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Lee MK, Park NH, Lee SY, Kim T. Context-Dependent and Locus-Specific Role of H3K36 Methylation in Transcriptional Regulation. J Mol Biol 2024:168796. [PMID: 39299382 DOI: 10.1016/j.jmb.2024.168796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 09/10/2024] [Accepted: 09/13/2024] [Indexed: 09/22/2024]
Abstract
H3K36 methylation is a critical histone modification involved in transcription regulation. It involves the mono (H3K36me1), di (H3K36me2), and/or tri-methylation (H3K36me3) of lysine 36 on histone H3 by methyltransferases. In yeast, Set2 catalyzes all three methylation states. By contrast, in higher eukaryotes, at least eight methyltransferases catalyze different methylation states, including SETD2 for H3K36me3 and the NSD family for H3K36me2 in vivo. Both Set2 and SETD2 interact with the phosphorylated CTD of RNA Pol II, which links H3K36 methylation to transcription. In yeast, H3K36me3 and H3K36me2 peak at the 3' ends of genes. In higher eukaryotes, this is also true for H3K36me3 but not for H3K36me2, which is enriched at the 5' ends of genes and intergenic regions, suggesting that H3K36me2 and H3K36me3 may play different regulatory roles. Whether H3K36me1 demonstrates preferential distribution remains unclear. H3K36me3 is essential for inhibiting transcription elongation. It also suppresses cryptic transcription by promoting histone deacetylation by the histone deacetylases Rpd3S (yeast) and variant NuRD (higher eukaryotes). H3K36me3 also facilitates DNA methylation by DNMT3B, thereby preventing spurious transcription initiation. H3K36me3 not only represses transcription since it promotes the activation of mRNA and cryptic promoters in response to environmental changes by targeting the histone acetyltransferase NuA3 in yeast. Further research is needed to elucidate the methylation state- and locus-specific functions of H3K36me1 and the mechanisms that regulate it.
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Affiliation(s)
- Min Kyung Lee
- Department of Life Sciences and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Na Hyun Park
- Department of Life Sciences and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Soo Young Lee
- Department of Life Sciences and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea
| | - TaeSoo Kim
- Department of Life Sciences and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea.
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De I, Weidenhausen J, Concha N, Müller CW. Structural insight into the DNMT1 reaction cycle by cryo-electron microscopy. PLoS One 2024; 19:e0307850. [PMID: 39226277 PMCID: PMC11371216 DOI: 10.1371/journal.pone.0307850] [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: 03/12/2024] [Accepted: 07/12/2024] [Indexed: 09/05/2024] Open
Abstract
DNMT1 is an essential DNA methyltransferase that catalyzes the transfer of methyl groups to CpG islands in DNA and generates a prominent epigenetic mark. The catalytic activity of DNMT1 relies on its conformational plasticity and ability to change conformation from an auto-inhibited to an activated state. Here, we present four cryo-EM reconstructions of apo DNMT1 and DNTM1: non-productive DNA, DNTM1: H3Ub2-peptide, DNTM1: productive DNA complexes. Our structures demonstrate the flexibility of DNMT1's N-terminal regulatory domains during the transition from an apo 'auto-inhibited' to a DNA-bound 'non-productive' and finally a DNA-bound 'productive' state of DNMT1. Furthermore, we address the regulation of DNMT1's methyltransferase activity by a DNMT1-selective small-molecule inhibitor and ubiquitinated histone H3. We observe that DNMT1 binds DNA in a 'non-productive' state despite the presence of the inhibitor and present the cryo-EM reconstruction of full-length DNMT1 in complex with a di-ubiquitinated H3 peptide analogue. Taken together, our results provide structural insights into the reaction cycle of DNMT1.
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Affiliation(s)
- Inessa De
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Jonas Weidenhausen
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Nestor Concha
- GlaxoSmithKline, Collegeville, PA, United States of America
| | - Christoph W. Müller
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
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3
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Shao Z, Lu J, Khudaverdyan N, Song J. Multi-layered heterochromatin interaction as a switch for DIM2-mediated DNA methylation. Nat Commun 2024; 15:6815. [PMID: 39122718 PMCID: PMC11315935 DOI: 10.1038/s41467-024-51246-4] [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: 04/12/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Functional crosstalk between DNA methylation, histone H3 lysine-9 trimethylation (H3K9me3) and heterochromatin protein 1 (HP1) is essential for proper heterochromatin assembly and genome stability. However, how repressive chromatin cues guide DNA methyltransferases for region-specific DNA methylation remains largely unknown. Here, we report structure-function characterizations of DNA methyltransferase Defective-In-Methylation-2 (DIM2) in Neurospora. The DNA methylation activity of DIM2 requires the presence of both H3K9me3 and HP1. Our structural study reveals a bipartite DIM2-HP1 interaction, leading to a disorder-to-order transition of the DIM2 target-recognition domain that is essential for substrate binding. Furthermore, the structure of DIM2-HP1-H3K9me3-DNA complex reveals a substrate-binding mechanism distinct from that for its mammalian orthologue DNMT1. In addition, the dual recognition of H3K9me3 peptide by the DIM2 RFTS and BAH1 domains allosterically impacts the DIM2-substrate binding, thereby controlling DIM2-mediated DNA methylation. Together, this study uncovers how multiple heterochromatin factors coordinately orchestrate an activity-switching mechanism for region-specific DNA methylation.
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Affiliation(s)
- Zengyu Shao
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Nelli Khudaverdyan
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA.
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4
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Khudaverdyan N, Lu J, Chen X, Herle G, Song J. The structure of DNA methyltransferase DNMT3C reveals an activity-tuning mechanism for DNA methylation. J Biol Chem 2024; 300:107633. [PMID: 39098534 PMCID: PMC11401227 DOI: 10.1016/j.jbc.2024.107633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 07/20/2024] [Accepted: 07/26/2024] [Indexed: 08/06/2024] Open
Abstract
DNA methylation is one of the major epigenetic mechanisms crucial for gene regulation and genome stability. De novo DNA methyltransferase DNMT3C is required for silencing evolutionarily young transposons during mice spermatogenesis. Mutation of DNMT3C led to a sterility phenotype that cannot be rescued by its homologs DNMT3A and DNMT3B. However, the structural basis of DNMT3C-mediated DNA methylation remains unknown. Here, we report the structure and mechanism of DNMT3C-mediated DNA methylation. The DNMT3C methyltransferase domain recognizes CpG-containing DNA in a manner similar to that of DNMT3A and DNMT3B, in line with their high sequence similarity. However, two evolutionary covariation sites, C543 and E590, diversify the substrate interaction among DNMT3C, DNMT3A, and DNMT3B, resulting in distinct DNA methylation activity and specificity between DNMT3C, DNMT3A, and DNMT3B in vitro. In addition, our combined structural and biochemical analysis reveals that the disease-causing rahu mutation of DNMT3C compromises its oligomerization and DNA-binding activities, explaining the loss of DNA methylation activity caused by this mutation. This study provides a mechanistic insight into DNMT3C-mediated DNA methylation that complements DNMT3A- and DNMT3B-mediated DNA methylation in mice, unraveling a regulatory mechanism by which evolutionary conservation and diversification fine-tune the activity of de novo DNA methyltransferases.
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Affiliation(s)
- Nelli Khudaverdyan
- Department of Biochemistry, University of California, Riverside, California, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, California, USA
| | - Xinyi Chen
- Department of Biochemistry, University of California, Riverside, California, USA
| | - Genevieve Herle
- Biophysics Program, University of California, Riverside, California, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, California, USA; Biophysics Program, University of California, Riverside, California, USA.
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5
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Qi Y, Meng X, Li J, He A, Hao J, Zhao X, Zhao R, Chen R, Zhang R. Evaluating the link between DIO3-FA27 promoter methylation, biochemical indices, and heart failure progression. Clin Epigenetics 2024; 16:57. [PMID: 38659084 PMCID: PMC11040988 DOI: 10.1186/s13148-024-01668-0] [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: 02/01/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
BACKGROUND Heart failure (HF) is a disease that poses a serious threat to individual health, and DNA methylation is an important mechanism in epigenetics, and its role in the occurrence and development of the disease has attracted more and more attention. The aim of this study was to evaluate the link between iodothyronine deiodinase 3 promoter region fragment FA27 (DIO3-FA27) methylation levels, biochemical indices, and HF. RESULTS The methylation levels of DIO3-FA27_CpG_11.12 and DIO3-FA27_CpG_23.24 significantly differed in HF patients with different degrees. Multivariate logistic regression analysis indicated that the relative HF risk in the third and fourth quartiles of activated partial thromboplastin time and fibrin degradation products. The results of the restricted cubic spline model showed that the methylation levels of DIO3-FA 27_CpG_11.12 and DIO3-FA 27_CpG_23.24 were associated with coagulation indicators, liver function, renal function, and blood routine. CONCLUSIONS Based on the differential analysis of CpG methylation levels based on DIO3-FA27, it was found that biochemical indicators combined with DIO3-FA27 promoter DNA methylation levels could increase the risk of worsening the severity classification of HF patients, which provided a solid foundation and new insights for the study of epigenetic regulation mechanisms in patients with HF.
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Affiliation(s)
- Yan Qi
- Department of Epidemiology and Health Statistics, School of Public Health, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi, China
| | - Xiangchao Meng
- Public Health Department, Jinan Children's Hospital, Jinan, 25000, Shandong, China
| | - Jing Li
- Department of Epidemiology and Health Statistics, School of Public Health, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi, China
| | - Aoyue He
- Department of Epidemiology and Health Statistics, School of Public Health, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi, China
| | - Jie Hao
- Department of Epidemiology and Health Statistics, School of Public Health, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi, China
| | - Xu Zhao
- Department of Epidemiology and Health Statistics, School of Public Health, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi, China
| | - Ruonan Zhao
- Department of Epidemiology and Health Statistics, School of Public Health, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi, China
| | - Rongrong Chen
- Department of Epidemiology and Health Statistics, School of Public Health, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi, China
| | - Rongqiang Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Shaanxi University of Chinese Medicine, Xianyang, 712046, Shaanxi, China.
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Zhang Y, Chen J, Zheng B, Teng J, Lou Z, Feng H, Zhao S, Xue L. Genome-wide identification, evolution of DNA methyltransferases and their expression under salinity stress in Larimichthys crocea. Int J Biol Macromol 2024; 264:130603. [PMID: 38447841 DOI: 10.1016/j.ijbiomac.2024.130603] [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: 10/25/2023] [Revised: 02/08/2024] [Accepted: 02/24/2024] [Indexed: 03/08/2024]
Abstract
DNA methyltransferases (Dnmts) are responsible for DNA methylation which influences patterns of gene expression and plays a crucial role in response to environmental changes. In this study, 7 LcDnmt genes were identified in the genome of large yellow croaker (Larimichthys crocea). The comprehensive analysis was conducted on gene structure, protein and location site of LcDnmts. LcDnmt proteins belonged to three groups (Dnmt1, Dnmt2, and Dnmt3) according to their conserved domains and phylogenetic analysis. Although Dnmt3 can be further divided into three sub groups (Dnmt3a, Dnmt3b, and Dnmt3l), there is no Dnmnt3l member in the large yellow croaker. Phylogenetic analysis revealed that the Dnmt family was highly conserved in teleosts. Expression patterns derived from the RNA-seq, qRT-PCR and Western blot analysis revealed that 2 LcDnmt genes (LcDnmt1 and LcDnmt3a2) significantly regulated under salinity stress in the liver, which was found to be dominantly expressed in the intestine and brain, respectively. These two genes may play an important role in the salinity stress of large yellow croaker and represent candidates for future functional analysis. Our results revealed the conservation of Dnmts during evolution and indicated a potential role of Dnmts in epigenetic regulation of response to salinity stress.
