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1
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Yakhnitsa V, Thompson J, Ponomareva O, Ji G, Kiritoshi T, Mahimainathan L, Molehin D, Pruitt K, Neugebauer V. Dysfunction of Small-Conductance Ca 2+-Activated Potassium (SK) Channels Drives Amygdala Hyperexcitability and Neuropathic Pain Behaviors: Involvement of Epigenetic Mechanisms. Cells 2024; 13:1055. [PMID: 38920682 PMCID: PMC11201618 DOI: 10.3390/cells13121055] [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: 04/29/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/27/2024] Open
Abstract
Neuroplasticity in the amygdala and its central nucleus (CeA) is linked to pain modulation and pain behaviors, but cellular mechanisms are not well understood. Here, we addressed the role of small-conductance Ca2+-activated potassium (SK) channels in pain-related amygdala plasticity. The facilitatory effects of the intra-CeA application of an SK channel blocker (apamin) on the pain behaviors of control rats were lost in a neuropathic pain model, whereas an SK channel activator (NS309) inhibited pain behaviors in neuropathic rats but not in sham controls, suggesting the loss of the inhibitory behavioral effects of amygdala SK channels. Brain slice electrophysiology found hyperexcitability of CeA neurons in the neuropathic pain condition due to the loss of SK channel-mediated medium afterhyperpolarization (mAHP), which was accompanied by decreased SK2 channel protein and mRNA expression, consistent with a pretranscriptional mechanisms. The underlying mechanisms involved the epigenetic silencing of the SK2 gene due to the increased DNA methylation of the CpG island of the SK2 promoter region and the change in methylated CpG sites in the CeA in neuropathic pain. This study identified the epigenetic dysregulation of SK channels in the amygdala (CeA) as a novel mechanism of neuropathic pain-related plasticity and behavior that could be targeted to control abnormally enhanced amygdala activity and chronic neuropathic pain.
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Affiliation(s)
- Vadim Yakhnitsa
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Jeremy Thompson
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Olga Ponomareva
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Guangchen Ji
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Center of Excellence for Translational Neuroscience and Therapeutics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Takaki Kiritoshi
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Lenin Mahimainathan
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Deborah Molehin
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Kevin Pruitt
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Volker Neugebauer
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Center of Excellence for Translational Neuroscience and Therapeutics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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2
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Zohourian N, Brown JAL. Current trends in clinical trials and the development of small molecule epigenetic inhibitors as cancer therapeutics. Epigenomics 2024; 16:671-680. [PMID: 38639711 PMCID: PMC11233149 DOI: 10.2217/epi-2023-0443] [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: 12/18/2023] [Accepted: 03/20/2024] [Indexed: 04/20/2024] Open
Abstract
Epigenetic mechanisms control and regulate normal chromatin structure and gene expression patterns, with epigenetic dysregulation observed in many different cancer types. Importantly, epigenetic modifications are reversible, offering the potential to silence oncogenes and reactivate tumor suppressors. Small molecule drugs manipulating these epigenetic mechanisms are at the leading edge of new therapeutic options for cancer treatment. The clinical use of histone deacetyltransferases inhibitors (HDACi) demonstrates the effectiveness of targeting epigenetic mechanisms for cancer treatment. Notably, the development of new classes of inhibitors, including lysine acetyltransferase inhibitors (KATi), are the future of epigenetic-based therapeutics. We outline the progress of current classes of small molecule epigenetic drugs for use against cancer (preclinical and clinical) and highlight the potential market growth in epigenetic-based therapeutics.
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Affiliation(s)
- Nazanin Zohourian
- Department of Biological Science, University of Limerick, Limerick, V94 T9PX, Ireland
| | - James AL Brown
- Department of Biological Science, University of Limerick, Limerick, V94 T9PX, Ireland
- Limerick Digital Cancer Research Centre (LDCRC), University of Limerick, Limerick, Ireland
- Health Research Institute (HRI), University of Limerick, Limerick, Ireland
- Bernal Institute, University of Limerick, Limerick, Ireland
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3
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Tsagkogeorga G, Santos-Rosa H, Alendar A, Leggate D, Rausch O, Kouzarides T, Weisser H, Han N. Predicting genes associated with RNA methylation pathways using machine learning. Commun Biol 2022; 5:868. [PMID: 36008532 PMCID: PMC9411552 DOI: 10.1038/s42003-022-03821-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/08/2022] [Indexed: 11/09/2022] Open
Abstract
RNA methylation plays an important role in functional regulation of RNAs, and has thus attracted an increasing interest in biology and drug discovery. Here, we collected and collated transcriptomic, proteomic, structural and physical interaction data from the Harmonizome database, and applied supervised machine learning to predict novel genes associated with RNA methylation pathways in human. We selected five types of classifiers, which we trained and evaluated using cross-validation on multiple training sets. The best models reached 88% accuracy based on cross-validation, and an average 91% accuracy on the test set. Using protein-protein interaction data, we propose six molecular sub-networks linking model predictions to previously known RNA methylation genes, with roles in mRNA methylation, tRNA processing, rRNA processing, but also protein and chromatin modifications. Our study exemplifies how access to large omics datasets joined by machine learning methods can be used to predict gene function.
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Affiliation(s)
- Georgia Tsagkogeorga
- STORM Therapeutics Ltd, Babraham Research Campus, Cambridge, UK.
- Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge, UK.
| | - Helena Santos-Rosa
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Andrej Alendar
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Dan Leggate
- STORM Therapeutics Ltd, Babraham Research Campus, Cambridge, UK
| | - Oliver Rausch
- STORM Therapeutics Ltd, Babraham Research Campus, Cambridge, UK
| | - Tony Kouzarides
- Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge, UK
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Hendrik Weisser
- STORM Therapeutics Ltd, Babraham Research Campus, Cambridge, UK.
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge, UK.
- Cambridge Centre for AI in Medicine, Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK.
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4
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Saliba AN, John AJ, Kaufmann SH. Resistance to venetoclax and hypomethylating agents in acute myeloid leukemia. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2021; 4:125-142. [PMID: 33796823 PMCID: PMC8011583 DOI: 10.20517/cdr.2020.95] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite the success of the combination of venetoclax with the hypomethylating agents (HMA) decitabine or azacitidine in inducing remission in older, previously untreated patients with acute myeloid leukemia (AML), resistance - primary or secondary - still constitutes a significant roadblock in the quest to prolong the duration of response. Here we review the proposed and proven mechanisms of resistance to venetoclax monotherapy, HMA monotherapy, and the doublet of venetoclax and HMA for the treatment of AML. We approach the mechanisms of resistance to HMAs and venetoclax in the light of the agents' mechanisms of action. We briefly describe potential therapeutic strategies to circumvent resistance to this promising combination, including alternative scheduling or the addition of other agents to the HMA and venetoclax backbone. Understanding the mechanisms of action and evolving resistance in AML remains a priority in order to maximize the benefit from novel drugs and combinations, identify new therapeutic targets, define potential prognostic markers, and avoid treatment failure.
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Affiliation(s)
- Antoine N Saliba
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - August J John
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Scott H Kaufmann
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN 55905, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA.,Division of Oncology Research, Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
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5
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Bai P, Lu X, Liu Y, Lan Y, Wang H, Fiedler S, Striar R, Wang C. Discovery of a Positron Emission Tomography Radiotracer Selectively Targeting the BD1 Bromodomains of BET Proteins. ACS Med Chem Lett 2021; 12:282-287. [PMID: 33603976 DOI: 10.1021/acsmedchemlett.0c00650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
In this paper, we report the design, synthesis, and biological evaluation of the first selective bromodomain and extra-terminal domain (BET) BD1 bromodomains of the PET radiotracer [18F]PB006. The standard compound PB006 showed high affinity and good selectivity toward BRD4 BD1 (K d = 100 nM and 29-fold selectively for BD1 over BD2) in an in vitro binding assay. PET imaging experiments in rodents were performed to evaluate the bioactivity of [18F]PB006 in vivo. A biodistribution study of [18F]PB006 in mice revealed high radiotracer uptake in peripheral tissues, such as liver and kidney, and moderate radiotracer uptake in the brain. Further blocking studies demonstrated the significant radioactivity decreasing (20-30% reduction compared with baseline) by pretreating unlabeled PB006 and JQ1, suggesting the high binding selectivity and specificity of [18F]PB006. Our study indicated that [18F]PB006 is a potent PET probe selectively targeting BET BD1, and further structural optimization of the radiotracer is still required to improve brain uptake to support neuroepigenetic imaging.
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Affiliation(s)
- Ping Bai
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xiaoxia Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P.R. China
| | - Yan Liu
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Yu Lan
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Hao Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Stephanie Fiedler
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Robin Striar
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Changning Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
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6
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Klutstein M. Cause and effect in epigenetics - where lies the truth, and how can experiments reveal it?: Epigenetic self-reinforcing loops obscure causation in cancer and aging. Bioessays 2020; 43:e2000262. [PMID: 33236359 DOI: 10.1002/bies.202000262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022]
Abstract
Epigenetic changes are implicated in aging and cancer. Sometimes, it is clear whether the causing agent of the condition is a genetic factor or epigenetic. In other cases, the causative factor is unclear, and could be either genetic or epigenetic. Is there a general role for epigenetic changes in cancer and aging? Here, I present the paradigm of causative roles executed by epigenetic changes. I discuss cases with clear roles of the epigenome in cancer and aging, and other cases showing involvement of other factors. I also present the possibility that sometimes causality is difficult to assign because of the presence of self-reinforcing loops in epigenetic regulation. Such loops hinder the identification of the causative factor. I provide an experimental framework by which the role of the epigenome can be examined in a better setting and where the presence of such loops could be investigated in more detail.
