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Gonzalez-Avalos E, Onodera A, Samaniego-Castruita D, Rao A, Ay F. Predicting gene expression state and prioritizing putative enhancers using 5hmC signal. Genome Biol 2024; 25:142. [PMID: 38825692 PMCID: PMC11145787 DOI: 10.1186/s13059-024-03273-z] [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: 04/03/2023] [Accepted: 05/11/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Like its parent base 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) is a direct epigenetic modification of cytosines in the context of CpG dinucleotides. 5hmC is the most abundant oxidized form of 5mC, generated through the action of TET dioxygenases at gene bodies of actively-transcribed genes and at active or lineage-specific enhancers. Although such enrichments are reported for 5hmC, to date, predictive models of gene expression state or putative regulatory regions for genes using 5hmC have not been developed. RESULTS Here, by using only 5hmC enrichment in genic regions and their vicinity, we develop neural network models that predict gene expression state across 49 cell types. We show that our deep neural network models distinguish high vs low expression state utilizing only 5hmC levels and these predictive models generalize to unseen cell types. Further, in order to leverage 5hmC signal in distal enhancers for expression prediction, we employ an Activity-by-Contact model and also develop a graph convolutional neural network model with both utilizing Hi-C data and 5hmC enrichment to prioritize enhancer-promoter links. These approaches identify known and novel putative enhancers for key genes in multiple immune cell subsets. CONCLUSIONS Our work highlights the importance of 5hmC in gene regulation through proximal and distal mechanisms and provides a framework to link it to genome function. With the recent advances in 6-letter DNA sequencing by short and long-read techniques, profiling of 5mC and 5hmC may be done routinely in the near future, hence, providing a broad range of applications for the methods developed here.
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Affiliation(s)
- Edahi Gonzalez-Avalos
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Atsushi Onodera
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Daniela Samaniego-Castruita
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA
| | - Anjana Rao
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA.
- Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Ferhat Ay
- La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, 92093, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA.
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2
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Liu X, Tang J, Wang Z, Zhu C, Deng H, Sun X, Yu G, Rong F, Chen X, Liao Q, Jia S, Liu W, Zha H, Fan S, Cai X, Gui JF, Xiao W. Oxygen enhances antiviral innate immunity through maintenance of EGLN1-catalyzed proline hydroxylation of IRF3. Nat Commun 2024; 15:3533. [PMID: 38670937 PMCID: PMC11053110 DOI: 10.1038/s41467-024-47814-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Oxygen is essential for aerobic organisms, but little is known about its role in antiviral immunity. Here, we report that during responses to viral infection, hypoxic conditions repress antiviral-responsive genes independently of HIF signaling. EGLN1 is identified as a key mediator of the oxygen enhancement of antiviral innate immune responses. Under sufficient oxygen conditions, EGLN1 retains its prolyl hydroxylase activity to catalyze the hydroxylation of IRF3 at proline 10. This modification enhances IRF3 phosphorylation, dimerization and nuclear translocation, leading to subsequent IRF3 activation. Furthermore, mice and zebrafish with Egln1 deletion, treatment with the EGLN inhibitor FG4592, or mice carrying an Irf3 P10A mutation are more susceptible to viral infections. These findings not only reveal a direct link between oxygen and antiviral responses, but also provide insight into the mechanisms by which oxygen regulates innate immunity.
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Affiliation(s)
- Xing Liu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- Hubei Hongshan Laboratory, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Jinhua Tang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing, P. R. China
| | - Zixuan Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Chunchun Zhu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Hongyan Deng
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Xueyi Sun
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Guangqing Yu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Fangjing Rong
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Xiaoyun Chen
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Qian Liao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Shuke Jia
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Wen Liu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Huangyuan Zha
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Sijia Fan
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Xiaolian Cai
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Jian-Fang Gui
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- Hubei Hongshan Laboratory, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Wuhan Xiao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China.
- Hubei Hongshan Laboratory, Wuhan, P. R. China.
- University of Chinese Academy of Sciences, Beijing, P. R. China.
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, P. R. China.
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Haidar L, Georgescu M, Drăghici GA, Bănățean-Dunea I, Nica DV, Șerb AF. DNA Methylation Machinery in Gastropod Mollusks. Life (Basel) 2024; 14:537. [PMID: 38672807 PMCID: PMC11050768 DOI: 10.3390/life14040537] [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: 03/11/2024] [Revised: 04/17/2024] [Accepted: 04/20/2024] [Indexed: 04/28/2024] Open
Abstract
The role of DNA methylation in mollusks is just beginning to be understood. This review synthesizes current knowledge on this potent molecular hallmark of epigenetic control in gastropods-the largest class of mollusks and ubiquitous inhabitants of diverse habitats. Their DNA methylation machinery shows a high degree of conservation in CG maintenance methylation mechanisms, driven mainly by DNMT1 homologues, and the presence of MBD2 and MBD2/3 proteins as DNA methylation readers. The mosaic-like DNA methylation landscape occurs mainly in a CG context and is primarily confined to gene bodies and housekeeping genes. DNA methylation emerges as a critical regulator of reproduction, development, and adaptation, with tissue-specific patterns being observed in gonadal structures. Its dynamics also serve as an important regulatory mechanism underlying learning and memory processes. DNA methylation can be affected by various environmental stimuli, including as pathogens and abiotic stresses, potentially impacting phenotypic variation and population diversity. Overall, the features of DNA methylation in gastropods are complex, being an essential part of their epigenome. However, comprehensive studies integrating developmental stages, tissues, and environmental conditions, functional annotation of methylated regions, and integrated genomic-epigenomic analyses are lacking. Addressing these knowledge gaps will advance our understanding of gastropod biology, ecology, and evolution.
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Affiliation(s)
- Laura Haidar
- Department of Functional Sciences, Physiology Discipline, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania;
- Center of Immuno-Physiology and Biotechnologies (CIFBIOTEH), “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
| | - Marius Georgescu
- Department of Functional Sciences, Physiology Discipline, Faculty of Medicine, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania;
- Center of Immuno-Physiology and Biotechnologies (CIFBIOTEH), “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timişoara, Romania
| | - George Andrei Drăghici
- Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania;
- Research Center for Pharmaco-Toxicological Evaluations, Faculty of Pharmacy, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania
| | - Ioan Bănățean-Dunea
- Biology and Plant Protection Department, Faculty of Agriculture, University of Life Sciences “King Mihai I” from Timișoara, Calea Aradului 119, 300645 Timișoara, Romania;
| | - Dragoș Vasile Nica
- The National Institute of Research—Development for Machines and Installations Designed for Agriculture and Food Industry (INMA), Bulevardul Ion Ionescu de la Brad 6, 077190 București, Romania
| | - Alina-Florina Șerb
- Department of Biochemistry and Pharmacology, Biochemistry Discipline, “Victor Babeș” University of Medicine and Pharmacy Timișoara, Eftimie Murgu Square No. 2, 300041 Timișoara, Romania;
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4
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Liu B, Xie D, Huang X, Jin S, Dai Y, Sun X, Li D, Bennett AM, Diano S, Huang Y. Skeletal muscle TET3 promotes insulin resistance through destabilisation of PGC-1α. Diabetologia 2024; 67:724-737. [PMID: 38216792 PMCID: PMC10904493 DOI: 10.1007/s00125-023-06073-5] [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: 08/29/2023] [Accepted: 11/17/2023] [Indexed: 01/14/2024]
Abstract
AIM/HYPOTHESIS The peroxisome proliferator-activated receptor-γ coactivator α (PGC-1α) plays a critical role in the maintenance of glucose, lipid and energy homeostasis by orchestrating metabolic programs in multiple tissues in response to environmental cues. In skeletal muscles, PGC-1α dysregulation has been associated with insulin resistance and type 2 diabetes but the underlying mechanisms have remained elusive. This research aims to understand the role of TET3, a member of the ten-eleven translocation (TET) family dioxygenases, in PGC-1α dysregulation in skeletal muscles in obesity and diabetes. METHODS TET expression levels in skeletal muscles were analysed in humans with or without type 2 diabetes, as well as in mouse models of high-fat diet (HFD)-induced or genetically induced (ob/ob) obesity/diabetes. Muscle-specific Tet3 knockout (mKD) mice were generated to study TET3's role in muscle insulin sensitivity. Genome-wide expression profiling (RNA-seq) of muscle tissues from wild-type (WT) and mKD mice was performed to mine deeper insights into TET3-mediated regulation of muscle insulin sensitivity. The correlation between PGC-1α and TET3 expression levels was investigated using muscle tissues and in vitro-derived myotubes. PGC-1α phosphorylation and degradation were analysed using in vitro assays. RESULTS TET3 expression was elevated in skeletal muscles of humans with type 2 diabetes and in HFD-fed and ob/ob mice compared with healthy controls. mKD mice exhibited enhanced glucose tolerance, insulin sensitivity and resilience to HFD-induced insulin resistance. Pathway analysis of RNA-seq identified 'Mitochondrial Function' and 'PPARα Pathway' to be among the top biological processes regulated by TET3. We observed higher PGC-1α levels (~25%) in muscles of mKD mice vs WT mice, and lower PGC-1α protein levels (~25-60%) in HFD-fed or ob/ob mice compared with their control counterparts. In human and murine myotubes, increased PGC-1α levels following TET3 knockdown contributed to improved mitochondrial respiration and insulin sensitivity. TET3 formed a complex with PGC-1α and interfered with its phosphorylation, leading to its destabilisation. CONCLUSIONS/INTERPRETATION Our results demonstrate an essential role for TET3 in the regulation of skeletal muscle insulin sensitivity and suggest that TET3 may be used as a potential therapeutic target for the metabolic syndrome. DATA AVAILABILITY Sequences are available from the Gene Expression Omnibus ( https://www.ncbi.nlm.nih.gov/geo/ ) with accession number of GSE224042.
