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Zhang S, Lin T, Xiong X, Chen C, Tan P, Wei Q. Targeting histone modifiers in bladder cancer therapy - preclinical and clinical evidence. Nat Rev Urol 2024; 21:495-511. [PMID: 38374198 DOI: 10.1038/s41585-024-00857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2024] [Indexed: 02/21/2024]
Abstract
Bladder cancer in the most advanced, muscle-invasive stage is lethal, and very limited therapeutic advances have been reported for decades. To date, cisplatin-based chemotherapy remains the first-line therapy for advanced bladder cancer. Late-line options have historically been limited. In the past few years, next-generation sequencing technology has enabled chromatin remodelling gene mutations to be characterized, showing that these alterations are more frequent in urothelial bladder carcinoma than in other cancer types. Histone modifiers have functional roles in tumour progression by modulating the expression of tumour suppressors and oncogenes and, therefore, have been considered as novel drug targets for cancer therapy. The roles of epigenetic reprogramming through histone modifications have been increasingly studied in bladder cancer, and the therapeutic efficacy of targeting those histone modifiers genetically or chemically is being assessed in preclinical studies. Results from preclinical studies in bladder cancer encouraged the investigation of some of these drugs in clinical trials, which yield mixed results. Further understanding of how alterations of histone modification mechanistically contribute to bladder cancer progression, drug resistance and tumour microenvironment remodelling will be required to facilitate clinical application of epigenetic drugs in bladder cancer.
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Affiliation(s)
- Shiyu Zhang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Tianhai Lin
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xingyu Xiong
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Chong Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Ping Tan
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
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2
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Curcio A, Rocca R, Alcaro S, Artese A. The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods. Pharmaceuticals (Basel) 2024; 17:620. [PMID: 38794190 PMCID: PMC11124352 DOI: 10.3390/ph17050620] [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: 04/18/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Histone deacetylases (HDACs) are crucial in gene transcription, removing acetyl groups from histones. They also influence the deacetylation of non-histone proteins, contributing to the regulation of various biological processes. Thus, HDACs play pivotal roles in various diseases, including cancer, neurodegenerative disorders, and inflammatory conditions, highlighting their potential as therapeutic targets. This paper reviews the structure and function of the four classes of human HDACs. While four HDAC inhibitors are currently available for treating hematological malignancies, numerous others are undergoing clinical trials. However, their non-selective toxicity necessitates ongoing research into safer and more efficient class-selective or isoform-selective inhibitors. Computational methods have aided the discovery of HDAC inhibitors with the desired potency and/or selectivity. These methods include ligand-based approaches, such as scaffold hopping, pharmacophore modeling, three-dimensional quantitative structure-activity relationships, and structure-based virtual screening (molecular docking). Moreover, recent developments in the field of molecular dynamics simulations, combined with Poisson-Boltzmann/molecular mechanics generalized Born surface area techniques, have improved the prediction of ligand binding affinity. In this review, we delve into the ways in which these methods have contributed to designing and identifying HDAC inhibitors.
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Affiliation(s)
- Antonio Curcio
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
| | - Roberta Rocca
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Campus “S. Venuta”, Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy; (A.C.); (S.A.); (A.A.)
- Net4Science S.r.l., Università degli Studi “Magna Græcia” di Catanzaro, Viale Europa, 88100 Catanzaro, Italy
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3
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Fan T, Yu Y, Chen YL, Gu P, Wong S, Xia ZY, Liu JA, Cheung CW. Histone deacetylase 5-induced deficiency of signal transducer and activator of transcription-3 acetylation contributes to spinal astrocytes degeneration in painful diabetic neuropathy. Glia 2023; 71:1099-1119. [PMID: 36579750 DOI: 10.1002/glia.24328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/24/2022] [Accepted: 12/15/2022] [Indexed: 12/30/2022]
Abstract
Diabetes patients with painful diabetic neuropathy (PDN) show severe spinal atrophy, suggesting pathological changes of the spinal cord contributes to central sensitization. However, the cellular changes and underlying molecular mechanisms within the diabetic spinal cord are less clear. By using a rat model of type 1 diabetes (T1D), we noted an extensive and irreversible spinal astrocyte degeneration at an early stage of T1D, which is highly associated with the chronification of PDN. Molecularly, acetylation of astrocytic signal transducer and activator of transcription-3 (STAT3) that is essential for maintaining the homeostatic astrocytes population was significantly impaired in the T1D model, resulting in a dramatic loss of spinal astrocytes and consequently promoting pain hypersensitivity. Mechanistically, class IIa histone deacetylase, HDAC5 were aberrantly activated in spinal astrocytes of diabetic rats, which promoted STAT3 deacetylation by direct protein-protein interactions, leading to the PDN phenotypes. Restoration of STAT3 signaling or inhibition of HDAC5 rescued astrocyte deficiency and attenuated PDN in the T1D model. Our work identifies the inhibitory axis of HDAC5-STAT3 induced astrocyte deficiency as a key mechanism underlying the pathogenesis of the diabetic spinal cord that paves the way for potential therapy development for PDN.
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Affiliation(s)
- Tingting Fan
- Department of Anaesthesiology, Laboratory and Clinical Research Institute for Pain, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Ying Yu
- Department of Anaesthesiology, Laboratory and Clinical Research Institute for Pain, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Yong-Long Chen
- Department of Anaesthesiology, Laboratory and Clinical Research Institute for Pain, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Pan Gu
- Department of Anaesthesiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Stanley Wong
- Department of Anaesthesiology, Laboratory and Clinical Research Institute for Pain, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Zheng-Yuan Xia
- Department of Medicine, State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong, Hong Kong SAR.,Department of Anesthesiology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jessica Aijia Liu
- Department of Neuroscience, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR
| | - Chi-Wai Cheung
- Department of Anaesthesiology, Laboratory and Clinical Research Institute for Pain, The University of Hong Kong, Hong Kong, Hong Kong SAR.,Department of Anaesthesiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
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4
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Sandonà M, Cavioli G, Renzini A, Cedola A, Gigli G, Coletti D, McKinsey TA, Moresi V, Saccone V. Histone Deacetylases: Molecular Mechanisms and Therapeutic Implications for Muscular Dystrophies. Int J Mol Sci 2023; 24:4306. [PMID: 36901738 PMCID: PMC10002075 DOI: 10.3390/ijms24054306] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/13/2023] [Accepted: 02/19/2023] [Indexed: 02/24/2023] Open
Abstract
Histone deacetylases (HDACs) are enzymes that regulate the deacetylation of numerous histone and non-histone proteins, thereby affecting a wide range of cellular processes. Deregulation of HDAC expression or activity is often associated with several pathologies, suggesting potential for targeting these enzymes for therapeutic purposes. For example, HDAC expression and activity are higher in dystrophic skeletal muscles. General pharmacological blockade of HDACs, by means of pan-HDAC inhibitors (HDACi), ameliorates both muscle histological abnormalities and function in preclinical studies. A phase II clinical trial of the pan-HDACi givinostat revealed partial histological improvement and functional recovery of Duchenne Muscular Dystrophy (DMD) muscles; results of an ongoing phase III clinical trial that is assessing the long-term safety and efficacy of givinostat in DMD patients are pending. Here we review the current knowledge about the HDAC functions in distinct cell types in skeletal muscle, identified by genetic and -omic approaches. We describe the signaling events that are affected by HDACs and contribute to muscular dystrophy pathogenesis by altering muscle regeneration and/or repair processes. Reviewing recent insights into HDAC cellular functions in dystrophic muscles provides new perspectives for the development of more effective therapeutic approaches based on drugs that target these critical enzymes.
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Affiliation(s)
| | - Giorgia Cavioli
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy
| | - Alessandra Renzini
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy
| | - Alessia Cedola
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), University of Rome “La Sapienza”, 00181 Rome, Italy
| | - Giuseppe Gigli
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), 73100 Lecce, Italy
| | - Dario Coletti
- Unit of Histology and Medical Embryology, Department of Human Anatomy, Histology, Forensic Medicine and Orthopedics, University of Rome “La Sapienza”, 00161 Rome, Italy
- CNRS UMR 8256, INSERM ERL U1164, Biological Adaptation and Aging B2A, Sorbonne Université, 75005 Paris, France
| | - Timothy A. McKinsey
- Department of Medicine, Division of Cardiology and Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Viviana Moresi
- Institute of Nanotechnology, National Research Council (CNR-NANOTEC), University of Rome “La Sapienza”, 00181 Rome, Italy
| | - Valentina Saccone
- IRCCS Fondazione Santa Lucia, 00143 Rome, Italy
- Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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5
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Lei I, Huang W, Noly PE, Naik S, Ghali M, Liu L, Pagani FD, Abou El Ela A, Pober JS, Pitt B, Platt JL, Cascalho M, Wang Z, Chen YE, Mortensen RM, Tang PC. Metabolic reprogramming by immune-responsive gene 1 up-regulation improves donor heart preservation and function. Sci Transl Med 2023; 15:eade3782. [PMID: 36753565 PMCID: PMC10068866 DOI: 10.1126/scitranslmed.ade3782] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Preservation quality of donor hearts is a key determinant of transplant success. Preservation duration beyond 4 hours is associated with primary graft dysfunction (PGD). Given transport time constraints, geographical limitations exist for donor-recipient matching, leading to donor heart underutilization. Here, we showed that metabolic reprogramming through up-regulation of the enzyme immune response gene 1 (IRG1) and its product itaconate improved heart function after prolonged preservation. Irg1 transcript induction was achieved by adding the histone deacetylase (HDAC) inhibitor valproic acid (VPA) to a histidine-tryptophan-ketoglutarate solution used for donor heart preservation. VPA increased acetylated H3K27 occupancy at the IRG1 enhancer and IRG1 transcript expression in human donor hearts. IRG1 converts aconitate to itaconate, which has both anti-inflammatory and antioxidant properties. Accordingly, our studies showed that Irg1 transcript up-regulation by VPA treatment increased nuclear translocation of nuclear factor erythroid 2-related factor 2 (Nrf2) in mice, which was accompanied by increased antioxidant protein expression [hemeoxygenase 1 (HO1) and superoxide dismutase 1 (SOD1)]. Deletion of Irg1 in mice (Irg1-/-) negated the antioxidant and cardioprotective effects of VPA. Consistent with itaconate's ability to inhibit succinate dehydrogenase, VPA treatment of human hearts increased itaconate availability and reduced succinate accumulation during preservation. VPA similarly increased IRG1 expression in pig donor hearts and improved its function in an ex vivo cardiac perfusion system both at the clinical 4-hour preservation threshold and at 10 hours. These results suggest that augmentation of cardioprotective immune-metabolomic pathways may be a promising therapeutic strategy for improving donor heart function in transplantation.