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Affiliation(s)
- Michael Klutstein
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
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7
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Guo X, Puttabyatappa M, Domino SE, Padmanabhan V. Developmental programming: Prenatal testosterone-induced changes in epigenetic modulators and gene expression in metabolic tissues of female sheep. Mol Cell Endocrinol 2020; 514:110913. [PMID: 32562712 PMCID: PMC7397566 DOI: 10.1016/j.mce.2020.110913] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/20/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022]
Abstract
Prenatal testosterone (T)-treated female sheep manifest peripheral insulin resistance and tissue-specific changes in insulin sensitivity with liver and muscle manifesting insulin resistance accompanied by inflammatory, oxidative and lipotoxic state. In contrast, visceral (VAT) and subcutaneous (SAT) adipose tissues are insulin sensitive in spite of VAT manifesting changes in inflammatory and oxidative state. We hypothesized that prenatal T-induced changes in tissue-specific insulin resistance arise from disrupted lipid storage and metabolism gene expression driven by changes in DNA and histone modifying enzymes. Changes in gene expression were assessed in liver, muscle and 4 adipose (VAT, SAT, epicardiac [ECAT] and perirenal [PRAT]) depots collected from control and prenatal T-treated female sheep. Prenatal T-treatment increased lipid droplet and metabolism genes PPARA and PLIN1 in liver, SREBF and PLIN1 in muscle and showed a trend for decrease in PLIN2 in PRAT. Among epigenetic modifying enzymes, prenatal T-treatment increased expression of 1) DNMT1 in liver and DNMT3A in VAT, PRAT, muscle and liver; 2) HDAC1 in ECAT, HDAC2 in muscle with decrease in HDAC3 in VAT; 3) EP300 in VAT and ECAT; and 4) KDM1A in VAT with increases in liver histone acetylation. Increased lipid storage and metabolism genes in liver and muscle are consistent with lipotoxicity in these tissues with increased histone acetylation likely contributing to increased liver PPARA. These findings are suggestive that metabolic defects in prenatal T-treated sheep may arise from changes in key genes mediated, in part, by tissue-specific changes in epigenetic-modifying enzymes.
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Affiliation(s)
- Xingzi Guo
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA; Department of Obstetrics and Gynecology, 3rd Xiangya Hospital, Central South University, Changsha, Hunan, 410008, PR China
| | | | - Steven E Domino
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor MI, USA
| | - Vasantha Padmanabhan
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor MI, USA.
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8
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Chen H, Zhao H, Xiang L, Wu H, Liang Y, Huang XA, Zhang J. Aldol sensor-inspired fluorescent probes for measuring protein citrullination. Org Biomol Chem 2020; 18:5120-5124. [PMID: 32598414 DOI: 10.1039/c9ob02737h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Protein citrullination is an important posttranslational modification on an arginine residue. However, high quality fluorescent probes for measuring the citrullination level and capturing citrullinated proteins are quite limited. Inspired by the similarity between acid-promoted citrulline-labeling reaction and aldol reaction, here we present "turn-on" and "turn-off" fluorescent probes for measuring citrulline levels based on the scaffold of aldol sensors. Further application of the modified probe showed great potential to simultaneously monitor and capture citrullinated peptides.
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Affiliation(s)
- Huihong Chen
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
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9
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Amjadi M, Hallaj T, Hildebrandt N. A sensitive homogeneous enzyme assay for euchromatic histone-lysine-N-methyltransferase 2 (G9a) based on terbium-to-quantum dot time-resolved FRET. ACTA ACUST UNITED AC 2020; 11:173-179. [PMID: 34336605 PMCID: PMC8314039 DOI: 10.34172/bi.2021.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 06/01/2020] [Accepted: 06/13/2020] [Indexed: 12/20/2022]
Abstract
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Introduction: Histone modifying enzymes include several classes of enzymes that are responsible for various post-translational modifications of histones such as methylation and acetylation. They are important epigenetic factors, which may involve several diseases and so their assay, as well as screening of their inhibitors, are of great importance. Herein, a bioassay based on terbium-to-quantum dot (Tb-to-QD) time-resolved Förster resonance energy transfer (TR-FRET) was developed for monitoring the activity of G9a, the euchromatic histone-lysine N-methyltransferase 2. Overexpression of G9a has been reported in some cancers such as ovarian carcinoma, lung cancer, multiple myeloma and brain cancer. Thus, inhibition of this enzyme is important for therapeutic purposes. Methods: In this assay, a biotinylated peptide was used as a G9a substrate in conjugation with streptavidin-coated ZnS/CdSe QD as FRET acceptor, and an anti-mark antibody labeled with Tb as a donor. Time-resolved fluorescence was used for measuring FRET ratios. Results: We examined three QDs, with emission wavelengths of 605, 655 and 705 nm, as FRET acceptors and investigated FRET efficiency between the Tb complex and each of them. Since the maximum FRET efficiency was obtained for Tb to QD705 (more than 50%), this pair was exploited for designing the enzyme assay. We showed that the method has excellent sensitivity and selectivity for the determination of G9a at concentrations as low as 20 pM. Furthermore, the designed assay was applied for screening of an enzyme inhibitor, S-(5’-Adenosyl)-L-homocysteine (SAH). Conclusion: It was shown that Tb-to-QD FRET is an outstanding platform for developing a homogenous assay for the G9a enzyme and its inhibitors. The obtained results confirmed that this assay was quite sensitive and could be used in the field of inhibitor screening.
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Affiliation(s)
- Mohammad Amjadi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 5166616471, Iran
| | - Tooba Hallaj
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 5166616471, Iran.,Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, Orsay, France.,Laboratoire Chimie Organique, Bioorganique, Réactivité et Analyse (COBRA), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France
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10
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Hallaj T, Amjadi M, Qiu X, Susumu K, Medintz IL, Hildebrandt N. Terbium-to-quantum dot Förster resonance energy transfer for homogeneous and sensitive detection of histone methyltransferase activity. NANOSCALE 2020; 12:13719-13730. [PMID: 32573632 DOI: 10.1039/d0nr03383a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The development of rapid, simple, and versatile biosensors for monitoring the activity of histone modifying enzymes (HMEs) is needed for the improvement of diagnostic assays, screening of HME inhibitors, and a better understanding of HME kinetics in different environments. Nanoparticles can play an important role in this regard by improving or complementing currently available enzyme detection technologies. Here, we present the development and application of a homogeneous methyltransferase (SET7/9) assay based on time-gated Förster resonance energy transfer (TG-FRET) between terbium complexes (Tb) and luminescent semiconductor quantum dots (QDs). Specific binding of a Tb-antibody conjugate to a SET7/9-methylated Lys4 on a histone H3(1-21) peptide substrate attached to the QD surface resulted in efficient FRET and provided the mechanism for monitoring the SET7/9 activity. Two common peptide-QD attachment strategies (biotin-streptavidin and polyhistidine-mediated self-assembly), two different QD colors (625 and 705 nm), and enzyme sensing with post- or pre-assembled QD-peptide conjugates demonstrated the broad applicability of this assay design. Limits of detection in the low picomolar concentration range, high selectivity tested against non-specific antibodies, enzymes, and co-factors, determination of the inhibition constants of the SET7/9 inhibitors SAH and (R)-PFI-2, and analysis of the co-factor (SAM) concentration-dependent enzyme kinetics of SET7/9 which followed the Michaelis-Menten model highlighted the excellent performance of this TG-FRET HME activity assay.
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Affiliation(s)
- Tooba Hallaj
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 5166616471, Iran. and Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia 5714783734, Iran
| | - Mohammad Amjadi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 5166616471, Iran.
| | - Xue Qiu
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France and School of Medicine and Pharmacy, Ocean University of China. 5, Yushan Road, 266003 Qingdao, Shandong, China
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, Washington, D.C. 20375, USA and KeyW Corporation, Hanover, Maryland 21076, USA
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, USA
| | - Niko Hildebrandt
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France and nanoFRET.com, Laboratoire COBRA (Chimie Organique, Bioorganique, Réactivité et Analyse), Université de Rouen Normandie, CNRS, INSA, 76821 Mont-Saint-Aignan, France.
