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Wang L, Feng J, Deng Y, Yang Q, Wei Q, Ye D, Rong X, Guo J. CCAAT/Enhancer-Binding Proteins in Fibrosis: Complex Roles Beyond Conventional Understanding. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9891689. [PMID: 36299447 PMCID: PMC9575473 DOI: 10.34133/2022/9891689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/18/2022] [Indexed: 07/29/2023]
Abstract
CCAAT/enhancer-binding proteins (C/EBPs) are a family of at least six identified transcription factors that contain a highly conserved basic leucine zipper domain and interact selectively with duplex DNA to regulate target gene expression. C/EBPs play important roles in various physiological processes, and their abnormal function can lead to various diseases. Recently, accumulating evidence has demonstrated that aberrant C/EBP expression or activity is closely associated with the onset and progression of fibrosis in several organs and tissues. During fibrosis, various C/EBPs can exert distinct functions in the same organ, while the same C/EBP can exert distinct functions in different organs. Modulating C/EBP expression or activity could regulate various molecular processes to alleviate fibrosis in multiple organs; therefore, novel C/EBPs-based therapeutic methods for treating fibrosis have attracted considerable attention. In this review, we will explore the features of C/EBPs and their critical functions in fibrosis in order to highlight new avenues for the development of novel therapies targeting C/EBPs.
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Affiliation(s)
- Lexun Wang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiaojiao Feng
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yanyue Deng
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Qianqian Yang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Quxing Wei
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Dewei Ye
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xianglu Rong
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiao Guo
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
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2
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Yoshinaga-Sakurai K, Rossman TG, Rosen BP. Regulation of arsenic methylation: identification of the transcriptional region of the human AS3MT gene. Cell Biol Toxicol 2022; 38:765-780. [PMID: 33956289 PMCID: PMC8571124 DOI: 10.1007/s10565-021-09611-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/27/2021] [Indexed: 12/19/2022]
Abstract
The human enzyme As(III) S-adenosylmethionine methyltransferase (AS3MT) catalyzes arsenic biotransformations and is considered to contribute to arsenic-related diseases. AS3MT is expressed in various tissues and cell types including liver, brain, adrenal gland, and peripheral blood mononuclear cells but not in human keratinocytes, urothelial, or brain microvascular endothelial cells. This indicates that AS3MT expression is regulated in a tissue/cell type-specific manner, but the mechanism of transcriptional regulation of expression of the AS3MT gene is not known. In this study, we define the DNA sequence of the core promoter region of the human AS3MT gene. We identify a GC box in the promoter to which the stress-related transcription factor Sp1 binds, indicating involvement of regulatory elements in AS3MT gene expression.
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Affiliation(s)
- Kunie Yoshinaga-Sakurai
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA
| | - Toby G Rossman
- Department of Environmental Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Barry P Rosen
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, 33199, USA.
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3
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Zhang J, Xiao J, Wang Y, Zheng X, Cui J, Wang C. A universal co-expression gene network and prognostic model for hepatic-biliary-pancreatic cancers identified by integrative analyses. FEBS Open Bio 2022; 12:2006-2024. [PMID: 36054420 PMCID: PMC9623511 DOI: 10.1002/2211-5463.13478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/12/2022] [Accepted: 08/25/2022] [Indexed: 01/25/2023] Open
Abstract
Hepatic, biliary and pancreatic cancers are a diverse set of malignancies with poor prognoses. It is possible that common molecular mechanisms are involved in the carcinogenesis of these cancers. Here, we identified LINC01537 and seven protein-coding genes by integrative analysis of transcriptomes of mRNAs, microRNAs and long non-coding RNAs from cholangiocarcinoma, hepatocellular carcinoma and pancreatic adenocarcinoma cohorts in TCGA. A predictive model constructed from seven biomarkers was established to successfully predict the survival rate of patients, which was then further verified in external cohorts. Additionally, patients with high-risk scores in our model were prone to epithelial-mesenchymal transition. Finally, activation of the biomarker PDE2A significantly attenuated migration and epithelial-mesenchymal transition in the HepG2 liver cancer cell line.
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Affiliation(s)
- Jing Zhang
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Juan Xiao
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and RepairAffiliated Hospital of Guilin Medical UniversityChina
| | - Yixuan Wang
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Xiao Zheng
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Jiajun Cui
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
| | - Chaochen Wang
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang UniversityHainingChina
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4
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Maldonato BJ, Vergara AG, Yadav J, Glass SM, Paragas EM, Li D, Lazarus P, McClay JL, Ning B, Daly AK, Russell LE. Epigenetics in drug disposition & drug therapy: symposium report of the 24 th North American meeting of the International Society for the Study of Xenobiotics (ISSX). Drug Metab Rev 2022; 54:318-330. [PMID: 35876105 PMCID: PMC9970013 DOI: 10.1080/03602532.2022.2101662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/10/2022] [Indexed: 11/03/2022]
Abstract
The 24th North American International Society for the Study of Xenobiotics (ISSX) meeting, held virtually from September 13 to 17, 2021, embraced the theme of "Broadening Our Horizons." This reinforces a key mission of ISSX: striving to share innovative science related to drug discovery and development. Session speakers and the ISSX New Investigators Group, which supports the scientific and professional development of student and early career ISSX members, elected to highlight the scientific content presented during the captivating session titled, "Epigenetics in Drug Disposition & Drug Therapy." The impact genetic variation has on drug response is well established; however, this session underscored the importance of investigating the role of epigenetics in drug disposition and drug discovery. Session speakers, Drs. Ning, McClay, and Lazarus, detailed mechanisms by which epigenetic players including long non-coding RNA (lncRNAs), microRNA (miRNAs), DNA methylation, and histone acetylation can alter the expression of genes involved in pharmacokinetics, pharmacodynamics, and toxicity. Dr. Ning detailed current knowledge about miRNAs and lncRNAs and the mechanisms by which they can affect the expression of drug metabolizing enzymes (DMEs) and nuclear receptors. Dr. Lazarus discussed the potential role of miRNAs on UDP-glucuronosyltransferase (UGT) expression and activity. Dr. McClay provided evidence that aging alters methylation and acetylation of DMEs in the liver, affecting gene expression and activity. These topics, compiled by the symposium organizers, presenters, and the ISSX New Investigators Group, are herein discussed, along with exciting future perspectives for epigenetics in drug disposition and drug discovery research.
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Affiliation(s)
- Benjamin J Maldonato
- Department of Nonclinical Development and Clinical Pharmacology, Revolution Medicines, Inc, Redwood City, CA, United States
| | - Ana G Vergara
- Department of ADME & Discovery Toxicology, Merck & Co., Inc, Rahway, NJ, United States
| | - Jaydeep Yadav
- Department of ADME & Discovery Toxicology, Merck & Co., Inc, Rahway, NJ, United States
| | - Sarah M Glass
- Janssen Research & Development, San Diego, CA, United States
| | | | - Dongying Li
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, United States
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, United States
| | - Joseph L McClay
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, United States
| | - Baitang Ning
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, United States
| | - Ann K Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Laura E Russell
- Drug Metabolism and Pharmacokinetics, AbbVie Inc, North Chicago, Illinois, United States
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5
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Suzuki T, Furuhata E, Maeda S, Kishima M, Miyajima Y, Tanaka Y, Lim J, Nishimura H, Nakanishi Y, Shojima A, Suzuki H. GATA6 is predicted to regulate DNA methylation in an in vitro model of human hepatocyte differentiation. Commun Biol 2022; 5:414. [PMID: 35508708 PMCID: PMC9068788 DOI: 10.1038/s42003-022-03365-1] [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: 04/12/2021] [Accepted: 04/14/2022] [Indexed: 01/02/2023] Open
Abstract
Hepatocytes are the dominant cell type in the human liver, with functions in metabolism, detoxification, and producing secreted proteins. Although gene regulation and master transcription factors involved in the hepatocyte differentiation have been extensively investigated, little is known about how the epigenome is regulated, particularly the dynamics of DNA methylation and the critical upstream factors. Here, by examining changes in the transcriptome and the methylome using an in vitro hepatocyte differentiation model, we show putative DNA methylation-regulating transcription factors, which are likely involved in DNA demethylation and maintenance of hypo-methylation in a differentiation stage-specific manner. Of these factors, we further reveal that GATA6 induces DNA demethylation together with chromatin activation in a binding-site-specific manner during endoderm differentiation. These results provide an insight into the spatiotemporal regulatory mechanisms exerted on the DNA methylation landscape by transcription factors and uncover an epigenetic role for transcription factors in early liver development. An integrated analysis of human induced pluripotent stem cells differentiating into hepatocyte-like cells unveils changes in DNA methylation and relevant transcription factors (like GATA6) that may influence hepatic development.
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Affiliation(s)
- Takahiro Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrated Medical Science (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Erina Furuhata
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrated Medical Science (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Shiori Maeda
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrated Medical Science (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Mami Kishima
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrated Medical Science (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yurina Miyajima
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrated Medical Science (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yuki Tanaka
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrated Medical Science (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Joanne Lim
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrated Medical Science (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Hajime Nishimura
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrated Medical Science (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yuri Nakanishi
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrated Medical Science (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Aiko Shojima
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrated Medical Science (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrated Medical Science (IMS), RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan.
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6
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Recalde M, Gárate-Rascón M, Herranz JM, Elizalde M, Azkona M, Unfried JP, Boix L, Reig M, Sangro B, Fernández-Barrena MG, Fortes P, Ávila MA, Berasain C, Arechederra M. DNA Methylation Regulates a Set of Long Non-Coding RNAs Compromising Hepatic Identity during Hepatocarcinogenesis. Cancers (Basel) 2022; 14:cancers14092048. [PMID: 35565178 PMCID: PMC9102946 DOI: 10.3390/cancers14092048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Hepatocarcinogenesis is a long process which implies the loss of hepatic functions. Our effort is to understand the mechanisms implicated in this pathological process in order to contribute to the development of new diagnostic markers and therapeutic targets. In this study we have identified a set of lncRNAs significantly downregulated in hepatocellular carcinoma (HCC) in correlation with the grade of tumor dedifferentiation and patients’ worse prognosis. Mechanistically, our results show that they are related with hepatic differentiation and at least a subset of those lncRNAs are essential to ensure the expression of other hepato-specific genes required for liver function. Moreover, we demonstrate that the expression of these lncRNAs in HCC is silenced by DNA methylation. All in all, we uncover connected epigenetic alterations involved in the progression of liver cancer and identify potential new biomarkers. Abstract Background: Long noncoding RNAs (lncRNAs) are emerging as key players in cancer, including hepatocellular carcinoma (HCC). Here we identify the mechanism implicated in the HCC inhibition of a set of lncRNAs, and their contribution to the process of hepatocarcinogenesis. Methods and Results: The top-ranked 35 lncRNAs downregulated in HCC (Top35 LNDH) were validated in several human HCC cohorts. We demonstrate that their inhibition is associated with promoter hypermethylation in HCC compared to control tissue, and in HCC human cell lines compared to primary hepatocytes. Moreover, demethylating treatment of HCC human cell lines induced the expression of these lncRNAs. The Top35 LNDH were preferentially expressed in the adult healthy liver compared to other tissues and fetal liver and were induced in well-differentiated HepaRG cells. Remarkably, their knockdown compromised the expression of other hepato-specific genes. Finally, the expression of the Top35 LNDH positively correlates with the grade of tumor differentiation and, more importantly, with a better patient prognosis. Conclusions: Our results demonstrate that the selected Top35 LNDH are not only part of the genes that compose the hepatic differentiated signature but participate in its establishment. Moreover, their downregulation through DNA methylation occurs during the process of hepatocarcinogenesis compromising hepatocellular differentiation and HCC patients’ prognosis.
