1
|
Occean JR, Yang N, Sun Y, Dawkins MS, Munk R, Belair C, Dar S, Anerillas C, Wang L, Shi C, Dunn C, Bernier M, Price NL, Kim JS, Cui CY, Fan J, Bhattacharyya M, De S, Maragkakis M, de Cabo R, Sidoli S, Sen P. Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging. Nat Commun 2024; 15:6357. [PMID: 39069555 PMCID: PMC11284234 DOI: 10.1038/s41467-024-50725-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 07/15/2024] [Indexed: 07/30/2024] Open
Abstract
DNA hydroxymethylation (5hmC), the most abundant oxidative derivative of DNA methylation, is typically enriched at enhancers and gene bodies of transcriptionally active and tissue-specific genes. Although aberrant genomic 5hmC has been implicated in age-related diseases, its functional role in aging remains unknown. Here, using mouse liver and cerebellum as model organs, we show that 5hmC accumulates in gene bodies associated with tissue-specific function and restricts the magnitude of gene expression changes with age. Mechanistically, 5hmC decreases the binding of splicing associated factors and correlates with age-related alternative splicing events. We found that various age-related contexts, such as prolonged quiescence and senescence, drive the accumulation of 5hmC with age. We provide evidence that this age-related transcriptionally restrictive function is conserved in mouse and human tissues. Our findings reveal that 5hmC regulates tissue-specific function and may play a role in longevity.
Collapse
Affiliation(s)
- James R Occean
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Na Yang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Yan Sun
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY, USA
| | - Marshall S Dawkins
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Cedric Belair
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Showkat Dar
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Lin Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Changyou Shi
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Christopher Dunn
- Flow Cytometry Unit, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Michel Bernier
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Nathan L Price
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Julie S Kim
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY, USA
| | - Chang-Yi Cui
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Jinshui Fan
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | | | - Supriyo De
- Computational Biology and Genomics Core, Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Manolis Maragkakis
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein School of Medicine, Bronx, NY, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, Baltimore, MD, USA.
| |
Collapse
|
2
|
Occean JR, Yang N, Sun Y, Dawkins MS, Munk R, Belair C, Dar S, Anerillas C, Wang L, Shi C, Dunn C, Bernier M, Price NL, Kim JS, Cui CY, Fan J, Bhattacharyya M, De S, Maragkakis M, deCabo R, Sidoli S, Sen P. Gene body DNA hydroxymethylation restricts the magnitude of transcriptional changes during aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.15.528714. [PMID: 36824863 PMCID: PMC9949049 DOI: 10.1101/2023.02.15.528714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
DNA hydroxymethylation (5hmC), the most abundant oxidative derivative of DNA methylation, is typically enriched at enhancers and gene bodies of transcriptionally active and tissue-specific genes. Although aberrant genomic 5hmC has been implicated in age-related diseases, its functional role in aging remains unknown. Here, using mouse liver and cerebellum as model organs, we show that 5hmC accumulates in gene bodies associated with tissue-specific function and restricts the magnitude of gene expression changes with age. Mechanistically, 5hmC decreases the binding of splicing associated factors and correlates with age-related alternative splicing events. We found that various age-related contexts, such as prolonged quiescence and senescence, drive the accumulation of 5hmC with age. We provide evidence that this age-related transcriptionally restrictive function is conserved in mouse and human tissues. Our findings reveal that 5hmC regulates tissue-specific function and may play a role in longevity.
Collapse
|
3
|
Huang W, Chen ACH, Wei X, Fong SW, Yeung WSB, Lee YL. Uncovering the role of TET2-mediated ENPEP activation in trophoblast cell fate determination. Cell Mol Life Sci 2024; 81:270. [PMID: 38886218 DOI: 10.1007/s00018-024-05306-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/24/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024]
Abstract
Early trophoblast differentiation is crucial for embryo implantation, placentation and fetal development. Dynamic changes in DNA methylation occur during preimplantation development and are critical for cell fate determination. However, the underlying regulatory mechanism remains unclear. Recently, we derived morula-like expanded potential stem cells from human preimplantation embryos (hEPSC-em), providing a valuable tool for studying early trophoblast differentiation. Data analysis on published datasets showed differential expressions of DNA methylation enzymes during early trophoblast differentiation in human embryos and hEPSC-em derived trophoblastic spheroids. We demonstrated downregulation of DNA methyltransferase 3 members (DNMT3s) and upregulation of ten-eleven translocation methylcytosine dioxygenases (TETs) during trophoblast differentiation. While DNMT inhibitor promoted trophoblast differentiation, TET inhibitor hindered the process and reduced implantation potential of trophoblastic spheroids. Further integrative analysis identified that glutamyl aminopeptidase (ENPEP), a trophectoderm progenitor marker, was hypomethylated and highly expressed in trophoblast lineages. Concordantly, progressive loss of DNA methylation in ENPEP promoter and increased ENPEP expression were detected in trophoblast differentiation. Knockout of ENPEP in hEPSC-em compromised trophoblast differentiation potency, reduced adhesion and invasion of trophoblastic spheroids, and impeded trophoblastic stem cell (TSC) derivation. Importantly, TET2 was involved in the loss of DNA methylation and activation of ENPEP expression during trophoblast differentiation. TET2-null hEPSC-em failed to produce TSC properly. Collectively, our results illustrated the crucial roles of ENPEP and TET2 in trophoblast fate commitments and the unprecedented TET2-mediated loss of DNA methylation in ENPEP promoter.
Collapse
Affiliation(s)
- Wen Huang
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China
- Centre for Translational Stem Cell Biology, Science Park, Sha Tin , Hong Kong, Special Administrative Region, China
| | - Andy Chun Hang Chen
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China
- Centre for Translational Stem Cell Biology, Science Park, Sha Tin , Hong Kong, Special Administrative Region, China
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Xujin Wei
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - Sze Wan Fong
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China
| | - William Shu Biu Yeung
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China.
- Centre for Translational Stem Cell Biology, Science Park, Sha Tin , Hong Kong, Special Administrative Region, China.
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
| | - Yin Lau Lee
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Special Administrative Region, China.
- Centre for Translational Stem Cell Biology, Science Park, Sha Tin , Hong Kong, Special Administrative Region, China.
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
| |
Collapse
|
4
|
Zhang J, Cao J, Liu Y, Zhao H. Advances in the Pathogenesis of Steroid-Associated Osteonecrosis of the Femoral Head. Biomolecules 2024; 14:667. [PMID: 38927070 PMCID: PMC11202272 DOI: 10.3390/biom14060667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/30/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Osteonecrosis of the femoral head (ONFH) is a refractory orthopedic condition characterized by bone cell ischemia, necrosis, bone trabecular fracture, and clinical symptoms such as pain, femoral head collapse, and joint dysfunction that can lead to disability. The disability rate of ONFH is very high, which imposes a significant economic burden on both families and society. Steroid-associated osteonecrosis of the femoral head (SANFH) is the most common type of ONFH. However, the pathogenesis of SANFH remains unclear, and it is an urgent challenge for orthopedic surgeons to explore it. In this paper, the pathogenesis of SANFH and its related signaling pathways were briefly reviewed to enhance comprehension of the pathogenesis and prevention of SANFH.
Collapse
Affiliation(s)
- Jie Zhang
- The First Clinical College of Medicine, Lanzhou University, Lanzhou 730000, China; (J.Z.); (J.C.); (Y.L.)
| | - Jianze Cao
- The First Clinical College of Medicine, Lanzhou University, Lanzhou 730000, China; (J.Z.); (J.C.); (Y.L.)
| | - Yongfei Liu
- The First Clinical College of Medicine, Lanzhou University, Lanzhou 730000, China; (J.Z.); (J.C.); (Y.L.)
| | - Haiyan Zhao
- Department of Orthopedics, The First Hospital of Lanzhou University, Lanzhou 730000, China
| |
Collapse
|
5
|
Ma T, Zhang Q, Zhang S, Yue D, Wang F, Ren Y, Zhang H, Wang Y, Wu Y, Liu LE, Yu F. Research progress of human key DNA and RNA methylation-related enzymes assay. Talanta 2024; 273:125872. [PMID: 38471421 DOI: 10.1016/j.talanta.2024.125872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/18/2024] [Accepted: 03/03/2024] [Indexed: 03/14/2024]
Abstract
Gene methylation-related enzymes (GMREs) are disfunction and aberrantly expressed in a variety of cancers, such as lung, gastric, and pancreatic cancers and have important implications for human health. Therefore,it is critical for early diagnosis and therapy of tumor to develop strategies that allow rapid and sensitive quantitative and qualitative detection of GMREs. With the development of modern analytical techniques and the application of various biosensors, there are numerous methods have been developed for analysis of GMREs. Therefore, this paper provides a systematic review of the strategies for level and activity assay of various GMREs including methyltransferases and demethylase. The detection methods mainly involve immunohistochemistry, colorimetry, fluorescence, chemiluminescence, electrochemistry, etc. Then, this review also addresses the coordinated role of various detection probes, novel nanomaterials, and signal amplification methods. The aim is to highlight potential challenges in the present field, to expand the analytical application of GMREs detection strategies, and to meet the urgent need for future disease diagnosis and intervention.
Collapse
Affiliation(s)
- Tiantian Ma
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Qiongwen Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuying Zhang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Dan Yue
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fanting Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yujie Ren
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Hengmiao Zhang
- School of Information Management, Zhengzhou University, Zhengzhou 450001, China
| | - Yinuo Wang
- Zhengzhou Foreign Language School, Zhengzhou 450001, China
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Li-E Liu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fei Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| |
Collapse
|
6
|
Wu X, Tang Y, Lu X, Liu Y, Liu X, Sun Q, Wang L, Huang W, Liu A, Liu L, Chao J, Zhang X, Qiu H. Endothelial cell-derived extracellular vesicles modulate the therapeutic efficacy of mesenchymal stem cells through IDH2/TET pathway in ARDS. Cell Commun Signal 2024; 22:293. [PMID: 38802896 PMCID: PMC11129421 DOI: 10.1186/s12964-024-01672-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Acute respiratory distress syndrome (ARDS) is a severe and fatal disease. Although mesenchymal stem cell (MSC)-based therapy has shown remarkable efficacy in treating ARDS in animal experiments, clinical outcomes have been unsatisfactory, which may be attributed to the influence of the lung microenvironment during MSC administration. Extracellular vesicles (EVs) derived from endothelial cells (EC-EVs) are important components of the lung microenvironment and play a crucial role in ARDS. However, the effect of EC-EVs on MSC therapy is still unclear. In this study, we established lipopolysaccharide (LPS) - induced acute lung injury model to evaluate the impact of EC-EVs on the reparative effects of bone marrow-derived MSC (BM-MSC) transplantation on lung injury and to unravel the underlying mechanisms. METHODS EVs were isolated from bronchoalveolar lavage fluid of mice with LPS - induced acute lung injury and patients with ARDS using ultracentrifugation. and the changes of EC-EVs were analysed using nanoflow cytometry analysis. In vitro assays were performed to establish the impact of EC-EVs on MSC functions, including cell viability and migration, while in vivo studies were performed to validate the therapeutic effect of EC-EVs on MSCs. RNA-Seq analysis, small interfering RNA (siRNA), and a recombinant lentivirus were used to investigate the underlying mechanisms. RESULTS Compared with that in non-ARDS patients, the quantity of EC-EVs in the lung microenvironment was significantly greater in patients with ARDS. EVs derived from lipopolysaccharide-stimulated endothelial cells (LPS-EVs) significantly decreased the viability and migration of BM-MSCs. Furthermore, engrafting BM-MSCs pretreated with LPS-EVs promoted the release of inflammatory cytokines and increased pulmonary microvascular permeability, aggravating lung injury. Mechanistically, LPS-EVs reduced the expression level of isocitrate dehydrogenase 2 (IDH2), which catalyses the formation of α-ketoglutarate (α-KG), an intermediate product of the tricarboxylic acid (TCA) cycle, in BM-MSCs. α-KG is a cofactor for ten-eleven translocation (TET) enzymes, which catalyse DNA hydroxymethylation in BM-MSCs. CONCLUSIONS This study revealed that EC-EVs in the lung microenvironment during ARDS can affect the therapeutic efficacy of BM-MSCs through the IDH2/TET pathway, providing potential strategies for improving the therapeutic efficacy of MSC-based therapy in the clinic.