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11
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Ogihara S, Komatsu T, Itoh Y, Miyake Y, Suzuki T, Yanagi K, Kimura Y, Ueno T, Hanaoka K, Kojima H, Okabe T, Nagano T, Urano Y. Metabolic-Pathway-Oriented Screening Targeting S-Adenosyl-l-methionine Reveals the Epigenetic Remodeling Activities of Naturally Occurring Catechols. J Am Chem Soc 2020; 142:21-26. [PMID: 31869215 DOI: 10.1021/jacs.9b08698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Methyl transfer reactions play important roles in many biological phenomena, wherein the methylation cofactor S-adenosyl-l-methionine (SAM) serves as the important currency to orchestrate those reactions. We have developed a fluorescent-probe-based high-throughput screening (HTS) system to search for the compounds that control cellular SAM levels. HTS with a drug repositioning library revealed the importance of catechol-O-methyltransferase (COMT) and its substrates in controlling the SAM concentrations and histone methylation levels in colorectal tumor cells.
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Affiliation(s)
| | | | - Yukihiro Itoh
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho, Sakyo-ku , Kyoto 606-0823 , Japan
| | - Yuka Miyake
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho, Sakyo-ku , Kyoto 606-0823 , Japan.,The Institute of Scientific and Industrial Research (ISIR) , Osaka University , 8-1 Mihogaoka, Ibaraki-shi , Osaka 567-0047 , Japan
| | - Takayoshi Suzuki
- Graduate School of Medical Science , Kyoto Prefectural University of Medicine , 1-5 Shimogamohangi-cho, Sakyo-ku , Kyoto 606-0823 , Japan.,The Institute of Scientific and Industrial Research (ISIR) , Osaka University , 8-1 Mihogaoka, Ibaraki-shi , Osaka 567-0047 , Japan
| | | | | | | | | | - Hirotatsu Kojima
- Drug Discovery Initiative , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Takayoshi Okabe
- Drug Discovery Initiative , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Tetsuo Nagano
- Drug Discovery Initiative , The University of Tokyo , 7-3-1 Hongo , Bunkyo-ku , Tokyo 113-0033 , Japan
| | - Yasuteru Urano
- Core Research for Evolutional Science and Technology (CREST) , Japan Agency for Medical Research and Development (AMED) , 1-7-1 Otemachi , Chiyoda-ku , Tokyo 100-0004 , Japan
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12
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C10ORF12 modulates PRC2 histone methyltransferase activity and H3K27me3 levels. Acta Pharmacol Sin 2019; 40:1457-1465. [PMID: 31186533 DOI: 10.1038/s41401-019-0247-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/05/2019] [Indexed: 01/03/2023]
Abstract
The polycomb repressive complex 2 (PRC2) catalyzes the methylation of histone H3 on lysine 27 (H3K27) to generate trimethyl-H3K27 (H3K27me3) marks, thereby leading to a repressive chromatin state that inhibits gene expression. C10ORF12 was recently identified as a novel PRC2 interactor. Here, we show that C10ORF12 specifically interacts with PRC2 through its middle region (positions 619-718). C10ORF12 significantly enhances the histone methyltransferase activity of PRC2 in vitro and dramatically increases the total H3K27me3 levels in HeLa cells. C10ORF12 also antagonizes Jarid2, which is an auxiliary factor of the PRC2.2 subcomplex, to promote increased H3K27me3 levels in HeLa cells. Moreover, C10ORF12 alters the substrate preference of PRC2. These results indicate that C10ORF12 functions as a positive regulator of PRC2 and facilitates PRC2-mediated H3K27me3 modification of chromatin. These findings provide new insight into the roles of C10ORF12 in regulating the activity of the PRC2 complex.
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13
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Guo X, Puttabyatappa M, Thompson RC, Padmanabhan V. Developmental Programming: Contribution of Epigenetic Enzymes to Antral Follicular Defects in the Sheep Model of PCOS. Endocrinology 2019; 160:2471-2484. [PMID: 31398247 PMCID: PMC6760338 DOI: 10.1210/en.2019-00389] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/22/2019] [Indexed: 12/27/2022]
Abstract
Prenatal testosterone (T)-treated sheep, similar to women with polycystic ovary syndrome (PCOS), manifest oligo-/anovulation, hyperandrogenism, and polyfollicular ovary. The polyfollicular ovarian morphology, a result of persistence of antral follicles, arises, in part, by transcriptional changes in key mediators of follicular development that, in turn, are driven by epigenetic mechanisms. We hypothesized that prenatal T excess induces, in a cell-specific manner, transcriptional changes in key mediators of follicular development associated with relevant changes in epigenetic machinery. Expression levels of key mediators of follicular development, DNA methyltransferases (DNMTs), and histone de-/methylases and de-/acetylases were determined in laser-capture microdissection-isolated antral follicular granulosa and theca and ovarian stromal cells from 21 months of age control and prenatal T-treated sheep (100 mg IM twice weekly from gestational day 30 to 90; term: 147 days). Changes in histone methylation were determined by immunofluorescence. Prenatal T treatment induced the following: (i) cell-specific changes in gene expression of key mediators of follicular development and steroidogenesis; (ii) granulosa, theca, and stromal cell-specific changes in DNMTs and histone de-/methylases and deacetylases, and (iii) increases in histone 3 trimethylation at lysine 9 in granulosa and histone 3 dimethylation at lysine 4 in theca cells. The pattern of histone methylation was consistent with the expression profile of histone de-/methylases in the respective cells. These findings suggest that changes in expression of key genes involved in the development of the polyfollicular phenotype in prenatal T-treated sheep are mediated, at least in part, by cell-specific changes in epigenetic-modifying enzymes.
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Affiliation(s)
- Xingzi Guo
- Department of Obstetrics and Gynecology, Xiangya Third Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | | | - Robert C Thompson
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan
| | - Vasantha Padmanabhan
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
- Correspondence: Vasantha Padmanabhan, PhD, Department of Pediatrics, University of Michigan, 7510 MSRB 1, 1500 West Medical Center Drive, Ann Arbor, Michigan 48109. E-mail:
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14
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Sipos F, Kiss AL, Constantinovits M, Tulassay Z, Műzes G. Modified Genomic Self-DNA Influences In Vitro Survival of HT29 Tumor Cells via TLR9- and Autophagy Signaling. Pathol Oncol Res 2019; 25:1505-1517. [PMID: 30465163 DOI: 10.1007/s12253-018-0544-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 11/16/2018] [Indexed: 02/08/2023]
Abstract
In relation of immunobiology, the consequence of the crosstalk between TLR9-signaling and autophagy is poorly documented in HT29 cancer cells. To assess the TLR9-mediated biologic effects of modified self-DNA sequences on cell kinetics and autophagy response HT29 cells were incubated separately with intact genomic (g), hypermethylated (m), fragmented (f), and hypermethylated/fragmented (m/f) self-DNAs. Cell viability, apoptosis, cell proliferation, colonosphere-formation were determined. Moreover, the relation of TLR9-signaling to autophagy response was assayed by real-time RT-PCR, immunocytochemistry and transmission electron microscopy (TEM). After incubation with g-, m-, and m/f-DNAs cell viability and proliferation decreased, while apoptosis increased. F-DNA treatment resulted in an increase of cell survival. Methylation of self-DNA resulted in decrease of TLR9 expression, while it did not influence the positive effect of DNA fragmentation on MyD88 and TRAF6 overexpression, and TNFα downregulation. Fragmentation of DNA abrogated the positive effect of methylation on IRAK2, NFκB and IL-8 mRNA upregulations. In case of the autophagy genes and proteins, g- and f-DNAs caused significant upregulation of Beclin1, Atg16L1, and LC3B. According to TEM analyses, autophagy was present in each group of tumor cells, but to a varying degree. Incubation with m-DNA suppressed tumor cell survival by inducing features of apoptotic cell death, and activated mitophagy. F-DNA treatment enhanced cell survival, and activated macroautophagy and lipophagy. Colonospheres were only present after m-DNA incubation. Our data provided evidence for a close existing interplay between TLR9-signaling and the autophagy response with remarkable influences on cell survival in HT29 cells subjected to modified self-DNA treatments.
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Affiliation(s)
- Ferenc Sipos
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi street 46, Budapest, 1088, Hungary.
| | - Anna L Kiss
- Department of Human Morphology and Developmental Biology, Semmelweis University, Budapest, 1094, Hungary
| | - Miklós Constantinovits
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi street 46, Budapest, 1088, Hungary
| | - Zsolt Tulassay
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi street 46, Budapest, 1088, Hungary
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, 1051, Hungary
| | - Györgyi Műzes
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi street 46, Budapest, 1088, Hungary
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15
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Fabini E, Talibov VO, Mihalic F, Naldi M, Bartolini M, Bertucci C, Del Rio A, Danielson UH. Unveiling the Biochemistry of the Epigenetic Regulator SMYD3. Biochemistry 2019; 58:3634-3645. [PMID: 31389685 DOI: 10.1021/acs.biochem.9b00420] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SET and MYND domain-containing protein 3 (SMYD3) is a lysine methyltransferase that plays a central role in a variety of cancer diseases, exerting its pro-oncogenic activity by methylation of key proteins, of both nuclear and cytoplasmic nature. However, the role of SMYD3 in the initiation and progression of cancer is not yet fully understood and further biochemical characterization is required to support the discovery of therapeutics targeting this enzyme. We have therefore developed robust protocols for production, handling, and crystallization of SMYD3 and biophysical and biochemical assays for clarification of SMYD3 biochemistry and identification of useful lead compounds. Specifically, a time-resolved biosensor assay was developed for kinetic characterization of SMYD3 interactions. Functional differences in SMYD3 interactions with its natural small molecule ligands SAM and SAH were revealed, with SAM forming a very stable complex. A variety of peptides mimicking putative substrates of SMYD3 were explored in order to expose structural features important for recognition. The interaction between SMYD3 and some peptides was influenced by SAM. A nonradioactive SMYD3 activity assay using liquid chromatography-mass spectrometry (LC-MS) analysis explored substrate features of importance also for methylation. Methylation was notable only toward MAP kinase kinase kinase 2 (MAP3K2_K260)-mimicking peptides, although binary and tertiary complexes were detected also with other peptides. The analysis supported a random bi-bi mechanistic model for SMYD3 methyltransferase catalysis. Our work unveiled complexities in SMYD3 biochemistry and resulted in procedures suitable for further studies and identification of novel starting points for design of effective and specific leads for this potential oncology target.