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Affiliation(s)
- Yu Zhang
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Jiaqian Chen
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Baoxiao Zheng
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Jian Teng
- School of Agricultural Science and Engineering, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Zhengjia Lou
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Huijie Feng
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China
| | - Shiqi Zhao
- School of Fishery, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
| | - Liangyi Xue
- College of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315832, China.
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7
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Presto P, Sehar U, Kopel J, Reddy PH. Mechanisms of pain in aging and age-related conditions: Focus on caregivers. Ageing Res Rev 2024; 95:102249. [PMID: 38417712 DOI: 10.1016/j.arr.2024.102249] [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: 09/28/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/01/2024]
Abstract
Pain is a complex, subjective experience that can significantly impact quality of life, particularly in aging individuals, by adversely affecting physical and emotional well-being. Whereas acute pain usually serves a protective function, chronic pain is a persistent pathological condition that contributes to functional deficits, cognitive decline, and emotional disturbances in the elderly. Despite substantial progress that has been made in characterizing age-related changes in pain, complete mechanistic details of pain processing mechanisms in the aging patient remain unknown. Pain is particularly under-recognized and under-managed in the elderly, especially among patients with Alzheimer's disease (AD), Alzheimer's disease-related dementias (ADRD), and other age-related conditions. Furthermore, difficulties in assessing pain in patients with AD/ADRD and other age-related conditions may contribute to the familial caregiver burden. The purpose of this article is to discuss the mechanisms and risk factors for chronic pain development and persistence, with a particular focus on age-related changes. Our article also highlights the importance of caregivers working with aging chronic pain patients, and emphasizes the urgent need for increased legislative awareness and improved pain management in these populations to substantially alleviate caregiver burden.
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Affiliation(s)
- Peyton Presto
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Ujala Sehar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Jonathan Kopel
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Nutritional Sciences Department, College of Human Sciences, Texas Tech University, Lubbock, TX 79409, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Public Health, School of Population and Public Health, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Neurology, Departments of School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
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8
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Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
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Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
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9
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Lim S, Lee KW, Kim JY, Kim KD. Consideration of SHP-1 as a Molecular Target for Tumor Therapy. Int J Mol Sci 2023; 25:331. [PMID: 38203502 PMCID: PMC10779157 DOI: 10.3390/ijms25010331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Abnormal activation of receptor tyrosine kinases (RTKs) contributes to tumorigenesis, while protein tyrosine phosphatases (PTPs) contribute to tumor control. One of the most representative PTPs is Src homology region 2 (SH2) domain-containing phosphatase 1 (SHP-1), which is associated with either an increased or decreased survival rate depending on the cancer type. Hypermethylation in the promoter region of PTPN6, the gene for the SHP-1 protein, is a representative epigenetic regulation mechanism that suppresses the expression of SHP-1 in tumor cells. SHP-1 comprises two SH2 domains (N-SH2 and C-SH2) and a catalytic PTP domain. Intramolecular interactions between the N-SH2 and PTP domains inhibit SHP-1 activity. Opening of the PTP domain by a conformational change in SHP-1 increases enzymatic activity and contributes to a tumor control phenotype by inhibiting the activation of the Janus kinase/signal transducer and activator of transcription (JAK/STAT3) pathway. Although various compounds that increase SHP-1 activation or expression have been proposed as tumor therapeutics, except sorafenib and its derivatives, few candidates have demonstrated clinical significance. In some cancers, SHP-1 expression and activation contribute to a tumorigenic phenotype by inducing a tumor-friendly microenvironment. Therefore, developing anticancer drugs targeting SHP-1 must consider the effect of SHP-1 on both cell biological mechanisms of SHP-1 in tumor cells and the tumor microenvironment according to the target cancer type. Furthermore, the use of combination therapies should be considered.
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Affiliation(s)
- Seyeon Lim
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Ki Won Lee
- Anti-Aging Bio Cell Factory—Regional Leading Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Jeong Yoon Kim
- Department of Pharmaceutical Engineering, Institute of Agricultural and Life Science (IALS), Gyeongsang National University, Jinju 52725, Republic of Korea;
| | - Kwang Dong Kim
- Division of Applied Life Science (BK21 Plus), Gyeongsang National University, Jinju 52828, Republic of Korea;
- Anti-Aging Bio Cell Factory—Regional Leading Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea;
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea
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10
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Lu J, Fang J, Zhu H, Liang KL, Khudaverdyan N, Song J. Structural basis for the allosteric regulation and dynamic assembly of DNMT3B. Nucleic Acids Res 2023; 51:12476-12491. [PMID: 37941146 PMCID: PMC10711551 DOI: 10.1093/nar/gkad972] [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: 03/29/2023] [Revised: 09/08/2023] [Accepted: 10/14/2023] [Indexed: 11/10/2023] Open
Abstract
Oligomerization of DNMT3B, a mammalian de novo DNA methyltransferase, critically regulates its chromatin targeting and DNA methylation activities. However, how the N-terminal PWWP and ADD domains interplay with the C-terminal methyltransferase (MTase) domain in regulating the dynamic assembly of DNMT3B remains unclear. Here, we report the cryo-EM structure of DNMT3B under various oligomerization states. The ADD domain of DNMT3B interacts with the MTase domain to form an autoinhibitory conformation, resembling the previously observed DNMT3A autoinhibition. Our combined structural and biochemical study further identifies a role for the PWWP domain and its associated ICF mutation in the allosteric regulation of DNMT3B tetramer, and a differential functional impact on DNMT3B by potential ADD-H3K4me0 and PWWP-H3K36me3 bindings. In addition, our comparative structural analysis reveals a coupling between DNMT3B oligomerization and folding of its substrate-binding sites. Together, this study provides mechanistic insights into the allosteric regulation and dynamic assembly of DNMT3B.
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Affiliation(s)
- Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| | - Jian Fang
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| | - Hongtao Zhu
- Vollum Institute, Oregon Health and Science University, Portland, OR, USA
| | | | - Nelli Khudaverdyan
- Department of Biochemistry, University of California, Riverside, CA92521, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA92521, USA
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11
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Djihinto OY, Meacci D, Medjigodo AA, Bernardini F, Djogbénou LS. Relative expression of key genes involved in nucleic acids methylation in Anopheles gambiae sensu stricto. MEDICAL AND VETERINARY ENTOMOLOGY 2023; 37:754-766. [PMID: 37417368 DOI: 10.1111/mve.12681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/21/2023] [Indexed: 07/08/2023]
Abstract
In vertebrates, enzymes responsible for DNA methylation, one of the epigenetic mechanisms, are encoded by genes falling into the cytosine methyltransferases genes family (Dnmt1, Dnmt3a,b and Dnmt3L). However, in Diptera, only the methyltransferase Dnmt2 was found, suggesting that DNA methylation might act differently for species in this order. Moreover, genes involved in epigenetic dynamics, such as Ten-eleven Translocation dioxygenases (TET) and Methyl-CpG-binding domain (MBDs), present in vertebrates, might play a role in insects. This work aimed at investigating nucleic acids methylation in the malaria vector Anopheles gambiae (Diptera: Culicidae) by analysing the expression of Dnmt2, TET2 and MBDs genes using quantitative real-time polymerase chain reaction (qRT-PCR) at pre-immature stages and in reproductive tissues of adult mosquitoes. In addition, the effect of two DNA methylation inhibitors on larval survival was evaluated. The qPCR results showed an overall low expression of Dnmt2 at all developmental stages and in adult reproductive tissues. In contrast, MBD and TET2 showed an overall higher expression. In adult mosquito reproductive tissues, the expression level of the three genes in males' testes was significantly higher than that in females' ovaries. The chemical treatments did not affect larval survival. The findings suggest that mechanisms other than DNA methylation underlie epigenetic regulation in An. gambiae.
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Affiliation(s)
- Oswald Y Djihinto
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Dario Meacci
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Adandé A Medjigodo
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
| | - Federica Bernardini
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
| | - Luc S Djogbénou
- Tropical Infectious Diseases Research Centre (TIDRC), University of Abomey-Calavi, Cotonou, Benin
- Institut Régional de Santé Publique (IRSP), University of Abomey-Calavi, Ouidah, Benin
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12
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Fu TY, Ji SS, Tian YL, Lin YG, Chen YM, Zhong QE, Zheng SC, Xu GF. Methyl-CpG binding domain (MBD)2/3 specifically recognizes and binds to the genomic mCpG site with a β-sheet in the MBD to affect embryonic development in Bombyx mori. INSECT SCIENCE 2023; 30:1607-1621. [PMID: 36915030 DOI: 10.1111/1744-7917.13195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/06/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
Methyl-CpG (mCpG) binding domain (MBD) proteins especially bind with methylated DNA, and are involved in many important biological processes; however, the binding mechanism between insect MBD2/3 and mCpG remains unclear. In this study, we identified 2 isoforms of the MBD2/3 gene in Bombyx mori, MBD2/3-S and MBD2/3-L. Binding analysis of MBD2/3-L, MBD2/3-S, and 7 mutant MBD2/3-L proteins deficient in β1-β6 or α1 in the MBD showed that β2-β3-turns in the β-sheet of the MBD are necessary for the formation of the MBD2/3-mCpG complex; furthermore, other secondary structures, namely, β4-β6 and an α-helix, play a role in stabilizing the β-sheet structure to ensure that the MBD is able to bind mCpG. In addition, sequence alignment and binding analyses of different insect MBD2/3s indicated that insect MBD2/3s have an intact and conserved MBD that binds to the mCpG of target genes. Furthermore, MBD2/3 RNA interference results showed that MBD2/3-L plays a role in regulating B. mori embryonic development, similar to that of DNA methylation; however, MBD2/3-S without β4-β6 and α-helix does not alter embryonic development. These results suggest that MBD2/3-L recognizes and binds to mCpG through the intact β-sheet structure in its MBD, thus ensuring silkworm embryonic development.
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Affiliation(s)
- Tong-Yu Fu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Shuang-Shun Ji
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yu-Lin Tian
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yi-Guang Lin
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yu-Mei Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Qi-En Zhong
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Si-Chun Zheng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Guan-Feng Xu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, China
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Fryar-Williams S, Tucker G, Strobel J, Huang Y, Clements P. Molecular Mechanism Biomarkers Predict Diagnosis in Schizophrenia and Schizoaffective Psychosis, with Implications for Treatment. Int J Mol Sci 2023; 24:15845. [PMID: 37958826 PMCID: PMC10650772 DOI: 10.3390/ijms242115845] [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: 09/02/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Diagnostic uncertainty and relapse rates in schizophrenia and schizoaffective disorder are relatively high, indicating the potential involvement of other pathological mechanisms that could serve as diagnostic indicators to be targeted for adjunctive treatment. This study aimed to seek objective evidence of methylenetetrahydrofolate reductase MTHFR C677T genotype-related bio markers in blood and urine. Vitamin and mineral cofactors related to methylation and indolamine-catecholamine metabolism were investigated. Biomarker status for 67 symptomatically well-defined cases and 67 asymptomatic control participants was determined using receiver operating characteristics, Spearman's correlation, and logistic regression. The 5.2%-prevalent MTHFR 677 TT genotype demonstrated a 100% sensitive and specific case-predictive biomarkers of increased riboflavin (vitamin B2) excretion. This was accompanied by low plasma zinc and indicators of a shift from low methylation to high methylation state. The 48.5% prevalent MTHFR 677 CC genotype model demonstrated a low-methylation phenotype with 93% sensitivity and 92% specificity and a negative predictive value of 100%. This model related to lower vitamin cofactors, high histamine, and HPLC urine indicators of lower vitamin B2 and restricted indole-catecholamine metabolism. The 46.3%-prevalent CT genotype achieved high predictive strength for a mixed methylation phenotype. Determination of MTHFR C677T genotype dependent functional biomarker phenotypes can advance diagnostic certainty and inform therapeutic intervention.