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Affiliation(s)
- Ienglam Lei
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wei Huang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pierre Emmanuel Noly
- Department of Cardiac Surgery, Université de Montréal, Montréal, Quebec H1T 1C8, Canada
| | - Suyash Naik
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Miriyam Ghali
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Liu Liu
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Francis D Pagani
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ashraf Abou El Ela
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jordan S Pober
- Department of Pathology, Yale University, New Haven, CT 06510, USA
| | - Bertram Pitt
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey L Platt
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marilia Cascalho
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhong Wang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Y Eugene Chen
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard M Mortensen
- Departments of Molecular and Integrative Physiology, Internal Medicine, and Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul C Tang
- Department of Cardiac Surgery, University of Michigan, Ann Arbor, MI 48109, USA
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6
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Xiang Z, Bai L, Zhou JQ, Cevallos RR, Sanders JR, Liu G, Bernard K, Sanders YY. Epigenetic regulation of IPF fibroblast phenotype by glutaminolysis. Mol Metab 2022; 67:101655. [PMID: 36526153 PMCID: PMC9827063 DOI: 10.1016/j.molmet.2022.101655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE Excessive extra-cellular-matrix production and uncontrolled proliferation of the fibroblasts are characteristics of many fibrotic diseases, including idiopathic pulmonary fibrosis (IPF). The fibroblasts have enhanced glutaminolysis with up-regulated glutaminase, GLS1, which converts glutamine to glutamate. Here, we investigated the role of glutaminolysis and glutaminolysis-derived metabolite α-ketoglutarate (α-KG) on IPF fibroblast phenotype and gene expression. METHODS Reduced glutamine conditions were carried out either using glutamine-free culture medium or silencing the expression of GLS1 with siRNA, with or without α-KG compensation. Cell phenotype has been characterized under these different conditions, and gene expression profile was examined by RNA-Seq. Specific profibrotic genes (Col3A1 and PLK1) expression were examined by real-time PCR and western blots. The levels of repressive histone H3K27me3, which demethylase activity is affected by glutaminolysis, were examined and H3K27me3 association with promoter region of Col3A1 and PLK1 were checked by ChIP assays. Effects of reduced glutaminolysis on fibrosis markers were checked in an animal model of lung fibrosis. RESULTS The lack of glutamine in the culture medium alters the profibrotic phenotype of activated fibroblasts. The addition of exogenous and glutaminolysis-derived metabolite α-KG to glutamine-free media barely restores the pro-fibrotic phenotype of activated fibroblasts. Many genes are down-regulated in glutamine-free medium, α-KG supplementation only rescues a limited number of genes. As α-KG is a cofactor for histone demethylases of H3K27me3, the reduced glutaminolysis alters H3K27me3 levels, and enriches H3K27me3 association with Col3A1 and PLK1 promoter region. Adding α-KG in glutamine-free medium depleted H3K27me3 association with Col3A1 promoter region but not that of PLK1. In a murine model of lung fibrosis, mice with reduced glutaminolysis showed markedly reduced fibrotic markers. CONCLUSIONS This study indicates that glutamine is critical for supporting pro-fibrotic fibroblast phenotype in lung fibrosis, partially through α-KG-dependent and -independent mechanisms, and supports targeting fibroblast metabolism as a therapeutic method for fibrotic diseases.
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Affiliation(s)
- Zheyi Xiang
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Le Bai
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jennifer Q. Zhou
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ricardo R. Cevallos
- Department of Biochemistry and Molecular Genetics, Birmingham, AL 35255, USA
| | - Jonathan R. Sanders
- Department of Biochemistry and Molecular Genetics, Birmingham, AL 35255, USA
| | - Gang Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Karen Bernard
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yan Y. Sanders
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA,Corresponding author: University of Alabama at Birmingham, 901 19th Street South, BMRII Room 408, Birmingham, AL 35294, USA.
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7
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Kapoor S, Damiani E, Wang S, Dharmanand R, Tripathi C, Tovar Perez JE, Dashwood WM, Rajendran P, Dashwood RH. BRD9 Inhibition by Natural Polyphenols Targets DNA Damage/Repair and Apoptosis in Human Colon Cancer Cells. Nutrients 2022; 14:nu14204317. [PMID: 36297001 PMCID: PMC9610492 DOI: 10.3390/nu14204317] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Epigenetic mechanisms play an important role in the etiology of colorectal cancer (CRC) and other malignancies due, in part, to deregulated bromodomain (BRD) functions. Inhibitors of the bromodomain and extraterminal (BET) family have entered into clinical trials as anticancer agents, and interest has grown in other acetyl 'reader' proteins as therapeutic targets, including non-BET member bromodomain-containing protein 9 (BRD9). We report here that overexpression of BRD9 is associated with poor prognosis in CRC patients, and that siRNA-mediated knockdown of BRD9 decreased cell viability and activated apoptosis in human colon cancer cells, coincident with increased DNA damage. Seeking natural compounds as BRD9 antagonists, molecular docking in silico identified several polyphenols such as Epigallocatechin-3-gallate (EGCG), Equol, Quercetin, and Aspalathin, with favorable binding energies, supported by BROMOscan® (DiscoverX) and isothermal titration calorimetry experiments. Polyphenols mimicked BRD9 knockdown and iBRD9 treatment in reducing colon cancer cell viability, inhibiting colony formation, and enhancing DNA damage and apoptosis. Normal colonic epithelial cells were unaffected, signifying cancer-specific effects. These findings suggest that natural polyphenols recognize and target BRD9 for inhibition, and might serve as useful lead compounds for bromodomain therapeutics in the clinical setting.
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Affiliation(s)
- Sabeeta Kapoor
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA
| | - Elisabetta Damiani
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, 60121 Ancona, Italy
| | - Shan Wang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Hangzhou 310030, China
| | - Ravirajan Dharmanand
- Center for Infectious & Inflammatory Diseases, Texas A&M Health, Houston, TX 77030, USA
| | - Chakrapani Tripathi
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA
| | | | - Wan Mohaiza Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA
| | - Praveen Rajendran
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA
- Department of Translational Medical Sciences, Texas A&M College of Medicine, Houston, TX 77030, USA
- Correspondence: (P.R.); (R.H.D.); Tel.: +1-713-677-7803 (P.R.); +1-713-677-7806 (R.H.D.)
| | - Roderick Hugh Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX 77030, USA
- Department of Translational Medical Sciences, Texas A&M College of Medicine, Houston, TX 77030, USA
- Correspondence: (P.R.); (R.H.D.); Tel.: +1-713-677-7803 (P.R.); +1-713-677-7806 (R.H.D.)
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Mattes RD, Rowe SB, Ohlhorst SD, Brown AW, Hoffman DJ, Liska DJ, Feskens EJM, Dhillon J, Tucker KL, Epstein LH, Neufeld LM, Kelley M, Fukagawa NK, Sunde RA, Zeisel SH, Basile AJ, Borth LE, Jackson E. Valuing the Diversity of Research Methods to Advance Nutrition Science. Adv Nutr 2022; 13:1324-1393. [PMID: 35802522 PMCID: PMC9340992 DOI: 10.1093/advances/nmac043] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 12/13/2022] Open
Abstract
The ASN Board of Directors appointed the Nutrition Research Task Force to develop a report on scientific methods used in nutrition science to advance discovery, interpretation, and application of knowledge in the field. The genesis of this report was growing concern about the tone of discourse among nutrition professionals and the implications of acrimony on the productive study and translation of nutrition science. Too often, honest differences of opinion are cast as conflicts instead of areas of needed collaboration. Recognition of the value (and limitations) of contributions from well-executed nutrition science derived from the various approaches used in the discipline, as well as appreciation of how their layering will yield the strongest evidence base, will provide a basis for greater productivity and impact. Greater collaborative efforts within the field of nutrition science will require an understanding that each method or approach has a place and function that should be valued and used together to create the nutrition evidence base. Precision nutrition was identified as an important emerging nutrition topic by the preponderance of task force members, and this theme was adopted for the report because it lent itself to integration of many approaches in nutrition science. Although the primary audience for this report is nutrition researchers and other nutrition professionals, a secondary aim is to develop a document useful for the various audiences that translate nutrition research, including journalists, clinicians, and policymakers. The intent is to promote accurate, transparent, verifiable evidence-based communication about nutrition science. This will facilitate reasoned interpretation and application of emerging findings and, thereby, improve understanding and trust in nutrition science and appropriate characterization, development, and adoption of recommendations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Leonard H Epstein
- University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | | | - Michael Kelley
- Michael Kelley Nutrition Science Consulting, Wauwatosa, WI, USA
| | - Naomi K Fukagawa
- USDA Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | | | - Steven H Zeisel
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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9
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King J, Patel M, Chandrasekaran S. Metabolism, HDACs, and HDAC Inhibitors: A Systems Biology Perspective. Metabolites 2021; 11:792. [PMID: 34822450 PMCID: PMC8620738 DOI: 10.3390/metabo11110792] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 01/15/2023] Open
Abstract
Histone deacetylases (HDACs) are epigenetic enzymes that play a central role in gene regulation and are sensitive to the metabolic state of the cell. The cross talk between metabolism and histone acetylation impacts numerous biological processes including development and immune function. HDAC inhibitors are being explored for treating cancers, viral infections, inflammation, neurodegenerative diseases, and metabolic disorders. However, how HDAC inhibitors impact cellular metabolism and how metabolism influences their potency is unclear. Discussed herein are recent applications and future potential of systems biology methods such as high throughput drug screens, cancer cell line profiling, single cell sequencing, proteomics, metabolomics, and computational modeling to uncover the interplay between metabolism, HDACs, and HDAC inhibitors. The synthesis of new systems technologies can ultimately help identify epigenomic and metabolic biomarkers for patient stratification and the design of effective therapeutics.
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Affiliation(s)
- Jacob King
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (J.K.); (M.P.)
| | - Maya Patel
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (J.K.); (M.P.)
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (J.K.); (M.P.)
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Bioinformatics and Computational Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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10
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Damiani E, Duran MN, Mohan N, Rajendran P, Dashwood RH. Targeting Epigenetic 'Readers' with Natural Compounds for Cancer Interception. J Cancer Prev 2020; 25:189-203. [PMID: 33409252 PMCID: PMC7783241 DOI: 10.15430/jcp.2020.25.4.189] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/03/2020] [Accepted: 12/05/2020] [Indexed: 12/14/2022] Open
Abstract
Natural compounds from diverse sources, including botanicals and commonly consumed foods and beverages, exert beneficial health effects via mechanisms that impact the epigenome and gene expression during disease pathogenesis. By targeting the so-called epigenetic 'readers', 'writers', and 'erasers', dietary phytochemicals can reverse abnormal epigenome signatures in cancer cells and preneoplastic stages. Thus, such agents provide avenues for cancer interception via prevention or treatment/therapeutic strategies. To date, much of the focus on dietary agents has been directed towards writers (e.g., histone acetyltransferases) and erasers (e.g., histone deacetylases), with less attention given to epigenetic readers (e.g., BRD proteins). The drug JQ1 was developed as a prototype epigenetic reader inhibitor, selectively targeting members of the bromodomain and extraterminal domain (BET) family, such as BRD4. Clinical trials with JQ1 as a single agent, or in combination with standard of care therapy, revealed antitumor efficacy but not without toxicity or resistance. In pursuit of second-generation epigenetic reader inhibitors, attention has shifted to natural sources, including dietary agents that might be repurposed as 'JQ1-like' bioactives. This review summarizes the current status of nascent research activity focused on natural compounds as inhibitors of BET and other epigenetic 'reader' proteins, with a perspective on future directions and opportunities.
