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Helsley RN, Zhou C. Epigenetic impact of endocrine disrupting chemicals on lipid homeostasis and atherosclerosis: a pregnane X receptor-centric view. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx017. [PMID: 29119010 PMCID: PMC5672952 DOI: 10.1093/eep/dvx017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/08/2017] [Accepted: 09/02/2017] [Indexed: 05/25/2023]
Abstract
Despite the major advances in developing diagnostic techniques and effective treatments, atherosclerotic cardiovascular disease (CVD) is still the leading cause of mortality and morbidity worldwide. While considerable progress has been achieved to identify gene variations and environmental factors that contribute to CVD, much less is known about the role of "gene-environment interactions" in predisposing individuals to CVD. Our chemical environment has significantly changed in the last few decades, and there are more than 100,000 synthetic chemicals in the market. Recent large-scale human population studies have associated exposure to certain chemicals including many endocrine disrupting chemicals (EDCs) with increased CVD risk, and animal studies have also confirmed that some EDCs can cause aberrant lipid homeostasis and increase atherosclerosis. However, the underlying mechanisms of how exposure to those EDCs influences CVD risk remain elusive. Numerous EDCs can activate the nuclear receptor pregnane X receptor (PXR) that functions as a xenobiotic sensor to regulate host xenobiotic metabolism. Recent studies have demonstrated the novel functions of PXR in lipid homeostasis and atherosclerosis. In addition to directly regulating transcription, PXR has been implicated in the epigenetic regulation of gene transcription. Exposure to many EDCs can also induce epigenetic modifications, but little is known about how the changes relate to the onset or progression of CVD. In this review, we will discuss recent research on PXR and EDCs in the context of CVD and propose that PXR may play a previously unrealized role in EDC-mediated epigenetic modifications that affect lipid homeostasis and atherosclerosis.
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Affiliation(s)
- Robert N Helsley
- Department of Pharmacology and Nutritional Sciences, Center for Metabolic Disease Research, University of Kentucky, Lexington, KY 40536, USA
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Changcheng Zhou
- Department of Pharmacology and Nutritional Sciences, Center for Metabolic Disease Research, University of Kentucky, Lexington, KY 40536, USA
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Yu Q, Shi X, Feng Y, Kent KC, Li L. Improving data quality and preserving HCD-generated reporter ions with EThcD for isobaric tag-based quantitative proteomics and proteome-wide PTM studies. Anal Chim Acta 2017; 968:40-49. [PMID: 28395773 PMCID: PMC5509462 DOI: 10.1016/j.aca.2017.03.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/03/2017] [Accepted: 03/02/2017] [Indexed: 11/22/2022]
Abstract
Mass spectrometry (MS)-based isobaric labeling has undergone rapid development in recent years due to its capability for high throughput quantitation. Apart from its originally designed use with collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD), isobaric tagging technique could also work with electron-transfer dissociation (ETD), which provides complementarity to CID and is preferred in sequencing peptides with post-translational modifications (PTMs). However, ETD suffers from long reaction time, reduced duty cycle and bias against peptides with lower charge states. In addition, common fragmentation mechanism in ETD results in altered reporter ion production, decreased multiplexing capability, and even loss of quantitation capability for some of the isobaric tags, including custom-designed dimethyl leucine (DiLeu) tags. Here, we demonstrate a novel electron-transfer/higher-energy collision dissociation (EThcD) approach that preserves original reporter ion channels, mitigates bias against lower charge states, improves sensitivity, and significantly improves data quality for quantitative proteomics and proteome-wide PTM studies. Systematic optimization was performed to achieve a balance between data quality and sensitivity. We provide direct comparison of EThcD with ETD and HCD for DiLeu- and TMT-labeled HEK cell lysate and IMAC enriched phosphopeptides. Results demonstrate improved data quality and phosphorylation localization accuracy while preserving sufficient reporter ion production. Biological studies were performed to investigate phosphorylation changes in a mouse vascular smooth muscle cell line treated with four different conditions. Overall, EThcD exhibits superior performance compared to conventional ETD and offers distinct advantages compared to HCD in isobaric labeling based quantitative proteomics and quantitative PTM studies.
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Affiliation(s)
- Qing Yu
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - Xudong Shi
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
| | - Yu Feng
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA
| | - K Craig Kent
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA; Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA.
