1
|
Chung MY, Kim BH. Fatty acids and epigenetics in health and diseases. Food Sci Biotechnol 2024; 33:3153-3166. [PMID: 39328231 PMCID: PMC11422405 DOI: 10.1007/s10068-024-01664-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 07/08/2024] [Accepted: 07/17/2024] [Indexed: 09/28/2024] Open
Abstract
Lipids are crucial for human health and reproduction and include diverse fatty acids (FAs), notably polyunsaturated FAs (PUFAs) and short-chain FAs (SCFAs) that are known for their health benefits. Bioactivities of PUFAs, including ω-6 and ω-3 FAs as well as SCFAs, have been widely studied in various tissues and diseases. Epigenetic regulation has been suggested as a significant mechanism affecting the progression of various diseases, including cancers and metabolic and inflammatory diseases. Epigenetics encompasses the reversible modulation of gene expression without altering the DNA sequence itself, mediated by mechanisms such as DNA methylation, histone acetylation, and chromatin remodeling. Bioactive FAs have been demonstrated to regulate gene expression via epigenetic modifications that are potentially important for modulating metabolic control and disease risk. This review paper discusses the evidence in support of bioactive FAs, including ω-6 and ω-3 FAs and SCFAs, eliciting various disease prevention via epigenetic regulation including methylation or acetylation. Graphical abstract
Collapse
Affiliation(s)
- Min-Yu Chung
- Department of Food and Nutrition, Gangseo University, Seoul, 07661 Republic of Korea
| | - Byung Hee Kim
- Department of Food and Nutrition, Sookmyung Women’s University, Seoul, 04310 Republic of Korea
| |
Collapse
|
2
|
Kremer M, Schulze S, Eisenbruch N, Nagel F, Vogt R, Berndt L, Dörre B, Palm GJ, Hoppen J, Girbardt B, Albrecht D, Sievers S, Delcea M, Baumann U, Schnetz K, Lammers M. Bacteria employ lysine acetylation of transcriptional regulators to adapt gene expression to cellular metabolism. Nat Commun 2024; 15:1674. [PMID: 38395951 PMCID: PMC10891134 DOI: 10.1038/s41467-024-46039-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
The Escherichia coli TetR-related transcriptional regulator RutR is involved in the coordination of pyrimidine and purine metabolism. Here we report that lysine acetylation modulates RutR function. Applying the genetic code expansion concept, we produced site-specifically lysine-acetylated RutR proteins. The crystal structure of lysine-acetylated RutR reveals how acetylation switches off RutR-DNA-binding. We apply the genetic code expansion concept in E. coli in vivo revealing the consequences of RutR acetylation on the transcriptional level. We propose a model in which RutR acetylation follows different kinetic profiles either reacting non-enzymatically with acetyl-phosphate or enzymatically catalysed by the lysine acetyltransferases PatZ/YfiQ and YiaC. The NAD+-dependent sirtuin deacetylase CobB reverses enzymatic and non-enzymatic acetylation of RutR playing a dual regulatory and detoxifying role. By detecting cellular acetyl-CoA, NAD+ and acetyl-phosphate, bacteria apply lysine acetylation of transcriptional regulators to sense the cellular metabolic state directly adjusting gene expression to changing environmental conditions.
Collapse
Affiliation(s)
- Magdalena Kremer
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Sabrina Schulze
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Nadja Eisenbruch
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Felix Nagel
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Robert Vogt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Leona Berndt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Babett Dörre
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Gottfried J Palm
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Jens Hoppen
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Britta Girbardt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Dirk Albrecht
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Susanne Sievers
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Mihaela Delcea
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Karin Schnetz
- Institute for Genetics, University of Cologne Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Michael Lammers
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
| |
Collapse
|
3
|
Delphin N, Aust C, Griffiths L, Fernandez F. Epigenetic Regulation in Schizophrenia: Focus on Methylation and Histone Modifications in Human Studies. Genes (Basel) 2024; 15:272. [PMID: 38540331 PMCID: PMC10970389 DOI: 10.3390/genes15030272] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 06/15/2024] Open
Abstract
Despite extensive research over the last few decades, the etiology of schizophrenia (SZ) remains unclear. SZ is a pathological disorder that is highly debilitating and deeply affects the lifestyle and minds of those affected. Several factors (one or in combination) have been reported as contributors to SZ pathogenesis, including neurodevelopmental, environmental, genetic and epigenetic factors. Deoxyribonucleic acid (DNA) methylation and post-translational modification (PTM) of histone proteins are potentially contributing epigenetic processes involved in transcriptional activity, chromatin folding, cell division and apoptotic processes, and DNA damage and repair. After establishing a summary of epigenetic processes in the context of schizophrenia, this review aims to highlight the current understanding of the role of DNA methylation and histone PTMs in this disorder and their potential roles in schizophrenia pathophysiology and pathogenesis.
Collapse
Affiliation(s)
- Natasha Delphin
- School of Health and Behavioural Sciences, Faculty of Health Sciences, Australian Catholic University, 1100 Nudgee Rd, Banyo, QLD 4014, Australia; (N.D.)
| | - Caitlin Aust
- School of Health and Behavioural Sciences, Faculty of Health Sciences, Australian Catholic University, 1100 Nudgee Rd, Banyo, QLD 4014, Australia; (N.D.)
| | - Lyn Griffiths
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia;
| | - Francesca Fernandez
- School of Health and Behavioural Sciences, Faculty of Health Sciences, Australian Catholic University, 1100 Nudgee Rd, Banyo, QLD 4014, Australia; (N.D.)
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia;
- Healthy Brain and Mind Research Centre, Australian Catholic University, Melbourne, VIC 3000, Australia
| |
Collapse
|
4
|
Wu KJ, Chen Q, Leung CH, Sun N, Gao F, Chen Z. Recent discoveries of the role of histone modifications and related inhibitors in pathological cardiac hypertrophy. Drug Discov Today 2024; 29:103878. [PMID: 38211819 DOI: 10.1016/j.drudis.2024.103878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/19/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Pathological cardiac hypertrophy is a common response of the heart to various pathological stimuli. In recent years, various histone modifications, including acetylation, methylation, phosphorylation and ubiquitination, have been identified to have crucial roles in regulating chromatin remodeling and cardiac hypertrophy. Novel drugs targeting these epigenetic changes have emerged as potential treatments for pathological cardiac hypertrophy. In this review, we provide a comprehensive summary of the roles of histone modifications in regulating the development of pathological cardiac hypertrophy, and discuss potential therapeutic targets that could be utilized for its treatment.
Collapse
Affiliation(s)
- Ke-Jia Wu
- Wuxi School of Medicine, Jiangnan University, Jiangsu 214082, PR China
| | - Qi Chen
- Wuxi School of Medicine, Jiangnan University, Jiangsu 214082, PR China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa 999078, Macau; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau; Macao Centre for Research and Development in Chinese Medicine, University of Macau, Taipa 999078, Macau; MoE Frontiers Science Centre for Precision Oncology, University of Macau, Taipa 999078, Macau.
| | - Ning Sun
- Wuxi School of Medicine, Jiangnan University, Jiangsu 214082, PR China.
| | - Fei Gao
- Department of Cardiology, Beijing An Zhen Hospital, Capital Medical University, Chaoyang District, Beijing 100029, PR China.
| | - Zhaoyang Chen
- Department of Cardiology, Heart Center of Fujian Province, Fujian Medical University Union Hospital, 29 Xin-Quan Road, Fuzhou, Fujian 350001, PR China.
| |
Collapse
|
5
|
Patel AB, He Y, Radhakrishnan I. Histone acetylation and deacetylation - Mechanistic insights from structural biology. Gene 2024; 890:147798. [PMID: 37726026 PMCID: PMC11253779 DOI: 10.1016/j.gene.2023.147798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/29/2023] [Accepted: 09/11/2023] [Indexed: 09/21/2023]
Abstract
Histones are subject to a diverse array of post-translational modifications. Among them, lysine acetylation is not only the most pervasive and dynamic modification but also highly consequential for regulating gene transcription. Although enzymes responsible for the addition and removal of acetyl groups were discovered almost 30 years ago, high-resolution structures of the enzymes in the context of their native complexes are only now beginning to become available, thanks to revolutionary technologies in protein structure determination and prediction. Here, we will review our current understanding of the molecular mechanisms of acetylation and deacetylation engendered by chromatin-modifying complexes, compare and contrast shared features, and discuss some of the pressing questions for future studies.
Collapse
Affiliation(s)
- Avinash B Patel
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Yuan He
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Ishwar Radhakrishnan
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| |
Collapse
|
6
|
Cao HY, Li L, Xue SL, Dai HP. Chidamide: Targeting epigenetic regulation in the treatment of hematological malignancy. Hematol Oncol 2023; 41:301-309. [PMID: 36251458 DOI: 10.1002/hon.3088] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/02/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
Epigenetic alterations frequently participate in the onset of hematological malignancies. Histone deacetylases (HDACs) are essential for regulating gene transcription and various signaling pathways. Targeting HDACs has become a novel treatment option for hematological malignancies. Chidamide is the first oral selective HDAC inhibitor for HDAC1, HDAC2, HDAC3, and HDAC10 and was first approved for the treatment of R/R peripheral T-cell lymphoma by the China Food and Drug Administration in 2014. Chidamide was also approved under the name Hiyasta (HBI-8000) in Japan in 2021. In vitro studies revealed that chidamide could inhibit proliferation and induce apoptosis via cell cycle arrest and the regulation of apoptotic proteins. In clinical studies, chidamide was also efficacious in multiple myeloma, acute leukemia and myelodysplastic syndrome. This review includes reported experimental and clinical data on chidamide monotherapy or chidamide treatment in combination with chemotherapy for various hematological malignancies, offering a rationale for the renewed exploration of this drug.