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Affiliation(s)
- Elisabetta Damiani
- Department of Life and Environmental Sciences, Polytechnic University of the Marche, Ancona, Italy
| | - Munevver N. Duran
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, TX, USA
| | - Nivedhitha Mohan
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, TX, USA
| | - Praveen Rajendran
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, TX, USA
| | - Roderick H. Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, TX, USA
- Department of Translational Medical Sciences, Texas A&M College of Medicine, Houston, TX, USA
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11
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Zeisel SH. Precision (Personalized) Nutrition: Understanding Metabolic Heterogeneity. Annu Rev Food Sci Technol 2020; 11:71-92. [DOI: 10.1146/annurev-food-032519-051736] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
People differ in their requirements for and responses to nutrients and bioactive molecules in the diet. Many inputs contribute to metabolic heterogeneity (including variations in genetics, epigenetics, microbiome, lifestyle, diet intake, and environmental exposure). Precision nutrition is not about developing unique prescriptions for individual people but rather about stratifying people into different subgroups of the population on the basis of biomarkers of the above-listed sources of metabolic variation and then using this stratification to better estimate the different subgroups’ dietary requirements, thereby enabling better dietary recommendations and interventions. The hope is that we will be able to subcategorize people into ever-smaller groups that can be targeted in terms of recommendations, but we will never achieve this at the individual level, thus, the choice of precision nutrition rather than personalized nutrition to designate this new field. This review focuses mainly on genetically related sources of metabolic heterogeneity and identifies challenges that need to be overcome to achieve a full understanding of the complex interactions between the many sources of metabolic heterogeneity that make people differ from one another in their requirements for and responses to foods. It also discusses the commercial applications of precision nutrition.
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Affiliation(s)
- Steven H. Zeisel
- Nutrition Research Institute, Department of Nutrition, University of North Carolina, Kannapolis, North Carolina 28081, USA
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12
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Ovejero-Benito MC, Reolid A, Sánchez-Jiménez P, Saiz-Rodríguez M, Muñoz-Aceituno E, Llamas-Velasco M, Martín-Vilchez S, Cabaleiro T, Román M, Ochoa D, Daudén E, Abad-Santos F. Histone modifications associated with biological drug response in moderate-to-severe psoriasis. Exp Dermatol 2019; 27:1361-1371. [PMID: 30260532 DOI: 10.1111/exd.13790] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/31/2018] [Accepted: 09/18/2018] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Epigenetic factors play an important role in psoriasis onset and development. Biological drugs are used to treat moderate-to-severe psoriasis patients resistant to conventional systemic drugs. Although they are safe and effective, some patients do not respond to them. Therefore, it is necessary to find biomarkers that could predict response to these therapies. OBJECTIVE To find epigenetic biomarkers that could predict response to biological drugs (ustekinumab, secukinumab, adalimumab, ixekizumab). MATERIALS AND METHODS Peripheral blood mononuclear cells (PBMCs) were isolated from 39 psoriasis patients treated with biological therapies before and after drug administration and from 42 healthy subjects. Afterwards, histones were extracted from PBMCs. Four histone modifications (H3 and H4 acetylation, H3K4 and H3K27 methylation) were determined by ELISA. Data were analysed by IBM-SPSS v.23. RESULTS AND CONCLUSIONS Psoriasis patients presented reduced levels of acetylated H3 and H4 and increased levels of methylated H3K4 compared to controls. Non-significant changes were observed after treatment administration in any of the histone modifications analysed. Nevertheless, significant changes in methylated H3K27 were found between responders and non-responders to biological drugs at 3 months. As 28% of these patients also presented psoriatic arthritis (PsA), the former analysis was repeated in the subsets of patients with or without PsA. In patients without PsA, significant changes in methylated H3K4 were found between responders and non-responders to biological drugs at 3 and 6 months. Although further studies should confirm these results, these findings suggest that H3K27 and H3K4 methylation may contribute to patients' response to biological drugs in psoriasis.
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Affiliation(s)
- María C Ovejero-Benito
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain
| | - Alejandra Reolid
- Dermatology Department, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria del Hospital de La Princesa (IIS-IP), Madrid, Spain
| | - Patricia Sánchez-Jiménez
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain
| | - Miriam Saiz-Rodríguez
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain
| | - Ester Muñoz-Aceituno
- Dermatology Department, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria del Hospital de La Princesa (IIS-IP), Madrid, Spain
| | - Mar Llamas-Velasco
- Dermatology Department, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria del Hospital de La Princesa (IIS-IP), Madrid, Spain
| | - Samuel Martín-Vilchez
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain
| | - Teresa Cabaleiro
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain
| | - Manuel Román
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain
| | - Dolores Ochoa
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain
| | - Esteban Daudén
- Dermatology Department, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria del Hospital de La Princesa (IIS-IP), Madrid, Spain
| | - Francisco Abad-Santos
- Clinical Pharmacology Department, Hospital Universitario de la Princesa, Instituto Teófilo Hernando, Universidad Autónoma de Madrid (UAM), Instituto de Investigación Sanitaria la Princesa (IIS-IP), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
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13
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Menendez JA, Cuyàs E, Folguera-Blasco N, Verdura S, Martin-Castillo B, Joven J, Alarcón T. In silico clinical trials for anti-aging therapies. Aging (Albany NY) 2019; 11:6591-6601. [PMID: 31444969 PMCID: PMC6738435 DOI: 10.18632/aging.102180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 08/09/2019] [Indexed: 12/19/2022]
Abstract
Therapeutic strategies targeting the hallmarks of aging can be broadly grouped into four categories, namely systemic (blood) factors, metabolic manipulation (diet regimens and dietary restriction mimetics), suppression of cellular senescence (senolytics), and cellular reprogramming, which likely have common characteristics and mechanisms of action. In evaluating the potential synergism of combining such strategies, however, we should consider the possibility of constraining trade-off phenotypes such as impairment in wound healing and immune response, tissue dysfunction and tumorigenesis. Moreover, we are rapidly learning that the benefit/risk ratio of aging-targeted interventions largely depends on intra- and inter-individual variations of susceptibility to the healthspan-, resilience-, and/or lifespan-promoting effects of the interventions. Here, we exemplify how computationally-generated proxies of the efficacy of a given lifespan/healthspan-promoting approach can predict the impact of baseline epigenetic heterogeneity on the positive outcomes of ketogenic diet and mTOR inhibition as single or combined anti-aging strategies. We therefore propose that stochastic biomathematical modeling and computational simulation platforms should be developed as in silico strategies to accelerate the performance of clinical trials targeting human aging, and to provide personalized approaches and robust biomarkers of healthy aging at the individual-to-population levels.
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Affiliation(s)
- Javier A Menendez
- ProCURE (Program Against Cancer Therapeutic Resistance),Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Elisabet Cuyàs
- ProCURE (Program Against Cancer Therapeutic Resistance),Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | | | - Sara Verdura
- ProCURE (Program Against Cancer Therapeutic Resistance),Metabolism and Cancer Group, Catalan Institute of Oncology, Girona, Spain.,Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | | | - Jorge Joven
- Unitat de Recerca Biomèdica (URB-CRB), Hospital Universitari de Sant Joan, Institut d'Investigació Sanitària Pere Virgili, Reus, Spain
| | - Tomás Alarcón
- ICREA, Barcelona, Spain.,Centre de Recerca Matemàtica (CRM), Barcelona, Spain.,Departament de Matemàtiques, Universitat Autònoma de Barcelona, Barcelona, Spain.,Barcelona Graduate School of Mathematics (BGSMath), Barcelona, Spain
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14
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Andreescu N, Puiu M, Niculescu M. Effects of Dietary Nutrients on Epigenetic Changes in Cancer. Methods Mol Biol 2019; 1856:121-139. [PMID: 30178249 DOI: 10.1007/978-1-4939-8751-1_7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Gene-nutrient interactions are important contributors to health management and disease prevention. Nutrition can alter gene expression, as well as the susceptibility to disease, including cancer, through epigenetic changes. Nutrients can influence the epigenetic status through several mechanisms, such as DNA methylation, histone modifications, and miRNA-dependent gene silencing. These alterations were associated with either increased or decreased risk for cancer development. There is convincing evidence indicating that several foods have protective roles in cancer prevention, by inhibiting tumor progression directly or through modifying tumor's microenvironment that leads to hostile conditions favorable to tumor initiation or growth. While nutritional intakes from foods cannot be adequately controlled for dosage, the role of nutrients in the epigenetics of cancer has led to more research aimed at developing nutriceuticals and drugs as cancer therapies. Clinical studies are needed to evaluate the optimum doses of dietary compounds, the safety profile of dosages, to establish the most efficient way of administration, and bioavailability, in order to maximize the beneficial effects already discovered, and to ensure replicability. Thus, nutrition represents a promising tool to be used not only in cancer prevention, but hopefully also in cancer treatment.
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Affiliation(s)
- Nicoleta Andreescu
- Medical Genetics Discipline, Center of Genomic Medicine, University of Medicine and Pharmacy "Victor Babes", Timisoara, Romania.
| | - Maria Puiu
- Medical Genetics Discipline, Center of Genomic Medicine, University of Medicine and Pharmacy "Victor Babes", Timisoara, Romania
| | - Mihai Niculescu
- Medical Genetics Discipline, Center of Genomic Medicine, University of Medicine and Pharmacy "Victor Babes", Timisoara, Romania
- Advanced Nutrigenomics, Hillsborough, NC, USA
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15
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Zeisel SH. A Conceptual Framework for Studying and Investing in Precision Nutrition. Front Genet 2019; 10:200. [PMID: 30936893 PMCID: PMC6431609 DOI: 10.3389/fgene.2019.00200] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 02/25/2019] [Indexed: 12/15/2022] Open
Abstract
Nutrients and food-derived bioactive molecules must transit complex metabolic pathways, and these pathways vary between people. Metabolic heterogeneity is caused by genetic variation, epigenetic variation, differences in microbiome composition and function, lifestyle differences and by variation in environmental exposures. This review discusses a number of these sources of metabolic heterogeneity and presents some of the research investments that will be needed to make applications of precision nutrition practical.