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Affiliation(s)
- Miriam Recalde
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
| | - María Gárate-Rascón
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
| | - José María Herranz
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
| | - María Elizalde
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
| | - María Azkona
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
| | - Juan P. Unfried
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain;
| | - Loreto Boix
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- Barcelona Clinic Liver Cancer (BCLC) Group, Liver Unit, Hospital Clínic de Barcelona, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - María Reig
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- Barcelona Clinic Liver Cancer (BCLC) Group, Liver Unit, Hospital Clínic de Barcelona, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Bruno Sangro
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- Hepatology Unit, Navarra University Clinic, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Maite G. Fernández-Barrena
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Puri Fortes
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Matías A. Ávila
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Carmen Berasain
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Correspondence: (C.B.); (M.A.); Tel.: +34-948194700 (C.B. & M.A.)
| | - María Arechederra
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Correspondence: (C.B.); (M.A.); Tel.: +34-948194700 (C.B. & M.A.)
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7
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The Central Role of Cytochrome P450 in Xenobiotic Metabolism-A Brief Review on a Fascinating Enzyme Family. J Xenobiot 2021; 11:94-114. [PMID: 34206277 PMCID: PMC8293344 DOI: 10.3390/jox11030007] [Citation(s) in RCA: 146] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
Human Cytochrome P450 (CYP) enzymes constitute a superfamily of membrane-bound hemoproteins that are responsible for the metabolism of a wide variety of clinically, physiologically, and toxicologically important compounds. These heme-thiolate monooxygenases play a pivotal role in the detoxification of xenobiotics, participating in the metabolism of many structurally diverge compounds. This short-review is intended to provide a summary on the major roles of CYPs in Phase I xenobiotic metabolism. The manuscript is focused on eight main topics that include the most relevant aspects of past and current CYP research. Initially, (I) a general overview of the main aspects of absorption, distribution, metabolism, and excretion (ADME) of xenobiotics are presented. This is followed by (II) a background overview on major achievements in the past of the CYP research field. (III) Classification and nomenclature of CYPs is briefly reviewed, followed by (IV) a summary description on CYP’s location and function in mammals. Subsequently, (V) the physiological relevance of CYP as the cornerstone of Phase I xenobiotic metabolism is highlighted, followed by (VI) reviewing both genetic determinants and (VI) nongenetic factors in CYP function and activity. The last topic of the review (VIII) is focused on the current challenges of the CYP research field.
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8
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Donia T, Khedr S, Salim EI, Hessien M. Trichostatin A sensitizes hepatoma cells to Taxol more than 5-Aza-dC and dexamethasone. Drug Metab Pers Ther 2021; 36:299-309. [PMID: 34773731 DOI: 10.1515/dmpt-2020-0186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/16/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES This work was designed to compare the sensitizing effects of epigenetic modifiers on cancer cells vs. that of glucocorticoids. Also, to evaluate their effects on genes involved in epigenetic changes and drug metabolism. METHODS Hepatoma cells (HepG2) were treated with the anticancer drug (Taxol), with a histone deacetylase inhibitor (Trichostatin A [TSA]), DNA methyltransferase inhibitor (5-Aza-dC) or dexamethasone (DEX). Cytotoxicity was assessed by MTT assay and the apoptosis was determined by Annexin V-FITC. The expression levels of HDAC1, HDAC3, Dnmt1, Dnmt3α, CYP1A2, CYP3A4, CYP2B6, CYP2C19 and CYP2D6 were monitored by qRT-PCR. RESULTS TSA, synergistically enhanced cells sensitivity with the anticancer effect of Taxol more than 5-Aza-dC and DEX. This was evidenced by the relative decrease in IC50 in cells cotreated with Taxol + TSA, Taxol + 5-Aza-dC or Taxol + DEX. Apoptosis was induced in 51.2, 16.9 and 41.3% of cells, respectively. In presence of Taxol, TSA induced four-fold increase in the expression of HDAC1 and downregulated Dnmt1&3α genes. CYP2D6 demonstrated progressive expression (up to 28-fold) with the increasing number of drugs. Moreover, the isoform overexpressed in cells treated with TSA + Taxol > DEX + Taxol > 5-Aza-dC + Taxol (6.4, 4.6 and 2.99, respectively). The investigated genes were clustered in two distinct subsets, where no coregulation was observed between HDAC1 and HDAC3. However, tight pairwise correlation-based cluster was seen between (CYP3A4/Dnmt3α and CYP2D6/CYP2C19). CONCLUSIONS The data reflects the sensitizing effect of acetylation modification by TSA on the responsiveness of hepatoma cells to anticancer therapy. The effect of histone deacetylase inhibition was more than hypomethylation and glucocorticoid effects. TSA exerts its role through its modulatory role on epigenetics and drugs metabolizing genes. Other modifiers (5-Aza-dC and DEX), however may adopt different mechanisms.
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Affiliation(s)
- Thoria Donia
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, Egypt
| | - Sherien Khedr
- College of Pharmacy, Arab Academy for Science, Technology & Maritime Transport, Alexandria, Egypt
| | - Elsayed I Salim
- Department of Zoology, Faculty of Science, Tanta University, Tanta, Egypt
| | - Mohamed Hessien
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, Egypt
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Donia T, Khedr S, Salim EI, Hessien M. Trichostatin A sensitizes hepatoma cells to Taxol more than 5-Aza-dC and dexamethasone. Drug Metab Pers Ther 2021; 0:dmdi-2020-0186. [PMID: 33818027 DOI: 10.1515/dmdi-2020-0186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/16/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES This work was designed to compare the sensitizing effects of epigenetic modifiers on cancer cells vs. that of glucocorticoids. Also, to evaluate their effects on genes involved in epigenetic changes and drug metabolism. METHODS Hepatoma cells (HepG2) were treated with the anticancer drug (Taxol), with a histone deacetylase inhibitor (Trichostatin A [TSA]), DNA methyltransferase inhibitor (5-Aza-dC) or dexamethasone (DEX). Cytotoxicity was assessed by MTT assay and the apoptosis was determined by Annexin V-FITC. The expression levels of HDAC1, HDAC3, Dnmt1, Dnmt3α, CYP1A2, CYP3A4, CYP2B6, CYP2C19 and CYP2D6 were monitored by qRT-PCR. RESULTS TSA, synergistically enhanced cells sensitivity with the anticancer effect of Taxol more than 5-Aza-dC and DEX. This was evidenced by the relative decrease in IC50 in cells cotreated with Taxol + TSA, Taxol + 5-Aza-dC or Taxol + DEX. Apoptosis was induced in 51.2, 16.9 and 41.3% of cells, respectively. In presence of Taxol, TSA induced four-fold increase in the expression of HDAC1 and downregulated Dnmt1&3α genes. CYP2D6 demonstrated progressive expression (up to 28-fold) with the increasing number of drugs. Moreover, the isoform overexpressed in cells treated with TSA + Taxol > DEX + Taxol > 5-Aza-dC + Taxol (6.4, 4.6 and 2.99, respectively). The investigated genes were clustered in two distinct subsets, where no coregulation was observed between HDAC1 and HDAC3. However, tight pairwise correlation-based cluster was seen between (CYP3A4/Dnmt3α and CYP2D6/CYP2C19). CONCLUSIONS The data reflects the sensitizing effect of acetylation modification by TSA on the responsiveness of hepatoma cells to anticancer therapy. The effect of histone deacetylase inhibition was more than hypomethylation and glucocorticoid effects. TSA exerts its role through its modulatory role on epigenetics and drugs metabolizing genes. Other modifiers (5-Aza-dC and DEX), however may adopt different mechanisms.
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Affiliation(s)
- Thoria Donia
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, Egypt
| | - Sherien Khedr
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, Egypt
| | - Elsayed I Salim
- Department of Zoology, Faculty of Science, Tanta University, Tanta, Egypt
| | - Mohamed Hessien
- Division of Biochemistry, Department of Chemistry, Faculty of Science, Tanta University, Tanta, Egypt
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Carvalho Henriques B, Yang EH, Lapetina D, Carr MS, Yavorskyy V, Hague J, Aitchison KJ. How Can Drug Metabolism and Transporter Genetics Inform Psychotropic Prescribing? Front Genet 2020; 11:491895. [PMID: 33363564 PMCID: PMC7753050 DOI: 10.3389/fgene.2020.491895] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/25/2020] [Indexed: 12/11/2022] Open
Abstract
Many genetic variants in drug metabolizing enzymes and transporters have been shown to be relevant for treating psychiatric disorders. Associations are strong enough to feature on drug labels and for prescribing guidelines based on such data. A range of commercial tests are available; however, there is variability in included genetic variants, methodology, and interpretation. We herein provide relevant background for understanding clinical associations with specific variants, other factors that are relevant to consider when interpreting such data (such as age, gender, drug-drug interactions), and summarize the data relevant to clinical utility of pharmacogenetic testing in psychiatry and the available prescribing guidelines. We also highlight areas for future research focus in this field.
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Affiliation(s)
| | - Esther H. Yang
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Diego Lapetina
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Michael S. Carr
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
| | - Vasyl Yavorskyy
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
| | - Joshua Hague
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Katherine J. Aitchison
- Department of Psychiatry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, AB, Canada
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11
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Molecular effects and retinopathy induced by hydroxychloroquine during SARS-CoV-2 therapy: Role of CYP450 isoforms and epigenetic modulations. Eur J Pharmacol 2020; 886:173454. [PMID: 32763298 PMCID: PMC7402235 DOI: 10.1016/j.ejphar.2020.173454] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 01/07/2023]
Abstract
Antimalaria drugs such as chloroquine (CQ) and hydroxychloroquine (HCQ) have been administered to several inflammatory diseases including rheumatoid arthritis and systemic lupus erythematosus, and infectious diseases such as acquired immune deficiency syndrome and influenza. Recently, several patients infected with novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were given HCQ, and showed a discrepant response. HCQ inhibits SARS-CoV-2 cell entry, and inflammatory cascade by interfering with lysosomal and endosomal activities, and autophagy, impeding virus-membrane fusion, and inhibiting cytokine production resulted from inflammatory pathways activation. Despite ongoing administration of HCQ in a wide spectrum of disorders, there are some reports about several side effects, especially retinopathy in some patients treated with HCQ. Cytochrome P450 (CYP450) and its isoforms are the main metabolizers of HCQ and CQ. Pharmacokinetic properties of CYP enzymes are influenced by CYP polymorphism, non-coding RNAs, and epigenetic mechanisms such as DNA methylation, and histone acetylation. Accumulating evidence about side effects of HCQ in some patients raise the possibility that different response of patients to HCQ might be due to difference in their genome. Therefore, CYP450 genotyping especially for CYP2D6 might be helpful to refine HCQ dosage. Also, regular control of retina should be considered for patients under HCQ treatment. The major focus of the present review is to discuss about the pharmacokinetic and pharmacodynamic properties of CQ and HCQ that may be influenced by epigenetic mechanisms, and consequently cause several side effects especially retinopathy during SARS-CoV-2 therapy.
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Wang X, Wei L, Yang J, Wang Y, Chen S, Yang K, Meng X, Zhang L. DNA methylation determines the regulation of pregnane X receptor on CYP3A4 expression. Clin Exp Pharmacol Physiol 2020; 48:250-259. [PMID: 33048369 DOI: 10.1111/1440-1681.13420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/22/2020] [Accepted: 10/07/2020] [Indexed: 11/30/2022]
Abstract
The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes. Here, we aimed to explore the potential relationship between DNA methylation and CYP3A4 expression. We analyzed the effect of a DNA methylation inhibitor, 5-aza-2-deoxycytidine, on pregnane X receptor (PXR) and CYP3A4 expression in HepG2 cells. In addition, pCpGL-CYP3A4-promoter and pCpGL-CYP3A4-enhancer plus promoter plasmids were constructed, methylated, and transfected. We found that treatment with 5-aza-2-deoxycytidine significantly increased the expression of PXR and CYP3A4 in a concentration- and time-dependent manner. In addition, CYP3A4 expression was significantly enhanced by overexpressing PXR via transfection of pSG5-PXR plasmids. Methylation of CYP3A4 enhancer inhibited CYP3A4 transcriptional activity mediated through PXR and inhibited the binding of PXR and CYP3A4 promoter. We also observed that when the promoter and enhancer of CYP3A4 were methylated, CYP3A4 expression did not increase after treatment with rifampicin. In conclusion, the investigation demonstrates that DNA methylation of CYP3A4 enhancer significantly inhibits CYP3A4 expression, mediated through PXR, which is not influenced by rifampicin.