Collapse
Affiliation(s)
- Han-Yu Cao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ling Li
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, California, USA
| | - Sheng-Li Xue
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hai-Ping Dai
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| |
Collapse
|
7
|
Stein RA, Riber L. Epigenetic effects of short-chain fatty acids from the large intestine on host cells. MICROLIFE 2023; 4:uqad032. [PMID: 37441522 PMCID: PMC10335734 DOI: 10.1093/femsml/uqad032] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/04/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
Adult humans harbor at least as many microbial cells as eukaryotic ones. The largest compartment of this diverse microbial population, the gut microbiota, encompasses the collection of bacteria, archaea, viruses, and eukaryotic organisms that populate the gastrointestinal tract, and represents a complex and dynamic ecosystem that has been increasingly implicated in health and disease. The gut microbiota carries ∼100-to-150-times more genes than the human genome and is intimately involved in development, homeostasis, and disease. Of the several microbial metabolites that have been studied, short-chain fatty acids emerge as a group of molecules that shape gene expression in several types of eukaryotic cells by multiple mechanisms, which include DNA methylation changes, histone post-translational modifications, and microRNA-mediated gene silencing. Butyric acid, one of the most extensively studied short-chain fatty acids, reaches higher concentrations in the colonic lumen, where it provides a source of energy for healthy colonocytes, and its concentrations decrease towards the bottom of the colonic crypts, where stem cells reside. The lower butyric acid concentration in the colonic crypts allows undifferentiated cells, such as stem cells, to progress through the cell cycle, pointing towards the importance of the crypts in providing them with a protective niche. In cancerous colonocytes, which metabolize relatively little butyric acid and mostly rely on glycolysis, butyric acid preferentially acts as a histone deacetylase inhibitor, leading to decreased cell proliferation and increased apoptosis. A better understanding of the interface between the gut microbiota metabolites and epigenetic changes in eukaryotic cells promises to unravel in more detail processes that occur physiologically and as part of disease, help develop novel biomarkers, and identify new therapeutic modalities.
Collapse
Affiliation(s)
- Richard A Stein
- Corresponding author. Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA. Tel: +1-917-684-9438; E-mail: ;
| | - Leise Riber
- Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| |
Collapse
|
8
|
Yang J, Xu J, Wang W, Zhang B, Yu X, Shi S. Epigenetic regulation in the tumor microenvironment: molecular mechanisms and therapeutic targets. Signal Transduct Target Ther 2023; 8:210. [PMID: 37217462 DOI: 10.1038/s41392-023-01480-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/17/2023] [Accepted: 04/28/2023] [Indexed: 05/24/2023] Open
Abstract
Over decades, researchers have focused on the epigenetic control of DNA-templated processes. Histone modification, DNA methylation, chromatin remodeling, RNA modification, and noncoding RNAs modulate many biological processes that are crucial to the development of cancers. Dysregulation of the epigenome drives aberrant transcriptional programs. A growing body of evidence suggests that the mechanisms of epigenetic modification are dysregulated in human cancers and might be excellent targets for tumor treatment. Epigenetics has also been shown to influence tumor immunogenicity and immune cells involved in antitumor responses. Thus, the development and application of epigenetic therapy and cancer immunotherapy and their combinations may have important implications for cancer treatment. Here, we present an up-to-date and thorough description of how epigenetic modifications in tumor cells influence immune cell responses in the tumor microenvironment (TME) and how epigenetics influence immune cells internally to modify the TME. Additionally, we highlight the therapeutic potential of targeting epigenetic regulators for cancer immunotherapy. Harnessing the complex interplay between epigenetics and cancer immunology to develop therapeutics that combine thereof is challenging but could yield significant benefits. The purpose of this review is to assist researchers in understanding how epigenetics impact immune responses in the TME, so that better cancer immunotherapies can be developed.
Collapse
Affiliation(s)
- Jing Yang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Bo Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Shanghai Pancreatic Cancer Institute, Shanghai, China.
- Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Shanghai Pancreatic Cancer Institute, Shanghai, China.
- Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| |
Collapse
|
9
|
Moena D, Vargas E, Montecino M. Epigenetic regulation during 1,25-dihydroxyvitamin D 3-dependent gene transcription. VITAMINS AND HORMONES 2023; 122:51-74. [PMID: 36863801 DOI: 10.1016/bs.vh.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Multiple evidence accumulated over the years, demonstrates that vitamin D-dependent physiological control in vertebrates occurs primarily through the regulation of target gene transcription. In addition, there has been an increasing appreciation of the role of the chromatin organization of the genome on the ability of the active form of vitamin D, 1,25(OH)2D3, and its specific receptor VDR to regulate gene expression. Chromatin structure in eukaryotic cells is principally modulated through epigenetic mechanisms including, but not limited to, a wide number of post-translational modifications of histone proteins and ATP-dependent chromatin remodelers, which are operative in different tissues during response to physiological cues. Hence, there is necessity to understand in depth the epigenetic control mechanisms that operate during 1,25(OH)2D3-dependent gene regulation. This chapter provides a general overview about epigenetic mechanisms functioning in mammalian cells and discusses how some of these mechanisms represent important components during transcriptional regulation of the model gene system CYP24A1 in response to 1,25(OH)2D3.
Collapse
Affiliation(s)
- Daniel Moena
- School of Bachelor in Science, Faculty of Life Sciences, Universidad Andres Bello, Concepcion, Chile
| | - Esther Vargas
- School of Medicine, Universidad Andres Bello, Santiago, Chile
| | - Martin Montecino
- Institute of Biomedical Sciences, Faculty of Medicine, Universidad Andres Bello, Santiago, Chile; Millenium Institute Center for Genome Regulation (CRG), Santiago, Chile.
| |
Collapse
|
10
|
Liu Y, Wen D, Ho C, Yu L, Zheng D, O'Reilly S, Gao Y, Li Q, Zhang Y. Epigenetics as a versatile regulator of fibrosis. J Transl Med 2023; 21:164. [PMID: 36864460 PMCID: PMC9983257 DOI: 10.1186/s12967-023-04018-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Fibrosis, a process caused by excessive deposition of extracellular matrix (ECM), is a common cause and outcome of organ failure and even death. Researchers have made many efforts to understand the mechanism of fibrogenesis and to develop therapeutic strategies; yet, the outcome remains unsatisfactory. In recent years, advances in epigenetics, including chromatin remodeling, histone modification, DNA methylation, and noncoding RNA (ncRNA), have provided more insights into the fibrotic process and have suggested the possibility of novel therapy for organ fibrosis. In this review, we summarize the current research on the epigenetic mechanisms involved in organ fibrosis and their possible clinical applications.
Collapse
Affiliation(s)
- Yangdan Liu
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Dongsheng Wen
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Chiakang Ho
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Li Yu
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Danning Zheng
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | | | - Ya Gao
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China.
| | - Qingfeng Li
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China.
| | - Yifan Zhang
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China.
| |
Collapse
|
11
|
Kumar A, Emdad L, Fisher PB, Das SK. Targeting epigenetic regulation for cancer therapy using small molecule inhibitors. Adv Cancer Res 2023; 158:73-161. [PMID: 36990539 DOI: 10.1016/bs.acr.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Cancer cells display pervasive changes in DNA methylation, disrupted patterns of histone posttranslational modification, chromatin composition or organization and regulatory element activities that alter normal programs of gene expression. It is becoming increasingly clear that disturbances in the epigenome are hallmarks of cancer, which are targetable and represent attractive starting points for drug creation. Remarkable progress has been made in the past decades in discovering and developing epigenetic-based small molecule inhibitors. Recently, epigenetic-targeted agents in hematologic malignancies and solid tumors have been identified and these agents are either in current clinical trials or approved for treatment. However, epigenetic drug applications face many challenges, including low selectivity, poor bioavailability, instability and acquired drug resistance. New multidisciplinary approaches are being designed to overcome these limitations, e.g., applications of machine learning, drug repurposing, high throughput virtual screening technologies, to identify selective compounds with improved stability and better bioavailability. We provide an overview of the key proteins that mediate epigenetic regulation that encompass histone and DNA modifications and discuss effector proteins that affect the organization of chromatin structure and function as well as presently available inhibitors as potential drugs. Current anticancer small-molecule inhibitors targeting epigenetic modified enzymes that have been approved by therapeutic regulatory authorities across the world are highlighted. Many of these are in different stages of clinical evaluation. We also assess emerging strategies for combinatorial approaches of epigenetic drugs with immunotherapy, standard chemotherapy or other classes of agents and advances in the design of novel epigenetic therapies.
Collapse
|
12
|
van Zundert B, Montecino M. Epigenetic Changes and Chromatin Reorganization in Brain Function: Lessons from Fear Memory Ensemble and Alzheimer’s Disease. Int J Mol Sci 2022; 23:ijms232012081. [PMID: 36292933 PMCID: PMC9602769 DOI: 10.3390/ijms232012081] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Healthy brain functioning in mammals requires a continuous fine-tuning of gene expression. Accumulating evidence over the last three decades demonstrates that epigenetic mechanisms and dynamic changes in chromatin organization are critical components during the control of gene transcription in neural cells. Recent genome-wide analyses show that the regulation of brain genes requires the contribution of both promoter and long-distance enhancer elements, which must functionally interact with upregulated gene expression in response to physiological cues. Hence, a deep comprehension of the mechanisms mediating these enhancer–promoter interactions (EPIs) is critical if we are to understand the processes associated with learning, memory and recall. Moreover, the onset and progression of several neurodegenerative diseases and neurological alterations are found to be strongly associated with changes in the components that support and/or modulate the dynamics of these EPIs. Here, we overview relevant discoveries in the field supporting the role of the chromatin organization and of specific epigenetic mechanisms during the control of gene transcription in neural cells from healthy mice subjected to the fear conditioning paradigm, a relevant model to study memory ensemble. Additionally, special consideration is dedicated to revising recent results generated by investigators working with animal models and human postmortem brain tissue to address how changes in the epigenome and chromatin architecture contribute to transcriptional dysregulation in Alzheimer’s disease, a widely studied neurodegenerative disease. We also discuss recent developments of potential new therapeutic strategies involving epigenetic editing and small chromatin-modifying molecules (or epidrugs).