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Affiliation(s)
- Stephanie Fryar-Williams
- Youth in Mind Research Institute, Unley, SA 5061, Australia
- The Queen Elizabeth Hospital, Woodville, SA 5011, Australia
- Basil Hetzel Institute for Translational Health Research, Woodville, SA 5011, Australia
- Department of Nanoscale BioPhotonics, Faculty of Health and Medical Sciences, School of Biomedicine, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Graeme Tucker
- Department of Public Health, Faculty of Health and Medical Sciences, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia;
| | - Jörg Strobel
- Department of Psychiatry, Faculty of Health and Medical Sciences, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia;
| | - Yichao Huang
- Waite Research Institute, The University of Adelaide, Urrbrae, SA 5064, Australia
| | - Peter Clements
- Waite Research Institute, The University of Adelaide, Urrbrae, SA 5064, Australia
- Department of Paediatrics, Faculty of Health and Medical Sciences, Adelaide Medical School, The University of Adelaide, Adelaide, SA 5000, Australia
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14
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Liu L, Niu L, Zheng X, Xiao F, Sun H, Deng W, Cai J. PD-L1 expression-related PI3K pathway correlates with immunotherapy efficacy in gastric cancer. Ther Adv Med Oncol 2023; 15:17588359231205853. [PMID: 37868079 PMCID: PMC10586003 DOI: 10.1177/17588359231205853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Background The programed death ligand-1 combined positive score (PD-L1 CPS), the only FDA-approved biomarker for immune checkpoint inhibitor therapy in gastric cancer (GC) patients, is an important but imperfect predictive biomarker. The molecular characteristics of tumors that influence the PD-L1 CPS are largely unknown and would be helpful for screening patients who would benefit from immunotherapy. Methods PD-L1 immunohistochemistry (IHC) and targeted next-generation sequencing techniques were used to compare genomic alterations in 492 GC patients in two groups (PD-L1 CPS ⩾ 1, positive; CPS < 1, negative). Screened PD-L1 expression-related factors were analyzed for immunotherapy efficacy in three distinct GC cohorts from public databases. Results Positive PD-L1 expression occurred in 40% of GC patients and was associated with a higher proportion of phosphatidylinositol 3-kinase (PI3K), SWItch/Sucrose NonFermentable (SWI/SNF), lysine demethylase (KDM), and DNA (cytosine-5)-methyltransferase (DNMT) (all p < 0.01), pathway alterations. Compared to wild-type GC patients, those with PI3K pathway alterations had a higher response rate (p = 0.002) and durable clinical benefit rate with immunotherapy (p = 0.023, p = 0.038) as well as longer progression-free survival (p = 0.084, p = 0.0076) and overall survival (p = 0.2, p = 0.037) with immunotherapy. Conclusion This study revealed PD-L1 expression-related factors in the tumor genome in a GC cohort. Alterations in the PI3K pathway associated with PD-L1 positivity were shown to be associated with better immunotherapy efficacy in three distinct GC cohorts from public databases. Our results provide a potential avenue for patient selection and rational immune combination development for GC patients.
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Affiliation(s)
- Langbiao Liu
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lei Niu
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Xue Zheng
- Genecast Biotechnology Co., Ltd, Wuxi City, Jiangsu, China
| | - Fei Xiao
- Genecast Biotechnology Co., Ltd, Wuxi City, Jiangsu, China
| | - Huaibo Sun
- Genecast Biotechnology Co., Ltd, Wuxi City, Jiangsu, China
| | - Wei Deng
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, No. 95, Yong’an Road, Xicheng District, Beijing 100050,China
| | - Jun Cai
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research & National Clinical Research Center for Digestive Diseases, Department of General Surgery, Beijing Friendship Hospital, Capital Medical University, No. 95, Yong’an Road, Xicheng District, Beijing, 100050, China
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15
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García-Ortiz MV, Cano-Ramírez P, Toledano-Fonseca M, Aranda E, Rodríguez-Ariza A. Diagnosing and monitoring pancreatic cancer through cell-free DNA methylation: progress and prospects. Biomark Res 2023; 11:88. [PMID: 37798621 PMCID: PMC10552233 DOI: 10.1186/s40364-023-00528-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/21/2023] [Indexed: 10/07/2023] Open
Abstract
Pancreatic cancer is one of the most challenging cancers due to its high mortality rates. Considering the late diagnosis and the limited survival benefit with current treatment options, it becomes imperative to optimize early detection, prognosis and prediction of treatment response. To address these challenges, significant research efforts have been undertaken in recent years to develop liquid-biopsy-based biomarkers for pancreatic cancer. In particular, an increasing number of studies point to cell-free DNA (cfDNA) methylation analysis as a promising non-invasive approach for the discovery and validation of epigenetic biomarkers with diagnostic or prognostic potential. In this review we provide an update on recent advancements in the field of cfDNA methylation analysis in pancreatic cancer. We discuss the relevance of DNA methylation in the context of pancreatic cancer, recent cfDNA methylation research, its clinical utility, and future directions for integrating cfDNA methylation analysis into routine clinical practice.
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Affiliation(s)
- María Victoria García-Ortiz
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain.
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain.
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain.
| | - Pablo Cano-Ramírez
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain
| | - Marta Toledano-Fonseca
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
| | - Enrique Aranda
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
- Department of Medicine, Faculty of Medicine, University of Córdoba, Córdoba, Spain
| | - Antonio Rodríguez-Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Andalusia-Roche Network Mixed Alliance in Precision Medical Oncology, Sevilla, Spain
- Cancer Network Biomedical Research Center (CIBERONC), Madrid, Spain
- Medical Oncology Department, Reina Sofía University Hospital, Córdoba, Spain
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16
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St John M, Tripathi T, Morgan AT, Amor DJ. To speak may draw on epigenetic writing and reading: Unravelling the complexity of speech and language outcomes across chromatin-related neurodevelopmental disorders. Neurosci Biobehav Rev 2023; 152:105293. [PMID: 37353048 DOI: 10.1016/j.neubiorev.2023.105293] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/11/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
Speech and language development are complex neurodevelopmental processes that are incompletely understood, yet current evidence suggests that speech and language disorders are prominent in those with disorders of chromatin regulation. This review aimed to unravel what is known about speech and language outcomes for individuals with chromatin-related neurodevelopmental disorders. A systematic literature search following PRISMA guidelines was conducted on 70 chromatin genes, to identify reports of speech/language outcomes across studies, including clinical reports, formal subjective measures, and standardised/objective measures. 3932 studies were identified and screened and 112 were systematically reviewed. Communication impairment was core across chromatin disorders, and specifically, chromatin writers and readers appear to play an important role in motor speech development. Identification of these relationships is important because chromatin disorders show promise as therapeutic targets due to the capacity for epigenetic modification. Further research is required using standardised and formal assessments to understand the nuanced speech/language profiles associated with variants in each gene, and the influence of chromatin dysregulation on the neurobiology of speech and language development.
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Affiliation(s)
- Miya St John
- Speech and Language, Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Audiology and Speech Pathology, University of Melbourne, VIC, Australia.
| | - Tanya Tripathi
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Parkville, VIC, Australia.
| | - Angela T Morgan
- Speech and Language, Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Audiology and Speech Pathology, University of Melbourne, VIC, Australia; Speech Genomics Clinic, Royal Children's Hospital, Parkville, VIC, Australia.
| | - David J Amor
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Parkville, VIC, Australia; Speech Genomics Clinic, Royal Children's Hospital, Parkville, VIC, Australia; Department of Paediatrics, University of Melbourne, VIC, Australia.
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17
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Chen Q, Liu B, Zeng Y, Hwang JW, Dai N, Corrêa I, Estecio M, Zhang X, Santos MA, Chen T, Cheng X. GSK-3484862 targets DNMT1 for degradation in cells. NAR Cancer 2023; 5:zcad022. [PMID: 37206360 PMCID: PMC10189803 DOI: 10.1093/narcan/zcad022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023] Open
Abstract
Maintenance of genomic methylation patterns at DNA replication forks by DNMT1 is the key to faithful mitotic inheritance. DNMT1 is often overexpressed in cancer cells and the DNA hypomethylating agents azacytidine and decitabine are currently used in the treatment of hematologic malignancies. However, the toxicity of these cytidine analogs and their ineffectiveness in treating solid tumors have limited wider clinical use. GSK-3484862 is a newly-developed, dicyanopyridine containing, non-nucleoside DNMT1-selective inhibitor with low cellular toxicity. Here, we show that GSK-3484862 targets DNMT1 for protein degradation in both cancer cell lines and murine embryonic stem cells (mESCs). DNMT1 depletion was rapid, taking effect within hours following GSK-3484862 treatment, leading to global hypomethylation. Inhibitor-induced DNMT1 degradation was proteasome-dependent, with no discernible loss of DNMT1 mRNA. In mESCs, GSK-3484862-induced Dnmt1 degradation requires the Dnmt1 accessory factor Uhrf1 and its E3 ubiquitin ligase activity. We also show that Dnmt1 depletion and DNA hypomethylation induced by the compound are reversible after its removal. Together, these results indicate that this DNMT1-selective degrader/inhibitor will be a valuable tool for dissecting coordinated events linking DNA methylation to gene expression and identifying downstream effectors that ultimately regulate cellular response to altered DNA methylation patterns in a tissue/cell-specific manner.
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Affiliation(s)
- Qin Chen
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
| | - Bigang Liu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
| | - Yang Zeng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX77030, USA
| | - Jee Won Hwang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
| | - Nan Dai
- New England Biolabs, Inc, Ipswich, MA 01938, USA
| | | | - Marcos R Estecio
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
| | - Margarida A Santos
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX77030, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
- Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX77030, USA
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Raval M, Mishra S, Tiwari AK. Epigenetic regulons in Alzheimer's disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:185-247. [DOI: 10.1016/bs.pmbts.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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19
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Li M, Zhang D. DNA methyltransferase-1 in acute myeloid leukaemia: beyond the maintenance of DNA methylation. Ann Med 2022; 54:2011-2023. [PMID: 35838271 PMCID: PMC9291682 DOI: 10.1080/07853890.2022.2099578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA methylation is considered an essential epigenetic event during leukaemogenesis and the emergence of drug resistance, which is primarily regulated by DNA methyltransferases. DNA methyltransferase-1 (DNMT1) is one of the members of DNA methyltransferases, in charge of maintaining established methylation. Recently, DNMT1 is shown to promote malignant events of cancers through the epigenetic and non-epigenetic processes. Increasing studies in solid tumours have identified DNMT1 as a therapeutic target and a regulator of therapy resistance; however, it is unclear whether DNMT1 is a critical regulator in acute myeloid leukaemia (AML) and how it works. In this review, we summarized the recent understanding of DNMT1 in normal haematopoiesis and AML and discussed the possible functions of DNMT1 in promoting the development of AML and predicting the sensitivity of hypomethylation agents to better understand the relationship between DNMT1 and AML and to look for new hope to treat AML patients.Key messagesThe function of DNA methyltransferase-1 in acute myeloid leukaemia.DNA methyltransferase-1 predicts the sensitivity of drug and involves the emergence of drug resistance.