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Affiliation(s)
- Steven H Zeisel
- Nutrition Research Institute, The University of North Carolina at Chapel Hill, Kannapolis, NC, United States
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16
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Zhang Q, Wang S, Chen J, Yu Z. Histone Deacetylases (HDACs) Guided Novel Therapies for T-cell lymphomas. Int J Med Sci 2019; 16:424-442. [PMID: 30911277 PMCID: PMC6428980 DOI: 10.7150/ijms.30154] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/19/2018] [Indexed: 12/20/2022] Open
Abstract
T-cell lymphomas are a heterogeneous group of cancers with different pathogenesis and poor prognosis. Histone deacetylases (HDACs) are epigenetic modifiers that modulate many key biological processes. In recent years, HDACs have been fully investigated for their roles and potential as drug targets in T-cell lymphomas. In this review, we have deciphered the modes of action of HDACs, HDAC inhibitors as single agents, and HDACs guided combination therapies in T-cell lymphomas. The overview of HDACs on the stage of T-cell lymphomas, and HDACs guided therapies both as single agents and combination regimens endow great opportunities for the cure of T-cell lymphomas.
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Affiliation(s)
- Qing Zhang
- Department of Minimally Invasive Intervention, Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, China
| | - Shaobin Wang
- Health Management Center of Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, China
| | - Junhui Chen
- Department of Minimally Invasive Intervention, Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, China
| | - Zhendong Yu
- China Central Laboratory of Peking University Shenzhen Hospital, Shenzhen, Guangdong, 518036, China
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17
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Klyuyeva A, Tuganova A, Kedishvili N, Popov KM. Tissue-specific kinase expression and activity regulate flux through the pyruvate dehydrogenase complex. J Biol Chem 2018; 294:838-851. [PMID: 30482839 DOI: 10.1074/jbc.ra118.006433] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/23/2018] [Indexed: 01/15/2023] Open
Abstract
The pyruvate dehydrogenase complex (PDC) is a multienzyme assembly that converts pyruvate to acetyl-CoA. As pyruvate and acetyl-CoA play central roles in cellular metabolism, understanding PDC regulation is pivotal to understanding the larger metabolic network. The activity of mammalian PDC is regulated through reversible phosphorylation governed by at least four isozymes of pyruvate dehydrogenase kinase (PDK). Deciphering which kinase regulates PDC in organisms at specific times or places has been challenging. In this study, we analyzed mouse strains carrying targeted mutations of individual isozymes to explore their role in regulating PDC activity. Analysis of protein content of PDK isozymes in major metabolic tissues revealed that PDK1 and PDK2 were ubiquitously expressed, whereas PDK3 and PDK4 displayed a rather limited tissue distribution. Measurement of kinase activity showed that PDK1 is the principal isozyme regulating hepatic PDC. PDK2 was largely responsible for inactivation of PDC in tissues of muscle origin and brown adipose tissue (BAT). PDK3 was the principal kinase regulating pyruvate dehydrogenase activity in kidney and brain. In a well-fed state, the tissue levels of PDK4 protein were fairly low. In most tissues tested, PDK4 ablation had little effect on the overall rates of inactivation of PDC in kinase reaction. Taken together, these data strongly suggest that the activity of PDC is regulated by different isozymes in different tissues. Furthermore, it appears that the overall flux through PDC in a given tissue largely reflects the properties of the PDK isozyme that is principally responsible for the regulation of PDC activity in that tissue.
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Affiliation(s)
- Alla Klyuyeva
- From the Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Alina Tuganova
- From the Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Natalia Kedishvili
- From the Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Kirill M Popov
- From the Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
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18
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Abstract
Epigenetics is the study of heritable mechanisms that can modify gene activity and phenotype without modifying the genetic code. The basis for the concept of epigenetics originated more than 2,000 yr ago as a theory to explain organismal development. However, the definition of epigenetics continues to evolve as we identify more of the components that make up the epigenome and dissect the complex manner by which they regulate and are regulated by cellular functions. A substantial and growing body of research shows that nutrition plays a significant role in regulating the epigenome. Here, we critically assess this diverse body of evidence elucidating the role of nutrition in modulating the epigenome and summarize the impact such changes have on molecular and physiological outcomes with regards to human health.
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Affiliation(s)
- Folami Y Ideraabdullah
- Departments of Genetics and Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina; and Departments of Nutrition and Pediatrics, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
| | - Steven H Zeisel
- Departments of Genetics and Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina; and Departments of Nutrition and Pediatrics, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
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19
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Pan P, Oshima K, Huang YW, Agle KA, Drobyski WR, Chen X, Zhang J, Yearsley MM, Yu J, Wang LS. Loss of FFAR2 promotes colon cancer by epigenetic dysregulation of inflammation suppressors. Int J Cancer 2018. [PMID: 29524208 DOI: 10.1002/ijc.31366] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Free fatty acid receptor 2 (FFAR2, also named GPR43), is activated by short-chain fatty acids (SCFAs), such as butyrate, that are produced when gut bacteria ferment dietary fiber. FFAR2 has been suggested to regulate colonic inflammation, which is a major risk factor for the development of colon cancer and is also linked to epigenetic dysregulation in colon carcinogenesis. The current study assessed whether FFAR2, acting as an epigenetic regulator, protects against colon carcinogenesis. To mimic the mild inflammation that promotes human colon cancer, we treated mice with dextran sodium sulfate (DSS) overnight, which avoids excessive inflammation but induces mild inflammation that promotes colon carcinogenesis in the ApcMin/+ and the azoxymethane (AOM)-treated mice. Our results showed that FFAR2 deficiency promotes the development of colon adenoma in the ApcMin/+ /DSS mice and the progression of adenoma to adenocarcinoma in the AOM/DSS mice. FFAR2's downstream cAMP-PKA-CREB pathway was enhanced, leading to overexpression of histone deacetylases (HDACs) in the FFAR2-deficient mice. ChIP-qPCR analysis revealed differential binding of H3K27me3 and H3K4me3 histone marks onto the promoter regions of inflammation suppressors (e.g., sfrp1, dkk3, socs1), resulting in decreased expression of these genes in the FFAR2-deficient mice. Also, more neutrophils infiltrated into tumors and colon lamina propria of the FFAR2-deficient mice. Depletion of neutrophils blocked the progression of colon tumors. In addition, FFAR2 is required for butyrate to suppress HDAC expression and hypermethylation of inflammation suppressors. Therefore, our results suggest that FFAR2 is an epigenetic tumor suppressor that acts at multiple stages of colon carcinogenesis.
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Affiliation(s)
- Pan Pan
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Kiyoko Oshima
- Department of Pathology, John Hopkins University, Baltimore, MD
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI
| | - Kimberle A Agle
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - William R Drobyski
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Xiao Chen
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Jianying Zhang
- Center for Biostatistics, The Ohio State University, Columbus, OH
| | | | - Jianhua Yu
- Division of Hematology, Department of Internal Medicine, College of Medicine, Comprehensive Cancer Center and The James Cancer Hospital, The Ohio State University, Columbus, OH
| | - Li-Shu Wang
- Division of Hematology and Oncology, Department of Medicine, Medical College of Wisconsin, RM C4930, 8701 Watertown Plank Rd, Milwaukee, WI, 53226
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20
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Neonatal Colonic Inflammation Epigenetically Aggravates Epithelial Inflammatory Responses to Injury in Adult Life. Cell Mol Gastroenterol Hepatol 2018; 6:65-78. [PMID: 29928672 PMCID: PMC6008258 DOI: 10.1016/j.jcmgh.2018.02.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/01/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Early life adversity is considered a risk factor for the development of gastrointestinal diseases, including inflammatory bowel disease. We hypothesized that early life colonic inflammation causes susceptibility to aggravated overexpression of interleukin (IL)1β. METHODS We developed a 2-hit rat model in which neonatal inflammation (NI) and adult inflammation (AI) were induced by trinitrobenzene sulfonic acid. RESULTS Aggravated immune responses were observed in NI + AI rats, including a sustained up-regulation of IL1β and other cytokines. In parallel with exacerbated loss of inhibitor of kappa B alpha expression, NI + AI rats showed hyperacetylation of histone H4K12 and increased V-Rel Avian Reticuloendotheliosis Viral Oncogene Homolog A binding on the IL1B promoter, accompanied by high levels of norepinephrine/epinephrine. Propranolol, a β-blocker, markedly ameliorated the inflammatory response and IL1β overexpression by mitigating against epigenetic modifications. Adrenalectomy abrogated NI-induced disease susceptibility whereas yohimbine sensitized the epithelium for exacerbated immune response. The macrophages of NI rats produced more IL1β than controls after exposure to lipopolysaccharide (LPS), suggesting hypersensitization; incubation with LPS plus Foradil (Sigma, St. Louis, MO), a β2-agonist, induced a greater IL1β expression than LPS alone. Epinephrine and Foradil also exacerbated LPS-induced IL1β activation in human THP-1-derived macrophages, by increasing acetylated H4K12, and these increases were abrogated by propranolol. CONCLUSIONS NI sensitizes the colon epithelium for exacerbated IL1β activation by increasing stress hormones that induce histone hyperacetylation, allowing greater access of nuclear factor-κB to the IL1B promoter and rendering the host susceptible to aggravated immune responses. Our findings suggest that β blockers have a therapeutic potential for inflammatory bowel disease susceptibility and establish a novel paradigm whereby NI induces epigenetic susceptibility to inflammatory bowel disease.
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Key Words
- AI, adult inflammation
- ChIP, chromatin immunoprecipitation
- Ctl, control
- Early Life Adversity
- Epinephrine
- H4K12ac, acetylated HRK12
- HDAC, histone deacetylase
- Histone Acetylation
- IBD, inflammatory bowel disease
- IL, interleukin
- Inflammatory Bowel Disease
- IκB, inhibitor of kappa B alpha
- LPS, lipopolysaccharide
- MPO, myeloperoxidase
- NF-κB
- NF-κB, nuclear factor-κB
- NI, neonatal inflammation
- PCR, polymerase chain reaction
- PMA, phorbol 12-myristate 13-acetate
- RNAP II, RNA polymerase II
- RelA, V-Rel Avian Reticuloendotheliosis Viral Oncogene Homolog A
- TNBS, 2,4,6-trinitrobenzene sulfonic acid
- Tnf, tumor necrosis factor
- mRNA, messenger RNA
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21
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Chen YS, Wang R, Dashwood WM, Löhr CV, Williams DE, Ho E, Mertens-Talcott S, Dashwood RH. A miRNA signature for an environmental heterocyclic amine defined by a multi-organ carcinogenicity bioassay in the rat. Arch Toxicol 2017; 91:3415-3425. [PMID: 28289824 PMCID: PMC5836314 DOI: 10.1007/s00204-017-1945-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/23/2017] [Indexed: 12/16/2022]
Abstract
Heterocyclic amines (HCAs) produced during high-temperature cooking have been studied extensively in terms of their genotoxic/genetic effects, but recent work has implicated epigenetic mechanisms involving non-coding RNAs. Colon tumors induced in the rat by 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) have altered microRNA (miRNA) signatures linked to dysregulated pluripotency factors, such as c-Myc and Krüppel-like factor 4 (KLF4). We tested the hypothesis that dysregulated miRNAs from PhIP-induced colon tumors would provide a "PhIP signature" for use in other target organs obtained from a 1-year carcinogenicity bioassay in the rat. Downstream targets that were corroborated in the rat were then investigated in human cancer datasets. The results confirmed that multiple let-7 family members were downregulated in PhIP-induced skin, colon, lung, small intestine, and Zymbal's gland tumors, and were associated with c-myc and Hmga2 upregulation. PhIP signature miRNAs with the profile mir-21high/mir-126low/mir-29clow/mir-215low/mir-145low were linked to reduced Klf4 levels in rat tumors, and in human pan-cancer and colorectal cancer. It remains to be determined whether this PhIP signature has predictive value, given that more than 20 different genotoxic HCAs are present in the human diet, plus other agents that likely induce or repress many of the same miRNAs. Future studies should define more precisely the miRNA signatures of other HCAs, and their possible value for human risk assessment.