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Affiliation(s)
- Beibei Liu
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
- Center of Reproductive Medicine, National Health Commission Key Laboratory of Advanced Reproductive Medicine and Fertility, Shengjing Hospital of China Medical University, Shenyang, China
| | - Di Xie
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
- Department of Reproductive Medicine, General Hospital of Central Theater Command, Wuhan, Hubei, China
| | - Xinmei Huang
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
- Department of Endocrinology, Fifth People's Hospital of Shanghai, Fudan University School of Medicine, Shanghai, China
| | - Sungho Jin
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY, USA
| | - Yangyang Dai
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoli Sun
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
- Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Jiangsu, China
| | - Da Li
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
- Center of Reproductive Medicine, National Health Commission Key Laboratory of Advanced Reproductive Medicine and Fertility, Shengjing Hospital of China Medical University, Shenyang, China
| | - Anton M Bennett
- Departments of Pharmacology and of Comparative Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, USA
| | - Sabrina Diano
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY, USA
| | - Yingqun Huang
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA.
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT, USA.
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5
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Zhang XJ, Han BB, Shao ZY, Yan R, Gao J, Liu T, Jin ZY, Lai W, Xu ZM, Wang CH, Zhang F, Gu C, Wang Y, Wang H, Walsh CP, Guo F, Xu GL, Du YR. Auto-suppression of Tet dioxygenases protects the mouse oocyte genome from oxidative demethylation. Nat Struct Mol Biol 2024; 31:42-53. [PMID: 38177668 DOI: 10.1038/s41594-023-01125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/14/2023] [Indexed: 01/06/2024]
Abstract
DNA cytosine methylation plays a vital role in repressing retrotransposons, and such derepression is linked with developmental failure, tumorigenesis and aging. DNA methylation patterns are formed by precisely regulated actions of DNA methylation writers (DNA methyltransferases) and erasers (TET, ten-eleven translocation dioxygenases). However, the mechanisms underlying target-specific oxidation of 5mC by TET dioxygenases remain largely unexplored. Here we show that a large low-complexity domain (LCD), located in the catalytic part of Tet enzymes, negatively regulates the dioxygenase activity. Recombinant Tet3 lacking LCD is shown to be hyperactive in converting 5mC into oxidized species in vitro. Endogenous expression of the hyperactive Tet3 mutant in mouse oocytes results in genome-wide 5mC oxidation. Notably, the occurrence of aberrant 5mC oxidation correlates with a consequent loss of the repressive histone mark H3K9me3 at ERVK retrotransposons. The erosion of both 5mC and H3K9me3 causes ERVK derepression along with upregulation of their neighboring genes, potentially leading to the impairment of oocyte development. These findings suggest that Tet dioxygenases use an intrinsic auto-regulatory mechanism to tightly regulate their enzymatic activity, thus achieving spatiotemporal specificity of methylome reprogramming, and highlight the importance of methylome integrity for development.
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Affiliation(s)
- Xiao-Jie Zhang
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bin-Bin Han
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhen-Yu Shao
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rui Yan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Juan Gao
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ting Liu
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Zi-Yang Jin
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhi-Mei Xu
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chao-Han Wang
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fengjuan Zhang
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chan Gu
- Changping Laboratory, Beijing, China
| | - Yin Wang
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Chinese Academy of Medical Sciences (RU069) and Zhongshan-Xuhui Hospital, Medical College of Fudan University, Shanghai, China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Colum P Walsh
- Genomic Medicine Research Group, Biomedical Sciences, Ulster University, Coleraine, UK
- Department of Cell Biology, Institute for Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Fan Guo
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Guo-Liang Xu
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Chinese Academy of Medical Sciences (RU069) and Zhongshan-Xuhui Hospital, Medical College of Fudan University, Shanghai, China.
| | - Ya-Rui Du
- CAS Key Laboratory of Epigenetic Regulation and Intervention, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
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6
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Boulet M, Gilbert G, Renaud Y, Schmidt-Dengler M, Plantié E, Bertrand R, Nan X, Jurkowski T, Helm M, Vandel L, Waltzer L. Adenine methylation is very scarce in the Drosophila genome and not erased by the ten-eleven translocation dioxygenase. eLife 2023; 12:RP91655. [PMID: 38126351 PMCID: PMC10735219 DOI: 10.7554/elife.91655] [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: 12/23/2023] Open
Abstract
N6-methyladenine (6mA) DNA modification has recently been described in metazoans, including in Drosophila, for which the erasure of this epigenetic mark has been ascribed to the ten-eleven translocation (TET) enzyme. Here, we re-evaluated 6mA presence and TET impact on the Drosophila genome. Using axenic or conventional breeding conditions, we found traces of 6mA by LC-MS/MS and no significant increase in 6mA levels in the absence of TET, suggesting that this modification is present at very low levels in the Drosophila genome but not regulated by TET. Consistent with this latter hypothesis, further molecular and genetic analyses showed that TET does not demethylate 6mA but acts essentially in an enzymatic-independent manner. Our results call for further caution concerning the role and regulation of 6mA DNA modification in metazoans and underline the importance of TET non-enzymatic activity for fly development.
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Affiliation(s)
- Manon Boulet
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
| | - Guerric Gilbert
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
| | - Yoan Renaud
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
| | - Martina Schmidt-Dengler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-UniversitätMainzGermany
| | - Emilie Plantié
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
| | - Romane Bertrand
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
| | - Xinsheng Nan
- School of Biosciences, Cardiff UniversityCardiffUnited Kingdom
| | | | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-UniversitätMainzGermany
| | - Laurence Vandel
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
| | - Lucas Waltzer
- Université Clermont Auvergne, CNRS, INSERM, iGReDClermont-FerrandFrance
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7
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Kim H, Jung I, Lee CH, An J, Ko M. Development of Novel Epigenetic Anti-Cancer Therapy Targeting TET Proteins. Int J Mol Sci 2023; 24:16375. [PMID: 38003566 PMCID: PMC10671484 DOI: 10.3390/ijms242216375] [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: 10/18/2023] [Revised: 11/12/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Epigenetic dysregulation, particularly alterations in DNA methylation and hydroxymethylation, plays a pivotal role in cancer initiation and progression. Ten-eleven translocation (TET) proteins catalyze the successive oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidized methylcytosines in DNA, thereby serving as central modulators of DNA methylation-demethylation dynamics. TET loss of function is causally related to neoplastic transformation across various cell types while its genetic or pharmacological activation exhibits anti-cancer effects, making TET proteins promising targets for epigenetic cancer therapy. Here, we developed a robust cell-based screening system to identify novel TET activators and evaluated their potential as anti-cancer agents. Using a carefully curated library of 4533 compounds provided by the National Cancer Institute, Bethesda, MD, USA, we identified mitoxantrone as a potent TET agonist. Through rigorous validation employing various assays, including immunohistochemistry and dot blot studies, we demonstrated that mitoxantrone significantly elevated 5hmC levels. Notably, this elevation manifested only in wild-type (WT) but not TET-deficient mouse embryonic fibroblasts, primary bone marrow-derived macrophages, and leukemia cell lines. Furthermore, mitoxantrone-induced cell death in leukemia cell lines occurred in a TET-dependent manner, indicating the critical role of TET proteins in mediating its anti-cancer effects. Our findings highlight mitoxantrone's potential to induce tumor cell death via a novel mechanism involving the restoration of TET activity, paving the way for targeted epigenetic therapies in cancer treatment.
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Affiliation(s)
- Hyejin Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; (H.K.); (I.J.)
| | - Inkyung Jung
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; (H.K.); (I.J.)
| | - Chan Hyeong Lee
- Department of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Jungeun An
- Department of Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea;
| | - Myunggon Ko
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea; (H.K.); (I.J.)
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
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8
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Zhang X, Zhang Y, Wang C, Wang X. TET (Ten-eleven translocation) family proteins: structure, biological functions and applications. Signal Transduct Target Ther 2023; 8:297. [PMID: 37563110 PMCID: PMC10415333 DOI: 10.1038/s41392-023-01537-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 08/12/2023] Open
Abstract
Ten-eleven translocation (TET) family proteins (TETs), specifically, TET1, TET2 and TET3, can modify DNA by oxidizing 5-methylcytosine (5mC) iteratively to yield 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC), and then two of these intermediates (5fC and 5caC) can be excised and return to unmethylated cytosines by thymine-DNA glycosylase (TDG)-mediated base excision repair. Because DNA methylation and demethylation play an important role in numerous biological processes, including zygote formation, embryogenesis, spatial learning and immune homeostasis, the regulation of TETs functions is complicated, and dysregulation of their functions is implicated in many diseases such as myeloid malignancies. In addition, recent studies have demonstrated that TET2 is able to catalyze the hydroxymethylation of RNA to perform post-transcriptional regulation. Notably, catalytic-independent functions of TETs in certain biological contexts have been identified, further highlighting their multifunctional roles. Interestingly, by reactivating the expression of selected target genes, accumulated evidences support the potential therapeutic use of TETs-based DNA methylation editing tools in disorders associated with epigenetic silencing. In this review, we summarize recent key findings in TETs functions, activity regulators at various levels, technological advances in the detection of 5hmC, the main TETs oxidative product, and TETs emerging applications in epigenetic editing. Furthermore, we discuss existing challenges and future directions in this field.