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Affiliation(s)
- Mengyuan Li
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Donghua Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
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20
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Moreira MTG, Pereira PR, Aquino A, Conte-Junior CA, Paschoalin VMF. Aldehyde Accumulation in Aged Alcoholic Beer: Addressing Acetaldehyde Impacts on Upper Aerodigestive Tract Cancer Risks. Int J Mol Sci 2022; 23:14147. [PMID: 36430619 PMCID: PMC9698545 DOI: 10.3390/ijms232214147] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022] Open
Abstract
Aldehydes, particularly acetaldehyde, are carcinogenic molecules and their concentrations in foodstuffs should be controlled to avoid upper aerodigestive tract (UADT) and liver cancers. Highly reactive, acetaldehyde forms DNA and protein adducts, impairing physiological functions and leading to the development of pathological conditions. The consumption of aged beer, outside of the ethanol metabolism, exposes habitual drinkers to this carcinogen, whose concentrations can be over-increased due to post-brewing chemical and biochemical reactions. Storage-related changes are a challenge faced by the brewing industry, impacting volatile compound formation and triggering flavor instability. Aldehydes are among the volatile compounds formed during beer aging, recognized as off-flavor compounds. To track and understand aldehyde formation through multiple pathways during beer storage, consequent changes in flavor but particularly quality losses and harmful compound formation, this systematic review reunited data on volatile compound profiles through gas chromatography analyses from 2011 to 2021. Conditions to avoid flavor instability and successful methods for reducing beer staling, and consequent acetaldehyde accumulation, were raised by exploring the dynamic conversion between free and bound-state aldehydes. Future research should focus on implementing sensory analyses to investigate whether adding aldehyde-binding agents, e.g., cysteine and bisulfite, would contribute to consumer acceptance, restore beer flavor, and minimize acetaldehyde-related health damage.
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Affiliation(s)
- Mariana Toledo Gonçalves Moreira
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, RJ, Brazil
| | - Patricia Ribeiro Pereira
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, RJ, Brazil
| | - Adriano Aquino
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, RJ, Brazil
| | - Carlos Adam Conte-Junior
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói 24220-000, RJ, Brazil
- Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, RJ, Brazil
- Analytical and Molecular Laboratorial Center (CLAn), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, RJ, Brazil
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-598, RJ, Brazil
| | - Vania Margaret Flosi Paschoalin
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, RJ, Brazil
- Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro 21941-909, RJ, Brazil
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Chen C, He M, Li X, Yu L, Liu Y, Yang Y, Li L, Jia J, Li B. H2O2/DEM-Promoted Maft Promoter Demethylation Drives Nrf2/ARE Activation in Zebrafish. Life (Basel) 2022; 12:life12091436. [PMID: 36143473 PMCID: PMC9503143 DOI: 10.3390/life12091436] [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: 07/28/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/22/2022] Open
Abstract
The Nrf2/ARE signaling pathway is a cell survival response pathway in response to environmental stresses. The Nrf2/ARE signaling pathway can be activated by stimulating cysteine residues at different positions in the Keap1. However, the epigenetic mechanisms of the Nrf2/ARE pathway under different stimuli are still poorly understood. In this study, we found that both hydrogen peroxide (H2O2) and Diethyl Maleate (DEM) activated the Nrf2/ARE signaling pathway at 120 hpf in zebrafish. H2O2 regulated the demethylation of the maft promoter by inhibiting the expression of methyltransferase. This promotes the mRNA expression of the Nrf2 binding factor maft, thereby promoting the downstream antioxidant genes. The methylation of the Nrf2/ARE signaling pathway was not significantly regulated by DEM. However, under oxidative stress, the methyltransferase inhibitors (decitabine and azacitidine) demethylated the promoter region of maft. It activated the expression of the maft, further improving the Nrf2/ARE signal pathway. At last, antioxidant target genes were activated. It was shown that H2O2 and DEM cooperated with methyltransferase inhibitors, providing an important reference for the treatment of oxidative stress-related diseases and breaking new ground for the study of the mechanism of methyltransferase inhibitors in the process of tumor chemotherapy.
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Affiliation(s)
- Ce Chen
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Mingyue He
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Xueting Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Lidong Yu
- School of Physics, Harbin Institute of Technology, Harbin 150080, China
| | - Yi Liu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Yan Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
| | - Li Li
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China
- Correspondence: (L.L.); (J.J.)
| | - Jianbo Jia
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China
- Correspondence: (L.L.); (J.J.)
| | - Bingsheng Li
- Key Laboratory of UV Light Emitting Materials and Technology of Ministry of Education, Northeast Normal University, Changchun 130024, China
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22
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Dogan F, Aljumaily RMK, Kitchen M, Forsyth NR. Physoxia Influences Global and Gene-Specific Methylation in Pluripotent Stem Cells. Int J Mol Sci 2022; 23:5854. [PMID: 35628663 PMCID: PMC9148100 DOI: 10.3390/ijms23105854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 12/10/2022] Open
Abstract
Pluripotent stem cells (PSC) possess unlimited proliferation, self-renewal, and a differentiation capacity spanning all germ layers. Appropriate culture conditions are important for the maintenance of self-renewal, pluripotency, proliferation, differentiation, and epigenetic states. Oxygen concentrations vary across different human tissues depending on precise cell location and proximity to vascularisation. The bulk of PSC culture-based research is performed in a physiologically hyperoxic, air oxygen (21% O2) environment, with numerous reports now detailing the impact of a physiologic normoxia (physoxia), low oxygen culture in the maintenance of stemness, survival, morphology, proliferation, differentiation potential, and epigenetic profiles. Epigenetic mechanisms affect multiple cellular characteristics including gene expression during development and cell-fate determination in differentiated cells. We hypothesized that epigenetic marks are responsive to a reduced oxygen microenvironment in PSCs and their differentiation progeny. Here, we evaluated the role of physoxia in PSC culture, the regulation of DNA methylation (5mC (5-methylcytosine) and 5hmC (5-hydroxymethylcytosine)), and the expression of regulatory enzyme DNMTs and TETs. Physoxia enhanced the functional profile of PSC including proliferation, metabolic activity, and stemness attributes. PSCs cultured in physoxia revealed the significant downregulation of DNMT3B, DNMT3L, TET1, and TET3 vs. air oxygen, accompanied by significantly reduced 5mC and 5hmC levels. The downregulation of DNMT3B was associated with an increase in its promoter methylation. Coupled with the above, we also noted decreased HIF1A but increased HIF2A expression in physoxia-cultured PSCs versus air oxygen. In conclusion, PSCs display oxygen-sensitive methylation patterns that correlate with the transcriptional and translational regulation of the de novo methylase DNMT3B.
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Affiliation(s)
- Fatma Dogan
- The Guy Hilton Research Laboratories, School of Pharmacy and Bioengineering, Faculty of Medicine and Health Sciences, Keele University, Stoke on Trent ST4 7QB, UK; (F.D.); (M.K.)
| | - Rakad M. Kh Aljumaily
- Department of Biology, College of Science, University of Baghdad, Baghdad 17635, Iraq;
| | - Mark Kitchen
- The Guy Hilton Research Laboratories, School of Pharmacy and Bioengineering, Faculty of Medicine and Health Sciences, Keele University, Stoke on Trent ST4 7QB, UK; (F.D.); (M.K.)
| | - Nicholas R. Forsyth
- The Guy Hilton Research Laboratories, School of Pharmacy and Bioengineering, Faculty of Medicine and Health Sciences, Keele University, Stoke on Trent ST4 7QB, UK; (F.D.); (M.K.)
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23
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Mechanism of cancer stemness maintenance in human liver cancer. Cell Death Dis 2022; 13:394. [PMID: 35449193 PMCID: PMC9023565 DOI: 10.1038/s41419-022-04848-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 11/08/2022]
Abstract
Primary liver cancer mainly includes the following four types: hepatocellular carcinoma (HCC), cholangiocarcinoma (CCA), hepatoblastoma (HB), and combined hepatocellular carcinoma and cholangiocarcinoma (cHCC-CCA). Recent studies have indicated that there are differences in cancer stem cell (CSC) properties among different types of liver cancer. Liver cancer stem cells (LCSCs), also called liver tumor-initiating cells, have been viewed as drivers of tumor initiation and metastasis. Many mechanisms and factors, such as mitophagy, mitochondrial dynamics, epigenetic modifications, the tumor microenvironment, and tumor plasticity, are involved in the regulation of cancer stemness in liver cancer. In this review, we analyze cancer stemness in different liver cancer types. Moreover, we further evaluate the mechanism of cancer stemness maintenance of LCSCs and discuss promising treatments for eradicating LCSCs.
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24
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Choubey P, Kaur H, Bansal K. Modulation of DNA/RNA Methylation Signaling Mediating Metabolic Homeostasis in Cancer. Subcell Biochem 2022; 100:201-237. [PMID: 36301496 DOI: 10.1007/978-3-031-07634-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nucleic acid methylation is a fundamental epigenetic mechanism that impinges upon several cellular attributes, including metabolism and energy production. The dysregulation of deoxyribonucleic acid (DNA)/ribonucleic acid (RNA) methylation can lead to metabolic rewiring in the cell, which in turn facilitates tumor development. Here, we review the current knowledge on the interplay between DNA/RNA methylation and metabolic programs in cancer cells. We also discuss the mechanistic role of these pathways in tumor development and progression.
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Affiliation(s)
- Pallawi Choubey
- Molecular Biology and Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, India
| | - Harshdeep Kaur
- Molecular Biology and Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, India
| | - Kushagra Bansal
- Molecular Biology and Genetics Unit (MBGU), Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, India.
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25
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Jurkowska RZ, Jeltsch A. Enzymology of Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:69-110. [DOI: 10.1007/978-3-031-11454-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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26
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Mensah IK, Norvil AB, AlAbdi L, McGovern S, Petell CJ, He M, Gowher H. Misregulation of the expression and activity of DNA methyltransferases in cancer. NAR Cancer 2021; 3:zcab045. [PMID: 34870206 PMCID: PMC8634572 DOI: 10.1093/narcan/zcab045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 12/15/2022] Open
Abstract
In mammals, DNA methyltransferases DNMT1 and DNMT3's (A, B and L) deposit and maintain DNA methylation in dividing and nondividing cells. Although these enzymes have an unremarkable DNA sequence specificity (CpG), their regional specificity is regulated by interactions with various protein factors, chromatin modifiers, and post-translational modifications of histones. Changes in the DNMT expression or interacting partners affect DNA methylation patterns. Consequently, the acquired gene expression may increase the proliferative potential of cells, often concomitant with loss of cell identity as found in cancer. Aberrant DNA methylation, including hypermethylation and hypomethylation at various genomic regions, therefore, is a hallmark of most cancers. Additionally, somatic mutations in DNMTs that affect catalytic activity were mapped in Acute Myeloid Leukemia cancer cells. Despite being very effective in some cancers, the clinically approved DNMT inhibitors lack specificity, which could result in a wide range of deleterious effects. Elucidating distinct molecular mechanisms of DNMTs will facilitate the discovery of alternative cancer therapeutic targets. This review is focused on: (i) the structure and characteristics of DNMTs, (ii) the prevalence of mutations and abnormal expression of DNMTs in cancer, (iii) factors that mediate their abnormal expression and (iv) the effect of anomalous DNMT-complexes in cancer.
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Affiliation(s)
- Isaiah K Mensah
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Lama AlAbdi
- Department of Zoology, Collage of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sarah McGovern
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | | | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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27
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Sun L, Lv S, Song T. O-GlcNAcylation links oncogenic signals and cancer epigenetics. Discov Oncol 2021; 12:54. [PMID: 35201498 PMCID: PMC8777512 DOI: 10.1007/s12672-021-00450-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/11/2021] [Indexed: 12/19/2022] Open
Abstract
Prevalent dysregulation of epigenetic modifications plays a pivotal role in cancer. Targeting epigenetic abnormality is a new strategy for cancer therapy. Understanding how conventional oncogenic factors cause epigenetic abnormality is of great basic and translational value. O-GlcNAcylation is a protein modification which affects physiology and pathophysiology. In mammals, O-GlcNAcylation is catalyzed by one single enzyme OGT and removed by one single enzyme OGA. O-GlcNAcylation is affected by the availability of the donor, UDP-GlcNAc, generated by the serial enzymatic reactions in the hexoamine biogenesis pathway (HBP). O-GlcNAcylation regulates a wide spectrum of substrates including many proteins involved in epigenetic modification. Like epigenetic modifications, abnormality of O-GlcNAcylation is also common in cancer. Studies have revealed substantial impact on HBP enzymes and OGT/OGA by oncogenic signals. In this review, we will first summarize how oncogenic signals regulate HBP enzymes, OGT and OGA in cancer. We will then integrate this knowledge with the up to date understanding how O-GlcNAcylation regulates epigenetic machinery. With this, we propose a signal axis from oncogenic signals through O-GlcNAcylation dysregulation to epigenetic abnormality in cancer. Further elucidation of this axis will not only advance our understanding of cancer biology but also provide new revenues towards cancer therapy.