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Affiliation(s)
- Ying-Shiuan Chen
- Center for Epigenetics and Disease Prevention, Texas A&M University College of Medicine, 2121 W Holcombe Blvd., Houston, TX, 77030, USA
| | - Rong Wang
- Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - Wan-Mohaiza Dashwood
- Center for Epigenetics and Disease Prevention, Texas A&M University College of Medicine, 2121 W Holcombe Blvd., Houston, TX, 77030, USA
| | - Christiane V Löhr
- College of Veterinary Medicine, Oregon State University, Corvallis, OR, USA
| | - David E Williams
- Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Emily Ho
- Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
- College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Susanne Mertens-Talcott
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roderick H Dashwood
- Center for Epigenetics and Disease Prevention, Texas A&M University College of Medicine, 2121 W Holcombe Blvd., Houston, TX, 77030, USA.
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Molecular and Cellular Medicine, Texas A&M College of Medicine, College Station, TX, USA.
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX, USA.
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22
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Byun SK, An TH, Son MJ, Lee DS, Kang HS, Lee EW, Han BS, Kim WK, Bae KH, Oh KJ, Lee SC. HDAC11 Inhibits Myoblast Differentiation through Repression of MyoD-Dependent Transcription. Mol Cells 2017; 40:667-676. [PMID: 28927261 PMCID: PMC5638774 DOI: 10.14348/molcells.2017.0116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 12/12/2022] Open
Abstract
Abnormal differentiation of muscle is closely associated with aging (sarcopenia) and diseases such as cancer and type II diabetes. Thus, understanding the mechanisms that regulate muscle differentiation will be useful in the treatment and prevention of these conditions. Protein lysine acetylation and methylation are major post-translational modification mechanisms that regulate key cellular processes. In this study, to elucidate the relationship between myogenic differentiation and protein lysine acetylation/methylation, we performed a PCR array of enzymes related to protein lysine acetylation/methylation during C2C12 myoblast differentiation. Our results indicated that the expression pattern of HDAC11 was substantially increased during myoblast differentiation. Furthermore, ectopic expression of HDAC11 completely inhibited myoblast differentiation, concomitant with reduced expression of key myogenic transcription factors. However, the catalytically inactive mutant of HDAC11 (H142/143A) did not impede myoblast differentiation. In addition, wild-type HDAC11, but not the inactive HDAC11 mutant, suppressed MyoD-induced promoter activities of MEF2C and MYOG (Myogenin), and reduced histone acetylation near the E-boxes, the MyoD binding site, of the MEF2C and MYOG promoters. Collectively, our results indicate that HDAC11 would suppress myoblast differentiation via regulation of MyoD-dependent transcription. These findings suggest that HDAC11 is a novel critical target for controlling myoblast differentiation.
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Affiliation(s)
- Sang Kyung Byun
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141,
Korea
| | - Tae Hyeon An
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141,
Korea
| | - Min Jeong Son
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
| | - Da Som Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
| | - Hyun Sup Kang
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141,
Korea
| | - Eun-Woo Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
| | - Baek Soo Han
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141,
Korea
| | - Won Kon Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141,
Korea
| | - Kwang-Hee Bae
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141,
Korea
| | - Kyoung-Jin Oh
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141,
Korea
| | - Sang Chul Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon 34141,
Korea
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23
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Ratovitski EA. Anticancer Natural Compounds as Epigenetic Modulators of Gene Expression. Curr Genomics 2017; 18:175-205. [PMID: 28367075 PMCID: PMC5345332 DOI: 10.2174/1389202917666160803165229] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/24/2015] [Accepted: 11/29/2015] [Indexed: 11/30/2022] Open
Abstract
Accumulating evidence shows that hallmarks of cancer include: "genetic and epigenetic alterations leading to inactivation of cancer suppressors, overexpression of oncogenes, deregulation of intracellular signaling cascades, alterations of cancer cell metabolism, failure to undergo cancer cell death, induction of epithelial to mesenchymal transition, invasiveness, metastasis, deregulation of immune response and changes in cancer microenvironment, which underpin cancer development". Natural compounds as bioactive ingredients isolated from natural sources (plants, fungi, marine life forms) have revolutionized the field of anticancer therapeutics and rapid developments in preclinical studies are encouraging. Natural compounds could affect the epigenetic molecular mechanisms that modulate gene expression, as well as DNA damage and repair mechanisms. The current review will describe the latest achievements in using naturally produced compounds targeting epigenetic regulators and modulators of gene transcription in vitro and in vivo to generate novel anticancer therapeutics.
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Affiliation(s)
- Edward A. Ratovitski
- Head and Neck Cancer Research Division, Department of Otolaryngology/Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
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24
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Abstract
Recent high-profile reports have reignited an interest in acetate metabolism in cancer. Acetyl-CoA synthetases that catalyse the conversion of acetate to acetyl-CoA have now been implicated in the growth of hepatocellular carcinoma, glioblastoma, breast cancer and prostate cancer. In this Review, we discuss how acetate functions as a nutritional source for tumours and as a regulator of cancer cell stress, and how preventing its (re)capture by cancer cells may provide an opportunity for therapeutic intervention.
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Affiliation(s)
- Zachary T Schug
- Cancer Metabolism Research Unit, Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, Scotland, UK
- Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
| | - Johan Vande Voorde
- Cancer Metabolism Research Unit, Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, Scotland, UK
| | - Eyal Gottlieb
- Cancer Metabolism Research Unit, Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, Scotland, UK
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25
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The Gut Microbiota and their Metabolites: Potential Implications for the Host Epigenome. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 902:33-44. [PMID: 27161349 DOI: 10.1007/978-3-319-31248-4_3] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The gut microbiota represents a metabolically active biomass of up to 2 kg in adult humans. Microbiota-derived molecules significantly contribute to the host metabolism. Large amounts of bacterial metabolites are taken up by the host and are subsequently utilized by the human body. For instance, short chain fatty acids produced by the gut microbiota are a major energy source of humans.It is widely accepted that microbiota-derived metabolites are used as fuel for beta-oxidation (short chain fatty acids) and participate in many metabolic processes (vitamins, such as folic acid). Apart from these direct metabolic effects, it also becomes more and more evident that these metabolites can interact with the mammalian epigenetic machinery. By interacting with histones and DNA they may be able to manipulate the host's chromatin state and functionality and hence its physiology and health.In this chapter, we summarize the current knowledge on possible interactions of different bacterial metabolites with the mammalian epigenetic machinery, mostly based on in vitro data. We discuss the putative impact on chromatin marks, for example histone modifications and DNA methylation. Subsequently, we speculate about possible beneficial and adverse consequences for the epigenome, the physiology and health of the host, as well as plausible future applications of this knowledge for in vivo translation to support personal health.
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Abstract
The search for a connection between diet and human cancer has a long history in cancer research, as has interest in the mechanisms by which dietary factors might increase or decrease cancer risk. The realization that altering diet can alter the epigenetic state of genes and that these epigenetic alterations might increase or decrease cancer risk is a more modern notion, driven largely by studies in animal models. The connections between diet and epigenetic alterations, on the one hand, and between epigenetic alterations and cancer, on the other, are supported by both observational studies in humans as well as animal models. However, the conclusion that diet is linked directly to epigenetic alterations and that these epigenetic alterations directly increase or decrease the risk of human cancer is much less certain. We suggest that true and measurable effects of diet or dietary supplements on epigenotype and cancer risk are most likely to be observed in longitudinal studies and at the extremes of the intersection of dietary risk factors and human population variability. Careful analysis of such outlier populations is most likely to shed light on the molecular mechanisms by which suspected environmental risk factors drive the process of carcinogenesis.
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Affiliation(s)
- Carmen Sapienza
- Fels Institute for Cancer Research and Molecular Biology and Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140;
| | - Jean-Pierre Issa
- Department of Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140;
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27
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Moos WH, Maneta E, Pinkert CA, Irwin MH, Hoffman ME, Faller DV, Steliou K. Epigenetic Treatment of Neuropsychiatric Disorders: Autism and Schizophrenia. Drug Dev Res 2016; 77:53-72. [PMID: 26899191 DOI: 10.1002/ddr.21295] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Neuropsychiatric disorders are a heterogeneous group of conditions that often share underlying mitochondrial dysfunction and biological pathways implicated in their pathogenesis, progression, and treatment. To date, these disorders have proven notoriously resistant to molecular-targeted therapies, and clinical options are relegated to interventional types, which do not address the core symptoms of the disease. In this review, we discuss emerging epigenetic-driven approaches using novel acylcarnitine esters (carnitinoids) that act on master regulators of antioxidant and cytoprotective genes and mitophagic pathways. These carnitinoids are actively transported, mitochondria-localizing, biomimetic coenzyme A surrogates of short-chain fatty acids, which inhibit histone deacetylase and may reinvigorate synaptic plasticity and protect against neuronal damage. We outline these neuroprotective effects in the context of treatment of neuropsychiatric disorders such as autism spectrum disorder and schizophrenia.
