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Jackson KD, Achour B, Lee J, Geffert RM, Beers JL, Latham BD. Novel Approaches to Characterize Individual Drug Metabolism and Advance Precision Medicine. Drug Metab Dispos 2023; 51:1238-1253. [PMID: 37419681 PMCID: PMC10506699 DOI: 10.1124/dmd.122.001066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023] Open
Abstract
Interindividual variability in drug metabolism can significantly affect drug concentrations in the body and subsequent drug response. Understanding an individual's drug metabolism capacity is important for predicting drug exposure and developing precision medicine strategies. The goal of precision medicine is to individualize drug treatment for patients to maximize efficacy and minimize drug toxicity. While advances in pharmacogenomics have improved our understanding of how genetic variations in drug-metabolizing enzymes (DMEs) affect drug response, nongenetic factors are also known to influence drug metabolism phenotypes. This minireview discusses approaches beyond pharmacogenetic testing to phenotype DMEs-particularly the cytochrome P450 enzymes-in clinical settings. Several phenotyping approaches have been proposed: traditional approaches include phenotyping with exogenous probe substrates and the use of endogenous biomarkers; newer approaches include evaluating circulating noncoding RNAs and liquid biopsy-derived markers relevant to DME expression and function. The goals of this minireview are to 1) provide a high-level overview of traditional and novel approaches to phenotype individual drug metabolism capacity, 2) describe how these approaches are being applied or can be applied to pharmacokinetic studies, and 3) discuss perspectives on future opportunities to advance precision medicine in diverse populations. SIGNIFICANCE STATEMENT: This minireview provides an overview of recent advances in approaches to characterize individual drug metabolism phenotypes in clinical settings. It highlights the integration of existing pharmacokinetic biomarkers with novel approaches; also discussed are current challenges and existing knowledge gaps. The article concludes with perspectives on the future deployment of a liquid biopsy-informed physiologically based pharmacokinetic strategy for patient characterization and precision dosing.
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Affiliation(s)
- Klarissa D Jackson
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.D.J., J.L., R.M.G., J.L.B., B.D.L.); and Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island (B.A.)
| | - Brahim Achour
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.D.J., J.L., R.M.G., J.L.B., B.D.L.); and Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island (B.A.)
| | - Jonghwa Lee
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.D.J., J.L., R.M.G., J.L.B., B.D.L.); and Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island (B.A.)
| | - Raeanne M Geffert
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.D.J., J.L., R.M.G., J.L.B., B.D.L.); and Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island (B.A.)
| | - Jessica L Beers
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.D.J., J.L., R.M.G., J.L.B., B.D.L.); and Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island (B.A.)
| | - Bethany D Latham
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.D.J., J.L., R.M.G., J.L.B., B.D.L.); and Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island (B.A.)
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2
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Bian J, Zhao J, Zhao Y, Hao X, He S, Li Y, Huang L. Impact of individual factors on DNA methylation of drug metabolism genes: A systematic review. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2023; 64:401-415. [PMID: 37522536 DOI: 10.1002/em.22567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 07/12/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023]
Abstract
Individual differences in drug response have always existed in clinical treatment. Many non-genetic factors show non-negligible impacts on personalized medicine. Emerging studies have demonstrated epigenetic could connect non-genetic factors and individual treatment differences. We used systematic retrieval methods and reviewed studies that showed individual factors' impact on DNA methylation of drug metabolism genes. In total, 68 studies were included, and half (n = 36) were cohort studies. Six aspects of individual factors were summarized from the perspective of personalized medicine: parental exposure, environmental pollutants exposure, obesity and diet, drugs, gender and others. The most research (n = 11) focused on ABCG1 methylation. The majority of studies showed non-genetic factors could result in a significant DNA methylation alteration in drug metabolism genes, which subsequently affects the pharmacokinetic processes. However, the underlying mechanism remained unknown. Finally, some viewpoints were presented for future research.
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Affiliation(s)
- Jialu Bian
- Department of Pharmacy, People's Hospital of Peking University, Beijing, China
- Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmaceutical Science, Peking University, Beijing, China
| | - Jinxia Zhao
- Department of Pharmacy, People's Hospital of Peking University, Beijing, China
- Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmaceutical Science, Peking University, Beijing, China
| | - Yinyu Zhao
- Department of Pharmacy, People's Hospital of Peking University, Beijing, China
- Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmaceutical Science, Peking University, Beijing, China
| | - Xu Hao
- Department of Pharmacy, People's Hospital of Peking University, Beijing, China
| | - Shiyu He
- Department of Pharmacy, People's Hospital of Peking University, Beijing, China
- Department of Pharmacy Administration and Clinical Pharmacy, School of Pharmaceutical Science, Peking University, Beijing, China
| | - Yuanyuan Li
- Department of Pharmacy, People's Hospital of Peking University, Beijing, China
| | - Lin Huang
- Department of Pharmacy, People's Hospital of Peking University, Beijing, China
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3
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Jin J, Zhong XB. Epigenetic Mechanisms Contribute to Intraindividual Variations of Drug Metabolism Mediated by Cytochrome P450 Enzymes. Drug Metab Dispos 2023; 51:672-684. [PMID: 36973001 PMCID: PMC10197210 DOI: 10.1124/dmd.122.001007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 02/24/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Significant interindividual and intraindividual variations on cytochrome P450 (CYP)-mediated drug metabolism exist in the general population globally. Genetic polymorphisms are one of the major contribution factors for interindividual variations, but epigenetic mechanisms mainly contribute to intraindividual variations, including DNA methylation, histone modifications, microRNAs, and long non-coding RNAs. The current review provides analysis of advanced knowledge in the last decade on contributions of epigenetic mechanisms to intraindividual variations on CYP-mediated drug metabolism in several situations, including (1) ontogeny, the developmental changes of CYP expression in individuals from neonates to adults; (2) increased activities of CYP enzymes induced by drug treatment; (3) increased activities of CYP enzymes in adult ages induced by drug treatment at neonate ages; and (4) decreased activities of CYP enzymes in individuals with drug-induced liver injury (DILI). Furthermore, current challenges, knowledge gaps, and future perspective of the epigenetic mechanisms in development of CYP pharmacoepigenetics are discussed. In conclusion, epigenetic mechanisms have been proven to contribute to intraindividual variations of drug metabolism mediated by CYP enzymes in age development, drug induction, and DILI conditions. The knowledge has helped understanding how intraindividual variation are generated. Future studies are needed to develop CYP-based pharmacoepigenetics to guide clinical applications for precision medicine with improved therapeutic efficacy and reduced risk of adverse drug reactions and toxicity. SIGNIFICANCE STATEMENT: Understanding epigenetic mechanisms in contribution to intraindividual variations of CYP-mediated drug metabolism may help to develop CYP-based pharmacoepigenetics for precision medicine to improve therapeutic efficacy and reduce adverse drug reactions and toxicity for drugs metabolized by CYP enzymes.