Collapse
Affiliation(s)
- Xiao Wu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Ying Tang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Xinxing Lu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Yigao Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Xu Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Qin Sun
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Lu Wang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Wei Huang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Airan Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Ling Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Jie Chao
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
- Department of Physiology, School of Medicine, Southeast University, Nanjing, 210009, China
| | - Xiwen Zhang
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China.
| | - Haibo Qiu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| |
Collapse
|
7
|
Zhang L, Mu Y, Li T, Hu J, Lin H, Zhang L. Molecular basis of an atypical dsDNA 5mC/6mA bifunctional dioxygenase CcTet from Coprinopsis cinerea in catalyzing dsDNA 5mC demethylation. Nucleic Acids Res 2024; 52:3886-3895. [PMID: 38324471 PMCID: PMC11040006 DOI: 10.1093/nar/gkae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/22/2023] [Accepted: 01/24/2024] [Indexed: 02/09/2024] Open
Abstract
The eukaryotic epigenetic modifications 5-methyldeoxycytosine (5mC) and N6-methyldeoxyadenine (6mA) have indispensable regulatory roles in gene expression and embryonic development. We recently identified an atypical bifunctional dioxygenase CcTet from Coprinopsis cinerea that works on both 5mC and 6mA demethylation. The nonconserved residues Gly331 and Asp337 of CcTet facilitate 6mA accommodation, while D337F unexpectedly abolishes 5mC oxidation activity without interfering 6mA demethylation, indicating a prominent distinct but unclear 5mC oxidation mechanism to the conventional Tet enzymes. Here, we assessed the molecular mechanism of CcTet in catalyzing 5mC oxidation by representing the crystal structure of CcTet-5mC-dsDNA complex. We identified the distinct mechanism by which CcTet recognizes 5mC-dsDNA compared to 6mA-dsDNA substrate. Moreover, Asp337 was found to have a central role in compensating for the loss of a critical 5mC-stablizing H-bond observed in conventional Tet enzymes, and stabilizes 5mC and subsequent intermediates through an H-bond with the N4 atom of the substrates. These findings improve our understanding of Tet enzyme functions in the dsDNA 5mC and 6mA demethylation pathways, and provide useful information for future discovery of small molecular probes targeting Tet enzymes in DNA active demethylation processes.
Collapse
Affiliation(s)
- Lin Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yajuan Mu
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Tingting Li
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jingyan Hu
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Houwen Lin
- Research Centre for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen 518055, China
| | - Liang Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| |
Collapse
|
8
|
Smithwick ER, Bhagi-Damodaran A, Damodaran AR. Equilibrium dialysis with HPLC detection to measure substrate binding affinity of a non-heme iron halogenase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.588023. [PMID: 38617253 PMCID: PMC11014511 DOI: 10.1101/2024.04.03.588023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Determination of substrate binding affinity (Kd) is critical to understanding enzyme function. An extensive number of methods have been developed and employed to study ligand/substrate binding, but the best approach depends greatly on the substrate and the enzyme in question. Below we describe how to measure the Kd of BesD, a non-heme iron halogenase, for its native substrate lysine using equilibrium dialysis with subsequent detection with High Performance Liquid Chromatography (HPLC). This method can be performed in anaerobic glove bag settings, requires readily available HPLC instrumentation for subsequent detection, and is adaptable to meet the needs of a variety of substrate affinity measurements.
Collapse
Affiliation(s)
- Elizabeth R. Smithwick
- Department of Chemistry, University of Minnesota -Twin Cities, 207 Pleasant St. SE. Minneapolis, MN 55455
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota -Twin Cities, 207 Pleasant St. SE. Minneapolis, MN 55455
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota -Twin Cities, 207 Pleasant St. SE. Minneapolis, MN 55455
| |
Collapse
|
9
|
Meng WY, Wang ZX, Zhang Y, Hou Y, Xue JH. Epigenetic marks or not? The discovery of novel DNA modifications in eukaryotes. J Biol Chem 2024; 300:106791. [PMID: 38403247 PMCID: PMC11065753 DOI: 10.1016/j.jbc.2024.106791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/24/2024] [Accepted: 02/04/2024] [Indexed: 02/27/2024] Open
Abstract
DNA modifications add another layer of complexity to the eukaryotic genome to regulate gene expression, playing critical roles as epigenetic marks. In eukaryotes, the study of DNA epigenetic modifications has been confined to 5mC and its derivatives for decades. However, rapid developing approaches have witnessed the expansion of DNA modification reservoirs during the past several years, including the identification of 6mA, 5gmC, 4mC, and 4acC in diverse organisms. However, whether these DNA modifications function as epigenetic marks requires careful consideration. In this review, we try to present a panorama of all the DNA epigenetic modifications in eukaryotes, emphasizing recent breakthroughs in the identification of novel DNA modifications. The characterization of their roles in transcriptional regulation as potential epigenetic marks is summarized. More importantly, the pathways for generating or eliminating these DNA modifications, as well as the proteins involved are comprehensively dissected. Furthermore, we briefly discuss the potential challenges and perspectives, which should be taken into account while investigating novel DNA modifications.
Collapse
Affiliation(s)
- Wei-Ying Meng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital affiliated to Tongji University, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zi-Xin Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital affiliated to Tongji University, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yunfang Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yujun Hou
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Jian-Huang Xue
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Tongji Hospital affiliated to Tongji University, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China.
| |
Collapse
|
10
|
Belle R, Saraç H, Salah E, Bhushan B, Szykowska A, Roper G, Tumber A, Kriaucionis S, Burgess-Brown N, Schofield CJ, Brown T, Kawamura A. Focused Screening Identifies Different Sensitivities of Human TET Oxygenases to the Oncometabolite 2-Hydroxyglutarate. J Med Chem 2024; 67:4525-4540. [PMID: 38294854 PMCID: PMC10983004 DOI: 10.1021/acs.jmedchem.3c01820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/10/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
Ten-eleven translocation enzymes (TETs) are Fe(II)/2-oxoglutarate (2OG) oxygenases that catalyze the sequential oxidation of 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine in eukaryotic DNA. Despite their roles in epigenetic regulation, there is a lack of reported TET inhibitors. The extent to which 2OG oxygenase inhibitors, including clinically used inhibitors and oncometabolites, modulate DNA modifications via TETs has been unclear. Here, we report studies on human TET1-3 inhibition by a set of 2OG oxygenase-focused inhibitors, employing both enzyme-based and cellular assays. Most inhibitors manifested similar potencies for TET1-3 and caused increases in cellular 5hmC levels. (R)-2-Hydroxyglutarate, an oncometabolite elevated in isocitrate dehydrogenase mutant cancer cells, showed different degrees of inhibition, with TET1 being less potently inhibited than TET3 and TET2, potentially reflecting the proposed role of TET2 mutations in tumorigenesis. The results highlight the tractability of TETs as drug targets and provide starting points for selective inhibitor design.
Collapse
Affiliation(s)
- Roman Belle
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Hilal Saraç
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
| | - Eidarus Salah
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Bhaskar Bhushan
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
| | - Aleksandra Szykowska
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Grace Roper
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
| | - Anthony Tumber
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Skirmantas Kriaucionis
- Ludwig
Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Nicola Burgess-Brown
- Centre
for Medicines Discovery, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Tom Brown
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Akane Kawamura
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- Chemistry
− School of Natural and Environmental Sciences, Bedson Building, Newcastle University, NE1 7RU Newcastle upon Tyne, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, University of Oxford, Wellcome Trust Centre for Human
Genetics, Roosevelt Drive, OX3 7BN Oxford, United Kingdom
| |
Collapse
|
11
|
Linowiecka K, Guz J, Dziaman T, Urbanowska-Domańska O, Zarakowska E, Szpila A, Szpotan J, Skalska-Bugała A, Mijewski P, Siomek-Górecka A, Różalski R, Gackowski D, Oliński R, Foksiński M. The level of active DNA demethylation compounds in leukocytes and urine samples as potential epigenetic biomarkers in breast cancer patients. Sci Rep 2024; 14:6481. [PMID: 38499584 PMCID: PMC10948817 DOI: 10.1038/s41598-024-56326-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
The active DNA demethylation process, which involves TET proteins, can affect DNA methylation pattern. TET dependent demethylation results in DNA hypomethylation by oxidation 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) and its derivatives. Moreover, TETs' activity may be upregulated by ascorbate. Given that aberrant DNA methylation of genes implicated in breast carcinogenesis may be involved in tumor progression, we wanted to determine whether breast cancer patients exert changes in the active DNA demethylation process. The study included blood samples from breast cancer patients (n = 74) and healthy subjects (n = 71). We analyzed the expression of genes involved in the active demethylation process (qRT-PCR), and 5-mC and its derivatives level (2D-UPLC MS/MS). The ascorbate level was determined using UPLC-MS. Breast cancer patients had significantly higher TET3 expression level, lower 5-mC and 5-hmC DNA levels. TET3 was significantly increased in luminal B breast cancer patients with expression of hormone receptors. Moreover, the ascorbate level in the plasma of breast cancer patients was decreased with the accompanying increase of sodium-dependent vitamin C transporters (SLC23A1 and SLC23A2). The presented study indicates the role of TET3 in DNA demethylation in breast carcinogenesis.
Collapse
Affiliation(s)
- Kinga Linowiecka
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland.
- Department of Human Biology, Institute of Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland.
| | - Jolanta Guz
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Tomasz Dziaman
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Olga Urbanowska-Domańska
- Department of Oncology, Professor Franciszek Lukaszczyk Oncology Centre, Romanowskiej 2, 85-796, Bydgoszcz, Poland
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Anna Szpila
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Justyna Szpotan
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
- Department of Human Biology, Institute of Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
| | - Aleksandra Skalska-Bugała
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Paweł Mijewski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Agnieszka Siomek-Górecka
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Rafał Różalski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Ryszard Oliński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Marek Foksiński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland.
| |
Collapse
|
12
|
Kriukienė E, Tomkuvienė M, Klimašauskas S. 5-Hydroxymethylcytosine: the many faces of the sixth base of mammalian DNA. Chem Soc Rev 2024; 53:2264-2283. [PMID: 38205583 DOI: 10.1039/d3cs00858d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Epigenetic phenomena play a central role in cell regulatory processes and are important factors for understanding complex human disease. One of the best understood epigenetic mechanisms is DNA methylation. In the mammalian genome, cytosines (C) in CpG dinucleotides were long known to undergo methylation at the 5-position of the pyrimidine ring (mC). Later it was found that mC can be oxidized to 5-hydroxymethylcytosine (hmC) or even further to 5-formylcytosine (fC) and to 5-carboxylcytosine (caC) by the action of 2-oxoglutarate-dependent dioxygenases of the TET family. These findings unveiled a long elusive mechanism of active DNA demethylation and bolstered a wave of studies in the area of epigenetic regulation in mammals. This review is dedicated to critical assessment of recent data on biochemical and chemical aspects of the formation and conversion of hmC in DNA, analytical techniques used for detection and mapping of this nucleobase in mammalian genomes as well as epigenetic roles of hmC in DNA replication, transcription, cell differentiation and human disease.