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Affiliation(s)
- Walter H Moos
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California San Francisco, San Francisco, CA, USA.,SRI Biosciences, A Division of SRI International, Menlo Park, CA, USA
| | - Eleni Maneta
- Department of Psychiatry, Boston Children's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Carl A Pinkert
- Department of Biological Sciences, College of Arts and Sciences, The University of Alabama, Tuscaloosa, AL, USA.,Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Michael H Irwin
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Michelle E Hoffman
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, USA
| | - Douglas V Faller
- Cancer Research Center, Boston University School of Medicine, Boston, MA, USA
| | - Kosta Steliou
- Cancer Research Center, Boston University School of Medicine, Boston, MA, USA.,PhenoMatriX, Inc., Boston, MA, USA
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28
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Rajendran P, Dashwood WM, Li L, Kang Y, Kim E, Johnson G, Fischer KA, Löhr CV, Williams DE, Ho E, Yamamoto M, Lieberman DA, Dashwood RH. Nrf2 status affects tumor growth, HDAC3 gene promoter associations, and the response to sulforaphane in the colon. Clin Epigenetics 2015; 7:102. [PMID: 26388957 PMCID: PMC4575421 DOI: 10.1186/s13148-015-0132-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/02/2015] [Indexed: 02/08/2023] Open
Abstract
Background The dietary agent sulforaphane (SFN) has been reported to induce nuclear factor erythroid 2 (NF-E2)-related factor 2 (Nrf2)-dependent pathways as well as inhibiting histone deacetylase (HDAC) activity. The current investigation sought to examine the relationships between Nrf2 status and HDAC expression in preclinical and translational studies. Results Wild type (WT) and Nrf2-deficient (Nrf2−/+) mice were treated with the colon carcinogen 1,2-dimethylhydrazine (DMH) followed by 400 ppm SFN in the diet (n = 35 mice/group). WT mice were more susceptible than Nrf2−/+ mice to tumor induction in the colon. Tumors from WT mice had higher HDAC levels globally and locally on genes such as cyclin-dependant kinase inhibitor 2a (Cdkn2a/p16) that were dysregulated during tumor development. The average tumor burden was reduced by SFN from 62.7 to 26.0 mm3 in WT mice and from 14.6 to 11.7 mm3 in Nrf2−/+ mice. The decreased antitumor activity of SFN in Nrf2−/+ mice coincided with attenuated Cdkn2a promoter interactions involving HDAC3. HDAC3 knockdown in human colon cancer cells recapitulated the effects of SFN on p16 induction. Human subjects given a broccoli sprout extract supplement (200 μmol SFN equivalents), or reporting more than five cruciferous vegetable servings per week, had increased p16 expression that was inversely associated with HDAC3 in circulating peripheral blood mononuclear cells (PBMCs) and in biopsies obtained during screening colonoscopy. Conclusions Nrf2 expression varies widely in both normal human colon and human colon cancers and likely contributes to the overall rate of tumor growth in the large intestine. It remains to be determined whether this influences global HDAC protein expression levels, as well as local HDAC interactions on genes dysregulated during human colon tumor development. If corroborated in future studies, Nrf2 status might serve as a biomarker of HDAC inhibitor efficacy in clinical trials using single agent or combination modalities to slow, halt, or regress the progression to later stages of solid tumors and hematological malignancies. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0132-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Praveen Rajendran
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, Houston, TX USA
| | - Wan-Mohaiza Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, Houston, TX USA
| | - Li Li
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, Houston, TX USA
| | - Yuki Kang
- Linus Pauling Institute, Oregon State University, Corvallis, OR USA
| | - Eunah Kim
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, Houston, TX USA
| | - Gavin Johnson
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, Houston, TX USA
| | - Kay A Fischer
- College of Veterinary Medicine, Oregon State University, Corvallis, OR USA
| | - Christiane V Löhr
- College of Veterinary Medicine, Oregon State University, Corvallis, OR USA
| | - David E Williams
- Linus Pauling Institute, Oregon State University, Corvallis, OR USA ; Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR USA
| | - Emily Ho
- Linus Pauling Institute, Oregon State University, Corvallis, OR USA ; College of Public Health and Human Sciences, Oregon State University, Corvallis, OR USA
| | - Masayuki Yamamoto
- Division of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi Japan
| | - David A Lieberman
- Department of Medicine, Oregon Health & Science University, Portland, OR USA
| | - Roderick H Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health Science Center, Houston, TX USA ; Department of Food Science & Nutrition, Texas A&M University, College Station, TX USA ; Department of Molecular & Cellular Medicine, Texas A&M University, College Station, TX USA ; Department of Clinical Cancer Prevention, MD Anderson Cancer Center, Houston, TX USA
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29
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Abstract
PURPOSE OF REVIEW To give an overview of recently published articles addressing the role of epigenetic modifications in rheumatoid arthritis (RA). Here we focused on DNA methylation and posttranslational histone modifications. RECENT FINDINGS Recent studies attempted to link epigenetic modifications with genetic or environmental risk factors for RA. There is evidence that histone deacetylases confer effects of environmental triggers such as smoking, diet or therapy on expression levels of target genes. Additionally, disturbed methylation patterns and cell-type specific histone methylation marks were identified as potential mediators of genetic risk in RA. Altered methylome signatures were found in several cell types in RA, first of all RA synovial fibroblasts, and contribute to the intrinsic fibroblast activation. The reversal of DNA hypomethylation by inhibiting the polyamine recycling pathway was suggested as new epigenetic therapy in RA. Moreover, targeting epigenetic reader proteins, such as bromodomain proteins, emerged as a new field in drug development and the first studies underscored the potential of these drugs not only in malignant and inflammatory conditions but also in autoimmune diseases. SUMMARY Epigenetic factors represent a promising area to link genetics, regulation of gene expression and environmental risk factors.
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30
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Abstract
Neuroglia, the "glue" that fills the space between neurons in the central nervous system, takes active part in nerve cell signaling. Neuroglial cells, astroglia, oligodendroglia, and microglia, are together about as numerous as neurons in the brain as a whole, and in the cerebral cortex grey matter, but the proportion varies widely among brain regions. Glial volume, however, is less than one-fifth of the tissue volume in grey matter. When stimulated by neurons or other cells, neuroglial cells release gliotransmitters by exocytosis, similar to neurotransmitter release from nerve endings, or by carrier-mediated transport or channel flux through the plasma membrane. Gliotransmitters include the common neurotransmitters glutamate and GABA, the nonstandard amino acid d-serine, the high-energy phosphate ATP, and l-lactate. The latter molecule is a "buffer" between glycolytic and oxidative metabolism as well as a signaling substance recently shown to act on specific lactate receptors in the brain. Complementing neurotransmission at a synapse, neuroglial transmission often implies diffusion of the transmitter over a longer distance and concurs with the concept of volume transmission. Transmission from glia modulates synaptic neurotransmission based on energetic and other local conditions in a volume of tissue surrounding the individual synapse. Neuroglial transmission appears to contribute significantly to brain functions such as memory, as well as to prevalent neuropathologies.
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Affiliation(s)
- Vidar Gundersen
- SN-Lab, Division of Anatomy, Department of Molecular Medicine, Institute of Basic Medical Sciences, and CMBN/SERTA/Healthy Brain Ageing Centre, University of Oslo, Oslo, Norway; Department of Neurology, Oslo University Hospital-Rikshospitalet, Oslo, Norway; Center for Healthy Aging, Department of Neuroscience and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; and Brain and Muscle Energy Group, Department of Oral Biology and Division of Anatomy, Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | - Jon Storm-Mathisen
- SN-Lab, Division of Anatomy, Department of Molecular Medicine, Institute of Basic Medical Sciences, and CMBN/SERTA/Healthy Brain Ageing Centre, University of Oslo, Oslo, Norway; Department of Neurology, Oslo University Hospital-Rikshospitalet, Oslo, Norway; Center for Healthy Aging, Department of Neuroscience and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; and Brain and Muscle Energy Group, Department of Oral Biology and Division of Anatomy, Department of Molecular Medicine, University of Oslo, Oslo, Norway
| | - Linda Hildegard Bergersen
- SN-Lab, Division of Anatomy, Department of Molecular Medicine, Institute of Basic Medical Sciences, and CMBN/SERTA/Healthy Brain Ageing Centre, University of Oslo, Oslo, Norway; Department of Neurology, Oslo University Hospital-Rikshospitalet, Oslo, Norway; Center for Healthy Aging, Department of Neuroscience and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; and Brain and Muscle Energy Group, Department of Oral Biology and Division of Anatomy, Department of Molecular Medicine, University of Oslo, Oslo, Norway
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31
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Busch C, Burkard M, Leischner C, Lauer UM, Frank J, Venturelli S. Epigenetic activities of flavonoids in the prevention and treatment of cancer. Clin Epigenetics 2015; 7:64. [PMID: 26161152 PMCID: PMC4497414 DOI: 10.1186/s13148-015-0095-z] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 06/17/2015] [Indexed: 02/07/2023] Open
Abstract
Aberrant epigenetic modifications are described in an increasing number of pathological conditions, including neurodegenerative diseases, cardiovascular diseases, diabetes mellitus type 2, obesity and cancer. The general reversibility of epigenetic changes makes them an attractive and promising target e.g. in the treatment of cancer. Thus, a growing number of epigenetically active compounds are currently tested in clinical trials for their therapeutic potential. Interestingly, many phytochemicals present in plant foods, particularly flavonoids, are suggested to be able to alter epigenetic cellular mechanisms. Flavonoids are natural phenol compounds that form a large group of secondary plant metabolites with interesting biological activities. They can be categorized into six major subclasses, which display diverse properties affecting the two best characterized epigenetic mechanisms: modulation of the DNA methylation status and histone acetylation. High dietary flavonoid intake has strongly been suggested to reduce the risk of numerous cancer entities in a large body of epidemiological studies. Established health-promoting effects of diets rich in fruit and vegetables are faced by efforts to use purified flavonoids as supplements or pharmaceuticals, whereupon data on the latter applications remain controversial. The purpose of this review is to give an overview of current research on flavonoids to further elucidate their potential in cancer prevention and therapy, thereby focusing on their distinct epigenetic activities.
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Affiliation(s)
- Christian Busch
- Division of Dermatologic Oncology, Department of Dermatology and Allergology, Medical University Hospital, Tuebingen, Germany
| | - Markus Burkard
- Division of Dermatologic Oncology, Department of Dermatology and Allergology, Medical University Hospital, Tuebingen, Germany ; Department of Internal Medicine I, Medical University Hospital, Otfried-Mueller-Str. 27, 72076 Tuebingen, Germany
| | - Christian Leischner
- Department of Internal Medicine I, Medical University Hospital, Otfried-Mueller-Str. 27, 72076 Tuebingen, Germany
| | - Ulrich M Lauer
- Department of Internal Medicine I, Medical University Hospital, Otfried-Mueller-Str. 27, 72076 Tuebingen, Germany
| | - Jan Frank
- Institute of Biological Chemistry and Nutrition, University of Hohenheim, Stuttgart, Germany
| | - Sascha Venturelli
- Department of Internal Medicine I, Medical University Hospital, Otfried-Mueller-Str. 27, 72076 Tuebingen, Germany
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32
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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: 1.8] [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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33
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Mathias RA, Guise AJ, Cristea IM. Post-translational modifications regulate class IIa histone deacetylase (HDAC) function in health and disease. Mol Cell Proteomics 2015; 14:456-70. [PMID: 25616866 DOI: 10.1074/mcp.o114.046565] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Class IIa histone deacetylases (HDACs4, -5, -7, and -9) modulate the physiology of the human cardiovascular, musculoskeletal, nervous, and immune systems. The regulatory capacity of this family of enzymes stems from their ability to shuttle between nuclear and cytoplasmic compartments in response to signal-driven post-translational modification. Here, we review the current knowledge of modifications that control spatial and temporal histone deacetylase functions by regulating subcellular localization, transcriptional functions, and cell cycle-dependent activity, ultimately impacting on human disease. We discuss the contribution of these modifications to cardiac and vascular hypertrophy, myoblast differentiation, neuronal cell survival, and neurodegenerative disorders.