Collapse
Affiliation(s)
- Brigitte van Zundert
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile
- CARE Biomedical Research Center, Santiago 8330005, Chile
- Correspondence: (B.v.Z.); (M.M.)
| | - Martin Montecino
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370186, Chile
- Millennium Institute Center for Genome Regulation CRG, Santiago 8370186, Chile
- Correspondence: (B.v.Z.); (M.M.)
| |
Collapse
|
13
|
Han Y, Nie J, Wang DW, Ni L. Mechanism of histone deacetylases in cardiac hypertrophy and its therapeutic inhibitors. Front Cardiovasc Med 2022; 9:931475. [PMID: 35958418 PMCID: PMC9360326 DOI: 10.3389/fcvm.2022.931475] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/06/2022] [Indexed: 12/03/2022] Open
Abstract
Cardiac hypertrophy is a key process in cardiac remodeling development, leading to ventricle enlargement and heart failure. Recently, studies show the complicated relation between cardiac hypertrophy and epigenetic modification. Post-translational modification of histone is an essential part of epigenetic modification, which is relevant to multiple cardiac diseases, especially in cardiac hypertrophy. There is a group of enzymes related in the balance of histone acetylation/deacetylation, which is defined as histone acetyltransferase (HAT) and histone deacetylase (HDAC). In this review, we introduce an important enzyme family HDAC, a key regulator in histone deacetylation. In cardiac hypertrophy HDAC I downregulates the anti-hypertrophy gene expression, including Kruppel-like factor 4 (Klf4) and inositol-5 phosphatase f (Inpp5f), and promote the development of cardiac hypertrophy. On the contrary, HDAC II binds to myocyte-specific enhancer factor 2 (MEF2), inhibit the assemble ability to HAT and protect against cardiac hypertrophy. Under adverse stimuli such as pressure overload and calcineurin stimulation, the HDAC II transfer to cytoplasm, and MEF2 can bind to nuclear factor of activated T cells (NFAT) or GATA binding protein 4 (GATA4), mediating inappropriate gene expression. HDAC III, also known as SIRTs, can interact not only to transcription factors, but also exist interaction mechanisms to other HDACs, such as HDAC IIa. We also present the latest progress of HDAC inhibitors (HDACi), as a potential treatment target in cardiac hypertrophy.
Collapse
Affiliation(s)
- Yu Han
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Jiali Nie
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Dao Wen Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
- *Correspondence: Dao Wen Wang,
| | - Li Ni
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
- Li Ni,
| |
Collapse
|
14
|
Tan SYX, Zhang J, Tee WW. Epigenetic Regulation of Inflammatory Signaling and Inflammation-Induced Cancer. Front Cell Dev Biol 2022; 10:931493. [PMID: 35757000 PMCID: PMC9213816 DOI: 10.3389/fcell.2022.931493] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
Epigenetics comprise a diverse array of reversible and dynamic modifications to the cell’s genome without implicating any DNA sequence alterations. Both the external environment surrounding the organism, as well as the internal microenvironment of cells and tissues, contribute to these epigenetic processes that play critical roles in cell fate specification and organismal development. On the other hand, dysregulation of epigenetic activities can initiate and sustain carcinogenesis, which is often augmented by inflammation. Chronic inflammation, one of the major hallmarks of cancer, stems from proinflammatory cytokines that are secreted by tumor and tumor-associated cells in the tumor microenvironment. At the same time, inflammatory signaling can establish positive and negative feedback circuits with chromatin to modulate changes in the global epigenetic landscape. In this review, we provide an in-depth discussion of the interconnected crosstalk between epigenetics and inflammation, specifically how epigenetic mechanisms at different hierarchical levels of the genome control inflammatory gene transcription, which in turn enact changes within the cell’s epigenomic profile, especially in the context of inflammation-induced cancer.
Collapse
Affiliation(s)
- Shawn Ying Xuan Tan
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jieqiong Zhang
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Wee-Wei Tee
- Chromatin Dynamics and Disease Epigenetics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| |
Collapse
|
15
|
Gopinathan G, Diekwisch TGH. Epigenetics and Early Development. J Dev Biol 2022; 10:jdb10020026. [PMID: 35735917 PMCID: PMC9225096 DOI: 10.3390/jdb10020026] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023] Open
Abstract
The epigenome controls all aspect of eukaryotic development as the packaging of DNA greatly affects gene expression. Epigenetic changes are reversible and do not affect the DNA sequence itself but rather control levels of gene expression. As a result, the science of epigenetics focuses on the physical configuration of chromatin in the proximity of gene promoters rather than on the mechanistic effects of gene sequences on transcription and translation. In the present review we discuss three prominent epigenetic modifications, DNA methylation, histone methylation/acetylation, and the effects of chromatin remodeling complexes. Specifically, we introduce changes to the methylated state of DNA through DNA methyltransferases and DNA demethylases, discuss the effects of histone tail modifications such as histone acetylation and methylation on gene expression and present the functions of major ATPase subunit containing chromatin remodeling complexes. We also introduce examples of how changes in these epigenetic factors affect early development in humans and mice. In summary, this review provides an overview over the most important epigenetic mechanisms and provides examples of the dramatic effects of epigenetic changes in early mammalian development.
Collapse
|
16
|
Vanegas JAG, Pacule HB, Capitão RM, Correia CRD, Terra WC, Campos VP, Oliveira DF. Methyl Esters of ( E)-Cinnamic Acid: Activity against the Plant-Parasitic Nematode Meloidogyne incognita and In Silico Interaction with Histone Deacetylase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6624-6633. [PMID: 35622462 DOI: 10.1021/acs.jafc.1c08142] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
(E)-Cinnamaldehyde is very active against Meloidogyne incognita but has low persistence in soil. To circumvent this problem, esters of cinnamic acid were evaluated as a substitute for (E)-cinnamaldehyde. The best results under assays with M. incognita second-stage juveniles (J2) were obtained for the methyl esters of (E)-p-fluoro- (13), (E)-p-chloro- (14), and (E)-p-bromocinnamic acid (15), which showed lethal concentrations to 50% (LC50) J2 of 168, 95, and 216 μg/mL, respectively. Under the same conditions, the LC50 values for the nematicides carbofuran and fluensulfone were 160 and 34 μg/mL, respectively. Substances 13-15 were also active against nematode eggs, which account for most of the M. incognita population in the field. According to an in silico study, substances 13-15 can act against the nematode through inhibition of histone deacetylase. Therefore, esters 13-15 and histone deacetylase are potentially useful for the rational design of new nematicides for the control of M. incognita.
Collapse
Affiliation(s)
- Javier A G Vanegas
- Laboratório de Produtos Naturais, Departamento de Química, Universidade Federal de Lavras, CEP 37200-900 Lavras, Minas Gerais, Brazil
| | - Horácio B Pacule
- Laboratório de Produtos Naturais, Departamento de Química, Universidade Federal de Lavras, CEP 37200-900 Lavras, Minas Gerais, Brazil
| | - Rebeca M Capitão
- Laboratório de Química Orgânica, Departamento de Química, Universidade Estadual de Campinas, CEP 13083-970, Campinas, São Paulo, Brazil
| | - Carlos R D Correia
- Laboratório de Química Orgânica, Departamento de Química, Universidade Estadual de Campinas, CEP 13083-970, Campinas, São Paulo, Brazil
| | - Willian C Terra
- Laboratório de Nematologia, Departamento de Fitopatologia, Universidade Federal de Lavras, CEP 37200-900, Lavras, Minas Gerais, Brazil
| | - Vicente P Campos
- Laboratório de Nematologia, Departamento de Fitopatologia, Universidade Federal de Lavras, CEP 37200-900, Lavras, Minas Gerais, Brazil
| | - Denilson F Oliveira
- Laboratório de Produtos Naturais, Departamento de Química, Universidade Federal de Lavras, CEP 37200-900 Lavras, Minas Gerais, Brazil
| |
Collapse
|
17
|
Pellerito C, Emanuele S, Giuliano M, Fiore T. Organotin(IV) complexes with epigenetic modulator ligands: New promising candidates in cancer therapy. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.120901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
18
|
Shen M, Chen Z, Ming M, Cheng Z, Sun J, Liang J, Shang T, Zhang Q, Zhou S, Ji Y, Ding F. The acetylome of adult mouse sciatic nerve. J Neurochem 2022; 162:262-275. [PMID: 35585794 DOI: 10.1111/jnc.15648] [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: 11/26/2021] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022]
Abstract
Lysine acetylation is a reversible post-translational modification (PTM) involved in multiple physiological functions. Recent studies have demonstrated the involvement of protein acetylation in modulating the biology of Schwann cells (SCs) and regeneration of the peripheral nervous system (PNS). However, the mechanisms underlying these processes remain partially understood. Here, we characterized the acetylome of the mouse sciatic nerve (SN) and investigated the cellular distribution of acetylated proteins. We identified 483 acetylated proteins containing 1,442 acetylation modification sites in the SN of adult C57BL/6 mice. Bioinformatics suggested that these acetylated SN proteins were mainly located in the myelin sheath, mitochondrial inner membrane, and cytoskeleton, and highlighted the significant differences between the mouse SN and brain acetylome. Manual annotation further indicated that most acetylated proteins (> 45%) were associated with mitochondria, energy metabolism, and cytoskeleton and cell adhesion. We verified three newly discovered acetylation-modified proteins, including neurofilament light polypeptide (NEFL), neurofilament medium/high polypeptide (NFM/H), and periaxin (PRX). Immunofluorescence illustrated that the acetylated proteins, including acetylated alpha-tubulin, were mainly co-localized with S100-positive SCs. Herein, we provided a comprehensive acetylome for the mouse SN and demonstrated that acetylated proteins in the SN were predominantly located in SCs. These results will extend our understanding and promote further study of the role and mechanism of protein acetylation in SC development and PNS regeneration.