Collapse
Affiliation(s)
- Edita Kriukienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Miglė Tomkuvienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| | - Saulius Klimašauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania.
| |
Collapse
|
13
|
Canberk S, Gonçalves J, Rios E, Povoa AA, Tastekin E, Sobrinho-Simões M, Uguz A, Aydin O, Ince U, Soares P, Máximo V. The Role of 5-Hydroxymethylcytosine as a Potential Epigenetic Biomarker in a Large Series of Thyroid Neoplasms. Endocr Pathol 2024; 35:25-39. [PMID: 38285158 PMCID: PMC10944390 DOI: 10.1007/s12022-024-09800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2024] [Indexed: 01/30/2024]
Abstract
Cytosine modifications at the 5-carbon position play a critical role in gene expression regulation and have been implicated in cancer development. 5-Hydroxymethylcytosine (5hmC), arising from 5-methylcytosine (5-mC) oxidation, has shown promise as a potential malignancy marker due to its depletion in various human cancers. However, its significance in thyroid tumors remains underexplored, primarily due to limited data. In our study, we evaluated 5hmC expression levels by immunohistochemistry in a cohort of 318 thyroid tumors. Our analysis revealed significant correlations between 5hmC staining extension scores and nodule size, vascular invasion, and oncocytic morphology. Nuclear 5hmC staining intensity demonstrated associations with focality, capsule status, extrathyroidal extension, vascular invasion, and oncocytic morphology. Follicular/oncocytic adenomas exhibited higher 5hmC expression than uncertain malignant potential (UMP) or noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTP), as well as malignant neoplasms, including papillary thyroid carcinomas (PTCs), oncocytic carcinomas (OCAs), follicular thyroid carcinomas (FTCs), and invasive encapsulated follicular variants of PTC (IEFV-PTC). TERT promoter mutation cases showed notably lower values for the 5hmC expression, while RAS (H, N, or K) mutations, particularly HRAS mutations, were associated with higher 5hmC expression. Additionally, we identified, for the first time, a significant link between 5hmC expression and oncocytic morphology. However, despite the merits of these discoveries, we acknowledge that 5hmC currently cannot segregate minimally invasive from widely invasive tumors, although 5hmC levels were lower in wi-FPTCs. Further research is needed to explore the potential clinical implications of 5hmC in thyroid tumors.
Collapse
Affiliation(s)
- Sule Canberk
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - João Gonçalves
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Elisabete Rios
- Department of Pathology, Faculty of Medicine of the University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Antónia A Povoa
- Department of General Surgery, Centro Hospitalar de Vila Nova de Gaia/Espinho (CHVNG/E), 4434-502, Vila Nova de Gaia, Portugal
| | - Ebru Tastekin
- Medical Faculty, Department of Pathology, Trakya University, Edirne, Turkey
| | - Manuel Sobrinho-Simões
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
- Department of Pathology, Faculty of Medicine of the University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Aysun Uguz
- Medical Faculty, Department of Pathology, Çukurova University, Adana, Turkey
| | - Ozlem Aydin
- Department of Pathology, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Umit Ince
- Department of Pathology, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Paula Soares
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
- Faculty of Medicine of the University of Porto (FMUP), Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal
- Department of Pathology, Faculty of Medicine of the University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Valdemar Máximo
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.
- Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.
- Faculty of Medicine of the University of Porto (FMUP), Alameda Professor Hernâni Monteiro, 4200-319, Porto, Portugal.
- Department of Pathology, Faculty of Medicine of the University of Porto, Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal.
| |
Collapse
|
14
|
Lee SM. Detecting DNA hydroxymethylation: exploring its role in genome regulation. BMB Rep 2024; 57:135-142. [PMID: 38449301 PMCID: PMC10979348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/15/2024] [Accepted: 02/01/2024] [Indexed: 03/08/2024] Open
Abstract
DNA methylation is one of the most extensively studied epigenetic regulatory mechanisms, known to play crucial roles in various organisms. It has been implicated in the regulation of gene expression and chromatin changes, ranging from global alterations during cell state transitions to locus-specific modifications. 5-hydroxymethylcytosine (5hmC) is produced by a major oxidation, from 5-methylcytosine (5mC), catalyzed by the ten-eleven translocation (TET) enzymes, and is gradually being recognized for its significant role in genome regulation. With the development of state-of-the-art experimental techniques, it has become possible to detect and distinguish 5mC and 5hmC at base resolution. Various techniques have evolved, encompassing chemical and enzymatic approaches, as well as thirdgeneration sequencing techniques. These advancements have paved the way for a thorough exploration of the role of 5hmC across a diverse array of cell types, from embryonic stem cells (ESCs) to various differentiated cells. This review aims to comprehensively report on recent techniques and discuss the emerging roles of 5hmC. [BMB Reports 2024; 57(3): 135-142].
Collapse
Affiliation(s)
- Sun-Min Lee
- Department of Physics, Konkuk Univeristy, Seoul 05029, Korea
| |
Collapse
|
15
|
Zhang L, Duan HC, Paduch M, Hu J, Zhang C, Mu Y, Lin H, He C, Kossiakoff AA, Jia G, Zhang L. The Molecular Basis of Human ALKBH3 Mediated RNA N 1 -methyladenosine (m 1 A) Demethylation. Angew Chem Int Ed Engl 2024; 63:e202313900. [PMID: 38158383 DOI: 10.1002/anie.202313900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
N1 -methyladenosine (m1 A) is a prevalent post-transcriptional RNA modification, and the distribution and dynamics of the modification play key epitranscriptomic roles in cell development. At present, the human AlkB Fe(II)/α-ketoglutarate-dependent dioxygenase family member ALKBH3 is the only known mRNA m1 A demethylase, but its catalytic mechanism remains unclear. Here, we present the structures of ALKBH3-oligo crosslinked complexes obtained with the assistance of a synthetic antibody crystallization chaperone. Structural and biochemical results showed that ALKBH3 utilized two β-hairpins (β4-loop-β5 and β'-loop-β'') and the α2 helix to facilitate single-stranded substrate binding. Moreover, a bubble-like region around Asp194 and a key residue inside the active pocket (Thr133) enabled specific recognition and demethylation of m1 A- and 3-methylcytidine (m3 C)-modified substrates. Mutation of Thr133 to the corresponding residue in the AlkB Fe(II)/α-ketoglutarate-dependent dioxygenase family members FTO or ALKBH5 converted ALKBH3 substrate selectivity from m1 A to N6 -methyladenosine (m6 A), as did Asp194 deletion. Our findings provide a molecular basis for understanding the mechanisms of substrate recognition and m1 A demethylation by ALKBH3. This study is expected to aid structure-guided design of chemical probes for further functional studies and therapeutic applications.
Collapse
Affiliation(s)
- Lin Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Hong-Chao Duan
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Marcin Paduch
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Jingyan Hu
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chi Zhang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yajuan Mu
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Houwen Lin
- Research Centre for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- Institute of Marine Biomedicine, Shenzhen Polytechnic, Shenzhen, 518055, China
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Anthony A Kossiakoff
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Peking-Tsinghua Center for Life Sciences, Beijing, 100871, China
| | - Liang Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| |
Collapse
|
16
|
He W, Yin X, Xu C, Liu X, Huang Y, Yang C, Xu Y, Hu L. Ascorbic Acid Reprograms Epigenome and Epitranscriptome by Reducing Fe(III) in the Catalytic Cycle of Dioxygenases. ACS Chem Biol 2024; 19:129-140. [PMID: 38100359 DOI: 10.1021/acschembio.3c00567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Ascorbic acid (ASC) has been reported to stimulate DNA iterative oxidase ten-eleven translocation (TET) enzymes, Jumonji C-domain-containing histone demethylases, and potentially RNA m6A demethylases FTO and ALKBH5 as a cofactor. Although ascorbic acid has been widely investigated in reprogramming DNA and histone methylation status in vitro, in cultured cells and mouse models, its specific role in the catalytic cycle of dioxygenases remains enigmatic. Here, we systematically investigated the stimulation of ASC toward TET2, ALKBH3, histone demethylases, and FTO. We find that ASC reprograms epitranscriptome by erasing the hypermethylated m6A sites in mRNA. Biochemistry and electron spin resonance assays demonstrate that ASC enters the active pocket of dioxygenases and reduces Fe(III), either incorporated upon protein synthesis or generated upon rebounding the hydroxyl radical during oxidation, into Fe(II). Finally, we propose a remedied model for the catalytic cycle of dioxygenases by adding in the essential cofactor, ASC, which refreshes and regenerates inactive dioxygenase through recycling Fe(III) into Fe(II) in a dynamic "hit-and-run" manner.
Collapse
Affiliation(s)
- Weizhi He
- Cancer Institute, Fudan university Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xiaotong Yin
- Cancer Institute, Fudan university Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Chu Xu
- Cancer Institute, Fudan university Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xiangyue Liu
- Cancer Institute, Fudan university Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yue Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Caiguang Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanhui Xu
- Cancer Institute, Fudan university Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Lulu Hu
- Cancer Institute, Fudan university Shanghai Cancer Center, Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai 200032, China
| |
Collapse
|
17
|
Treadway CJ, Boyer JA, Yang S, Yang H, Liu M, Li Z, Cheng M, Marzluff WF, Ye D, Xiong Y, Baldwin AS, Zhang Q, Brown NG. Using NMR to Monitor TET-Dependent Methylcytosine Dioxygenase Activity and Regulation. ACS Chem Biol 2024; 19:15-21. [PMID: 38193366 PMCID: PMC11075173 DOI: 10.1021/acschembio.3c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
The active removal of DNA methylation marks is governed by the ten-eleven translocation (TET) family of enzymes (TET1-3), which iteratively oxidize 5-methycytosine (5mC) into 5-hydroxymethycytosine (5hmC), and then 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TET proteins are frequently mutated in myeloid malignancies or inactivated in solid tumors. These methylcytosine dioxygenases are α-ketoglutarate (αKG)-dependent and are, therefore, sensitive to metabolic homeostasis. For example, TET2 is activated by vitamin C (VC) and inhibited by specific oncometabolites. However, understanding the regulation of the TET2 enzyme by different metabolites and its activity remains challenging because of limitations in the methods used to simultaneously monitor TET2 substrates, products, and cofactors during catalysis. Here, we measure TET2-dependent activity in real time using NMR. Additionally, we demonstrate that in vitro activity of TET2 is highly dependent on the presence of VC in our system and is potently inhibited by an intermediate metabolite of the TCA cycle, oxaloacetate (OAA). Despite these opposing effects on TET2 activity, the binding sites of VC and OAA on TET2 are shared with αKG. Overall, our work suggests that NMR can be effectively used to monitor TET2 catalysis and illustrates how TET activity is regulated by metabolic and cellular conditions at each oxidation step.
Collapse
Affiliation(s)
- Colton J. Treadway
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Joshua A Boyer
- Department. of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Shiyue Yang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Hui Yang
- Molecular & Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai College of Medicine, Fudan University, Shanghai 200032, China
- Present address: Department of Neurosurgery, Huashan Hospital, Institute for Translational Brain Research, Shanghai College of Medicine, Fudan University, Shanghai, 200032, China
| | - Mengxi Liu
- Molecular & Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai College of Medicine, Fudan University, Shanghai 200032, China
- Present address: Plexium, Inc., San Diego, CA 92121, United States
| | - Zhijun Li
- Department. of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Meng Cheng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - William F. Marzluff
- Department. of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Dan Ye
- Molecular & Cell Biology Lab, Institutes of Biomedical Sciences, Shanghai College of Medicine, Fudan University, Shanghai 200032, China
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Present address: Cullgen, Inc., 12730 High Bluff Drive, San Diego, CA, 92130, United States
| | - Albert S. Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Qi Zhang
- Department. of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Nicholas G. Brown
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| |
Collapse
|
18
|
Li Q, Fan J, Zhou Z, Ma Z, Che Z, Wu Y, Yang X, Liang P, Li H. AID-induced CXCL12 upregulation enhances castration-resistant prostate cancer cell metastasis by stabilizing β-catenin expression. iScience 2023; 26:108523. [PMID: 38162032 PMCID: PMC10755053 DOI: 10.1016/j.isci.2023.108523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 11/14/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Prostate cancer (PCa) is one of the most common malignant diseases of urinary system and has poor prognosis after progression to castration-resistant prostate cancer (CRPC), and increased cytosine methylation heterogeneity is associated with the more aggressive phenotype of PCa cell line. Activation-induced cytidine deaminase (AID) is a multifunctional enzyme and contributes to antibody diversification. However, the dysregulation of AID participates in the progression of multiple diseases and related with certain oncogenes through demethylation. Nevertheless, the role of AID in PCa remains elusive. We observed a significant upregulation of AID expression in PCa samples, which exhibited a negative correlation with E-cadherin expression. Furthermore, AID expression is remarkably higher in CRPC cells than that in HSPC cells, and AID induced the demethylation of CXCL12, which is required to stabilize the Wnt signaling pathway executor β-catenin and EMT procedure. Our study suggests that AID drives CRPC metastasis by demethylation and can be a potential therapeutic target for CRPC.
