51
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Pronier E, Imanci A, Selimoglu-Buet D, Badaoui B, Itzykson R, Roger T, Jego C, Naimo A, Francillette M, Breckler M, Wagner-Ballon O, Figueroa ME, Aglave M, Gautheret D, Porteu F, Bernard OA, Vainchenker W, Delhommeau F, Solary E, Droin NM. Macrophage migration inhibitory factor is overproduced through EGR1 in TET2 low resting monocytes. Commun Biol 2022; 5:110. [PMID: 35115654 PMCID: PMC8814058 DOI: 10.1038/s42003-022-03057-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 01/06/2022] [Indexed: 12/14/2022] Open
Abstract
Somatic mutation in TET2 gene is one of the most common clonal genetic events detected in age-related clonal hematopoiesis as well as in chronic myelomonocytic leukemia (CMML). In addition to being a pre-malignant state, TET2 mutated clones are associated with an increased risk of death from cardiovascular disease, which could involve cytokine/chemokine overproduction by monocytic cells. Here, we show in mice and in human cells that, in the absence of any inflammatory challenge, TET2 downregulation promotes the production of MIF (macrophage migration inhibitory factor), a pivotal mediator of atherosclerotic lesion formation. In healthy monocytes, TET2 is recruited to MIF promoter and interacts with the transcription factor EGR1 and histone deacetylases. Disruption of these interactions as a consequence of TET2-decreased expression favors EGR1-driven transcription of MIF gene and its secretion. MIF favors monocytic differentiation of myeloid progenitors. These results designate MIF as a chronically overproduced chemokine and a potential therapeutic target in patients with clonal TET2 downregulation in myeloid cells. To improve our understanding of the pathological role of TET2 mutations, Pronier, Imanci et al. use mice and human cells to show that TET2 downregulation promotes the production of macrophage migration inhibitory factor (MIF). In addition they show that whilst TET2 is recruited to the MIF promoter in healthy monocytes, decreased TET2 expression results in chronic overproduction of MIF - suggesting that MIF signaling could therefore constitute a potential therapeutic target for conditions associated with TET2 mutations.
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Affiliation(s)
- Elodie Pronier
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Owkin Lab, Owkin, Inc., New York, NY, 10003, USA
| | - Aygun Imanci
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
| | - Dorothée Selimoglu-Buet
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
| | - Bouchra Badaoui
- AP-HP, Hôpitaux Universitaires Henri-Mondor, Département d'Hématologie et Immunologie Biologiques, 94000, Créteil, France
| | - Raphael Itzykson
- AP-HP, Service Hématologie Adultes, Hôpital Saint-Louis, 75010, Paris, France
| | - Thierry Roger
- Infectious Disease Service, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, 1011, Lausanne, Switzerland
| | - Chloé Jego
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
| | - Audrey Naimo
- INSERM US23, CNRS UMS 3655, AMMICa, Genomic platform, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Maëla Francillette
- INSERM US23, CNRS UMS 3655, AMMICa, Genomic platform, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Marie Breckler
- INSERM US23, CNRS UMS 3655, AMMICa, Genomic platform, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Orianne Wagner-Ballon
- AP-HP, Hôpitaux Universitaires Henri-Mondor, Département d'Hématologie et Immunologie Biologiques, 94000, Créteil, France.,Université Paris Est Créteil, INSERM, IMRB, Equipe 9, 94010, Créteil, France
| | - Maria E Figueroa
- Human Genetics, University of Miami Miller School of Medicine, 33136, Miami, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 33136, Miami, USA
| | - Marine Aglave
- INSERM US23, CNRS UMS 3655, AMMICa, Bioinformatic platform, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Daniel Gautheret
- INSERM US23, CNRS UMS 3655, AMMICa, Bioinformatic platform, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Françoise Porteu
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
| | - Olivier A Bernard
- Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France.,INSERM U1170, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - William Vainchenker
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France
| | - François Delhommeau
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, 75012, Paris, France.,AP-HP, Sorbonne Université, Hôpital Saint-Antoine, Service d'Hématologie et Immunologie Biologique, 75012, Paris, France
| | - Eric Solary
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France.,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France.,Hematology department, Gustave Roussy Cancer Center, 94805, Villejuif, France
| | - Nathalie M Droin
- INSERM U1287, Gustave Roussy Cancer Center, 94805, Villejuif, France. .,Université Paris Saclay, Faculté de Médecine, 94270, Le Kremlin-Bicêtre, France. .,INSERM US23, CNRS UMS 3655, AMMICa, Genomic platform, Gustave Roussy Cancer Center, 94805, Villejuif, France.
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52
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Bernstein C. DNA Methylation and Establishing Memory. Epigenet Insights 2022; 15:25168657211072499. [PMID: 35098021 PMCID: PMC8793415 DOI: 10.1177/25168657211072499] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/17/2021] [Indexed: 11/30/2022] Open
Abstract
A single event can cause a life-long memory. Memories physically reside in neurons, and changes in neuronal gene expression are considered to be central to memory. Early models proposed that specific DNA methylations of cytosines in neuronal DNA encode memories in a stable biochemical form. This review describes recent research that elucidates the molecular mechanisms used by the mammalian brain to form DNA methylcytosine encoded memories. For example, neuron activation initiates cytosine demethylation by stimulating DNA topoisomerase II beta (TOP2B) protein to make a temporary DNA double-strand break (repaired within about 2 hours) at a promoter of an immediate early gene, EGR1, allowing expression of this gene. The EGR1 proteins then recruit methylcytosine dioxygenase TET1 proteins to initiate demethylation at several hundred genes, facilitating expression of those genes. Initiation of demethylation of cytosine also occurs when OGG1 localizes at oxidized guanine in a methylated CpG site and recruits TET1 for initiation of demethylation at that site. DNMT3A2 is another immediate early gene upregulated by synaptic activity. DNMT3A2 protein catalyzes de novo DNA methylations. These several mechanisms convert external experiences into DNA methylations and initiated demethylations of neuronal DNA cytosines, causing changes in gene expression that are the basis of long-term memories.
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Affiliation(s)
- Carol Bernstein
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
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53
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Oliveira Paiva AM, Friggen AH, Douwes R, Wittekoek B, Smits WK. Practical observations on the use of fluorescent reporter systems in Clostridioides difficile. Antonie van Leeuwenhoek 2022; 115:297-323. [PMID: 35039954 DOI: 10.1007/s10482-021-01691-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/19/2021] [Indexed: 12/18/2022]
Abstract
Fluorescence microscopy is a valuable tool to study a broad variety of bacterial cell components and dynamics thereof. For Clostridioides difficile, the fluorescent proteins CFPopt, mCherryOpt and phiLOV2.1, and the self-labelling tags SNAPCd and HaloTag, hereafter collectively referred as fluorescent systems, have been described to explore different cellular pathways. In this study, we sought to characterize previously used fluorescent systems in C. difficile cells. We performed single cell analyses using fluorescence microscopy of exponentially growing C. difficile cells harbouring different fluorescent systems, either expressing these separately in the cytosol or fused to the C-terminus of HupA, under defined conditions. We show that the intrinsic fluorescence of C. difficile cells increases during growth, independent of sigB or spo0A. However, when C. difficile cells are exposed to environmental oxygen autofluorescence is enhanced. Cytosolic overexpression of the different fluorescent systems alone, using the same expression signals, showed heterogeneous expression of the fluorescent systems. High levels of mCherryOpt were toxic for C. difficile cells limiting the applicability of this fluorophore as a transcriptional reporter. When fused to HupA, a C. difficile histone-like protein, the fluorescent systems behaved similarly and did not affect the HupA overproduction phenotype. The present study compares several commonly used fluorescent systems for application as transcriptional or translational reporters in microscopy and summarizes the limitations and key challenges for live-cell imaging of C. difficile. Due to independence of molecular oxygen and fluorescent signal, SNAPCd appears the most suitable candidate for live-cell imaging in C. difficile to date.
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Affiliation(s)
- Ana M Oliveira Paiva
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbial Cell Biology, Leiden, The Netherlands.,Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198, Gif-sur-Yvette, France
| | - Annemieke H Friggen
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbial Cell Biology, Leiden, The Netherlands
| | - Roxanne Douwes
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - Bert Wittekoek
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands. .,Center for Microbial Cell Biology, Leiden, The Netherlands.
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54
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Chakravarti R, Lenka SK, Gautam A, Singh R, Ravichandiran V, Roy S, Ghosh D. A Review on CRISPR-Mediated Epigenome Editing: A Future Directive for Therapeutic Management of Cancer. Curr Drug Targets 2022; 23:836-853. [DOI: 10.2174/1389450123666220117105531] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/15/2021] [Accepted: 12/14/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Recent studies have shed light on the role of epigenetic marks in certain diseases like cancer, type II diabetes mellitus (T2DM), obesity, and cardiovascular dysfunction, to name a few. Epigenetic marks like DNA methylation and histone acetylation are randomly altered in the disease state. It has been seen that methylation of DNA and histones can result in down-regulation of gene expression, whereas histone acetylation, ubiquitination, and phosphorylation are linked to enhanced expression of genes. How can we precisely target such epigenetic aberrations to prevent the advent of diseases? The answer lies in the amalgamation of the efficient genome editing technique, CRISPR, with certain effector molecules that can alter the status of epigenetic marks as well as employ certain transcriptional activators or repressors. In this review, we have discussed the rationale of epigenetic editing as a therapeutic strategy and how CRISPR-Cas9 technology coupled with epigenetic effector tags can efficiently edit epigenetic targets. In the later part, we have discussed how certain epigenetic effectors are tagged with dCas9 to elicit epigenetic changes in cancer. Increased interest in exploring the epigenetic background of cancer and non-communicable diseases like type II diabetes mellitus and obesity accompanied with technological breakthroughs has made it possible to perform large-scale epigenome studies.
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Affiliation(s)
- Rudra Chakravarti
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Swadhin Kumar Lenka
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Syamal Roy
- CSIR-Indian Institute of Chemical Biology, Jadavpur, Kolkata, India
| | - Dipanjan Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, India
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55
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Pradhan RK, Ramakrishna W. Transposons: Unexpected players in cancer. Gene 2022; 808:145975. [PMID: 34592349 DOI: 10.1016/j.gene.2021.145975] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 12/21/2022]
Abstract
Transposons are repetitive DNA sequences encompassing about half of the human genome. They play a vital role in genome stability maintenance and contribute to genomic diversity and evolution. Their activity is regulated by various mechanisms considering the deleterious effects of these mobile elements. Various genetic risk factors and environmental stress conditions affect the regulatory pathways causing alteration of transposon expression. Our knowledge of the biological role of transposons is limited especially in various types of cancers. Retrotransposons of different types (LTR-retrotransposons, LINEs and SINEs) regulate a plethora of genes that have a role in cell reprogramming, tumor suppression, cell cycle, apoptosis, cell adhesion and migration, and DNA repair. The regulatory mechanisms of transposons, their deregulation and different mechanisms underlying transposon-mediated carcinogenesis in humans focusing on the three most prevalent types, lung, breast and colorectal cancers, were reviewed. The modes of regulation employed include alternative splicing, deletion, insertion, duplication in genes and promoters resulting in upregulation, downregulation or silencing of genes.