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Affiliation(s)
- Lidong Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China.
| | - Suli Lv
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China
| | - Tanjing Song
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, China.
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28
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Miao W, Dai J, Wang Y, Wang Q, Lu C, La Y, Niu J, Tan F, Zhou S, Wu Y, Chen H, La H. Roles of IDM3 and SDJ1/2/3 in Establishment and/or Maintenance of DNA Methylation in Arabidopsis. PLANT & CELL PHYSIOLOGY 2021; 62:1409-1422. [PMID: 34185870 DOI: 10.1093/pcp/pcab091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Previous studies had demonstrated that in Arabidopsis, IDM3 is involved in ROS1-mediated DNA demethylation pathway, and SUVH-SDJ complex functions as a DNA methylation reader complex for enhancing gene transcription, which presumably recruits ROS1 to the promoters of target genes for DNA demethylation. Here, our analyses, however, showed that the IDM3 and SDJ1/2/3, the components of the SUVH-SDJ complex, are implicated in establishing and/or maintaining DNA methylation as well through DDR (DRD1-DMS3-RDM1) complex. idm3-3 or sdj1/2/3 mutations led to genome-wide DNA hypomethylation, and both mutants shared a large number of common hypo-DMRs (Differentially Methylated Regions) with rdm1-4 and dms3-4, suggesting that IDM3 and SDJ1/2/3 help establish and/or maintain DNA methylation, mediated by RdDM pathway, at a subset of genomic regions largely through DDR complex. IDM3 is able to strongly interact with RDM1 and DMS3, but weakly with SDJ1 and SDJ3; SDJ1 and SDJ3 is capable of interacting separately with RDM1 and DMS3. Furthermore, comparisons of DNA methylation features in idm3-3 and sdj1/2/3 indicated that idm3-3 and sdj1/2/3 mutations make differential impacts on DNA methylation levels and patterns on a genome-wide scale, indicating that they are targeted to quite distinct genomic regions for aiding in DNA methylation. Further analyses on ChIP-seq data demonstrated that RDM1, DMS3 and NRPE1 are enriched in IDM3- and SDJ1/2/3-targted regions. Altogether, our results provide clear demonstration that IDM3 and SDJ1/2/3 play a part in establishing and/or maintaining DNA methylation of a group of genomic regions, through the DDR complex.
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Affiliation(s)
- Wei Miao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jie Dai
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yutong Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Qianqian Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Chong Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yumei La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jiayu Niu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Feng Tan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Shaoxia Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Huhui Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Honggui La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
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29
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King EA, Peairs EM, Uthappa DM, Villa JK, Goff CM, Burrow NK, Deitch RT, Martin AK, Young DD. Photoregulation of PRMT-1 Using a Photolabile Non-Canonical Amino Acid. Molecules 2021; 26:molecules26165072. [PMID: 34443661 PMCID: PMC8398576 DOI: 10.3390/molecules26165072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/24/2022] Open
Abstract
Protein methyltransferases are vital to the epigenetic modification of gene expression. Thus, obtaining a better understanding of and control over the regulation of these crucial proteins has significant implications for the study and treatment of numerous diseases. One ideal mechanism of protein regulation is the specific installation of a photolabile-protecting group through the use of photocaged non-canonical amino acids. Consequently, PRMT1 was caged at a key tyrosine residue with a nitrobenzyl-protected Schultz amino acid to modulate protein function. Subsequent irradiation with UV light removes the caging group and restores normal methyltransferase activity, facilitating the spatial and temporal control of PRMT1 activity. Ultimately, this caged PRMT1 affords the ability to better understand the protein’s mechanism of action and potentially regulate the epigenetic impacts of this vital protein.
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30
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Zhu Y, Wang X, Zhou X, Ding L, Liu D, Xu H. DNMT1-mediated PPARα methylation aggravates damage of retinal tissues in diabetic retinopathy mice. Biol Res 2021; 54:25. [PMID: 34362460 PMCID: PMC8348846 DOI: 10.1186/s40659-021-00347-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 07/21/2021] [Indexed: 02/06/2023] Open
Abstract
Background Peroxisome proliferator-activated receptor alpha (PPARα) is associated with diabetic retinopathy (DR), and the underlying mechanism is still unclear. Aim of this work was to investigate the mechanism of PPARα in DR. Methods Human retinal capillary pericytes (HRCPs) were treated with high glucose (HG) to induce DR cell model. DR mouse model was established by streptozotocin injection, and then received 5-Aza-2-deoxycytidine (DAC; DNA methyltransferase inhibitor) treatment. Hematoxylin–eosin staining was performed to assess retinal tissue damage. PPARα methylation was examined by Methylation-Specific PCR. Flow cytometry and DCFH-DA fluorescent probe was used to estimate apoptosis and reactive oxygen species (ROS). The interaction between DNA methyltransferase-1 (DNMT1) and PPARα promoter was examined by Chromatin Immunoprecipitation. Quantitative real-time PCR and western blot were performed to assess gene and protein expression. Results HG treatment enhanced the methylation levels of PPARα, and repressed PPARα expression in HRCPs. The levels of apoptotic cells and ROS were significantly increased in HRCPs in the presence of HG. Moreover, DNMT1 was highly expressed in HG-treated HRCPs, and DNMT1 interacted with PPARα promoter. PPARα overexpression suppressed apoptosis and ROS levels of HRCPs, which was rescued by DNMT1 up-regulation. In DR mice, DAC treatment inhibited PPARα methylation and reduced damage of retinal tissues. Conclusion DNMT1-mediated PPARα methylation promotes apoptosis and ROS levels of HRCPs and aggravates damage of retinal tissues in DR mice. Thus, this study may highlight novel insights into DR pathogenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s40659-021-00347-1.
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Affiliation(s)
- Ying Zhu
- Eye Center of Xiangya Hospital, Central South University, No. 87 Xiangya Road, Hunan, 410008, Changsha, China
| | - Xinru Wang
- Eye Center of Xiangya Hospital, Central South University, No. 87 Xiangya Road, Hunan, 410008, Changsha, China
| | - Xiaoyun Zhou
- Department of Ophthalmology, The First Hospital of Changsha, 311 Yingpan Road, Hunan, Changsha, China
| | - Lexi Ding
- Eye Center of Xiangya Hospital, Central South University, No. 87 Xiangya Road, Hunan, 410008, Changsha, China
| | - Dan Liu
- Eye Center of Xiangya Hospital, Central South University, No. 87 Xiangya Road, Hunan, 410008, Changsha, China
| | - Huizhuo Xu
- Eye Center of Xiangya Hospital, Central South University, No. 87 Xiangya Road, Hunan, 410008, Changsha, China.
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31
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Yang T, Liu X, Kumar SK, Jin F, Dai Y. Decoding DNA methylation in epigenetics of multiple myeloma. Blood Rev 2021; 51:100872. [PMID: 34384602 DOI: 10.1016/j.blre.2021.100872] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 02/08/2023]
Abstract
Dysregulation of DNA methylation in B cells has been observed during their neoplastic transformation and therefore closely associated with various B-cell malignancies including multiple myeloma (MM), a malignancy of terminally differentiated plasma cells. Emerging evidence has unveiled pronounced alterations in DNA methylation in MM, including both global and gene-specific changes that can affect genome stability and gene transcription. Moreover, dysregulated expression of DNA methylation-modifying enzymes has been related with myelomagenesis, disease progression, and poor prognosis. However, the functional roles of the epigenetic abnormalities involving DNA methylation in MM remain elusive. In this article, we review current understanding of the alterations in DNA methylome and DNA methylation modifiers in MM, particularly focusing on DNA methyltransferases (DNMTs) and tet methylcytosine dioxygenases (TETs). We also discuss how these DNA methylation modifiers may be regulated and function in MM cells, therefore providing a rationale for developing novel epigenetic therapies targeting DNA methylation in MM.
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Affiliation(s)
- Ting Yang
- Laboratory of Cancer Precision Medicine, the First Hospital of Jilin University, 519 Dongminzhu Street, Changchun, Jilin 130061, China.
| | - Xiaobo Liu
- Laboratory of Cancer Precision Medicine, the First Hospital of Jilin University, 519 Dongminzhu Street, Changchun, Jilin 130061, China.
| | - Shaji K Kumar
- Division of Hematology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA.
| | - Fengyan Jin
- Department of Hematology, Cancer Center, the First Hospital of Jilin University, 71 Xinmin Street, Changchun, Jilin 130012, China.
| | - Yun Dai
- Laboratory of Cancer Precision Medicine, the First Hospital of Jilin University, 519 Dongminzhu Street, Changchun, Jilin 130061, China.
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32
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Methyltransferase-like protein 7A (METTL7A) promotes cell survival and osteogenic differentiation under metabolic stress. Cell Death Discov 2021; 7:154. [PMID: 34226523 PMCID: PMC8257615 DOI: 10.1038/s41420-021-00555-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/07/2021] [Accepted: 05/29/2021] [Indexed: 12/24/2022] Open
Abstract
While bone has an inherent capacity to heal itself, it is very difficult to reconstitute large bone defects. Regenerative medicine, including stem cell implantation, has been studied as a novel solution to treat these conditions. However, when the local vascularity is impaired, even the transplanted cells undergo rapid necrosis before differentiating into osteoblasts and regenerating bone. Thus, to increase the effectiveness of stem cell transplantation, it is quintessential to improve the viability of the implanted stem cells. In this study, given that the regulation of glucose may hold the key to stem cell survival and osteogenic differentiation, we investigated the molecules that can replace the effect of glucose under ischemic microenvironment of stem cell transplantation in large bone defects. By analyzing differentially expressed genes under glucose-supplemented and glucose-free conditions, we explored markers such as methyltransferase-like protein 7A (METTL7A) that are potentially related to cell survival and osteogenic differentiation. Overexpression of METTL7A gene enhanced the osteogenic differentiation and viability of human bone marrow stem cells (hBMSCs) in glucose-free conditions. When the in vivo effectiveness of METTL7A-transfected cells in bone regeneration was explored in a rat model of critical-size segmental long-bone defect, METTL7A-transfected hBMSCs showed significantly better regenerative potential than the control vector-transfected hBMSCs. DNA methylation profiles showed a large difference in methylation status of genes related to osteogenesis and cell survival between hBMSCs cultured in glucose-supplemented condition and those cultured in glucose-free condition. Interestingly, METTL7A overexpression altered the methylation status of related genes to favor osteogenic differentiation and cell survival. In conclusion, it is suggested that a novel factor METTL7A enhances osteogenic differentiation and viability of hBMSCs by regulating the methylation status of genes related to osteogenesis or survival.
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33
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Wu Y, Wang CZ, Wan JY, Yao H, Yuan CS. Dissecting the Interplay Mechanism between Epigenetics and Gut Microbiota: Health Maintenance and Disease Prevention. Int J Mol Sci 2021; 22:6933. [PMID: 34203243 PMCID: PMC8267743 DOI: 10.3390/ijms22136933] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/10/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota exists throughout the full life cycle of the human body, and it has been proven to have extensive impacts on health and disease. Accumulating evidence demonstrates that the interplay between gut microbiota and host epigenetics plays a multifaceted role in health maintenance and disease prevention. Intestinal microflora, along with their metabolites, could regulate multiple epigenetic pathways; e.g., DNA methylation, miRNA, or histone modification. Moreover, epigenetic factors can serve as mediators to coordinate gut microbiota within the host. Aiming to dissect this interplay mechanism, the present review summarizes the research profile of gut microbiota and epigenetics in detail, and further interprets the biofunctions of this interplay, especially the regulation of intestinal inflammation, the improvement of metabolic disturbances, and the inhibition of colitis events. This review provides new insights into the interplay of epigenetics and gut microbiota, and attempts to reveal the mysteries of health maintenance and disease prevention from this new perspective.