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Affiliation(s)
- Jing Jin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
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Dehdari H, Moradian F, Barzegar A, Ebrahimzadeh MA. CYP1A1 contiguous hypermethylation within a putative CpG block is associated with breast cancer progression: Feasibility to define boundary motives. Exp Cell Res 2022; 413:113062. [PMID: 35167827 DOI: 10.1016/j.yexcr.2022.113062] [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: 07/06/2021] [Revised: 02/03/2022] [Accepted: 02/11/2022] [Indexed: 11/04/2022]
Abstract
Having broad specificity for xenobiotics metabolism throughout the body, cytochrome P450 (CYP) isoform 1A1 is of key relevance for carcinogenesis. However, the oncogenic potential of its altered transcription and the underlying mechanism has not been well-established in breast cancer. Direct bisulfite sequencing PCR (BSP) of the CYP1A1 promoter, enriched by 113 CpGs within and flanking the xenobiotic response elements (XREs) 2 to 10, in paired cancerous and normal tissues from 40 breast cancer patients revealed three distinctly methylated patterns; unmethylated (XREs 2 to 6) and completely methylated (XREs 7 and 8) CpGs, in common for the normal and cancerous tissues, and a putative 171bp CpG block (XREs 9 and 10) contiguously hypermethylated in the tumor tissues. Increased transcription of CYP1A1, observed for the cancerous tissues, was correlated with the hypermethylation of given CpG block, besides simultaneously being associated with upregulation of the anti-apoptotic BCL-2. Clinical value of the methylation changes, investigated based on the comparisons between the tissue cohorts of different clinicopathological features, exhibited gradual hypermethylation of the corresponding CpG block following disease progression as well as lymphatic involvement. Hypermethylation of given CpG block may has potential to be used as a biomarker for diagnosis and progression of breast cancer.
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Affiliation(s)
- Hossein Dehdari
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Fatemeh Moradian
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, Sari, Iran
| | - Ali Barzegar
- Department of Basic Sciences, Sari Agricultural Sciences and Natural Resources University, Sari, Iran.
| | - Mohammad Ali Ebrahimzadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
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Golestanian R, Barzegar A, Mianji GR, Ebrahimzadeh MA, Fatemi B. Evaluation of alternations in DNA methylation of CYP3A4 gene upstream regulatory elements in gastric cancer and in response to Diazinon treatment. Curr Drug Metab 2022; 23:242-250. [PMID: 35331105 DOI: 10.2174/1389200223666220324094645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Little is known about cytochrome P450 3A4 (CYP3A4) DNA methylation and transcription alterations in gastric cancer. OBJECTIVE In this paper, we initially aimed to address the effect of diazinon pesticide on DNA methylation and transcription changes of the CYP3A4 gene in a human gastric cell line. In the next step, we studied the methylation differences of CpG sites within the upstream regulatory regions of the CYP3A4 gene among human gastric cancerous and healthy tissues. METHODS For the in vitro assay, the methylation changes of the C/EBP response element and transcript level of the CYP3A4 gene were studied following treatment of the AGS cell line with various concentrations of diazinon pesticide. In the next phase, the methylation percentages of 24 CpG sites within or around the upstream regulatory elements including near promoter, C/EBP binding site, XREM, and CLEM4 in 11 specimens of human gastric cancer tissue were compared to their adjacent healthy tissues. RESULTS Treatment with 10 µM Diazinon significantly increased the CYP3A4 gene transcription by approximately 27-fold, which was correlated with the hypermethylation of 3 CpGs in C/EBP binding sites including -5998, -5731 and -5725 (p<0.001 for all comparisons). Results of bisulfite sequencing revealed that the CpG sites which are located in -1521 (p=0.003), -1569 (p=0.027), -10813 (p=0.003), -10851 (p=0.001) and -10895 (p=0.0) bp from transcription start site, were significantly hypermethylated in cancerous tissues comparing to their healthy cohort. CONCLUSION Hypermethylation of CLEM4 and a region near the core promoter may have a significant association with gastric cancer incidence.
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Affiliation(s)
- Ramin Golestanian
- Department of Basic Sciences, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran
| | - Ali Barzegar
- Department of Basic Sciences, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran
| | - Ghodrat Rahimi Mianji
- Faculty of Animal Science and Fisheries, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran
| | - Mohammad Ali Ebrahimzadeh
- Pharmaceutical Sciences Research Center, School of Pharmacy, Mazandaran University of Medical Science, Sari, Iran
| | - Behnaz Fatemi
- Department of Basic Sciences, Sari University of Agricultural Sciences and Natural Resources, Sari, Iran
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6
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Neumann E, Schreeck F, Herberg J, Jacqz Aigrain E, Maitland-van der Zee AH, Pérez-Martínez A, Hawcutt DB, Schaeffeler E, Rane A, de Wildt SN, Schwab M. How paediatric drug development and use could benefit from OMICs: a c4c expert group white paper. Br J Clin Pharmacol 2022; 88:5017-5033. [PMID: 34997627 DOI: 10.1111/bcp.15216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/01/2022] Open
Abstract
The safety and efficacy of pharmacotherapy in children, particularly preterms, neonates, and infants, is limited by a paucity of good quality data from prospective clinical drug trials. A specific challenge is the establishment of valid biomarkers. OMICs technologies may support these efforts, by complementary information about targeted and non-targeted molecules through systematic characterization and quantitation of biological samples. OMICs technologies comprise at least genomics, epigenomics, transcriptomics, proteomics, metabolomics, and microbiomics in addition to the patient's phenotype. OMICs technologies are in part hypothesis-generating allowing an in depth understanding of disease pathophysiology and pharmacological mechanisms. Application of OMICs technologies in paediatrics faces major challenges before routine adoption. First, developmental processes need to be considered, including a sub-division into specific age groups as developmental changes clearly impact OMICs data. Second, compared to the adult population, the number of patients is limited as well as type and amount of necessary biomaterial, especially in neonates and preterms. Thus, advanced trial designs and biostatistical methods, non-invasive biomarkers, innovative biobanking concepts including data and samples from healthy children, as well as analytical approaches (e.g. liquid biopsies) should be addressed to overcome these obstacles. The ultimate goal is to link OMICs technologies with innovative analysis tools, like artificial intelligence at an early stage. The use of OMICs data based on a feasible approach will contribute to identify complex phenotypes and subpopulations of patients to improve development of medicines for children with potential economic advantages.
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Affiliation(s)
- Eva Neumann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany
| | - Filippa Schreeck
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany
| | - Jethro Herberg
- Department of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Evelyne Jacqz Aigrain
- Pediatric Pharmacology and Pharmacogenetics, Hopital Universitaire Saint-Louis, Paris, France.,Clinical Investigation Center CIC1426, Hôpital Robert Debre, Paris, France.,Pharmacology, University of Paris, Paris, France
| | | | - Antonio Pérez-Martínez
- Institute for Health Research (IdiPAZ), La Paz University Hospital, Madrid, Spain.,Pediatric Onco-Hematology Department, La Paz University Hospital, Madrid, Spain.,Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain
| | - Daniel B Hawcutt
- Department of Women's and Children's Health, University of Liverpool, UK.,NIHR Alder Hey Clinical Research Facility, Alder Hey Children's Hospital, Liverpool, UK
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany
| | - Anders Rane
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Saskia N de Wildt
- Department of Pharmacology and Toxicology, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands.,Intensive Care and Department of Paediatric Surgery, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany.,Departments of Clinical Pharmacology, and of Biochemistry and Pharmacy, University of Tuebingen, Tuebingen, Germany
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Collins JM, Wang D. Cytochrome P450 3A4 (CYP3A4) protein quantification using capillary western blot technology and total protein normalization. J Pharmacol Toxicol Methods 2021; 112:107117. [PMID: 34474151 DOI: 10.1016/j.vascn.2021.107117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/27/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022]
Abstract
The western blot (WB) is the predominate method for protein quantification, frequently used in pharmacological and toxicological studies. To control for technical variation, WB signals are normalized through immunodetection of an internal standard "house-keeping" gene or total protein quantification via staining of the same blot or a duplicate, sister blot. Increasing evidence suggests that house-keeping genes are subject to change after drug treatment or under disease states, causing protein quantification errors in WB. Recent advances in automated capillary-based WB technologies enable measurement of the protein of interest, internal standards, and total protein in a single capillary. Using this approach, we quantified cytochrome P450 3A4 (CYP3A4) across 179 liver samples and compared normalization by both β-actin and total protein to determine which better functions as an internal standard. CYP3A4 is responsible for metabolism of a wide array of xenobiotics and is known to exhibit large inter-person variation, making it a good candidate to evaluate protein quantification. We observed significant differences in β-actin protein levels between liver samples (~20-fold) and found better correlation between CYP3A4 protein and mRNA using total protein normalization than β-actin, indicating total protein normalization to be less error prone for estimation of CYP3A4. Furthermore, by using total protein normalization, we confirmed significant association between CYP3A4 protein expression and the functional CYP3A4 variant CYP3A4*22, which contains two linked SNPs rs35599367 and rs62471956. Our results indicate that the automatic capillary WB instrument combined with total protein normalization provides a high throughput and robust approach for protein quantification.