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Affiliation(s)
- Xiaofei Wang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Luman Wei
- Department of Pharmacy, Zhengzhou People's Hospital, Zhengzhou, China
| | - Jingke Yang
- Laboratory of Cardiovascular Disease and Drug Research, The 7th People's Hospital of Zhengzhou, Zhengzhou, China
| | - Yiting Wang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Shitong Chen
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Kun Yang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Xiangguang Meng
- Laboratory of Cardiovascular Disease and Drug Research, The 7th People's Hospital of Zhengzhou, Zhengzhou, China
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
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Ruoß M, Vosough M, Königsrainer A, Nadalin S, Wagner S, Sajadian S, Huber D, Heydari Z, Ehnert S, Hengstler JG, Nussler AK. Towards improved hepatocyte cultures: Progress and limitations. Food Chem Toxicol 2020; 138:111188. [PMID: 32045649 DOI: 10.1016/j.fct.2020.111188] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/31/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
Abstract
Hepatotoxicity is among the most frequent reasons for drug withdrawal from the market. Therefore, there is an urgent need for reliable predictive in vitro tests, which unfailingly identify hepatotoxic drug candidates, reduce drug development time, expenses and the number of test animals. Currently, human hepatocytes represent the gold standard. However, the use of hepatocytes is challenging since the cells are not constantly available and lose their metabolic activity in culture. To solve these problems many different approaches have been developed in the past decades. The aim of this review is to present these approaches and to discuss the possibilities and limitations as well as future opportunities and directions.
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Affiliation(s)
- Marc Ruoß
- Department of Traumatology, Siegfried Weller Institute, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Alfred Königsrainer
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Silvio Nadalin
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Silvia Wagner
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, Tübingen, Germany
| | - Sahar Sajadian
- Department of Traumatology, Siegfried Weller Institute, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Diana Huber
- Department of Traumatology, Siegfried Weller Institute, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Zahra Heydari
- Department of Regenerative Medicine, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sabrina Ehnert
- Department of Traumatology, Siegfried Weller Institute, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Technical University of Dortmund, Dortmund, Germany
| | - Andreas K Nussler
- Department of Traumatology, Siegfried Weller Institute, Eberhard Karls University Tübingen, Tübingen, Germany.
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14
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Methylation of adenosine at the N6 position post-transcriptionally regulates hepatic P450s expression. Biochem Pharmacol 2020; 171:113697. [DOI: 10.1016/j.bcp.2019.113697] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022]
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15
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Loss of alanine-glyoxylate and serine-pyruvate aminotransferase expression accelerated the progression of hepatocellular carcinoma and predicted poor prognosis. J Transl Med 2019; 17:390. [PMID: 31771612 PMCID: PMC6880547 DOI: 10.1186/s12967-019-02138-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 11/13/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Accumulated studies reported abnormal gene expression profiles of hepatocellular carcinoma (HCC) by cDNA microarray. We tried to merge cDNA microarray data from different studies to search for stably changed genes, and to find out better diagnostic and prognostic markers for HCC. METHODS A systematic review was performed by searching publications indexed in Pubmed from March 1, 2001 to July 1, 2016. Studies that reporting cDNA microarray profiles in HCC, containing both tumor and nontumor data and published in English-language were retrieved. The differentially expressed genes from eligible studies were summarized and ranked according to the frequency. High frequency genes were subjected to survival analyses. The expression and prognostic value of alanine-glyoxylate and serine-pyruvate aminotransferase (AGXT) was further evaluated in HCC datasets in Oncomine and an independent HCC tissue array cohort. The role of AGXT in HCC progression was evaluated by proliferation and migration assays in a human HCC cell line. RESULTS A total of 43 eligible studies that containing 1917 HCC patients were included, a list of 2022 non redundant abnormally expressed genes in HCC were extracted. The frequencies of reported genes were ranked. We finally obtained a list of only five genes (AGXT; ALDOB; CYP2E1; IGFBP3; TOP2A) that were differentially expressed in tumor and nontumor tissues across studies and were significantly correlated to HCC prognosis. Only AGXT had not been reported in HCC. Reduced expression of AGXT reflected poor differentiation of HCC and predicts poor survival. Knocking down of AGXT enhanced cell proliferation and migration of HCC cell line. CONCLUSIONS The present study supported the feasibility and necessity of systematic review on discovering new and reliable biomarkers for HCC. We also identified a list of high frequency prognostic genes and emphasized a critical role of AGXT deletion during HCC progression.
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Li H, Lampe JN. Neonatal cytochrome P450 CYP3A7: A comprehensive review of its role in development, disease, and xenobiotic metabolism. Arch Biochem Biophys 2019; 673:108078. [PMID: 31445893 DOI: 10.1016/j.abb.2019.108078] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/17/2019] [Accepted: 08/18/2019] [Indexed: 12/14/2022]
Abstract
The human cytochrome P450 CYP3A7, once thought to be an enzyme exclusive to fetal livers, has more recently been identified in neonates and developing infants as old as 24 months post-gestational age. CYP3A7 has been demonstrated to metabolize two endogenous compounds that are known to be important in the growth and development of the fetus and neonate, namely dehydroepiandrosterone sulfate (DHEA-S) and all-trans retinoic acid (atRA). In addition, it is also known to metabolize a variety of drugs and xenobiotics, albeit generally to a lesser extent relative to CYP3A4/5. CYP3A7 is an important component in the development and protection of the fetal liver and additionally plays a role in certain disease states, such as cancer and adrenal hyperplasia. Ultimately, a full understanding of the expression, regulation, and metabolic properties of CYP3A7 is needed to provide neonates with appropriate individualized pharmacotherapy. This article summarizes the current state of knowledge of CYP3A7, including its discovery, distribution, alleles, RNA splicing, expression and regulation, metabolic properties, substrates, and inhibitors.
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Affiliation(s)
- Haixing Li
- Sino-German Joint Research Institute Nanchang University, 235 East Nanjing Road, Nanchang, 330047, Jiangxi, PR China
| | - Jed N Lampe
- University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Mail Stop C238, 12850 E. Montview Blvd., Aurora, CO, 80045, USA.
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Ruoß M, Damm G, Vosough M, Ehret L, Grom-Baumgarten C, Petkov M, Naddalin S, Ladurner R, Seehofer D, Nussler A, Sajadian S. Epigenetic Modifications of the Liver Tumor Cell Line HepG2 Increase Their Drug Metabolic Capacity. Int J Mol Sci 2019; 20:ijms20020347. [PMID: 30654452 PMCID: PMC6358789 DOI: 10.3390/ijms20020347] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/12/2019] [Accepted: 01/14/2019] [Indexed: 01/31/2023] Open
Abstract
Although human liver tumor cells have reduced metabolic functions as compared to primary human hepatocytes (PHH) they are widely used for pre-screening tests of drug metabolism and toxicity. The aim of the present study was to modify liver cancer cell lines in order to improve their drug-metabolizing activities towards PHH. It is well-known that epigenetics is strongly modified in tumor cells and that epigenetic regulators influence the expression and function of Cytochrome P450 (CYP) enzymes through altering crucial transcription factors responsible for drug-metabolizing enzymes. Therefore, we screened the epigenetic status of four different liver cancer cell lines (Huh7, HLE, HepG2 and AKN-1) which were reported to have metabolizing drug activities. Our results showed that HepG2 cells demonstrated the highest similarity compared to PHH. Thus, we modified the epigenetic status of HepG2 cells towards 'normal' liver cells by 5-Azacytidine (5-AZA) and Vitamin C exposure. Then, mRNA expression of Epithelial-mesenchymal transition (EMT) marker SNAIL and CYP enzymes were measured by PCR and determinate specific drug metabolites, associated with CYP enzymes by LC/MS. Our results demonstrated an epigenetic shift in HepG2 cells towards PHH after exposure to 5-AZA and Vitamin C which resulted in a higher expression and activity of specific drug metabolizing CYP enzymes. Finally, we observed that 5-AZA and Vitamin C led to an increased expression of Hepatocyte nuclear factor 4α (HNF4α) and E-Cadherin and a significant down regulation of Snail1 (SNAIL), the key transcriptional repressor of E-Cadherin. Our study shows, that certain phase I genes and their enzyme activities are increased by epigenetic modification in HepG2 cells with a concomitant reduction of EMT marker gene SNAIL. The enhancing of liver specific functions in hepatoma cells using epigenetic modifiers opens new opportunities for the usage of cell lines as a potential liver in vitro model for drug testing and development.
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Affiliation(s)
- Marc Ruoß
- Siegfried Weller Institute, BG Trauma Clinic, Eberhard Karls University Tübingen, 72076 Tübingen, Germany.
| | - Georg Damm
- Department of Hepatobiliary Surgery and Visceral Transplantation, University of Leipzig, 04103 Leipzig, Germany.
| | - Massoud Vosough
- Royan Institute for Stem Cell Biology and Technology, Department of Stem Cells and Developmental Biology, Tehran 16635-148, Iran.
| | - Lisa Ehret
- Siegfried Weller Institute, BG Trauma Clinic, Eberhard Karls University Tübingen, 72076 Tübingen, Germany.
| | - Carl Grom-Baumgarten
- Siegfried Weller Institute, BG Trauma Clinic, Eberhard Karls University Tübingen, 72076 Tübingen, Germany.
| | - Martin Petkov
- Siegfried Weller Institute, BG Trauma Clinic, Eberhard Karls University Tübingen, 72076 Tübingen, Germany.
| | - Silvio Naddalin
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, 72076 Tübingen, Germany.
| | - Ruth Ladurner
- Department of General, Visceral and Transplant Surgery, University Hospital Tübingen, 72076 Tübingen, Germany.
| | - Daniel Seehofer
- Department of Hepatobiliary Surgery and Visceral Transplantation, University of Leipzig, 04103 Leipzig, Germany.
| | - Andreas Nussler
- Siegfried Weller Institute, BG Trauma Clinic, Eberhard Karls University Tübingen, 72076 Tübingen, Germany.
| | - Sahar Sajadian
- Siegfried Weller Institute, BG Trauma Clinic, Eberhard Karls University Tübingen, 72076 Tübingen, Germany.
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Li D, Tolleson WH, Yu D, Chen S, Guo L, Xiao W, Tong W, Ning B. Regulation of cytochrome P450 expression by microRNAs and long noncoding RNAs: Epigenetic mechanisms in environmental toxicology and carcinogenesis. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2019; 37:180-214. [PMID: 31305208 PMCID: PMC6737535 DOI: 10.1080/10590501.2019.1639481] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Environmental exposures to hazardous chemicals are associated with a variety of human diseases and disorders, including cancers. Phase I metabolic activation and detoxification reactions catalyzed by cytochrome P450 enzymes (CYPs) affect the toxicities of many xenobiotic compounds. Proper regulation of CYP expression influences their biological effects. Noncoding RNAs (ncRNAs) are involved in regulating CYP expression, and ncRNA expression is regulated in response to environmental chemicals. The mechanistic interactions between ncRNAs and CYPs associated with the toxicity and carcinogenicity of environmental chemicals are described in this review, focusing on microRNA-dependent CYP regulation. The role of long noncoding RNAs in regulating CYP expression is also presented and new avenues of research concerning this regulatory mechanism are described.