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Affiliation(s)
- Yuqi Wu
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China;
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Chong-Zhi Wang
- Tang Center for Herbal Medicine Research, The University of Chicago, Chicago, IL 60637, USA; (C.-Z.W.); (C.-S.Y.)
- Department of Anesthesia and Critical Care, The University of Chicago, Chicago, IL 60637, USA
| | - Jin-Yi Wan
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China;
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Haiqiang Yao
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China;
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Chun-Su Yuan
- Tang Center for Herbal Medicine Research, The University of Chicago, Chicago, IL 60637, USA; (C.-Z.W.); (C.-S.Y.)
- Department of Anesthesia and Critical Care, The University of Chicago, Chicago, IL 60637, USA
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Khrabrova DA, Yakubovskaya MG, Gromova ES. AML-Associated Mutations in DNA Methyltransferase DNMT3A. BIOCHEMISTRY (MOSCOW) 2021; 86:307-318. [PMID: 33838631 DOI: 10.1134/s000629792103007x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In mammals, DNA methylation is an essential epigenetic modification necessary for the maintenance of genome stability, regulation of gene expression, and other processes. Carcinogenesis is accompanied by multiple changes in the DNA methylation pattern and DNA methyltransferase (DNMT) genes; these changes are often associated with poor disease prognosis. Human DNA methyltransferase DNMT3A is responsible for de novo DNA methylation. Missense mutations in the DNMT3A gene occur frequently at the early stages of tumor development and are often observed in hematologic malignances, especially in acute myeloid leukemia (AML), with a prevalence of the R882H mutation. This mutation is the only one that has been extensively studied using both model DNA substrates and cancer cell lines. Biochemical characterization of other DNMT3A mutants is necessary to assess their potential effects on the DNMT3A functioning. In this review, we describe DNMT3A mutations identified in AML with special emphasis on the missense mutations in the DNMT3A catalytic domain. The impact of R882H and less common missense mutations on the DNMT3A activity toward model DNA substrates and in cancer cell lines is discussed together with the underlying molecular mechanisms. Understanding general features of these mechanisms will be useful for further development of novel approaches for early diagnostics of hematologic diseases and personalized cancer therapy.
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Affiliation(s)
- Dariya A Khrabrova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Marianna G Yakubovskaya
- Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, 115478, Russia
| | - Elizaveta S Gromova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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35
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Jin N, George TL, Otterson GA, Verschraegen C, Wen H, Carbone D, Herman J, Bertino EM, He K. Advances in epigenetic therapeutics with focus on solid tumors. Clin Epigenetics 2021; 13:83. [PMID: 33879235 PMCID: PMC8056722 DOI: 10.1186/s13148-021-01069-7] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 04/04/2021] [Indexed: 02/06/2023] Open
Abstract
Epigenetic ("above genetics") modifications can alter the gene expression without altering the DNA sequence. Aberrant epigenetic regulations in cancer include DNA methylation, histone methylation, histone acetylation, non-coding RNA, and mRNA methylation. Epigenetic-targeted agents have demonstrated clinical activities in hematological malignancies and therapeutic potential in solid tumors. In this review, we describe mechanisms of various epigenetic modifications, discuss the Food and Drug Administration-approved epigenetic agents, and focus on the current clinical investigations of novel epigenetic monotherapies and combination therapies in solid tumors.
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Affiliation(s)
- Ning Jin
- The Ohio State University Comprehensive Cancer Center - Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Tiffany L George
- The Ohio State University Comprehensive Cancer Center - Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Gregory A Otterson
- The Ohio State University Comprehensive Cancer Center - Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Claire Verschraegen
- The Ohio State University Comprehensive Cancer Center - Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Haitao Wen
- The Ohio State University Comprehensive Cancer Center - Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - David Carbone
- The Ohio State University Comprehensive Cancer Center - Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - James Herman
- Department of Medicine, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Erin M Bertino
- The Ohio State University Comprehensive Cancer Center - Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA.
| | - Kai He
- The Ohio State University Comprehensive Cancer Center - Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA.
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Wang D, Wen Y, Zhang Z, Yang S, Liu X, Cai C, An Q, Lyu S, He H, Xie J, Lei C, Chen H, Ru B, Wang E, Huang Y. DNA methylation status of SERPINA3 gene involved in mRNA expression in three cattle breeds. Anim Biotechnol 2021; 33:1289-1295. [PMID: 33847248 DOI: 10.1080/10495398.2021.1886944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA methylation could take part in the gene expression and acts an important role in muscle development. In this study, DNA methylation and expression in adipose and muscle tissues were examined at the same time to evaluate the extent of epigenetic modifications and gene expression on the differentially methylated region (DMR) in SERPINA3. Chain reaction of bisulfite sequencing polymerase (BSP) was used to compared difference among DNA methylation patterns. The result of quantitative real-time PCR (qPCR) analysis showed that there was an extensive expression of SERPINA3 gene in tissue and there was a significant difference existing in muscle and adipose between Jiaxian cattle and individual of other breeds with increasing hybridization (p < 0.05). The statistic analyses indicated that DNA methylation patterns had a significant influence to the level of mRNA in tissue of fat and muscle. This study may be an important reference for investigating development of muscle tissue in cattle, and may promote the process of cattle molecular breeding.
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Affiliation(s)
- Dahui Wang
- College of Agriculture and Forestry Engineering, Tongren Unviersity, Tongren, Guizhou, People's Republic of China
| | - Yifan Wen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Shizhen Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Cuicui Cai
- Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan, Ningxia, People's Republic of China
| | - Qingming An
- College of Agriculture and Forestry Engineering, Tongren Unviersity, Tongren, Guizhou, People's Republic of China
| | - Shijie Lyu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Hua He
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Jianliang Xie
- Guyuan Branch of Ningxia Academy of Agriculture and Forestry Sciences, Guyuan, Ningxia, People's Republic of China
| | - ChuZhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
| | - Baorui Ru
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan, People's Republic of China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, People's Republic of China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People's Republic of China
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Hegde M, Joshi MB. Comprehensive analysis of regulation of DNA methyltransferase isoforms in human breast tumors. J Cancer Res Clin Oncol 2021; 147:937-971. [PMID: 33604794 PMCID: PMC7954751 DOI: 10.1007/s00432-021-03519-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/10/2021] [Indexed: 12/14/2022]
Abstract
Significant reprogramming of epigenome is widely described during pathogenesis of breast cancer. Transformation of normal cell to hyperplastic cell and to neoplastic phenotype is associated with aberrant DNA (de)methylation, which, through promoter and enhancer methylation changes, activates oncogenes and silence tumor suppressor genes in variety of tumors including breast. DNA methylation, one of the major epigenetic mechanisms is catalyzed by evolutionarily conserved isoforms namely, DNMT1, DNMT3A and DNMT3B in humans. Over the years, studies have demonstrated intricate and complex regulation of DNMT isoforms at transcriptional, translational and post-translational levels. The recent findings of allosteric regulation of DNMT isoforms and regulation by other interacting chromatin modifying proteins emphasizes functional integrity and their contribution for the development of breast cancer and progression. DNMT isoforms are regulated by several intrinsic and extrinsic parameters. In the present review, we have extensively performed bioinformatics analysis of expression of DNMT isoforms along with their transcriptional and post-transcriptional regulators such as transcription factors, interacting proteins, hormones, cytokines and dietary elements along with their significance during pathogenesis of breast tumors. Our review manuscript provides a comprehensive understanding of key factors regulating DNMT isoforms in breast tumor pathology and documents unsolved issues.
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Affiliation(s)
- Mangala Hegde
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Planetarium Complex, Manipal, 576104, India
| | - Manjunath B Joshi
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Planetarium Complex, Manipal, 576104, India.
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Singh M, Kumar V, Sehrawat N, Yadav M, Chaudhary M, Upadhyay SK, Kumar S, Sharma V, Kumar S, Dilbaghi N, Sharma AK. Current paradigms in epigenetic anticancer therapeutics and future challenges. Semin Cancer Biol 2021; 83:422-440. [PMID: 33766649 DOI: 10.1016/j.semcancer.2021.03.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 12/14/2020] [Accepted: 03/16/2021] [Indexed: 12/16/2022]
Abstract
Any alteration at the genetic or epigenetic level, may result in multiplex of diseases including tumorigenesis which ultimately results in the cancer development. Restoration of the normal epigenome by reversing the epigenetic alterations have been reported in tumors paving the way for development of an effective epigenetic treatment in cancer. However, delineating various epigenetic events has been a challenging task so far despite substantial progress in understanding DNA methylation and histone modifications during transcription of genes. Many inhibitors in the form of epigenetic drugs mostly targeting chromatin and histone modifying enzymes including DNA methyltransferase (DNMT) enzyme inhibitors and a histone deacetylases (HDACs) inhibitor, have been in use subsequent to the approval by FDA for cancer treatment. Similarly, other inhibitory drugs, such as FK228, suberoylanilide hydroxamic acid (SAHA) and MS-275, have been successfully tested in clinical studies. Despite all these advancements, still we see a hazy view as far as a promising epigenetic anticancer therapy is concerned. The challenges are to have more specific and effective inhibitors with negligible side effects. Moreover, the alterations seen in tumors are not well understood for which one has to gain deeper insight into the tumor pathology as well. Current review focusses on such epigenetic alterations occurring in cancer and the effective strategies to utilize such alterations for potential therapeutic use and treatment in cancer.
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Affiliation(s)
- Manoj Singh
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Vikas Kumar
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Nirmala Sehrawat
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Mukesh Yadav
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Mayank Chaudhary
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Sushil K Upadhyay
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Sunil Kumar
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India
| | - Varruchi Sharma
- Department of Biotechnology, Sri Guru Gobind Singh College Sector-26, Chandigarh, UT, 160019, India
| | - Sandeep Kumar
- Department of Bio& Nanotechnology, Guru Jambheshwar University of Science & Technology, Hisar, Haryana, 125001, India
| | - Neeraj Dilbaghi
- Department of Bio& Nanotechnology, Guru Jambheshwar University of Science & Technology, Hisar, Haryana, 125001, India
| | - Anil K Sharma
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, 133207, Haryana, India.
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Zhang Y, Rong D, Li B, Wang Y. Targeting Epigenetic Regulators with Covalent Small-Molecule Inhibitors. J Med Chem 2021; 64:7900-7925. [PMID: 33599482 DOI: 10.1021/acs.jmedchem.0c02055] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetic regulation of gene expression plays a critical role in various physiological processes, and epigenetic dysregulation is implicated in a number of diseases, prominently including cancer. Epigenetic regulators have been validated as potential therapeutic targets, and significant progress has been made in the discovery and development of epigenetic-based inhibitors. However, successful epigenetic drug discovery is still facing challenges, including moderate selectivity, limited efficacy, and acquired drug resistance. Inspired by the advantages of covalent small-molecule inhibitors, targeted covalent inhibition has attracted increasing interest in epigenetic drug discovery. In this review, we comprehensively summarize the structure-based design and characterization of covalent inhibitors targeting epigenetic writers, readers, and erasers and highlight their potential benefits in enhancing selectivity across the enzyme family and improving in vivo efficacy. We also discuss the challenges and opportunities of covalent small-molecule inhibitors and hope to shed light on future epigenetic drug discovery.