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Affiliation(s)
- Xinchao Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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9
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Sergeeva A, Davydova K, Perenkov A, Vedunova M. Mechanisms of human DNA methylation, alteration of methylation patterns in physiological processes and oncology. Gene 2023:147487. [PMID: 37211289 DOI: 10.1016/j.gene.2023.147487] [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: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
DNA methylation is one of the epigenetic modifications of the genome, the essence of which is the attachment of a methyl group to nitrogenous bases. In the eukaryote genome, cytosine is methylated in the vast majority of cases. About 98% of cytosines are methylated as part of CpG dinucleotides. They, in turn, form CpG islands, which are clusters of these dinucleotides. Islands located in the regulatory elements of genes are in particular interest. They are assumed to play an important role in the regulation of gene expression in humans. Besides that, cytosine methylation serves the functions of genomic imprinting, transposon suppression, epigenetic memory maintenance, X- chromosome inactivation, and embryonic development. Of particular interest are the enzymatic processes of methylation and demethylation. The methylation process always depends on the work of enzymatic complexes and is very precisely regulated. The methylation process largely depends on the functioning of three groups of enzymes: writers, readers and erasers. Writers include proteins of the DNMT family, readers are proteins containing the MBD, BTB/POZ or SET- and RING-associated domains and erasers are proteins of the TET family. Whereas demethylation can be performed not only by enzymatic complexes, but also passively during DNA replication. Hence, the maintenance of DNA methylation is important. Changes in methylation patterns are observed during embryonic development, aging, and cancers. In both aging and cancer, massive hypomethylation of the genome with local hypermethylation is observed. In this review, we will review the current understanding of the mechanisms of DNA methylation and demethylation in humans, the structure and distribution of CpG islands, the role of methylation in the regulation of gene expression, embryogenesis, aging, and cancer development.
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Affiliation(s)
- A Sergeeva
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - K Davydova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - A Perenkov
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - M Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
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10
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Enkhmandakh B, Joshi P, Robson P, Vijaykumar A, Mina M, Shin DG, Bayarsaihan D. Single-cell Transcriptome Landscape of DNA Methylome Regulators Associated with Orofacial Clefts in the Mouse Dental Pulp. Cleft Palate Craniofac J 2023:10556656231172296. [PMID: 37161276 DOI: 10.1177/10556656231172296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
OBJECTIVE Significant evidence links epigenetic processes governing the dynamics of DNA methylation and demethylation to an increased risk of syndromic and nonsyndromic cleft lip and/or cleft palate (CL/P). Previously, we characterized mesenchymal stem/stromal cells (MSCs) at different stages of osteogenic differentiation in the mouse incisor dental pulp. The main objective of this research was to characterize the transcriptional landscape of regulatory genes associated with DNA methylation and demethylation at a single-cell resolution. DESIGN We used single-cell RNA sequencing (scRNA-seq) data to characterize transcriptome in individual subpopulations of MSCs in the mouse incisor dental pulp. SETTINGS The biomedical research institution. PATIENTS/PARTICIPANTS This study did not include patients. INTERVENTIONS This study collected and analyzed data on the single-cell RNA expssion in the mouse incisor dental pulp. MAIN OUTCOME MEASURE(S) Molecular regulators of DNA methylation/demethylation exhibit differential transcriptional landscape in different subpopulations of osteogenic progenitor cells. RESULTS scRNA-seq analysis revealed that genes encoding DNA methylation and demethylation enzymes (DNA methyltransferases and members of the ten-eleven translocation family of methylcytosine dioxygenases), methyl-DNA binding domain proteins, as well as transcription factors and chromatin remodeling proteins that cooperate with DNA methylation machinery are differentially expressed within distinct subpopulations of MSCs that undergo different stages of osteogenic differentiation. CONCLUSIONS These findings suggest some mechanistic insights into a potential link between epigenetic alterations and multifactorial causes of CL/P phenotypes.
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Affiliation(s)
- Badam Enkhmandakh
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Pujan Joshi
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Single Cell Biology Laboratory, Farmington, CT, USA
| | - Anushree Vijaykumar
- Department of Craniofacial Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Mina Mina
- Department of Craniofacial Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Dong-Guk Shin
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, USA
| | - Dashzeveg Bayarsaihan
- Center for Regenerative Medicine and Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, Farmington, CT, USA
- Institute for System Genomics, University of Connecticut, Storrs, CT, USA
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11
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Wang Z, Quan Y, Hu M, Xu Y, Chen Y, Jin P, Ma J, Chen X, Fan J, Fan X, Gong Y, Li M, Wang Y. VGLL4-TEAD1 promotes vascular smooth muscle cell differentiation from human pluripotent stem cells via TET2. J Mol Cell Cardiol 2023; 176:21-32. [PMID: 36657637 DOI: 10.1016/j.yjmcc.2023.01.005] [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: 10/16/2022] [Revised: 12/21/2022] [Accepted: 01/13/2023] [Indexed: 01/18/2023]
Abstract
The Hippo signaling pathway plays a critical role in cardiovascular development and stem cell differentiation. Using microarray profiling, we found that the Hippo pathway components vestigial-like family member 4 (VGLL4) and TEA domain transcription factor 1 (TEAD1) were upregulated during vascular smooth muscle cell (VSMC) differentiation from H1 ESCs (H1 embryonic stem cells). To further explore the role and molecular mechanisms of VGLL4 in regulating VSMC differentiation, we generated a VGLL4-knockdown H1 ESC line (heterozygous knockout) using the CRISPR/Cas9 system and found that VGLL4 knockdown inhibited VSMC specification. In contrast, overexpression of VGLL4 using the PiggyBac transposon system facilitated VSMC differentiation. We confirmed that this effect was mediated via TEAD1 and VGLL4 interaction. In addition, bioinformatics analysis revealed that Ten-eleven-translocation 2 (TET2), a DNA dioxygenase, is a target of TEAD1, and a luciferase assay further verified that TET2 is the target of the VGLL4-TEAD1 complex. Indeed, TET2 overexpression promoted VSMC marker gene expression and countered the VGLL4 knockdown-mediated inhibitory effects on VSMC differentiation. In summary, we revealed a novel role of VGLL4 in promoting VSMC differentiation from hESCs and identified TET2 as a new target of the VGLL4-TEAD1 complex, which may demethylate VSMC marker genes and facilitate VSMC differentiation. This study provides new insights into the VGLL4-TEAD1-TET2 axis in VSMC differentiation and vascular development.
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Affiliation(s)
- Zuxuan Wang
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China
| | - Yingyi Quan
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China
| | - Minjie Hu
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China
| | - Yubin Xu
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China
| | - Yuhao Chen
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China
| | - Peifeng Jin
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325015, Zhejiang, China
| | - Jianshe Ma
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China
| | - Xiufang Chen
- Cardiac Regeneration Research Institute, School of Basic Medical Science, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China
| | - Junming Fan
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China
| | - Xiaofang Fan
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China
| | - Yongsheng Gong
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China
| | - Ming Li
- Cardiac Regeneration Research Institute, School of Basic Medical Science, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China
| | - Yongyu Wang
- Institute of Hypoxia Medicine, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China; Cardiac Regeneration Research Institute, School of Basic Medical Science, Wenzhou Medical University, Wenzhou 325015, Zhejiang, China.
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12
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Epigenetic Modification of Cytosines in Hematopoietic Differentiation and Malignant Transformation. Int J Mol Sci 2023; 24:ijms24021727. [PMID: 36675240 PMCID: PMC9863985 DOI: 10.3390/ijms24021727] [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: 12/24/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The mammalian DNA methylation landscape is established and maintained by the combined activities of the two key epigenetic modifiers, DNA methyltransferases (DNMT) and Ten-eleven-translocation (TET) enzymes. Once DNMTs produce 5-methylcytosine (5mC), TET proteins fine-tune the DNA methylation status by consecutively oxidizing 5mC to 5-hydroxymethylcytosine (5hmC) and further oxidized derivatives. The 5mC and oxidized methylcytosines are essential for the maintenance of cellular identity and function during differentiation. Cytosine modifications with DNMT and TET enzymes exert pleiotropic effects on various aspects of hematopoiesis, including self-renewal of hematopoietic stem/progenitor cells (HSPCs), lineage determination, differentiation, and function. Under pathological conditions, these enzymes are frequently dysregulated, leading to loss of function. In particular, the loss of DNMT3A and TET2 function is conspicuous in diverse hematological disorders, including myeloid and lymphoid malignancies, and causally related to clonal hematopoiesis and malignant transformation. Here, we update recent advances in understanding how the maintenance of DNA methylation homeostasis by DNMT and TET proteins influences normal hematopoiesis and malignant transformation, highlighting the potential impact of DNMT3A and TET2 dysregulation on clonal dominance and evolution of pre-leukemic stem cells to full-blown malignancies. Clarification of the normal and pathological functions of DNA-modifying epigenetic regulators will be crucial to future innovations in epigenetic therapies for treating hematological disorders.
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13
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Chen GD, Fatima I, Xu Q, Rozhkova E, Fessing MY, Mardaryev AN, Sharov AA, Xu GL, Botchkarev VA. DNA dioxygenases Tet2/3 regulate gene promoter accessibility and chromatin topology in lineage-specific loci to control epithelial differentiation. SCIENCE ADVANCES 2023; 9:eabo7605. [PMID: 36630508 PMCID: PMC9833667 DOI: 10.1126/sciadv.abo7605] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 12/05/2022] [Indexed: 05/03/2023]
Abstract
Execution of lineage-specific differentiation programs requires tight coordination between many regulators including Ten-eleven translocation (TET) family enzymes, catalyzing 5-methylcytosine oxidation in DNA. Here, by using Keratin 14-Cre-driven ablation of Tet genes in skin epithelial cells, we demonstrate that ablation of Tet2/Tet3 results in marked alterations of hair shape and length followed by hair loss. We show that, through DNA demethylation, Tet2/Tet3 control chromatin accessibility and Dlx3 binding and promoter activity of the Krt25 and Krt28 genes regulating hair shape, as well as regulate interactions between the Krt28 gene promoter and distal enhancer. Moreover, Tet2/Tet3 also control three-dimensional chromatin topology in Keratin type I/II gene loci via DNA methylation-independent mechanisms. These data demonstrate the essential roles for Tet2/3 in establishment of lineage-specific gene expression program and control of Dlx3/Krt25/Krt28 axis in hair follicle epithelial cells and implicate modulation of DNA methylation as a novel approach for hair growth control.