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Affiliation(s)
- Rommel A Mathias
- From the ‡Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544; §Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia
| | - Amanda J Guise
- From the ‡Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544
| | - Ileana M Cristea
- From the ‡Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544;
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34
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HDAC8 and STAT3 repress BMF gene activity in colon cancer cells. Cell Death Dis 2014; 5:e1476. [PMID: 25321483 PMCID: PMC4237248 DOI: 10.1038/cddis.2014.422] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/27/2014] [Accepted: 09/02/2014] [Indexed: 12/31/2022]
Abstract
Histone deacetylase (HDAC) inhibitors are undergoing clinical trials as anticancer agents, but some exhibit resistance mechanisms linked to anti-apoptotic Bcl-2 functions, such as BH3-only protein silencing. HDAC inhibitors that reactivate BH3-only family members might offer an improved therapeutic approach. We show here that a novel seleno-α-keto acid triggers global histone acetylation in human colon cancer cells and activates apoptosis in a p21-independent manner. Profiling of multiple survival factors identified a critical role for the BH3-only member Bcl-2-modifying factor (Bmf). On the corresponding BMF gene promoter, loss of HDAC8 was associated with signal transducer and activator of transcription 3 (STAT3)/specificity protein 3 (Sp3) transcription factor exchange and recruitment of p300. Treatment with a p300 inhibitor or transient overexpression of exogenous HDAC8 interfered with BMF induction, whereas RNAi-mediated silencing of STAT3 activated the target gene. This is the first report to identify a direct target gene of HDAC8 repression, namely, BMF. Interestingly, the repressive role of HDAC8 could be uncoupled from HDAC1 to trigger Bmf-mediated apoptosis. These findings have implications for the development of HDAC8-selective inhibitors as therapeutic agents, beyond the reported involvement of HDAC8 in childhood malignancy.
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35
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Bassett SA, Barnett MPG. The role of dietary histone deacetylases (HDACs) inhibitors in health and disease. Nutrients 2014; 6:4273-301. [PMID: 25322459 PMCID: PMC4210916 DOI: 10.3390/nu6104273] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 10/06/2014] [Accepted: 10/06/2014] [Indexed: 12/30/2022] Open
Abstract
Modification of the histone proteins associated with DNA is an important process in the epigenetic regulation of DNA structure and function. There are several known modifications to histones, including methylation, acetylation, and phosphorylation, and a range of factors influence each of these. Histone deacetylases (HDACs) remove the acetyl group from lysine residues within a range of proteins, including transcription factors and histones. Whilst this means that their influence on cellular processes is more complex and far-reaching than histone modifications alone, their predominant function appears to relate to histones; through deacetylation of lysine residues they can influence expression of genes encoded by DNA linked to the histone molecule. HDAC inhibitors in turn regulate the activity of HDACs, and have been widely used as therapeutics in psychiatry and neurology, in which a number of adverse outcomes are associated with aberrant HDAC function. More recently, dietary HDAC inhibitors have been shown to have a regulatory effect similar to that of pharmacological HDAC inhibitors without the possible side-effects. Here, we discuss a number of dietary HDAC inhibitors, and how they may have therapeutic potential in the context of a whole food.
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Affiliation(s)
- Shalome A Bassett
- Food Nutrition & Health Team, Food & Bio-based Products Group, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North 4442, New Zealand.
| | - Matthew P G Barnett
- Food Nutrition & Health Team, Food & Bio-based Products Group, AgResearch Limited, Grasslands Research Centre, Tennent Drive, Palmerston North 4442, New Zealand.
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Joven J, Micol V, Segura-Carretero A, Alonso-Villaverde C, Menéndez JA. Polyphenols and the modulation of gene expression pathways: can we eat our way out of the danger of chronic disease? Crit Rev Food Sci Nutr 2014; 54:985-1001. [PMID: 24499117 DOI: 10.1080/10408398.2011.621772] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Plant-derived dietary polyphenols may improve some disease states and promote health. Experimental evidence suggests that this is partially attributable to changes in gene expression. The rational use of bioactive food components may therefore present an opportunity to activate or repress selected gene expression pathways and, consequently, to manage or prevent disease. It remains to be determined whether this use of bioactive food components can be done safely. This article reviews the associated controversies and limitations of polyphenol therapy. There is a paucity of clinical data on the rational use of polyphenols, including a lack of knowledge on effective dosage, actual chemical formulations, bioavailability, distribution in tissues, the effect of genetic variations, differences in gut microflora, the synergistic (or antagonistic) effects observed in extracts, and the possible interaction between polyphenols and lipid domains of cell membranes that may alter the function of relevant receptors. The seminal question of why plants make substances that benefit humans remains unanswered, and there is still much to learn in terms of correlative versus causal effects of human exposure to various nutrients. The available data strongly suggest significant effects at the molecular level that represent interactions with the epigenome. The advent of relatively simple technologies is helping the field of epigenetics progress and facilitating the acquisition of multiple types of data that were previously difficult to obtain. In this review, we summarize the molecular basis of the epigenetic regulation of gene expression and the epigenetic changes associated with the consumption of polyphenols that illustrate how modifications in human nutrition may become relevant to health and disease.
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Affiliation(s)
- Jorge Joven
- a Centre de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV , Universitat Rovira i Virgili , Calle Sant Llorenç 21 , 43201 , Reus , Spain
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el Bahhaj F, Dekker FJ, Martinet N, Bertrand P. Delivery of epidrugs. Drug Discov Today 2014; 19:1337-52. [DOI: 10.1016/j.drudis.2014.03.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 02/28/2014] [Accepted: 03/19/2014] [Indexed: 12/22/2022]
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Naturally occurring plant polyphenols as potential therapies for inherited neuromuscular diseases. Future Med Chem 2014; 5:2091-101. [PMID: 24215348 DOI: 10.4155/fmc.13.165] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
There are several lines of laboratory-based evidence emerging to suggest that purified polyphenol compounds such as resveratrol, found naturally in red grapes, epigallocatechin galate from green tea and curcumin from turmeric, might be useful for the treatment of various inherited neuromuscular diseases, including spinal muscular atrophy, Duchenne muscular dystrophy and Charcot-Marie-Tooth disease. Here, we critically examine the scientific evidence related to the known molecular effects that these polyphenols have on different models of inherited neuromuscular disease, with particular attention to problems with the validity of in vitro evidence. We also present proteomic evidence that polyphenols have in vitro effects on cells related to metal ion chelation in cell-culture media. Although their precise mechanisms of action remain somewhat elusive, polyphenols could be an attractive approach to therapy for inherited neuromuscular disease, especially since they may be safer to use on young children, compared with some of the other drug candidates.
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Abstract
Inflammatory bowel disease includes ulcerative colitis and Crohn's disease, which are both inflammatory disorders of the gastrointestinal tract. Both types of inflammatory bowel disease have a complex etiology, resulting from a genetically determined susceptibility interacting with environmental factors, including the diet and gut microbiota. Genome Wide Association Studies have implicated more than 160 single-nucleotide polymorphisms in disease susceptibility. Consideration of the different pathways suggested to be involved implies that specific dietary interventions are likely to be appropriate, dependent upon the nature of the genes involved. Epigenetics and the gut microbiota are also responsive to dietary interventions. Nutrigenetics may lead to personalized nutrition for disease prevention and treatment, while nutrigenomics may help to understand the nature of the disease and individual response to nutrients.
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Affiliation(s)
- Lynnette R Ferguson
- Discipline of Nutrition, Faculty of Medical & Health Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand and Nutrigenomics New Zealand, Auckland, New Zealand.
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Sun S, Han Y, Liu J, Fang Y, Tian Y, Zhou J, Ma D, Wu P. Trichostatin A targets the mitochondrial respiratory chain, increasing mitochondrial reactive oxygen species production to trigger apoptosis in human breast cancer cells. PLoS One 2014; 9:e91610. [PMID: 24626188 PMCID: PMC3953478 DOI: 10.1371/journal.pone.0091610] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/11/2014] [Indexed: 02/06/2023] Open
Abstract
AIM Histone deacetylase inhibitors (HDACIs)-based therapies have stimulated interest via their anti-tumor activities, including apoptosis induction, cell cycle arrest, cell differentiation, and autophagy. However, the mechanisms of HDACI-associated anti-tumor activity are not yet clearly defined. The aim of this study was to explore the key events of Trichostatin A (TSA), a classic HDACI agent, against breast cancer cells. METHODS The MCF-7, MDA-MB-231 and MCF-10A cell lines were evaluated with colony-forming and cell viability assays. Apoptosis and cell cycle distribution were detected by flow cytometry. Mitochondrial function was measured with biochemical assays, flow cytometry and transmission electron microscopy. RESULTS TSA inhibited breast cancer cell viability and proliferation, without affecting MCF-10A cell. TSA-induced breast cancer cell apoptosis was initiated by G2-M arrest and depended on mitochondrial reactive oxygen species (ROS) produced subsequent to reduced mitochondrial respiratory chain activity. The enhanced mitochondrial ROS production and apoptosis in cancer cells were markedly attenuated by antioxidants, such as N-acetyl cysteine (NAC), reduced glutathione (GSH) and Vitamin C. CONCLUSION The present study demonstrated that TSA-induced cell death by arresting cell cycle in G2-M phase and was dependent on production of mitochondria-derived ROS, which was derived from impaired mitochondrial respiratory chain.
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Affiliation(s)
- Shujuan Sun
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yingyan Han
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Liu
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Fang
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Tian
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianfeng Zhou
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Ma
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- * E-mail: (DM); (PW)
| | - Peng Wu
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- * E-mail: (DM); (PW)
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Abstract
The etiology of colon cancer is complex, yet it is undoubtedly impacted by intestinal microbiota. Whether the contribution to colon carcinogenesis is generated through the presence of an overall dysbiosis or by specific pathogens is still a matter for debate. However, it is apparent that interactions between microbiota and the host are mediated by a variety of processes, including signaling cascades, the immune system, host metabolism, and regulation of gene transcription. To fully appreciate the role of microbiota in colon carcinogenesis, it will be necessary to expand efforts to define populations in niche environments, such as colonic crypts, explore cross talk between the host and the microbiota, and more completely define the metabolomic profile of the microbiota. These efforts must be pursued with appreciation that dietary substrates and other environmental modifiers mediate changes in the microbiota, as well as their metabolism and functional characteristics.
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Health promoting effects of brassica-derived phytochemicals: from chemopreventive and anti-inflammatory activities to epigenetic regulation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2013; 2013:964539. [PMID: 24454992 PMCID: PMC3885109 DOI: 10.1155/2013/964539] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 11/20/2013] [Indexed: 12/19/2022]
Abstract
A high intake of brassica vegetables may be associated with a decreased chronic disease risk. Health promoting effects of Brassicaceae have been partly attributed to glucosinolates and in particular to their hydrolyzation products including isothiocyanates. In vitro and in vivo studies suggest a chemopreventive activity of isothiocyanates through the redox-sensitive transcription factor Nrf2. Furthermore, studies in cultured cells, in laboratory rodents, and also in humans support an anti-inflammatory effect of brassica-derived phytochemicals. However, the underlying mechanisms of how these compounds mediate their health promoting effects are yet not fully understood. Recent findings suggest that brassica-derived compounds are regulators of epigenetic mechanisms. It has been shown that isothiocyanates may inhibit histone deacetylase transferases and DNA-methyltransferases in cultured cells. Only a few papers have dealt with the effect of brassica-derived compounds on epigenetic mechanisms in laboratory animals, whereas data in humans are currently lacking. The present review aims to summarize the current knowledge regarding the biological activities of brassica-derived phytochemicals regarding chemopreventive, anti-inflammatory, and epigenetic pathways.