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Affiliation(s)
- Yi Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Deqin Rong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Bingbing Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Yuanxiang Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
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Abhishek S, Nakarakanti NK, Deeksha W, Rajakumara E. Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA. Int J Biol Macromol 2021; 170:514-522. [PMID: 33359809 DOI: 10.1016/j.ijbiomac.2020.12.149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 11/25/2022]
Abstract
Non-CpG DNA methylation (non-mCpG) is enriched in the genome of brain neurons and germline cells in mammals. Accumulation of non-mCpG during postnatal brain development correlates with gene regulation and inactivation of distal regulatory elements. Recently, UHRF1 has been found to contribute to de novo non-CpG methylation, however, whether UHRF1 could recognize non-mCpG is unknown. Here, we have demonstrated through calorimetric measurements that the UHRF1 SRA can recognize mCpH and fully-mCpHpG, types of non-mCpG. Our ITC binding studies endorse the preferential reading of hemi-mCpG by UHRF1 SRA and also show 6-fold weaker binding for fully-mCpG than hemi-mCpG. Despite presence of symmetrical (5-methyl cytosine) 5mCs, stoichiometry of 1:1 for UHRF1 SRA binding to fully-mCpG indicates that UHRF1 SRA may not form a stable complex with fully-mCpG DNA. Contrarily, UHRF1 SRA recognizes fully-mCpHpG with a stoichiometry of 2:1 protein to DNA duplex with binding affinity higher than fully-mCpG. Our crystal structure of UHRF1 SRA bound to fully-mCpHpG DNA reveals dual flip-out mechanism of 5mC recognition. Metadynamics studies corroborates with ITC data that UHRF1 SRA could not form a stable complex with fully-mCpG DNA. Altogether, this study demonstrates that UHRF1 SRA recognizes non-mCpG DNA and exhibits contrasting mechanisms for hemi-mCpG and fully-mCpHpG DNA recognition.
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Affiliation(s)
- Suman Abhishek
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Naveen Kumar Nakarakanti
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Waghela Deeksha
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India
| | - Eerappa Rajakumara
- Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India.
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Sanaei M, Kavoosi F. Effect of Zebularine in Comparison to Trichostatin A on the Intrinsic and Extrinsic Apoptotic Pathway, Cell Viability, and Apoptosis in Hepatocellular Carcinoma SK-Hep 1, Human Colorectal Cancer SW620, and Human Pancreatic Cancer PaCa-44 Cell Lines. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 20:310-323. [PMID: 34903991 PMCID: PMC8653687 DOI: 10.22037/ijpr.2021.115097.15196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aberrant histone modifications or promoter region hypermethylation of tumor suppressor genes (TSGs) have been recognized as the important epigenetic molecular mechanism in cancer induction. The potential anticancer activities of histone deacetylase inhibitors (HDACIs) and DNA methyltransferase inhibitors (DNMTIs) have been investigated in recent years. The current study was assigned to investigate the effect of trichostatin A (HDACI) in comparison to zebularine (DNMTI) on the intrinsic pro-apoptotic (Bax, Bim, and Bak) and anti-apoptotic (Bcl-2, Mcl-1, and Bcl-xL) genes and extrinsic (DR4, DR5, FAS, FAS-L, and TRAIL genes) pathways, DNA methyltransferase 1, 3a, and 3b, histone deacetylase inhibitors 1, 2, and 3, cell viability, and apoptosis in hepatocellular carcinoma (HCC) SK-Hep 1, colorectal cancer SW620, and pancreatic cancer PaCa-44 cell lines. The SK-Hep 1, SW620, and PaCa-44 cells were cultured and treated with TSA and zebularine. To determine cell apoptosis, cell viability, and the relative gene expression level, flow cytometry assay, MTT assay, and qRT-PCR were done respectively. The result indicated that zebularine and TSA changed the expression level of the Bax, Bak, Bim Bcl-2, Bcl-xL, Mcl-1, DR4, DR5, FAS, FAS-L, TRAIL, DNA methyltransferase 1, 3a, and 3b, histone deacetylase inhibitors 1, 2, and 3 by which induced cell apoptosis and inhibit cell growth in all three cell lines. Concluding, TSA induced its role through both extrinsic and intrinsic apoptotic pathways in three cell lines, whereas, zebularine played its role via both pathways in the SK-Hep 1cell line, it had no significant effect on Bcl-2, Bcl-xL, and Mcl-1 gene expression in SW620 and PaCa-44 cell lines.
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Romanowska K, Sobecka A, Rawłuszko-Wieczorek AA, Suchorska WM, Golusiński W. Head and Neck Squamous Cell Carcinoma: Epigenetic Landscape. Diagnostics (Basel) 2020; 11:diagnostics11010034. [PMID: 33375464 PMCID: PMC7823717 DOI: 10.3390/diagnostics11010034] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 02/06/2023] Open
Abstract
Head and neck squamous carcinoma (HNSCC) constitutes the sixth most prevalent cancer worldwide. The molecular pathogenesis of HNSCC includes disorders in cell cycle, intercellular signaling, proliferation, squamous cell differentiation and apoptosis. In addition to the genetic mutations, changes in HNSCC are also characterized by the accumulation of epigenetic alterations such as DNA methylation, histone modifications, non-coding RNA activity and RNA methylation. In fact, some of them may promote cancer formation and progression by controlling the gene expression machinery, hence, they could be used as biomarkers in the clinical surveillance of HNSCC or as targets for therapeutic strategies. In this review, we focus on the current knowledge regarding epigenetic modifications observed in HNSCC and its predictive value for cancer development.
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Affiliation(s)
- Kamila Romanowska
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, 61-866 Poznan, Poland; (A.S.); (W.G.)
- Department of Medical Physics, Radiobiology Laboratory, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, 61-866 Poznan, Poland;
- Correspondence:
| | - Agnieszka Sobecka
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, 61-866 Poznan, Poland; (A.S.); (W.G.)
- Department of Medical Physics, Radiobiology Laboratory, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, 61-866 Poznan, Poland;
| | | | - Wiktoria M. Suchorska
- Department of Medical Physics, Radiobiology Laboratory, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, 61-866 Poznan, Poland;
| | - Wojciech Golusiński
- Department of Head and Neck Surgery, Poznan University of Medical Sciences, The Greater Poland Cancer Centre, 61-866 Poznan, Poland; (A.S.); (W.G.)
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Thaulow J, Song Y, Lindeman LC, Kamstra JH, Lee Y, Xie L, Aleström P, Salbu B, Tollefsen KE. Epigenetic, transcriptional and phenotypic responses in Daphnia magna exposed to low-level ionizing radiation. ENVIRONMENTAL RESEARCH 2020; 190:109930. [PMID: 32738623 DOI: 10.1016/j.envres.2020.109930] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/18/2020] [Accepted: 07/10/2020] [Indexed: 06/11/2023]
Abstract
Ionizing radiation is known to induce oxidative stress and DNA damage as well as epigenetic effects in aquatic organisms. Epigenetic changes can be part of the adaptive responses to protect organisms from radiation-induced damage, or act as drivers of toxicity pathways leading to adverse effects. To investigate the potential roles of epigenetic mechanisms in low-dose ionizing radiation-induced stress responses, an ecologically relevant crustacean, adult Daphnia magna were chronically exposed to low and medium level external 60Co gamma radiation ranging from 0.4, 1, 4, 10, and 40 mGy/h for seven days. Biological effects at the molecular (global DNA methylation, histone modification, gene expression), cellular (reactive oxygen species formation), tissue/organ (ovary, gut and epidermal histology) and organismal (fecundity) levels were investigated using a suite of effect assessment tools. The results showed an increase in global DNA methylation associated with loci-specific alterations of histone H3K9 methylation and acetylation, and downregulation of genes involved in DNA methylation, one-carbon metabolism, antioxidant defense, DNA repair, apoptosis, calcium signaling and endocrine regulation of development and reproduction. Temporal changes of reactive oxygen species (ROS) formation were also observed with an apparent transition from ROS suppression to induction from 2 to 7 days after gamma exposure. The cumulative fecundity, however, was not significantly changed by the gamma exposure. On the basis of the new experimental evidence and existing knowledge, a hypothetical model was proposed to provide in-depth mechanistic understanding of the roles of epigenetic mechanisms in low dose ionizing radiation induced stress responses in D. magna.
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Affiliation(s)
- Jens Thaulow
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349, Oslo, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - You Song
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349, Oslo, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway.
| | - Leif C Lindeman
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Jorke H Kamstra
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of Veterinary Medicine, Institute for Risk Assessment Sciences, Utrecht University, PO Box 80177, NL-3508 TD, Utrecht, the Netherlands
| | - YeonKyeong Lee
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of BioSciences, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Li Xie
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349, Oslo, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
| | - Peter Aleström
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway
| | - Brit Salbu
- Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
| | - Knut Erik Tollefsen
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, N-0349, Oslo, Norway; Centre for Environmental Radioactivity (CERAD), Norwegian University of Life Sciences (NMBU), Post box 5003, N-1432 Ås, Norway; Norwegian University of Life Sciences (NMBU), Faculty of Environmental Sciences and Natural Resource Management (MINA), P.O. Box 5003, N-1432 Ås, Norway
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Cervena K, Siskova A, Buchler T, Vodicka P, Vymetalkova V. Methylation-Based Therapies for Colorectal Cancer. Cells 2020; 9:E1540. [PMID: 32599894 PMCID: PMC7349319 DOI: 10.3390/cells9061540] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/22/2020] [Accepted: 06/23/2020] [Indexed: 02/08/2023] Open
Abstract
Colorectal carcinogenesis (CRC) is caused by the gradual long-term accumulation of both genetic and epigenetic changes. Recently, epigenetic alterations have been included in the classification of the CRC molecular subtype, and this points out their prognostic impact. As epigenetic modifications are reversible, they may represent relevant therapeutic targets. DNA methylation, catalyzed by DNA methyltransferases (DNMTs), regulates gene expression. For many years, the deregulation of DNA methylation has been considered to play a substantial part in CRC etiology and evolution. Despite considerable advances in CRC treatment, patient therapy response persists as limited, and their profit from systemic therapies are often hampered by the introduction of chemoresistance. In addition, inter-individual changes in therapy response in CRC patients can arise from their specific (epi)genetic compositions. In this review article, we summarize the options of CRC treatment based on DNA methylation status for their predictive value. This review also includes the therapy outcomes based on the patient's methylation status in CRC patients. In addition, the current challenge of research is to develop therapeutic inhibitors of DNMT. Based on the essential role of DNA methylation in CRC development, the application of DNMT inhibitors was recently proposed for the treatment of CRC patients, especially in patients with DNA hypermethylation.
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Affiliation(s)
- Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14 200 Prague, Czech Republic; (K.C.); (A.S.); (P.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
| | - Anna Siskova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14 200 Prague, Czech Republic; (K.C.); (A.S.); (P.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
| | - Tomas Buchler
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Videnska 800, 140 59 Prague, Czech Republic;
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14 200 Prague, Czech Republic; (K.C.); (A.S.); (P.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 14 200 Prague, Czech Republic; (K.C.); (A.S.); (P.V.)
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 76, 323 00 Pilsen, Czech Republic
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Ciernikova S, Earl J, García Bermejo ML, Stevurkova V, Carrato A, Smolkova B. Epigenetic Landscape in Pancreatic Ductal Adenocarcinoma: On the Way to Overcoming Drug Resistance? Int J Mol Sci 2020; 21:ijms21114091. [PMID: 32521716 PMCID: PMC7311973 DOI: 10.3390/ijms21114091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/02/2020] [Accepted: 06/06/2020] [Indexed: 12/24/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive solid malignancies due to the rapid rate of metastasis and high resistance to currently applied cancer therapies. The complex mechanism underlying the development and progression of PDAC includes interactions between genomic, epigenomic, and signaling pathway alterations. In this review, we summarize the current research findings on the deregulation of epigenetic mechanisms in PDAC and the influence of the epigenome on the dynamics of the gene expression changes underlying epithelial–mesenchymal transition (EMT), which is responsible for the invasive phenotype of cancer cells and, therefore, their metastatic potential. More importantly, we provide an overview of the studies that uncover potentially actionable pathways. These studies provide a scientific basis to test epigenetic drug efficacy in synergy with other anticancer therapies in future clinical trials, in order to reverse acquired therapy resistance. Thus, epigenomics has the potential to generate relevant new knowledge of both a biological and clinical impact. Moreover, the potential, hurdles, and challenges of predictive biomarker discoveries will be discussed, with a special focus on the promise of liquid biopsies.