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Affiliation(s)
- Guo-Dong Chen
- Department of Dermatology, Boston University, Boston, MA, USA
| | - Iqra Fatima
- Department of Dermatology, Boston University, Boston, MA, USA
| | - Qin Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Elena Rozhkova
- Department of Dermatology, Boston University, Boston, MA, USA
| | - Michael Y. Fessing
- Centre for Skin Sciences, School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | - Andrei N. Mardaryev
- Centre for Skin Sciences, School of Chemistry and Biosciences, University of Bradford, Bradford, UK
| | | | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
- Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Medical College of Fudan University, Shanghai, China
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14
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Wu F, Li X, Looso M, Liu H, Ding D, Günther S, Kuenne C, Liu S, Weissmann N, Boettger T, Atzberger A, Kolahian S, Renz H, Offermanns S, Gärtner U, Potente M, Zhou Y, Yuan X, Braun T. Spurious transcription causing innate immune responses is prevented by 5-hydroxymethylcytosine. Nat Genet 2023; 55:100-111. [PMID: 36539616 PMCID: PMC9839451 DOI: 10.1038/s41588-022-01252-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 10/26/2022] [Indexed: 12/24/2022]
Abstract
Generation of functional transcripts requires transcriptional initiation at regular start sites, avoiding production of aberrant and potentially hazardous aberrant RNAs. The mechanisms maintaining transcriptional fidelity and the impact of spurious transcripts on cellular physiology and organ function have not been fully elucidated. Here we show that TET3, which successively oxidizes 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) and other derivatives, prevents aberrant intragenic entry of RNA polymerase II pSer5 into highly expressed genes of airway smooth muscle cells, assuring faithful transcriptional initiation at canonical start sites. Loss of TET3-dependent 5hmC production in SMCs results in accumulation of spurious transcripts, which stimulate the endosomal nucleic-acid-sensing TLR7/8 signaling pathway, thereby provoking massive inflammation and airway remodeling resembling human bronchial asthma. Furthermore, we found that 5hmC levels are substantially lower in human asthma airways compared with control samples. Suppression of spurious transcription might be important to prevent chronic inflammation in asthma.
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Affiliation(s)
- Fan Wu
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Xiang Li
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Mario Looso
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Hang Liu
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Dong Ding
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Günther
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Shuya Liu
- grid.418032.c0000 0004 0491 220XDepartment of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany ,grid.13648.380000 0001 2180 3484Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Norbert Weissmann
- grid.440517.3Cardiopulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany ,grid.8664.c0000 0001 2165 8627Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Thomas Boettger
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ann Atzberger
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Saeed Kolahian
- grid.10253.350000 0004 1936 9756Philipps University of Marburg - Medical Faculty, Center for Tumor- and Immunobiology (ZTI), Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Marburg, Germany
| | - Harald Renz
- grid.10253.350000 0004 1936 9756Philipps University of Marburg - Medical Faculty, Center for Tumor- and Immunobiology (ZTI), Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Marburg, Germany
| | - Stefan Offermanns
- grid.418032.c0000 0004 0491 220XDepartment of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ulrich Gärtner
- Institute for Anatomy und Cell Biology, Giessen, Germany
| | - Michael Potente
- grid.418032.c0000 0004 0491 220XAngiogenesis and Metabolism Laboratory, Max-Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Yonggang Zhou
- grid.418032.c0000 0004 0491 220XDepartment of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Xuejun Yuan
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany. .,Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany.
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15
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Wang D, Wu W, Callen E, Pavani R, Zolnerowich N, Kodali S, Zong D, Wong N, Noriega S, Nathan WJ, Matos-Rodrigues G, Chari R, Kruhlak MJ, Livak F, Ward M, Caldecott K, Di Stefano B, Nussenzweig A. Active DNA demethylation promotes cell fate specification and the DNA damage response. Science 2022; 378:983-989. [PMID: 36454826 PMCID: PMC10196940 DOI: 10.1126/science.add9838] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Neurons harbor high levels of single-strand DNA breaks (SSBs) that are targeted to neuronal enhancers, but the source of this endogenous damage remains unclear. Using two systems of postmitotic lineage specification-induced pluripotent stem cell-derived neurons and transdifferentiated macrophages-we show that thymidine DNA glycosylase (TDG)-driven excision of methylcytosines oxidized with ten-eleven translocation enzymes (TET) is a source of SSBs. Although macrophage differentiation favors short-patch base excision repair to fill in single-nucleotide gaps, neurons also frequently use the long-patch subpathway. Disrupting this gap-filling process using anti-neoplastic cytosine analogs triggers a DNA damage response and neuronal cell death, which is dependent on TDG. Thus, TET-mediated active DNA demethylation promotes endogenous DNA damage, a process that normally safeguards cell identity but can also provoke neurotoxicity after anticancer treatments.
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Affiliation(s)
- Dongpeng Wang
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Nicholas Zolnerowich
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Srikanth Kodali
- Stem Cells and Regenerative Medicine, Center for Cell and Gene Therapy, Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Nancy Wong
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Santiago Noriega
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - William J. Nathan
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | | | - Raj Chari
- Genome Modification Core, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael J. Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Ferenc Livak
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
| | - Michael Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Keith Caldecott
- Genome Damage and Stability Centre, University of Sussex, Falmer Brighton, UK
| | - Bruno Di Stefano
- Stem Cells and Regenerative Medicine, Center for Cell and Gene Therapy, Department of Molecular and Cellular Biology and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, MD, USA
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16
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Ren Y. Regulatory mechanism and biological function of UHRF1–DNMT1-mediated DNA methylation. Funct Integr Genomics 2022; 22:1113-1126. [DOI: 10.1007/s10142-022-00918-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
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17
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Xie D, Stutz B, Li F, Chen F, Lv H, Sestan-Pesa M, Catarino J, Gu J, Zhao H, Stoddard CE, Carmichael GG, Shanabrough M, Taylor HS, Liu ZW, Gao XB, Horvath TL, Huang Y. TET3 epigenetically controls feeding and stress response behaviors via AGRP neurons. J Clin Invest 2022; 132:162365. [PMID: 36189793 PMCID: PMC9525119 DOI: 10.1172/jci162365] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
The TET family of dioxygenases promote DNA demethylation by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine (5hmC). Hypothalamic agouti-related peptide-expressing (AGRP-expressing) neurons play an essential role in driving feeding, while also modulating nonfeeding behaviors. Besides AGRP, these neurons produce neuropeptide Y (NPY) and the neurotransmitter GABA, which act in concert to stimulate food intake and decrease energy expenditure. Notably, AGRP, NPY, and GABA can also elicit anxiolytic effects. Here, we report that in adult mouse AGRP neurons, CRISPR-mediated genetic ablation of Tet3, not previously known to be involved in central control of appetite and metabolism, induced hyperphagia, obesity, and diabetes, in addition to a reduction of stress-like behaviors. TET3 deficiency activated AGRP neurons, simultaneously upregulated the expression of Agrp, Npy, and the vesicular GABA transporter Slc32a1, and impeded leptin signaling. In particular, we uncovered a dynamic association of TET3 with the Agrp promoter in response to leptin signaling, which induced 5hmC modification that was associated with a chromatin-modifying complex leading to transcription inhibition, and this regulation occurred in both the mouse models and human cells. Our results unmasked TET3 as a critical central regulator of appetite and energy metabolism and revealed its unexpected dual role in the control of feeding and other complex behaviors through AGRP neurons.
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Affiliation(s)
- Di Xie
- Department of Obstetrics, Gynecology and Reproductive Sciences.,Yale Center for Molecular and Systems Metabolism, and
| | - Bernardo Stutz
- Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Feng Li
- Department of Obstetrics, Gynecology and Reproductive Sciences.,Yale Center for Molecular and Systems Metabolism, and
| | - Fan Chen
- Department of Obstetrics, Gynecology and Reproductive Sciences
| | - Haining Lv
- Department of Obstetrics, Gynecology and Reproductive Sciences.,Yale Center for Molecular and Systems Metabolism, and
| | - Matija Sestan-Pesa
- Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jonatas Catarino
- Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jianlei Gu
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Christopher E Stoddard
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Gordon G Carmichael
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Marya Shanabrough
- Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hugh S Taylor
- Department of Obstetrics, Gynecology and Reproductive Sciences
| | - Zhong-Wu Liu
- Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Xiao-Bing Gao
- Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tamas L Horvath
- Department of Obstetrics, Gynecology and Reproductive Sciences.,Yale Center for Molecular and Systems Metabolism, and.,Department of Comparative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Neuroscience, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yingqun Huang
- Department of Obstetrics, Gynecology and Reproductive Sciences.,Yale Center for Molecular and Systems Metabolism, and
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18
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Chen HY, Almonte-Loya A, Lay FY, Hsu M, Johnson E, González-Avalos E, Yin J, Bruno RS, Ma Q, Ghoneim HE, Wozniak DJ, Harrison FE, Lio CWJ. Epigenetic remodeling by vitamin C potentiates plasma cell differentiation. eLife 2022; 11:73754. [PMID: 36069787 PMCID: PMC9451539 DOI: 10.7554/elife.73754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Ascorbate (vitamin C) is an essential micronutrient in humans. The severe chronic deficiency of ascorbate, termed scurvy, has long been associated with increased susceptibility to infections. How ascorbate affects the immune system at the cellular and molecular levels remained unclear. From a micronutrient analysis, we identified ascorbate as a potent enhancer for antibody response by facilitating the IL-21/STAT3-dependent plasma cell differentiation in mouse and human B cells. The effect of ascorbate is unique as other antioxidants failed to promote plasma cell differentiation. Ascorbate is especially critical during early B cell activation by poising the cells to plasma cell lineage without affecting the proximal IL-21/STAT3 signaling and the overall transcriptome. As a cofactor for epigenetic enzymes, ascorbate facilitates TET2/3-mediated DNA modification and demethylation of multiple elements at the Prdm1 locus. DNA demethylation augments STAT3 association at the Prdm1 promoter and a downstream enhancer, thus ensuring efficient gene expression and plasma cell differentiation. The results suggest that an adequate level of ascorbate is required for antibody response and highlight how micronutrients may regulate the activity of epigenetic enzymes to regulate gene expression. Our findings imply that epigenetic enzymes can function as sensors to gauge the availability of metabolites and influence cell fate decisions.