Collapse
Affiliation(s)
- Mi Shen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Zixin Chen
- Department of Immunology, College of Life science and Technology, Jinan University, Guangzhou, China
| | - Mengru Ming
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Zhenghui Cheng
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Junjie Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Jingyun Liang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Tongxin Shang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Qi Zhang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Songlin Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| | - Yuhua Ji
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China.,Department of Immunology, College of Life science and Technology, Jinan University, Guangzhou, China
| | - Fei Ding
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Jiangsu Clinical Medicine Center of Tissue Engineering and Nerve Injury Repair, Nantong University, Nantong, China
| |
Collapse
|
19
|
Liu J, Li JN, Wu H, Liu P. The Status and Prospects of Epigenetics in the Treatment of Lymphoma. Front Oncol 2022; 12:874645. [PMID: 35463343 PMCID: PMC9033274 DOI: 10.3389/fonc.2022.874645] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
The regulation of gene transcription by epigenetic modifications is closely related to many important life processes and is a hot research topic in the post-genomic era. Since the emergence of international epigenetic research in the 1990s, scientists have identified a variety of chromatin-modifying enzymes and recognition factors, and have systematically investigated their three-dimensional structures, substrate specificity, and mechanisms of enzyme activity regulation. Studies of the human tumor genome have revealed the close association of epigenetic factors with various malignancies, and we have focused more on mutations in epigenetically related regulatory enzymes and regulatory recognition factors in lymphomas. A number of studies have shown that epigenetic alterations are indeed widespread in the development and progression of lymphoma and understanding these mechanisms can help guide clinical efforts. In contrast to chemotherapy which induces cytotoxicity, epigenetic therapy has the potential to affect multiple cellular processes simultaneously, by reprogramming cells to achieve a therapeutic effect in lymphoma. Epigenetic monotherapy has shown promising results in previous clinical trials, and several epigenetic agents have been approved for use in the treatment of lymphoma. In addition, epigenetic therapies in combination with chemotherapy and/or immunotherapy have been used in various clinical trials. In this review, we present several important epigenetic modalities of regulation associated with lymphoma, summarize the corresponding epigenetic drugs in lymphoma, and look at the future of epigenetic therapies in lymphoma.
Collapse
Affiliation(s)
- Jiaxin Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Jia-Nan Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Hongyu Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Panpan Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| |
Collapse
|
20
|
Li W, Jones K, Burke TJ, Hossain MA, Lariscy L. Epigenetic Regulation of Nucleotide Excision Repair. Front Cell Dev Biol 2022; 10:847051. [PMID: 35465333 PMCID: PMC9023881 DOI: 10.3389/fcell.2022.847051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022] Open
Abstract
Genomic DNA is constantly attacked by a plethora of DNA damaging agents both from endogenous and exogenous sources. Nucleotide excision repair (NER) is the most versatile repair pathway that recognizes and removes a wide range of bulky and/or helix-distorting DNA lesions. Even though the molecular mechanism of NER is well studied through in vitro system, the NER process inside the cell is more complicated because the genomic DNA in eukaryotes is tightly packaged into chromosomes and compacted into a nucleus. Epigenetic modifications regulate gene activity and expression without changing the DNA sequence. The dynamics of epigenetic regulation play a crucial role during the in vivo NER process. In this review, we summarize recent advances in our understanding of the epigenetic regulation of NER.
Collapse
|
21
|
Gomathi K, Rohini M, Partridge NC, Selvamurugan N. Regulation of transforming growth factor-β1-stimulation of Runx2 acetylation for matrix metalloproteinase 13 expression in osteoblastic cells. Biol Chem 2022; 403:305-315. [PMID: 34643076 DOI: 10.1515/hsz-2021-0292] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 09/30/2021] [Indexed: 01/12/2023]
Abstract
Transforming growth factor beta 1 (TGF-β1) functions as a coupling factor between bone development and resorption. Matrix metalloproteinase 13 (MMP13) is important in bone remodeling, and skeletal dysplasia is caused by a deficiency in MMP13 expre-ssion. Runx2, a transcription factor is essential for bone development, and MMP13 is one of its target genes. TGF-β1 promoted Runx2 phosphorylation, which was necessary for MMP13 production in osteoblastic cells, as we previously shown. Since the phosphorylation of some proteins causes them to be degraded by the ubiquitin/proteasome pathway, we hypothesized that TGF-β1 might stabilize the phosphorylated Runx2 protein for its activity by other post-translational modification (PTM). This study demonstrated that TGF-β1-stimulated Runx2 acetylation in rat osteoblastic cells. p300, a histone acetyltransferase interacted with Runx2, and it promoted Runx2 acetylation upon TGF-β1-treatment in these cells. Knockdown of p300 decreased the TGF-β1-stimulated Runx2 acetylation and MMP13 expression in rat osteoblastic cells. TGF-β1-treatment stimulated the acetylated Runx2 bound at the MMP13 promoter, and knockdown of p300 reduced this effect in these cells. Overall, our studies identified the transcriptional regulation of MMP13 by TGF-β1 via Runx2 acetylation in rat osteoblastic cells, and these findings contribute to the knowledge of events presiding bone metabolism.
Collapse
Affiliation(s)
- Kanagaraj Gomathi
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Muthukumar Rohini
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Nicola C Partridge
- Department of Molecular Pathobiology, New York University College Dentistry, New York, NY, USA
| | - Nagarajan Selvamurugan
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| |
Collapse
|
22
|
Yildiz I, Yildiz BS. Computational Analysis of Histone Deacetylase 10 Mechanism by the ONIOM Method: A Complementary Approach to X-ray and Kinetics Studies. ACS OMEGA 2022; 7:6393-6402. [PMID: 35224400 PMCID: PMC8868106 DOI: 10.1021/acsomega.1c07055] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Histone deacetylase 10 (HDAC 10) catalyzes deacetylation of N8-acetylspermidine into spermidine in the cytosolic region of eukaryotic cells. Inhibition of HDAC 10 has clinical importance in certain types of cancers. Recently, X-ray crystal structures corresponding to the substrate-bound, tetrahedral intermediate-bound, and product-bound enzymes have been resolved using variant forms of humanized HDAC 10. Based on these structures, it was proposed that Y307 residue polarizes the carbonyl of the acetyl group in N8-acetylspermidine together with a zinc atom, which is coordinated by D174, H176, D267, and an H2O molecule. The H2O molecule undergoes nucleophilic addition to the carbonyl carbon of N8-acetylspermidine to form the tetrahedral intermediate. During this process, it is suggested that H136 acts as a general base to deprotonate the H2O molecule. It is further proposed that the protonation of the amide N atom of the tetrahedral intermediate by H137 causes the deacetylation forming the final products, spermidine and acetate ion. In this study, computational models based on the ONIOM method were employed to study the proposed mechanism for the two steps of the deacetylation process based on the crystal structure of the substrate-bound enzyme. The energy profiles of each step as well as the roles of the active site residues were investigated for the catalysis. The calculated activation barrier is in good agreement with the reported kcat value.
Collapse
Affiliation(s)
- Ibrahim Yildiz
- Chemistry
Department, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Banu Sizirici Yildiz
- CIVE
Department, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| |
Collapse
|
23
|
Tanemoto F, Mimura I. Therapies Targeting Epigenetic Alterations in Acute Kidney Injury-to-Chronic Kidney Disease Transition. Pharmaceuticals (Basel) 2022; 15:ph15020123. [PMID: 35215236 PMCID: PMC8877070 DOI: 10.3390/ph15020123] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 12/04/2022] Open
Abstract
Acute kidney injury (AKI) was previously thought to be a merely transient event; however, recent epidemiological evidence supports the existence of a causal relationship between AKI episodes and subsequent progression to chronic kidney disease (CKD). Although the pathophysiology of this AKI-to-CKD transition is not fully understood, it is mediated by the interplay among multiple components of the kidney including tubular epithelial cells, endothelial cells, pericytes, inflammatory cells, and myofibroblasts. Epigenetic alterations including histone modification, DNA methylation, non-coding RNAs, and chromatin conformational changes, are also expected to be largely involved in the pathophysiology as a “memory” of the initial injury that can persist and predispose to chronic progression of fibrosis. Each epigenetic modification has a great potential as a therapeutic target of AKI-to-CKD transition; timely and target-specific epigenetic interventions to the various temporal stages of AKI-to-CKD transition will be the key to future therapeutic applications in clinical practice. This review elaborates on the latest knowledge of each mechanism and the currently available therapeutic agents that target epigenetic modification in the context of AKI-to-CKD transition. Further studies will elucidate more detailed mechanisms and novel therapeutic targets of AKI-to-CKD transition.
Collapse
|
24
|
Jang S, Hwang J, Jeong HS. The Role of Histone Acetylation in Mesenchymal Stem Cell Differentiation. Chonnam Med J 2022; 58:6-12. [PMID: 35169553 PMCID: PMC8813658 DOI: 10.4068/cmj.2022.58.1.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 11/06/2022] Open
Abstract
The mechanism and action concerning epigenetic modifications, especially that of histone modifications, are not fully understood. However, it is clear that histone modifications play an essential role in several biological processes that are involved in cell proliferation and differentiation. In this article, we focused on how histone acetylation may result in differentiation into mesenchymal stem cells as well as histone acetylation function. Moreover, histone acetylation followed by the action of histone deacetylase inhibitors, which can result in the differentiation of stem cells into other types of cells such as adipocytes, chondrocytes, osteocytes, neurons, and other lineages, were also reviewed.
Collapse
Affiliation(s)
- Sujeong Jang
- Department of Physiology, Chonnam National University Medical School, Hwasun, Korea
| | - Jinsu Hwang
- Department of Physiology, Chonnam National University Medical School, Hwasun, Korea
| | - Han-Seong Jeong
- Department of Physiology, Chonnam National University Medical School, Hwasun, Korea
| |
Collapse
|
25
|
Tuong ZK, Stewart BJ, Guo SA, Clatworthy MR. Epigenetics and tissue immunity-Translating environmental cues into functional adaptations. Immunol Rev 2021; 305:111-136. [PMID: 34821397 DOI: 10.1111/imr.13036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 12/21/2022]
Abstract
There is an increasing appreciation that many innate and adaptive immune cell subsets permanently reside within non-lymphoid organs, playing a critical role in tissue homeostasis and defense. The best characterized are macrophages and tissue-resident T lymphocytes that work in concert with organ structural cells to generate appropriate immune responses and are functionally shaped by organ-specific environmental cues. The interaction of tissue epithelial, endothelial and stromal cells is also required to attract, differentiate, polarize and maintain organ immune cells in their tissue niche. All of these processes require dynamic regulation of cellular transcriptional programmes, with epigenetic mechanisms playing a critical role, including DNA methylation and post-translational histone modifications. A failure to appropriately regulate immune cell transcription inevitably results in inadequate or inappropriate immune responses and organ pathology. Here, with a focus on the mammalian kidney, an organ which generates differing regional environmental cues (including hypersalinity and hypoxia) due to its physiological functions, we will review the basic concepts of tissue immunity, discuss the technologies available to profile epigenetic modifications in tissue immune cells, including those that enable single-cell profiling, and consider how these mechanisms influence the development, phenotype, activation and function of different tissue immune cell subsets, as well as the immunological function of structural cells.