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Affiliation(s)
- Edoardo Fabini
- Department of Pharmacy and Biotechnology , Alma Mater Studiorum University of Bologna , Bologna , Italy.,Institute of Organic Synthesis and Photoreactivity (ISOF) , National Research Council (CNR) , Bologna , Italy
| | | | - Filip Mihalic
- Department of Chemistry - BMC , Uppsala University , Uppsala , Sweden
| | - Marina Naldi
- Department of Pharmacy and Biotechnology , Alma Mater Studiorum University of Bologna , Bologna , Italy.,Center for Applied Biomedical Research (C.R.B.A.) , S. Orsola-Malpighi Hospital , Bologna , Italy
| | - Manuela Bartolini
- Department of Pharmacy and Biotechnology , Alma Mater Studiorum University of Bologna , Bologna , Italy
| | - Carlo Bertucci
- Department of Pharmacy and Biotechnology , Alma Mater Studiorum University of Bologna , Bologna , Italy
| | - Alberto Del Rio
- Institute of Organic Synthesis and Photoreactivity (ISOF) , National Research Council (CNR) , Bologna , Italy.,Innovamol Consulting Srl , Modena , Italy
| | - U Helena Danielson
- Department of Chemistry - BMC , Uppsala University , Uppsala , Sweden.,Science for Life Laboratory , Uppsala University , Uppsala , Sweden
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16
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Ponnusamy L, Mahalingaiah PKS, Singh KP. Epigenetic reprogramming and potential application of epigenetic-modifying drugs in acquired chemotherapeutic resistance. Adv Clin Chem 2019; 94:219-259. [PMID: 31952572 DOI: 10.1016/bs.acc.2019.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Chemotherapy is the most common clinical choice of treatment for cancer, however, acquired chemoresistance is a major challenge that limits the successful outcome of this option. Systematic review of in vitro, in vivo, preclinical and clinical studies suggests that acquired chemoresistance is polygenic, progressive, and involve both genetic and epigenetic heterogeneities and perturbations. Various mechanisms that confer resistance to chemotherapy are tightly controlled by epigenetic regulations. Poised epigenetic plasticity and temporal increase in epigenetic alterations upon chemotherapy make chemoresistance likely an epigenetic-driven process. The transient and reversible nature of epigenetic modulations enable ways to intervene the epigenetic re-programing associated with acquired chemoresistance via application of epigenetic modifying drugs. This review discusses recent understandings behind the various mechanisms of acquired chemoresistance that are under the control of epigenetic drivers, potential application of epigenetic-based drugs in resensitizing refractory cancers to chemotherapy, the limitations and future scope for clinical application of epigenetic therapeutics in successfully addressing chemoresistance.
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Affiliation(s)
- Logeswari Ponnusamy
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, TX, United States
| | - Prathap Kumar S Mahalingaiah
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, TX, United States
| | - Kamaleshwar P Singh
- Department of Environmental Toxicology, The Institute of Environmental and Human Health (TIEHH), Texas Tech University, Lubbock, TX, United States.
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17
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Samarajeewa A, Jacques BE, Dabdoub A. Therapeutic Potential of Wnt and Notch Signaling and Epigenetic Regulation in Mammalian Sensory Hair Cell Regeneration. Mol Ther 2019; 27:904-911. [PMID: 30982678 PMCID: PMC6520458 DOI: 10.1016/j.ymthe.2019.03.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 02/07/2023] Open
Abstract
Hearing loss is one of the most prevalent sensory deficits worldwide and can result from the death of mechanosensory hair cells that transduce auditory signals in the cochlea. The mammalian cochlea lacks the capacity to regenerate these hair cells once damaged, and currently there are no biological therapies for hearing loss. Understanding the signaling pathways responsible for hair cell development can inform regenerative strategies and identify targets for treating hearing loss. The canonical Wnt and Notch pathways are critical for cochlear development; they converge on several key molecules, such as Atoh1, to regulate prosensory specification, proliferation, hair cell differentiation, and cellular organization. Much work has focused on Wnt and Notch modulation in the neonatal mouse cochlea, where they can promote hair cell regeneration. However, this regenerative response is limited in the adult cochlea and this might be attributed to age-dependent epigenetic modifications. Indeed, the epigenetic status at key gene loci undergoes dynamic changes during cochlear development, maturation, and aging. Therefore, strategies to improve regenerative success in the adult cochlea might require the modulation of Wnt, Notch, or other pathways, as well as targeted epigenetic modifications to alter the activity of key genes critical for supporting cell proliferation or transdifferentiation.
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Affiliation(s)
- Anshula Samarajeewa
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Alain Dabdoub
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Otolaryngology - Head & Neck Surgery, University of Toronto, Toronto, ON M5G 2C4, Canada.
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18
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Chaturvedi SS, Ramanan R, Waheed SO, Karabencheva-Christova TG, Christov CZ. Structure-function relationships in KDM7 histone demethylases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 117:113-125. [DOI: 10.1016/bs.apcsb.2019.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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19
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Matt SM, Zimmerman JD, Lawson MA, Bustamante AC, Uddin M, Johnson RW. Inhibition of DNA Methylation With Zebularine Alters Lipopolysaccharide-Induced Sickness Behavior and Neuroinflammation in Mice. Front Neurosci 2018; 12:636. [PMID: 30279646 PMCID: PMC6153314 DOI: 10.3389/fnins.2018.00636] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 08/24/2018] [Indexed: 12/24/2022] Open
Abstract
Activity of DNA methyltransferases (DNMTs), the enzymes that catalyze DNA methylation, is dynamically regulated in the brain. DNMT inhibitors alter DNA methylation globally in the brain and at individual neural plasticity-associated genes, but how DNMT inhibitors centrally influence lipopolysaccharide (LPS)-induced neuroinflammation is not known. We investigated whether the DMNT inhibitor, zebularine, would alter sickness behavior, DNA methylation of the Il-1β promoter and expression of inflammatory genes in hippocampus and microglia. Contrary to our hypothesis that zebularine may exaggerate LPS-induced sickness response and neuroinflammation, adult mice treated with an intracerebroventricular (ICV) injection of zebularine prior to LPS had surprisingly faster recovery of burrowing behavior compared to mice treated with LPS. Further, genes of inflammatory markers, epigenetic regulators, and the microglial sensory apparatus (i.e., the sensome) were differentially expressed by zebularine alone or in combination with LPS. Bisulfite pyrosequencing revealed that ICV zebularine led to decreased DNA methylation of two CpG sites near the Il-1β proximal promoter alone or in combination with LPS. Zebularine treated mice still exhibited decreased DNA methylation 48 h after treatment when LPS-induced sickness behavior as well as hippocampal and microglial gene expression were similar to control mice. Taken together, these data suggest that decreased DNA methylation, specifically of the Il-1β promoter region, with a DNMT inhibitor in the brain disrupts molecular mechanisms of neuroinflammation.