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Affiliation(s)
- Joseph M Collins
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States of America
| | - Danxin Wang
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States of America.
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8
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Emerging noninvasive methylation biomarkers of cancer prognosis and drug response prediction. Semin Cancer Biol 2021; 83:584-595. [PMID: 33757849 DOI: 10.1016/j.semcancer.2021.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/15/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022]
Abstract
Cancer is the second leading cause of death worldwide being responsible for 9.6 million deaths in 2018. Epigenetic alterations are key in directing the aberrant expression of tumor-associated genes that drive cellular malignant transformation and cancer progression. Among epigenetic alterations, DNA methylation is the most deeply studied one in relation to environmental exposure. Tissue biopsies have traditionally been the main procedure by which a small sample of body tissue is excised to confirm cancer diagnosis or to indicate the primary site when cancer has spread. In contrast, the analysis of circulating tumor-derived material, or tumor circulome, by means of liquid biopsy of peripheral blood, urine, saliva or sputum is a noninvasive, fast and reproducible alternative to tissue biopsy. Recently, the assessment of epigenetic alterations such as DNA methylation and hydroxymethylation in circulating free DNA has been proved possible. These marks can be associated to prognosis and response to a variety of treatments including chemotherapy, hormonotherapy or immunotherapy. Epigenetic biomarkers may offer some advantages over RNA or genetic biomarkers given their stability in bodily fluids and their high tissue-specificity. While many challenges are still ahead, the unique advantages of these types of biomarkers is urging the scientific community to persevere in their clinical validation and integration into reliable prediction models. This review aims at recapitulating the emerging noninvasive DNA methylated biomarkers of importance for prediction of prognosis and drug response in cancer.
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A new parameter in multiple myeloma: CYP3A4*1B single nucleotide polymorphism. Ann Hematol 2020; 100:421-427. [PMID: 33170343 PMCID: PMC7653211 DOI: 10.1007/s00277-020-04339-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 11/03/2020] [Indexed: 12/19/2022]
Abstract
Multiple myeloma (MM) is a disease caused by malignant plasma cells, causing free light chain release accompanying the increase in monoclonal immunoglobulin. Cytochrome P450 (CYP) is one of the large and functional enzyme families composed of various hemoproteins. This protein network has been shown to play a role in many treatment steps in current practices. We aimed to investigate the relationship between genotypes of CYP3A4*1B and treatment response and prognosis of MM. Seventy-two patients diagnosed with MM between January 2016 and 2020 and 100 healthy people to create a control group participated in our study. Genotypes were classified in 3 separate groups as NN, MN, and MM. Both PFS and OS were significantly higher in the NN genotype (p = 0.001, p = 0.014). Being under the age of 65 was 27.988 times more protective for OS and 4.496 times for PFS (p = 0.006, p = 0.017). NN genotype was shown to be 41.666-fold protective for OS and 3.144-fold protective for PFS (p = 0.004, p = 0.030). This study demonstrated that CYP3A4*1B NN genotype, which is an important cytochrome p450 member for the treatment of MM, was 41.666-fold protective for OS and 3.144-fold protective for PFS. It was shown in this study for the first time in the literature as a valuable contribution.
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10
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Hypomethylation of the XRE -1383 site is associated with the upregulation of CYP1A1 in gastric adenocarcinoma. Gene 2020; 769:145216. [PMID: 33069801 DOI: 10.1016/j.gene.2020.145216] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/12/2020] [Accepted: 10/02/2020] [Indexed: 01/08/2023]
Abstract
Owing to its broad substrate specificity of mainly xenobiotics and its preferential extrahepatic expression, cytochrome P450 1A1 (CYP1A1) is a principle member of the CYP detoxifying enzyme superfamily involving in carcinogenesis. Methylation status of 93 CpG sites, densely scattered within approximately 1.5 kb 5' regulatory region of CYP1A1, and its association with gene transcription was analyzed in tissue cohorts dissected from 40 patients with gastric cancer. Bisulfite sequencing and the resulting methylation percentages revealed dynamically methylated CpG sites located within or around xenobiotic response elements (XRE) 4-10, and a region of consistent hypermethylation located near proximal promoter, encompassing XRE2-3. Statistical analysis revealed significant differences of the methylation percentages at the CpG sites -1415 (0.032) and -1524 (P = 0.041) (located at the close upstream region of XRE10) between cancerous and normal gastric tissues as well as between those with and without lymphatic involvement. Quantitative real time PCR analysis showed that the CYP1A1 gene expression significantly increases in cancerous tissues compared to their normal tissue cohort, and is significantly associated with hypomethylation at the CpG site -1383 (P = 0.018) within the XRE10 motif. These data suggest that the variably methylated CpG site from the 5' regulatory region of CYP1A1, corresponding with the XRE10 regulatory region, is associated with its gene upregulation thus, is likely involved in gastric cancer incidence and metastasis. Methylation analysis of the CpG sites located within or around the XRE10 motif of the CYP1A1 promoter can be used as a potential marker to evaluate individual susceptibility to gastric cancer.
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11
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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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Abstract
The CYP3A4 enzyme is the most abundant drug-metabolizing enzyme in the liver, metabolizing ~50% of commonly used medications. CYP3A4 displays large interperson variability in expression and enzyme activity with unknown causes. This study aims to identify cis-acting regulatory elements controlling the transcription of CYP3A4, using chromatin conformation capture (4C and 3C assays), chromatin immunoprecipitation followed by quantitative PCR (ChIP-qPCR), clustered regularly interspaced short palindromic repeats (CRISPR)-mediated deletions of genomic regions and reporter gene assays in primary culture human hepatocytes and hepatic cell lines. 4C assays identified four regions (R1-R4) interacting with the CYP3A4 promoter, one of which overlaps with the previously identified upstream enhancers CLEM4/XREM (R2) while the other three are novel. ChIP-qPCR, reporter gene assays and CRISPR-mediated deletion experiments indicate regulatory roles for both R2 and R4. Interestingly, the deletion of R4 increased CYP3A4 while decreasing CYP3A43 expression, possibly due to competitive domain-domain interactions within the CYP3A cluster, supported by deletion of R4 increasing interaction between the CYP3A4 promoter and R2. We also identified a single nucleotide polymorphism rs62471956 within R4, with the variant allele A having increased transcriptional activity in a reporter gene assay. The rs62471956 A allele is associated with higher CYP3A43 expression and lower CYP3A4 expression in a cohort of 136 liver samples, further supporting the opposing effects of R4 on CYP3A4 and CYP3A43. rs62471956 is in complete linkage disequilibrium with CYP3A4*22, potentially contributing to reduced expression of CYP3A4*22. These results validate previously identified enhancers (CLEM4 and XREM) of CYP3A4 and demonstrate additional regulatory mechanisms underlying CYP3A4 transcriptional control via competitive domain-domain interactions within the CYP3A cluster.