Collapse
Affiliation(s)
- Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Shuang Andrew Guo
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK.,Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| |
Collapse
|
26
|
Liu M, Guo L, Fu Y, Huo M, Qi Q, Zhao G. Bacterial protein acetylation and its role in cellular physiology and metabolic regulation. Biotechnol Adv 2021; 53:107842. [PMID: 34624455 DOI: 10.1016/j.biotechadv.2021.107842] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/22/2021] [Accepted: 10/03/2021] [Indexed: 12/28/2022]
Abstract
Protein acetylation is an evolutionarily conserved posttranslational modification. It affects enzyme activity, metabolic flux distribution, and other critical physiological and biochemical processes by altering protein size and charge. Protein acetylation may thus be a promising tool for metabolic regulation to improve target production and conversion efficiency in fermentation. Here we review the role of protein acetylation in bacterial physiology and metabolism and describe applications of protein acetylation in fermentation engineering and strategies for regulating acetylation status. Although protein acetylation has become a hot topic, the regulatory mechanisms have not been fully characterized. We propose future research directions in protein acetylation.
Collapse
Affiliation(s)
- Min Liu
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China; CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Likun Guo
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Yingxin Fu
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Meitong Huo
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China
| | - Guang Zhao
- State Key Laboratory of Microbial Technology, Shandong University, 266237 Qingdao, China; CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
| |
Collapse
|
27
|
He R, Dantas A, Riabowol K. Histone Acetyltransferases and Stem Cell Identity. Cancers (Basel) 2021; 13:2407. [PMID: 34067525 PMCID: PMC8156521 DOI: 10.3390/cancers13102407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/02/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
Acetylation of histones is a key epigenetic modification involved in transcriptional regulation. The addition of acetyl groups to histone tails generally reduces histone-DNA interactions in the nucleosome leading to increased accessibility for transcription factors and core transcriptional machinery to bind their target sequences. There are approximately 30 histone acetyltransferases and their corresponding complexes, each of which affect the expression of a subset of genes. Because cell identity is determined by gene expression profile, it is unsurprising that the HATs responsible for inducing expression of these genes play a crucial role in determining cell fate. Here, we explore the role of HATs in the maintenance and differentiation of various stem cell types. Several HAT complexes have been characterized to play an important role in activating genes that allow stem cells to self-renew. Knockdown or loss of their activity leads to reduced expression and or differentiation while particular HATs drive differentiation towards specific cell fates. In this study we review functions of the HAT complexes active in pluripotent stem cells, hematopoietic stem cells, muscle satellite cells, mesenchymal stem cells, neural stem cells, and cancer stem cells.
Collapse
Affiliation(s)
- Ruicen He
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (R.H.); (A.D.)
- Department of Molecular Genetics, Temerty School of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Arthur Dantas
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (R.H.); (A.D.)
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Karl Riabowol
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (R.H.); (A.D.)
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| |
Collapse
|
28
|
Vidaurre V, Chen X. Epigenetic regulation of drosophila germline stem cell maintenance and differentiation. Dev Biol 2021; 473:105-118. [PMID: 33610541 DOI: 10.1016/j.ydbio.2021.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/26/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022]
Abstract
Gametogenesis is one of the most extreme cellular differentiation processes that takes place in Drosophila male and female germlines. This process begins at the germline stem cell, which undergoes asymmetric cell division (ACD) to produce a self-renewed daughter that preserves its stemness and a differentiating daughter cell that undergoes epigenetic and genomic changes to eventually produce haploid gametes. Research in molecular genetics and cellular biology are beginning to take advantage of the continually advancing genomic tools to understand: (1) how germ cells are able to maintain their identity throughout the adult reproductive lifetime, and (2) undergo differentiation in a balanced manner. In this review, we focus on the epigenetic mechanisms that address these two questions through their regulation of germline-soma communication to ensure germline stem cell identity and activity.
Collapse
Affiliation(s)
- Velinda Vidaurre
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD, 21218, USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Baltimore, MD, 21218, USA.
| |
Collapse
|
29
|
Caballero‐Camino FJ, Rivilla I, Herraez E, Briz O, Santos‐Laso A, Izquierdo‐Sanchez L, Lee‐Law PY, Rodrigues PM, Munoz‐Garrido P, Jin S, Peixoto E, Richard S, Gradilone SA, Perugorria MJ, Esteller M, Bujanda L, Marin JJ, Banales JM, Cossío FP. Synthetic Conjugates of Ursodeoxycholic Acid Inhibit Cystogenesis in Experimental Models of Polycystic Liver Disease. Hepatology 2021; 73:186-203. [PMID: 32145077 PMCID: PMC7891670 DOI: 10.1002/hep.31216] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/11/2020] [Accepted: 02/23/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND AIMS Polycystic liver diseases (PLDs) are genetic disorders characterized by progressive development of symptomatic biliary cysts. Current surgical and pharmacological approaches are ineffective, and liver transplantation represents the only curative option. Ursodeoxycholic acid (UDCA) and histone deacetylase 6 inhibitors (HDAC6is) have arisen as promising therapeutic strategies, but with partial benefits. APPROACH AND RESULTS Here, we tested an approach based on the design, synthesis, and validation of a family of UDCA synthetic conjugates with selective HDAC6i capacity (UDCA-HDAC6i). Four UDCA-HDAC6i conjugates presented selective HDAC6i activity, UDCA-HDAC6i #1 being the most promising candidate. UDCA orientation within the UDCA-HDAC6i structure was determinant for HDAC6i activity and selectivity. Treatment of polycystic rats with UDCA-HDAC6i #1 reduced their hepatomegaly and cystogenesis, increased UDCA concentration, and inhibited HDAC6 activity in liver. In cystic cholangiocytes UDCA-HDAC6i #1 restored primary cilium length and exhibited potent antiproliferative activity. UDCA-HDAC6i #1 was actively transported into cells through BA and organic cation transporters. CONCLUSIONS These UDCA-HDAC6i conjugates open a therapeutic avenue for PLDs.
Collapse
Affiliation(s)
- Francisco J. Caballero‐Camino
- Department of Organic Chemistry ICenter of Innovation in Advanced Chemistry (ORFEO‐CINQA)University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU)Donostia International Physics Center (DIPC)Donostia‐San SebastianSpain,Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUPV/EHUDonostia‐San SebastianSpain
| | - Ivan Rivilla
- Department of Organic Chemistry ICenter of Innovation in Advanced Chemistry (ORFEO‐CINQA)University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU)Donostia International Physics Center (DIPC)Donostia‐San SebastianSpain
| | - Elisa Herraez
- Experimental Hepatology and Drug Targeting (HEVEFARM)Biomedical Research Institute of Salamanca (IBSAL)University of SalamancaSalamancaSpain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd)Carlos III National Institute of HealthMadridSpain
| | - Oscar Briz
- Experimental Hepatology and Drug Targeting (HEVEFARM)Biomedical Research Institute of Salamanca (IBSAL)University of SalamancaSalamancaSpain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd)Carlos III National Institute of HealthMadridSpain
| | - Alvaro Santos‐Laso
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUPV/EHUDonostia‐San SebastianSpain
| | - Laura Izquierdo‐Sanchez
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUPV/EHUDonostia‐San SebastianSpain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd)Carlos III National Institute of HealthMadridSpain
| | - Pui Y. Lee‐Law
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUPV/EHUDonostia‐San SebastianSpain
| | - Pedro M. Rodrigues
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUPV/EHUDonostia‐San SebastianSpain
| | - Patricia Munoz‐Garrido
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUPV/EHUDonostia‐San SebastianSpain
| | - Sujeong Jin
- The Hormel InstituteUniversity of MinnesotaAustinMN,Masonic Cancer CenterUniversity of MinnesotaMinneapolisMN
| | - Estanislao Peixoto
- The Hormel InstituteUniversity of MinnesotaAustinMN,Masonic Cancer CenterUniversity of MinnesotaMinneapolisMN
| | - Seth Richard
- The Hormel InstituteUniversity of MinnesotaAustinMN,Masonic Cancer CenterUniversity of MinnesotaMinneapolisMN
| | - Sergio A. Gradilone
- The Hormel InstituteUniversity of MinnesotaAustinMN,Masonic Cancer CenterUniversity of MinnesotaMinneapolisMN
| | - Maria J. Perugorria
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUPV/EHUDonostia‐San SebastianSpain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd)Carlos III National Institute of HealthMadridSpain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC)BarcelonaSpain,Centro de Investigacion Biomedica en Red Cancer (CIBERONC)MadridSpain,Institucio Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain,Physiological Sciences DepartmentSchool of Medicine and Health SciencesUniversity of Barcelona (UB)BarcelonaSpain
| | - Luis Bujanda
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUPV/EHUDonostia‐San SebastianSpain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd)Carlos III National Institute of HealthMadridSpain
| | - Jose J.G. Marin
- Experimental Hepatology and Drug Targeting (HEVEFARM)Biomedical Research Institute of Salamanca (IBSAL)University of SalamancaSalamancaSpain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd)Carlos III National Institute of HealthMadridSpain
| | - Jesus M. Banales
- Department of Liver and Gastrointestinal DiseasesBiodonostia Health Research InstituteDonostia University HospitalUPV/EHUDonostia‐San SebastianSpain,National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd)Carlos III National Institute of HealthMadridSpain,IKERBASQUEBasque Foundation for ScienceBilbaoSpain
| | - Fernando P. Cossío
- Department of Organic Chemistry ICenter of Innovation in Advanced Chemistry (ORFEO‐CINQA)University of the Basque Country/Euskal Herriko Unibertsitatea (UPV/EHU)Donostia International Physics Center (DIPC)Donostia‐San SebastianSpain
| |
Collapse
|
30
|
Epigenetic Regulation of Pulmonary Arterial Hypertension-Induced Vascular and Right Ventricular Remodeling: New Opportunities? Int J Mol Sci 2020; 21:ijms21238901. [PMID: 33255338 PMCID: PMC7727715 DOI: 10.3390/ijms21238901] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022] Open
Abstract
Pulmonary artery hypertension (PAH) is a rare chronic disease with high impact on patients’ quality of life and currently no available cure. PAH is characterized by constant remodeling of the pulmonary artery by increased proliferation and migration of pulmonary arterial smooth muscle cells (PASMCs), fibroblasts (FBs) and endothelial cells (ECs). This remodeling eventually leads to increased pressure in the right ventricle (RV) and subsequent right ventricle hypertrophy (RVH) which, when left untreated, progresses into right ventricle failure (RVF). PAH can not only originate from heritable mutations, but also develop as a consequence of congenital heart disease, exposure to drugs or toxins, HIV, connective tissue disease or be idiopathic. While much attention was drawn into investigating and developing therapies related to the most well understood signaling pathways in PAH, in the last decade, a shift towards understanding the epigenetic mechanisms driving the disease occurred. In this review, we reflect on the different epigenetic regulatory factors that are associated with the pathology of RV remodeling, and on their relevance towards a better understanding of the disease and subsequently, the development of new and more efficient therapeutic strategies.