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Schmitz-Rixen T, Keese M, Hakimi M, Peters A, Böckler D, Nelson K, Grundmann RT. Ruptured abdominal aortic aneurysm—epidemiology, predisposing factors, and biology. Langenbecks Arch Surg 2016; 401:275-88. [DOI: 10.1007/s00423-016-1401-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/04/2016] [Indexed: 12/19/2022]
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Seffer I, Nemeth Z, Hoffmann G, Matics R, Seffer AG, Koller A. Unexplored potentials of epigenetic mechanisms of plants and animals-theoretical considerations. GENETICS & EPIGENETICS 2013; 5:23-41. [PMID: 25512705 PMCID: PMC4222336 DOI: 10.4137/geg.s11752] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Morphological and functional changes of cells are important for adapting to environmental changes and associated with continuous regulation of gene expressions. Genes are regulated–in part–by epigenetic mechanisms resulting in alternating patterns of gene expressions throughout life. Epigenetic changes responding to the environmental and intercellular signals can turn on/off specific genes, but do not modify the DNA sequence. Most epigenetic mechanisms are evolutionary conserved in eukaryotic organisms, and several homologs of epigenetic factors are present in plants and animals. Moreover, in vitro studies suggest that the plant cytoplasm is able to induce a nuclear reassembly of the animal cell, whereas others suggest that the ooplasm is able to induce condensation of plant chromatin. Here, we provide an overview of the main epigenetic mechanisms regulating gene expression and discuss fundamental epigenetic mechanisms and factors functioning in both plants and animals. Finally, we hypothesize that animal genome can be reprogrammed by epigenetic factors from the plant protoplast.
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Affiliation(s)
| | - Zoltan Nemeth
- Seffer-Renner Medical Clinic, Budapest, Hungary. ; Department of Pathophysiology and Gerontology, Medical School, and Szentagothai Res Centre, University of Pecs, Pecs, Hungary
| | - Gyula Hoffmann
- Institute of Biology, Faculty of Sciences, University of Pecs, Pecs, Hungary
| | - Robert Matics
- Department of Pathophysiology and Gerontology, Medical School, and Szentagothai Res Centre, University of Pecs, Pecs, Hungary
| | - A Gergely Seffer
- Surgery Clinic, Medical School, University of Pecs, Pecs, Hungary
| | - Akos Koller
- Department of Pathophysiology and Gerontology, Medical School, and Szentagothai Res Centre, University of Pecs, Pecs, Hungary. ; Department of Physiology, New York Medical College, Valhalla NY, USA
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Schleithoff C, Voelter-Mahlknecht S, Dahmke IN, Mahlknecht U. On the epigenetics of vascular regulation and disease. Clin Epigenetics 2012; 4:7. [PMID: 22621747 PMCID: PMC3438017 DOI: 10.1186/1868-7083-4-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/09/2012] [Indexed: 12/16/2022] Open
Abstract
Consolidated knowledge is accumulating as to the role of epigenetic regulatory mechanisms in the physiology of vascular development and vascular tone as well as in the pathogenesis of cardiovascular disease. The modulation of gene expression through modification of the epigenome by structural changes of the chromatin architecture without alterations of the associated genomic DNA sequence is part of the cellular response to environmental changes. Such environmental conditions, which are finally being translated into adaptations of the cardiovascular system, also comprise pathological conditions such as atherosclerosis or myocardial infarction. This review summarizes recent findings on the epigenetics of vascular regulation and disease and presents nutritional and pharmacological approaches as novel epigenetic strategies in the prevention and treatment of cardiovascular disease.
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Affiliation(s)
- Christina Schleithoff
- Saarland University Medical Center, Department of Internal Medicine, Division of Immunotherapy and Gene Therapy, Homburg, Saar, D-66421, Germany
| | - Susanne Voelter-Mahlknecht
- Institute of Occupational and Social Medicine and Health Services Research, University of Tuebingen, Wilhelmstrasse 27, D-72074, Tuebingen, Germany
| | - Indra Navina Dahmke
- Saarland University Medical Center, Department of Internal Medicine, Division of Immunotherapy and Gene Therapy, Homburg, Saar, D-66421, Germany
| | - Ulrich Mahlknecht
- Saarland University Medical Center, Department of Internal Medicine, Division of Immunotherapy and Gene Therapy, Homburg, Saar, D-66421, Germany
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Furdas SD, Shekfeh S, Kannan S, Sippl W, Jung M. Rhodaninecarboxylic acids as novel inhibitors of histoneacetyltransferases. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md00211f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Virtual screening has identified rhodanine containing carboxylic acids as new inhibitors of histone acetyltransferases.