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56
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Català-Moll F, Ferreté-Bonastre AG, Godoy-Tena G, Morante-Palacios O, Ciudad L, Barberà L, Fondelli F, Martínez-Cáceres EM, Rodríguez-Ubreva J, Li T, Ballestar E. Vitamin D receptor, STAT3, and TET2 cooperate to establish tolerogenesis. Cell Rep 2022; 38:110244. [DOI: 10.1016/j.celrep.2021.110244] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/27/2021] [Accepted: 12/20/2021] [Indexed: 12/21/2022] Open
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57
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Structure and Function of TET Enzymes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:239-267. [DOI: 10.1007/978-3-031-11454-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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58
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Zhao H, Lu J, Yan T, Han F, Sun J, Yin X, Chen L, Shen C, Wunderlich M, Yun W, Yang L, Chen L, Su D, Bohlander SK, Wang F, Mulloy JC, Li C, Chen J, Huang H, Jiang X. Opioid receptor signaling suppresses leukemia through both catalytic and non-catalytic functions of TET2. Cell Rep 2022; 38:110253. [DOI: 10.1016/j.celrep.2021.110253] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/24/2021] [Accepted: 12/21/2021] [Indexed: 01/12/2023] Open
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59
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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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60
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Wang G, Han JJ. Connections between metabolism and epigenetic modifications in cancer. MEDICAL REVIEW (BERLIN, GERMANY) 2021; 1:199-221. [PMID: 37724300 PMCID: PMC10388788 DOI: 10.1515/mr-2021-0015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/19/2021] [Indexed: 09/20/2023]
Abstract
How cells sense and respond to environmental changes is still a key question. It has been identified that cellular metabolism is an important modifier of various epigenetic modifications, such as DNA methylation, histone methylation and acetylation and RNA N6-methyladenosine (m6A) methylation. This closely links the environmental nutrient availability to the maintenance of chromatin structure and gene expression, and is crucial to regulate cellular homeostasis, cell growth and differentiation. Cancer metabolic reprogramming and epigenetic alterations are widely observed, and facilitate cancer development and progression. In cancer cells, oncogenic signaling-driven metabolic reprogramming modifies the epigenetic landscape via changes in the key metabolite levels. In this review, we briefly summarized the current evidence that the abundance of key metabolites, such as S-adenosyl methionine (SAM), acetyl-CoA, α-ketoglutarate (α-KG), 2-hydroxyglutarate (2-HG), uridine diphospho-N-acetylglucosamine (UDP-GlcNAc) and lactate, affected by metabolic reprogramming plays an important role in dynamically regulating epigenetic modifications in cancer. An improved understanding of the roles of metabolic reprogramming in epigenetic regulation can contribute to uncover the underlying mechanisms of metabolic reprogramming in cancer development and identify the potential targets for cancer therapies.
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Affiliation(s)
- Guangchao Wang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jingdong J. Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
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61
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He N, Ma D, Tan Y, Liu M. Upregulation of O-GlcNAc transferase is involved in the pathogenesis of acute myeloid leukemia. Asia Pac J Clin Oncol 2021; 18:e318-e328. [PMID: 34821067 DOI: 10.1111/ajco.13685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/23/2021] [Indexed: 01/11/2023]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is the most common acute leukemia in adults. Patients have a low survival rate and a high recurrence rate, and AML is a highly heterogeneous disease without an effective and specific targeted therapy. AIMS Therefore, it is urgent to explore new AML markers to enable early diagnosis and find drug targets for individualized treatment. RESULTS Herein, we demonstrate that O-linked-N-acetylglucosamine transferase (OGT) is significantly upregulated in AML tissues compared with normal tissues. The high level of OGT expression is significantly related to poor overall survival (OS) in AML. Inhibition of OGT can inhibit AML cell proliferation and promote AML cell apoptosis. CONCLUSION These results suggest that OGT plays an important role in the pathogenesis of AML, and may become a potential biomarker and molecular drug target for precision therapy for AML.
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Affiliation(s)
- Na He
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China.,Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Daoxin Ma
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yanjie Tan
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Min Liu
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
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62
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Sun L, Lv S, Song T. O-GlcNAcylation links oncogenic signals and cancer epigenetics. Discov Oncol 2021; 12:54. [PMID: 35201498 PMCID: PMC8777512 DOI: 10.1007/s12672-021-00450-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/11/2021] [Indexed: 12/19/2022] Open
Abstract
Prevalent dysregulation of epigenetic modifications plays a pivotal role in cancer. Targeting epigenetic abnormality is a new strategy for cancer therapy. Understanding how conventional oncogenic factors cause epigenetic abnormality is of great basic and translational value. O-GlcNAcylation is a protein modification which affects physiology and pathophysiology. In mammals, O-GlcNAcylation is catalyzed by one single enzyme OGT and removed by one single enzyme OGA. O-GlcNAcylation is affected by the availability of the donor, UDP-GlcNAc, generated by the serial enzymatic reactions in the hexoamine biogenesis pathway (HBP). O-GlcNAcylation regulates a wide spectrum of substrates including many proteins involved in epigenetic modification. Like epigenetic modifications, abnormality of O-GlcNAcylation is also common in cancer. Studies have revealed substantial impact on HBP enzymes and OGT/OGA by oncogenic signals. In this review, we will first summarize how oncogenic signals regulate HBP enzymes, OGT and OGA in cancer. We will then integrate this knowledge with the up to date understanding how O-GlcNAcylation regulates epigenetic machinery. With this, we propose a signal axis from oncogenic signals through O-GlcNAcylation dysregulation to epigenetic abnormality in cancer. Further elucidation of this axis will not only advance our understanding of cancer biology but also provide new revenues towards cancer therapy.
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Affiliation(s)
- Lidong Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China.
| | - Suli Lv
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China
| | - Tanjing Song
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China.
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63
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Seyama R, Tsuchida N, Okada Y, Sakata S, Hamada K, Azuma Y, Hamanaka K, Fujita A, Koshimizu E, Miyatake S, Mizuguchi T, Makino S, Itakura A, Okada S, Okamoto N, Ogata K, Uchiyama Y, Matsumoto N. Two families with TET3-related disorder showing neurodevelopmental delay with craniofacial dysmorphisms. J Hum Genet 2021; 67:157-164. [PMID: 34719681 DOI: 10.1038/s10038-021-00986-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/25/2021] [Accepted: 10/09/2021] [Indexed: 01/21/2023]
Abstract
TET3 at 2p13.1 encodes tet methylcytosine dioxygenase 3, a demethylation enzyme that converts 5-methylcytosine to 5-hydroxymethylcytosine. Beck et al. reported that patients with TET3 abnormalities in either an autosomal dominant or recessive inheritance fashion clinically showed global developmental delay, intellectual disability, and dysmorphisms. In this study, exome sequencing identified both mono- and biallelic TET3 variants in two families: a de novo variant NM_001287491.1:c.3028 A > G:p.(Asn1010Asp), and compound heterozygous variants NM_001287491.1:c.[2077 C > T];[2896 T > G],p.[Gln693*];[Cys966Gly]. Despite the different inheritance modes, the affected individuals showed similar phenotypic features. Including these three patients, only 14 affected individuals have been reported to date. The accumulation of data regarding individuals with TET3-related disorder is necessary to describe their clinical spectrum.
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Affiliation(s)
- Rie Seyama
- Department of Human Genetics, Yokohama City University, Yokohama, Japan.,Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Yasuyuki Okada
- Department of Pediatrics, National Hospital Organization Higashihiroshima Medical Center, Higashihiroshima, Japan
| | - Sonoko Sakata
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Yokohama City University, Yokohama, Japan
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University, Yokohama, Japan.,Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University, Yokohama, Japan
| | - Shintaro Makino
- Department of Obstetrics and Gynecology, Juntendo University Urayasu Hospital, Chiba, Japan
| | - Atsuo Itakura
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University, Yokohama, Japan.
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64
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Wang X, Rosikiewicz W, Sedkov Y, Martinez T, Hansen BS, Schreiner P, Christensen J, Xu B, Pruett-Miller SM, Helin K, Herz HM. PROSER1 mediates TET2 O-GlcNAcylation to regulate DNA demethylation on UTX-dependent enhancers and CpG islands. Life Sci Alliance 2021; 5:5/1/e202101228. [PMID: 34667079 PMCID: PMC8548262 DOI: 10.26508/lsa.202101228] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 01/18/2023] Open
Abstract
PROSER1 promotes the interaction between TET2 and the glycosyltransferase OGT to regulate TET2 O-GlcNAcylation and stability on genomic elements that depend on the activity of the MLL3/4 complexes. DNA methylation at enhancers and CpG islands usually leads to gene repression, which is counteracted by DNA demethylation through the TET protein family. However, how TET enzymes are recruited and regulated at these genomic loci is not fully understood. Here, we identify TET2, the glycosyltransferase OGT and a previously undescribed proline and serine rich protein, PROSER1 as interactors of UTX, a component of the enhancer-associated MLL3/4 complexes. We find that PROSER1 mediates the interaction between OGT and TET2, thus promoting TET2 O-GlcNAcylation and protein stability. In addition, PROSER1, UTX, TET1/2, and OGT colocalize on many genomic elements genome-wide. Loss of PROSER1 results in lower enrichment of UTX, TET1/2, and OGT at enhancers and CpG islands, with a concomitant increase in DNA methylation and transcriptional down-regulation of associated target genes and increased DNA hypermethylation encroachment at H3K4me1-predisposed CpG islands. Furthermore, we provide evidence that PROSER1 acts as a more general regulator of OGT activity by controlling O-GlcNAcylation of multiple other chromatin signaling pathways. Taken together, this study describes for the first time a regulator of TET2 O-GlcNAcylation and its implications in mediating DNA demethylation at UTX-dependent enhancers and CpG islands and supports an important role for PROSER1 in regulating the function of various chromatin-associated proteins via OGT-mediated O-GlcNAcylation.
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Affiliation(s)
- Xiaokang Wang
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yurii Sedkov
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Tanner Martinez
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Baranda S Hansen
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Patrick Schreiner
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jesper Christensen
- Biotech Research and Innovation Centre and The Novo Nordisk Foundation for Stem Cell Biology, University of Copenhagen, Copenhagen, Denmark
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kristian Helin
- Biotech Research and Innovation Centre and The Novo Nordisk Foundation for Stem Cell Biology, University of Copenhagen, Copenhagen, Denmark.,Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Hans-Martin Herz
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
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65
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Cavalieri V. The Expanding Constellation of Histone Post-Translational Modifications in the Epigenetic Landscape. Genes (Basel) 2021; 12:genes12101596. [PMID: 34680990 PMCID: PMC8535662 DOI: 10.3390/genes12101596] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/02/2021] [Accepted: 10/05/2021] [Indexed: 12/17/2022] Open
Abstract
The emergence of a nucleosome-based chromatin structure accompanied the evolutionary transition from prokaryotes to eukaryotes. In this scenario, histones became the heart of the complex and precisely timed coordination between chromatin architecture and functions during adaptive responses to environmental influence by means of epigenetic mechanisms. Notably, such an epigenetic machinery involves an overwhelming number of post-translational modifications at multiple residues of core and linker histones. This review aims to comprehensively describe old and recent evidence in this exciting field of research. In particular, histone post-translational modification establishing/removal mechanisms, their genomic locations and implication in nucleosome dynamics and chromatin-based processes, as well as their harmonious combination and interdependence will be discussed.