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Affiliation(s)
- Sona Ciernikova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia;
- Correspondence: ; Tel.: +421-2-3229-5198
| | - Julie Earl
- Molecular Epidemiology and Predictive Tumor Markers Group, Medical Oncology Research Laboratory, Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9100, 28034 Madrid, Spain; (J.E.); (A.C.)
| | - María Laura García Bermejo
- Biomarkers and Therapeutic Targets Group, Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9100, 28034 Madrid, Spain;
| | - Viola Stevurkova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia;
| | - Alfredo Carrato
- Molecular Epidemiology and Predictive Tumor Markers Group, Medical Oncology Research Laboratory, Ramón y Cajal Health Research Institute (IRYCIS), Carretera Colmenar Km 9100, 28034 Madrid, Spain; (J.E.); (A.C.)
| | - Bozena Smolkova
- Department of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 05 Bratislava, Slovakia;
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Li Z, Zhang D, Li Q, Yang X, Zhang R, Zhang D, Yang X, Wang C, Tan X, Xiong Y. Effects of methylation of deiodinase 3 gene on gene expression and severity of Kashin-Beck disease. J Cell Physiol 2020; 235:9946-9957. [PMID: 32458485 DOI: 10.1002/jcp.29809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/21/2020] [Accepted: 05/09/2020] [Indexed: 12/26/2022]
Abstract
Kashin-Beck disease (KBD) is a complex endemic osteoarthropathy, which mainly occurs in the northeast to southwest China. Iodothyronine deiodinases 3 (DIO3) is one of the selenoproteins, which is closely related to bone metabolism and unclear to KBD. This study aims to investigate the role and associated mechanisms of methylation and expression of DIO3 with disease severity in patients with KBD. We performed a bioinformatics analysis first to identify the biological mechanisms involved in selenoproteins. The methylation status of the DIO3 gene and DIO3 gene expression, as well as DIO3-related regulatory genes in patients with KBD, were analyzed. We found that 15 CpG sites of six selenoproteins were hypomethylated with 5-azacytidine treatment. DIO3 hypermethylation was associated with an increased risk of KBD and may lead to downregulation of DIO3 gene expression as well as be an indicator of the severity of KBD, which may provide a new insight for gene-environment correlations and interactions in etiology and pathogenesis of KBD.
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Affiliation(s)
- Zhaofang Li
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Di Zhang
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Qiang Li
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Xiaoli Yang
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Rongqiang Zhang
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Dandan Zhang
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Xuena Yang
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Chen Wang
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Xiwang Tan
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
| | - Yongmin Xiong
- Institute of Endemic Diseases and Key Laboratory of Trace Elements and Endemic Diseases, National Health Commission of the People's Republic of China, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China
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S-Adenosine Methionine (SAMe) and Valproic Acid (VPA) as Epigenetic Modulators: Special Emphasis on their Interactions Affecting Nervous Tissue during Pregnancy. Int J Mol Sci 2020; 21:ijms21103721. [PMID: 32466248 PMCID: PMC7279375 DOI: 10.3390/ijms21103721] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/19/2020] [Accepted: 05/22/2020] [Indexed: 12/15/2022] Open
Abstract
S-adenosylmethionine (SAMe) is involved in many transmethylation reactions in most living organisms and is also required in the synthesis of several substances such as monoamine neurotransmitters and the N-methyl-D-aspartate (NMDA) receptor. Due to its important role as an epigenetic modulator, we discuss in some length the process of DNA methylation and demethylation and the critical periods of epigenetic modifications in the embryo, fetus, and thereafter. We also discuss the effects of SAMe deficiency and the attempts to use SAMe for therapeutic purposes such as the treatment of major depressive disorder, Alzheimer disease, and other neuropsychiatric disorders. SAMe is an approved food additive and as such is also used during pregnancy. Yet, there seems to scanty data on the possible effects of SAMe on the developing embryo and fetus. Valproic acid (VPA) is a well-tolerated and effective antiepileptic drug that is also used as a mood stabilizer. Due to its high teratogenicity, it is contraindicated in pregnancy. A major mechanism of its action is histone deacetylase inhibition, and therefore, it acts as an epigenetic modulator, mainly on the brain. This prompted clinical trials using VPA for additional indications i.e., treating degenerative brain disease such as Alzheimer disease, dementia, HIV, and even cancer. Therefore, we discuss the possible effects of VPA and SAMe on the conceptus and early postnatally, during periods of susceptibility to epigenetic modifications. VPA is also used as an inducer of autistic-like behavior in rodents and was found by us to modify gene expression when administered during the first postnatal week but not when administered to the pregnant dams on day 12 of gestation. In contrast, SAMe modified gene expression when administered on day 12 of pregnancy but not postnatally. If administered together, VPA prevented the changes in gene expression induced by prenatal SAMe administration, and SAMe prevented the gene expression changes and autistic-like behavior induced by early postnatal VPA. It is concluded that both VPA and SAMe are powerful epigenetic modifiers with antagonistic actions on the brain that will probably be used in the future more extensively for the treatment of a variety of epigenetic diseases of the nervous system.
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Huber TD, Clinger JA, Liu Y, Xu W, Miller MD, Phillips GN, Thorson JS. Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes. ACS Chem Biol 2020; 15:695-705. [PMID: 32091873 DOI: 10.1021/acschembio.9b00943] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structural conservation among methyltransferases (MTs) and MT functional redundancy is a major challenge to the cellular study of individual MTs. As a first step toward the development of an alternative biorthogonal platform for MTs and other AdoMet-utilizing enzymes, we describe the evaluation of 38 human methionine adenosyltransferase II-α (hMAT2A) mutants in combination with 14 non-native methionine analogues to identify suitable bioorthogonal mutant/analogue pairings. Enabled by the development and implementation of a hMAT2A high-throughput (HT) assay, this study revealed hMAT2A K289L to afford a 160-fold inversion of the hMAT2A selectivity index for a non-native methionine analogue over the native substrate l-Met. Structure elucidation of K289L revealed the mutant to be folded normally with minor observed repacking within the modified substrate pocket. This study highlights the first example of exchanging l-Met terminal carboxylate/amine recognition elements within the hMAT2A active-site to enable non-native bioorthgonal substrate utilization. Additionally, several hMAT2A mutants and l-Met substrate analogues produced AdoMet analogue products with increased stability. As many AdoMet-producing (e.g., hMAT2A) and AdoMet-utlizing (e.g., MTs) enzymes adopt similar active-site strategies for substrate recognition, the proof of concept first generation hMAT2A engineering highlighted herein is expected to translate to a range of AdoMet-utilizing target enzymes.
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Affiliation(s)
- Tyler D. Huber
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | | | - Yang Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | | | | | | | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
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Liu X, Wang X, Liu N, Zhu K, Zhang S, Duan X, Huang Y, Jin Z, Jaypaul H, Wu Y, Chen H. TET2 is involved in DNA hydroxymethylation, cell proliferation and inflammatory response in keratinocytes. Mol Med Rep 2020; 21:1941-1949. [PMID: 32319620 PMCID: PMC7057829 DOI: 10.3892/mmr.2020.10989] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/29/2020] [Indexed: 12/15/2022] Open
Abstract
DNA methylation and hydroxymethylation are the most common epigenetic modifications associated with the cell cycle and the inflammatory response. The present study aimed to investigate the role of 5-hydroxymethyl-cytosine (5-hmC) and ten-eleven translocation-2 (TET2) in keratinocytes. Following TET2 knockdown, dot blot analysis was performed to assess the levels of 5-hmC in keratinocytes, using HaCaT cells. Subsequently, the viability and cell cycle of HaCaT cells were assessed by MTT, Cell Counting Kit-8 assay and flow cytometric assays. Cyclin-dependent kinase inhibitor 2A and proinflammatory cytokine protein and mRNA expression levels were also detected. The present results suggested that TET2 may play an important role in regulating cellular proliferation by mediating DNA hydroxymethylation in HaCaT cells. In addition, TET2 knockdown decreased the production of proinflammatory cytokines, including lipocalin 2, S100 calcium binding protein A7, matrix metallopeptidase 9, C-X-C motif chemokine ligand 1, interferon regulatory factor 7 and interleukin-7 receptor. The present study suggested that TET2 regulated cell viability, apoptosis and the expression of inflammatory mediators in keratinocytes. Collectively, the results indicated that TET2 knockdown may relieve inflammatory responses in the skin.
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Affiliation(s)
- Xinxin Liu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hebei 430022, P.R. China
| | - Xin Wang
- Department of Dermatology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Nian Liu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hebei 430022, P.R. China
| | - Ke Zhu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hebei 430022, P.R. China
| | - Song Zhang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hebei 430022, P.R. China
| | - Xiaoru Duan
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hebei 430022, P.R. China
| | - Yuqiong Huang
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hebei 430022, P.R. China
| | - Zilin Jin
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hebei 430022, P.R. China
| | - Himanshu Jaypaul
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hebei 430022, P.R. China
| | - Yan Wu
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hebei 430022, P.R. China
| | - Hongxiang Chen
- Department of Dermatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hebei 430022, P.R. China
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Lu Y, Dai J, Yang L, La Y, Zhou S, Qiang S, Wang Q, Tan F, Wu Y, Kong W, La H. Involvement of MEM1 in DNA demethylation in Arabidopsis. PLANT MOLECULAR BIOLOGY 2020; 102:307-322. [PMID: 31902068 DOI: 10.1007/s11103-019-00949-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/16/2019] [Indexed: 06/10/2023]
Abstract
MEM1 participates in ROS1-mediated DNA demethylation pathway, and acts functionally as ROS3 to counteract the effects of RdDM pathway.mem1mutation leads to large numbers of hyper-DMRs inArabidopsisgenome. In higher plants, DNA methylation performs important functions in silencing transcribed genes and transposable elements (TEs). Active DNA demethylation mediated by REPRESSOR OF SILENCING 1 (ROS1) is able to antagonize the action of DNA methylation caused by RNA-directed DNA methylation (RdDM) pathway, which plays critical roles in keeping DNA methylation at a proper level. In this study, a new mutant named mem1 (for methylation elevated mutant 1) was isolated from a genetic screen of T-DNA insertional mutant population for lines with elevated DNA methylation at a particular locus through Chop-PCR method. MEM1 possesses a Zf-C3HC domain, and is localized in nucleus as well as highly expressed in cotyledons. Whole-genome bisulfite sequencing data showed that knockout mutation of MEM1 leads to 4519 CG, 1793 CHG and 12739 CHH hyper-DMRs (for differentially methylated regions). Further analysis indicated that there are 2751, 2216 and 2042 overlapped CG hyper-DMRs between mem1-1and three mutants, i.e. ros1-4, rdd and ros3-2, respectively; 797, 2514, and 6766 overlapped CHH hyper-DMRs were observed between mem1-1 and three such mutants, respectively; mem1 nrpd1-3 and mem1 rdm1 double mutants showed nearly complete or partial loss of hypermethylation at 4 tested loci, suggesting that MEM1 performs similar functions as DNA glycosylase/lyases in counteracting excessive DNA methylation, and MEM1 plays important roles as REPRESSOR OF SILENCING 3 (ROS3) in erasing CHH methylation caused by the RdDM pathway. Together, these data demonstrate the involvement of MEM1 in ROS1-mediated DNA demethylation pathway and functional connections between MEM1 and ROS3.
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Affiliation(s)
- Yanke Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jie Dai
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Liu Yang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yumei La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shaoxia Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Sheng Qiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qianqian Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Feng Tan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Weiwen Kong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Honggui La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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