Collapse
|
31
|
Montalvo-Casimiro M, González-Barrios R, Meraz-Rodriguez MA, Juárez-González VT, Arriaga-Canon C, Herrera LA. Epidrug Repurposing: Discovering New Faces of Old Acquaintances in Cancer Therapy. Front Oncol 2020; 10:605386. [PMID: 33312959 PMCID: PMC7708379 DOI: 10.3389/fonc.2020.605386] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022] Open
Abstract
Gene mutations are strongly associated with tumor progression and are well known in cancer development. However, recently discovered epigenetic alterations have shown the potential to greatly influence tumoral response to therapy regimens. Such epigenetic alterations have proven to be dynamic, and thus could be restored. Due to their reversible nature, the promising opportunity to improve chemotherapy response using epigenetic therapy has arisen. Beyond helping to understand the biology of the disease, the use of modern clinical epigenetics is being incorporated into the management of the cancer patient. Potential epidrug candidates can be found through a process known as drug repositioning or repurposing, a promising strategy for the discovery of novel potential targets in already approved drugs. At present, novel epidrug candidates have been identified in preclinical studies and some others are currently being tested in clinical trials, ready to be repositioned. This epidrug repurposing could circumvent the classic paradigm where the main focus is the development of agents with one indication only, while giving patients lower cost therapies and a novel precision medical approach to optimize treatment efficacy and reduce toxicity. This review focuses on the main approved epidrugs, and their druggable targets, that are currently being used in cancer therapy. Also, we highlight the importance of epidrug repurposing by the rediscovery of known chemical entities that may enhance epigenetic therapy in cancer, contributing to the development of precision medicine in oncology.
Collapse
Affiliation(s)
- Michel Montalvo-Casimiro
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Rodrigo González-Barrios
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Marco Antonio Meraz-Rodriguez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | | | - Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
| | - Luis A. Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Mexico City, Mexico
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| |
Collapse
|
32
|
Ramazi S, Allahverdi A, Zahiri J. Evaluation of post-translational modifications in histone proteins: A review on histone modification defects in developmental and neurological disorders. J Biosci 2020. [DOI: 10.1007/s12038-020-00099-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
33
|
Kozako T, Itoh Y, Honda SI, Suzuki T. Epigenetic Control Using Small Molecules in Cancer. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/978-3-030-32857-3_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
34
|
Duman M, Martinez-Moreno M, Jacob C, Tapinos N. Functions of histone modifications and histone modifiers in Schwann cells. Glia 2020; 68:1584-1595. [PMID: 32034929 DOI: 10.1002/glia.23795] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 01/25/2023]
Abstract
Schwann cells (SCs) are the main glial cells present in the peripheral nervous system (PNS). Their primary functions are to insulate peripheral axons to protect them from the environment and to enable fast conduction of electric signals along big caliber axons by enwrapping them in a thick myelin sheath rich in lipids. In addition, SCs have the peculiar ability to foster axonal regrowth after a lesion by demyelinating and converting into repair cells that secrete neurotrophic factors and guide axons back to their former target to finally remyelinate regenerated axons. The different steps of SC development and their role in the maintenance of PNS integrity and regeneration after lesion are controlled by various factors among which transcription factors and chromatin-remodeling enzymes hold major functions. In this review, we discussed how histone modifications and histone-modifying enzymes control SC development, maintenance of PNS integrity and response to injury. The functions of histone modifiers as part of chromatin-remodeling complexes are discussed in another review published in the same issue of Glia.
Collapse
Affiliation(s)
- Mert Duman
- Faculty of Biology, Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Margot Martinez-Moreno
- Department of Neurosurgery, Molecular Neuroscience & Neuro-Oncology Laboratory, Brown University, Providence, Rhode Island
| | - Claire Jacob
- Faculty of Biology, Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nikos Tapinos
- Department of Neurosurgery, Molecular Neuroscience & Neuro-Oncology Laboratory, Brown University, Providence, Rhode Island
| |
Collapse
|
35
|
Gomathi K, Akshaya N, Srinaath N, Moorthi A, Selvamurugan N. Regulation of Runx2 by post-translational modifications in osteoblast differentiation. Life Sci 2020; 245:117389. [PMID: 32007573 DOI: 10.1016/j.lfs.2020.117389] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 01/27/2023]
Abstract
Osteogenesis is the process of new bone formation where transcription factors play an important role in controlling cell proliferation and differentiation. Runt-related transcription factor 2 (Runx2), a key transcription factor, regulates the differentiation of mesenchymal stem cells into osteoblasts, which further mature into osteocytes. Runx2 acts as a modulator such that it can either stimulate or inhibit the osteoblast differentiation. A defect/alteration in the expression/activity of this gene may lead to skeletal dysplasia. Runx2 thus serves as the best therapeutic model gene for studying bone and bone-related diseases. In this review, we briefly outline the regulation of Runx2 and its activity at the post-translational levels by the virtue of phosphorylation, acetylation, and ubiquitination in controlling the bone homeostasis.
Collapse
Affiliation(s)
- K Gomathi
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - N Akshaya
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - N Srinaath
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - A Moorthi
- Faculty of Allied Health Sciences, Chettinad Hospital and Research Institute, Chettinad Academy of Research and Education, Kelambakkam, Tamil Nadu, India
| | - N Selvamurugan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India.
| |
Collapse
|
36
|
Itoh Y. Drug Discovery Researches on Modulators of Lysine-Modifying Enzymes Based on Strategic Chemistry Approaches. Chem Pharm Bull (Tokyo) 2020; 68:34-45. [DOI: 10.1248/cpb.c19-00741] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yukihiro Itoh
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine
| |
Collapse
|
37
|
Sharma S, Ahmed M, Akhter Y. Fungal acetyltransferases structures, mechanisms and inhibitors: A review. Int J Biol Macromol 2019; 157:626-640. [PMID: 31786301 DOI: 10.1016/j.ijbiomac.2019.11.214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022]
Abstract
Acetylation of proteins is vital and mediate many processes within the cells like protein interactions, intercellular localization, protein stability, transcriptional regulation, enzyme activity and many more. Acetylation, an evolutionarily conserved process, attracted more attention due to its key regulatory role in many cellular processes and its effect on proteome and metabolome. In eukaryotes, protein acetylation also contribute to the epigenetic regulation of gene expression. Acetylation involves the transfer of acetyl group from donor acetyl coenzyme A to a suitable acceptor molecule and the reaction is catalyzed by acetyltransferase enzymes. The review focuses on current understanding of different acetyltransferase families: their discovery, structure and catalytic mechanism in fungal species. Fungal acetyltransferases use divergent catalytic mechanisms and carry out catalysis in a substrate-specific manner. The studies have explored different fungal acetyltransferases in relation to secondary metabolite production and the fungal pathogenesis. Although, the functions and catalytic mechanism of acetyltransferases are well known, however further enhanced knowledge may improve their utilization in various applications of biotechnology.
Collapse
Affiliation(s)
- Shikha Sharma
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Mushtaq Ahmed
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, VidyaVihar, Raebareli Road, Lucknow, Uttar Pradesh 226025, India.
| |
Collapse
|
38
|
Epigenetic mechanisms underlying the therapeutic effects of HDAC inhibitors in chronic myeloid leukemia. Biochem Pharmacol 2019; 173:113698. [PMID: 31706847 DOI: 10.1016/j.bcp.2019.113698] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/05/2019] [Indexed: 12/20/2022]
Abstract
Chronic myeloid leukemia (CML) is a hematological disorder caused by the oncogenic BCR-ABL fusion protein in more than 90% of patients. Despite the striking improvements in the management of CML patients since the introduction of tyrosine kinase inhibitors (TKis), the appearance of TKi resistance and side effects lead to treatment failure, justifying the need of novel therapeutic approaches. Histone deacetylase inhibitors (HDACis), able to modulate gene expression patterns and important cellular signaling pathways through the regulation of the acetylation status of both histone and non-histone protein targets, have been reported to display promising anti-leukemic properties alone or in combination with TKis. This review summarizes pre-clinical and clinical studies that investigated the mechanisms underlying the anticancer potential of HDACis and discusses the rationale for a combination of HDACis with TKis as a therapeutic option in CML.