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Affiliation(s)
- Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90128 Palermo, Italy
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66
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Sapozhnikov DM, Szyf M. Unraveling the functional role of DNA demethylation at specific promoters by targeted steric blockage of DNA methyltransferase with CRISPR/dCas9. Nat Commun 2021; 12:5711. [PMID: 34588447 PMCID: PMC8481236 DOI: 10.1038/s41467-021-25991-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/07/2021] [Indexed: 01/10/2023] Open
Abstract
Despite four decades of research to support the association between DNA methylation and gene expression, the causality of this relationship remains unresolved. Here, we reaffirm that experimental confounds preclude resolution of this question with existing strategies, including recently developed CRISPR/dCas9 and TET-based epigenetic editors. Instead, we demonstrate a highly effective method using only nuclease-dead Cas9 and guide RNA to physically block DNA methylation at specific targets in the absence of a confounding flexibly-tethered enzyme, thereby enabling the examination of the role of DNA demethylation per se in living cells, with no evidence of off-target activity. Using this method, we probe a small number of inducible promoters and find the effect of DNA demethylation to be small, while demethylation of CpG-rich FMR1 produces larger changes in gene expression. This method could be used to reveal the extent and nature of the contribution of DNA methylation to gene regulation.
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Affiliation(s)
- Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC, Canada.
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67
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TET3 promotes AML growth and epigenetically regulates glucose metabolism and leukemic stem cell associated pathways. Leukemia 2021; 36:416-425. [PMID: 34462525 DOI: 10.1038/s41375-021-01390-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/07/2021] [Accepted: 08/17/2021] [Indexed: 11/09/2022]
Abstract
Acute myeloid leukemia (AML) is considered a poor prognosis malignancy where patients exhibit altered glucose metabolism and stem cell signatures that contribute to AML growth and maintenance. Here, we report that the epigenetic factor, Ten-Eleven Translocation 3 (TET3) dioxygenase is overexpressed in AML patients and functionally validated human leukemic stem cells (LSCs), is required for leukemic growth by virtue of its regulation of glucose metabolism in AML cells. In human AML cells, TET3 maintains 5-hydroxymethylcytosine (5hmC) epigenetic marks and expression of early myeloid progenitor program, critical glucose metabolism and STAT5A signaling pathway genes, which also positively correlate with TET3 expression in AML patients. Consequently, TET3 depletion impedes hexokinase activity and L-Lactate production in AML cells. Conversely, overexpression of TET3 in healthy human hematopoietic stem progenitors (HSPCs) upregulates the expression of glucose metabolism, STAT5A signaling and AML associated genes, and impairs normal HSPC lineage differentiation in vitro. Finally, TET3 depletion renders AML cells highly sensitive to blockage of the TET3 downstream pathways glycolysis and STAT5 signaling via the combination of 2-Deoxy-D-glucose and STAT5 inhibitor which preferentially targets AML cells but spares healthy CD34+ HSPCs.
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68
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Shams R, Ito Y, Miyatake H. Evaluation of the Binding Kinetics of RHEB with mTORC1 by In-Cell and In Vitro Assays. Int J Mol Sci 2021; 22:ijms22168766. [PMID: 34445471 PMCID: PMC8395731 DOI: 10.3390/ijms22168766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/04/2021] [Accepted: 08/13/2021] [Indexed: 11/16/2022] Open
Abstract
The mammalian/mechanistic target of rapamycin complex 1 (mTORC1) is activated by the small G-protein, Ras homolog enriched in brain (RHEB–GTPase). On lysosome, RHEB activates mTORC1 by binding the domains of N-heat, M-heat, and the focal adhesion targeting (FAT) domain, which allosterically regulates ATP binding in the active site for further phosphorylation. The crucial role of RHEB in regulating growth and survival through mTORC1 makes it a targetable site for anti-cancer therapeutics. However, the binding kinetics of RHEB to mTORC1 is still unknown at the molecular level. Therefore, we studied the kinetics by in vitro and in-cell protein–protein interaction (PPI) assays. To this end, we used the split-luciferase system (NanoBiT®) for in-cell studies and prepared proteins for the in vitro measurements. Consequently, we demonstrated that RHEB binds to the whole mTOR both in the presence or absence of GTPγS, with five-fold weaker affinity in the presence of GTPγS. In addition, RHEB bound to the truncated mTOR fragments of N-heat domain (∆N, aa 60–167) or M-heat domain (∆M, aa 967–1023) with the same affinity in the absence of GTP. The reconstructed binding site of RHEB, ∆N-FAT-M, however, bound to RHEB with the same affinity as ∆N-M, indicating that the FAT domain (∆FAT, aa 1240–1360) is dispensable for RHEB binding. Furthermore, RHEB bound to the truncated kinase domain (∆ATP, aa 2148–2300) with higher affinity than to ∆N-FAT-M. In conclusion, RHEB engages two different binding sites of mTOR, ∆N-FAT-M and ∆ATP, with higher affinity for ∆ATP, which likely regulates the kinase activity of mTOR through multiple different biding modes.
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Affiliation(s)
- Raef Shams
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, RIKEN, Wako 351-0198, Saitama, Japan; (R.S.); (Y.I.)
- Department of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City 338-8570, Saitama, Japan
| | - Yoshihiro Ito
- Emergent Bioengineering Materials Research Team, RIKEN Center for Emergent Matter Science, RIKEN, Wako 351-0198, Saitama, Japan; (R.S.); (Y.I.)
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako 351-0198, Saitama, Japan
| | - Hideyuki Miyatake
- Department of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama City 338-8570, Saitama, Japan
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako 351-0198, Saitama, Japan
- Correspondence: ; Tel.: +81-48-467-4979
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69
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Li L, Qiu Y, Miao M, Liu Z, Li W, Zhu Y, Wang Q. Reduction of Tet2 exacerbates early stage Alzheimer's pathology and cognitive impairments in 2×Tg-AD mice. Hum Mol Genet 2021; 29:1833-1852. [PMID: 31943063 DOI: 10.1093/hmg/ddz282] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/20/2019] [Accepted: 11/19/2019] [Indexed: 12/29/2022] Open
Abstract
Abnormal modification of 5-hydroxymethylcytosine (5hmC) is closely related to the occurrence of Alzheimer's disease (AD). However, the role of 5hmC and its writers, ten-eleven translocation (Tet) proteins, in regulating the pathogenesis of AD remains largely unknown. We detected a significant decrease in 5hmC and Tet2 levels in the hippocampus of aged APPswe/PSEN1 double-transgenic (2×Tg-AD) mice that coincides with abundant amyloid-β (Aβ) plaque accumulation. On this basis, we examined the reduction of Tet2 expression in the hippocampus at early disease stages, which caused a decline of 5hmC levels and led young 2×Tg-AD mice to present with advanced stages of AD-related pathological hallmarks, including Aβ accumulation, GFAP-positive astrogliosis and Iba1-positive microglia overgrowth as well as the overproduction of pro-inflammatory factors. Additionally, the loss of Tet2 in the 2×Tg-AD mice at 5 months of age accelerated hippocampal-dependent learning and memory impairments compared to age-matched control 2×Tg-AD mice. In contrast, restoring Tet2 expression in adult neural stem cells isolated from aged 2×Tg-AD mice hippocampi increased 5hmC levels and increased their regenerative capacity, suggesting that Tet2 might be an exciting target for rejuvenating the brain during aging and AD. Further, hippocampal RNA sequencing data revealed that the expression of altered genes identified in both Tet2 knockdown and control 2×Tg-AD mice was significantly associated with inflammation response. Finally, we demonstrated that Tet2-mediated 5hmC epigenetic modifications regulate AD pathology by interacting with HDAC1. These results suggest a combined approach for the regulation and treatment of AD-related memory impairment and cognitive symptoms by increasing Tet2 via HDAC1 suppression.
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Affiliation(s)
- Liping Li
- Ningbo Key Laboratory of Behavioral Neuroscience, Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo 315211, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Yisha Qiu
- Ningbo Key Laboratory of Behavioral Neuroscience, Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo 315211, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Miao Miao
- Ningbo Key Laboratory of Behavioral Neuroscience, Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo 315211, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Zhitao Liu
- Faculty of Sports Science, Ningbo University, Ningbo 315211, China
| | - Wanyi Li
- Faculty of Sports Science, Ningbo University, Ningbo 315211, China
| | - Yiyi Zhu
- Ningbo Key Laboratory of Behavioral Neuroscience, Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo 315211, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
| | - Qinwen Wang
- Ningbo Key Laboratory of Behavioral Neuroscience, Department of Physiology and Pharmacology, Ningbo University School of Medicine, Ningbo 315211, China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo 315211, China
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70
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Hai R, He L, Shu G, Yin G. Characterization of Histone Deacetylase Mechanisms in Cancer Development. Front Oncol 2021; 11:700947. [PMID: 34395273 PMCID: PMC8360675 DOI: 10.3389/fonc.2021.700947] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/05/2021] [Indexed: 02/01/2023] Open
Abstract
Over decades of studies, accumulating evidence has suggested that epigenetic dysregulation is a hallmark of tumours. Post-translational modifications of histones are involved in tumour pathogenesis and development mainly by influencing a broad range of physiological processes. Histone deacetylases (HDACs) and histone acetyltransferases (HATs) are pivotal epigenetic modulators that regulate dynamic processes in the acetylation of histones at lysine residues, thereby influencing transcription of oncogenes and tumour suppressor genes. Moreover, HDACs mediate the deacetylation process of many nonhistone proteins and thus orchestrate a host of pathological processes, such as tumour pathogenesis. In this review, we elucidate the functions of HDACs in cancer.
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Affiliation(s)
- Rihan Hai
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China.,School of Basic Medical Sciences, Central South University, Changsha, China
| | - Liuer He
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China.,School of Basic Medical Sciences, Central South University, Changsha, China
| | - Guang Shu
- School of Basic Medical Sciences, Central South University, Changsha, China
| | - Gang Yin
- Department of Pathology, Xiangya Hospital, School of Basic Medical Sciences, Central South University, Changsha, China
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71
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Qin W, Scicluna BP, van der Poll T. The Role of Host Cell DNA Methylation in the Immune Response to Bacterial Infection. Front Immunol 2021; 12:696280. [PMID: 34394088 PMCID: PMC8358789 DOI: 10.3389/fimmu.2021.696280] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Host cells undergo complex transcriptional reprogramming upon infection. Epigenetic changes play a key role in the immune response to bacteria, among which DNA modifications that include methylation have received much attention in recent years. The extent of DNA methylation is well known to regulate gene expression. Whilst historically DNA methylation was considered to be a stable epigenetic modification, accumulating evidence indicates that DNA methylation patterns can be altered rapidly upon exposure of cells to changing environments and pathogens. Furthermore, the action of proteins regulating DNA methylation, particularly DNA methyltransferases and ten-eleven translocation methylcytosine dioxygenases, may be modulated, at least in part, by bacteria. This review discusses the principles of DNA methylation, and recent insights about the regulation of host DNA methylation during bacterial infection.