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Affiliation(s)
- Dongying Li
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - William H Tolleson
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Dianke Yu
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Si Chen
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Lei Guo
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Wenming Xiao
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Weida Tong
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Baitang Ning
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
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Zhao Y, Zhou C, Yu H, Zhang W, Cheng F, Yu H, Zhou D, Li B, Liu J, Dai J, Zhong J, Chen M, Huang T, Pan R, Duan S, Hu Z. Association between the methylation of six apoptosis‑associated genes with autism spectrum disorder. Mol Med Rep 2018; 18:4629-4634. [PMID: 30221723 DOI: 10.3892/mmr.2018.9473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/17/2018] [Indexed: 11/05/2022] Open
Abstract
Excessive apoptosis hinders the process of brain maturation and is regarded as one of the principal risk factors for the development of autism spectrum disorder (ASD). The aim of the present study was to investigate the association between the methylation of six apoptosis‑associated genes [transforming growth factor β 1 (TGFB1), BCL2 associated X, apoptosis regulator, insulin like growth factor binding protein 3, protein kinase C β 1, presenilin 2 and C‑C motif chemokine ligand 2] and ASD. Using quantitative methylation‑specific polymerase chain reaction technology, DNA methylation levels were detected in 42 autistic and 26 control subjects. The logistic regression analysis results demonstrated that of the six genes, only TGFB1 was significantly hypomethylated in peripheral blood samples from children with autism compared with control samples (mean percentage of methylated reference, 0.011% vs. 0.019%; age‑adjusted P=0.028). In addition, TGFB1 methylation was identified to be positively associated with the interaction ability score from the Autism Behavior Checklist (r=0.452; P=0.035). These data suggested that decreased TGFB1 methylation may contribute to the development of ASD.
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Affiliation(s)
- Yuanzhi Zhao
- Department of Child Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang 315211, P.R. China
| | - Cong Zhou
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Hang Yu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Wenwu Zhang
- Department of Child Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang 315211, P.R. China
| | - Fang Cheng
- Department of Child Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang 315211, P.R. China
| | - Haihang Yu
- Department of Child Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang 315211, P.R. China
| | - Dongsheng Zhou
- Department of Child Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang 315211, P.R. China
| | - Bin Li
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jing Liu
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Dai
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Zhong
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Min Chen
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Tianyi Huang
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Ranran Pan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Shiwei Duan
- Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Zhenyu Hu
- Department of Child Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang 315211, P.R. China
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20
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Ashida R, Okamura Y, Ohshima K, Kakuda Y, Uesaka K, Sugiura T, Ito T, Yamamoto Y, Sugino T, Urakami K, Kusuhara M, Yamaguchi K. CYP3A4 Gene Is a Novel Biomarker for Predicting a Poor Prognosis in Hepatocellular Carcinoma. Cancer Genomics Proteomics 2018; 14:445-453. [PMID: 29109094 DOI: 10.21873/cgp.20054] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/02/2017] [Accepted: 10/03/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND/AIM Project HOPE (High-tech Omics-based Patient Evaluation) began in 2014 using integrated gene expression profiling (GEP) of cancer tissues as well as diathesis of each patient who underwent operation at our Institution. The aim of this study was to identify novel genes displaying altered gene expression related to the survival and early recurrence after hepatectomy for hepatocellular carcinoma (HCC) using the results of integrated GEP analysis. MATERIALS AND METHODS The present study included 92 patients. Genes with aberrant expression were selected by the difference of expression levels with ≥10-fold change between tumor and non-tumor tissues. RESULTS GEP analysis showed that down-regulation was frequently observed in the PRSS8 (64%), CYP3A4 (61%) and EPCAM (57%) genes. Multivariate analysis revealed tumor stage ≥II (p=0.008) and down-regulation of the CYP3A4 gene (p=0.036) as independent predictor for overall survival. Furthermore, multivariate analysis identified maximum tumor diameter ≥74mm (p=0.008), presence of intrahepatic-metastasis (p=0.020), and down-regulation of CYP3A4 gene (p=0.019) as independent predictors for early recurrence. CONCLUSION CYP3A4 was identified as a novel tumor suppressor gene related to a poor prognosis in HCC.
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Affiliation(s)
- Ryo Ashida
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan.,Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yukiyasu Okamura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yuko Kakuda
- Division of Pathology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Katsuhiko Uesaka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Teiichi Sugiura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Takaaki Ito
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Yusuke Yamamoto
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Masatoshi Kusuhara
- Regional Resources Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center Hospital and Research Institute, Shizuoka, Japan
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21
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Gailhouste L, Liew LC, Yasukawa K, Hatada I, Tanaka Y, Nakagama H, Ochiya T. Differentiation Therapy by Epigenetic Reconditioning Exerts Antitumor Effects on Liver Cancer Cells. Mol Ther 2018; 26:1840-1854. [PMID: 29759938 PMCID: PMC6035736 DOI: 10.1016/j.ymthe.2018.04.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 02/07/2023] Open
Abstract
Primary liver tumors are mainly represented by hepatocellular carcinoma (HCC), one of the most aggressive and resistant forms of cancer. Liver tumorigenesis is characterized by an accumulation of epigenetic abnormalities, leading to gene extinction and loss of hepatocyte differentiation. The aim of this work was to investigate the feasibility of converting liver cancer cells toward a less aggressive and differentiated phenotype using a process called epigenetic reconditioning. Here, we showed that an epigenetic regimen with non-cytotoxic doses of the demethylating compound 5-azacytidine (5-AZA) promoted an anti-cancer response by inhibiting HCC cell tumorigenicity. Furthermore, epigenetic reconditioning improved sorafenib response. Remarkably, epigenetic treatment was associated with a significant restoration of differentiation, as attested by the increased expression of characteristic hepatocyte markers in reconditioned cells. In particular, we showed that reexpression of these epigenetically silenced liver genes following 5-AZA treatment or after knockdown of DNA methyltransferase 1 (DNMT1) was the result of regional CpG demethylation. Lastly, we confirmed the efficacy of HCC differentiation therapy by epigenetic reconditioning using an in vivo tumor growth model. In summary, this work demonstrates that epigenetic reconditioning using the demethylating compound 5-AZA shows therapeutic significance for liver cancer and is potentially attractive for the treatment of solid tumors.
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Affiliation(s)
- Luc Gailhouste
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan.
| | - Lee Chuen Liew
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ken Yasukawa
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Yasuhito Tanaka
- Department of Virology and Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Hitoshi Nakagama
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; National Cancer Center, Tokyo, Japan
| | - Takahiro Ochiya
- Division of Molecular and Cellular Medicine, National Cancer Center Research Institute, Tokyo, Japan.
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22
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Jahangiri R, Mosaffa F, Emami Razavi A, Teimoori‐Toolabi L, Jamialahmadi K. Altered DNA methyltransferases promoter methylation and mRNA expression are associated with tamoxifen response in breast tumors. J Cell Physiol 2018; 233:7305-7319. [DOI: 10.1002/jcp.26562] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/23/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Rosa Jahangiri
- Department of Medical BiotechnologyFaculty of MedicineMashhad University of Medical SciencesMashhadIran
| | - Fatemeh Mosaffa
- Biotechnology Research CenterPharmaceutical Technology InstituteMashhad University of Medical SciencesMashhadIran
- Department of Pharmaceutical BiotechnologySchool of PharmacyMashhad University of Medical SciencesMashhadIran
| | - Amirnader Emami Razavi
- Iran National Tumor BankCancer Biology Research CenterCancer Institute of IranTehran University of Medical SciencesTehranIran
| | | | - Khadijeh Jamialahmadi
- Biotechnology Research CenterPharmaceutical Technology InstituteMashhad University of Medical SciencesMashhadIran
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23
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Burns KE, Shepherd P, Finlay G, Tingle MD, Helsby NA. Indirect regulation of CYP2C19 gene expression via DNA methylation. Xenobiotica 2017; 48:781-792. [DOI: 10.1080/00498254.2017.1372648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Kathryn Elisa Burns
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand,
| | - Phillip Shepherd
- School of Medical Sciences, University of Auckland, Auckland, New Zealand, and
| | - Graeme Finlay
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand,
| | - Malcolm Drummond Tingle
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | - Nuala Ann Helsby
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand,
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24
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Tan W, Zhu Z, Ye L, Leung LK. Methylation dictates PI.f-specific CYP19 transcription in human glial cells. Mol Cell Endocrinol 2017; 452:131-137. [PMID: 28559115 DOI: 10.1016/j.mce.2017.05.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 05/24/2017] [Accepted: 05/24/2017] [Indexed: 01/31/2023]
Abstract
CYP19 is the single copy gene encoding for the estrogen synthetic enzyme aromatase. Alternate splicing of the promoter is the regulatory mechanism of this gene. In the brain, estrogen is synthesized in neuronal and glial cells and the gene is mainly regulated by the alternate promoter PI.f. The hormone produced in this vicinity has been associated with maintaining normal brain functions. Previously, epigenetic regulation has been shown in the promoters PII and I.3 of CYP19 in adipocytes. In the present study, the methylation of PI.f in CYP19 was examined in glial cells. Treatment of the hypomethylating agent 5-aza-2'deoxycytidine increased CYP19 mRNA species in U87 MG cells while little changes were observed in the other glia cell lines. As PI.f is also chiefly used in T98G cells with high expression of CYP19, the methylation statuses of the promoter in these two cell models were compared. Our results showed that treating U87 MG cells with 10 μM 5-aza-2'deoxycytidine significantly induced a ∼10-fold increase in CYP19 transcription and ∼80% increase in aromatase activity. In contrast, the same treatment did not change either endpoint in T98G cells. Further investigation illustrated the CpGs in PI.f were differentially methylated in the two cell lines; 63% and 37% of the 14 CpG sites were methylated in U87 MG and T98G cells respectively. In conclusion, this study illustrated that the brain-specific PI.f derived CYP19 expression can be regulated by DNA methylation.
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Affiliation(s)
- Wenjuan Tan
- Biochemistry Programme, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Zhiping Zhu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing 211166, China.
| | - Lai K Leung
- Biochemistry Programme, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong; Food and Nutritional Sciences Programme, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong.
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25
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Enane FO, Shuen WH, Gu X, Quteba E, Przychodzen B, Makishima H, Bodo J, Ng J, Chee CL, Ba R, Seng Koh L, Lim J, Cheong R, Teo M, Hu Z, Ng KP, Maciejewski J, Radivoyevitch T, Chung A, Ooi LL, Tan YM, Cheow PC, Chow P, Chan CY, Lim KH, Yerian L, Hsi E, Toh HC, Saunthararajah Y. GATA4 loss of function in liver cancer impedes precursor to hepatocyte transition. J Clin Invest 2017; 127:3527-3542. [PMID: 28758902 DOI: 10.1172/jci93488] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/08/2017] [Indexed: 12/18/2022] Open
Abstract
The most frequent chromosomal structural loss in hepatocellular carcinoma (HCC) is of the short arm of chromosome 8 (8p). Genes on the remaining homologous chromosome, however, are not recurrently mutated, and the identity of key 8p tumor-suppressor genes (TSG) is unknown. In this work, analysis of minimal commonly deleted 8p segments to identify candidate TSG implicated GATA4, a master transcription factor driver of hepatocyte epithelial lineage fate. In a murine model, liver-conditional deletion of 1 Gata4 allele to model the haploinsufficiency seen in HCC produced enlarged livers with a gene expression profile of persistent precursor proliferation and failed hepatocyte epithelial differentiation. HCC mimicked this gene expression profile, even in cases that were morphologically classified as well differentiated. HCC with intact chromosome 8p also featured GATA4 loss of function via GATA4 germline mutations that abrogated GATA4 interactions with a coactivator, MED12, or by inactivating mutations directly in GATA4 coactivators, including ARID1A. GATA4 reintroduction into GATA4-haploinsufficient HCC cells or ARID1A reintroduction into ARID1A-mutant/GATA4-intact HCC cells activated hundreds of hepatocyte genes and quenched the proliferative precursor program. Thus, disruption of GATA4-mediated transactivation in HCC suppresses hepatocyte epithelial differentiation to sustain replicative precursor phenotype.