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Affiliation(s)
- Heng-Yi Chen
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Ana Almonte-Loya
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States.,Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States
| | - Fang-Yun Lay
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Michael Hsu
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Eric Johnson
- Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States
| | - Edahí González-Avalos
- Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States
| | - Jieyun Yin
- Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States
| | - Richard S Bruno
- Human Nutrition Program, The Ohio State University, Columbus, OH, United States
| | - Qin Ma
- Biomedical Informatics, The Ohio State University, Columbus, OH, United States.,Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States.,Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Daniel J Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Fiona E Harrison
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Chan-Wang Jerry Lio
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States.,Division of Gene Expression and Signaling, La Jolla Institute for Immunology, San Diego, CA, United States.,Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, OH, United States
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19
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Germline Abnormalities in DNA Methylation and Histone Modification and Associated Cancer Risk. Curr Hematol Malig Rep 2022; 17:82-93. [PMID: 35653077 DOI: 10.1007/s11899-022-00665-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW Somatic mutations in DNA methyltransferases and other DNA methylation associated genes have been found in a wide variety of cancers. Germline mutations in these genes have been associated with several rare hereditary disorders. Among the described germline/congenital disorders, neurological dysfunction and/or growth abnormalities appear to be a common phenotype. Here, we outline known germline abnormalities and examine the cancer risks associated with these mutations. RECENT FINDINGS The increased use and availability of sequencing techniques in the clinical setting has expanded the identification of germline abnormalities involving DNA methylation machinery. This has provided additional cases to study these rare hereditary disorders and their predisposition to cancer. Studying these syndromes may offer an opportunity to better understand the contribution of these genes in cancer development.
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20
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Morgan RC, Kee BL. Genomic and Transcriptional Mechanisms Governing Innate-like T Lymphocyte Development. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:208-216. [PMID: 35821098 DOI: 10.4049/jimmunol.2200141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/18/2022] [Indexed: 12/16/2022]
Abstract
Innate-like lymphocytes are a subset of lymphoid cells that function as a first line of defense against microbial infection. These cells are activated by proinflammatory cytokines or broadly expressed receptors and are able to rapidly perform their effector functions owing to a uniquely primed chromatin state that is acquired as a part of their developmental program. These cells function in many organs to protect against disease, but they release cytokines and cytotoxic mediators that can also lead to severe tissue pathologies. Therefore, harnessing the capabilities of these cells for therapeutic interventions will require a deep understanding of how these cells develop and regulate their effector functions. In this review we discuss recent advances in the identification of the transcription factors and the genomic regions that guide the development and function of invariant NKT cells and we highlight related mechanisms in other innate-like lymphocytes.
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Affiliation(s)
- Roxroy C Morgan
- Committee on Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL; and
| | - Barbara L Kee
- Cancer Biology and Immunology, Department of Pathology, University of Chicago, Chicago, IL
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21
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Gerecke C, Egea Rodrigues C, Homann T, Kleuser B. The Role of Ten-Eleven Translocation Proteins in Inflammation. Front Immunol 2022; 13:861351. [PMID: 35386689 PMCID: PMC8977485 DOI: 10.3389/fimmu.2022.861351] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/28/2022] [Indexed: 12/11/2022] Open
Abstract
Ten-eleven translocation proteins (TET1-3) are dioxygenases that oxidize 5-methyldeoxycytosine, thus taking part in passive and active demethylation. TETs have shown to be involved in immune cell development, affecting from self-renewal of stem cells and lineage commitment to terminal differentiation. In fact, dysfunction of TET proteins have been vastly associated with both myeloid and lymphoid leukemias. Recently, there has been accumulating evidence suggesting that TETs regulate immune cell function during innate and adaptive immune responses, thereby modulating inflammation. In this work, we pursue to review the current and recent evidence on the mechanistic aspects by which TETs regulate immune cell maturation and function. We will also discuss the complex interplay of TET expression and activity by several factors to modulate a multitude of inflammatory processes. Thus, modulating TET enzymes could be a novel pharmacological approach to target inflammation-related diseases and myeloid and lymphoid leukemias, when their activity is dysregulated.
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Affiliation(s)
- Christian Gerecke
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Caue Egea Rodrigues
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Thomas Homann
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Burkhard Kleuser
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
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22
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Xie D, Chen F, Zhang Y, Shi B, Song J, Chaudhari K, Yang SH, Zhang GJ, Sun X, Taylor HS, Li D, Huang Y. Let-7 underlies metformin-induced inhibition of hepatic glucose production. Proc Natl Acad Sci U S A 2022; 119:e2122217119. [PMID: 35344434 PMCID: PMC9169108 DOI: 10.1073/pnas.2122217119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/26/2022] [Indexed: 12/16/2022] Open
Abstract
SignificanceA clear mechanistic understanding of metformin's antidiabetic effects is lacking. This is because suprapharmacological concentrations of metformin have been used in most studies. Using mouse models and human primary hepatocytes, we show that metformin, at clinically relevant doses, suppresses hepatic glucose production by activating a conserved regulatory pathway encompassing let-7, TET3, and a fetal isoform of hepatocyte nuclear factor 4 alpha (HNF4α). We demonstrate that metformin no longer has potent antidiabetic actions in a liver-specific let-7 loss-of-function mouse model and that hepatic delivery of let-7 ameliorates hyperglycemia and improves glucose homeostasis. Our results thus reveal an important role of the hepatic let-7/TET3/HNF4α axis in mediating the therapeutic effects of metformin and suggest that targeting this axis may be a potential therapeutic for diabetes.
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Affiliation(s)
- Di Xie
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT 06520
| | - Fan Chen
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510
| | - Yuanyuan Zhang
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510
| | - Bei Shi
- Medical Basic Experimental Teaching Center, China Medical University, Shenyang 110004, China
| | - Jiahui Song
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Kiran Chaudhari
- Department of Pharmacology and Neuroscience, Institute for Healthy Aging, University of North Texas Health Science Center, Fort Worth, TX 76107
| | - Shao-Hua Yang
- Department of Pharmacology and Neuroscience, Institute for Healthy Aging, University of North Texas Health Science Center, Fort Worth, TX 76107
| | - Gary J. Zhang
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510
| | - Xiaoli Sun
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510
| | - Hugh S. Taylor
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510
| | - Da Li
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yingqun Huang
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510
- Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT 06520
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23
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Gabed N, Verret F, Peticca A, Kryvoruchko I, Gastineau R, Bosson O, Séveno J, Davidovich O, Davidovich N, Witkowski A, Kristoffersen JB, Benali A, Ioannou E, Koutsaviti A, Roussis V, Gâteau H, Phimmaha S, Leignel V, Badawi M, Khiar F, Francezon N, Fodil M, Pasetto P, Mouget JL. What Was Old Is New Again: The Pennate Diatom Haslea ostrearia (Gaillon) Simonsen in the Multi-Omic Age. Mar Drugs 2022; 20:md20040234. [PMID: 35447907 PMCID: PMC9033121 DOI: 10.3390/md20040234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
The marine pennate diatom Haslea ostrearia has long been known for its characteristic blue pigment marennine, which is responsible for the greening of invertebrate gills, a natural phenomenon of great importance for the oyster industry. For two centuries, this taxon was considered unique; however, the recent description of a new blue Haslea species revealed unsuspected biodiversity. Marennine-like pigments are natural blue dyes that display various biological activities—e.g., antibacterial, antioxidant and antiproliferative—with a great potential for applications in the food, feed, cosmetic and health industries. Regarding fundamental prospects, researchers use model organisms as standards to study cellular and physiological processes in other organisms, and there is a growing and crucial need for more, new and unconventional model organisms to better correspond to the diversity of the tree of life. The present work, thus, advocates for establishing H. ostrearia as a new model organism by presenting its pros and cons—i.e., the interesting aspects of this peculiar diatom (representative of benthic-epiphytic phytoplankton, with original behavior and chemodiversity, controlled sexual reproduction, fundamental and applied-oriented importance, reference genome, and transcriptome will soon be available); it will also present the difficulties encountered before this becomes a reality as it is for other diatom models (the genetics of the species in its infancy, the transformation feasibility to be explored, the routine methods needed to cryopreserve strains of interest).
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Affiliation(s)
- Noujoud Gabed
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Gournes Pediados, 71003 Heraklion, Greece; (N.G.); (J.B.K.); (A.B.)