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Affiliation(s)
- Wanhai Qin
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Brendon P Scicluna
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Tom van der Poll
- Center of Experimental & Molecular Medicine, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Division of Infectious Diseases, Amsterdam University Medical Centers, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
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72
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Nakajima H, Murakami K. O-GlcNAcylation: Implications in normal and malignant hematopoiesis. Exp Hematol 2021; 101-102:16-24. [PMID: 34302904 DOI: 10.1016/j.exphem.2021.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
Posttranslational protein modification through addition of the O-linked β-N-acetyl-D-glucosamine (O-GlcNAc) moiety to serine or threonine residues, termed O-GlcNAcylation, is a highly dynamic process conserved throughout eukaryotes. O-GlcNAcylation is reversibly catalyzed by a single pair of enzymes, O-GlcNAc transferase and O-GlcNAcase, and it acts as a fundamental regulator for a wide variety of biological processes including gene expression, cell cycle regulation, metabolism, stress response, cellular signaling, epigenetics, and proteostasis. O-GlcNAcylation is regulated by various intracellular or extracellular cues such as metabolic status, nutrient availability, and stress. Studies over decades have unveiled the profound biological significance of this unique protein modification in normal physiology and pathologic processes of diverse cell types or tissues. In hematopoiesis, recent studies have indicated the essential and pleiotropic roles of O-GlcNAcylation in differentiation, proliferation, and function of hematopoietic cells including T cells, B cells, myeloid progenitors, and hematopoietic stem and progenitor cells. Moreover, aberrant O-GlcNAcylation is implicated in the development of hematologic malignancies with dysregulated epigenetics, metabolism, and gene transcription. Thus, it is now recognized that O-GlcNAcylation is one of the key regulators of normal and malignant hematopoiesis.
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Affiliation(s)
- Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
| | - Koichi Murakami
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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73
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Traube FR, Özdemir D, Sahin H, Scheel C, Glück AF, Geserich AS, Oganesian S, Kostidis S, Iwan K, Rahimoff R, Giorgio G, Müller M, Spada F, Biel M, Cox J, Giera M, Michalakis S, Carell T. Redirected nuclear glutamate dehydrogenase supplies Tet3 with α-ketoglutarate in neurons. Nat Commun 2021; 12:4100. [PMID: 34215750 PMCID: PMC8253819 DOI: 10.1038/s41467-021-24353-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/11/2021] [Indexed: 12/14/2022] Open
Abstract
Tet3 is the main α-ketoglutarate (αKG)-dependent dioxygenase in neurons that converts 5-methyl-dC into 5-hydroxymethyl-dC and further on to 5-formyl- and 5-carboxy-dC. Neurons possess high levels of 5-hydroxymethyl-dC that further increase during neural activity to establish transcriptional plasticity required for learning and memory functions. How αKG, which is mainly generated in mitochondria as an intermediate of the tricarboxylic acid cycle, is made available in the nucleus has remained an unresolved question in the connection between metabolism and epigenetics. We show that in neurons the mitochondrial enzyme glutamate dehydrogenase, which converts glutamate into αKG in an NAD+-dependent manner, is redirected to the nucleus by the αKG-consumer protein Tet3, suggesting on-site production of αKG. Further, glutamate dehydrogenase has a stimulatory effect on Tet3 demethylation activity in neurons, and neuronal activation increases the levels of αKG. Overall, the glutamate dehydrogenase-Tet3 interaction might have a role in epigenetic changes during neural plasticity. α-ketoglutarate (αKG) is an intermediate in the tricarboxylic acid cycle that is required in the nucleus for genomic DNA demethylation by Tet3. Here, the authors show that the enzyme glutamate dehydrogenase, which converts glutamate to αKG, is redirected from the mitochondria to the nucleus.
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Affiliation(s)
- Franziska R Traube
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dilara Özdemir
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hanife Sahin
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Constanze Scheel
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andrea F Glück
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Anna S Geserich
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sabine Oganesian
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sarantos Kostidis
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Katharina Iwan
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - René Rahimoff
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Grazia Giorgio
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Markus Müller
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabio Spada
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin Biel
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jürgen Cox
- Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martin Giera
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Stylianos Michalakis
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany. .,Department of Ophthalmology, University Hospital, LMU Munich, Munich, Germany.
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany.
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74
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Li J, Li L, Sun X, Deng T, Huang G, Li X, Xie Z, Zhou Z. Role of Tet2 in Regulating Adaptive and Innate Immunity. Front Cell Dev Biol 2021; 9:665897. [PMID: 34222235 PMCID: PMC8247589 DOI: 10.3389/fcell.2021.665897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/25/2021] [Indexed: 12/16/2022] Open
Abstract
Accumulated evidence indicates that epigenetic modifications play central roles in gene expression regulation and participate in developing many autoimmune and autoinflammatory diseases. Mechanistically, epigenetic modifications act as a bridge between environmental and cellular factors and susceptibility genes. DNA methylation is a critical epigenetic modification that is regulated by ten-eleven translocation (TET) enzymes. Accumulating evidence has revealed that TET family proteins function as gene regulators and antitumor drug targets mainly because of their ability to oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Recently, the effect of Tet2, an essential TET protein, on the development of autoimmune diseases has been explored. In this review, we summarize the current understanding of Tet2 in immune response regulation, clarify the mechanisms of Tet2 in B and T cell differentiation and function, and discuss the opposing effects of Tet2 on inflammatory gene expression in the immune system to provide new potential therapeutic targets for related diseases.
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Affiliation(s)
- Jiaqi Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lifang Li
- Department of Ultrasound, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiaoxiao Sun
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Tuo Deng
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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Dick A, Chen A. The role of TET proteins in stress-induced neuroepigenetic and behavioural adaptations. Neurobiol Stress 2021; 15:100352. [PMID: 34189192 PMCID: PMC8220100 DOI: 10.1016/j.ynstr.2021.100352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/21/2021] [Accepted: 06/05/2021] [Indexed: 12/27/2022] Open
Abstract
Over the past decade, critical, non-redundant roles of the ten-eleven translocation (TET) family of dioxygenase enzymes have been identified in the brain during developmental and postnatal stages. Specifically, TET-mediated active demethylation, involving the iterative oxidation of 5-methylcytosine to 5-hydroxymethylcytosine and subsequent oxidative derivatives, is dynamically regulated in response to environmental stimuli such as neuronal activity, learning and memory processes, and stressor exposure. Such changes may therefore perpetuate stable and dynamic transcriptional patterns within neuronal populations required for neuroplasticity and behavioural adaptation. In this review, we will highlight recent evidence supporting a role of TET protein function and active demethylation in stress-induced neuroepigenetic and behavioural adaptations. We further explore potential mechanisms by which TET proteins may mediate both the basal and pathological embedding of stressful life experiences within the brain of relevance to stress-related psychiatric disorders.
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Affiliation(s)
- Alec Dick
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
- Corresponding author.
| | - Alon Chen
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
- The Ruhman Family Laboratory for Research on the Neurobiology of Stress, Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
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76
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Sun L, Zhang H, Gao P. Metabolic reprogramming and epigenetic modifications on the path to cancer. Protein Cell 2021; 13:877-919. [PMID: 34050894 PMCID: PMC9243210 DOI: 10.1007/s13238-021-00846-7] [Citation(s) in RCA: 203] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/02/2021] [Indexed: 02/07/2023] Open
Abstract
Metabolic rewiring and epigenetic remodeling, which are closely linked and reciprocally regulate each other, are among the well-known cancer hallmarks. Recent evidence suggests that many metabolites serve as substrates or cofactors of chromatin-modifying enzymes as a consequence of the translocation or spatial regionalization of enzymes or metabolites. Various metabolic alterations and epigenetic modifications also reportedly drive immune escape or impede immunosurveillance within certain contexts, playing important roles in tumor progression. In this review, we focus on how metabolic reprogramming of tumor cells and immune cells reshapes epigenetic alterations, in particular the acetylation and methylation of histone proteins and DNA. We also discuss other eminent metabolic modifications such as, succinylation, hydroxybutyrylation, and lactylation, and update the current advances in metabolism- and epigenetic modification-based therapeutic prospects in cancer.
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Affiliation(s)
- Linchong Sun
- Guangzhou First People's Hospital, School of Medicine, Institutes for Life Sciences, South China University of Technology, Guangzhou, 510006, China.
| | - Huafeng Zhang
- The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230027, China. .,CAS Centre for Excellence in Cell and Molecular Biology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Ping Gao
- Guangzhou First People's Hospital, School of Medicine, Institutes for Life Sciences, South China University of Technology, Guangzhou, 510006, China. .,School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, 510006, China. .,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China.
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77
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De Dieuleveult M, Bizet M, Colin L, Calonne E, Bachman M, Li C, Stancheva I, Miotto B, Fuks F, Deplus R. The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome. Epigenetics 2021; 17:422-443. [PMID: 33960278 DOI: 10.1080/15592294.2021.1917152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ten-Eleven Translocation (TET) proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) leading to a dynamic epigenetic state of DNA that can influence transcription and chromatin organization. While TET proteins interact with complexes involved in transcriptional repression and activation, the overall understanding of the molecular mechanisms involved in TET-mediated regulation of gene expression still remains limited. Here, we show that TET proteins interact with the chromatin remodelling protein lymphoid-specific helicase (LSH/HELLS) in vivo and in vitro. In mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESCs) knock out of Lsh leads to a significant reduction of 5-hydroxymethylation amount in the DNA. Whole genome sequencing of 5hmC in wild-type versus Lsh knock-out MEFs and ESCs showed that in absence of Lsh, some regions of the genome gain 5hmC while others lose it, with mild correlation with gene expression changes. We further show that differentially hydroxymethylated regions did not completely overlap with differentially methylated regions indicating that changes in 5hmC distribution upon Lsh knock-out are not a direct consequence of 5mC decrease. Altogether, our results suggest that LSH, which interacts with TET proteins, contributes to the regulation of 5hmC levels and distribution in MEFs and ESCs.
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Affiliation(s)
- Maud De Dieuleveult
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium.,Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Laurence Colin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Martin Bachman
- Medicines Discovery Catapult, Alderley Park, Macclesfield, UK
| | - Chao Li
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Irina Stancheva
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Benoit Miotto
- Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
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78
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O-GlcNAcylation and O-GlcNAc Cycling Regulate Gene Transcription: Emerging Roles in Cancer. Cancers (Basel) 2021; 13:cancers13071666. [PMID: 33916244 PMCID: PMC8037238 DOI: 10.3390/cancers13071666] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/26/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary O-linked β-N-acetylglucosamine (O-GlcNAc) is a post-translational modification (PTM) linking nutrient flux through the hexosamine biosynthetic pathway (HBP) to gene transcription. Mounting experimental and clinical data implicates aberrant O-GlcNAcylation in the development and progression of cancer. Herein, we discuss how alteration of O-GlcNAc-regulated transcriptional mechanisms leads to atypical gene expression in cancer. We discuss the challenges associated with studying O-GlcNAc function and present several new approaches for studies of O-GlcNAc-regulated transcription. Abstract O-linked β-N-acetylglucosamine (O-GlcNAc) is a single sugar post-translational modification (PTM) of intracellular proteins linking nutrient flux through the Hexosamine Biosynthetic Pathway (HBP) to the control of cis-regulatory elements in the genome. Aberrant O-GlcNAcylation is associated with the development, progression, and alterations in gene expression in cancer. O-GlcNAc cycling is defined as the addition and subsequent removal of the modification by O-GlcNAc Transferase (OGT) and O-GlcNAcase (OGA) provides a novel method for cells to regulate various aspects of gene expression, including RNA polymerase function, epigenetic dynamics, and transcription factor activity. We will focus on the complex relationship between phosphorylation and O-GlcNAcylation in the regulation of the RNA Polymerase II (RNAP II) pre-initiation complex and the regulation of the carboxyl-terminal domain of RNAP II via the synchronous actions of OGT, OGA, and kinases. Additionally, we discuss how O-GlcNAcylation of TATA-box binding protein (TBP) alters cellular metabolism. Next, in a non-exhaustive manner, we will discuss the current literature on how O-GlcNAcylation drives gene transcription in cancer through changes in transcription factor or chromatin remodeling complex functions. We conclude with a discussion of the challenges associated with studying O-GlcNAcylation and present several new approaches for studying O-GlcNAc regulated transcription that will advance our understanding of the role of O-GlcNAc in cancer.