Collapse
Affiliation(s)
- Qi Li
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
- Department of Urology, TianYou Hospital affiliated to Wuhan University of Science & Technology, Wuhan, Hubei Province, China
| | - Jinfeng Fan
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Zhiyan Zhou
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Zhe Ma
- The First Hospital of Tsinghua University, Beijing, China
| | - Zhifei Che
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Yaoxi Wu
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Xiangli Yang
- Department of Urology, TianYou Hospital affiliated to Wuhan University of Science & Technology, Wuhan, Hubei Province, China
| | - Peiyu Liang
- Department of Urology, the First Affiliated Hospital of Hainan Medical College, Haikou, Hainan Province, China
| | - Haoyong Li
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| |
Collapse
|
19
|
Maity J, Majumder S, Pal R, Saha B, Mukhopadhyay PK. Ascorbic acid modulates immune responses through Jumonji-C domain containing histone demethylases and Ten eleven translocation (TET) methylcytosine dioxygenase. Bioessays 2023; 45:e2300035. [PMID: 37694689 DOI: 10.1002/bies.202300035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023]
Abstract
Ascorbic acid is a redox regulator in many physiological processes. Besides its antioxidant activity, many intriguing functions of ascorbic acid in the expression of immunoregulatory genes have been suggested. Ascorbic acid acts as a co-factor for the Fe+2 -containing α-ketoglutarate-dependent Jumonji-C domain-containing histone demethylases (JHDM) and Ten eleven translocation (TET) methylcytosine dioxygenasemediated epigenetic modulation. By influencing JHDM and TET, ascorbic acid facilitates the differentiation of double negative (CD4- CD8- ) T cells to double positive (CD4+ CD8+ ) T cells and of T-helper cells to different effector subsets. Ascorbic acid modulates plasma cell differentiation and promotes early differentiation of hematopoietic stem cells (HSCs) to NK cells. These findings indicate that ascorbic acid plays a significant role in regulating both innate and adaptive immune cells, opening up new research areas in Immunonutrition. Being a water-soluble vitamin and a safe micro-nutrient, ascorbic acid can be used as an adjunct therapy for many disorders of the immune system.
Collapse
Affiliation(s)
- Jeet Maity
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | - Ranjana Pal
- Department of Life Sciences, Presidency University, Kolkata, India
| | | | | |
Collapse
|
20
|
Seethy AA, Pethusamy K, Kushwaha T, Kumar G, Talukdar J, Chaubey R, Sundaram UD, Mahapatra M, Saxena R, Dhar R, Inampudi KK, Karmakar S. Alterations of the expression of TET2 and DNA 5-hmC predict poor prognosis in Myelodysplastic Neoplasms. BMC Cancer 2023; 23:1035. [PMID: 37884893 PMCID: PMC10601240 DOI: 10.1186/s12885-023-11449-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Myelodysplastic Neoplasms (MDS) are clonal stem cell disorders characterized by ineffective hematopoiesis and progression to acute myeloid leukemia, myelodysplasia-related (AML-MR). A major mechanism of pathogenesis of MDS is the aberration of the epigenetic landscape of the hematopoietic stem cells and/or progenitor cells, especially DNA cytosine methylation, and demethylation. Data on TET2, the predominant DNA demethylator of the hematopoietic system, is limited, particularly in the MDS patients from India, whose biology may differ since these patients present at a relatively younger age. We studied the expression and the variants of TET2 in Indian MDS and AML-MR patients and their effects on 5-hydroxymethyl cytosine (5-hmC, a product of TET2 catalysis) and on the prognosis of MDS patients. RESULTS Of the 42 MDS patients, cytogenetics was available for 31 sub-categorized according to the Revised International Prognostic Scoring System (IPSS-R). Their age resembled that of the previous studies from India. Bone marrow nucleated cells (BMNCs) were also obtained from 13 patients with AML-MR, 26 patients with de-novo AML, and 11 subjects with morphologically normal bone marrow. The patients had a significantly lower TET2 expression which was more pronounced in AML-MR and the IPSS-R higher-risk MDS categories. The 5-hmC levels in higher-risk MDS and AML-MR correlated with TET2 expression, suggesting a possible mechanistic role in the loss of TET2 expression. The findings on TET2 and 5-hmC were also confirmed at the tissue level using immunohistochemistry. Pathogenic variants of TET2 were found in 7 of 24 patient samples (29%), spanning across the IPSS-R prognostic categories. One of the variants - H1778R - was found to affect local and global TET2 structure when studied using structural predictions and molecular dynamics simulations. Thus, it is plausible that some pathogenic variants in TET2 can compromise the structure of TET2 and hence in the formation of 5-hmC. CONCLUSIONS IPSS-R higher-risk MDS categories and AML-MR showed a reduction in TET2 expression, which was not apparent in lower-risk MDS. DNA 5-hmC levels followed a similar pattern. Overall, a decreased TET2 expression and a low DNA 5-hmC level are predictors of advanced disease and adverse outcome in MDS in the population studied, i.e., MDS patients from India.
Collapse
Affiliation(s)
- Ashikh A Seethy
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
- Department of Biochemistry, All India Institute of Medical Sciences, Guwahati, India
| | - Karthikeyan Pethusamy
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Tushar Kushwaha
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Gaurav Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Joyeeta Talukdar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Rekha Chaubey
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Udayakumar Dharmalingam Sundaram
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
- Department of Hematopathology, Medanta - The Medicity, Gurgaon, India
| | - Manoranjan Mahapatra
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
| | - Renu Saxena
- Department of Hematology, All India Institute of Medical Sciences, New Delhi, India
- Department of Hematopathology, Medanta - The Medicity, Gurgaon, India
| | - Ruby Dhar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Krishna K Inampudi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Subhradip Karmakar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
| |
Collapse
|
21
|
Martella G, Motwani NH, Khan Z, Sousa PFM, Gorokhova E, Motwani HV. Simultaneous RNA and DNA Adductomics Using Single Data-Independent Acquisition Mass Spectrometry Analysis. Chem Res Toxicol 2023; 36:1471-1482. [PMID: 37566384 PMCID: PMC10523582 DOI: 10.1021/acs.chemrestox.3c00041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Indexed: 08/12/2023]
Abstract
Adductomics studies are used for the detection and characterization of various chemical modifications (adducts) of nucleic acids and proteins. The advancements in liquid chromatography coupled with high-resolution tandem mass spectrometry (HRMS/MS) have resulted in efficient methods for qualitative and quantitative adductomics. We developed an HRMS-based method for the simultaneous analysis of RNA and DNA adducts in a single run and demonstrated its application using Baltic amphipods, useful sentinels of environmental disturbances, as test organisms. The novelty of this method is screening for RNA and DNA adducts by a single injection on an Orbitrap HRMS instrument using full scan and data-independent acquisition. The MS raw files were processed with an open-source program, nLossFinder, to identify and distinguish RNA and DNA adducts based on the characteristic neutral loss of ribonucleosides and 2'-deoxyribonucleosides, respectively. In the amphipods, in addition to the nearly 150 putative DNA adducts characterized earlier, we detected 60 putative RNA adducts. For the structural identification of the detected RNA adducts, the MODOMICS database was used. The identified RNA adducts included simple mono- and dimethylation and other larger functional groups on different ribonucleosides and deaminated product inosine. However, 54 of these RNA adducts are not yet structurally identified, and further work on their characterization may uncover new layers of information related to the transcriptome and help understand their biological significance. Considering the susceptibility of nucleic acids to environmental factors, including pollutants, the developed multi-adductomics methodology with further advancement has the potential to provide biomarkers for diagnostics of pollution effects in biota.
Collapse
Affiliation(s)
- Giulia Martella
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| | - Nisha H. Motwani
- School
of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge SE-14189, Sweden
| | - Zareen Khan
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| | - Pedro F. M. Sousa
- Department
of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106 91, Sweden
| | - Elena Gorokhova
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| | - Hitesh V. Motwani
- Department
of Environmental Science, Stockholm University, Stockholm SE-106 91, Sweden
| |
Collapse
|
22
|
de Vries I, Ammerlaan D, Heidebrecht T, Celie PH, Geerke DP, Joosten RP, Perrakis A. Distant sequence regions of JBP1 contribute to J-DNA binding. Life Sci Alliance 2023; 6:e202302150. [PMID: 37328191 PMCID: PMC10276184 DOI: 10.26508/lsa.202302150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/18/2023] Open
Abstract
Base-J (β-D-glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J-binding protein 1 (JBP1) that has a thymidine hydroxylase domain and a J-DNA-binding domain (JDBD). How the thymidine hydroxylase domain synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here, we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for molecular dynamics simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. Α high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.
Collapse
Affiliation(s)
- Ida de Vries
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Danique Ammerlaan
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tatjana Heidebrecht
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Patrick Hn Celie
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan P Geerke
- Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMS) and Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Robbie P Joosten
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anastassis Perrakis
- Oncode Institute and Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
23
|
Zhang X, Zhang Y, Wang C, Wang X. TET (Ten-eleven translocation) family proteins: structure, biological functions and applications. Signal Transduct Target Ther 2023; 8:297. [PMID: 37563110 PMCID: PMC10415333 DOI: 10.1038/s41392-023-01537-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 08/12/2023] Open
Abstract
Ten-eleven translocation (TET) family proteins (TETs), specifically, TET1, TET2 and TET3, can modify DNA by oxidizing 5-methylcytosine (5mC) iteratively to yield 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC), and then two of these intermediates (5fC and 5caC) can be excised and return to unmethylated cytosines by thymine-DNA glycosylase (TDG)-mediated base excision repair. Because DNA methylation and demethylation play an important role in numerous biological processes, including zygote formation, embryogenesis, spatial learning and immune homeostasis, the regulation of TETs functions is complicated, and dysregulation of their functions is implicated in many diseases such as myeloid malignancies. In addition, recent studies have demonstrated that TET2 is able to catalyze the hydroxymethylation of RNA to perform post-transcriptional regulation. Notably, catalytic-independent functions of TETs in certain biological contexts have been identified, further highlighting their multifunctional roles. Interestingly, by reactivating the expression of selected target genes, accumulated evidences support the potential therapeutic use of TETs-based DNA methylation editing tools in disorders associated with epigenetic silencing. In this review, we summarize recent key findings in TETs functions, activity regulators at various levels, technological advances in the detection of 5hmC, the main TETs oxidative product, and TETs emerging applications in epigenetic editing. Furthermore, we discuss existing challenges and future directions in this field.
Collapse
Affiliation(s)
- Xinchao Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| |
Collapse
|
24
|
Palit D, Kundu S, Pain PK, Sarma R, Manna D. A Chemical Model of a TET Enzyme for Selective Oxidation of Hydroxymethyl Cytosine to Formyl Cytosine. Inorg Chem 2023. [PMID: 37339080 DOI: 10.1021/acs.inorgchem.3c00063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Methylation/demethylation of cytosines in DNA is central to epigenetics, which plays crucial roles in the regulation of about half of all human genes. Although the methylation mechanism, which downregulates gene expression, has been sufficiently decoded; the demethylation pathway, which upregulates gene expression, still holds questions to be answered. Demethylation of 5-methylcytosine by ten-eleven translocation (TET) enzymes yields understudied but epigenetically relevant intermediates, 5-hydroxymethyl (5-hmC), 5-formyl (5-fC), and 5-carboxyl (5-caC) cytosines. Here we report an iron complex, FeIIITAML (TAML = tetraamido macrocyclic ligand), which can facilitate selective oxidation of 5-hmC to its oxidative derivatives by forming a high-valent Fe-oxo intermediate in the presence of H2O2 under physiologically relevant conditions. Detailed HPLC analyses supported by a wide reaction condition optimization for the 5-hmC → 5-fC oxidation provides us with a chemical model of the TET enzyme. This study shines light on future efforts for a better understanding of the roles of 5-hmC and the TET enzyme mechanism and potentially novel therapeutic methods.