Collapse
|
39
|
Sanaei M, Kavoosi F. Histone Deacetylases and Histone Deacetylase Inhibitors: Molecular Mechanisms of Action in Various Cancers. Adv Biomed Res 2019; 8:63. [PMID: 31737580 PMCID: PMC6839273 DOI: 10.4103/abr.abr_142_19] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/22/2019] [Accepted: 09/23/2019] [Indexed: 01/15/2023] Open
Abstract
Epigenetic modifications such as histone modification play an important role in tumorigenesis. There are several evidence that histone deacetylases (HDACs) play a key role in cancer induction and progression by histone deacetylation. Besides, histone acetylation is being accessed as a therapeutic target because of its role in regulating gene expression. HDAC inhibitors (HDACIs) are a family of synthetic and natural compounds that differ in their target specificities and activities. They affect markedly cancer cells, inducing cell differentiation, cell cycle arrest and cell death, reduction of angiogenesis, and modulation of the immune system. Here, we summarize the mechanisms of HDACs and the HDACIs in several cancers. An online search of different sources such as PubMed, ISI, and Scopus was performed to find available data on mechanisms and pathways of HDACs and HDACIs in different cancers. The result indicated that HDACs induce cancer through multiple mechanisms in various tissues. This effect can be inhibited by HDACIs which affect cancer cell by different pathways such as cell differentiation, cell cycle arrest, and cell death. In conclusion, these findings indicate that the HDACs play a major role in carcinogenesis through various pathways, and HDACIs can inhibit HDAC activity by multiple mechanisms resulting in cell cycle arrest, cell growth inhibition, and apoptosis induction.
Collapse
Affiliation(s)
- Masumeh Sanaei
- From the Research Center for Noncommunicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Fraidoon Kavoosi
- From the Research Center for Noncommunicable Diseases, Jahrom University of Medical Sciences, Jahrom, Iran
| |
Collapse
|
40
|
Keiser AA, Wood MA. Examining the contribution of histone modification to sex differences in learning and memory. Learn Mem 2019; 26:318-331. [PMID: 31416905 PMCID: PMC6699407 DOI: 10.1101/lm.048850.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 07/08/2019] [Indexed: 01/04/2023]
Abstract
The epigenome serves as a signal integration platform that encodes information from experience and environment that adds tremendous complexity to the regulation of transcription required for memory, beyond the directions encoded in the genome. To date, our understanding of how epigenetic mechanisms integrate information to regulate gene expression required for memory is primarily obtained from male derived data despite sex-specific life experiences and sex differences in consolidation and retrieval of memory, and in the molecular mechanisms that mediate these processes. In this review, we examine the contribution of chromatin modification to learning and memory in both sexes. We provide examples of how exposure to a number of internal and external factors influence the epigenome in sex-similar and sex-specific ways that may ultimately impact transcription required for memory processes. We also pose a number of key open questions and identify areas requiring further investigation as we seek to understand how histone modifying mechanisms shape memory in females.
Collapse
Affiliation(s)
- Ashley A Keiser
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, California 92697, USA
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, Center for the Neurobiology of Learning and Memory, University of California, Irvine, Irvine, California 92697, USA
| |
Collapse
|
41
|
Ghanbari M, Safaralizadeh R, Mohammadi K. A Review on Important Histone Acetyltransferase (HAT) Enzymes as Targets for Cancer Therapy. CURRENT CANCER THERAPY REVIEWS 2019. [DOI: 10.2174/1573394714666180720152100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
At the present time, cancer is one of the most lethal diseases worldwide. There are various factors involved in the development of cancer, including genetic factors, lifestyle, nutrition, and so on. Recent studies have shown that epigenetic factors have a critical role in the initiation and development of tumors. The histone post-translational modifications (PTMs) such as acetylation, methylation, phosphorylation, and other PTMs are important mechanisms that regulate the status of chromatin structure and this regulation leads to the control of gene expression. The histone acetylation is conducted by histone acetyltransferase enzymes (HATs), which are involved in transferring an acetyl group to conserved lysine amino acids of histones and consequently increase gene expression. On the basis of similarity in catalytic domains of HATs, these enzymes are divided into different groups such as families of GNAT, MYST, P300/CBP, SRC/P160, and so on. These enzymes have effective roles in apoptosis, signaling pathways, metastasis, cell cycle, DNA repair and other related mechanisms deregulated in cancer. Abnormal activation of HATs leads to uncontrolled amplification of cells and incidence of malignancy signs. This indicates that HAT might be an important target for effective cancer treatments, and hence there would be a need for further studies and designing of therapeutic drugs on this basis. In this study, we have reviewed the important roles of HATs in different human malignancies.
Collapse
Affiliation(s)
- Mohammad Ghanbari
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Kiyanoush Mohammadi
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| |
Collapse
|
42
|
Abstract
Acetylation is a posttranslational modification conserved in all domains of life that is carried out by N-acetyltransferases. While acetylation can occur on Nα-amino groups, this review will focus on Nε-acetylation of lysyl residues and how the posttranslational modification changes the cellular physiology of bacteria. Up until the late 1990s, acetylation was studied in eukaryotes in the context of chromatin maintenance and gene expression. At present, bacterial protein acetylation plays a prominent role in central and secondary metabolism, virulence, transcription, and translation. Given the diversity of niches in the microbial world, it is not surprising that the targets of bacterial protein acetyltransferases are very diverse, making their biochemical characterization challenging. The paradigm for acetylation in bacteria involves the acetylation of acetyl-CoA synthetase, whose activity must be tightly regulated to maintain energy charge homeostasis. While this paradigm has provided much mechanistic detail for acetylation and deacetylation, in this review we discuss advances in the field that are changing our understanding of the physiological role of protein acetylation in bacteria.
Collapse
Affiliation(s)
- Chelsey M VanDrisse
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA;
| | | |
Collapse
|
43
|
Elías-Villalobos A, Barrales RR, Ibeas JI. Chromatin modification factors in plant pathogenic fungi: Insights from Ustilago maydis. Fungal Genet Biol 2019; 129:52-64. [PMID: 30980908 DOI: 10.1016/j.fgb.2019.04.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 03/25/2019] [Accepted: 04/08/2019] [Indexed: 01/10/2023]
Abstract
Adaptation to the environment is a requirement for the survival of every organism. For pathogenic fungi this also implies coping with the different conditions that occur during the infection cycle. After detecting changes to external media, organisms must modify their gene expression patterns in order to accommodate the new circumstances. Control of gene expression is a complex process that involves the coordinated action of multiple regulatory elements. Chromatin modification is a well-known mechanism for controlling gene expression in response to environmental changes in all eukaryotes. In pathogenic fungi, chromatin modifications are known to play crucial roles in controlling host interactions and their virulence capacity, yet little is known about the specific genes they directly target and to which signals they respond. The smut fungus Ustilago maydis is an excellent model system in which multiple molecular and cellular approaches are available to study biotrophic interactions. Many target genes regulated during the infection process have been well studied, however, how they are controlled and specifically how chromatin modifications affect gene regulation in the context of infection is not well known in this organism. Here, we analyse the presence of chromatin modifying enzymes and complexes in U. maydis and discuss their putative roles in this plant pathogen in the context of findings from other organisms, including other plant pathogens such as Magnaporthe oryzae and Fusarium graminearum. We propose U. maydis as a remarkable organism with interesting chromatin features, which would allow finding new functions of chromatin modifications during plant pathogenesis.
Collapse
Affiliation(s)
- Alberto Elías-Villalobos
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR5237-Centre National de la Recherche Scientifique-Université de Montpellier, Montpellier, France.
| | - Ramón R Barrales
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, de Sevilla-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Sevilla, Spain.
| | - José I Ibeas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide, de Sevilla-Consejo Superior de Investigaciones Científicas-Junta de Andalucía, Sevilla, Spain
| |
Collapse
|
44
|
The Role of Nucleosomes in Epigenetic Gene Regulation. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
|
45
|
Elsen GE, Bedogni F, Hodge RD, Bammler TK, MacDonald JW, Lindtner S, Rubenstein JLR, Hevner RF. The Epigenetic Factor Landscape of Developing Neocortex Is Regulated by Transcription Factors Pax6→ Tbr2→ Tbr1. Front Neurosci 2018; 12:571. [PMID: 30186101 PMCID: PMC6113890 DOI: 10.3389/fnins.2018.00571] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022] Open
Abstract
Epigenetic factors (EFs) regulate multiple aspects of cerebral cortex development, including proliferation, differentiation, laminar fate, and regional identity. The same neurodevelopmental processes are also regulated by transcription factors (TFs), notably the Pax6→ Tbr2→ Tbr1 cascade expressed sequentially in radial glial progenitors (RGPs), intermediate progenitors, and postmitotic projection neurons, respectively. Here, we studied the EF landscape and its regulation in embryonic mouse neocortex. Microarray and in situ hybridization assays revealed that many EF genes are expressed in specific cortical cell types, such as intermediate progenitors, or in rostrocaudal gradients. Furthermore, many EF genes are directly bound and transcriptionally regulated by Pax6, Tbr2, or Tbr1, as determined by chromatin immunoprecipitation-sequencing and gene expression analysis of TF mutant cortices. Our analysis demonstrated that Pax6, Tbr2, and Tbr1 form a direct feedforward genetic cascade, with direct feedback repression. Results also revealed that each TF regulates multiple EF genes that control DNA methylation, histone marks, chromatin remodeling, and non-coding RNA. For example, Tbr1 activates Rybp and Auts2 to promote the formation of non-canonical Polycomb repressive complex 1 (PRC1). Also, Pax6, Tbr2, and Tbr1 collectively drive massive changes in the subunit isoform composition of BAF chromatin remodeling complexes during differentiation: for example, a novel switch from Bcl7c (Baf40c) to Bcl7a (Baf40a), the latter directly activated by Tbr2. Of 11 subunits predominantly in neuronal BAF, 7 were transcriptionally activated by Pax6, Tbr2, or Tbr1. Using EFs, Pax6→ Tbr2→ Tbr1 effect persistent changes of gene expression in cell lineages, to propagate features such as regional and laminar identity from progenitors to neurons.