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Lauschke VM, Zhou Y, Ingelman-Sundberg M. Novel genetic and epigenetic factors of importance for inter-individual differences in drug disposition, response and toxicity. Pharmacol Ther 2019; 197:122-152. [PMID: 30677473 PMCID: PMC6527860 DOI: 10.1016/j.pharmthera.2019.01.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Individuals differ substantially in their response to pharmacological treatment. Personalized medicine aspires to embrace these inter-individual differences and customize therapy by taking a wealth of patient-specific data into account. Pharmacogenomic constitutes a cornerstone of personalized medicine that provides therapeutic guidance based on the genomic profile of a given patient. Pharmacogenomics already has applications in the clinics, particularly in oncology, whereas future development in this area is needed in order to establish pharmacogenomic biomarkers as useful clinical tools. In this review we present an updated overview of current and emerging pharmacogenomic biomarkers in different therapeutic areas and critically discuss their potential to transform clinical care. Furthermore, we discuss opportunities of technological, methodological and institutional advances to improve biomarker discovery. We also summarize recent progress in our understanding of epigenetic effects on drug disposition and response, including a discussion of the only few pharmacogenomic biomarkers implemented into routine care. We anticipate, in part due to exciting rapid developments in Next Generation Sequencing technologies, machine learning methods and national biobanks, that the field will make great advances in the upcoming years towards unlocking the full potential of genomic data.
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Key Words
- 5cac, 5- carboxylcytosine
- 5fc, 5- formylcytosine
- 5hmc, 5-hydroxymethylcytosine
- abc-hss, abacavir hypersensitivity syndrome.
- all, acute lymphoblastic leukemia
- cat, catalase
- cftr, cystic fibrosis transmembrane conductance regulator
- chip, chromatin immunoprecipitation
- cnvs, copy number variations
- cpic, clinical pharmacogenetics implementation consortium
- dhr, drug hypersensitivity reactions
- dihs, drug-induced hypersensitivity syndrome.
- dili, drug-induced liver injury
- dnmts, dna methyltransferases
- dpwg, dutch pharmacogenetics working group
- dress, drug rash with eosinophilia and systemic symptoms
- eqtl, quantitative trait locus
- gpcr, g-protein coupled receptor
- gst, glutathione-s-transferase
- hdacs, histone deacetylases
- maf, minor allele frequencies
- mpe, maculopapular exanthema
- ms, multiple sclerosis
- pm, poor metabolism
- oxbs-seq, oxidative bisulfite sequencing
- prc2, polycomb repressive complex 2
- ptms, posttranslational modifications
- ra, retinoic acid
- scar, severe cutaneous adverse reaction
- sjs, stevens-johnson syndrome
- snvs, single nucleotide variations
- tab-seq, tet-assisted bisulfite sequencing
- ten, toxic epidermal necrolysis
- um, ultrarapid metabolism
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Affiliation(s)
- Volker M Lauschke
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Biomedicum 5B, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Biomedicum 5B, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Biomedicum 5B, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
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14
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Dempsey JL, Cui JY. Regulation of Hepatic Long Noncoding RNAs by Pregnane X Receptor and Constitutive Androstane Receptor Agonists in Mouse Liver. Drug Metab Dispos 2019; 47:329-339. [PMID: 30593543 PMCID: PMC6382996 DOI: 10.1124/dmd.118.085142] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/21/2018] [Indexed: 12/28/2022] Open
Abstract
Altered expression of long noncoding RNAs (lncRNAs) by environmental chemicals modulates the expression of xenobiotic biotransformation-related genes and may serve as therapeutic targets and novel biomarkers of exposure. The pregnane X receptor (PXR/NR1I2) is a critical xenobiotic-sensing nuclear receptor that regulates the expression of many drug-processing genes, and it has similar target-gene profiles and DNA-binding motifs with another xenobiotic-sensing nuclear receptor, namely, constitutive andronstrane receptor (CAR/Nr1i3). To test our hypothesis that lncRNAs are regulated by PXR in concert with protein-coding genes (PCGs) and to compare the PXR-targeted lncRNAs with CAR-targeted lncRNAs, RNA-Seq was performed from livers of adult male C57BL/6 mice treated with corn oil, the PXR agonist PCN, or the CAR agonist 1, 4-bis[2-(3,5-dichloropyridyloxy)]benzene (TCPOBOP). Among 125,680 known lncRNAs, 3843 were expressed in liver, and 193 were differentially regulated by PXR (among which 40% were also regulated by CAR). Most PXR- or CAR-regulated lncRNAs were mapped to the introns and 3'-untranslated regions (UTRs) of PCGs, as well as intergenic regions. Combining the RNA-Seq data with a published PXR chromatin immunoprecipitation coupled with high-throughput sequencing; cytochrome P450 (P450; ChIP-Seq) data set, we identified 774 expressed lncRNAs with direct PXR-DNA binding sites, and 26.8% of differentially expressed lncRNAs had changes in PXR-DNA binding after PCN exposure. De novo motif analysis identified colocalization of PXR with liver receptor homolog (LRH-1), which regulates bile acid synthesis after PCN exposure. There was limited overlap of PXR binding with an epigenetic mark for transcriptional activation (histone-H3K4-di-methylation, H3K4me2) but no overlap with epigenetic marks for transcriptional silencing [H3 lysine 27 tri-methylation (H3K27me3) and DNA methylation]. Among differentially expressed lncRNAs, 264 were in proximity of PCGs, and the lncRNA-PCG pairs displayed a high coregulatory pattern by PXR and CAR activation. This study was among the first to demonstrate that lncRNAs are regulated by PXR and CAR activation and that they may be important regulators of PCGs involved in xenobiotic metabolism.
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Affiliation(s)
- Joseph L Dempsey
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
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Liver-enriched Genes are Associated with the Prognosis of Patients with Hepatocellular Carcinoma. Sci Rep 2018; 8:11197. [PMID: 30046116 PMCID: PMC6060164 DOI: 10.1038/s41598-018-29237-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/29/2018] [Indexed: 02/07/2023] Open
Abstract
Tissue-enriched genes are highly expressed in one particular tissue type and represent distinct physiological processes. The dynamic profile of tissue-enriched genes during tumorigenesis and progression remains largely unstudied. Here, we identified tissue-enriched genes from 12 tissue types based on RNA sequencing data from the Cancer Genome Atlas (TCGA), and found that the liver had the largest number of such genes among the 12 tissue types. The characteristics of liver-enriched genes were further investigated. Most liver-enriched genes were downregulated and metabolism-related genes, which were associated with pathological stage and dedifferentiation in patients with hepatocellular carcinoma (HCC). Hypermethylation might be a mechanism underlying the downregulation of liver-enriched genes. We constructed a liver-enriched gene set and demonstrated that it is associated with the prognosis of the patients with HCC both in the TCGA cohort and the Gene Expression Omnibus (GEO) datasets. Moreover, we discovered that the degree of the dissimilarity between tumors and normal tissues was correlated with the prognosis of patients with HCC and the biological behaviours of the tumors. These results will help identify prognostic biomarkers of patients with HCC, and enhance our understanding of the molecular mechanisms of hepatocarcinogenesis and progression.