Collapse
Affiliation(s)
- Dipanwita Palit
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, MP 462066, India
| | - Shubhankar Kundu
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, MP 462066, India
| | - Pritam Kumar Pain
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, MP 462066, India
| | - Rajdeep Sarma
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, MP 462066, India
| | - Debasish Manna
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal, MP 462066, India
| |
Collapse
|
25
|
Abstract
DNA-editing enzymes perform chemical reactions on DNA nucleobases. These reactions can change the genetic identity of the modified base or modulate gene expression. Interest in DNA-editing enzymes has burgeoned in recent years due to the advent of clustered regularly interspaced short palindromic repeat-associated (CRISPR-Cas) systems, which can be used to direct their DNA-editing activity to specific genomic loci of interest. In this review, we showcase DNA-editing enzymes that have been repurposed or redesigned and developed into programmable base editors. These include deaminases, glycosylases, methyltransferases, and demethylases. We highlight the astounding degree to which these enzymes have been redesigned, evolved, and refined and present these collective engineering efforts as a paragon for future efforts to repurpose and engineer other families of enzymes. Collectively, base editors derived from these DNA-editing enzymes facilitate programmable point mutation introduction and gene expression modulation by targeted chemical modification of nucleobases.
Collapse
Affiliation(s)
- Kartik L Rallapalli
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA;
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA;
| |
Collapse
|
26
|
Peng Z, Ma J, Christov CZ, Karabencheva-Christova T, Lehnert N, Li D. Kinetic Studies on the 2-Oxoglutarate/Fe(II)-Dependent Nucleic Acid Modifying Enzymes from the AlkB and TET Families. DNA 2023; 3:65-84. [PMID: 38698914 PMCID: PMC11065319 DOI: 10.3390/dna3020005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Nucleic acid methylations are important genetic and epigenetic biomarkers. The formation and removal of these markers is related to either methylation or demethylation. In this review, we focus on the demethylation or oxidative modification that is mediated by the 2-oxoglutarate (2-OG)/Fe(II)-dependent AlkB/TET family enzymes. In the catalytic process, most enzymes oxidize 2-OG to succinate, in the meantime oxidizing methyl to hydroxymethyl, leaving formaldehyde and generating demethylated base. The AlkB enzyme from Escherichia coli has nine human homologs (ALKBH1-8 and FTO) and the TET family includes three members, TET1 to 3. Among them, some enzymes have been carefully studied, but for certain enzymes, few studies have been carried out. This review focuses on the kinetic properties of those 2-OG/Fe(II)-dependent enzymes and their alkyl substrates. We also provide some discussions on the future directions of this field.
Collapse
Affiliation(s)
- Zhiyuan Peng
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Jian Ma
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, MI 49931, USA
| | | | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Deyu Li
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| |
Collapse
|
27
|
Xiang J, Zhang J, Liao L, Jiang B, Yuan R, Xiang Y. Label-free and sensitive fluorescent sensing of ten-eleven translocation enzyme via cascaded recycling signal amplifications. Anal Chim Acta 2023; 1251:341025. [PMID: 36925297 DOI: 10.1016/j.aca.2023.341025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/14/2023] [Accepted: 02/25/2023] [Indexed: 03/03/2023]
Abstract
The sensitive detection of ten-eleven translocation (TET) dioxygenase is of significance for understanding the demethylation mechanism of 5-methylocytosine (5mC), which is responsible for a wide range of biological functions that can affect gene expression in eukaryotic species. Here, a non-label and sensitive fluorescence biosensing method for TET assay using TET1 as the model target molecule is established on the basis of target-triggered Mg2+-dependent DNAzyme and catalytic hairpin assembly (CHA)-mediated multiple signal amplification cascades. 5mC sites in the hairpin DNA probe are first oxidized by TET1 into 5-carboxycytosine, which are further reduced by pyridine borane into dihydrouracil, followed by its recognition and cleavage by the USER enzyme to liberate active DNAzyme and G-quadruplex sequences from the probe. The DNAzyme further cyclically cleaves the substrate hairpins to trigger subsequent CHA reaction and DNAzyme cleavage cycles for yielding many G-quadruplex strands. Thioflavin T dye then intercalates into G-quadruplexes to cause a magnificent increase of fluorescence for high sensitivity assay of TET1 with 47 fM detection limit. And, application of this method for TET1 monitoring in diluted serum has also been confirmed.
Collapse
Affiliation(s)
- Jie Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Junyi Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Lei Liao
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China
| | - Bingying Jiang
- School of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing, 400054, PR China.
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China
| | - Yun Xiang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, PR China.
| |
Collapse
|
28
|
Feng LL, Liu RY, An K, Tang S, Wu J, Yang Q. TET3 as a non-invasive screening tool for the detection of fibrosis in patients with chronic liver disease. Sci Rep 2023; 13:6382. [PMID: 37076545 PMCID: PMC10115894 DOI: 10.1038/s41598-023-33564-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/14/2023] [Indexed: 04/21/2023] Open
Abstract
Ten-eleven translocation protein 3 (TET3) is one of the key enzymes in DNA demethylation which can be expressed in liver tissues. However, the clinical value of TET3 for diagnosis and treatment of chronic liver disease have not been reported previously. We investigated the diagnostic accuracy of serum TET3 as a non-invasive screening tool for liver fibrosis. 212 patients with chronic liver disease from were enrolled in this study. Enzyme-linked immunosorbent assay was used to measure the serum levels of TET3. Receiver operating characteristics (ROC) were determined to examine the diagnostic accuracy of TET3 and combination model for diagnosis fibrosis. Serum TET3 level in fibrosis cases was significantly higher than that in non-fibrosis and controls, respectively. The areas under the ROC curve of the TET3 and fibrosis-4 index for liver fibrosis were 0.863 and 0.813, and 0.916 and 0.957 for liver cirrhosis. The combination of TET3 and fibrosis-4 index had a highly promising positive predictive value for detecting liver fibrosis and cirrhosis different stages of (93.5% and 100%) as compared with each diagnostic tool alone. TET3 is related to the development of liver fibrosis and cirrhosis. The TET3-fibrosis-4 model enhances discriminatory power and represents a promising non-invasive tool for the diagnosis and screening of liver fibrosis.
Collapse
Affiliation(s)
- Lin-Lin Feng
- Academic Research, Department of Pathology and Pathophysiology, College of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, China
- Clinical Laboratory Center, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou Province, China
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research On Common Chronic Diseases, Guizhou Medical University, Guiyang, 550025, Guizhou Province, China
| | - Ran-Yang Liu
- Academic Research, Department of Pathology and Pathophysiology, College of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, China
| | - Kun An
- Hepatopathy Laboratory, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou Province, China
| | - Shuang Tang
- Academic Research, Department of Pathology and Pathophysiology, College of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, China
| | - Jun Wu
- Hepatopathy Laboratory, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, Guizhou Province, China
| | - Qin Yang
- Academic Research, Department of Pathology and Pathophysiology, College of Basic Medical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, China.
| |
Collapse
|
29
|
Du X, Yang Z, Xie G, Wang C, Zhang L, Yan K, Yang M, Li S, Zhu JK, Du J. Molecular basis of the plant ROS1-mediated active DNA demethylation. NATURE PLANTS 2023; 9:271-279. [PMID: 36624257 DOI: 10.1038/s41477-022-01322-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Active DNA demethylation plays a crucial role in eukaryotic gene imprinting and antagonizing DNA methylation. The plant-specific REPRESSOR OF SILENCING 1/DEMETER (ROS1/DME) family of enzymes directly excise 5-methyl-cytosine (5mC), representing an efficient DNA demethylation pathway distinct from that of animals. Here, we report the cryo-electron microscopy structures of an Arabidopsis ROS1 catalytic fragment in complex with substrate DNA, mismatch DNA and reaction intermediate, respectively. The substrate 5mC is flipped-out from the DNA duplex and subsequently recognized by the ROS1 base-binding pocket through hydrophobic and hydrogen-bonding interactions towards the 5-methyl group and Watson-Crick edge respectively, while the different protonation states of the bases determine the substrate preference for 5mC over T:G mismatch. Together with the structure of the reaction intermediate complex, our structural and biochemical studies revealed the molecular basis for substrate specificity, as well as the reaction mechanism underlying 5mC demethylation by the ROS1/DME family of plant-specific DNA demethylases.
Collapse
Affiliation(s)
- Xuan Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen, China
| | - Zhenlin Yang
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Guohui Xie
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Changshi Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Laixing Zhang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Kaige Yan
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Maojun Yang
- Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Sisi Li
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen, China
| | - Jian-Kang Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Advanced Biotechnology, Southern University of Science and Technology, Shenzhen, China
- Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| |
Collapse
|
30
|
Scott V, Dey D, Kuwik J, Hinkelman K, Waldman M, Islam K. Allele-Specific Chemical Rescue of Histone Demethylases Using Abiotic Cofactors. ACS Chem Biol 2022; 17:3321-3330. [PMID: 34496208 DOI: 10.1021/acschembio.1c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Closely related protein families evolved from common ancestral genes present a significant hurdle in developing member- and isoform-specific chemical probes, owing to their similarity in fold and function. In this piece of work, we explore an allele-specific chemical rescue strategy to activate a "dead" variant of a wildtype protein using synthetic cofactors and demonstrate its successful application to the members of the alpha-ketoglutarate (αKG)-dependent histone demethylase 4 (KDM4) family. We show that a mutation at a specific residue in the catalytic site renders the variant inactive toward the natural cosubstrate. In contrast, αKG derivatives bearing appropriate stereoelectronic features endowed the mutant with native-like demethylase activity while remaining refractory to a set of wild type dioxygenases. The orthogonal enzyme-cofactor pairs demonstrated site- and degree-specific lysine demethylation on a full-length chromosomal histone in the cellular milieu. Our work offers a strategy to modulate a specific histone demethylase by identifying and engineering a conserved phenylalanine residue, which acts as a gatekeeper in the KDM4 subfamily, to sensitize the enzyme toward a novel set of αKG derivatives. The orthogonal pairs developed herein will serve as probes to study the role of degree-specific lysine demethylation in mammalian gene expression. Furthermore, this approach to overcome active site degeneracy is expected to have general application among all human αKG-dependent dioxygenases.
Collapse
Affiliation(s)
- Valerie Scott
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Debasis Dey
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Jordan Kuwik
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Kathryn Hinkelman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Megan Waldman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
31
|
Palei S, Weisner J, Vogt M, Gontla R, Buchmuller B, Ehrt C, Grabe T, Kleinbölting S, Müller M, Clever GH, Rauh D, Summerer D. A high-throughput effector screen identifies a novel small molecule scaffold for inhibition of ten-eleven translocation dioxygenase 2. RSC Med Chem 2022; 13:1540-1548. [PMID: 36545435 PMCID: PMC9749932 DOI: 10.1039/d2md00186a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/29/2022] [Indexed: 12/24/2022] Open
Abstract
Ten-eleven translocation dioxygenases (TETs) are the erasers of 5-methylcytosine (mC), the central epigenetic regulator of mammalian DNA. TETs convert mC to three oxidized derivatives with unique physicochemical properties and inherent regulatory potential, and it initializes active demethylation by the base excision repair pathway. Potent small molecule inhibitors would be useful tools to study TET functions by conditional control. To facilitate the discovery of such tools, we here report a high-throughput screening pipeline and its application to screen and validate 31.5k compounds for inhibition of TET2. Using a homogenous fluorescence assay, we discover a novel quinoline-based scaffold that we further validate with an orthogonal semi-high throughput MALDI-MS assay for direct monitoring of substrate turnover. Structure-activity relationship (SAR) studies involving >20 derivatives of this scaffold led to the identification of optimized inhibitors, and together with computational studies suggested a plausible model for its mode of action.