- Oran High School of Biological Sciences (ESSBO), Cellular and Molecular Biology Department, Oran 31000, Algeria
- Laboratoire d’Aquaculture et Bioremediation AquaBior, Université d’Oran 1, Oran 31000, Algeria
| | - Frédéric Verret
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Gournes Pediados, 71003 Heraklion, Greece; (N.G.); (J.B.K.); (A.B.)
- Correspondence: ; Tel.: +30-2810-337-852
| | - Aurélie Peticca
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Igor Kryvoruchko
- Department of Biology, United Arab Emirates University (UAEU), Al Ain P.O. Box 15551, United Arab Emirates;
| | - Romain Gastineau
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16, 70-383 Szczecin, Poland; (R.G.); (N.D.); (A.W.)
| | - Orlane Bosson
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Julie Séveno
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Olga Davidovich
- Karadag Scientific Station, Natural Reserve of the Russian Academy of Sciences, Kurortnoe, 98188 Feodosiya, Russia;
| | - Nikolai Davidovich
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16, 70-383 Szczecin, Poland; (R.G.); (N.D.); (A.W.)
- Karadag Scientific Station, Natural Reserve of the Russian Academy of Sciences, Kurortnoe, 98188 Feodosiya, Russia;
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16, 70-383 Szczecin, Poland; (R.G.); (N.D.); (A.W.)
| | - Jon Bent Kristoffersen
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Gournes Pediados, 71003 Heraklion, Greece; (N.G.); (J.B.K.); (A.B.)
| | - Amel Benali
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research (HCMR), Gournes Pediados, 71003 Heraklion, Greece; (N.G.); (J.B.K.); (A.B.)
- Laboratoire d’Aquaculture et Bioremediation AquaBior, Université d’Oran 1, Oran 31000, Algeria
- Laboratoire de Génétique Moléculaire et Cellulaire, Université des Sciences et de la Technologie d’Oran Mohamed BOUDIAF-USTO-MB, BP 1505, El M’naouer, Oran 31000, Algeria
| | - Efstathia Ioannou
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (E.I.); (A.K.); (V.R.)
| | - Aikaterini Koutsaviti
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (E.I.); (A.K.); (V.R.)
| | - Vassilios Roussis
- Section of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece; (E.I.); (A.K.); (V.R.)
| | - Hélène Gâteau
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Suliya Phimmaha
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Vincent Leignel
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Myriam Badawi
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Feriel Khiar
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Nellie Francezon
- Institut des Molécules et Matériaux du Mans, UMR CNRS 6283, Le Mans Université, Avenue Olivier Messiaen, 2085 Le Mans, France; (N.F.); (P.P.)
| | - Mostefa Fodil
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
| | - Pamela Pasetto
- Institut des Molécules et Matériaux du Mans, UMR CNRS 6283, Le Mans Université, Avenue Olivier Messiaen, 2085 Le Mans, France; (N.F.); (P.P.)
| | - Jean-Luc Mouget
- Laboratoire Biologie des Organismes, Stress, Santé, Environnement (BiOSSE), Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, France; (A.P.); (O.B.); (J.S.); (H.G.); (S.P.); (V.L.); (M.B.); (F.K.); (M.F.); (J.-L.M.)
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24
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Gardiner J, Ghoshal B, Wang M, Jacobsen SE. CRISPR-Cas-mediated transcriptional control and epi-mutagenesis. PLANT PHYSIOLOGY 2022; 188:1811-1824. [PMID: 35134247 PMCID: PMC8968285 DOI: 10.1093/plphys/kiac033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/13/2022] [Indexed: 05/24/2023]
Abstract
Tools for sequence-specific DNA binding have opened the door to new approaches in investigating fundamental questions in biology and crop development. While there are several platforms to choose from, many of the recent advances in sequence-specific targeting tools are focused on developing Clustered Regularly Interspaced Short Palindromic Repeats- CRISPR Associated (CRISPR-Cas)-based systems. Using a catalytically inactive Cas protein (dCas), this system can act as a vector for different modular catalytic domains (effector domains) to control a gene's expression or alter epigenetic marks such as DNA methylation. Recent trends in developing CRISPR-dCas systems include creating versions that can target multiple copies of effector domains to a single site, targeting epigenetic changes that, in some cases, can be inherited to the next generation in the absence of the targeting construct, and combining effector domains and targeting strategies to create synergies that increase the functionality or efficiency of the system. This review summarizes and compares DNA targeting technologies, the effector domains used to target transcriptional control and epi-mutagenesis, and the different CRISPR-dCas systems used in plants.
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Affiliation(s)
| | | | - Ming Wang
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, USA
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25
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Balsalobre A, Drouin J. Pioneer factors as master regulators of the epigenome and cell fate. Nat Rev Mol Cell Biol 2022; 23:449-464. [PMID: 35264768 DOI: 10.1038/s41580-022-00464-z] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 12/23/2022]
Abstract
Pioneer factors are transcription factors with the unique ability to initiate opening of closed chromatin. The stability of cell identity relies on robust mechanisms that maintain the epigenome and chromatin accessibility to transcription factors. Pioneer factors counter these mechanisms to implement new cell fates through binding of DNA target sites in closed chromatin and introduction of active-chromatin histone modifications, primarily at enhancers. As master regulators of enhancer activation, pioneers are thus crucial for the implementation of correct cell fate decisions in development, and as such, they hold tremendous potential for therapy through cellular reprogramming. The power of pioneer factors to reshape the epigenome also presents an Achilles heel, as their misexpression has major pathological consequences, such as in cancer. In this Review, we discuss the emerging mechanisms of pioneer factor functions and their roles in cell fate specification, cellular reprogramming and cancer.
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Affiliation(s)
- Aurelio Balsalobre
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada.
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26
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Crouch J, Shvedova M, Thanapaul RJRS, Botchkarev V, Roh D. Epigenetic Regulation of Cellular Senescence. Cells 2022; 11:672. [PMID: 35203320 PMCID: PMC8870565 DOI: 10.3390/cells11040672] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 02/04/2023] Open
Abstract
Senescence is a complex cellular stress response that abolishes proliferative capacity and generates a unique secretory pattern that is implicated in organismal aging and age-related disease. How a cell transitions to a senescent state is multifactorial and often requires transcriptional regulation of multiple genes. Epigenetic alterations to DNA and chromatin are powerful regulators of genome architecture and gene expression, and they play a crucial role in mediating the induction and maintenance of senescence. This review will highlight the changes in chromatin, DNA methylation, and histone alterations that establish and maintain cellular senescence, alongside the specific epigenetic regulation of the senescence-associated secretory phenotype (SASP).
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Affiliation(s)
- Jack Crouch
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Maria Shvedova
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Rex Jeya Rajkumar Samdavid Thanapaul
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
| | - Vladimir Botchkarev
- Department of Dermatology, Boston University School of Medicine, Boston, MA 02118, USA;
| | - Daniel Roh
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Boston University School of Medicine, Boston, MA 02118, USA; (J.C.); (M.S.); (R.J.R.S.T.)
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27
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Caldecott KW, Ward ME, Nussenzweig A. The threat of programmed DNA damage to neuronal genome integrity and plasticity. Nat Genet 2022; 54:115-120. [PMID: 35145299 DOI: 10.1038/s41588-021-01001-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023]
Abstract
The neuronal genome is particularly sensitive to loss or attenuation of DNA repair, and many neurological diseases ensue when DNA repair is impaired. It is well-established that the neuronal genome is subjected to stochastic DNA damage, most likely because of extensive oxidative stress in the brain. However, recent studies have identified unexpected high levels of 'programmed' DNA breakage in neurons, which we propose arise during physiological DNA metabolic processes intrinsic to neuronal development, differentiation and maintenance. The role of programmed DNA breaks in normal neuronal physiology and disease remains relatively unexplored thus far. However, bulk and single-cell sequencing analyses of neurodegenerative diseases have revealed age-related somatic mutational signatures that are enriched in regulatory regions of the genome. Here, we explore a paradigm of DNA repair in neurons, in which the genome is safeguarded from erroneous impacts of programmed genome breakage intrinsic to normal neuronal function.
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Affiliation(s)
- Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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28
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Chen Z, Huang Y, Cao D, Qiu S, Chen B, Li J, Bao Y, Wei Q, Han P, Liu L. Vitamin C Intake and Cancers: An Umbrella Review. Front Nutr 2022; 8:812394. [PMID: 35127793 PMCID: PMC8812486 DOI: 10.3389/fnut.2021.812394] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/13/2021] [Indexed: 12/13/2022] Open
Abstract
Based on the existing systematic reviews and meta-analyses, we conducted this umbrella review aiming at evaluating the quality of evidence, validity and biases of the relationship between vitamin C (VC) intake and incidence and outcomes of multiple cancers. We identified 22 cancer outcomes within 3,562 articles. VC consumption was associated with lower incidence of bladder cancer, breast cancer, cervical tumors, endometrial cancer, esophageal cancer, gastric cancer, glioma, lung cancer, pancreatic cancer, prostate cancer, renal cell cancer, and total cancer occurrence. VC intake was also related to decreased risk of breast cancer prognosis (recurrence, cancer-specific mortality, and all-cause mortality).