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Affiliation(s)
- Stephanie M Matt
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Animal Sciences Laboratory, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jalisa D Zimmerman
- Animal Sciences Laboratory, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Marcus A Lawson
- Animal Sciences Laboratory, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Angela C Bustamante
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Monica Uddin
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Department of Psychology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Rodney W Johnson
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Animal Sciences Laboratory, Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States.,Integrative Immunology and Behavior Program, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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20
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Adeegbe DO, Liu S, Hattersley MM, Bowden M, Zhou CW, Li S, Vlahos R, Grondine M, Dolgalev I, Ivanova EV, Quinn MM, Gao P, Hammerman PS, Bradner JE, Diehl JA, Rustgi AK, Bass AJ, Tsirigos A, Freeman GJ, Chen H, Wong KK. BET Bromodomain Inhibition Cooperates with PD-1 Blockade to Facilitate Antitumor Response in Kras-Mutant Non-Small Cell Lung Cancer. Cancer Immunol Res 2018; 6:1234-1245. [PMID: 30087114 DOI: 10.1158/2326-6066.cir-18-0077] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/22/2018] [Accepted: 08/02/2018] [Indexed: 12/24/2022]
Abstract
KRAS mutation is present in approximately 30% of human lung adenocarcinomas. Although recent advances in targeted therapy have shown great promise, effective targeting of KRAS remains elusive, and concurrent alterations in tumor suppressors render KRAS-mutant tumors even more resistant to existing therapies. Contributing to the refractoriness of KRAS-mutant tumors are immunosuppressive mechanisms, such as increased presence of suppressive regulatory T cells (Treg) in tumors and elevated expression of the inhibitory receptor PD-1 on tumor-infiltrating T cells. Treatment with BET bromodomain inhibitors is beneficial for hematologic malignancies, and they have Treg-disruptive effects in a non-small cell lung cancer (NSCLC) model. Targeting PD-1-inhibitory signals through PD-1 antibody blockade also has substantial therapeutic impact in lung cancer, although these outcomes are limited to a minority of patients. We hypothesized that the BET bromodomain inhibitor JQ1 would synergize with PD-1 blockade to promote a robust antitumor response in lung cancer. In the present study, using Kras+/LSL-G12D ; Trp53L/L (KP) mouse models of NSCLC, we identified cooperative effects between JQ1 and PD-1 antibody. The numbers of tumor-infiltrating Tregs were reduced and activation of tumor-infiltrating T cells, which had a T-helper type 1 (Th1) cytokine profile, was enhanced, underlying their improved effector function. Furthermore, lung tumor-bearing mice treated with this combination showed robust and long-lasting antitumor responses compared with either agent alone, culminating in substantial improvement in the overall survival of treated mice. Thus, combining BET bromodomain inhibition with immune checkpoint blockade offers a promising therapeutic approach for solid malignancies such as lung adenocarcinoma. Cancer Immunol Res; 6(10); 1234-45. ©2018 AACR.
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Affiliation(s)
- Dennis O Adeegbe
- Laura & Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York.
| | - Shengwu Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Maureen M Hattersley
- Oncology Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, Massachusetts
| | - Michaela Bowden
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Chensheng W Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Shuai Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Raven Vlahos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Michael Grondine
- Oncology Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, Massachusetts
| | - Igor Dolgalev
- Applied Bioinformatics Laboratories and Department of Pathology, New York University School of Medicine, New York, New York
| | - Elena V Ivanova
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.,Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Max M Quinn
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Peng Gao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Peter S Hammerman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - James E Bradner
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - J Alan Diehl
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina
| | - Anil K Rustgi
- Division of Gastroenterology, Departments of Medicine and Genetics, Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Adam J Bass
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories and Department of Pathology, New York University School of Medicine, New York, New York
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Huawei Chen
- Oncology Innovative Medicines Unit, AstraZeneca R&D Boston, Waltham, Massachusetts
| | - Kwok-Kin Wong
- Laura & Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York.
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21
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I-7ab inhibited the growth of TNBC cells via targeting HDAC3 and promoting the acetylation of p53. Biomed Pharmacother 2018; 99:220-226. [DOI: 10.1016/j.biopha.2018.01.063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/29/2017] [Accepted: 01/11/2018] [Indexed: 11/24/2022] Open
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22
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Bayat S, Shekari Khaniani M, Choupani J, Alivand MR, Mansoori Derakhshan S. HDACis (class I), cancer stem cell, and phytochemicals: Cancer therapy and prevention implications. Biomed Pharmacother 2018; 97:1445-1453. [DOI: 10.1016/j.biopha.2017.11.065] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 12/12/2022] Open
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23
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Systematic discovery of drug action mechanisms by an integrated chemical genomics approach: identification of functional disparities between azacytidine and decitabine. Oncotarget 2017; 7:27363-78. [PMID: 27036028 PMCID: PMC5053656 DOI: 10.18632/oncotarget.8455] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 03/16/2016] [Indexed: 01/22/2023] Open
Abstract
Polypharmacology (the ability of a drug to affect more than one molecular target) is considered a basic property of many therapeutic small molecules. Herein, we used a chemical genomics approach to systematically analyze polypharmacology by integrating several analytical tools, including the LINCS (Library of Integrated Cellular Signatures), STITCH (Search Tool for Interactions of Chemicals), and WebGestalt (WEB-based GEne SeT AnaLysis Toolkit). We applied this approach to identify functional disparities between two cytidine nucleoside analogs: azacytidine (AZA) and decitabine (DAC). AZA and DAC are structurally and mechanistically similar DNA-hypomethylating agents. However, their metabolism and destinations in cells are distinct. Due to their differential incorporation into RNA or DNA, functional disparities between AZA and DAC are expected. Indeed, different cytotoxicities of AZA and DAC toward human colorectal cancer cell lines were observed, in which cells were more sensitive to AZA. Based on a polypharmacological analysis, we found that AZA transiently blocked protein synthesis and induced an acute apoptotic response that was antagonized by concurrently induced cytoprotective autophagy. In contrast, DAC caused cell cycle arrest at the G2/M phase associated with p53 induction. Therefore, our study discriminated functional disparities between AZA and DAC, and also demonstrated the value of this chemical genomics approach that can be applied to discover novel drug action mechanisms.
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24
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Zheng Y, Liu Q, Shen H, Yang G. To increase the incorporation efficiency of genetically encoding N ε-acetyllysine in recombinant protein. Protein Expr Purif 2017; 145:59-63. [PMID: 28986241 DOI: 10.1016/j.pep.2017.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/22/2017] [Accepted: 10/01/2017] [Indexed: 11/25/2022]
Abstract
Reversible Nε-lysine (Nε-Lys) acetylation is a dynamic post-translational modification. Genetic incorporation of Nε-acetyllysine (Nε-AcK) into the specific site of a protein is a powerful method for producing recombinant protein with acetylation and studying the functional role of protein acetylation. Because of the universal existence of deacetylase such as CobB in vivo, the acetyl group of Nε-AcK may be removed from recombinant protein. So in the process of incorporating acetyl lysine into protein, nicotinamide (NAM), a lysine deacetylase (KDAC) inhibitor, is needed to inhibit the KDAC activity and protect the acetyl group of Nε-acetyllysine incorporated from removal in vivo. In this study, we knocked out cobB gene from an E. coli strain and used it as host for incorporating of Nε-AcK into recombinant protein by expanding genetic code. Comparing with the addition of KDAC inhibitor, this is a novel method to protect the acetyl group of Nε-acetyllysine from deacetylation by using cobB knockout strain. Thus, this method provides a better way for protecting recombinant acetylated protein from deacetylation. By knocking out cobB gene from the strain of E. coli, we successfully produced homogeneous acetylated protein by expanding genetic code with a high effectiveness. This method will also provide a good reference for genetically introducing other varieties of modified amino acids into protein.
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Affiliation(s)
- Yueting Zheng
- College of Animal, Sciences and Veterinary Medicine, Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, Henan Agricultural University, Zhengzhou, Henan 450002, PR China
| | - Qitao Liu
- College of Animal, Sciences and Veterinary Medicine, Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, Henan Agricultural University, Zhengzhou, Henan 450002, PR China
| | - Huanhuan Shen
- College of Animal, Sciences and Veterinary Medicine, Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, Henan Agricultural University, Zhengzhou, Henan 450002, PR China
| | - Guoyu Yang
- College of Animal, Sciences and Veterinary Medicine, Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, Henan Agricultural University, Zhengzhou, Henan 450002, PR China.
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25
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Shi Y, Wang XX, Zhuang YW, Jiang Y, Melcher K, Xu HE. Structure of the PRC2 complex and application to drug discovery. Acta Pharmacol Sin 2017; 38:963-976. [PMID: 28414199 PMCID: PMC5519257 DOI: 10.1038/aps.2017.7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/10/2017] [Indexed: 02/07/2023]
Abstract
The polycomb repressive complexes 2 (PRC2) complex catalyzes tri-methylation of histone H3 lysine 27 (H3K27), a repressive chromatin marker associated with gene silencing. Overexpression and mutations of PRC2 are found in a wide variety of cancers, making the catalytic activity of PRC2 an important target of cancer therapy. This review highlights recent structural breakthroughs of the human PRC2 complex bound to the H3K27 peptide and a small molecule inhibitor, which provide critically needed insight into PRC2-targeted drug discovery.
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Affiliation(s)
- Yi Shi
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiao-xi Wang
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - You-wen Zhuang
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yi Jiang
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Karsten Melcher
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - H Eric Xu
- Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Laboratory of Structural Sciences, Van Andel Research Institute, Grand Rapids, MI 49503, USA
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26
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Obesity and Weight Control: Is There Light at the End of the Tunnel? Curr Nutr Rep 2017. [DOI: 10.1007/s13668-017-0206-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ponomarev I, Stelly CE, Morikawa H, Blednov YA, Mayfield RD, Harris RA. Mechanistic insights into epigenetic modulation of ethanol consumption. Alcohol 2017; 60:95-101. [PMID: 28433417 DOI: 10.1016/j.alcohol.2017.01.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 12/16/2022]
Abstract
There is growing evidence that small-molecule inhibitors of epigenetic modulators, such as histone deacetylases (HDAC) and DNA methyltransferases (DNMT), can reduce voluntary ethanol consumption in animal models, but molecular and cellular processes underlying this behavioral effect are poorly understood. We used C57BL/6J male mice to investigate the effects of two FDA-approved drugs, decitabine (a DNMT inhibitor) and SAHA (an HDAC inhibitor), on ethanol consumption using two tests: binge-like drinking in the dark (DID) and chronic intermittent every other day (EOD) drinking. Decitabine but not SAHA reduced ethanol consumption in both tests. We further investigated decitabine's effects on the brain's reward pathway by gene expression profiling in the ventral tegmental area (VTA), using RNA sequencing and electrophysiological recordings from VTA dopaminergic neurons. Decitabine-induced decreases in EOD drinking were associated with global changes in gene expression, implicating regulation of cerebral blood flow, extracellular matrix organization, and neuroimmune functions in decitabine actions. In addition, an in vivo administration of decitabine shortened ethanol-induced excitation of VTA dopaminergic neurons in vitro, suggesting that decitabine reduces ethanol drinking via changes in the reward pathway. Taken together, our data suggest a contribution of both neuronal and non-neuronal mechanisms in the VTA in the regulation of ethanol consumption. Decitabine and other epigenetic compounds have been approved for cancer treatment, and understanding their mechanisms of actions in the brain may assist in repurposing these drugs and developing novel therapies for central disorders, including drug addiction.