Collapse
Affiliation(s)
- Shubhendu Palei
- Department of Chemistry and Chemical Biology, TU Dortmund University and, Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Jörn Weisner
- Department of Chemistry and Chemical Biology, TU Dortmund University and, Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Melina Vogt
- Department of Chemistry and Chemical Biology, TU Dortmund University and, Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Rajesh Gontla
- Department of Chemistry and Chemical Biology, TU Dortmund University and, Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Benjamin Buchmuller
- Department of Chemistry and Chemical Biology, TU Dortmund University and, Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Christiane Ehrt
- Department of Chemistry and Chemical Biology, TU Dortmund University and, Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Tobias Grabe
- Department of Chemistry and Chemical Biology, TU Dortmund University and, Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Silke Kleinbölting
- Department of Chemistry and Chemical Biology, TU Dortmund University and, Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Matthias Müller
- Department of Chemistry and Chemical Biology, TU Dortmund University and, Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Guido H Clever
- Department of Chemistry and Chemical Biology, TU Dortmund University and, Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Daniel Rauh
- Department of Chemistry and Chemical Biology, TU Dortmund University and, Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn Str. 4a 44227 Dortmund Germany
| | - Daniel Summerer
- Department of Chemistry and Chemical Biology, TU Dortmund University and, Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) Otto-Hahn Str. 4a 44227 Dortmund Germany
| |
Collapse
|
32
|
Chhatbar K, Connelly J, Webb S, Kriaucionis S, Bird A. A critique of the hypothesis that CA repeats are primary targets of neuronal MeCP2. Life Sci Alliance 2022; 5:5/12/e202201522. [PMID: 36122935 PMCID: PMC9485053 DOI: 10.26508/lsa.202201522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/24/2022] Open
Abstract
The DNA-binding protein MeCP2 is reported to bind methylated cytosine in CG and CA motifs in genomic DNA, but it was recently proposed that arrays of tandemly repeated CA containing either methylated or hydroxymethylated cytosine are the primary targets for MeCP2 binding and function. Here we investigated the predictions of this hypothesis using a range of published datasets. We failed to detect enrichment of cytosine modification at genomic CA repeat arrays in mouse brain regions and found no evidence for preferential MeCP2 binding at CA repeats. Moreover, we did not observe a correlation between the CA repeat density near genes and their degree of transcriptional deregulation when MeCP2 was absent. Our results do not provide support for the hypothesis that CA repeats are key mediators of MeCP2 function. Instead, we found that CA repeats are subject to CAC methylation to a degree that is typical of the surrounding genome and contribute modestly to MeCP2-mediated modulation of gene expression in accordance with their content of this canonical target motif.
Collapse
Affiliation(s)
- Kashyap Chhatbar
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, Edinburgh, UK.,Informatics Forum, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - John Connelly
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, Edinburgh, UK
| | - Shaun Webb
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, Edinburgh, UK
| | | | - Adrian Bird
- Wellcome Centre for Cell Biology, University of Edinburgh, The Michael Swann Building, Edinburgh, UK
| |
Collapse
|
33
|
Zheng Y, Cui X, Zhou Y, Zhang H, Cao L, Gao L, Yin H, Ai S. MXene Enhanced Photoactivity of Bi 2O 3/Bi 2S 3 Heterojunction with G-wire Superstructure for Photoelectrochemical Detection of TET1 Protein. ACS Sens 2022; 7:3116-3125. [PMID: 36205635 DOI: 10.1021/acssensors.2c01600] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Ten-eleven translocation 1 (TET1) protein has the potential to accelerate the oxygenation of 5-methylcytosine to 5-hydroxymethylcytosine (5hmC); then the -CH2OH of 5hmC can further covalently react with -SH catalyzed by M.HhaI methyltransferase. A brand-new photoelectrochemical (PEC) detection technique for the TET1 protein was created in light of this. For this objective, the Bi2O3/Bi2S3 heterojunction was first prepared by a one-pot hydrothermal method and served for photosensitive materials. For further enhancing the photoactivity, Bi2O3/Bi2S3 was blended with MXene to form an energy band-matched structure, thus improving the migration kinetics of photogenerated carriers. For achieving a high sensitivity of detection, a DNA Walker incorporated with the nicking endonuclease (Nb.BbvCI enzyme)-assisted signal amplification strategy was presented to output exponential G-quadruplex fragments. Self-assembly of the free G-quadruplex sequence into a G-wire superstructure with the assistance of Mg2+ provided more loading sites for MB and amplified the PEC signal. The linear range of the biosensor was 0.1-10 μg/mL with a detection limit of 0.024 μg/mL (S/N = 3) for TET1 protein under optimal experimental conditions. The suitability of the proposed method was evaluated by inhibitor screening experiments and the influence of environmental degradation on the activity of TET1 protein.
Collapse
Affiliation(s)
- Yulin Zheng
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Xiaoting Cui
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Haowei Zhang
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Lulu Cao
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Lanlan Gao
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Huanshun Yin
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Shiyun Ai
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| |
Collapse
|
34
|
Pospíšil Š, Panattoni A, Gracias F, Sýkorová V, Hausnerová VV, Vítovská D, Šanderová H, Krásný L, Hocek M. Epigenetic Pyrimidine Nucleotides in Competition with Natural dNTPs as Substrates for Diverse DNA Polymerases. ACS Chem Biol 2022; 17:2781-2788. [PMID: 35679536 PMCID: PMC9594043 DOI: 10.1021/acschembio.2c00342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Five 2'-deoxyribonucleoside triphosphates (dNTPs) derived from epigenetic pyrimidines (5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, 5-hydroxymethyluracil, and 5-formyluracil) were prepared and systematically studied as substrates for nine DNA polymerases in competition with natural dNTPs by primer extension experiments. The incorporation of these substrates was evaluated by a restriction endonucleases cleavage-based assay and by a kinetic study of single nucleotide extension. All of the modified pyrimidine dNTPs were good substrates for the studied DNA polymerases that incorporated a significant percentage of the modified nucleotides into DNA even in the presence of natural nucleotides. 5-Methylcytosine dNTP was an even better substrate for most polymerases than natural dCTP. On the other hand, 5-hydroxymethyl-2'-deoxyuridine triphosphate was not the best substrate for SPO1 DNA polymerase, which naturally synthesizes 5hmU-rich genomes of the SPO1 bacteriophage. The results shed light onto the possibility of gene silencing through recycling and random incorporation of epigenetic nucleotides and into the replication of modified bacteriophage genomes.
Collapse
Affiliation(s)
- Šimon Pospíšil
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic,Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Alessandro Panattoni
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Filip Gracias
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Veronika Sýkorová
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Viola Vaňková Hausnerová
- Lab.
of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Dragana Vítovská
- Lab.
of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Hana Šanderová
- Lab.
of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Libor Krásný
- Lab.
of Microbial Genetics and Gene Expression, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, CZ-14220 Prague 4, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic,Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic,E-mail:
| |
Collapse
|
35
|
RNA modifications: importance in immune cell biology and related diseases. Signal Transduct Target Ther 2022; 7:334. [PMID: 36138023 PMCID: PMC9499983 DOI: 10.1038/s41392-022-01175-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 08/31/2022] [Indexed: 11/16/2022] Open
Abstract
RNA modifications have become hot topics recently. By influencing RNA processes, including generation, transportation, function, and metabolization, they act as critical regulators of cell biology. The immune cell abnormality in human diseases is also a research focus and progressing rapidly these years. Studies have demonstrated that RNA modifications participate in the multiple biological processes of immune cells, including development, differentiation, activation, migration, and polarization, thereby modulating the immune responses and are involved in some immune related diseases. In this review, we present existing knowledge of the biological functions and underlying mechanisms of RNA modifications, including N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, and adenosine-to-inosine (A-to-I) RNA editing, and summarize their critical roles in immune cell biology. Via regulating the biological processes of immune cells, RNA modifications can participate in the pathogenesis of immune related diseases, such as cancers, infection, inflammatory and autoimmune diseases. We further highlight the challenges and future directions based on the existing knowledge. All in all, this review will provide helpful knowledge as well as novel ideas for the researchers in this area.
Collapse
|
36
|
Antonyová V, Tatar A, Brogyányi T, Kejík Z, Kaplánek R, Vellieux F, Abramenko N, Sinica A, Hajduch J, Novotný P, Masters BS, Martásek P, Jakubek M. Targeting of the Mitochondrial TET1 Protein by Pyrrolo[3,2- b]pyrrole Chelators. Int J Mol Sci 2022; 23:ijms231810850. [PMID: 36142763 PMCID: PMC9505425 DOI: 10.3390/ijms231810850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
Targeting of epigenetic mechanisms, such as the hydroxymethylation of DNA, has been intensively studied, with respect to the treatment of many serious pathologies, including oncological disorders. Recent studies demonstrated that promising therapeutic strategies could potentially be based on the inhibition of the TET1 protein (ten-eleven translocation methylcytosine dioxygenase 1) by specific iron chelators. Therefore, in the present work, we prepared a series of pyrrolopyrrole derivatives with hydrazide (1) or hydrazone (2–6) iron-binding groups. As a result, we determined that the basic pyrrolo[3,2-b]pyrrole derivative 1 was a strong inhibitor of the TET1 protein (IC50 = 1.33 μM), supported by microscale thermophoresis and molecular docking. Pyrrolo[3,2-b]pyrroles 2–6, bearing substituted 2-hydroxybenzylidene moieties, displayed no significant inhibitory activity. In addition, in vitro studies demonstrated that derivative 1 exhibits potent anticancer activity and an exclusive mitochondrial localization, confirmed by Pearson’s correlation coefficient of 0.92.
Collapse
Affiliation(s)
- Veronika Antonyová
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
- BIOCEV, First Faculty of Medicine, Charles University, 252 20 Vestec, Czech Republic
| | - Ameneh Tatar
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Tereza Brogyányi
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
- Institute of Pathological Physiology, First Faculty of Medicine, Charles University, 128 53 Prague, Czech Republic
| | - Zdeněk Kejík
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
- BIOCEV, First Faculty of Medicine, Charles University, 252 20 Vestec, Czech Republic
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Robert Kaplánek
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
- BIOCEV, First Faculty of Medicine, Charles University, 252 20 Vestec, Czech Republic
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Fréderic Vellieux
- BIOCEV, First Faculty of Medicine, Charles University, 252 20 Vestec, Czech Republic
| | - Nikita Abramenko
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
- BIOCEV, First Faculty of Medicine, Charles University, 252 20 Vestec, Czech Republic
| | - Alla Sinica
- BIOCEV, First Faculty of Medicine, Charles University, 252 20 Vestec, Czech Republic
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Jan Hajduch
- BIOCEV, First Faculty of Medicine, Charles University, 252 20 Vestec, Czech Republic
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Petr Novotný
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
- BIOCEV, First Faculty of Medicine, Charles University, 252 20 Vestec, Czech Republic
| | - Bettie Sue Masters
- Duke University Medical Center, Department of Biochemistry, Durham, NC 27707, USA
| | - Pavel Martásek
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
- Correspondence: (P.M.); (M.J.)
| | - Milan Jakubek
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Ke Karlovu 455/2, 128 08 Prague, Czech Republic
- BIOCEV, First Faculty of Medicine, Charles University, 252 20 Vestec, Czech Republic
- Department of Analytical Chemistry, Faculty of Chemical Engineering, University of Chemistry and Technology, 166 28 Prague, Czech Republic
- Correspondence: (P.M.); (M.J.)
| |
Collapse
|
37
|
Bisht D, Arora A, Sachan M. Role of DNA De-methylation intermediate '5-hydroxymethylcytosine' in ovarian cancer management: A comprehensive review. Biomed Pharmacother 2022; 155:113674. [PMID: 36099791 DOI: 10.1016/j.biopha.2022.113674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Ovarian cancer remains the most eminent silent killer, with high morbidity and mortality among all gynaecological cancers. The advanced-stage patient's diagnosis has a low survival rate caused by its asymptomatic progression and diverse histopathological sub-types, wherefore in poor prognosis and highly recurring malignancy with multidrug resistance towards chemotherapy. Epigenetic biomarkers open promising avenues of intriguing research to combat OC malignancy, furthermore a tool for its early diagnosis. 5-hydroxymethycytosine (5-hmC), alias the sixth base of the genome, is an intermediate formed during the recently established DNA demethylation process and catalysed via ten-eleven translocation (TET) family of enzymes. It plays a significant role in regulating gene expression and has sparked interest in various cancer types. This review summarizes the role of active DNA demethylation process, its enzymes and intermediate 5-hmC in epigenetic landscape of ovarian cancer as a potent biomarker for clinical translation in identification of therapeutic targets, diagnostic and prognostic evaluation.