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Affiliation(s)
- Zeyu Chen
- Department of Urology, Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- West China School of Clinical Medicine, Sichuan University, Chengdu, China
| | - Yin Huang
- Department of Urology, Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- West China School of Clinical Medicine, Sichuan University, Chengdu, China
| | - Dehong Cao
- Department of Urology, Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Shi Qiu
- Department of Urology, Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Bo Chen
- Department of Urology, Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- West China School of Clinical Medicine, Sichuan University, Chengdu, China
| | - Jin Li
- Department of Urology, Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- West China School of Clinical Medicine, Sichuan University, Chengdu, China
| | - Yige Bao
- Department of Urology, Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Qiang Wei
- Department of Urology, Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Ping Han
- Department of Urology, Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Ping Han
| | - Liangren Liu
- Department of Urology, Institute of Urology, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
- Liangren Liu
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29
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Onodera A, Kiuchi M, Kokubo K, Nakayama T. Epigenetic regulation of inflammation by CxxC domain‐containing proteins*. Immunol Rev 2022. [DOI: 10.1111/imr.13056
expr 964170082 + 969516512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Affiliation(s)
- Atsushi Onodera
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
- Institute for Global Prominent Research Chiba University Chiba Japan
| | - Masahiro Kiuchi
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
| | - Kota Kokubo
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
| | - Toshinori Nakayama
- Department of Immunology Graduate School of Medicine Chiba University Chiba Japan
- AMED‐CREST, AMED Chiba Japan
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30
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TET deficiency perturbs mature B cell homeostasis and promotes oncogenesis associated with accumulation of G-quadruplex and R-loop structures. Nat Immunol 2021; 23:99-108. [PMID: 34937926 PMCID: PMC8772520 DOI: 10.1038/s41590-021-01087-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 11/02/2021] [Indexed: 01/02/2023]
Abstract
Enzymes of the TET family are methylcytosine dioxygenases that undergo frequent mutational or functional inactivation in human cancers. Recurrent loss-of-function mutations in TET proteins are frequent in human diffuse large B cell lymphoma (DLBCL). Here, we investigate the role of TET proteins in B cell homeostasis and development of B cell lymphomas with features of DLBCL. We show that deletion of Tet2 and Tet3 genes in mature B cells in mice perturbs B cell homeostasis and results in spontaneous development of germinal center (GC)-derived B cell lymphomas with increased G-quadruplexes and R-loops. At a genome-wide level, G-quadruplexes and R-loops were associated with increased DNA double-strand breaks (DSBs) at immunoglobulin switch regions. Deletion of the DNA methyltransferase DNMT1 in TET-deficient B cells prevented expansion of GC B cells, diminished the accumulation of G-quadruplexes and R-loops and delayed B lymphoma development, consistent with the opposing functions of DNMT and TET enzymes in DNA methylation and demethylation. Clustered regularly interspaced short palindromic repeats (CRISPR)-mediated depletion of nucleases and helicases that regulate G-quadruplexes and R-loops decreased the viability of TET-deficient B cells. Our studies suggest a molecular mechanism by which TET loss of function might predispose to the development of B cell malignancies.
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31
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Onodera A, Kiuchi M, Kokubo K, Nakayama T. Epigenetic regulation of inflammation by CxxC domain-containing proteins. Immunol Rev 2021; 305:137-151. [PMID: 34935162 DOI: 10.1111/imr.13056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/03/2021] [Accepted: 11/12/2021] [Indexed: 12/14/2022]
Abstract
Epigenetic regulation of gene transcription in the immune system is important for proper control of protective and pathogenic inflammation. Aberrant epigenetic modifications are often associated with dysregulation of the immune cells, including lymphocytes and macrophages, leading to pathogenic inflammation and autoimmune diseases. Two classical epigenetic markers-histone modifications and DNA cytosine methylation, the latter is the 5 position of the cytosine base in the context of CpG dinucleotides-play multiple roles in the immune system. CxxC domain-containing proteins, which basically bind to the non-methylated CpG (i.e., epigenetic "readers"), often function as "writers" of the epigenetic markers via their catalytic domain within the proteins or by interacting with other epigenetic modifiers. We herein report the most recent advances in our understanding of the functions of CxxC domain-containing proteins in the immune system and inflammation, mainly focusing on T cells and macrophages.
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Affiliation(s)
- Atsushi Onodera
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Institute for Global Prominent Research, Chiba University, Chiba, Japan
| | - Masahiro Kiuchi
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Kota Kokubo
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan.,AMED-CREST, AMED, Chiba, Japan
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32
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TET3- and OGT-Dependent Expression of Genes Involved in Epithelial-Mesenchymal Transition in Endometrial Cancer. Int J Mol Sci 2021; 22:ijms222413239. [PMID: 34948036 PMCID: PMC8708691 DOI: 10.3390/ijms222413239] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 12/16/2022] Open
Abstract
TET3 is a member of the TET (ten-eleven translocation) proteins family that catalyzes the conversion of the 5-methylcytosine into 5-hydroxymethylcytosine. TET proteins can also affect chromatin modifications and gene expression independently of their enzymatic activity via interactions with other proteins. O-GlcNAc transferase (OGT), the enzyme responsible for modification of proteins via binding of N-acetylglucosamine residues, is one of the proteins whose action may be dependent on TET3. Here, we demonstrated that in endometrial cancer cells both TET3 and OGT affected the expression of genes involved in epithelial to mesenchymal transition (EMT), i.e., FOXC1, TWIST1, and ZEB1. OGT overexpression was caused by an increase in TWIST1 and ZEB1 levels in HEC-1A and Ishikawa cells, which was associated with increased O-GlcNAcylation of histone H2B and trimethylation of H3K4. The TET3 had the opposite effect on gene expressions and histone modifications. OGT and TET3 differently affected FOXC1 expression and the migratory potential of HEC-1A and Ishikawa cells. Analysis of gene expressions in cancer tissue samples from endometrial cancer patients confirmed the association between OGT or TET3 and EMT genes. Our results contribute to the knowledge of the role of the TET3/OGT relationship in the complex mechanism supporting endometrial cancer progression.
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33
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Liu T, Guo L, Liu G, Hu X, Li X, Zhang J, Dai Z, Yu P, Jiang M, Wang J, Zhang J. Molecular Characterization of the Clinical and Tumor Immune Microenvironment Signature of 5-methylcytosine-Related Regulators in non-small Cell Lung Cancer. Front Cell Dev Biol 2021; 9:779367. [PMID: 34858994 PMCID: PMC8632062 DOI: 10.3389/fcell.2021.779367] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/19/2021] [Indexed: 12/28/2022] Open
Abstract
Background: DNA methylation is an important epigenetic modification, among which 5-methylcytosine methylation (5mC) is generally associated with tumorigenesis. Nonetheless, the potential roles of 5mC regulators in the tumor microenvironment (TME) remain unclear. Methods: The 5mC modification patterns of 1,374 lung adenocarcinoma samples were analyzed systematically. The correlation between the 5mC modification and tumor microenvironment cell infiltration was further assessed. The 5mCscore was developed to evaluate tumor mutation burden, immune check-point inhibitor response, and the clinical prognosis of individual tumors. Results: Three 5mC modification patterns were established based on the clinical characteristics of 21 5mC regulators. According to the differential expression of 5mC regulators, three distinct 5mC gene cluster were also identified, which showed distinct TME immune cell infiltration patterns and clinical prognoses. The 5mCscore was constructed to evaluate the tumor mutation burden, immune check-point inhibitor response, and prognosis characteristics. We found that patients with a low 5mCscore had significant immune cell infiltration and increased clinical benefit. Conclusion: This study indicated that the 5mC modification is involved in regulating TME infiltration remodeling. Targeting 5mC modification regulators might be a novel strategy to treat lung cancer.
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Affiliation(s)
- Taisheng Liu
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Liyi Guo
- The Sixth People's Hospital of Huizhou City, Huiyang Hospital Affiliated to Southern Medical University, Huizhou, China
| | - Guihong Liu
- Department of Radiation Oncology, DongGuan Tungwah Hospital, Dongguan, China
| | - Xiaoshan Hu
- Department of Internal Medicine of Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Xiaoning Li
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jinye Zhang
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Zili Dai
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou, China
| | - Peng Yu
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou, China
| | - Ming Jiang
- Department of Breast Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jian Wang
- Department of Thoracic Surgery, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Guangzhou, China
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34
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Yue X, Samaniego-Castruita D, González-Avalos E, Li X, Barwick BG, Rao A. Whole-genome analysis of TET dioxygenase function in regulatory T cells. EMBO Rep 2021; 22:e52716. [PMID: 34288360 PMCID: PMC8339674 DOI: 10.15252/embr.202152716] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022] Open
Abstract
TET methylcytosine dioxygenases are essential for the stability and function of regulatory T cells (Treg cells), which maintain immune homeostasis and self‐tolerance and express the lineage‐determining transcription factor Foxp3. Here, we use whole‐genome analyses to show that the transcriptional program and epigenetic features (DNA modification, chromatin accessibility) of Treg cells are attenuated in the absence of Tet2 and Tet3. Conversely, the addition of the TET activator vitamin C during TGFβ‐induced iTreg cell differentiation in vitro potentiates the expression of Treg signature genes and alters the epigenetic landscape to better resemble that of Treg cells generated in vivo. Vitamin C enhances IL‐2 responsiveness in iTreg cells by increasing IL2Rα expression, STAT5 phosphorylation, and STAT5 binding, mimicking the IL‐2/STAT5 dependence of Treg cells generated in vivo. In summary, TET proteins play essential roles in maintaining Treg molecular features and promoting their dependence on IL‐2. TET activity during endogenous Treg development and potentiation of TET activity by vitamin C during iTreg differentiation are necessary to maintain the transcriptional and epigenetic features of Treg cells.