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Affiliation(s)
- Igor Ponomarev
- Waggoner Center for Alcohol and Addiction Research, USA; The College of Pharmacy, The University of Texas at Austin, 2500 Speedway A4800, Austin, TX, 78712, USA.
| | | | | | | | | | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, USA; The College of Pharmacy, The University of Texas at Austin, 2500 Speedway A4800, Austin, TX, 78712, USA
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28
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Gan X, Wang H, Yu Y, Yi W, Zhu S, Li E, Liang Y. Epigenetically repressing human cytomegalovirus lytic infection and reactivation from latency in THP-1 model by targeting H3K9 and H3K27 histone demethylases. PLoS One 2017; 12:e0175390. [PMID: 28407004 PMCID: PMC5391200 DOI: 10.1371/journal.pone.0175390] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/26/2017] [Indexed: 12/21/2022] Open
Abstract
Human Cytomegalovirus (hCMV) infects a broad range of the population and establishes life-long latency in the infected individuals. Periodically the latently infected virus can reactivate and becomes a significant cause of morbidity and mortality in immunocompromised individuals. In latent infection, the viral genome is suppressed in a heterochromatic state and viral gene transcription is silenced. Upon reactivation, the repressive chromatin is remodeled to an active form, allowing viral lytic gene transcription, initiated by the expression of viral Immediate Early (IE) genes. During this process, a number of histone modification enzymes, including histone demethylases (HDMs), play important roles in driving IE expression, but the mechanisms involved are not fully understood. To get a better understanding of these mechanisms, we focused on two HDMs, KDM4 and KDM6, which reverse the repressive histone H3-lysine 9 and lysine 27 methylation, respectively. Our studies show that in lytic infection, both demethylases are important in the activation of viral IE gene expression. Simultaneous disruption of both via genetic or chemical methods leads to severely impaired viral IE gene expression and viral replication. Additionally, in an experimental latency-reactivation model in THP-1 cells, the KDM6 family member JMJD3 is induced upon viral reactivation and its knockdown resulted in reduced IE gene transcription. These findings suggest pharmacological inhibition of these HDMs may potentially block hCMV lytic infection and reactivation, and control the viral infection associated diseases, which are of significant unmet medical needs.
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Affiliation(s)
- Xin Gan
- China Novartis Institutes for Biomedical Research, 4218 JinKe Rd, Pudong, Shanghai, P.R. China
| | - Haifeng Wang
- China Novartis Institutes for Biomedical Research, 4218 JinKe Rd, Pudong, Shanghai, P.R. China
| | - Yanyan Yu
- China Novartis Institutes for Biomedical Research, 4218 JinKe Rd, Pudong, Shanghai, P.R. China
| | - Wei Yi
- China Novartis Institutes for Biomedical Research, 4218 JinKe Rd, Pudong, Shanghai, P.R. China
| | - Shanshan Zhu
- China Novartis Institutes for Biomedical Research, 4218 JinKe Rd, Pudong, Shanghai, P.R. China
| | - En Li
- China Novartis Institutes for Biomedical Research, 4218 JinKe Rd, Pudong, Shanghai, P.R. China
| | - Yu Liang
- China Novartis Institutes for Biomedical Research, 4218 JinKe Rd, Pudong, Shanghai, P.R. China
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29
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Prachayasittikul V, Prathipati P, Pratiwi R, Phanus-Umporn C, Malik AA, Schaduangrat N, Seenprachawong K, Wongchitrat P, Supokawej A, Prachayasittikul V, Wikberg JES, Nantasenamat C. Exploring the epigenetic drug discovery landscape. Expert Opin Drug Discov 2017; 12:345-362. [PMID: 28276705 DOI: 10.1080/17460441.2017.1295954] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Epigenetic modification has been implicated in a wide range of diseases and the ability to modulate such systems is a lucrative therapeutic strategy in drug discovery. Areas covered: This article focuses on the concepts and drug discovery aspects of epigenomics. This is achieved by providing a survey of the following concepts: (i) factors influencing epigenetics, (ii) diseases arising from epigenetics, (iii) epigenetic enzymes as druggable targets along with coverage of existing FDA-approved drugs and pharmacological agents, and (iv) drug repurposing/repositioning as a means for rapid discovery of pharmacological agents targeting epigenetics. Expert opinion: Despite significant interests in targeting epigenetic modifiers as a therapeutic route, certain classes of target proteins are heavily studied while some are less characterized. Thus, such orphan target proteins are not yet druggable with limited report of active modulators. Current research points towards a great future with novel drugs directed to the many complex multifactorial diseases of humans, which are still often poorly understood and difficult to treat.
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Affiliation(s)
- Veda Prachayasittikul
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Philip Prathipati
- b National Institutes of Biomedical Innovation, Health and Nutrition , Osaka , Japan
| | - Reny Pratiwi
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Chuleeporn Phanus-Umporn
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Aijaz Ahmad Malik
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Nalini Schaduangrat
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Kanokwan Seenprachawong
- c Department of Clinical Microscopy, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Prapimpun Wongchitrat
- d Center for Research and Innovation, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Aungkura Supokawej
- c Department of Clinical Microscopy, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Virapong Prachayasittikul
- e Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - Jarl E S Wikberg
- f Department of Pharmaceutical Biosciences , Uppsala University , Uppsala , Sweden
| | - Chanin Nantasenamat
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
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30
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Picchi GFA, Zulkievicz V, Krieger MA, Zanchin NT, Goldenberg S, de Godoy LMF. Post-translational Modifications of Trypanosoma cruzi Canonical and Variant Histones. J Proteome Res 2017; 16:1167-1179. [DOI: 10.1021/acs.jproteome.6b00655] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | - Vanessa Zulkievicz
- Instituto Carlos Chagas, Fiocruz Parana, Curitiba, Paraná 81350-010, Brazil
| | - Marco A. Krieger
- Instituto Carlos Chagas, Fiocruz Parana, Curitiba, Paraná 81350-010, Brazil
| | - Nilson T. Zanchin
- Instituto Carlos Chagas, Fiocruz Parana, Curitiba, Paraná 81350-010, Brazil
| | - Samuel Goldenberg
- Instituto Carlos Chagas, Fiocruz Parana, Curitiba, Paraná 81350-010, Brazil
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31
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Wan S, Bhati AP, Zasada SJ, Wall I, Green D, Bamborough P, Coveney PV. Rapid and Reliable Binding Affinity Prediction of Bromodomain Inhibitors: A Computational Study. J Chem Theory Comput 2017; 13:784-795. [PMID: 28005370 PMCID: PMC5312866 DOI: 10.1021/acs.jctc.6b00794] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Binding free energies of bromodomain inhibitors are calculated with recently formulated approaches, namely ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling). A set of compounds is provided by GlaxoSmithKline, which represents a range of chemical functionality and binding affinities. The predicted binding free energies exhibit a good Spearman correlation of 0.78 with the experimental data from the 3-trajectory ESMACS, and an excellent correlation of 0.92 from the TIES approach where applicable. Given access to suitable high end computing resources and a high degree of automation, we can compute individual binding affinities in a few hours with precisions no greater than 0.2 kcal/mol for TIES, and no larger than 0.34 and 1.71 kcal/mol for the 1- and 3-trajectory ESMACS approaches.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
| | - Agastya P Bhati
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
| | - Stefan J Zasada
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
| | - Ian Wall
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Darren Green
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Paul Bamborough
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
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32
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Kimura Y, Komatsu T, Yanagi K, Hanaoka K, Ueno T, Terai T, Kojima H, Okabe T, Nagano T, Urano Y. Development of Chemical Tools to Monitor and Control Isoaspartyl Peptide Methyltransferase Activity. Angew Chem Int Ed Engl 2016; 56:153-157. [DOI: 10.1002/anie.201608677] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/07/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Yusuke Kimura
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Precursory Research for Embryonic Science and Technology, PRESTO, Japan, Science and Technology Agency, JST; 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kouichi Yanagi
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takuya Terai
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Hirotatsu Kojima
- Discovery Initiative (DDI); The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Okabe
- Discovery Initiative (DDI); The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tetsuo Nagano
- Discovery Initiative (DDI); The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Medicine; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Core Research for Evolutional Science and Technology, CREST, Investigator, Japan, Agency for Medical Research and Development, AMED; 1-7-1 Otemachi Chiyoda-ku Tokyo 100-0004 Japan
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
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33
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Kimura Y, Komatsu T, Yanagi K, Hanaoka K, Ueno T, Terai T, Kojima H, Okabe T, Nagano T, Urano Y. Development of Chemical Tools to Monitor and Control Isoaspartyl Peptide Methyltransferase Activity. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yusuke Kimura
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Precursory Research for Embryonic Science and Technology, PRESTO, Japan, Science and Technology Agency, JST 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kouichi Yanagi
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kenjiro Hanaoka
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takuya Terai
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Hirotatsu Kojima
- Discovery Initiative (DDI) The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Okabe
- Discovery Initiative (DDI) The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Tetsuo Nagano
- Discovery Initiative (DDI) The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Medicine The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Core Research for Evolutional Science and Technology, CREST, Investigator, Japan, Agency for Medical Research and Development, AMED 1-7-1 Otemachi Chiyoda-ku Tokyo 100-0004 Japan
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
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Abstract
Nucleosomes function to tightly package DNA into chromosomes, but the nucleosomal landscape becomes disrupted during active processes such as replication, transcription, and repair. The realization that many proteins responsible for chromatin regulation are frequently mutated in cancer has drawn attention to chromatin dynamics; however, the basic mechanisms whereby nucleosomes are disrupted and reassembled is incompletely understood. Here, I present an overview of chromatin dynamics as has been elucidated in model organisms, in which our understanding is most advanced. A basic understanding of chromatin dynamics during normal developmental processes can provide the context for understanding how this machinery can go awry during oncogenesis.