Collapse
Affiliation(s)
- Gina E. Elsen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Francesco Bedogni
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Rebecca D. Hodge
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Theo K. Bammler
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Susan Lindtner
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, United States
| | - John L. R. Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, United States
| | - Robert F. Hevner
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
- Department of Neurological Surgery, School of Medicine, University of Washington, Seattle, WA, United States
| |
Collapse
|
46
|
Yang Q, Yang Y, Zhou N, Tang K, Lau WB, Lau B, Wang W, Xu L, Yang Z, Huang S, Wang X, Yi T, Zhao X, Wei Y, Wang H, Zhao L, Zhou S. Epigenetics in ovarian cancer: premise, properties, and perspectives. Mol Cancer 2018; 17:109. [PMID: 30064416 PMCID: PMC6069741 DOI: 10.1186/s12943-018-0855-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 07/11/2018] [Indexed: 01/04/2023] Open
Abstract
Malignant ovarian tumors bear the highest mortality rate among all gynecological cancers. Both late tumor diagnosis and tolerance to available chemical therapy increase patient mortality. Therefore, it is both urgent and important to identify biomarkers facilitating early identification and novel agents preventing recurrence. Accumulating evidence demonstrates that epigenetic aberrations (particularly histone modifications) are crucial in tumor initiation and development. Histone acetylation and methylation are respectively regulated by acetyltransferases-deacetylases and methyltransferases-demethylases, both of which are implicated in ovarian cancer pathogenesis. In this review, we summarize the most recent discoveries pertaining to ovarian cancer development arising from the imbalance of histone acetylation and methylation, and provide insight into novel therapeutic interventions for the treatment of ovarian carcinoma.
Collapse
Affiliation(s)
- Qilian Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Yuqing Yang
- Nanchang University, Nanchang, People's Republic of China
| | - Nianxin Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Kexin Tang
- Sichuan Normal University Affiliated Middle School, Chengdu, People's Republic of China
| | - Wayne Bond Lau
- Department of Emergency Medicine, Thomas Jefferson University Hospital, Philadelphia, USA
| | - Bonnie Lau
- Department of Surgery, Emergency Medicine, Kaiser Santa Clara Medical Center, Affiliate of Stanford University, Stanford, USA
| | - Wei Wang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China
| | - Lian Xu
- Department of Pathology, West China Second University Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Zhengnan Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Shuang Huang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China
| | - Tao Yi
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Xia Zhao
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Yuquan Wei
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China
| | - Hongjing Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China.
| | - Linjie Zhao
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China.
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, 610041, People's Republic of China.
| |
Collapse
|
47
|
He H, Hu Z, Xiao H, Zhou F, Yang B. The tale of histone modifications and its role in multiple sclerosis. Hum Genomics 2018; 12:31. [PMID: 29933755 PMCID: PMC6013900 DOI: 10.1186/s40246-018-0163-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 06/08/2018] [Indexed: 02/08/2023] Open
Abstract
Epigenetics defines the persistent modifications of gene expression in a manner that does not involve the corresponding alterations in DNA sequences. It includes modifications of DNA nucleotides, nucleosomal remodeling, and post-translational modifications (PTMs). It is becoming evident that PTMs which act singly or in combination to form “histone codes” orchestrate the chromatin structure and dynamic functions. PTMs of histone tails have been demonstrated to influence numerous biological developments, as well as disease onset and progression. Multiple sclerosis (MS) is an autoimmune inflammatory demyelinating and neurodegenerative disease of the central nervous system, of which the precise pathophysiological mechanisms remain to be fully elucidated. There is a wealth of emerging evidence that epigenetic modifications may confer risk for MS, which provides new insights into MS. Histone PTMs, one of the key events that regulate gene activation, seem to play a prominent role in the epigenetic mechanism of MS. In this review, we summarize recent studies in our understanding of the epigenetic language encompassing histone, with special emphasis on histone acetylation and histone lysine methylation, two of the best characterized histone modifications. We also discuss how the current studies address histone acetylation and histone lysine methylation influencing pathophysiology of MS and how future studies could be designed to establish optimized therapeutic strategies for MS.
Collapse
Affiliation(s)
- Hui He
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China
| | - Zhiping Hu
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China
| | - Han Xiao
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China
| | - Fangfang Zhou
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China
| | - Binbin Yang
- Department of Neurology, 2nd Xiangya Hospital, Central South University, No 139, Renmin Road, Changsha, Hunan Province, China.
| |
Collapse
|
48
|
Itoh Y. Chemical Protein Degradation Approach and its Application to Epigenetic Targets. CHEM REC 2018; 18:1681-1700. [PMID: 29893461 DOI: 10.1002/tcr.201800032] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/24/2018] [Indexed: 12/17/2022]
Abstract
In addition to traditional drugs, such as enzyme inhibitors, receptor agonists/antagonists, and protein-protein interaction inhibitors as well as genetic technology, such as RNA interference and the CRISPR/Cas9 system, protein knockdown approaches using proteolysis-targeting chimeras (PROTACs) have attracted much attention. PROTACs, which induce selective degradation of their target protein via the ubiquitin-proteasome system, are useful for the down-regulation of various proteins, including disease-related proteins and epigenetic proteins. Recent reports have shown that chemical protein knockdown is possible not only in cells, but also in vivo and this approach is expected to be used as the therapeutic strategy for several diseases. Thus, this approach may be a significant technique to complement traditional drugs and genetic ablation and will be more widely used for drug discovery and chemical biology studies in the future. In this personal account, a history of chemical protein knockdown is introduced, and its features, recent progress in the epigenetics field, and future outlooks are discussed.
Collapse
Affiliation(s)
- Yukihiro Itoh
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-0823, Japan
| |
Collapse
|
49
|
Epigenetics in teleost fish: From molecular mechanisms to physiological phenotypes. Comp Biochem Physiol B Biochem Mol Biol 2018; 224:210-244. [PMID: 29369794 DOI: 10.1016/j.cbpb.2018.01.006] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 02/07/2023]
Abstract
While the field of epigenetics is increasingly recognized to contribute to the emergence of phenotypes in mammalian research models across different developmental and generational timescales, the comparative biology of epigenetics in the large and physiologically diverse vertebrate infraclass of teleost fish remains comparatively understudied. The cypriniform zebrafish and the salmoniform rainbow trout and Atlantic salmon represent two especially important teleost orders, because they offer the unique possibility to comparatively investigate the role of epigenetic regulation in 3R and 4R duplicated genomes. In addition to their sequenced genomes, these teleost species are well-characterized model species for development and physiology, and therefore allow for an investigation of the role of epigenetic modifications in the emergence of physiological phenotypes during an organism's lifespan and in subsequent generations. This review aims firstly to describe the evolution of the repertoire of genes involved in key molecular epigenetic pathways including histone modifications, DNA methylation and microRNAs in zebrafish, rainbow trout, and Atlantic salmon, and secondly, to discuss recent advances in research highlighting a role for molecular epigenetics in shaping physiological phenotypes in these and other teleost models. Finally, by discussing themes and current limitations of the emerging field of teleost epigenetics from both theoretical and technical points of view, we will highlight future research needs and discuss how epigenetics will not only help address basic research questions in comparative teleost physiology, but also inform translational research including aquaculture, aquatic toxicology, and human disease.
Collapse
|
50
|
Dent JR, Martins VF, Svensson K, LaBarge SA, Schlenk NC, Esparza MC, Buckner EH, Meyer GA, Hamilton DL, Schenk S, Philp A. Muscle-specific knockout of general control of amino acid synthesis 5 (GCN5) does not enhance basal or endurance exercise-induced mitochondrial adaptation. Mol Metab 2017; 6:1574-1584. [PMID: 29111103 PMCID: PMC5699915 DOI: 10.1016/j.molmet.2017.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 09/29/2017] [Accepted: 10/10/2017] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE Lysine acetylation is an important post-translational modification that regulates metabolic function in skeletal muscle. The acetyltransferase, general control of amino acid synthesis 5 (GCN5), has been proposed as a regulator of mitochondrial biogenesis via its inhibitory action on peroxisome proliferator activated receptor-γ coactivator-1α (PGC-1α). However, the specific contribution of GCN5 to skeletal muscle metabolism and mitochondrial adaptations to endurance exercise in vivo remain to be defined. We aimed to determine whether loss of GCN5 in skeletal muscle enhances mitochondrial density and function, and the adaptive response to endurance exercise training. METHODS We used Cre-LoxP methodology to generate mice with muscle-specific knockout of GCN5 (mKO) and floxed, wildtype (WT) littermates. We measured whole-body energy expenditure, as well as markers of mitochondrial density, biogenesis, and function in skeletal muscle from sedentary mice, and mice that performed 20 days of voluntary endurance exercise training. RESULTS Despite successful knockdown of GCN5 activity in skeletal muscle of mKO mice, whole-body energy expenditure as well as skeletal muscle mitochondrial abundance and maximal respiratory capacity were comparable between mKO and WT mice. Further, there were no genotype differences in endurance exercise-mediated mitochondrial biogenesis or increases in PGC-1α protein content. CONCLUSION These results demonstrate that loss of GCN5 in vivo does not promote metabolic remodeling in mouse skeletal muscle.
Collapse
Affiliation(s)
- Jessica R Dent
- School of Sport, Exercise and Rehabilitation Sciences, University of Birmingham, UK
| | - Vitor F Martins
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA; Biomedical Sciences Graduate Program, University of California, La Jolla, San Diego, CA, USA
| | - Kristoffer Svensson
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA
| | - Samuel A LaBarge
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA
| | - Noah C Schlenk
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA
| | - Mary C Esparza
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA
| | - Elisa H Buckner
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA
| | - Gretchen A Meyer
- Program in Physical Therapy, Washington University School of Medicine, St Louis, MO, USA
| | | | - Simon Schenk
- Department of Orthopaedic Surgery, University of California, La Jolla, San Diego, CA, USA; Biomedical Sciences Graduate Program, University of California, La Jolla, San Diego, CA, USA.
| | - Andrew Philp
- School of Sport, Exercise and Rehabilitation Sciences, University of Birmingham, UK.
| |
Collapse
|