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Affiliation(s)
- Xiaojing Yue
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Daniela Samaniego-Castruita
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.,Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Edahí González-Avalos
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.,Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Xiang Li
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA
| | - Benjamin G Barwick
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.,Department of Pharmacology and Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA
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35
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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36
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Onodera A, González-Avalos E, Lio CWJ, Georges RO, Bellacosa A, Nakayama T, Rao A. Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells. Genome Biol 2021; 22:186. [PMID: 34158086 PMCID: PMC8218415 DOI: 10.1186/s13059-021-02384-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 05/21/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND TET enzymes mediate DNA demethylation by oxidizing 5-methylcytosine (5mC) in DNA to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Since these oxidized methylcytosines (oxi-mCs) are not recognized by the maintenance methyltransferase DNMT1, DNA demethylation can occur through "passive," replication-dependent dilution when cells divide. A distinct, replication-independent ("active") mechanism of DNA demethylation involves excision of 5fC and 5caC by the DNA repair enzyme thymine DNA glycosylase (TDG), followed by base excision repair. RESULTS Here by analyzing inducible gene-disrupted mice, we show that DNA demethylation during primary T cell differentiation occurs mainly through passive replication-dependent dilution of all three oxi-mCs, with only a negligible contribution from TDG. In addition, by pyridine borane sequencing (PB-seq), a simple recently developed method that directly maps 5fC/5caC at single-base resolution, we detect the accumulation of 5fC/5caC in TDG-deleted T cells. We also quantify the occurrence of concordant demethylation within and near enhancer regions in the Il4 locus. In an independent system that does not involve cell division, macrophages treated with liposaccharide accumulate 5hmC at enhancers and show altered gene expression without DNA demethylation; loss of TET enzymes disrupts gene expression, but loss of TDG has no effect. We also observe that mice with long-term (1 year) deletion of Tdg are healthy and show normal survival and hematopoiesis. CONCLUSIONS We have quantified the relative contributions of TET and TDG to cell differentiation and DNA demethylation at representative loci in proliferating T cells. We find that TET enzymes regulate T cell differentiation and DNA demethylation primarily through passive dilution of oxi-mCs. In contrast, while we observe a low level of active, replication-independent DNA demethylation mediated by TDG, this process does not appear to be essential for immune cell activation or differentiation.
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Affiliation(s)
- Atsushi Onodera
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
- Institute for Global Prominent Research, Chiba University, 1-33, Yayoicho, Inage-ku, Chiba, 263-8522, Japan
| | - Edahí González-Avalos
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Chan-Wang Jerry Lio
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Present address: Department of Microbial Infection and Immunity, Ohio State University, 460 W 12th Ave, Columbus, OH, 43210, USA
| | - Romain O Georges
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Alfonso Bellacosa
- Cancer Signaling and Epigenetics Program & Cancer Epigenetics Institute, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - Toshinori Nakayama
- Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
- AMED-CREST, AMED, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA.
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37
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Epigenetics of addiction. Neurochem Int 2021; 147:105069. [PMID: 33992741 DOI: 10.1016/j.neuint.2021.105069] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/16/2021] [Accepted: 05/09/2021] [Indexed: 11/22/2022]
Abstract
Substance use disorders are complex biopsychosocial disorders that have substantial negative neurocognitive impact in various patient populations. These diseases involve the compulsive use of licit or illicit substances despite adverse medicolegal consequences and appear to be secondary to long-lasting epigenetic and transcriptional adaptations in brain reward and non-reward circuits. The accumulated evidence supports the notion that repeated drug use causes changes in post-translational histone modifications and in DNA methylation/hydroxymethylation processes in several brain regions. This review provides an overview of epigenetic changes reported in models of cocaine, methamphetamine, and opioid use disorders. The accumulated data suggest that future therapeutic interventions should focus on the development of epigenetic drugs against addictive diseases.
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38
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Wu W, Hill SE, Nathan WJ, Paiano J, Callen E, Wang D, Shinoda K, van Wietmarschen N, Colón-Mercado JM, Zong D, De Pace R, Shih HY, Coon S, Parsadanian M, Pavani R, Hanzlikova H, Park S, Jung SK, McHugh PJ, Canela A, Chen C, Casellas R, Caldecott KW, Ward ME, Nussenzweig A. Neuronal enhancers are hotspots for DNA single-strand break repair. Nature 2021; 593:440-444. [PMID: 33767446 PMCID: PMC9827709 DOI: 10.1038/s41586-021-03468-5] [Citation(s) in RCA: 108] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023]
Abstract
Defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons1,2. The cellular genome is subjected to a constant barrage of endogenous DNA damage, but surprisingly little is known about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here we show that post-mitotic neurons accumulate unexpectedly high levels of DNA single-strand breaks (SSBs) at specific sites within the genome. Genome-wide mapping reveals that SSBs are located within enhancers at or near CpG dinucleotides and sites of DNA demethylation. These SSBs are repaired by PARP1 and XRCC1-dependent mechanisms. Notably, deficiencies in XRCC1-dependent short-patch repair increase DNA repair synthesis at neuronal enhancers, whereas defects in long-patch repair reduce synthesis. The high levels of SSB repair in neuronal enhancers are therefore likely to be sustained by both short-patch and long-patch processes. These data provide the first evidence of site- and cell-type-specific SSB repair, revealing unexpected levels of localized and continuous DNA breakage in neurons. In addition, they suggest an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair.
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Affiliation(s)
- Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sarah E Hill
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - William J Nathan
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.,Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jacob Paiano
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Dongpeng Wang
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Kenta Shinoda
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | - Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Raffaella De Pace
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Han-Yu Shih
- National Eye Institute, NIH, Bethesda, MD, USA
| | - Steve Coon
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Maia Parsadanian
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Hana Hanzlikova
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Solji Park
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Cancer Institute, NIH, Bethesda, MD, USA.,NIH Regulome Project, NIH, Bethesda, MD, USA
| | - Seol Kyoung Jung
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Cancer Institute, NIH, Bethesda, MD, USA.,NIH Regulome Project, NIH, Bethesda, MD, USA
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Andres Canela
- The Hakubi Center for Advanced Research and Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Chongyi Chen
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Cancer Institute, NIH, Bethesda, MD, USA.,NIH Regulome Project, NIH, Bethesda, MD, USA
| | - Keith W Caldecott
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic. .,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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39
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TET family dioxygenases and the TET activator vitamin C in immune responses and cancer. Blood 2021; 136:1394-1401. [PMID: 32730592 DOI: 10.1182/blood.2019004158] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/13/2020] [Indexed: 12/21/2022] Open
Abstract
Vitamin C serves as a cofactor for Fe(II) and 2-oxoglutarate-dependent dioxygenases including TET family enzymes, which catalyze the oxidation of 5-methylcytosine into 5-hydroxymethylcytosine and further oxidize methylcytosines. Loss-of-function mutations in epigenetic regulators such as TET genes are prevalent in hematopoietic malignancies. Vitamin C deficiency is frequently observed in cancer patients. In this review, we discuss the role of vitamin C and TET proteins in cancer, with a focus on hematopoietic malignancies, T regulatory cells, and other immune system cells.
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40
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Rao A. Scientific divagations: from signaling and transcription to chromatin changes in T cells. Nat Immunol 2021; 21:1473-1476. [PMID: 33173218 DOI: 10.1038/s41590-020-00823-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.
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41
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Proshkina E, Shaposhnikov M, Moskalev A. Genome-Protecting Compounds as Potential Geroprotectors. Int J Mol Sci 2020; 21:E4484. [PMID: 32599754 PMCID: PMC7350017 DOI: 10.3390/ijms21124484] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Throughout life, organisms are exposed to various exogenous and endogenous factors that cause DNA damages and somatic mutations provoking genomic instability. At a young age, compensatory mechanisms of genome protection are activated to prevent phenotypic and functional changes. However, the increasing stress and age-related deterioration in the functioning of these mechanisms result in damage accumulation, overcoming the functional threshold. This leads to aging and the development of age-related diseases. There are several ways to counteract these changes: 1) prevention of DNA damage through stimulation of antioxidant and detoxification systems, as well as transition metal chelation; 2) regulation of DNA methylation, chromatin structure, non-coding RNA activity and prevention of nuclear architecture alterations; 3) improving DNA damage response and repair; 4) selective removal of damaged non-functional and senescent cells. In the article, we have reviewed data about the effects of various trace elements, vitamins, polyphenols, terpenes, and other phytochemicals, as well as a number of synthetic pharmacological substances in these ways. Most of the compounds demonstrate the geroprotective potential and increase the lifespan in model organisms. However, their genome-protecting effects are non-selective and often are conditioned by hormesis. Consequently, the development of selective drugs targeting genome protection is an advanced direction.
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Affiliation(s)
- Ekaterina Proshkina
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (E.P.); (M.S.)
| | - Mikhail Shaposhnikov
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (E.P.); (M.S.)
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Centre, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russia; (E.P.); (M.S.)
- Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky prosp., 167001 Syktyvkar, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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42
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Lio CWJ, Huang SCC. Circles of Life: linking metabolic and epigenetic cycles to immunity. Immunology 2020; 161:165-174. [PMID: 32418209 DOI: 10.1111/imm.13207] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/04/2020] [Indexed: 12/15/2022] Open
Abstract
Metabolites are the essential substrates for epigenetic modification enzymes to write or erase the epigenetic blueprint in cells. Hence, the availability of nutrients and activity of metabolic pathways strongly influence the enzymatic function. Recent studies have shed light on the choreography between metabolome and epigenome in the control of immune cell differentiation and function, with a major focus on histone modifications. Yet, despite its importance in gene regulation, DNA methylation and its relationship with metabolism is relatively unclear. In this review, we will describe how the metabolic flux can influence epigenetic networks in innate and adaptive immune cells, with a focus on the DNA methylation cycle and the metabolites S-adenosylmethionine and α-ketoglutarate. Future directions will be discussed for this rapidly emerging field.
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Affiliation(s)
- Chan-Wang Jerry Lio
- Division of Signaling and Gene Expression, La Jolla Institute, San Diego, CA, USA.,Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA
| | - Stanley Ching-Cheng Huang
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA.,Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
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