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Affiliation(s)
- Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
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35
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Chemical probes for methyl lysine reader domains. Curr Opin Chem Biol 2016; 33:135-41. [PMID: 27348158 DOI: 10.1016/j.cbpa.2016.06.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 12/14/2022]
Abstract
The primary intent of a chemical probe is to establish the relationship between a molecular target, usually a protein whose function is modulated by the probe, and the biological consequences of that modulation. In order to fulfill this purpose, a chemical probe must be profiled for selectivity, mechanism of action, and cellular activity, as the cell is the minimal system in which 'biology' can be explored. This review provides a brief overview of progress towards chemical probes for methyl lysine reader domains with a focus on recent progress targeting chromodomains.
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36
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Komatsu T, Virdee S. ICBS and ECBS Chemical Biology Meeting 2015 - Let Them Come to Berlin! ACS Chem Biol 2016; 11:1159-66. [PMID: 27198933 DOI: 10.1021/acschembio.6b00268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Toru Komatsu
- Graduate
School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- JST PRESTO, Tokyo, Japan
| | - Satpal Virdee
- MRC
Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
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37
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Langley GW, Brinkø A, Münzel M, Walport LJ, Schofield CJ, Hopkinson RJ. Analysis of JmjC Demethylase-Catalyzed Demethylation Using Geometrically-Constrained Lysine Analogues. ACS Chem Biol 2016; 11:755-62. [PMID: 26555343 DOI: 10.1021/acschembio.5b00738] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamic post-translational modifications of histones play important roles in the regulation of transcription in animals. The demethylation of N(ε)-methyl lysine residues in the N-terminal tail of histone H3 is catalyzed by demethylases, of which the largest family is the ferrous iron and 2-oxoglutarate dependent demethylases (JmjC KDMs), which catalyze demethylation via initial hydroxylation of the N-methyl groups. We report studies on the conformational requirements of the JmjC KDM substrates using N-methylated lysine analogues prepared by metathesis reactions of suitably protected N-allylglycine. The results support the proposed requirement for a positively charged N(ε)-amino group in JmjC KDM catalysis. Demethylation of a trans-C-4/C-5 dehydrolysine substrate analogue was observed with representative KDM4 subfamily members KDM4A, KDM4B and KDM4E, and KDM7B, which are predicted, based on crystallographic analyses, to bind the N(ε)-methylated lysine residue in different conformations during catalysis. This information may be useful in the design of JmjC KDM selective inhibitors.
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Affiliation(s)
- Gareth W Langley
- Chemistry Research Laboratory , 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Anne Brinkø
- Chemistry Research Laboratory , 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
- Department of Chemistry, Aarhus University , Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Martin Münzel
- Chemistry Research Laboratory , 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Louise J Walport
- Chemistry Research Laboratory , 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | | | - Richard J Hopkinson
- Chemistry Research Laboratory , 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
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38
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Edwards B, Lesnick J, Wang J, Tang N, Peters C. Miniaturization of High-Throughput Epigenetic Methyltransferase Assays with Acoustic Liquid Handling. ACTA ACUST UNITED AC 2016; 21:208-16. [DOI: 10.1177/2211068215610861] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 01/04/2023]
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39
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Zhang G, Huang R. Facile synthesis of SAM-peptide conjugates through alkyl linkers targeting protein N-terminal methyltransferase 1. RSC Adv 2016; 6:6768-6771. [PMID: 27588169 DOI: 10.1039/c5ra20625a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We report the first chemical synthesis of SAM-peptide conjugates through alkyl linkers to prepare bisubstrate analogs for protein methyltransferases. We demonstrate its application by developing a series of bisubstrate inhibitors for protein N-terminal methyltransferase 1 and the most potent one exhibits a Ki value of 310 ± 55 nM.
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Affiliation(s)
- Gang Zhang
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery & Development, Virginia Commonwealth University, Richmond, VA, 23219, USA
| | - Rong Huang
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery & Development, Virginia Commonwealth University, Richmond, VA, 23219, USA
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40
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Pharmacological modulation of HDAC1 and HDAC6 in vivo in a zebrafish model: Therapeutic implications for Parkinson’s disease. Pharmacol Res 2016; 103:328-39. [DOI: 10.1016/j.phrs.2015.11.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/27/2015] [Accepted: 11/29/2015] [Indexed: 11/22/2022]
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41
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Bi X, Yang R, Feng X, Rhodes D, Liu CF. Semisynthetic UbH2A reveals different activities of deubiquitinases and inhibitory effects of H2A K119 ubiquitination on H3K36 methylation in mononucleosomes. Org Biomol Chem 2015; 14:835-9. [PMID: 26615908 DOI: 10.1039/c5ob02323h] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using a genetically incorporated azidonorleucine for ubiquitin installation, we prepared multi-milligram quantities of H2AK119ub (ubH2A). With a native isopeptide linkage, the synthetic ubH2A was used to study the activity of deubiquitinases and crosstalk between H2A ubiquitination and H3K36 methylation in the context of chemically defined mononucleosomes.
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Affiliation(s)
- Xiaobao Bi
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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42
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Unlocking the potential of chemical probes for methyl-lysine reader proteins. Future Med Chem 2015; 7:1831-3. [PMID: 26393394 DOI: 10.4155/fmc.15.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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43
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Finley A, Copeland RA. Small molecule control of chromatin remodeling. ACTA ACUST UNITED AC 2015; 21:1196-210. [PMID: 25237863 DOI: 10.1016/j.chembiol.2014.07.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 06/26/2014] [Accepted: 07/21/2014] [Indexed: 01/16/2023]
Abstract
Control of cellular transcriptional programs is based on reversible changes in chromatin conformation that affect access of the transcriptional machinery to specific gene promoters. Chromatin conformation is in turn controlled by the concerted effects of reversible, covalent modification of the DNA and histone components of chromatin, along with topographical changes in DNA-histone interactions; all of these chromatin-modifying reactions are catalyzed by specific enzymes and are communicated to the transcriptional machinery by proteins that recognize and bind to unique, covalent modifications at specific chromatin sites (so-called reader proteins). Over the past decade, considerable progress has been made in the discovery of potent and selective small molecule modulators of specific chromatin-modifying proteins. Here we review the progress that has been made toward small molecule control of these mechanisms and the potential clinical applications of such small molecule modulators of chromatin remodeling.
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Affiliation(s)
- Aidan Finley
- Epizyme, Inc., 400 Technology Square, 4th Floor, Cambridge, MA 02139, USA
| | - Robert A Copeland
- Epizyme, Inc., 400 Technology Square, 4th Floor, Cambridge, MA 02139, USA.
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44
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Andreoli F, Del Rio A. Computer-aided Molecular Design of Compounds Targeting Histone Modifying Enzymes. Comput Struct Biotechnol J 2015; 13:358-65. [PMID: 26082827 PMCID: PMC4459771 DOI: 10.1016/j.csbj.2015.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 04/24/2015] [Accepted: 04/30/2015] [Indexed: 02/06/2023] Open
Abstract
Growing evidences show that epigenetic mechanisms play crucial roles in the genesis and progression of many physiopathological processes. As a result, research in epigenetic grew at a fast pace in the last decade. In particular, the study of histone post-translational modifications encountered an extraordinary progression and many modifications have been characterized and associated to fundamental biological processes and pathological conditions. Histone modifications are the catalytic result of a large set of enzyme families that operate covalent modifications on specific residues at the histone tails. Taken together, these modifications elicit a complex and concerted processing that greatly contribute to the chromatin remodeling and may drive different pathological conditions, especially cancer. For this reason, several epigenetic targets are currently under validation for drug discovery purposes and different academic and industrial programs have been already launched to produce the first pre-clinical and clinical outcomes. In this scenario, computer-aided molecular design techniques are offering important tools, mainly as a consequence of the increasing structural information available for these targets. In this mini-review we will briefly discuss the most common types of known histone modifications and the corresponding operating enzymes by emphasizing the computer-aided molecular design approaches that can be of use to speed-up the efforts to generate new pharmaceutically relevant compounds.