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What We Have Learned about Autism Spectrum Disorder from Valproic Acid. PATHOLOGY RESEARCH INTERNATIONAL 2013; 2013:712758. [PMID: 24381784 PMCID: PMC3871912 DOI: 10.1155/2013/712758] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/16/2013] [Accepted: 10/17/2013] [Indexed: 12/29/2022]
Abstract
Two recent epidemiological investigations in children exposed to valproic acid (VPA) treatment in utero have reported a significant risk associated with neurodevelopmental disorders and autism spectrum disorder (ASD) in particular. Parallel to this work, there is a growing body of animal research literature using VPA as an animal model of ASD. In this focused review we first summarize the epidemiological evidence linking VPA to ASD and then comment on two important neurobiological findings linking VPA to ASD clinicopathology, namely, accelerated or early brain overgrowth and hyperexcitable networks. Improving our understanding of how the drug VPA can alter early development of neurological systems will ultimately improve our understanding of ASD.
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Schilderink R, Verseijden C, de Jonge WJ. Dietary inhibitors of histone deacetylases in intestinal immunity and homeostasis. Front Immunol 2013; 4:226. [PMID: 23914191 PMCID: PMC3730085 DOI: 10.3389/fimmu.2013.00226] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Accepted: 07/18/2013] [Indexed: 12/31/2022] Open
Abstract
Intestinal epithelial cells (IECs) are integral players in homeostasis of immunity and host defense in the gut and are under influence of the intestinal microbiome. Microbial metabolites and dietary components, including short chain fatty acids (acetate, propionate, and butyrate, SCFAs), have an impact on the physiology of IECs at multiple levels, including the inhibition of deacetylases affecting chromatin remodeling and global changes in transcriptional activity. The number and diversity of butyrate-producing bacteria is subject to factors related to age, disease, and to diet. At physiological levels, SCFAs are inhibitors of histone deacetylases (HDACs) which may explain the transcriptional effects of SCFAs on epithelial cells, although many effects of SCFAs on colonic mucosa can be ascribed to mechanisms beyond HDAC inhibition. Interference with this type of post-translational modification has great potential in cancer and different inflammatory diseases, because HDAC inhibition has anti-proliferative and anti-inflammatory effects in vitro, and in in vivo models of intestinal inflammation. Hence, the influence of dietary modulators on HDAC activity in epithelia is likely to be an important determinant of its responses to inflammatory and microbial challenges.
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Affiliation(s)
- R Schilderink
- Tytgat Institute for Liver and Intestinal Research, Department of Gastroenterology and Hepatology, Academic Medical Center , Amsterdam , Netherlands
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Rajendran P, Kidane AI, Yu TW, Dashwood WM, Bisson WH, Löhr CV, Ho E, Williams DE, Dashwood RH. HDAC turnover, CtIP acetylation and dysregulated DNA damage signaling in colon cancer cells treated with sulforaphane and related dietary isothiocyanates. Epigenetics 2013; 8:612-23. [PMID: 23770684 PMCID: PMC3857341 DOI: 10.4161/epi.24710] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Histone deacetylases (HDACs) and acetyltransferases have important roles in the regulation of protein acetylation, chromatin dynamics and the DNA damage response. Here, we show in human colon cancer cells that dietary isothiocyanates (ITCs) inhibit HDAC activity and increase HDAC protein turnover with the potency proportional to alkyl chain length, i.e., AITC < sulforaphane (SFN) < 6-SFN < 9-SFN. Molecular docking studies provided insights into the interactions of ITC metabolites with HDAC3, implicating the allosteric site between HDAC3 and its co-repressor. ITCs induced DNA double-strand breaks and enhanced the phosphorylation of histone H2AX, ataxia telangiectasia and Rad3-related protein (ATR) and checkpoint kinase-2 (CHK2). Depending on the ITC and treatment conditions, phenotypic outcomes included cell growth arrest, autophagy and apoptosis. Coincident with the loss of HDAC3 and HDAC6, as well as SIRT6, ITCs enhanced the acetylation and subsequent degradation of critical repair proteins, such as CtIP, and this was recapitulated in HDAC knockdown experiments. Importantly, colon cancer cells were far more susceptible than non-cancer cells to ITC-induced DNA damage, which persisted in the former case but was scarcely detectable in non-cancer colonic epithelial cells under the same conditions. Future studies will address the mechanistic basis for dietary ITCs preferentially exploiting HDAC turnover mechanisms and faulty DNA repair pathways in colon cancer cells vs. normal cells.
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Steliou K, Boosalis MS, Perrine SP, Sangerman J, Faller DV. Butyrate histone deacetylase inhibitors. Biores Open Access 2013; 1:192-8. [PMID: 23514803 PMCID: PMC3559235 DOI: 10.1089/biores.2012.0223] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In addition to being a part of the metabolic fatty acid fuel cycle, butyrate is also capable of inducing growth arrest in a variety of normal cell types and senescence-like phenotypes in gynecological cancer cells, inhibiting DNA synthesis and cell growth in colonic tumor cell lines, suppressing hTERT mRNA expression and telomerase activity in human prostate cancer cells, and inducing stem cell differentiation and apoptosis by DNA fragmentation. It regulates gene expression by inhibiting histone deacetylases (HDACs), enhances memory recovery and formation in mice, stimulates neurogenesis in the ischemic brain, promotes osteoblast formation, selectively blocks cell replication in transformed cells (compared to healthy cells), and can prevent and treat diet-induced obesity and insulin resistance in mouse models of obesity, as well as stimulate fetal hemoglobin expression in individuals with hematologic diseases such as the thalassemias and sickle-cell disease, in addition to a multitude of other biochemical effects in vivo. However, efforts to exploit the potential of butyrate in the clinical treatment of cancer and other medical disorders are thwarted by its poor pharmacological properties (short half-life and first-pass hepatic clearance) and the multigram doses needed to achieve therapeutic concentrations in vivo. Herein, we review some of the methods used to overcome these difficulties with an emphasis on HDAC inhibition.
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Affiliation(s)
- Kosta Steliou
- PhenoMatriX, Inc. , Boston, Massachusetts. ; Cancer Research Center, Boston University School of Medicine , Boston, Massachusetts
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Russo D, Durante C, Bulotta S, Puppin C, Puxeddu E, Filetti S, Damante G. Targeting histone deacetylase in thyroid cancer. Expert Opin Ther Targets 2012; 17:179-93. [DOI: 10.1517/14728222.2013.740013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Simpson NE, Tryndyak VP, Pogribna M, Beland FA, Pogribny IP. Modifying metabolically sensitive histone marks by inhibiting glutamine metabolism affects gene expression and alters cancer cell phenotype. Epigenetics 2012; 7:1413-20. [PMID: 23117580 PMCID: PMC3528696 DOI: 10.4161/epi.22713] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The interplay of metabolism and epigenetic regulatory mechanisms has become a focal point for a better understanding of cancer development and progression. In this study, we have acquired data supporting previous observations that demonstrate glutamine metabolism affects histone modifications in human breast cancer cell lines. Treatment of non-invasive epithelial (T-47D and MDA-MB-361) and invasive mesenchymal (MDA-MB-231 and Hs-578T) breast cancer cell lines with the glutaminase inhibitor, Compound 968, resulted in cytotoxicity in all cell lines, with the greatest effect being observed in MDA-MB-231 breast cancer cells. Compound 968-treatment induced significant downregulation of 20 critical cancer-related genes, the majority of which are anti-apoptotic and/or promote metastasis, including AKT, BCL2, BCL2L1, CCND1, CDKN3, ERBB2, ETS1, E2F1, JUN, KITLG, MYB, and MYC. Histone H3K4me3, a mark of transcriptional activation, was reduced at the promoters of all but one of these critical cancer genes. The decrease in histone H3K4me3 at global and gene-specific levels correlated with reduced expression of SETD1 and ASH2L, genes encoding the histone H3K4 methyltransferase complex. Further, the expression of other epigenetic regulatory genes, known to be downregulated during apoptosis (e.g., DNMT1, DNMT3B, SETD1 and SIRT1), was also downregulated by Compound 968. These changes in gene expression and histone modifications were accompanied by the activation of apoptosis, and decreased invasiveness and resistance of MDA-MB-231 cells to chemotherapeutic drug doxorubicin. The results of this study provide evidence to a link between cytotoxicity caused by inhibiting glutamine metabolism with alterations of the epigenome of breast cancer cells and suggest that modification of intracellular metabolism may enhance the efficiency of epigenetic therapy.
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Affiliation(s)
- Natalie E. Simpson
- Division of Biochemical Toxicology; National Center for Toxicological Research; Jefferson, AR USA
| | - Volodymyr P. Tryndyak
- Division of Biochemical Toxicology; National Center for Toxicological Research; Jefferson, AR USA
| | - Marta Pogribna
- Division of Biochemical Toxicology; National Center for Toxicological Research; Jefferson, AR USA
| | - Frederick A. Beland
- Division of Biochemical Toxicology; National Center for Toxicological Research; Jefferson, AR USA
| | - Igor P. Pogribny
- Division of Biochemical Toxicology; National Center for Toxicological Research; Jefferson, AR USA
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Bergersen LH, Gjedde A. Is lactate a volume transmitter of metabolic states of the brain? FRONTIERS IN NEUROENERGETICS 2012; 4:5. [PMID: 22457647 PMCID: PMC3307048 DOI: 10.3389/fnene.2012.00005] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Accepted: 03/01/2012] [Indexed: 11/13/2022]
Abstract
We present the perspective that lactate is a volume transmitter of cellular signals in brain that acutely and chronically regulate the energy metabolism of large neuronal ensembles. From this perspective, we interpret recent evidence to mean that lactate transmission serves the maintenance of network metabolism by two different mechanisms, one by regulating the formation of cAMP via the lactate receptor GPR81, the other by adjusting the NADH/NAD(+) redox ratios, both linked to the maintenance of brain energy turnover and possibly cerebral blood flow. The role of lactate as mediator of metabolic information rather than metabolic substrate answers a number of questions raised by the controversial oxidativeness of astrocytic metabolism and its contribution to neuronal function.
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Affiliation(s)
- Linda H Bergersen
- The Brain and Muscle Energy Group, Centre for Molecular Biology and Neuroscience, Institute for Basic Medical Sciences, University of Oslo, Oslo, Norway
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