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Affiliation(s)
- Francis O Enane
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Wai Ho Shuen
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Xiaorong Gu
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ebrahem Quteba
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Bartlomiej Przychodzen
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Hideki Makishima
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Juraj Bodo
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Joanna Ng
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Chit Lai Chee
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Rebecca Ba
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Lip Seng Koh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Janice Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Rachael Cheong
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Marissa Teo
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Zhenbo Hu
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Kwok Peng Ng
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Jaroslaw Maciejewski
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Tomas Radivoyevitch
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, USA
| | - Alexander Chung
- Department of Hepato-pancreato-biliary and Transplant Surgery and
| | | | - Yu Meng Tan
- Department of Hepato-pancreato-biliary and Transplant Surgery and
| | - Peng-Chung Cheow
- Department of Hepato-pancreato-biliary and Transplant Surgery and
| | - Pierce Chow
- Department of Hepato-pancreato-biliary and Transplant Surgery and
| | - Chung Yip Chan
- Department of Hepato-pancreato-biliary and Transplant Surgery and
| | - Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, Singapore
| | - Lisa Yerian
- Clinical Pathology, Pathology Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Eric Hsi
- Clinical Pathology, Pathology Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Han Chong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Yogen Saunthararajah
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA
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26
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Huang TH, Wu SY, Huang YJ, Wei PL, Wu ATH, Chao TY. The identification and validation of Trichosstatin A as a potential inhibitor of colon tumorigenesis and colon cancer stem-like cells. Am J Cancer Res 2017; 7:1227-1237. [PMID: 28560069 PMCID: PMC5446486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 04/13/2017] [Indexed: 06/07/2023] Open
Abstract
Colon cancer is one of the most prevalent cancer types in developed countries. Metastasis and drug resistance are two contributing factors to the high mortality rate. Accumulating evidence suggest that cancer stem-like cells (CSCs) represents as a major contributor to these malignant features. Here, we identified and isolated colon cancer stem-like cells using side-population (SP) method from human colon cancer cell lines. SP colon cells demonstrate cancer stem-like cell properties including enhanced sphere-forming ability and resistance towards fluorouracil (5-FU). The CSC properties were associated with the increased expression level of major oncogenic and stem cell markers including β-catenin, NF-kB, Akt/mTOR, KRAS and c-Myc. Trichostatin A (TSA), an antifungal antibiotic also a HDAC inhibitor, was found to function not only to decrease the expression of oncogenic markers but also the colon CSC properties. Importantly, TSA and 5-FU combined treatment synergistically suppressed colon cancer viability. Finally, in vivo results demonstrated that TSA alone and in combination with 5-FU effectively suppressed colon tumorigenesis. Collectively, this study provides preclinical evidence that TSA may function as a potential colon cancer therapeutic agent by targeting CSC and overcoming 5-FU resistance.
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Affiliation(s)
- Tse-Hung Huang
- Department of Traditional Chinese Medicine, Chang Gung Memorial HospitalKeelung, Taiwan
- School of Traditional Chinese Medicine, Chang Gung UniversityTaoyuan, Taiwan
- School of Nursing, National Taipei University of Nursing and Health SciencesTaipei, Taiwan
| | - Szu-Yuan Wu
- Department of Radiation Oncology, Wan Fang Hospital, Taipei Medical UniversityTaipei, Taiwan
- Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical UniversityTaipei, Taiwan
| | - Yan-Jiun Huang
- Division of Colorectal Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei Medical UniversityTaipei, Taiwan
- Department of Surgery, College of Medicine, Taipei Medical UniversityTaipei, Taiwan
- Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical UniversityTaipei, Taiwan
| | - Po-Li Wei
- Division of Colorectal Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei Medical UniversityTaipei, Taiwan
- Department of Surgery, College of Medicine, Taipei Medical UniversityTaipei, Taiwan
| | - Alexander TH Wu
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical UniversityTaipei, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical CenterTaipei 114, Taiwan
| | - Tsu-Yi Chao
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical UniversityTaipei, Taiwan
- Department of Medical Research & Education, Taipei Medical University-Shuang Ho HospitalNew Taipei, Taiwan
- Division of Hematology and Oncology, Department of Internal Medicine, Taipei Medical University-Shuang Ho HospitalNew Taipei, Taiwan
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27
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Nakamura K, Aizawa K, Aung KH, Yamauchi J, Tanoue A. Zebularine upregulates expression of CYP genes through inhibition of DNMT1 and PKR in HepG2 cells. Sci Rep 2017; 7:41093. [PMID: 28112215 PMCID: PMC5253741 DOI: 10.1038/srep41093] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/14/2016] [Indexed: 01/22/2023] Open
Abstract
Drug-induced hepatotoxicity is one of the major reasons cited for drug withdrawal. Therefore, it is of extreme importance to detect human hepatotoxic candidates as early as possible during the drug development process. In this study, we aimed to enhance hepatocyte functions such as CYP gene expression in HepG2 cells, one of the most extensively used cell lines in evaluating hepatotoxicity of chemicals and drugs. We found that zebularine, a potent inhibitor of DNA methylation, remarkably upregulates the expression of CYP genes in HepG2 cells. In addition, we revealed that the upregulation of CYP gene expression by zebularine was mediated through the inhibition of both DNA methyltransferase 1 (DNMT1) and double-stranded RNA-dependent protein kinase (PKR). Furthermore, HepG2 cells treated with zebularine were more sensitive than control cells to drug toxicity. Taken together, our results show that zebularine may make HepG2 cells high-functioning and thus could be useful for evaluating the hepatotoxicity of chemicals and drugs speedily and accurately in in-vitro systems. The finding that zebularine upregulates CYP gene expression through DNMT1 and PKR modulation sheds light on the mechanisms controlling hepatocyte function and thus may aid in the development of new in-vitro systems using high-functioning hepatocytes.
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Affiliation(s)
- Kazuaki Nakamura
- Department of Pharmacology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Kazuko Aizawa
- Department of Pharmacology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Kyaw Htet Aung
- Department of Pharmacology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Junji Yamauchi
- Department of Pharmacology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
| | - Akito Tanoue
- Department of Pharmacology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo, 157-8535, Japan
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28
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Lolodi O, Wang YM, Wright WC, Chen T. Differential Regulation of CYP3A4 and CYP3A5 and its Implication in Drug Discovery. Curr Drug Metab 2017; 18:1095-1105. [PMID: 28558634 PMCID: PMC5709240 DOI: 10.2174/1389200218666170531112038] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/29/2017] [Accepted: 05/08/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND Cancer cells use several mechanisms to resist the cytotoxic effects of drugs, resulting in tumor progression and invasion. One such mechanism capitalizes on the body's natural defense against xenobiotics by increasing the rate of xenobiotic efflux and metabolic inactivation. Xenobiotic metabolism typically involves conversion of parent molecules to more soluble and easily excreted derivatives in reactions catalyzed by Phase I and Phase II drug metabolizing enzymes. METHODS We performed a structured search of peer-reviewed literature on P450 (CYP) 3A, with a focus on CYP3A4 and CYP3A5. RESULTS Recent reports indicate that components of the xenobiotic response system are upregulated in some diseases, including many cancers. Such components include the pregnane X receptor (PXR), CYP3A4 and CYP3A5 enzymes. The CYP3A enzymes are a subset of the numerous enzymes that are transcriptionally activated following the interaction of PXR and many ligands. CONCLUSION Intense research is ongoing to understand the functional ramifications of aberrant expression of these components in diseased states with the goal of designing novel drugs that can selectively target them.
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Affiliation(s)
- Ogheneochukome Lolodi
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yue-Ming Wang
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - William C. Wright
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, Tennessee, USA
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29
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Letsou W, Cai L. Noncommutative Biology: Sequential Regulation of Complex Networks. PLoS Comput Biol 2016; 12:e1005089. [PMID: 27560383 PMCID: PMC4999240 DOI: 10.1371/journal.pcbi.1005089] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 07/28/2016] [Indexed: 12/21/2022] Open
Abstract
Single-cell variability in gene expression is important for generating distinct cell types, but it is unclear how cells use the same set of regulatory molecules to specifically control similarly regulated genes. While combinatorial binding of transcription factors at promoters has been proposed as a solution for cell-type specific gene expression, we found that such models resulted in substantial information bottlenecks. We sought to understand the consequences of adopting sequential logic wherein the time-ordering of factors informs the final outcome. We showed that with noncommutative control, it is possible to independently control targets that would otherwise be activated simultaneously using combinatorial logic. Consequently, sequential logic overcomes the information bottleneck inherent in complex networks. We derived scaling laws for two noncommutative models of regulation, motivated by phosphorylation/neural networks and chromosome folding, respectively, and showed that they scale super-exponentially in the number of regulators. We also showed that specificity in control is robust to the loss of a regulator. Lastly, we connected these theoretical results to real biological networks that demonstrate specificity in the context of promiscuity. These results show that achieving a desired outcome often necessitates roundabout steps. DNA is the blueprint of life. Yet the order in which a cell follows these instructions makes it capable of generating thousands of different fates. How this information is extracted from underlying gene regulatory networks is unclear, especially given that biological networks are highly interconnected, and that the number of signaling pathways is relatively small (approximately 5–10). The conventional approach for increasing the information capacity of a limited set of regulators is to use them in combination. Surprisingly, combinatorial logic does not increase the diversity of target configurations or cell fates, but instead causes information bottlenecks. A different approach, called sequential logic, uses noncommutative sequences of a small set of regulators to drive networks to a large number of novel configurations. If certain targets are first protected, then even promiscuous regulators can activate specific subsets of lineage-specific targets. In this paper we show how sequential logic outperforms combinatorial logic, and argue that noncommutative sequences underlie a number of cases of biological regulation, e.g. how a small number of signaling pathways generates a large diversity of cell types in development. In addition to explaining biological networks, sequential logic may be a general experimental design strategy in synthetic and single-cell biology.
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Affiliation(s)
- William Letsou
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Long Cai
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
- * E-mail:
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30
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Lemche E, Chaban OS, Lemche AV. Neuroendocrinological and Epigenetic Mechanisms Subserving Autonomic Imbalance and HPA Dysfunction in the Metabolic Syndrome. Front Neurosci 2016; 10:142. [PMID: 27147943 PMCID: PMC4830841 DOI: 10.3389/fnins.2016.00142] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/21/2016] [Indexed: 12/18/2022] Open
Abstract
Impact of environmental stress upon pathophysiology of the metabolic syndrome (MetS) has been substantiated by epidemiological, psychophysiological, and endocrinological studies. This review discusses recent advances in the understanding of causative roles of nutritional factors, sympathomedullo-adrenal (SMA) and hypothalamic-pituitary adrenocortical (HPA) axes, and adipose tissue chronic low-grade inflammation processes in MetS. Disturbances in the neuroendocrine systems for leptin, melanocortin, and neuropeptide Y (NPY)/agouti-related protein systems have been found resulting directly in MetS-like conditions. The review identifies candidate risk genes from factors shown critical for the functioning of each of these neuroendocrine signaling cascades. In its meta-analytic part, recent studies in epigenetic modification (histone methylation, acetylation, phosphorylation, ubiquitination) and posttranscriptional gene regulation by microRNAs are evaluated. Several studies suggest modification mechanisms of early life stress (ELS) and diet-induced obesity (DIO) programming in the hypothalamic regions with populations of POMC-expressing neurons. Epigenetic modifications were found in cortisol (here HSD11B1 expression), melanocortin, leptin, NPY, and adiponectin genes. With respect to adiposity genes, epigenetic modifications were documented for fat mass gene cluster APOA1/C3/A4/A5, and the lipolysis gene LIPE. With regard to inflammatory, immune and subcellular metabolism, PPARG, NKBF1, TNFA, TCF7C2, and those genes expressing cytochrome P450 family enzymes involved in steroidogenesis and in hepatic lipoproteins were documented for epigenetic modifications.