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16
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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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17
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Lauschke VM, Barragan I, Ingelman-Sundberg M. Pharmacoepigenetics and Toxicoepigenetics: Novel Mechanistic Insights and Therapeutic Opportunities. Annu Rev Pharmacol Toxicol 2017; 58:161-185. [PMID: 29029592 DOI: 10.1146/annurev-pharmtox-010617-053021] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Pharmacological treatment and exposure to xenobiotics can cause substantial changes in epigenetic signatures. The majority of these epigenetic changes, caused by the compounds in question, occur downstream of transcriptional activation mechanisms, whereby the epigenetic alterations can create a transcriptional memory and stably modulate cell function. The increasing understanding of epigenetic mechanisms and their importance in disease has prompted the development of therapeutic interventions that target epigenetic modulatory mechanisms, particularly in oncology where inhibitors of epigenetic-modifying proteins (epidrugs) have been successfully used in treatment, mostly in combination with standard-of-care chemotherapy, either provoking direct cytotoxicity or inhibiting resistance to anticancer drugs. In addition, emerging methods for detecting epigenetically modified DNA in bodily fluids may provide information about tumor phenotype or drug treatment success. However, it is important to note that many technical pitfalls, such as the nondeconvolution of methylcytosine and hydroxymethylcytosine, compromise epigenetic analyses and the interpretation of results. In this review, we provide an update on the field, with an emphasis on the novel therapeutic opportunities made possible by epidrugs.
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Affiliation(s)
- Volker M Lauschke
- Pharmacogenetics Section, Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden;
| | - Isabel Barragan
- Pharmacoepigenetics Group, Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Magnus Ingelman-Sundberg
- Pharmacogenetics Section, Department of Physiology and Pharmacology, Karolinska Institutet, SE-171 77 Stockholm, Sweden;
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18
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Combined study of genetic and epigenetic biomarker risperidone treatment efficacy in Chinese Han schizophrenia patients. Transl Psychiatry 2017; 7:e1170. [PMID: 28696411 PMCID: PMC5538123 DOI: 10.1038/tp.2017.143] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/06/2017] [Accepted: 05/06/2017] [Indexed: 02/06/2023] Open
Abstract
Nowadays, risperidone is an atypical antipsychotic drug that has been increasingly used for treatment and maintenance therapy in schizophrenia. However, partially affected by genetic or environmental factors, there is significant difference in treatment outcomes among patients. In this study, we aimed to interpret the difference between good and poor responders treated with risperidone in both genetic and epigenetic levels in 288 mainland Chinese patients. We recruited a Henan cohort including 98 patients as initial discovery group and then confirmed our results in Shanghai cohort. In genetic studies, we found 10 candidate single-nucleotide polymorphisms (SNPs) and 2 rare variants in Henan cohort by next-generation sequencing of 100 risperidone-response-related genes. After replication in Shanghai cohort by massarray platform, ultimately, rs6706232 and rs4818 were significantly associated with risperidone response in the two cohort meta-analysis (P=0.024 and 0.04, respectively). Besides, we also selected another reported 17 candidate SNPs associated with risperidone drug response to replicate in our mainland Chinese samples, while, we found no significant SNPs after Bonferroni correction. In epigenetic studies, we investigated the methylation status in promoters or gene-coding region of risperidone drug response-related genes including CYP3A4, CYP2D6, ABCB1, HTR2A, DRD2. Totally we found seven significant CpG sites in the meta-analysis with Bonferroni-corrected PCYP3A4_CpG_-36=0.0014, PCYP3A4_CpG_-258=0.0013, PCYP3A4_CpG_-296=0.0014, PCYP3A4_CpG_-367:-372:-374=0.028, PCYP2D6_CpG_193=0.012, PCYP2D6_CpG_242:244:250=0.00076 and PCYP2D6_CpG_284=0.034, respectively. As genetic and epigenetic factors may interactively affect drug response, we finally carried out a multivariant interaction analysis with multifactor dimensionality reduction and discovered a significant four-locus model (CYP3A4_CpG_-82:-86 +rs6280+rs1800497+rs6265, P=0.038) affecting drug response. These findings could partially explain different risperidone response outcome in Chinese population in a systematic level.
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Multicentric Case-Control Study on Azathioprine Dose and Pharmacokinetics in Early-onset Pediatric Inflammatory Bowel Disease. Inflamm Bowel Dis 2017; 23:628-634. [PMID: 28296824 DOI: 10.1097/mib.0000000000001051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Early-onset inflammatory bowel disease (IBD) is generally aggressive, with a high probability of complications and need of surgery. Despite the introduction of highly effective biological drugs, treatment with azathioprine continues to be important even for early-onset IBD; however, in these patients azathioprine response seems to be reduced. This study evaluated azathioprine doses, metabolite concentrations, and their associations with patients' age in children with IBD treated at 6 tertiary pediatric referral centers. METHODS Azathioprine doses, metabolites, and clinical effects were assessed after at least 3 months of therapy in 17 early-onset (age < 6 yr, cases) and 51 nonearly-onset (aged > 12 and <18 yrs, controls) patients with IBD. Azathioprine dose was titrated on therapeutic efficacy (response and adverse effects). Azathioprine metabolites and thiopurine methyltransferase activity were determined by high-performance liquid chromatography with ultra violet-vis detection (HPLC-UV) methods. RESULTS Frequency of patients in remission was similar among early-onset and control groups, respectively (82% and 84%, P value = 0.72). Early-onset patients required higher doses of azathioprine (median 2.7 versus 2.0 mg·kg·d, P value = 1.1 × 10). Different doses resulted in comparable azathioprine active thioguanine nucleotide metabolite concentrations (median 263 versus 366 pmol/8 × 10 erythrocytes, P value = 0.41) and methylmercaptopurine nucleotide concentrations (median 1455 versus 1532 pmol/8 × 10 erythrocytes, P value = 0.60). Lower ratios between thioguanine nucleotide metabolites and azathioprine doses were found in early-onset patients (median 98 versus 184 pmol/8 × 10 erythrocytes·mg·kg·d, P value = 0.017). Interestingly, early-onset patients presented also higher thiopurine methyltransferase activity (median 476 versus 350 nmol methylmercaptopurine/mg hemoglobin/h, P-value = 0.046). CONCLUSIONS This study demonstrated that patients with early-onset IBD present increased inactivating azathioprine metabolism, likely because of elevated activity of the enzyme thiopurine methyltransferase.