Collapse
Affiliation(s)
- Deepa Bisht
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211004, Uttar Pradesh, India
| | - Arisha Arora
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039 Assam, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj 211004, Uttar Pradesh, India.
| |
Collapse
|
38
|
Ravichandran M, Rafalski D, Davies CI, Ortega-Recalde O, Nan X, Glanfield CR, Kotter A, Misztal K, Wang AH, Wojciechowski M, Rażew M, Mayyas IM, Kardailsky O, Schwartz U, Zembrzycki K, Morison IM, Helm M, Weichenhan D, Jurkowska RZ, Krueger F, Plass C, Zacharias M, Bochtler M, Hore TA, Jurkowski TP. Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function. SCIENCE ADVANCES 2022; 8:eabm2427. [PMID: 36070377 PMCID: PMC9451156 DOI: 10.1126/sciadv.abm2427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
TET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic domain of mammalian TET enzymes favor CGs embedded within basic helix-loop-helix and basic leucine zipper domain transcription factor-binding sites, with up to 250-fold preference in vitro. Crystal structures and molecular dynamics calculations show that sequence preference is caused by intrasubstrate interactions and CG flanking sequence indirectly affecting enzyme conformation. TET sequence preferences are physiologically relevant as they explain the rates of DNA demethylation in TET-rescue experiments in culture and in vivo within the zygote and germ line. Most and least favorable TET motifs represent DNA sites that are bound by methylation-sensitive immediate-early transcription factors and octamer-binding transcription factor 4 (OCT4), respectively, illuminating TET function in transcriptional responses and pluripotency support.
Collapse
Affiliation(s)
- Mirunalini Ravichandran
- Department of Anatomy, University of California, San Francisco, 513 Parnassus Avenue, HSW 1301, San Francisco, CA 94143, USA
- Universität Stuttgart, Abteilung Biochemie, Institute für Biochemie und Technische Biochemie, Allmandring 31, Stuttgart D-70569, Germany
| | - Dominik Rafalski
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
| | - Claudia I. Davies
- University of Otago, Department of Anatomy, Dunedin 9016, New Zealand
| | | | - Xinsheng Nan
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | | | - Annika Kotter
- Johannes-Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Sciences, Staudingerweg 5, 55128 Mainz, Germany
| | - Katarzyna Misztal
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
| | - Andrew H. Wang
- University of Otago, Department of Anatomy, Dunedin 9016, New Zealand
| | - Marek Wojciechowski
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
| | - Michał Rażew
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
| | - Issam M. Mayyas
- University of Otago, Department of Pathology, Dunedin 9016, New Zealand
| | - Olga Kardailsky
- University of Otago, Department of Anatomy, Dunedin 9016, New Zealand
| | - Uwe Schwartz
- University of Regensburg, Computational Core Unit, 93053 Regensburg, Germany
| | - Krzysztof Zembrzycki
- Institute of Fundamental Technological Research, Department of Biosystems and Soft Matter PAS, Pawińskiego 5B, Warsaw, Poland
| | - Ian M. Morison
- University of Otago, Department of Pathology, Dunedin 9016, New Zealand
| | - Mark Helm
- Johannes-Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Sciences, Staudingerweg 5, 55128 Mainz, Germany
| | - Dieter Weichenhan
- German Cancer Research Center (DKFZ), Division of Cancer Epigenomics, Heidelberg, Germany
| | - Renata Z. Jurkowska
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Christoph Plass
- German Cancer Research Center (DKFZ), Division of Cancer Epigenomics, Heidelberg, Germany
| | - Martin Zacharias
- Physics Department, Technical University of Munich, James-Franck Str. 1, 85748 Garching, Germany
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology in Warsaw (IIMCB), Trojdena 4, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS (IBB), Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Timothy A. Hore
- University of Otago, Department of Anatomy, Dunedin 9016, New Zealand
| | - Tomasz P. Jurkowski
- Universität Stuttgart, Abteilung Biochemie, Institute für Biochemie und Technische Biochemie, Allmandring 31, Stuttgart D-70569, Germany
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| |
Collapse
|
39
|
Turpin M, Salbert G. 5-methylcytosine turnover: Mechanisms and therapeutic implications in cancer. Front Mol Biosci 2022; 9:976862. [PMID: 36060265 PMCID: PMC9428128 DOI: 10.3389/fmolb.2022.976862] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
DNA methylation at the fifth position of cytosine (5mC) is one of the most studied epigenetic mechanisms essential for the control of gene expression and for many other biological processes including genomic imprinting, X chromosome inactivation and genome stability. Over the last years, accumulating evidence suggest that DNA methylation is a highly dynamic mechanism driven by a balance between methylation by DNMTs and TET-mediated demethylation processes. However, one of the main challenges is to understand the dynamics underlying steady state DNA methylation levels. In this review article, we give an overview of the latest advances highlighting DNA methylation as a dynamic cycling process with a continuous turnover of cytosine modifications. We describe the cooperative actions of DNMT and TET enzymes which combine with many additional parameters including chromatin environment and protein partners to govern 5mC turnover. We also discuss how mathematical models can be used to address variable methylation levels during development and explain cell-type epigenetic heterogeneity locally but also at the genome scale. Finally, we review the therapeutic implications of these discoveries with the use of both epigenetic clocks as predictors and the development of epidrugs that target the DNA methylation/demethylation machinery. Together, these discoveries unveil with unprecedented detail how dynamic is DNA methylation during development, underlying the establishment of heterogeneous DNA methylation landscapes which could be altered in aging, diseases and cancer.
Collapse
Affiliation(s)
- Marion Turpin
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
| | - Gilles Salbert
- Sp@rte Team, UMR6290 CNRS, Institute of Genetics and Development of Rennes, Rennes, France
- University of Rennes 1, Rennes, France
- *Correspondence: Gilles Salbert,
| |
Collapse
|
40
|
Liu Y, Chen C, Wang X, Sun Y, Zhang J, Chen J, Shi Y. An Epigenetic Role of Mitochondria in Cancer. Cells 2022; 11:cells11162518. [PMID: 36010594 PMCID: PMC9406960 DOI: 10.3390/cells11162518] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are not only the main energy supplier but are also the cell metabolic center regulating multiple key metaborates that play pivotal roles in epigenetics regulation. These metabolites include acetyl-CoA, α-ketoglutarate (α-KG), S-adenosyl methionine (SAM), NAD+, and O-linked beta-N-acetylglucosamine (O-GlcNAc), which are the main substrates for DNA methylation and histone post-translation modifications, essential for gene transcriptional regulation and cell fate determination. Tumorigenesis is attributed to many factors, including gene mutations and tumor microenvironment. Mitochondria and epigenetics play essential roles in tumor initiation, evolution, metastasis, and recurrence. Targeting mitochondrial metabolism and epigenetics are promising therapeutic strategies for tumor treatment. In this review, we summarize the roles of mitochondria in key metabolites required for epigenetics modification and in cell fate regulation and discuss the current strategy in cancer therapies via targeting epigenetic modifiers and related enzymes in metabolic regulation. This review is an important contribution to the understanding of the current metabolic-epigenetic-tumorigenesis concept.
Collapse
Affiliation(s)
- Yu’e Liu
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Chao Chen
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, China
| | - Xinye Wang
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Yihong Sun
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
| | - Jin Zhang
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Juxiang Chen
- Department of Neurosurgery, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai 200433, China
- Correspondence: (J.C.); (Y.S.)
| | - Yufeng Shi
- Tongji University Cancer Center, Shanghai Tenth People’s Hospital of Tongji University, School of Medicine, Tongji University, Shanghai 200092, China
- Clinical Center for Brain and Spinal Cord Research, Tongji University, Shanghai 200092, China
- Correspondence: (J.C.); (Y.S.)
| |
Collapse
|
41
|
Germline Abnormalities in DNA Methylation and Histone Modification and Associated Cancer Risk. Curr Hematol Malig Rep 2022; 17:82-93. [PMID: 35653077 DOI: 10.1007/s11899-022-00665-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW Somatic mutations in DNA methyltransferases and other DNA methylation associated genes have been found in a wide variety of cancers. Germline mutations in these genes have been associated with several rare hereditary disorders. Among the described germline/congenital disorders, neurological dysfunction and/or growth abnormalities appear to be a common phenotype. Here, we outline known germline abnormalities and examine the cancer risks associated with these mutations. RECENT FINDINGS The increased use and availability of sequencing techniques in the clinical setting has expanded the identification of germline abnormalities involving DNA methylation machinery. This has provided additional cases to study these rare hereditary disorders and their predisposition to cancer. Studying these syndromes may offer an opportunity to better understand the contribution of these genes in cancer development.
Collapse
|
42
|
Long-Term Treatment with Bortezomib Induces Specific Methylation Changes in Differentiated Neuronal Cells. Cancers (Basel) 2022; 14:cancers14143402. [PMID: 35884461 PMCID: PMC9319119 DOI: 10.3390/cancers14143402] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary We exposed LUHMES cells, differentiated into mature neurons, to bortezomib (BTZ) in two treatment cycles and analyzed the methylomes of these cells after each cycle, controlling the analysis for the methylation changes potentially induced by the long-term culture. Our results show that BTZ induces methylation changes that may affect cell morphogenesis, neurogenesis, and neurotransmission. These changes are specifically enriched within transcription factor binding sites of EBF, PAX, DLX, LHX, and HNF family members, which have been shown to regulate neurogenesis and neuronal differentiation. We further show that the observed methylation changes are not present in the SH-SY5Y cells that we used to study mechanisms of development of BTZ resistance. Altogether, our results show that BTZ treatment induces very specific changes in the methylomes of neuronal cells. Abstract Bortezomib (BTZ) is proteasome inhibitor, effectively used in the treatment of multiple myeloma, but frequently discontinued due to peripheral neuropathy, which develops in patients after consecutive treatment cycles. The molecular mechanisms affected by BTZ in neuronal cells, which result in neuropathy, remain unknown. However, BTZ is unlikely to lead to permanent morphological nerve damage, because neuropathy reverses after discontinuation of treatment, and nerve cells have very limited renewal capacity. We have previously shown that BTZ induces methylation changes in SH-SY5Y cells, which take part in the development of treatment resistance. Here, we hypothesized that BTZ affects the methylomes of mature neurons, and these changes are associated with BTZ neurotoxicity. Thus, we studied methylomes of neuronal cells, differentiated from the LUHMES cell line, after cycles of treatment with BTZ. Our results show that BTZ induces specific methylation changes in mature neurons, which are not present in SH-SY5Y cells after BTZ treatment. These changes appear to affect genes involved in morphogenesis, neurogenesis, and neurotransmission. Furthermore, identified methylation changes are significantly enriched within binding sites of transcription factors previously linked to neuron physiology, including EBF, PAX, DLX, LHX, and HNF family members. Altogether, our results indicate that methylation changes are likely to be involved in BTZ neurotoxicity.
