gege Yan
- Department of Pharmacology and Regenerative Medicine, The University of Illinois College of Medicine, Chicago, IL, USA
- Division of Cardiology, Department of Medicine, The University of Illinois College of Medicine, Chicago, IL, USA
| | - Sang-Ging Ong
- Department of Pharmacology and Regenerative Medicine, The University of Illinois College of Medicine, Chicago, IL, USA.
- Division of Cardiology, Department of Medicine, The University of Illinois College of Medicine, Chicago, IL, USA.
| | - Jalees Rehman
- Department of Biochemistry and Molecular Genetics, The University of Illinois College of Medicine, Chicago, IL, USA.
- Department of Pharmacology and Regenerative Medicine, The University of Illinois College of Medicine, Chicago, IL, USA.
- Division of Cardiology, Department of Medicine, The University of Illinois College of Medicine, Chicago, IL, USA.
- University of Illinois Cancer Center, Chicago, IL, USA.
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Huang F, Luo X, Ou Y, Gao Z, Tang Q, Chu Z, Zhu X, He Y. Control of histone demethylation by nuclear-localized α-ketoglutarate dehydrogenase. Science 2023; 381:eadf8822. [PMID: 37440635 DOI: 10.1126/science.adf8822] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/19/2023] [Indexed: 07/15/2023]
Abstract
Methylations on nucleosomal histones play fundamental roles in regulating eukaryotic transcription. Jumonji C domain-containing histone demethylases (JMJs) dynamically control the level of histone methylations. However, how JMJ activity is generally regulated is unknown. We found that the tricarboxylic acid cycle-associated enzyme α-ketoglutarate (α-KG) dehydrogenase (KGDH) entered the nucleus, where it interacted with various JMJs to regulate α-KG-dependent histone demethylations by JMJs, and thus controlled genome-wide gene expression in plants. We show that nuclear targeting is regulated by environmental signals and that KGDH is enriched at thousands of loci in Arabidopsis thaliana. Chromatin-bound KGDH catalyzes α-KG decarboxylation and thus may limit its local availability to KGDH-coupled JMJs, inhibiting histone demethylation. Thus, our results uncover a regulatory mechanism for histone demethylations by JMJs.
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Affiliation(s)
- Fei Huang
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
| | - Xiao Luo
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
| | - Yang Ou
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
| | - Zhaoxu Gao
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qiming Tang
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai, 200032, China
| | - Zhenzhen Chu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
| | - Xinguang Zhu
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai, 200032, China
| | - Yuehui He
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
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Elías-López AL, Vázquez-Mena O, Sferruzzi-Perri AN. Mitochondrial dysfunction in the offspring of obese mothers and it's transmission through damaged oocyte mitochondria: Integration of mechanisms. Biochim Biophys Acta Mol Basis Dis 2023:166802. [PMID: 37414229 DOI: 10.1016/j.bbadis.2023.166802] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/23/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
In vivo and in vitro studies demonstrate that mitochondria in the oocyte, are susceptible to damage by suboptimal pre/pregnancy conditions, such as obesity. These suboptimal conditions have been shown to induce mitochondrial dysfunction (MD) in multiple tissues of the offspring, suggesting that mitochondria of oocytes that pass from mother to offspring, can carry information that can programme mitochondrial and metabolic dysfunction of the next generation. They also suggest that transmission of MD could increase the risk of obesity and other metabolic diseases in the population inter- and trans-generationally. In this review, we examined whether MD observed in offspring tissues of high energetic demand, is the result of the transmission of damaged mitochondria from obese mothers' oocytes to the offspring. The contribution of genome-independent mechanisms (namely mitophagy) in this transmission were also explored. Finally, potential interventions aimed at improving oocyte/embryo health were investigated, to see if they may provide an opportunity to halter the generational effects of MD.
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Affiliation(s)
- A L Elías-López
- Dirección de Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico.
| | | | - A N Sferruzzi-Perri
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, UK.
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Gu Y, Xu J, Sun F, Cheng J. Elevated intracellular pH of zygotes during mouse aging causes mitochondrial dysfunction associated with poor embryo development. Mol Cell Endocrinol 2023:111991. [PMID: 37336488 DOI: 10.1016/j.mce.2023.111991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023]
Abstract
The mortality of preimplantation embryos is positively correlated with maternal age. However, the underlying mechanism for the poor quality of embryos remains unclear. Here, we found that aging caused elevated intracellular pH (pHi) in zygotes, which could trigger aberrant mitochondrial membrane potential, increased reactive oxygen species (ROS) levels, and poor embryo development. Moreover, single-cell transcriptome sequencing of mouse zygotes identified 120 genes that were significantly differentially expressed (DE) between young and older zygotes. These include genes such as Slc14a1, Fxyd5, CD74, and Bst, which are related to cell division, ion transporter, and cell differentiation. Further analysis indicated that these DE genes were enriched in apoptosis, the NF-kappa B signaling pathway, and the chemokine signaling pathway, which might be the key regulatory pathway affecting the quality of zygotes and subsequent embryo development. Taken together, our study helps elucidate the poor quality and development of older preimplantation embryos.
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Affiliation(s)
- Yimin Gu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Junjie Xu
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China; Department of Obstetrics and Gynecology, The Second Hospital of Shanxi Medical University, 7, Taiyuan, 030001, China
| | - Fei Sun
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China.
| | - Jinmei Cheng
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China.
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Solomou G, Finch A, Asghar A, Bardella C. Mutant IDH in Gliomas: Role in Cancer and Treatment Options. Cancers (Basel) 2023; 15:cancers15112883. [PMID: 37296846 DOI: 10.3390/cancers15112883] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
Altered metabolism is a common feature of many cancers and, in some cases, is a consequence of mutation in metabolic genes, such as the ones involved in the TCA cycle. Isocitrate dehydrogenase (IDH) is mutated in many gliomas and other cancers. Physiologically, IDH converts isocitrate to α-ketoglutarate (α-KG), but when mutated, IDH reduces α-KG to D2-hydroxyglutarate (D2-HG). D2-HG accumulates at elevated levels in IDH mutant tumours, and in the last decade, a massive effort has been made to develop small inhibitors targeting mutant IDH. In this review, we summarise the current knowledge about the cellular and molecular consequences of IDH mutations and the therapeutic approaches developed to target IDH mutant tumours, focusing on gliomas.
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Affiliation(s)
- Georgios Solomou
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Division of Academic Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
- Wellcome MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Alina Finch
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Asim Asghar
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Chiara Bardella
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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