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20
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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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21
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Mooij MG, Nies AT, Knibbe CAJ, Schaeffeler E, Tibboel D, Schwab M, de Wildt SN. Development of Human Membrane Transporters: Drug Disposition and Pharmacogenetics. Clin Pharmacokinet 2016; 55:507-24. [PMID: 26410689 PMCID: PMC4823323 DOI: 10.1007/s40262-015-0328-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Membrane transporters play an essential role in the transport of endogenous and exogenous compounds, and consequently they mediate the uptake, distribution, and excretion of many drugs. The clinical relevance of transporters in drug disposition and their effect in adults have been shown in drug–drug interaction and pharmacogenomic studies. Little is known, however, about the ontogeny of human membrane transporters and their roles in pediatric pharmacotherapy. As they are involved in the transport of endogenous substrates, growth and development may be important determinants of their expression and activity. This review presents an overview of our current knowledge on human membrane transporters in pediatric drug disposition and effect. Existing pharmacokinetic and pharmacogenetic data on membrane substrate drugs frequently used in children are presented and related, where possible, to existing ex vivo data, providing a basis for developmental patterns for individual human membrane transporters. As data for individual transporters are currently still scarce, there is a striking information gap regarding the role of human membrane transporters in drug therapy in children.
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Affiliation(s)
- Miriam G Mooij
- Intensive Care and Department of Pediatric Surgery, Erasmus MC-Sophia Children's Hospital, Room Sp-3458, Wytemaweg 80, PO-box 2060, 3000 CB, Rotterdam, The Netherlands
| | - Anne T Nies
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Catherijne A J Knibbe
- Faculty of Science, Leiden Academic Centre for Research, Pharmacology, Leiden, The Netherlands.,Hospital Pharmacy and Clinical Pharmacology, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Dick Tibboel
- Intensive Care and Department of Pediatric Surgery, Erasmus MC-Sophia Children's Hospital, Room Sp-3458, Wytemaweg 80, PO-box 2060, 3000 CB, Rotterdam, The Netherlands
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,Department of Clinical Pharmacology, University Hospital Tuebingen, Tuebingen, Germany
| | - Saskia N de Wildt
- Intensive Care and Department of Pediatric Surgery, Erasmus MC-Sophia Children's Hospital, Room Sp-3458, Wytemaweg 80, PO-box 2060, 3000 CB, Rotterdam, The Netherlands.
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22
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Majchrzak-Celińska A, Baer-Dubowska W. Pharmacoepigenetics: an element of personalized therapy? Expert Opin Drug Metab Toxicol 2016; 13:387-398. [PMID: 27860490 DOI: 10.1080/17425255.2017.1260546] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Epigenetics is a rapidly growing field describing heritable alterations in gene expression that do not involve DNA sequence variations. Advances in epigenetics and epigenomics have influenced pharmacology, leading to the development of a new specialty, pharmacoepigenetics, the study of the epigenetic basis for the individual variation in drug response. Areas covered: We present an overview of the major epigenetic mechanisms and their effects on the expression of drug metabolizing enzymes and drug transporters, as well as the epigenetic status of drug protein targets affecting therapy response. Recent advances in the development of pharmacoepigenetic biomarkers and epidrugs are also discussed. Expert opinion: There is growing evidence that pharmacoepigenetics has the potential to become an important element of personalized medicine. Epigenetic modifications influence drug response, but they can also be modulated by drugs. Moreover, they can be monitored not only in the affected tissue, but also in body fluids. Nevertheless, there are very few examples of epigenetic biomarkers implemented in the clinical setting. Explanation of the interplay between genomic and epigenomic changes will contribute to the personalized medicine approach. Ultimately, both genetic biomarkers and epigenetic mechanisms should be taken into consideration in predicting drug response in the course of successful personalized therapy.
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Affiliation(s)
| | - Wanda Baer-Dubowska
- a Department of Pharmaceutical Biochemistry , Poznan University of Medical Sciences , Poznań , Poland
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23
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Liu X, Beith J, Low SK, Boddy AV. The path to implementation of personalized medicine of aromatase inhibitors in patients with breast cancer. Pharmacogenomics 2016; 17:1861-1864. [PMID: 27790931 DOI: 10.2217/pgs-2016-0141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Xiaoman Liu
- Faculty of Pharmacy, University of Sydney, Sydney, NSW 2006, Australia
| | - Jane Beith
- Chris O'Brien Lifehouse Centre, Sydney, NSW 2006, Australia
| | - Siew-Kee Low
- Faculty of Pharmacy, University of Sydney, Sydney, NSW 2006, Australia
| | - Alan V Boddy
- Faculty of Pharmacy, University of Sydney, Sydney, NSW 2006, Australia
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24
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Lauschke VM, Ingelman-Sundberg M. The Importance of Patient-Specific Factors for Hepatic Drug Response and Toxicity. Int J Mol Sci 2016; 17:E1714. [PMID: 27754327 PMCID: PMC5085745 DOI: 10.3390/ijms17101714] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 09/23/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023] Open
Abstract
Responses to drugs and pharmacological treatments differ considerably between individuals. Importantly, only 50%-75% of patients have been shown to react adequately to pharmacological interventions, whereas the others experience either a lack of efficacy or suffer from adverse events. The liver is of central importance in the metabolism of most drugs. Because of this exposed status, hepatotoxicity is amongst the most common adverse drug reactions and hepatic liabilities are the most prevalent reason for the termination of development programs of novel drug candidates. In recent years, more and more factors were unveiled that shape hepatic drug responses and thus underlie the observed inter-individual variability. In this review, we provide a comprehensive overview of different principle mechanisms of drug hepatotoxicity and illustrate how patient-specific factors, such as genetic, physiological and environmental factors, can shape drug responses. Furthermore, we highlight other parameters, such as concomitantly prescribed medications or liver diseases and how they modulate drug toxicity, pharmacokinetics and dynamics. Finally, we discuss recent progress in the field of in vitro toxicity models and evaluate their utility in reflecting patient-specific factors to study inter-individual differences in drug response and toxicity, as this understanding is necessary to pave the way for a patient-adjusted medicine.
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Affiliation(s)
- Volker M Lauschke
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, SE-17177 Stockholm, Sweden.
| | - Magnus Ingelman-Sundberg
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, SE-17177 Stockholm, Sweden.
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Developmental regulation of CYP3A4 and CYP3A7 in Chinese Han population. Drug Metab Pharmacokinet 2016; 31:433-444. [PMID: 27727071 DOI: 10.1016/j.dmpk.2016.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 07/12/2016] [Accepted: 08/30/2016] [Indexed: 01/06/2023]
Abstract
CYP3A4 and CYP3A7 are generally served as the major adult and fetal liver forms, respectively, and exhibited a developmental switch during liver maturation. The objective of this study was to explore the potential mechanisms associated with the developmental switch of CYP3A4 and CYP3A7 in the Chinese Han population. We analyzed CYP3A4/7, nuclear receptors, and epigenetic modifications in human liver samples. We found that the expression levels of CYP3A4 mRNA in adults were significantly higher than the levels in fetus. In contrast, CYP3A7 mRNA expression reached a maximal level at an estimated gestational age of 25 weeks and then substantially decreased during the first year after birth. We also found that the expression level of hepatocyte nuclear factor 4 alpha (HNF4A) was most associated with CYP3A4 expression in adult liver; whereas the expression level of glucocorticoid receptor (GR) was intensively correlated with CYP3A7 expression in fetal liver. Furthermore, we illustrated the dynamic changes of H3K4me2 and H3K27me3 in the developmental switch of CYP3A7 and CYP3A4. In summary, our data suggested that HNF4A and GR, and epigenetic changes of H3K4me2 and H3K27me3 are associated with the ontogenic expressions of CYP3A4/3A7 in the livers of the Chinese Han population.