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79
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Lin CH, Liao CC, Chen MY, Chou TY. Feedback Regulation of O-GlcNAc Transferase through Translation Control to Maintain Intracellular O-GlcNAc Homeostasis. Int J Mol Sci 2021; 22:ijms22073463. [PMID: 33801653 PMCID: PMC8037101 DOI: 10.3390/ijms22073463] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/14/2022] Open
Abstract
Protein O-GlcNAcylation is a dynamic post-translational modification involving the attachment of N-acetylglucosamine (GlcNAc) to the hydroxyl groups of Ser/Thr residues on numerous nucleocytoplasmic proteins. Two enzymes are responsible for O-GlcNAc cycling on substrate proteins: O-GlcNAc transferase (OGT) catalyzes the addition while O-GlcNAcase (OGA) helps the removal of GlcNAc. O-GlcNAcylation modifies protein functions; therefore, dysregulation of O-GlcNAcylation affects cell physiology and contributes to pathogenesis. To maintain homeostasis of cellular O-GlcNAcylation, there exists feedback regulation of OGT and OGA expression responding to fluctuations of O-GlcNAc levels; yet, little is known about the molecular mechanisms involved. In this study, we investigated the O-GlcNAc-feedback regulation of OGT and OGA expression in lung cancer cells. Results suggest that, upon alterations in O-GlcNAcylation, the regulation of OGA expression occurs at the mRNA level and likely involves epigenetic mechanisms, while modulation of OGT expression is through translation control. Further analyses revealed that the eukaryotic translation initiation factor 4E-binding protein 1 (4E-BP1) contributes to the downregulation of OGT induced by hyper-O-GlcNAcylation; the S5A/S6A O-GlcNAcylation-site mutant of 4E-BP1 cannot support this regulation, suggesting an important role of O-GlcNAcylation. The results provide additional insight into the molecular mechanisms through which cells may fine-tune intracellular O-GlcNAc levels to maintain homeostasis.
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Affiliation(s)
- Chia-Hung Lin
- Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
| | - Chen-Chung Liao
- Metabolomics-Proteomics Research Center, National Yang-Ming University, Taipei 11221, Taiwan;
- Metabolomics-Proteomics Research Center, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
| | - Mei-Yu Chen
- Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei 11221, Taiwan
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Cancer Progression Research Center, National Yang-Ming University, Taipei 11221, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Correspondence: (M.-Y.C.); (T.-Y.C.); Tel.: +886-2-2826-7269 (M.-Y.C.); +886-2-2875-7022 (T.-Y.C.)
| | - Teh-Ying Chou
- Division of Molecular Pathology, Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
- Cancer Progression Research Center, National Yang-Ming University, Taipei 11221, Taiwan
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Institute of Clinical Medicine, National Yang-Ming University, Taipei 11221, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Correspondence: (M.-Y.C.); (T.-Y.C.); Tel.: +886-2-2826-7269 (M.-Y.C.); +886-2-2875-7022 (T.-Y.C.)
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80
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Nutrient regulation of the flow of genetic information by O-GlcNAcylation. Biochem Soc Trans 2021; 49:867-880. [PMID: 33769449 DOI: 10.1042/bst20200769] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 01/10/2023]
Abstract
O-linked-β-N-acetylglucosamine (O-GlcNAc) is a post-translational modification (PTM) that is actively added to and removed from thousands of intracellular proteins. As a PTM, O-GlcNAcylation tunes the functions of a protein in various ways, such as enzymatic activity, transcriptional activity, subcellular localization, intermolecular interactions, and degradation. Its regulatory roles often interplay with the phosphorylation of the same protein. Governed by 'the Central Dogma', the flow of genetic information is central to all cellular activities. Many proteins regulating this flow are O-GlcNAc modified, and their functions are tuned by the cycling sugar. Herein, we review the regulatory roles of O-GlcNAcylation on the epigenome, in DNA replication and repair, in transcription and in RNA processing, in protein translation and in protein turnover.
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81
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Joiner CM, Hammel FA, Janetzko J, Walker S. Protein Substrates Engage the Lumen of O-GlcNAc Transferase's Tetratricopeptide Repeat Domain in Different Ways. Biochemistry 2021; 60:847-853. [PMID: 33709700 PMCID: PMC8040631 DOI: 10.1021/acs.biochem.0c00981] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glycosylation of nuclear and cytoplasmic proteins is an essential post-translational modification in mammals. O-GlcNAc transferase (OGT), the sole enzyme responsible for this modification, glycosylates more than 1000 unique nuclear and cytoplasmic substrates. How OGT selects its substrates is a fundamental question that must be answered to understand OGT's unusual biology. OGT contains a long tetratricopeptide repeat (TPR) domain that has been implicated in substrate selection, but there is almost no information about how changes to this domain affect glycosylation of individual substrates. By profiling O-GlcNAc in cell extracts and probing glycosylation of purified substrates, we show here that ladders of asparagines and aspartates that extend the full length of OGT's TPR lumen control substrate glycosylation. Different substrates are sensitive to changes in different regions of OGT's TPR lumen. We also found that substrates with glycosylation sites close to the C-terminus bypass lumenal binding. Our findings demonstrate that substrates can engage OGT in a variety of different ways for glycosylation.
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Affiliation(s)
- Cassandra M. Joiner
- Department of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston MA 02115, USA
| | - Forrest A. Hammel
- Department of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston MA 02115, USA
- Program in Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - John Janetzko
- Department of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston MA 02115, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
| | - Suzanne Walker
- Department of Microbiology, Harvard Medical School, 4 Blackfan Circle, Boston MA 02115, USA
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82
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Xu Y, Sun X, Zhang R, Cao T, Cai SY, Boyer JL, Zhang X, Li D, Huang Y. A Positive Feedback Loop of TET3 and TGF-β1 Promotes Liver Fibrosis. Cell Rep 2021; 30:1310-1318.e5. [PMID: 32023451 PMCID: PMC7063678 DOI: 10.1016/j.celrep.2019.12.092] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/14/2019] [Accepted: 12/24/2019] [Indexed: 02/08/2023] Open
Abstract
Pathological activation of TGF-β signaling is universal in fibrosis. Aberrant TGF-β signaling in conjunction with transdifferentiation of hepatic stellate cells (HSCs) into fibrogenic myofibroblasts plays a central role in liver fibrosis. Here we report that the DNA demethylase TET3 is anomalously upregulated in fibrotic livers in both humans and mice. We demonstrate that in human HSCs, TET3 promotes profibrotic gene expression by upregulation of multiple key TGF-β pathway genes, including TGFB1. TET3 binds to target gene promoters, inducing demethylation, which in turn facilitates chromatin remodeling and transcription. We also reveal a positive feedback loop between TGF-β1 and TET3 in both HSCs and hepatocytes. Furthermore, TET3 knockdown ameliorates liver fibrosis in mice. Our results uncover a TET3/TGF-β1 positive feedback loop as a crucial determinant of liver fibrosis and suggest that inhibiting TET3 may represent a therapeutic strategy for liver fibrosis and perhaps other fibrotic diseases. Xu et al. unmask a positive feedback loop between chromatin demethylase TET3 and TGF-β1 in stressed hepatocytes and stellate cells in humans and mice. Activation of this loop stimulates expression of fibrotic genes, whereas knockdown of TET3 reduces liver fibrosis in mice, suggesting a strategy for treating fibrosis.
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Affiliation(s)
- Yetao Xu
- Department of Obstetrics, Gynecology, & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA; Center of Reproductive Medicine, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Jiangsu 211166, China
| | - Xiaoli Sun
- Department of Obstetrics, Gynecology, & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA; Center of Reproductive Medicine, Department of Obstetrics and Gynecology, Affiliated Hospital of Nantong University, Jiangsu 226001, China
| | - Ruling Zhang
- Department of Obstetrics, Gynecology, & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200080, China
| | - Tiefeng Cao
- Department of Obstetrics, Gynecology, & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA; Department of Gynecology and Obstetrics, First Affiliated Hospital of Sun Yat-Sen University, Guangdong 510070, China
| | - Shi-Ying Cai
- Liver Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - James L Boyer
- Liver Center, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Xuchen Zhang
- Pathology Department, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Da Li
- Department of Obstetrics, Gynecology, & Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06510, USA; Center of Reproductive Medicine, Department of Obstetrics and Gynecology, 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, USA.
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83
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Liu Y, Yao RZ, Lian S, Liu P, Hu YJ, Shi HZ, Lv HM, Yang YY, Xu B, Li SZ. O-GlcNAcylation: the "stress and nutrition receptor" in cell stress response. Cell Stress Chaperones 2021; 26:297-309. [PMID: 33159661 PMCID: PMC7925768 DOI: 10.1007/s12192-020-01177-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
O-GlcNAcylation is an atypical, reversible, and dynamic glycosylation that plays a critical role in maintaining the normal physiological functions of cells by regulating various biological processes such as signal transduction, proteasome activity, apoptosis, autophagy, transcription, and translation. It can also respond to environmental changes and physiological signals to play the role of "stress receptor" and "nutrition sensor" in a variety of stress responses and biological processes. Even, a homeostatic disorder of O-GlcNAcylation may cause many diseases. Therefore, O-GlcNAcylation and its regulatory role in stress response are reviewed in this paper.
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Affiliation(s)
- Yang Liu
- National Experimental Teaching Demonstration Center of Animal Medicine Foundation, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Rui-Zhi Yao
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, 028000, People's Republic of China
| | - Shuai Lian
- National Experimental Teaching Demonstration Center of Animal Medicine Foundation, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Peng Liu
- National Experimental Teaching Demonstration Center of Animal Medicine Foundation, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Ya-Jie Hu
- National Experimental Teaching Demonstration Center of Animal Medicine Foundation, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Hong-Zhao Shi
- National Experimental Teaching Demonstration Center of Animal Medicine Foundation, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Hong-Ming Lv
- National Experimental Teaching Demonstration Center of Animal Medicine Foundation, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Yu-Ying Yang
- National Experimental Teaching Demonstration Center of Animal Medicine Foundation, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China
| | - Bin Xu
- National Experimental Teaching Demonstration Center of Animal Medicine Foundation, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China.
| | - Shi-Ze Li
- National Experimental Teaching Demonstration Center of Animal Medicine Foundation, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, 163319, People's Republic of China.