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Affiliation(s)
- Erwin Lemche
- Section of Cognitive Neuropsychiatry, Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London London, UK
| | - Oleg S Chaban
- Section of Psychosomatic Medicine, Bogomolets National Medical University Kiev, Ukraine
| | - Alexandra V Lemche
- Department of Medical Science, Institute of Clinical Research Berlin, Germany
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Vyhlidal CA, Bi C, Ye SQ, Leeder JS. Dynamics of Cytosine Methylation in the Proximal Promoters of CYP3A4 and CYP3A7 in Pediatric and Prenatal Livers. ACTA ACUST UNITED AC 2016; 44:1020-6. [PMID: 26772622 DOI: 10.1124/dmd.115.068726] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/14/2016] [Indexed: 11/22/2022]
Abstract
Members of the human CYP3A family of metabolizing enzymes exhibit developmental changes in expression whereby CYP3A7 is expressed in fetal tissues, followed by a transition to expression of CYP3A4 in the first months of life. Despite knowledge about the general pattern of CYP3A activity in human development, the mechanisms that regulate developmental expression remain poorly understood. Epigenetic changes, including cytosine methylation, have been suggested to play a role in the regulation of CYP3A expression. The objective of this study was to investigate changes in cytosine methylation of the CYP3A4 and CYP3A7 genes in human pediatric and prenatal livers. The methylation status of cytosine-phospho-guanine dinucleotides was determined in 16 pediatric liver samples using methyl-seq and confirmed by bisulfite sequencing of 48 pediatric and 34 prenatal liver samples. Samples were separated by age into five groups (prenatal, < 1 year of age, 1.8-6 years, 7-11 years, and 12-17 years). Methyl-seq anaylsis revealed that cytosines in the proximal promoter of CYP3A7 are hypomethylated in neonates compared with adolescents (P < 0.001). In contrast, a cytosine 383 base pair upstream of CYP3A4 is hypermethylated in liver samples from neonates compared with adolescents (P = 0.00001). Developmental changes in methylation of cytosines in the proximal promoters of CYP3A4 and CYP3A7 in pediatric livers were confirmed by bisulfite sequencing. In addition, the methylation status of cytosine in the CYP3A4 and CYP3A7 proximal promoters correlated with changes in developmental expression of mRNA for the two enzymes.
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Affiliation(s)
- Carrie A Vyhlidal
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation (C.A.V., C.B., J.S.L.), and Division of Experimental and Translational Genetics (S.Q.Y.), Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Chengpeng Bi
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation (C.A.V., C.B., J.S.L.), and Division of Experimental and Translational Genetics (S.Q.Y.), Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Shui Qing Ye
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation (C.A.V., C.B., J.S.L.), and Division of Experimental and Translational Genetics (S.Q.Y.), Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - J Steven Leeder
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation (C.A.V., C.B., J.S.L.), and Division of Experimental and Translational Genetics (S.Q.Y.), Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
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Mátis G, Kulcsár A, Petrilla J, Hermándy-Berencz K, Neogrády Z. Feed-drug interaction of orally applied butyrate and phenobarbital on hepatic cytochrome P450 activity in chickens. J Anim Physiol Anim Nutr (Berl) 2015; 100:637-42. [PMID: 26614344 DOI: 10.1111/jpn.12416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 08/27/2015] [Indexed: 11/26/2022]
Abstract
The expression of hepatic drug-metabolizing cytochrome P450 (CYP) enzymes may be affected by several nutrition-derived compounds, such as by the commonly applied feed additive butyrate, possibly leading to feed-drug interactions. The aim of this study was to provide some evidence if butyrate can alter the activity of hepatic CYPs in chickens exposed to CYP-inducing xenobiotics, monitoring for the first time the possibility of such interaction. Ross 308 chickens in the grower phase were treated with daily intracoelomal phenobarbital (PB) injection (80 mg/kg BW), applied as a non-specific CYP-inducer, simultaneously with two different doses of intra-ingluvial sodium butyrate boluses (0.25 and 1.25 g/kg BW) for 5 days. Activity of CYP2H and CYP3A subfamilies was assessed by specific enzyme assays from isolated liver microsomes. According to our results, the lower dose of orally administered butyrate significantly attenuated the PB-triggered elevation of both hepatic CYP2H and CYP3A activities, which might be in association with the partly common signalling pathways of butyrate and CYP-inducing drugs, such as that of PB. Based on these data, butyrate may take part in pharmacoepigenetic interactions with simultaneously applied drugs or other CYP-inducing xenobiotics, with possible consequences for food safety and pharmacotherapy. Butyrate was found to be capable to maintain physiological CYP activity by attenuating CYP induction, underlining the safety of butyrate application in poultry nutrition.
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Affiliation(s)
- G Mátis
- Department of Physiology and Biochemistry, Faculty of Veterinary Science, Szent István University, Budapest, Hungary
| | - A Kulcsár
- Department of Physiology and Biochemistry, Faculty of Veterinary Science, Szent István University, Budapest, Hungary
| | - J Petrilla
- Department of Physiology and Biochemistry, Faculty of Veterinary Science, Szent István University, Budapest, Hungary
| | - K Hermándy-Berencz
- Department of Physiology and Biochemistry, Faculty of Veterinary Science, Szent István University, Budapest, Hungary
| | - Zs Neogrády
- Department of Physiology and Biochemistry, Faculty of Veterinary Science, Szent István University, Budapest, Hungary
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Quetglas EG, Mujagic Z, Wigge S, Keszthelyi D, Wachten S, Masclee A, Reinisch W. Update on pathogenesis and predictors of response of therapeutic strategies used in inflammatory bowel disease. World J Gastroenterol 2015; 21:12519-12543. [PMID: 26640330 PMCID: PMC4658608 DOI: 10.3748/wjg.v21.i44.12519] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 09/14/2015] [Indexed: 02/06/2023] Open
Abstract
The search for biomarkers that characterize specific aspects of inflammatory bowel disease (IBD), has received substantial interest in the past years and is moving forward rapidly with the help of modern technologies. Nevertheless, there is a direct demand to identify adequate biomarkers for predicting and evaluating therapeutic response to different therapies. In this subset, pharmacogenetics deserves more attention as part of the endeavor to provide personalized medicine. The ultimate goal in this area is the adjustment of medication for a patient’s specific genetic background and thereby to improve drug efficacy and safety rates. The aim of the following review is to utilize the latest knowledge on immunopathogenesis of IBD and update the findings on the field of Immunology and Genetics, to evaluate the response to the different therapies. In the present article, more than 400 publications were reviewed but finally 287 included based on design, reproducibility (or expectancy to be reproducible and translationable into humans) or already measured in humans. A few tests have shown clinical applicability. Other, i.e., genetic associations for the different therapies in IBD have not yet shown consistent or robust results. In the close future it is anticipated that this, cellular and genetic material, as well as the determination of biomarkers will be implemented in an integrated molecular diagnostic and prognostic approach to manage IBD patients.
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Samal J, Kandpal M, Vivekanandan P. Hepatitis B “e” antigen-mediated inhibition of HBV replication fitness and transcription efficiency in vitro. Virology 2015; 484:234-240. [DOI: 10.1016/j.virol.2015.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/25/2015] [Accepted: 06/02/2015] [Indexed: 01/04/2023]
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Li H, Zhang C, Ni F, Guo S, Wang W, Liu J, Lu X, Huang H, Zhang W. Gestational N-hexane inhalation alters the expression of genes related to ovarian hormone production and DNA methylation states in adult female F1 rat offspring. Toxicol Lett 2015; 239:141-51. [PMID: 26410608 DOI: 10.1016/j.toxlet.2015.09.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/27/2015] [Accepted: 09/23/2015] [Indexed: 11/15/2022]
Abstract
Research has revealed that n-hexane can disrupt adult female endocrine functions; however, few reports have focused on endocrine changes in adult F1 females after maternal exposure during gestation. In this study, female Wistar rats inhaled 100, 500, 2500, or 12,500 ppm n-hexane for 4 h daily during their initial 20 gestational days. The F1 female offspring exhibited abnormal oestrus cycles. Compared with the controls, the in vitro-cultured ovarian granulosa cells of the 12,500 ppm group showed significantly reduced in vitro progesterone and oestradiol secretion. Elevated progesterone secretion was observed in the 500 ppm group, and decreased and significantly upregulated mRNA expression of the Star, Cyp11a1, Cyp17a1, and Hsd3b genes was observed in the 12,500 ppm and 500 ppm groups, respectively. The protein expression levels were consistent with the mRNA expression levels. Methylation screening of the promoter regions of these genes was performed using MeDIP-chip and confirmed by methylation-sensitive high-resolution melting (MS-HRM), and the observed methylation state changes of the promoter regions were correlated with the gene expression levels. The results suggest that the hormone levels in the female offspring after gestational n-hexane inhalation correspond to the expression levels and DNA methylation states of the hormone production genes.
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Affiliation(s)
- Hong Li
- Department of Pharmaceuticals, Fujian Health College, Fuzhou 350101, China
| | - Chenyun Zhang
- Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350004, China
| | - Feng Ni
- Department of Pharmaceuticals, Fujian Health College, Fuzhou 350101, China
| | - Suhua Guo
- Department of Pharmaceuticals, Fujian Health College, Fuzhou 350101, China
| | - Wenxiang Wang
- Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350004, China
| | - Jing Liu
- Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350004, China
| | - Xiaoli Lu
- Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350004, China
| | - Huiling Huang
- Union Hospital of Fujian Medical University, Fuzhou 350000, China.
| | - Wenchang Zhang
- Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350004, China.
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Pulido-Salgado M, Vidal-Taboada JM, Saura J. C/EBPβ and C/EBPδ transcription factors: Basic biology and roles in the CNS. Prog Neurobiol 2015; 132:1-33. [PMID: 26143335 DOI: 10.1016/j.pneurobio.2015.06.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/08/2015] [Accepted: 06/16/2015] [Indexed: 02/01/2023]
Abstract
CCAAT/enhancer binding protein (C/EBP) β and C/EBPδ are transcription factors of the basic-leucine zipper class which share phylogenetic, structural and functional features. In this review we first describe in depth their basic molecular biology which includes fascinating aspects such as the regulated use of alternative initiation codons in the C/EBPβ mRNA. The physical interactions with multiple transcription factors which greatly opens the number of potentially regulated genes or the presence of at least five different types of post-translational modifications are also remarkable molecular mechanisms that modulate C/EBPβ and C/EBPδ function. In the second part, we review the present knowledge on the localization, expression changes and physiological roles of C/EBPβ and C/EBPδ in neurons, astrocytes and microglia. We conclude that C/EBPβ and C/EBPδ share two unique features related to their role in the CNS: whereas in neurons they participate in memory formation and synaptic plasticity, in glial cells they regulate the pro-inflammatory program. Because of their role in neuroinflammation, C/EBPβ and C/EBPδ in microglia are potential targets for treatment of neurodegenerative disorders. Any strategy to reduce C/EBPβ and C/EBPδ activity in neuroinflammation needs to take into account its potential side-effects in neurons. Therefore, cell-specific treatments will be required for the successful application of this strategy.
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Affiliation(s)
- Marta Pulido-Salgado
- Biochemistry and Molecular Biology Unit, School of Medicine, University of Barcelona, IDIBAPS, Casanova 143, planta 3, 08036 Barcelona, Spain
| | - Jose M Vidal-Taboada
- Biochemistry and Molecular Biology Unit, School of Medicine, University of Barcelona, IDIBAPS, Casanova 143, planta 3, 08036 Barcelona, Spain
| | - Josep Saura
- Biochemistry and Molecular Biology Unit, School of Medicine, University of Barcelona, IDIBAPS, Casanova 143, planta 3, 08036 Barcelona, Spain.
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He Y, Chevillet JR, Liu G, Kim TK, Wang K. The effects of microRNA on the absorption, distribution, metabolism and excretion of drugs. Br J Pharmacol 2015; 172:2733-47. [PMID: 25296724 PMCID: PMC4439871 DOI: 10.1111/bph.12968] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 09/18/2014] [Accepted: 09/26/2014] [Indexed: 12/17/2022] Open
Abstract
The importance of genetic factors (e.g. sequence variation) in the absorption, distribution, metabolism, excretion (ADME) and overall efficacy of therapeutic agents is well established. Our ability to identify, interpret and utilize these factors is the subject of much clinical investigation and therapeutic development. However, drug ADME and efficacy are also heavily influenced by epigenetic factors such as DNA/histone methylation and non-coding RNAs [especially microRNAs (miRNAs)]. Results from studies using tools, such as in silico miRNA target prediction, in vitro functional assays, nucleic acid profiling/sequencing and high-throughput proteomics, are rapidly expanding our knowledge of these factors and their effects on drug metabolism. Although these studies reveal a complex regulation of drug ADME, an increased understanding of the molecular interplay between the genome, epigenome and transcriptome has the potential to provide practically useful strategies to facilitate drug development, optimize therapeutic efficacy, circumvent adverse effects, yield novel diagnostics and ultimately become an integral component of personalized medicine.