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Fisel P, Schaeffeler E, Schwab M. DNA Methylation of ADME Genes. Clin Pharmacol Ther 2016; 99:512-27. [PMID: 27061006 DOI: 10.1002/cpt.343] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 12/13/2022]
Abstract
The epigenetic regulation of expression of genes involved in the absorption, distribution, metabolism, and excretion (ADME) of drugs contributes to interindividual variability in drug response. Epigenetic mechanisms include DNA methylation, histone modifications, and miRNAs. This review systematically outlines the influence of DNA methylation on ADME gene expression and highlights the consequences for interindividual variability in drug response or drug-induced toxicity and the implications for personalized medicine.
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Affiliation(s)
- P Fisel
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany
| | - E Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany
| | - M Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,Department of Clinical Pharmacology, University Hospital Tübingen, Tübingen, Germany.,Department of Pharmacy and Biochemistry, University of Tübingen, Tübingen, 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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Huse SM, Gruppuso PA, Boekelheide K, Sanders JA. Patterns of gene expression and DNA methylation in human fetal and adult liver. BMC Genomics 2015; 16:981. [PMID: 26589361 PMCID: PMC4654795 DOI: 10.1186/s12864-015-2066-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/13/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is an important epigenetic control mechanism that has been shown to be associated with gene silencing through the course of development, maturation and aging. However, only limited data are available regarding the relationship between methylation and gene expression in human development. RESULTS We analyzed the methylome and transcriptome of three human fetal liver samples (gestational age 20-22 weeks) and three adult human liver samples. Genes whose expression differed between fetal and adult numbered 7,673. Adult overexpression was associated with metabolic pathways and, in particular, cytochrome P450 enzymes while fetal overexpression reflected enrichment for DNA replication and repair. Analysis for DNA methylation using the Illumina Infinium 450 K HumanMethylation BeadChip showed that 42% of the quality filtered 426,154 methylation sites differed significantly between adult and fetal tissue (q ≤ 0.05). Differences were small; 69% of the significant sites differed in their mean methylation beta value by ≤0.2. There was a trend among all sites toward higher methylation in the adult samples with the most frequent difference in beta being 0.1. Characterization of the relationship between methylation and expression revealed a clear difference between fetus and adult. Methylation of genes overexpressed in fetal liver showed the same pattern as seen for genes that were similarly expressed in fetal and adult liver. In contrast, adult overexpressed genes showed fetal hypermethylation that differed from the similarly expressed genes. An examination of gene region-specific methylation showed that sites proximal to the transcription start site or within the first exon with a significant fetal-adult difference in beta (>0.2) showed an inverse relationship with gene expression. CONCLUSIONS Nearly half of the CpGs in human liver show a significant difference in methylation comparing fetal and adult samples. Sites proximal to the transcription start site or within the first exon that show a transition from hypermethylation in the fetus to hypomethylation or intermediate methylation in the adult are associated with inverse changes in gene expression. In contrast, increases in methylation going from fetal to adult are not associated with fetal-to-adult decreased expression. These findings indicate fundamentally different roles for and/or regulation of DNA methylation in human fetal and adult liver.
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Affiliation(s)
- Susan M Huse
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Philip A Gruppuso
- Department of Pediatrics, Rhode Island Hospital and Brown University, Providence, RI, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Kim Boekelheide
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Jennifer A Sanders
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
- Department of Pediatrics, Rhode Island Hospital and Brown University, Providence, RI, USA.
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Habano W, Kawamura K, Iizuka N, Terashima J, Sugai T, Ozawa S. Analysis of DNA methylation landscape reveals the roles of DNA methylation in the regulation of drug metabolizing enzymes. Clin Epigenetics 2015; 7:105. [PMID: 26421064 PMCID: PMC4587720 DOI: 10.1186/s13148-015-0136-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/15/2015] [Indexed: 12/24/2022] Open
Abstract
Background Drug metabolizing enzymes (DMEs) exhibit dramatic inter- and intra-individual variability in expression and activity. However, the mechanisms determining this variability have not been fully elucidated. The aim of this study was to evaluate the biological significance of DNA methylation in the regulation of DME genes by genome-wide integrative analysis. Results DNA methylation and mRNA expression profiles of human tissues and hepatoma cells were examined by microarrays. The data were combined with GEO datasets of liver tissues, and integrative analysis was performed on selected DME genes. Detailed DNA methylation statuses at individual CpG sites were evaluated by DNA methylation mapping. From analysis of 20 liver tissues, highly variable DNA methylation was observed in 37 DME genes, 7 of which showed significant inverse correlations between DNA methylation and mRNA expression. In hepatoma cells, treatment with a demethylating agent resulted in upregulation of 5 DME genes, which could be explained by DNA methylation status. Interestingly, some DMEs were suggested to act as tumor-suppressor or housekeeper based on their unique DNA methylation features. Moreover, tissue-specific and age-dependent expression of UDP-glucuronosyltransferase 1A splicing variants was associated with DNA methylation status of individual first exons. Conclusions Some DME genes were regulated by DNA methylation, potentially resulting in inter- and intra-individual differences in drug metabolism. Analysis of DNA methylation landscape facilitated elucidation of the role of DNA methylation in the regulation of DME genes, such as mediator of inter-individual variability, guide for correct alternative splicing, and potential tumor-suppressor or housekeeper. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0136-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wataru Habano
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba-Cho, Shiwa-Gun 028-3694 Japan
| | - Kohei Kawamura
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba-Cho, Shiwa-Gun 028-3694 Japan
| | - Natsuki Iizuka
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba-Cho, Shiwa-Gun 028-3694 Japan
| | - Jun Terashima
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba-Cho, Shiwa-Gun 028-3694 Japan
| | - Tamotsu Sugai
- Department of Diagnostic Pathology, School of Medicine, Iwate Medical University, Iwate, Japan
| | - Shogo Ozawa
- Department of Pharmacodynamics and Molecular Genetics, School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba-Cho, Shiwa-Gun 028-3694 Japan
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Park HJ, Choi YJ, Kim JW, Chun HS, Im I, Yoon S, Han YM, Song CW, Kim H. Differences in the Epigenetic Regulation of Cytochrome P450 Genes between Human Embryonic Stem Cell-Derived Hepatocytes and Primary Hepatocytes. PLoS One 2015; 10:e0132992. [PMID: 26177506 PMCID: PMC4503736 DOI: 10.1371/journal.pone.0132992] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/23/2015] [Indexed: 12/30/2022] Open
Abstract
Human pluripotent stem cell-derived hepatocytes have the potential to provide in vitro model systems for drug discovery and hepatotoxicity testing. However, these cells are currently unsuitable for drug toxicity and efficacy testing because of their limited expression of genes encoding drug-metabolizing enzymes, especially cytochrome P450 (CYP) enzymes. Transcript levels of major CYP genes were much lower in human embryonic stem cell-derived hepatocytes (hESC-Hep) than in human primary hepatocytes (hPH). To verify the mechanism underlying this reduced expression of CYP genes, including CYP1A1, CYP1A2, CYP1B1, CYP2D6, and CYP2E1, we investigated their epigenetic regulation in terms of DNA methylation and histone modifications in hESC-Hep and hPH. CpG islands of CYP genes were hypermethylated in hESC-Hep, whereas they had an open chromatin structure, as represented by hypomethylation of CpG sites and permissive histone modifications, in hPH. Inhibition of DNA methyltransferases (DNMTs) during hepatic maturation induced demethylation of the CpG sites of CYP1A1 and CYP1A2, leading to the up-regulation of their transcription. Combinatorial inhibition of DNMTs and histone deacetylases (HDACs) increased the transcript levels of CYP1A1, CYP1A2, CYP1B1, and CYP2D6. Our findings suggest that limited expression of CYP genes in hESC-Hep is modulated by epigenetic regulatory factors such as DNMTs and HDACs.