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84
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Shin EM, Huynh VT, Neja SA, Liu CY, Raju A, Tan K, Tan NS, Gunaratne J, Bi X, Iyer LM, Aravind L, Tergaonkar V. GREB1: An evolutionarily conserved protein with a glycosyltransferase domain links ERα glycosylation and stability to cancer. SCIENCE ADVANCES 2021; 7:7/12/eabe2470. [PMID: 33731348 PMCID: PMC7968844 DOI: 10.1126/sciadv.abe2470] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 01/29/2021] [Indexed: 05/03/2023]
Abstract
What covalent modifications control the temporal ubiquitination of ERα and hence the duration of its transcriptional activity remain poorly understood. We show that GREB1, an ERα-inducible enzyme, catalyzes O-GlcNAcylation of ERα at residues T553/S554, which stabilizes ERα protein by inhibiting association with the ubiquitin ligase ZNF598. Loss of GREB1-mediated glycosylation of ERα results in reduced cellular ERα levels and insensitivity to estrogen. Higher GREB1 expression in ERα+ve breast cancer is associated with greater survival in response to tamoxifen, an ERα agonist. Mice lacking Greb1 exhibit growth and fertility defects reminiscent of phenotypes in ERα-null mice. In summary, this study identifies GREB1, a protein with an evolutionarily conserved domain related to DNA-modifying glycosyltransferases of bacteriophages and kinetoplastids, as the first inducible and the only other (apart from OGT) O-GlcNAc glycosyltransferase in mammalian cytoplasm and ERα as its first substrate.
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Affiliation(s)
- Eun Myoung Shin
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Vinh Thang Huynh
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research, Singapore 138673, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sultan Abda Neja
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Chia Yi Liu
- Bioprocessing Technology Institute (BTI), A*STAR, Singapore, Singapore
| | - Anandhkumar Raju
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Kelly Tan
- Bioprocessing Technology Institute (BTI), A*STAR, Singapore, Singapore
| | - Nguan Soon Tan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive,, Singapore 637551, Singapore
| | - Jayantha Gunaratne
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117594, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute (BTI), A*STAR, Singapore, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Vinay Tergaonkar
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research, Singapore 138673, Singapore.
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore
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85
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Broome R, Chernukhin I, Jamieson S, Kishore K, Papachristou EK, Mao SQ, Tejedo CG, Mahtey A, Theodorou V, Groen AJ, D'Santos C, Balasubramanian S, Farcas AM, Siersbæk R, Carroll JS. TET2 is a component of the estrogen receptor complex and controls 5mC to 5hmC conversion at estrogen receptor cis-regulatory regions. Cell Rep 2021; 34:108776. [PMID: 33626359 PMCID: PMC7921846 DOI: 10.1016/j.celrep.2021.108776] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/05/2021] [Accepted: 01/29/2021] [Indexed: 01/10/2023] Open
Abstract
Estrogen receptor-α (ER) drives tumor development in ER-positive (ER+) breast cancer. The transcription factor GATA3 has been closely linked to ER function, but its precise role in this setting remains unclear. Quantitative proteomics was used to assess changes to the ER complex in response to GATA3 depletion. Unexpectedly, few proteins were lost from the ER complex in the absence of GATA3, with the only major change being depletion of the dioxygenase TET2. TET2 binding constituted a near-total subset of ER binding in multiple breast cancer models, with loss of TET2 associated with reduced activation of proliferative pathways. TET2 knockdown did not appear to change global methylated cytosine (5mC) levels; however, oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) was significantly reduced, and these events occurred at ER enhancers. These findings implicate TET2 in the maintenance of 5hmC at ER sites, providing a potential mechanism for TET2-mediated regulation of ER target genes.
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Affiliation(s)
- Rebecca Broome
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Igor Chernukhin
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Stacey Jamieson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Merck Sharp & Dohme (UK) Limited, 120 Moorgate, London EC2M 6UR, UK
| | - Kamal Kishore
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Shi-Qing Mao
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | | | - Areeb Mahtey
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Vasiliki Theodorou
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology - Hellas Nikolaou Plastira 100, 70013 Heraklion, Crete, Greece
| | - Arnoud J Groen
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Clive D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Anca Madalina Farcas
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; Bioscience, Oncology R&D, AstraZeneca, Cambridge CB2 0RE, UK.
| | - Rasmus Siersbæk
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK; University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jason S Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK.
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86
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Muha V, Authier F, Szoke-Kovacs Z, Johnson S, Gallagher J, McNeilly A, McCrimmon RJ, Teboul L, van Aalten DMF. Loss of O-GlcNAcase catalytic activity leads to defects in mouse embryogenesis. J Biol Chem 2021; 296:100439. [PMID: 33610549 PMCID: PMC7988489 DOI: 10.1016/j.jbc.2021.100439] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/02/2021] [Accepted: 02/17/2021] [Indexed: 02/08/2023] Open
Abstract
O-GlcNAcylation is an essential post-translational modification that has been implicated in neurodevelopmental and neurodegenerative disorders. O-GlcNAcase (OGA), the sole enzyme catalyzing the removal of O-GlcNAc from proteins, has emerged as a potential drug target. OGA consists of an N-terminal OGA catalytic domain and a C-terminal pseudo histone acetyltransferase (HAT) domain with unknown function. To investigate phenotypes specific to loss of OGA catalytic activity and dissect the role of the HAT domain, we generated a constitutive knock-in mouse line, carrying a mutation of a catalytic aspartic acid to alanine. These mice showed perinatal lethality and abnormal embryonic growth with skewed Mendelian ratios after day E18.5. We observed tissue-specific changes in O-GlcNAc homeostasis regulation to compensate for loss of OGA activity. Using X-ray microcomputed tomography on late gestation embryos, we identified defects in the kidney, brain, liver, and stomach. Taken together, our data suggest that developmental defects during gestation may arise upon prolonged OGA inhibition specifically because of loss of OGA catalytic activity and independent of the function of the HAT domain.
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Affiliation(s)
- Villő Muha
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Florence Authier
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Sara Johnson
- The Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, UK
| | - Jennifer Gallagher
- Division of Molecular & Clinical Medicine, University of Dundee, Dundee, UK
| | - Alison McNeilly
- System Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Rory J McCrimmon
- Division of Molecular & Clinical Medicine, University of Dundee, Dundee, UK
| | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell Institute, Oxfordshire, UK
| | - Daan M F van Aalten
- Division of Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.
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87
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Itkonen HM, Loda M, Mills IG. O-GlcNAc Transferase - An Auxiliary Factor or a Full-blown Oncogene? Mol Cancer Res 2021; 19:555-564. [PMID: 33472950 DOI: 10.1158/1541-7786.mcr-20-0926] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/05/2020] [Accepted: 01/07/2021] [Indexed: 11/16/2022]
Abstract
The β-linked N-acetyl-d-glucosamine (GlcNAc) is a posttranslational modification of serine and threonine residues catalyzed by the enzyme O-GlcNAc transferase (OGT). Increased OGT expression is a feature of most human cancers and inhibition of OGT decreases cancer cell proliferation. Antiproliferative effects are attributed to posttranslational modifications of known regulators of cancer cell proliferation, such as MYC, FOXM1, and EZH2. In general, OGT amplifies cell-specific phenotype, for example, OGT overexpression enhances reprogramming efficiency of mouse embryonic fibroblasts into stem cells. Genome-wide screens suggest that certain cancers are particularly dependent on OGT, and understanding these addictions is important when considering OGT as a target for cancer therapy. The O-GlcNAc modification is involved in most cellular processes, which raises concerns of on-target undesirable effects of OGT-targeting therapy. Yet, emerging evidence suggest that, much like proteasome inhibitors, specific compounds targeting OGT elicit selective antiproliferative effects in cancer cells, and can prime malignant cells to other treatments. It is, therefore, essential to gain mechanistic insights on substrate specificity for OGT, develop reagents to more specifically enrich for O-GlcNAc-modified proteins, identify O-GlcNAc "readers," and develop OGT small-molecule inhibitors. Here, we review the relevance of OGT in cancer progression and the potential targeting of this metabolic enzyme as a putative oncogene.
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Affiliation(s)
- Harri M Itkonen
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, New York.,The Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,The New York Genome Center, New York, New York
| | - Ian G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom. .,PCUK/Movember Centre of Excellence for Prostate Cancer Research, Patrick G Johnston Centre, for Cancer Research (PGJCCR), Queen's University Belfast, Belfast, United Kingdom
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88
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Tsiouplis NJ, Bailey DW, Chiou LF, Wissink FJ, Tsagaratou A. TET-Mediated Epigenetic Regulation in Immune Cell Development and Disease. Front Cell Dev Biol 2021; 8:623948. [PMID: 33520997 PMCID: PMC7843795 DOI: 10.3389/fcell.2020.623948] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
TET proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidation products in DNA. The oxidized methylcytosines (oxi-mCs) facilitate DNA demethylation and are also novel epigenetic marks. TET loss-of-function is strongly associated with cancer; TET2 loss-of-function mutations are frequently observed in hematological malignancies that are resistant to conventional therapies. Importantly, TET proteins govern cell fate decisions during development of various cell types by activating a cell-specific gene expression program. In this review, we seek to provide a conceptual framework of the mechanisms that fine tune TET activity. Then, we specifically focus on the multifaceted roles of TET proteins in regulating gene expression in immune cell development, function, and disease.
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Affiliation(s)
- Nikolas James Tsiouplis
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States
| | - David Wesley Bailey
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States.,University of North Carolina Center of Translational Immunology, Chapel Hill, NC, United States.,University of North Carolina Institute of Inflammatory Disease, Chapel Hill, NC, United States
| | - Lilly Felicia Chiou
- University of North Carolina Curriculum in Genetics and Molecular Biology, Chapel Hill, NC, United States
| | - Fiona Jane Wissink
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States
| | - Ageliki Tsagaratou
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC, United States.,University of North Carolina Center of Translational Immunology, Chapel Hill, NC, United States.,University of North Carolina Institute of Inflammatory Disease, Chapel Hill, NC, United States.,University of North Carolina Curriculum in Genetics and Molecular Biology, Chapel Hill, NC, United States.,University of North Carolina Department of Genetics, Chapel Hill, NC, United States.,University of North Carolina Department of Microbiology and Immunology, Chapel Hill, NC, United States
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89
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Rasmussen KD, Helin K. ChIP-Sequencing of TET Proteins. Methods Mol Biol 2021; 2272:251-262. [PMID: 34009619 DOI: 10.1007/978-1-0716-1294-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
TET proteins are methylcytosine dioxygenases that interact directly with chromatin to shape the DNA methylation landscape. To increase the understanding of TET protein function in a specific cellular context, it is important to be able to map the interactions between TET proteins and DNA. This ChIP-seq protocol details our procedure to analyze TET2 bound DNA in disuccinimidyl glutarate (DSG) and formaldehyde-crosslinked chromatin but can also be adapted to study other TET enzymes.
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Affiliation(s)
- Kasper D Rasmussen
- Centre for Gene Regulation & Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Kristian Helin
- Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Copenhagen, Denmark.
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90
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Huang Z, Yu J, Cui W, Johnson BK, Kim K, Pfeifer GP. The chromosomal protein SMCHD1 regulates DNA methylation and the 2c-like state of embryonic stem cells by antagonizing TET proteins. SCIENCE ADVANCES 2021; 7:7/4/eabb9149. [PMID: 33523915 PMCID: PMC7817097 DOI: 10.1126/sciadv.abb9149] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 11/24/2020] [Indexed: 05/15/2023]
Abstract
5-Methylcytosine (5mC) oxidases, the ten-eleven translocation (TET) proteins, initiate DNA demethylation, but it is unclear how 5mC oxidation is regulated. We show that the protein SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1) is found in complexes with TET proteins and negatively regulates TET activities. Removal of SMCHD1 from mouse embryonic stem (ES) cells induces DNA hypomethylation, preferentially at SMCHD1 target sites and accumulation of 5-hydroxymethylcytosine (5hmC), along with promoter demethylation and activation of the Dux double-homeobox gene. In the absence of SMCHD1, ES cells acquire a two-cell (2c) embryo-like state characterized by activation of an early embryonic transcriptome that is substantially imposed by Dux Using Smchd1/Tet1/Tet2/Tet3 quadruple-knockout cells, we show that DNA demethylation, activation of Dux, and other genes upon SMCHD1 loss depend on TET proteins. These data identify SMCHD1 as an antagonist of the 2c-like state of ES cells and of TET-mediated DNA demethylation.