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Affiliation(s)
- Federico Andreoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
| | - Alberto Del Rio
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum, University of Bologna, Via S. Giacomo 14, 40126 Bologna, Italy
- Institute of Organic Synthesis and Photoreactivity, National Research Council, Via P. Gobetti, 101 40129 Bologna, Italy
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Zhang G, Richardson SL, Mao Y, Huang R. Design, synthesis, and kinetic analysis of potent protein N-terminal methyltransferase 1 inhibitors. Org Biomol Chem 2015; 13:4149-54. [PMID: 25712161 PMCID: PMC4857722 DOI: 10.1039/c5ob00120j] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The protein N-terminal methyltransferase 1 (NTMT1) methylates the α-N-terminal amines of proteins. NTMT1 is upregulated in a variety of cancers and knockdown of NTMT1 results in cell mitotic defects. Therefore, NTMT1 inhibitors could be potential anticancer therapeutics. This study describes the design and synthesis of the first inhibitor targeting NTMT1. A novel bisubstrate analogue (NAM-TZ-SPKRIA) was shown to be a potent inhibitor (Ki = 0.20 μM) for NTMT1 and was selective versus protein lysine methyltransferase G9a and arginine methyltransferase 1. NAM-TZ-SPKRIA was found to exhibit a competitive inhibition pattern for both substrates, and mass spectrometry experiments revealed that the inhibitor substantially suppressed the methylation progression. Our results demonstrate the feasibility of using a triazole group to link an S-adenosyl-L-methionine analog with a peptide substrate to construct bisubstrate analogues as NTMT1 potent and selective inhibitors. This study lays a foundation to further discover small molecule NTMT1 inhibitors to interrogate its biological functions, and suggests a general strategy for the development of selective protein methyltransferase inhibitors.
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Affiliation(s)
- Gang Zhang
- Department of Medicinal Chemistry, and the Institute of Structural Biology & Drug Discovery, Virginia Commonwealth University, Richmond, VA, USA.
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A novel class I histone deacetylase inhibitor, I-7ab, induces apoptosis and arrests cell cycle progression in human colorectal cancer cells. Biomed Pharmacother 2015; 71:70-8. [DOI: 10.1016/j.biopha.2015.02.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 02/15/2015] [Indexed: 12/18/2022] Open
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Richardson SL, Mao Y, Zhang G, Hanjra P, Peterson DL, Huang R. Kinetic mechanism of protein N-terminal methyltransferase 1. J Biol Chem 2015; 290:11601-10. [PMID: 25771539 DOI: 10.1074/jbc.m114.626846] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Indexed: 01/10/2023] Open
Abstract
The protein N-terminal methyltransferase 1 (NTMT1) catalyzes the transfer of the methyl group from the S-adenosyl-l-methionine to the protein α-amine, resulting in formation of S-adenosyl-l-homocysteine and α-N-methylated proteins. NTMT1 is an interesting potential anticancer target because it is overexpressed in gastrointestinal cancers and plays an important role in cell mitosis. To gain insight into the biochemical mechanism of NTMT1, we have characterized the kinetic mechanism of recombinant NTMT1 using a fluorescence assay and mass spectrometry. The results of initial velocity, product, and dead-end inhibition studies indicate that methylation by NTMT1 proceeds via a random sequential Bi Bi mechanism. In addition, our processivity studies demonstrate that NTMT1 proceeds via a distributive mechanism for multiple methylations. Together, our studies provide new knowledge about the kinetic mechanism of NTMT1 and lay the foundation for the development of mechanism-based inhibitors.
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Affiliation(s)
- Stacie L Richardson
- From the Department of Medicinal Chemistry, the Institute for Structural Biology and Drug Discovery, and
| | - Yunfei Mao
- From the Department of Medicinal Chemistry, the Institute for Structural Biology and Drug Discovery, and
| | - Gang Zhang
- From the Department of Medicinal Chemistry, the Institute for Structural Biology and Drug Discovery, and
| | - Pahul Hanjra
- From the Department of Medicinal Chemistry, the Institute for Structural Biology and Drug Discovery, and
| | - Darrell L Peterson
- the Institute for Structural Biology and Drug Discovery, and the Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia 23219
| | - Rong Huang
- From the Department of Medicinal Chemistry, the Institute for Structural Biology and Drug Discovery, and
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48
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Kristie TM. Dynamic modulation of HSV chromatin drives initiation of infection and provides targets for epigenetic therapies. Virology 2015; 479-480:555-61. [PMID: 25702087 DOI: 10.1016/j.virol.2015.01.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/25/2015] [Accepted: 01/30/2015] [Indexed: 10/24/2022]
Abstract
Upon infection, the genomes of herpesviruses undergo a striking transition from a non-nucleosomal structure to a chromatin structure. The rapid assembly and modulation of nucleosomes during the initial stage of infection results in an overlay of complex regulation that requires interactions of a plethora of chromatin modulation components. For herpes simplex virus, the initial chromatin dynamic is dependent on viral and host cell transcription factors and coactivators that mediate the balance between heterochromatic suppression of the viral genome and the euchromatin transition that allows and promotes the expression of viral immediate early genes. Strikingly similar to lytic infection, in sensory neurons this dynamic transition between heterochromatin and euchromatin governs the establishment, maintenance, and reactivation from the latent state. Chromatin dynamics in both the lytic infection and latency-reactivation cycles provides opportunities to shift the balance using small molecule epigenetic modulators to suppress viral infection, shedding, and reactivation from latency.
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Affiliation(s)
- Thomas M Kristie
- Molecular Genetics Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health Bld 33, Rm 3W20B.7 33 North Drive,, Bethesda, MA 20892, USA.
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Hill JM, Quenelle DC, Cardin RD, Vogel JL, Clement C, Bravo FJ, Foster TP, Bosch-Marce M, Raja P, Lee JS, Bernstein DI, Krause PR, Knipe DM, Kristie TM. Inhibition of LSD1 reduces herpesvirus infection, shedding, and recurrence by promoting epigenetic suppression of viral genomes. Sci Transl Med 2014; 6:265ra169. [PMID: 25473037 PMCID: PMC4416407 DOI: 10.1126/scitranslmed.3010643] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Herpesviruses are highly prevalent and maintain lifelong latent reservoirs, thus posing challenges to the control of herpetic disease despite the availability of antiviral pharmaceuticals that target viral DNA replication. The initiation of herpes simplex virus infection and reactivation from latency is dependent on a transcriptional coactivator complex that contains two required histone demethylases, LSD1 (lysine-specific demethylase 1) and a member of the JMJD2 family (Jumonji C domain-containing protein 2). Inhibition of either of these enzymes results in heterochromatic suppression of the viral genome and blocks infection and reactivation in vitro. We demonstrate that viral infection can be epigenetically suppressed in three animal models of herpes simplex virus infection and disease. Treating animals with the monoamine oxidase inhibitor tranylcypromine to inhibit LSD1 suppressed viral lytic infection, subclinical shedding, and reactivation from latency in vivo. This phenotypic suppression was correlated with enhanced epigenetic suppression of the viral genome and suggests that, even during latency, the chromatin state of the virus is dynamic. Therefore, epi-pharmaceuticals may represent a promising approach to treat herpetic diseases.
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Affiliation(s)
- James M Hill
- Department of Ophthalmology and Department of Microbiology, Immunology, and Parasitology, LSU Eye Center, Louisiana State University Health Science Center School of Medicine, New Orleans, LA 70112, USA
| | - Debra C Quenelle
- Department of Pediatric Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rhonda D Cardin
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Jodi L Vogel
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christian Clement
- Department of Ophthalmology and Department of Microbiology, Immunology, and Parasitology, LSU Eye Center, Louisiana State University Health Science Center School of Medicine, New Orleans, LA 70112, USA
| | - Fernando J Bravo
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Timothy P Foster
- Department of Ophthalmology and Department of Microbiology, Immunology, and Parasitology, LSU Eye Center, Louisiana State University Health Science Center School of Medicine, New Orleans, LA 70112, USA
| | - Marta Bosch-Marce
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20852, USA
| | - Priya Raja
- Department of Microbiology and Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Jennifer S Lee
- Department of Microbiology and Immunology, Harvard Medical School, Boston, MA 02115, USA. Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - David I Bernstein
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Philip R Krause
- Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20852, USA
| | - David M Knipe
- Department of Microbiology and Immunology, Harvard Medical School, Boston, MA 02115, USA. Harvard Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas M Kristie
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Burgio E, Lopomo A, Migliore L. Obesity and diabetes: from genetics to epigenetics. Mol Biol Rep 2014; 42:799-818. [DOI: 10.1007/s11033-014-3751-z] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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