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Affiliation(s)
- Y He
- Institute of Medical Systems Biology, Guangdong Medical CollegeDongguan, Guangdong, China
| | | | - G Liu
- Department of Chemistry and Biochemistry, North Dakota State UniversityFargo, ND, USA
| | - T K Kim
- Institute for Systems BiologySeattle, WA, USA
| | - K Wang
- Institute for Systems BiologySeattle, WA, USA
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Seripa D, Panza F, Daragjati J, Paroni G, Pilotto A. Measuring pharmacogenetics in special groups: geriatrics. Expert Opin Drug Metab Toxicol 2015; 11:1073-88. [PMID: 25990744 DOI: 10.1517/17425255.2015.1041919] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION The cytochrome P450 (CYP) enzymes oxidize about 80% of the most commonly used drugs. Older patients form a very interesting clinical group in which an increased prevalence of adverse drug reactions (ADRs) and therapeutic failures (TFs) is observed. Might CYP drug metabolism change with age, and justify the differences in drug response observed in a geriatric setting? AREAS COVERED A complete overview of the CYP pharmacogenetics with a focus on the epigenetic CYP gene regulation by DNA methylation in the context of advancing age, in which DNA methylation might change. EXPERT OPINION Responder phenotypes consist of a continuum spanning from ADRs to TFs, with the best responders at the midpoint. CYP genetics is the basis of this continuum on which environmental and physiological factors act, modeling the phenotype observed in clinical practice. Physiological age-related changes in DNA methylation, the main epigenetic mechanisms regulating gene expression in humans, results in a physiological decrease in CYP gene expression with advancing age. This may be one of the physiological changes that, together with increased drug use, contributed to the higher prevalence of ADRs and TFs observed in the geriatric setting, thus, making geriatrics a special group for pharmacogenetics.
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Affiliation(s)
- Davide Seripa
- IRCCS Casa Sollievo della Sofferenza, Geriatric Unit and Gerontology-Geriatrics Research Laboratory, Department of Medical Sciences , San Giovanni Rotondo, Foggia , Italy
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Peng L, Zhong X. Epigenetic regulation of drug metabolism and transport. Acta Pharm Sin B 2015; 5:106-12. [PMID: 26579435 PMCID: PMC4629221 DOI: 10.1016/j.apsb.2015.01.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/04/2015] [Accepted: 01/06/2015] [Indexed: 12/18/2022] Open
Abstract
The drug metabolism is a biochemical process on modification of pharmaceutical substances through specialized enzymatic systems. Changes in the expression of drug-metabolizing enzyme genes can affect drug metabolism. Recently, epigenetic regulation of drug-metabolizing enzyme genes has emerged as an important mechanism. Epigenetic regulation refers to heritable factors of genomic modifications that do not involve changes in DNA sequence. Examples of such modifications include DNA methylation, histone modifications, and non-coding RNAs. This review examines the widespread effect of epigenetic regulations on genes involved in drug metabolism, and also suggests a network perspective of epigenetic regulation. The epigenetic mechanisms have important clinical implications and may provide insights into effective drug development and improve safety of drug therapy.
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Key Words
- CAR, constitutive androstane receptor
- DNA methylation
- DNMTs, DNA methyltransferases
- Drug metabolism
- Epigenetics
- H3K27me3, histone 3 lysine 27 trimethylation
- H3K36me3, histone 3 lysine 36 trimethylation
- H3K4me1, histone 3 lysine 4 monomethylation
- H3K4me2, histone 3 lysine 4 dimethylation
- H3K4me3, histone 3 lysine 4 trimethylation
- H3K9me2, histone 3 lysine 9 dimethylation
- H3K9me3, histone 3 lysine 9 trimethylation
- HATs, histone acetyltransferases
- HDAC, histone deacetylases
- Histone modification
- Non-coding RNA
- P450s, cytochrome P450s
- SULTs, sulfotransferases
- TSS, transcription start sites
- Transporter
- UGTs, UDP-glucuronosyltransferases
- UTR, untranslated region
- lncRNAs, long non-coding RNAs
- miRNAs, microRNAs
- ncRNAs, non-coding RNAs
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Iwao T, Kodama N, Kondo Y, Kabeya T, Nakamura K, Horikawa T, Niwa T, Kurose K, Matsunaga T. Generation of enterocyte-like cells with pharmacokinetic functions from human induced pluripotent stem cells using small-molecule compounds. Drug Metab Dispos 2015; 43:603-10. [PMID: 25650381 DOI: 10.1124/dmd.114.062604] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The small intestine plays an important role in all aspects of pharmacokinetics, but there is no system for the comprehensive evaluation of small-intestinal pharmacokinetics, including drug metabolism and absorption. In this study, we aimed to construct an intestinal pharmacokinetics evaluation system and to generate pharmacokinetically functional enterocytes from human induced pluripotent stem cells. Using activin A and fibroblast growth factor 2, we differentiated these stem cells into intestinal stem cell-like cells, and the resulting cells were differentiated into enterocytes in a medium containing epidermal growth factor and small-molecule compounds. The differentiated cells expressed intestinal marker genes and drug transporters. The expression of sucrase-isomaltase, an intestine-specific marker, was markedly increased by small-molecule compounds. The cells exhibited activities of drug-metabolizing enzymes expressed in enterocytes, including CYP1A1/2, CYP2C9, CYP2C19, CYP2D6, CYP3A4/5, UGT, and sulfotransferase. Fluorescence-labeled dipeptide uptake into the cells was observed and was inhibited by ibuprofen, an inhibitor of the intestinal oligopeptide transporter solute carrier 15A1/PEPT1. CYP3A4 mRNA expression level was increased by these compounds and induced by the addition of 1α,25-dihydroxyvitamin D3. CYP3A4/5 activity was also induced by 1α,25-dihydroxyvitamin D3 in cells differentiated in the presence of the compounds. All these results show that we have generated enterocyte-like cells that have pharmacokinetic functions, and we have identified small-molecule compounds that are effective for promoting intestinal differentiation and the gain of pharmacokinetic functions. Our enterocyte-like cells would be useful material for developing a novel evaluation system to predict human intestinal pharmacokinetics.
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Affiliation(s)
- Takahiro Iwao
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., N.K., Y.K., K.N., T.M.); Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., T.K., K.N., T.M.); DMPK Research Laboratory, Mitsubishi Tanabe Pharma Corporation, Toda, Saitama, Japan (T.H., T.N.); Research & Development Department, Japan Bioindustry Association, Tokyo, Japan (T.N.); and The Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan (K.K.)
| | - Nao Kodama
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., N.K., Y.K., K.N., T.M.); Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., T.K., K.N., T.M.); DMPK Research Laboratory, Mitsubishi Tanabe Pharma Corporation, Toda, Saitama, Japan (T.H., T.N.); Research & Development Department, Japan Bioindustry Association, Tokyo, Japan (T.N.); and The Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan (K.K.)
| | - Yuki Kondo
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., N.K., Y.K., K.N., T.M.); Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., T.K., K.N., T.M.); DMPK Research Laboratory, Mitsubishi Tanabe Pharma Corporation, Toda, Saitama, Japan (T.H., T.N.); Research & Development Department, Japan Bioindustry Association, Tokyo, Japan (T.N.); and The Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan (K.K.)
| | - Tomoki Kabeya
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., N.K., Y.K., K.N., T.M.); Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., T.K., K.N., T.M.); DMPK Research Laboratory, Mitsubishi Tanabe Pharma Corporation, Toda, Saitama, Japan (T.H., T.N.); Research & Development Department, Japan Bioindustry Association, Tokyo, Japan (T.N.); and The Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan (K.K.)
| | - Katsunori Nakamura
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., N.K., Y.K., K.N., T.M.); Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., T.K., K.N., T.M.); DMPK Research Laboratory, Mitsubishi Tanabe Pharma Corporation, Toda, Saitama, Japan (T.H., T.N.); Research & Development Department, Japan Bioindustry Association, Tokyo, Japan (T.N.); and The Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan (K.K.)
| | - Takashi Horikawa
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., N.K., Y.K., K.N., T.M.); Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., T.K., K.N., T.M.); DMPK Research Laboratory, Mitsubishi Tanabe Pharma Corporation, Toda, Saitama, Japan (T.H., T.N.); Research & Development Department, Japan Bioindustry Association, Tokyo, Japan (T.N.); and The Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan (K.K.)
| | - Takuro Niwa
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., N.K., Y.K., K.N., T.M.); Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., T.K., K.N., T.M.); DMPK Research Laboratory, Mitsubishi Tanabe Pharma Corporation, Toda, Saitama, Japan (T.H., T.N.); Research & Development Department, Japan Bioindustry Association, Tokyo, Japan (T.N.); and The Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan (K.K.)
| | - Kouichi Kurose
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., N.K., Y.K., K.N., T.M.); Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., T.K., K.N., T.M.); DMPK Research Laboratory, Mitsubishi Tanabe Pharma Corporation, Toda, Saitama, Japan (T.H., T.N.); Research & Development Department, Japan Bioindustry Association, Tokyo, Japan (T.N.); and The Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan (K.K.)
| | - Tamihide Matsunaga
- Department of Clinical Pharmacy, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., N.K., Y.K., K.N., T.M.); Educational Research Center for Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan (T.I., T.K., K.N., T.M.); DMPK Research Laboratory, Mitsubishi Tanabe Pharma Corporation, Toda, Saitama, Japan (T.H., T.N.); Research & Development Department, Japan Bioindustry Association, Tokyo, Japan (T.N.); and The Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan (K.K.)
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Abstract
CYP3A ranks among the most abundant cytochrome P450 enzymes in the liver, playing a dominant role in metabolic elimination of clinically used drugs. A main member in CYP3A family, CYP3A4 expression and activity vary considerably among individuals, attributable to genetic and non-genetic factors, affecting drug dosage and efficacy. However, the extent of genetic influence has remained unclear. This review assesses current knowledge on the genetic factors influencing CYP3A4 activity. Coding region CYP3A4 polymorphisms are rare and account for only a small portion of inter-person variability in CYP3A metabolism. Except for the promoter allele CYP3A4*1B with ambiguous effect on expression, common CYP3A4 regulatory polymorphisms were thought to be lacking. Recent studies have identified a relatively common regulatory polymorphism, designated CYP3A4*22 with robust effects on hepatic CYP3A4 expression. Combining CYP3A4*22 with CYP3A5 alleles *1, *3 and *7 has promise as a biomarker predicting overall CYP3A activity. Also contributing to variable expression, the role of polymorphisms in transcription factors and microRNAs is discussed.
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Affiliation(s)
- Danxin Wang
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-614-292-7336; Fax: +1-614-292-7232
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Bolleyn J, Fraczek J, Rogiers V, Vanhaecke T. Epigenetic Modifications as Antidedifferentiation Strategy for Primary Hepatocytes in Culture. Methods Mol Biol 2015; 1250:203-211. [PMID: 26272144 DOI: 10.1007/978-1-4939-2074-7_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A well-known problem of cultured primary hepatocytes is their rapid dedifferentiation. During the last years, several strategies to counteract this phenomenon have been developed, of which changing the in vitro environment is the most popular one. However, mimicking the in vivo setting in vitro by adding soluble media additives or the restoration of both cell-cell and cell-extracellular matrix contacts is not sufficient and only delays the dedifferentiation process instead of counteracting it. In this chapter, new strategies to prevent the deterioration of the liver-specific phenotype of primary hepatocytes in culture by targeting the (epi)genetic mechanisms that drive hepatocellular gene expression are described.