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Affiliation(s)
- Silviya D. Furdas
- Institute of Pharmaceutical Sciences
- Albert-Ludwigs-Unversity of Freiburg
- Freiburg
- Germany
| | - Suhaib Shekfeh
- Department of Pharmaceutical Chemistry
- Martin-Luther University of Halle-Wittenberg
- Germany
| | | | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry
- Martin-Luther University of Halle-Wittenberg
- Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences
- Albert-Ludwigs-Unversity of Freiburg
- Freiburg
- Germany
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Liu D, Glaser AP, Patibandla S, Blum A, Munson PJ, McCoy JP, Raghavachari N, Cannon RO. Transcriptional profiling of CD133(+) cells in coronary artery disease and effects of exercise on gene expression. Cytotherapy 2011; 13:227-36. [PMID: 21235297 DOI: 10.3109/14653249.2010.491611] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND AIMS Bone marrow (BM)-derived progenitor cells are under investigation for cardiovascular repair but may be altered by disease. Our aim was to identify differences in gene expression in CD133(+) cells of patients with coronary artery disease (CAD) and healthy controls, and determine whether exercise modifies gene expression. METHODS CD133(+) cells were flow-sorted from 10 CAD patients and four controls, and total RNA was isolated for microarray-based gene expression profiling. Genes that were found to be differentially regulated in patients were analyzed further to investigate whether exercise had any normalizing effect on CD133(+) cells in CAD patients following 3 months of an exercise program. RESULTS Improvement in effort tolerance and increases in the number of CD133(+) cells were observed in CAD patients after 3 months of exercise. Gene expression analysis of the CD133(+) cells identified 82 differentially expressed genes (2-fold cut-off, 25% false-discovery rate and % present calls) in patients compared with controls, of which 59 were found to be up-regulated and 23 down-regulated. These genes were found to be involved in carbohydrate metabolism, cell cycle, cellular development and signaling, and molecular transport. Following completion of the exercise program, gene expression patterns resembled those of controls in seven of 10 patients. CONCLUSIONS Alterations in gene expression of BM-derived CD133(+) progenitor cells were found in CAD patients, which in part may be normalized by exercise.
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Affiliation(s)
- Delong Liu
- Genomics Core, National Institutes of Health, Bethesda, Maryland, USA
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Krishna SM, Dear AE, Norman PE, Golledge J. Genetic and epigenetic mechanisms and their possible role in abdominal aortic aneurysm. Atherosclerosis 2010; 212:16-29. [PMID: 20347091 DOI: 10.1016/j.atherosclerosis.2010.02.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 01/29/2010] [Accepted: 02/04/2010] [Indexed: 11/30/2022]
Abstract
Abdominal aortic aneurysm (AAA) is a common disease associated with significant cardiovascular morbidity and mortality. The pathogenesis of AAA is poorly defined, making targeting of new therapies problematic. Current evidence favours an interaction of multiple environmental and genetic factors in the initiation and progression of AAA. Epigenetics is the term used to define the properties of the genome that are not explained by the primary sequence, but are due to the modifications of DNA and/or associated proteins. Previous research indicates the association of gene specific promoter DNA hyper-methylation and global DNA hypo-methylation with atherosclerosis. Evidence also suggests an important role for epigenetic processes such as histone acetylation in cardiovascular diseases including atherosclerosis and restenosis. Altered DNA methylation or histone acetylation occur in inflammation, cellular proliferation and remodelling processes and therefore maybe relevant to the pathology of AAA. Important risk factors for AAA, including cigarette smoking, older age, male gender and hypertension, have been linked with epigenetic effects and thus could act in this way to promote AAA. In this review, we discuss the potential role of epigenetic mechanisms in AAA. Since epigenetic alterations are to some extent reversible, further study of this area may identify new treatment targets for AAA.
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Affiliation(s)
- Smriti M Krishna
- Vascular Biology Unit, School of Medicine, James Cook University, Townsville, Queensland 4811, Australia
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