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Affiliation(s)
- Zhijun Huang
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jiyoung Yu
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
- Asan Medical Center, University of Ulsan, College of Medicine, Songpa, Seoul, South Korea
| | - Wei Cui
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Benjamin K Johnson
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Kyunggon Kim
- Asan Medical Center, University of Ulsan, College of Medicine, Songpa, Seoul, South Korea
| | - Gerd P Pfeifer
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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91
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Murakami K, Kurotaki D, Kawase W, Soma S, Fukuchi Y, Kunimoto H, Yoshimi R, Koide S, Oshima M, Hishiki T, Hayakawa N, Matsuura T, Oda M, Yanagisawa K, Kobayashi H, Haraguchi M, Atobe Y, Funakoshi K, Iwama A, Takubo K, Okamoto S, Tamura T, Nakajima H. OGT Regulates Hematopoietic Stem Cell Maintenance via PINK1-Dependent Mitophagy. Cell Rep 2021; 34:108579. [PMID: 33406421 DOI: 10.1016/j.celrep.2020.108579] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 07/04/2020] [Accepted: 12/09/2020] [Indexed: 01/07/2023] Open
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) is a unique enzyme introducing O-GlcNAc moiety on target proteins, and it critically regulates various cellular processes in diverse cell types. However, its roles in hematopoietic stem and progenitor cells (HSPCs) remain elusive. Here, using Ogt conditional knockout mice, we show that OGT is essential for HSPCs. Ogt is highly expressed in HSPCs, and its disruption induces rapid loss of HSPCs with increased reactive oxygen species and apoptosis. In particular, Ogt-deficient hematopoietic stem cells (HSCs) lose quiescence, cannot be maintained in vivo, and become vulnerable to regenerative and competitive stress. Interestingly, Ogt-deficient HSCs accumulate defective mitochondria due to impaired mitophagy with decreased key mitophagy regulator, Pink1, through dysregulation of H3K4me3. Furthermore, overexpression of PINK1 restores mitophagy and the number of Ogt-deficient HSCs. Collectively, our results reveal that OGT critically regulates maintenance and stress response of HSCs by ensuring mitochondrial quality through PINK1-dependent mitophagy.
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Affiliation(s)
- Koichi Murakami
- Division of Hematology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan; Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan
| | - Daisuke Kurotaki
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Wataru Kawase
- Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Shunsuke Soma
- Division of Hematology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yumi Fukuchi
- Division of Hematology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hiroyoshi Kunimoto
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Ryusuke Yoshimi
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Shuhei Koide
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8039, Japan
| | - Motohiko Oshima
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8039, Japan
| | - Takako Hishiki
- Clinical and Translational Research Center, Keio University School of Medicine, Tokyo 160-8582, Japan; Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Noriyo Hayakawa
- Clinical and Translational Research Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tomomi Matsuura
- Clinical and Translational Research Center, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Mayumi Oda
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kiichi Yanagisawa
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Hiroshi Kobayashi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Miho Haraguchi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Yoshitoshi Atobe
- Department of Neuroanatomy, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Kengo Funakoshi
- Department of Neuroanatomy, Yokohama City University School of Medicine, Yokohama 236-0004, Japan
| | - Atsushi Iwama
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, Chiba 260-8670, Japan; Division of Stem Cell and Molecular Medicine, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8039, Japan
| | - Keiyo Takubo
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Shinichiro Okamoto
- Division of Hematology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tomohiko Tamura
- Advanced Medical Research Center, Yokohama City University, Yokohama 236-0004, Japan; Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan.
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92
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Sheikh MA, Emerald BS, Ansari SA. Stem cell fate determination through protein O-GlcNAcylation. J Biol Chem 2021; 296:100035. [PMID: 33154167 PMCID: PMC7948975 DOI: 10.1074/jbc.rev120.014915] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022] Open
Abstract
Embryonic and adult stem cells possess the capability of self-renewal and lineage-specific differentiation. The intricate balance between self-renewal and differentiation is governed by developmental signals and cell-type-specific gene regulatory mechanisms. A perturbed intra/extracellular environment during lineage specification could affect stem cell fate decisions resulting in pathology. Growing evidence demonstrates that metabolic pathways govern epigenetic regulation of gene expression during stem cell fate commitment through the utilization of metabolic intermediates or end products of metabolic pathways as substrates for enzymatic histone/DNA modifications. UDP-GlcNAc is one such metabolite that acts as a substrate for enzymatic mono-glycosylation of various nuclear, cytosolic, and mitochondrial proteins on serine/threonine amino acid residues, a process termed protein O-GlcNAcylation. The levels of GlcNAc inside the cells depend on the nutrient availability, especially glucose. Thus, this metabolic sensor could modulate gene expression through O-GlcNAc modification of histones or other proteins in response to metabolic fluctuations. Herein, we review evidence demonstrating how stem cells couple metabolic inputs to gene regulatory pathways through O-GlcNAc-mediated epigenetic/transcriptional regulatory mechanisms to govern self-renewal and lineage-specific differentiation programs. This review will serve as a primer for researchers seeking to better understand how O-GlcNAc influences stemness and may catalyze the discovery of new stem-cell-based therapeutic approaches.
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Affiliation(s)
- Muhammad Abid Sheikh
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE; Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE
| | - Suraiya Anjum Ansari
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE; Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, UAE.
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93
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Qiao Z, Zhang S, Hu T, Lan F, Yu D, Ge G, Li C, Fang S, Chen Q. Tet2 regulates Barx2 expression in undifferentiated and early differentiated mouse embryonic stem cells. Biochem Biophys Res Commun 2020; 533:1212-1218. [PMID: 33069358 DOI: 10.1016/j.bbrc.2020.09.095] [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: 09/10/2020] [Accepted: 09/23/2020] [Indexed: 11/24/2022]
Abstract
The methylcytosine oxidase TET proteins play important roles in DNA demethylation and development. In developing embryos, TET2 are upregulated during pre-implantation development, and significantly expressed in the trophectoderm and inner cell mass. In this study, we identified Barx2 as a new target of Tet2. Tet2 bound and demethylated the promoter of Barx2 in mouse embryonic stem cells (mESCs) to maintain the expression of Barx2. During mESC differentiation, Tet2 bound the promoter of Barx2 in day 4 embryonic bodies but not in day 8 EBs. However, Barx2 expression remained unchanged. Thus, Tet2 functioned as a demethylase and maintained the expression of Barx2 in undifferentiated and early differentiated mESCs.
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Affiliation(s)
- Zijun Qiao
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Shiqiang Zhang
- Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Tao Hu
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Fei Lan
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Dingdang Yu
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Guangbo Ge
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Changwei Li
- Shanghai Key Laboratory for the Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopedics, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197, Ruijin 2nd Road, Shanghai, 200025, China.
| | - Shengquan Fang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
| | - Qilong Chen
- Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China; Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
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94
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Konzman D, Abramowitz LK, Steenackers A, Mukherjee MM, Na HJ, Hanover JA. O-GlcNAc: Regulator of Signaling and Epigenetics Linked to X-linked Intellectual Disability. Front Genet 2020; 11:605263. [PMID: 33329753 PMCID: PMC7719714 DOI: 10.3389/fgene.2020.605263] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 10/20/2020] [Indexed: 12/13/2022] Open
Abstract
Cellular identity in multicellular organisms is maintained by characteristic transcriptional networks, nutrient consumption, energy production and metabolite utilization. Integrating these cell-specific programs are epigenetic modifiers, whose activity is often dependent on nutrients and their metabolites to function as substrates and co-factors. Emerging data has highlighted the role of the nutrient-sensing enzyme O-GlcNAc transferase (OGT) as an epigenetic modifier essential in coordinating cellular transcriptional programs and metabolic homeostasis. OGT utilizes the end-product of the hexosamine biosynthetic pathway to modify proteins with O-linked β-D-N-acetylglucosamine (O-GlcNAc). The levels of the modification are held in check by the O-GlcNAcase (OGA). Studies from model organisms and human disease underscore the conserved function these two enzymes of O-GlcNAc cycling play in transcriptional regulation, cellular plasticity and mitochondrial reprogramming. Here, we review these findings and present an integrated view of how O-GlcNAc cycling may contribute to cellular memory and transgenerational inheritance of responses to parental stress. We focus on a rare human genetic disorder where mutant forms of OGT are inherited or acquired de novo. Ongoing analysis of this disorder, OGT- X-linked intellectual disability (OGT-XLID), provides a window into how epigenetic factors linked to O-GlcNAc cycling may influence neurodevelopment.
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Affiliation(s)
| | | | | | | | | | - John A. Hanover
- Laboratory of Cellular and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
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95
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Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J. Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response. Nat Commun 2020; 11:5898. [PMID: 33214551 PMCID: PMC7678849 DOI: 10.1038/s41467-020-19579-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
O-GlcNAc modification plays critical roles in regulating the stress response program and cellular homeostasis. However, systematic and multi-omics studies on the O-GlcNAc regulated mechanism have been limited. Here, comprehensive data are obtained by a chemical reporter-based method to survey O-GlcNAc function in human breast cancer cells stimulated with the genotoxic agent adriamycin. We identify 875 genotoxic stress-induced O-GlcNAc chromatin-associated proteins (OCPs), including 88 O-GlcNAc chromatin-associated transcription factors and cofactors (OCTFs), subsequently map their genomic loci, and construct a comprehensive transcriptional reprogramming network. Notably, genotoxicity-induced O-GlcNAc enhances the genome-wide interactions of OCPs with chromatin. The dynamic binding switch of hundreds of OCPs from enhancers to promoters is identified as a crucial feature in the specific transcriptional activation of genes involved in the adaptation of cancer cells to genotoxic stress. The OCTF nuclear respiratory factor 1 (NRF1) is found to be a key response regulator in O-GlcNAc-modulated cellular homeostasis. These results provide a valuable clue suggesting that OCPs act as stress sensors by regulating the expression of various genes to protect cancer cells from genotoxic stress. Protein O-GlcNAcylation is involved in regulating gene expression and maintaining cellular homeostasis. Here, the authors develop a chemical reporter-based strategy for the proteomic profiling and genome-wide mapping of genotoxic stress-induced O-GlcNAcylated chromatin-associated proteins.
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Affiliation(s)
- Yubo Liu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Qiushi Chen
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Nana Zhang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Keren Zhang
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China
| | - Tongyi Dou
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Yu Cao
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Yimin Liu
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Kun Li
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Xinya Hao
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Xueqin Xie
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Wenli Li
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China
| | - Yan Ren
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen, China.
| | - Jianing Zhang
- School of Life and Pharmaceutical Sciences, Dalian University of Technology, Panjin, China.