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Affiliation(s)
- Jennifer Bolleyn
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
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43
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Englert NA, Luo G, Goldstein JA, Surapureddi S. Epigenetic modification of histone 3 lysine 27: mediator subunit MED25 is required for the dissociation of polycomb repressive complex 2 from the promoter of cytochrome P450 2C9. J Biol Chem 2014; 290:2264-78. [PMID: 25391650 DOI: 10.1074/jbc.m114.579474] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The Mediator complex is vital for the transcriptional regulation of eukaryotic genes. Mediator binds to nuclear receptors at target response elements and recruits chromatin-modifying enzymes and RNA polymerase II. Here, we examine the involvement of Mediator subunit MED25 in the epigenetic regulation of human cytochrome P450 2C9 (CYP2C9). MED25 is recruited to the CYP2C9 promoter through association with liver-enriched HNF4α, and we show that MED25 influences the H3K27 status of the HNF4α binding region. This region was enriched for the activating marker H3K27ac and histone acetyltransferase CREBBP after MED25 overexpression but was trimethylated when MED25 expression was silenced. The epigenetic regulator Polycomb repressive complex (PRC2), which represses expression by methylating H3K27, plays an important role in target gene regulation. Silencing MED25 correlated with increased association of PRC2 not only with the promoter region chromatin but with HNF4α itself. We confirmed the involvement of MED25 for fully functional preinitiation complex recruitment and transcriptional output in vitro. Formaldehyde-assisted isolation of regulatory elements (FAIRE) revealed chromatin conformation changes that were reliant on MED25, indicating that MED25 induced a permissive chromatin state that reflected increases in CYP2C9 mRNA. For the first time, we showed evidence that a functionally relevant human gene is transcriptionally regulated by HNF4α via MED25 and PRC2. CYP2C9 is important for the metabolism of many exogenous chemicals including pharmaceutical drugs as well as endogenous substrates. Thus, MED25 is important for regulating the epigenetic landscape resulting in transcriptional activation of a highly inducible gene, CYP2C9.
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Affiliation(s)
- Neal A Englert
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - George Luo
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Joyce A Goldstein
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Sailesh Surapureddi
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
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Björkhem-Bergman L, Johansson M, Morgenstern R, Rane A, Ekström L. Prenatal expression of thioredoxin reductase 1 (TRXR1) and microsomal glutathione transferase 1 (MGST1) in humans. FEBS Open Bio 2014; 4:886-91. [PMID: 25379386 PMCID: PMC4215115 DOI: 10.1016/j.fob.2014.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 10/07/2014] [Accepted: 10/08/2014] [Indexed: 11/24/2022] Open
Abstract
Thioredoxin reductase 1 (TRXR1) and microsomal glutathione transferase 1 (MGST1) are important redox and detoxifying enzymes in adult life. The aim of this study was to investigate the expression of these enzymes during fetal life. In addition, the role of gene methylation was studied since this might play an important role in the on-and-off switch of gene expression between fetal and adult life. To this end, the expression of the TRXR1-encoding gene TXNRD1 and the MGST1-encoding gene MGST1 was studied in fetal tissues. The mean mRNA expression of TXNRD1 in fetal livers were seven times higher compared to the mean expression in adult livers (p < 0.001). Of the six studied splice variants of TXNRD1, four had a significantly higher expression in the fetal livers as compared to adult livers. The mean expression of MGST1 was twofold higher in adult compared to fetal liver tissue (p = 0.01). For MGST1 the alternative first exon 1B was the predominant splice variant in both fetal and adult liver samples. The highest mRNA expression of both TXNRD1 and MGST1 was found in fetal adrenals, whereas expression was lower in fetal liver, lungs and kidneys. There was a significant correlation between the hepatic expression of TXNRD1 and MGST1. Treatment with the demethylating agent 5-AZA resulted in decreased levels of TXNRD1 in human liver HepG2 cells but did not affect the expression of MGST1. In conclusion, the expression of TXNRD1 is higher in fetuses than in adults and might be of importance during fetal life. Hepatic TXNRD1 and MGST1 are co-expressed in both fetuses and adults suggesting common regulatory mechanisms.
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Affiliation(s)
- Linda Björkhem-Bergman
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, SE-141 86 Stockholm, Sweden
| | - Maria Johansson
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, SE-141 86 Stockholm, Sweden
| | - Ralf Morgenstern
- Institute of Environmental Medicine, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Anders Rane
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, SE-141 86 Stockholm, Sweden
| | - Lena Ekström
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Huddinge, SE-141 86 Stockholm, Sweden
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Chen Y, Yin D, Li L, Deng YC, Tian W. Screening aberrant methylation profile in esophageal squamous cell carcinoma for Kazakhs in Xinjiang area of China. Mol Biol Rep 2014; 42:457-64. [DOI: 10.1007/s11033-014-3788-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 09/30/2014] [Indexed: 11/28/2022]
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46
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Meaney S. Epigenetic regulation of cholesterol homeostasis. Front Genet 2014; 5:311. [PMID: 25309573 PMCID: PMC4174035 DOI: 10.3389/fgene.2014.00311] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 08/20/2014] [Indexed: 01/15/2023] Open
Abstract
Although best known as a risk factor for cardiovascular disease, cholesterol is a vital component of all mammalian cells. In addition to key structural roles, cholesterol is a vital biochemical precursor for numerous biologically important compounds including oxysterols and bile acids, as well as acting as an activator of critical morphogenic systems (e.g., the Hedgehog system). A variety of sophisticated regulatory mechanisms interact to coordinate the overall level of cholesterol in cells, tissues and the entire organism. Accumulating evidence indicates that in additional to the more “traditional” regulatory schemes, cholesterol homeostasis is also under the control of epigenetic mechanisms such as histone acetylation and DNA methylation. The available evidence supporting a role for these mechanisms in the control of cholesterol synthesis, elimination, transport and storage are the focus of this review.
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Affiliation(s)
- Steve Meaney
- School of Biological Sciences, College of Sciences and Health, Dublin Institute of Technology Dublin, Ireland ; Environmental Sustainability and Health Institute, Dublin Institute of Technology Dublin, Ireland
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Sun Q, Xie Y, Wang G, Li J. Identification of genes in HepG2 cells that respond to DNA methylation and histone deacetylation inhibitor treatment. Exp Ther Med 2014; 8:813-817. [PMID: 25120605 PMCID: PMC4113545 DOI: 10.3892/etm.2014.1789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 05/14/2014] [Indexed: 12/21/2022] Open
Abstract
Previous studies have demonstrated that epigenetics has an important role in the regulation of gene expression in cancer. Epigenetics is the study of reversible, heritable changes in gene function, which occur independently from changes in the DNA sequence. DNA methylation and histone deacetylation are the two most important epigenetic modifications. DNA methylation was one of the first discovered epigenetic modifications and it may lead to changes in chromatin structure, DNA conformation and DNA stability, thereby controlling gene expression. Sample data on the HepG2 cell line from the Gene Expression Omnibus database under GSE5230 accession number were obtained and GEOquery and the limma package were then used to analyze the data and identify differentially expressed genes using Gene Otology. This was conducted in order to investigate the effect on gene expression of inhibiting DNA methylation and histone deacetylation, and to explore the potential role of epigenetics in the development and treatment of hepatic carcinoma. It was found that inhibition of DNA methylation and histone deacetylation affected not only substance metabolism, but also the immune activity in HepG2 cells. Furthermore, common target sites for transcription factors were identified in the differentially expressed genes. It may be concluded that the inhibition of DNA methylation and histone deacetylation contributes to the treatment of hepatic carcinoma and may provide a novel therapeutic strategy for the treatment of hepatic cancer.
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Affiliation(s)
- Qiang Sun
- General Surgery Department, The Second Artillery General Hospital of PLA, Beijing 100088, P.R. China
| | - Yu Xie
- General Surgery Department, The Second Artillery General Hospital of PLA, Beijing 100088, P.R. China
| | - Guojing Wang
- General Surgery Department, The Second Artillery General Hospital of PLA, Beijing 100088, P.R. China
| | - Jidong Li
- Surgical Oncology Department, Chinese PLA General Hospital, Beijing 100853, P.R. China
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Wang Z, Curry E, Montana G. Network-guided regression for detecting associations between DNA methylation and gene expression. ACTA ACUST UNITED AC 2014; 30:2693-701. [PMID: 24919878 DOI: 10.1093/bioinformatics/btu361] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION High-throughput profiling in biological research has resulted in the availability of a wealth of data cataloguing the genetic, epigenetic and transcriptional states of cells. These data could yield discoveries that may lead to breakthroughs in the diagnosis and treatment of human disease, but require statistical methods designed to find the most relevant patterns from millions of potential interactions. Aberrant DNA methylation is often a feature of cancer, and has been proposed as a therapeutic target. However, the relationship between DNA methylation and gene expression remains poorly understood. RESULTS We propose Network-sparse Reduced-Rank Regression (NsRRR), a multivariate regression framework capable of using prior biological knowledge expressed as gene interaction networks to guide the search for associations between gene expression and DNA methylation signatures. We use simulations to show the advantage of our proposed model in terms of variable selection accuracy over alternative models that do not use prior network information. We discuss an application of NsRRR to The Cancer Genome Atlas datasets on primary ovarian tumours. AVAILABILITY AND IMPLEMENTATION R code implementing the NsRRR model is available at http://www2.imperial.ac.uk/∼gmontana CONTACT giovanni.montana@kcl.ac.uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zi Wang
- Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Edward Curry
- Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK
| | - Giovanni Montana
- Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK Department of Mathematics, Imperial College London, London SW7 2AZ, Division of Cancer, Imperial College London, Hammersmith Hospital, London W12 0NN and Department of Biomedical Engineering, King's College London, St Thomas' Hospital, London SE1 7EH, UK
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49
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Tu T, Budzinska MA, Maczurek AE, Cheng R, Di Bartolomeo A, Warner FJ, McCaughan GW, McLennan SV, Shackel NA. Novel aspects of the liver microenvironment in hepatocellular carcinoma pathogenesis and development. Int J Mol Sci 2014; 15:9422-58. [PMID: 24871369 PMCID: PMC4100103 DOI: 10.3390/ijms15069422] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a prevalent primary liver cancer that is derived from hepatocytes and is characterised by high mortality rate and poor prognosis. While HCC is driven by cumulative changes in the hepatocyte genome, it is increasingly recognised that the liver microenvironment plays a pivotal role in HCC propensity, progression and treatment response. The microenvironmental stimuli that have been recognised as being involved in HCC pathogenesis are diverse and include intrahepatic cell subpopulations, such as immune and stellate cells, pathogens, such as hepatitis viruses, and non-cellular factors, such as abnormal extracellular matrix (ECM) and tissue hypoxia. Recently, a number of novel environmental influences have been shown to have an equally dramatic, but previously unrecognized, role in HCC progression. Novel aspects, including diet, gastrointestinal tract (GIT) microflora and circulating microvesicles, are now being recognized as increasingly important in HCC pathogenesis. This review will outline aspects of the HCC microenvironment, including the potential role of GIT microflora and microvesicles, in providing new insights into tumourigenesis and identifying potential novel targets in the treatment of HCC.
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Affiliation(s)
- Thomas Tu
- Liver Cell Biology, Centenary Institute, Sydney, NSW 2050, Australia.
| | | | | | - Robert Cheng
- Liver Cell Biology, Centenary Institute, Sydney, NSW 2050, Australia.
| | - Anna Di Bartolomeo
- School of Medicine, University of Adelaide, Adelaide, SA 5005, Australia.
| | - Fiona J Warner
- Liver Cell Biology, Centenary Institute, Sydney, NSW 2050, Australia.
| | | | - Susan V McLennan
- Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia.
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50
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Oda S, Fukami T, Yokoi T, Nakajima M. Epigenetic regulation of the tissue-specific expression of human UDP-glucuronosyltransferase (UGT) 1A10. Biochem Pharmacol 2014; 87:660-7. [DOI: 10.1016/j.bcp.2013.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 11/04/2013] [Accepted: 11/04/2013] [Indexed: 11/28/2022]
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