Collapse
|
43
|
Xu Y, Zhong L, Wei H, Li Y, Xie J, Xie L, Chen X, Guo X, Yin P, Li S, Zeng J, Li XJ, Lin L. Brain Region- and Age-Dependent 5-Hydroxymethylcytosine Activity in the Non-Human Primate. Front Aging Neurosci 2022; 14:934224. [PMID: 35912074 PMCID: PMC9326314 DOI: 10.3389/fnagi.2022.934224] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/15/2022] [Indexed: 11/24/2022] Open
Abstract
Because of the difficulty in collecting fresh brains of humans at different ages, it remains unknown how epigenetic regulation occurs in the primate brains during aging. In the present study, we examined the genomic distribution of 5hmC, an indicator of DNA methylation, in the brain regions of non-human primates (rhesus monkey) at the ages of 2 (juvenile), 8 (young adult), and 17 (old) years. We found that genomic 5hmC distribution was accumulated in the monkey brain as age increased and displayed unique patterns in the cerebellum and striatum in an age-dependent manner. We also observed a correlation between differentially hydroxymethylated regions (DhMRs) and genes that contribute to brain region-related functions and diseases. Our studies revealed, for the first time, the brain-region and age-dependent 5hmC modifications in the non-human primate and the association of these 5hmC modifications with brain region-specific function and potentially aging-related brain diseases.
Collapse
Affiliation(s)
- Yanru Xu
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Liying Zhong
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Huixian Wei
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Yuwei Li
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Jiaxiang Xie
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Leijie Xie
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xiusheng Chen
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Xiangyu Guo
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Peng Yin
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Shihua Li
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Junwei Zeng
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiao-Jiang Li
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
| | - Li Lin
- Guangdong Key Laboratory of Nonhuman Primate Models of Human Diseases, Key Laboratory of CNS Regeneration (Ministry of Education), Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, Guangzhou, China
- *Correspondence: Li Lin
| |
Collapse
|
44
|
Sun L, Chai X, Xiao P, Liu X, Deng F. The Effect of Zinc Finger Domain Protein Spalt Like Transcription Factor 4 (SALL4A)-Mediated DNA Demethylation on Cardiac Development and Function. J BIOMATER TISS ENG 2022. [DOI: 10.1166/jbt.2022.3056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
SALL4 is one of the important members of SALL4 gene family and participates in embryo development, including organogenesis, maintenance and reconstruction of pluripotency, such as heart development and function. This study explores the effects of SALL4A-mediated DNA demethylation on
heart development and function. The ventricular weight/body weight, ventricular diameter, septal thickness, LVEF% and LVFS% of the SALL4A gene knockout and normal SD mice were compared. ChIP/DIP-Seq and RNA-Seq technology were used to assess the mechanism by how SALL4Adependent DNA demethylation
affects heart development and function. We found that compared with control group of SD mice, the ventricular weight/body weight of SD mice in SALL4A knockout group was significantly lower. In addition, SALL4A knockout group showed significantly lower interval thickness, LVEF%, LVFS% and other
indicators related to heart development than normal SD mice. In addition, SALL4A-mediated DNA demethylation was closely related to TET. Both TET1 and TET2 were enriched in the SALL4A binding site. SALL4A targeted 5hmC gene in vitro and occupied the enhancer in mouse embryonic stem cells
(ESCs) to promote 5hmC oxidation depending on TET enzyme. Therefore, SALL4A promoted oxidation of 5hmC and caused DNA demethylation which finally affected heart development and function. In conclusion, SALL4A, as a gene that can target and bind 5hmC, promotes the oxidation of 5hmC by stabilizing
TET enzyme binding, thereby regulating the DNA demethylation process in ESCs to further regulate heart development and function.
Collapse
Affiliation(s)
- Luoying Sun
- Department of Emergency, Hunan Provincial Brain Hospital, Changsha, Hunan, 410007, China
| | - Xiaoli Chai
- Department of Cardiovascular Diseases, Hunan Provincial Brain Hospital, Changsha, Hunan, 410007, China
| | - Pengfei Xiao
- Department of Oncology, Hunan Provincial Brain Hospital, Changsha, Hunan, 410007, China
| | - Xiulan Liu
- Department of Emergency, Hunan Provincial Brain Hospital, Changsha, Hunan, 410007, China
| | - Feimeng Deng
- Department of Stroke Prevention and Treatment, Hunan Provincial Brain Hospital, Changsha, Hunan, 410007, China
| |
Collapse
|
45
|
Joshi K, Liu S, Breslin S J P, Zhang J. Mechanisms that regulate the activities of TET proteins. Cell Mol Life Sci 2022; 79:363. [PMID: 35705880 DOI: 10.1007/s00018-022-04396-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/16/2022] [Accepted: 05/23/2022] [Indexed: 02/08/2023]
Abstract
The ten-eleven translocation (TET) family of dioxygenases consists of three members, TET1, TET2, and TET3. All three TET enzymes have Fe+2 and α-ketoglutarate (α-KG)-dependent dioxygenase activities, catalyzing the 1st step of DNA demethylation by converting 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), and further oxidize 5hmC to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Gene knockout studies demonstrated that all three TET proteins are involved in the regulation of fetal organ generation during embryonic development and normal tissue generation postnatally. TET proteins play such roles by regulating the expression of key differentiation and fate-determining genes via (1) enzymatic activity-dependent DNA methylation of the promoters and enhancers of target genes; and (2) enzymatic activity-independent regulation of histone modification. Interacting partner proteins and post-translational regulatory mechanisms regulate the activities of TET proteins. Mutations and dysregulation of TET proteins are involved in the pathogenesis of human diseases, specifically cancers. Here, we summarize the research on the interaction partners and post-translational modifications of TET proteins. We also discuss the molecular mechanisms by which these partner proteins and modifications regulate TET functioning and target gene expression. Such information will help in the design of medications useful for targeted therapy of TET-mutant-related diseases.
Collapse
Affiliation(s)
- Kanak Joshi
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Shanhui Liu
- School of Life Sciences, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Peter Breslin S J
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA.,Departments of Molecular/Cellular Physiology and Biology, Loyola University Medical Center and Loyola University Chicago, Chicago, IL, 60660, USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA. .,Departments of Pathology and Radiation Oncology, Loyola University Medical Center, Maywood, IL, 60153, USA.
| |
Collapse
|
46
|
A fungal dioxygenase CcTet serves as a eukaryotic 6mA demethylase on duplex DNA. Nat Chem Biol 2022; 18:733-741. [PMID: 35654845 DOI: 10.1038/s41589-022-01041-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 03/31/2022] [Indexed: 12/24/2022]
Abstract
N6-methyladenosine (6mA) is a DNA modification that has recently been found to play regulatory roles during mammalian early embryo development and mitochondrial transcription. We found that a dioxygenase CcTet from the fungus Coprinopsis cinerea is also a dsDNA 6mA demethylase. It oxidizes 6mA to the intermediate N6-hydroxymethyladenosine (6hmA) with robust activity of 6mA-containing duplex DNA (dsDNA) as well as isolated genomics DNA. Structural characterization revealed that CcTet utilizes three flexible loop regions and two key residues-D337 and G331-in the active pocket to preferentially recognize substrates on dsDNA. A CcTet D337F mutant protein retained the catalytic activity on 6mA but lost activity on 5-methylcytosine. Our findings uncovered a 6mA demethylase that works on dsDNA, suggesting potential 6mA demethylation in fungi and elucidating 6mA recognition and the catalytic mechanism of CcTet. The CcTet D337F mutant protein also provides a chemical biology tool for future functional manipulation of DNA 6mA in vivo.
Collapse
|
47
|
Chakrapani A, Ruiz‐Larrabeiti O, Pohl R, Svoboda M, Krásný L, Hocek M. Glucosylated 5‐Hydroxymethylpyrimidines as Epigenetic DNA Bases Regulating Transcription and Restriction Cleavage. Chemistry 2022; 28:e202200911. [DOI: 10.1002/chem.202200911] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Indexed: 12/13/2022]
Affiliation(s)
- Aswathi Chakrapani
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science Charles University Hlavova 8 CZ-12843 Prague 2 Czech Republic
| | - Olatz Ruiz‐Larrabeiti
- Dept. of Microbial Genetics and Gene Expression Institute of Microbiology Czech Academy of Sciences 14220 Prague 4 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Svoboda
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Libor Krásný
- Dept. of Microbial Genetics and Gene Expression Institute of Microbiology Czech Academy of Sciences 14220 Prague 4 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry, Faculty of Science Charles University Hlavova 8 CZ-12843 Prague 2 Czech Republic
| |
Collapse
|
48
|
Weirath NA, Hurben AK, Chao C, Pujari SS, Cheng T, Liu S, Tretyakova NY. Small Molecule Inhibitors of TET Dioxygenases: Bobcat339 Activity Is Mediated by Contaminating Copper(II). ACS Med Chem Lett 2022; 13:792-798. [PMID: 35586434 PMCID: PMC9109264 DOI: 10.1021/acsmedchemlett.1c00677] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
Ten eleven translocation (TET) dioxygenases 1-3 are non-heme Fe(II) and α-ketoglutarate dependent enzymes that catalyze oxidation of 5-methylcytosine (5mC) in DNA to hydroxymethyl-C, formyl-C, and carboxy-C. This typically leads to gene activation and epigenetic remodeling. Most known inhibitors of TET are α-ketoglutarate mimics that may interfere with other α-ketoglutarate dependent enzymes. Recently, a novel cytosine-based inhibitor of TET, Bobcat339, was reported to have mid-μM inhibitory activity against TET1 and TET2. The molecule is now sold as a TET inhibitor by several vendors. We independently prepared Bobcat339 in our laboratory and observed that it had minimal inhibitory activity against human TET1 and TET2 via a quantitative LC-ESI-MS/MS assay. Furthermore, the inhibitory activity of commercial Bobcat339 preparations was directly correlated with Cu(II) content. We therefore conclude that Bobcat339 alone is not capable of inhibiting TET enzymes at the reported concentrations, and that its activity is enhanced by contaminating Cu(II).
Collapse
Affiliation(s)
- Nicholas A. Weirath
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, Minnesota 55455, United States
| | - Alexander K. Hurben
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, Minnesota 55455, United States
| | - Christopher Chao
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, Minnesota 55455, United States
| | - Suresh S. Pujari
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, Minnesota 55455, United States
| | - Tao Cheng
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, Minnesota 55912, United States
| | - Shujun Liu
- The Hormel Institute, University of Minnesota, 801 16th Avenue NE, Austin, Minnesota 55912, United States
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry and Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
49
|
Albracht SP. Hypothesis: mutual dependency of ascorbate and calcidiol for optimal performance of the immune system. Med Hypotheses 2022. [DOI: 10.1016/j.mehy.2022.110845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
50
|
Besaratinia A, Caceres A, Tommasi S. DNA Hydroxymethylation in Smoking-Associated Cancers. Int J Mol Sci 2022; 23:2657. [PMID: 35269796 PMCID: PMC8910185 DOI: 10.3390/ijms23052657] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 02/01/2023] Open
Abstract
5-hydroxymethylcytosine (5-hmC) was first detected in mammalian DNA five decades ago. However, it did not take center stage in the field of epigenetics until 2009, when ten-eleven translocation 1 (TET1) was found to oxidize 5-methylcytosine to 5-hmC, thus offering a long-awaited mechanism for active DNA demethylation. Since then, a remarkable body of research has implicated DNA hydroxymethylation in pluripotency, differentiation, neural system development, aging, and pathogenesis of numerous diseases, especially cancer. Here, we focus on DNA hydroxymethylation in smoking-associated carcinogenesis to highlight the diagnostic, therapeutic, and prognostic potentials of this epigenetic mark. We describe the significance of 5-hmC in DNA demethylation, the importance of substrates and cofactors in TET-mediated DNA hydroxymethylation, the regulation of TETs and related genes (isocitrate dehydrogenases, fumarate hydratase, and succinate dehydrogenase), the cell-type dependency and genomic distribution of 5-hmC, and the functional role of 5-hmC in the epigenetic regulation of transcription. We showcase examples of studies on three major smoking-associated cancers, including lung, bladder, and colorectal cancers, to summarize the current state of knowledge, outstanding questions, and future direction in the field.
Collapse
Affiliation(s)
- Ahmad Besaratinia
- Department of Population & Public Health Sciences, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA; (A.C.); (S.T.)
| | | | | |
Collapse
|