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96
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Kunimoto H, Nakajima H. TET2: A cornerstone in normal and malignant hematopoiesis. Cancer Sci 2020; 112:31-40. [PMID: 33048426 PMCID: PMC7780023 DOI: 10.1111/cas.14688] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/04/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022] Open
Abstract
Regulation of genome‐wide DNA methylation is fundamental for a variety of biological processes such as mammalian development, stem cell function, cellular proliferation/differentiation, and oncogenesis. Among the regulators of DNA methylation, ten‐eleven translocation 2 (TET2) is one of the most frequently mutated genes in clonal hematopoiesis of indeterminate potential and in various hematological malignancies, underscoring a pivotal role for TET2 in blood homeostasis and hematopoietic transformation. TET2 oxidizes methylated cytosines to further modify cytosines, which behave as intermediates in active/passive DNA demethylation processes. TET2 itself associates with histone modifiers, thereby regulating histone modifications and expression of target genes. A number of studies have reported pleiotropic effects of TET2 on hematopoietic stem cell self‐renewal, hematopoietic differentiation, genome instability and inflammatory response. Recent single‐cell genomics studies have identified gene promoters as well as transcription factor binding sites as TET2‐targeted genetic loci in which disruption of DNA methylation can fundamentally modify hematopoietic differentiation and promote leukemogenesis. TET2 mutations show convergent cooperativity with other disease alleles in signaling molecules, epigenetic modifiers, and spliceosome factors in hematopoietic transformation. Future studies focusing on the molecular basis of stem cell and immune regulation by TET2 loss will further deepen our understanding of the entire landscape of pathophysiology and molecular vulnerabilities of TET2‐mutated hematological malignancies.
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Affiliation(s)
- Hiroyoshi Kunimoto
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hideaki Nakajima
- Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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97
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Li HJ, Wang Y, Li BX, Yang Y, Guan F, Pang XC, Li X. Roles of ten-eleven translocation family proteins and their O-linked β-N-acetylglucosaminylated forms in cancer development. Oncol Lett 2020; 21:1. [PMID: 33240407 PMCID: PMC7681232 DOI: 10.3892/ol.2020.12262] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022] Open
Abstract
Members of the ten-eleven translocation (TET) protein family of which three mammalian TET proteins have been discovered so far, catalyze the sequential oxidation of 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine which serve an important role in embryonic development and tumor progression. O-GlcNAcylation (O-linked β-N-acetylglucosaminylation) is a reversible post-translational modification known to serve important roles in tumorigenesis and metastasis especially in hematopoietic malignancies such as myelodysplastic syndromes, chronic myelomonocytic leukemia and acute myeloid leukemia. O-GlcNAcylation activity requires only two enzymes: O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA). OGT catalyzes attachment of GlcNAc sugar to serine, threonine and cytosine residues in proteins, while OGA hydrolyzes O-GlcNAc attached to proteins. Numerous recent studies have demonstrated that TETs can be O-GlcNAcylated by OGT, with consequent alteration of TET activity and stability. The present review focuses on the cellular, biological and biochemical functions of TET and its O-GlcNAcylated form and proposes a model of the role of TET/OGT complex in regulation of target proteins during cancer development. In addition, the present review provides directions for future research in this area.
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Affiliation(s)
- Hong-Jiao Li
- Key Laboratory of Resource Biology and Biotechnology Western China, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P.R. China.,Hematology Institute, School of Medicine, Northwest University, Xi'an, Shaanxi 710069, P.R. China
| | - Yi Wang
- Department of Hematology, Provincial People's Hospital, Xi'an, Shaanxi 710069, P.R. China
| | - Bing-Xin Li
- Key Laboratory of Resource Biology and Biotechnology Western China, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P.R. China.,Hematology Institute, School of Medicine, Northwest University, Xi'an, Shaanxi 710069, P.R. China
| | - Yang Yang
- Key Laboratory of Resource Biology and Biotechnology Western China, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P.R. China
| | - Feng Guan
- Key Laboratory of Resource Biology and Biotechnology Western China, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P.R. China
| | - Xing-Chen Pang
- Key Laboratory of Resource Biology and Biotechnology Western China, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P.R. China.,Hematology Institute, School of Medicine, Northwest University, Xi'an, Shaanxi 710069, P.R. China
| | - Xiang Li
- Key Laboratory of Resource Biology and Biotechnology Western China, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, P.R. China.,Hematology Institute, School of Medicine, Northwest University, Xi'an, Shaanxi 710069, P.R. China.,Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu 214000, P.R. China
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98
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Xiang P, Li F, Ma Z, Yue J, Lu C, You Y, Hou L, Yin B, Qiang B, Shu P, Peng X. HCF-1 promotes cell cycle progression by regulating the expression of CDC42. Cell Death Dis 2020; 11:907. [PMID: 33097698 PMCID: PMC7584624 DOI: 10.1038/s41419-020-03094-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 08/09/2020] [Accepted: 09/09/2020] [Indexed: 11/16/2022]
Abstract
The eukaryotic cell cycle involves a highly orchestrated series of events in which the cellular genome is replicated during a synthesis (S) phase and each of the two resulting copies are segregated properly during mitosis (M). Host cell factor-1 (HCF-1) is a transcriptional co-regulator that is essential for and has been implicated in basic cellular processes, such as transcriptional regulation and cell cycle progression. Although a series of HCF-1 transcriptional targets have been identified, few functional clues have been provided, especially for chromosome segregation. Our results showed that HCF-1 activated CDC42 expression by binding to the −881 to −575 region upstream of the CDC42 transcription start site, and the regulation of CDC42 expression by HCF-1 was correlated with cell cycle progression. The overexpression of a spontaneously cycling and constitutively active CDC42 mutant (CDC42F28L) rescued G1 phase delay and multinucleate defects in mitosis upon the loss of HCF-1. Therefore, these results establish that HCF-1 ensures proper cell cycle progression by regulating the expression of CDC42, which indicates a possible mechanism of cell cycle coordination and the regulation mode of typical Rho GTPases.
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Affiliation(s)
- Pan Xiang
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Fei Li
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Zhihua Ma
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Jiping Yue
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Cailing Lu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yuangang You
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Lin Hou
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Bin Yin
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Boqin Qiang
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Pengcheng Shu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China.
| | - Xiaozhong Peng
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Medical Primate Research Center, Neuroscience Center, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China. .,Institute of Medical Biology, Chinese Academy of Medical Sciences, Peking Union Medical College, Kunming, China.
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99
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Inhibition of O-GlcNAc transferase activates tumor-suppressor gene expression in tamoxifen-resistant breast cancer cells. Sci Rep 2020; 10:16992. [PMID: 33046784 PMCID: PMC7552408 DOI: 10.1038/s41598-020-74083-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
In this study, we probed the importance of O-GlcNAc transferase (OGT) activity for the survival of tamoxifen-sensitive (TamS) and tamoxifen-resistant (TamR) breast cancer cells. Tamoxifen is an antagonist of estrogen receptor (ERα), a transcription factor expressed in over 50% of breast cancers. ERα-positive breast cancers are successfully treated with tamoxifen; however, a significant number of patients develop tamoxifen-resistant disease. We show that in vitro development of tamoxifen-resistance is associated with increased sensitivity to the OGT small molecule inhibitor OSMI-1. Global transcriptome profiling revealed that TamS cells adapt to OSMI-1 treatment by increasing the expression of histone genes. This is known to mediate chromatin compaction. In contrast, TamR cells respond to OGT inhibition by activating the unfolded protein response and by significantly increasing ERRFI1 expression. ERRFI1 is an endogenous inhibitor of ERBB-signaling, which is a known driver of tamoxifen-resistance. We show that ERRFI1 is selectively downregulated in ERα-positive breast cancers and breast cancers driven by ERBB2. This likely occurs via promoter methylation. Finally, we show that increased ERRFI1 expression is associated with extended survival in patients with ERα-positive tumors (p = 9.2e-8). In summary, we show that tamoxifen-resistance is associated with sensitivity to OSMI-1, and propose that this is explained in part through an epigenetic activation of the tumor-suppressor ERRFI1 in response to OSMI-1 treatment.
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100
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Lan J, Rajan N, Bizet M, Penning A, Singh NK, Guallar D, Calonne E, Li Greci A, Bonvin E, Deplus R, Hsu PJ, Nachtergaele S, Ma C, Song R, Fuentes-Iglesias A, Hassabi B, Putmans P, Mies F, Menschaert G, Wong JJL, Wang J, Fidalgo M, Yuan B, Fuks F. Functional role of Tet-mediated RNA hydroxymethylcytosine in mouse ES cells and during differentiation. Nat Commun 2020; 11:4956. [PMID: 33009383 PMCID: PMC7532169 DOI: 10.1038/s41467-020-18729-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/01/2020] [Indexed: 12/23/2022] Open
Abstract
Tet-enzyme-mediated 5-hydroxymethylation of cytosines in DNA plays a crucial role in mouse embryonic stem cells (ESCs). In RNA also, 5-hydroxymethylcytosine (5hmC) has recently been evidenced, but its physiological roles are still largely unknown. Here we show the contribution and function of this mark in mouse ESCs and differentiating embryoid bodies. Transcriptome-wide mapping in ESCs reveals hundreds of messenger RNAs marked by 5hmC at sites characterized by a defined unique consensus sequence and particular features. During differentiation a large number of transcripts, including many encoding key pluripotency-related factors (such as Eed and Jarid2), show decreased cytosine hydroxymethylation. Using Tet-knockout ESCs, we find Tet enzymes to be partly responsible for deposition of 5hmC in mRNA. A transcriptome-wide search further reveals mRNA targets to which Tet1 and Tet2 bind, at sites showing a topology similar to that of 5hmC sites. Tet-mediated RNA hydroxymethylation is found to reduce the stability of crucial pluripotency-promoting transcripts. We propose that RNA cytosine 5-hydroxymethylation by Tets is a mark of transcriptome flexibility, inextricably linked to the balance between pluripotency and lineage commitment. TET mediated RNA-hydroxymethylation (5hmC) has been detected in mammals, but its physiological role remains unclear. Here the authors map 5hmC during embryonic stem cell (ESC) differentiation and find that Tet-mediated RNA hydroxymethylation reduces the stability of crucial pluripotency related transcripts.
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Affiliation(s)
- Jie Lan
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Nicholas Rajan
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Audrey Penning
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Nitesh K Singh
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Diana Guallar
- CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Andrea Li Greci
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Elise Bonvin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Phillip J Hsu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, and Howard Hughes Medical Institute, University of Chicago, Chicago, IL, 60637, USA
| | - Sigrid Nachtergaele
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, and Howard Hughes Medical Institute, University of Chicago, Chicago, IL, 60637, USA
| | - Chengjie Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, 430072, Wuhan, People's Republic of China
| | - Renhua Song
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Alejandro Fuentes-Iglesias
- CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Bouchra Hassabi
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Pascale Putmans
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Frédérique Mies
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Gerben Menschaert
- Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Lab of Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium
| | - Justin J L Wong
- Epigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Jianlong Wang
- Department of Medicine, Columbia Center for Human Development (CCHD), Columbia University Irving Medical Center (CUIMC), New York, NY, 10032, USA
| | - Miguel Fidalgo
- CiMUS, Universidade de Santiago de Compostela-Health Research Institute (IDIS), Santiago de Compostela, Coruña, Spain
| | - Bifeng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, 430072, Wuhan, People's Republic of China
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB Cancer Research Center (U-CRC), Welbio Investigator, Université Libre de Bruxelles (ULB), Brussels, Belgium. .,WELBIO (Walloon Excellence in Lifesciences & Biotechnology), Brussels, Belgium.
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