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Affiliation(s)
- Han-Jin Park
- Department of Biological Sciences and Center for Stem Cell Differentiation, Korea Advanced Institute of Science and Technology, Daejeon, 305–701, Republic of Korea
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 305–343, Republic of Korea
| | - Young-Jun Choi
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 305–343, Republic of Korea
- Human and Environmental Toxicology, School of Engineering, University of Science and Technology, Daejeon, 303–333, Republic of Korea
| | - Ji Woo Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 305–343, Republic of Korea
| | - Hang-Suk Chun
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 305–343, Republic of Korea
| | - Ilkyun Im
- Department of Biological Sciences and Center for Stem Cell Differentiation, Korea Advanced Institute of Science and Technology, Daejeon, 305–701, Republic of Korea
| | - Seokjoo Yoon
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 305–343, Republic of Korea
- Human and Environmental Toxicology, School of Engineering, University of Science and Technology, Daejeon, 303–333, Republic of Korea
| | - Yong-Mahn Han
- Department of Biological Sciences and Center for Stem Cell Differentiation, Korea Advanced Institute of Science and Technology, Daejeon, 305–701, Republic of Korea
| | - Chang-Woo Song
- Department of Inhalation Research, Korea Institute of Toxicology, Jeollabuk-do, 580–185, Republic of Korea
- Human and Environmental Toxicology, School of Engineering, University of Science and Technology, Daejeon, 303–333, Republic of Korea
| | - Hyemin Kim
- Department of Predictive Toxicology, Korea Institute of Toxicology, Daejeon, 305–343, Republic of Korea
- * E-mail:
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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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Role of DNA Methylation on the Expression of the Anthracycline Metabolizing Enzyme AKR7A2 in Human Heart. Cardiovasc Toxicol 2015; 16:182-92. [PMID: 25962911 DOI: 10.1007/s12012-015-9327-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The intracardiac synthesis of anthracycline alcohol metabolites by aldo-keto reductases (AKRs) contributes to the pathogenesis of anthracycline-related cardiotoxicity. AKR7A2 is the most abundant anthracycline reductase in hearts from donors with and without Down syndrome (DS), and its expression varies between individuals (≈tenfold). We investigated whether DNA methylation impacts AKR7A2 expression in hearts from donors with (n = 11) and without DS (n = 30). Linear models were used to test for associations between methylation status and cardiac AKR7A2 expression. In hearts from donors without DS, DNA methylation status at CpG site -865 correlated with AKR7A2 mRNA (Pearson's regression coefficient, r = -0.4051, P = 0.0264) and AKR7A2 protein expression (r = -0.5818, P = 0.0071). In heart tissue from donors with DS, DNA methylation status at CpG site -232 correlated with AKR7A2 protein expression (r = 0.8659, P = 0.0025). Multiple linear regression modeling revealed that methylation at several CpG sites is associated with the synthesis of cardiotoxic daunorubicinol. AKR7A2 methylation status in lymphoblastoid cell lines from donors with and without DS was examined to explore potential parallelisms between cardiac tissue and lymphoid cells. These results suggest that DNA methylation impacts AKR7A2 expression and the synthesis of cardiotoxic daunorubicinol.
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Turner RM, Park BK, Pirmohamed M. Parsing interindividual drug variability: an emerging role for systems pharmacology. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:221-41. [PMID: 25950758 PMCID: PMC4696409 DOI: 10.1002/wsbm.1302] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/08/2015] [Accepted: 04/15/2015] [Indexed: 12/25/2022]
Abstract
There is notable interindividual heterogeneity in drug response, affecting both drug efficacy and toxicity, resulting in patient harm and the inefficient utilization of limited healthcare resources. Pharmacogenomics is at the forefront of research to understand interindividual drug response variability, but although many genotype-drug response associations have been identified, translation of pharmacogenomic associations into clinical practice has been hampered by inconsistent findings and inadequate predictive values. These limitations are in part due to the complex interplay between drug-specific, human body and environmental factors influencing drug response and therefore pharmacogenomics, whilst intrinsically necessary, is by itself unlikely to adequately parse drug variability. The emergent, interdisciplinary and rapidly developing field of systems pharmacology, which incorporates but goes beyond pharmacogenomics, holds significant potential to further parse interindividual drug variability. Systems pharmacology broadly encompasses two distinct research efforts, pharmacologically-orientated systems biology and pharmacometrics. Pharmacologically-orientated systems biology utilizes high throughput omics technologies, including next-generation sequencing, transcriptomics and proteomics, to identify factors associated with differential drug response within the different levels of biological organization in the hierarchical human body. Increasingly complex pharmacometric models are being developed that quantitatively integrate factors associated with drug response. Although distinct, these research areas complement one another and continual development can be facilitated by iterating between dynamic experimental and computational findings. Ultimately, quantitative data-derived models of sufficient detail will be required to help realize the goal of precision medicine.
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Affiliation(s)
- Richard M Turner
- The Wolfson Centre for Personalised Medicine, Institute for Translational Medicine, University of Liverpool, Liverpool, UK
| | - B Kevin Park
- MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | - Munir Pirmohamed
- The Wolfson Centre for Personalised Medicine, Institute for Translational Medicine, University of Liverpool, Liverpool, UK
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KUANG ZEMIN, HUANG ZHIJUN, LI YING, YANG GUOPING, LIU MEILIN, YUAN HONG. Overexpression of CYP3A5 attenuates inducibility and activity of CYP3A4 in HepG2 cells. Mol Med Rep 2014; 11:2868-74. [DOI: 10.3892/mmr.2014.3022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 10/01/2014] [Indexed: 11/06/2022] Open
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36
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Bonder MJ, Kasela S, Kals M, Tamm R, Lokk K, Barragan I, Buurman WA, Deelen P, Greve JW, Ivanov M, Rensen SS, van Vliet-Ostaptchouk JV, Wolfs MG, Fu J, Hofker MH, Wijmenga C, Zhernakova A, Ingelman-Sundberg M, Franke L, Milani L. Genetic and epigenetic regulation of gene expression in fetal and adult human livers. BMC Genomics 2014; 15:860. [PMID: 25282492 PMCID: PMC4287518 DOI: 10.1186/1471-2164-15-860] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/24/2014] [Indexed: 01/07/2023] Open
Abstract
Background The liver plays a central role in the maintenance of homeostasis and health in general. However, there is substantial inter-individual variation in hepatic gene expression, and although numerous genetic factors have been identified, less is known about the epigenetic factors. Results By analyzing the methylomes and transcriptomes of 14 fetal and 181 adult livers, we identified 657 differentially methylated genes with adult-specific expression, these genes were enriched for transcription factor binding sites of HNF1A and HNF4A. We also identified 1,000 genes specific to fetal liver, which were enriched for GATA1, STAT5A, STAT5B and YY1 binding sites. We saw strong liver-specific effects of single nucleotide polymorphisms on both methylation levels (28,447 unique CpG sites (meQTL)) and gene expression levels (526 unique genes (eQTL)), at a false discovery rate (FDR) < 0.05. Of the 526 unique eQTL associated genes, 293 correlated significantly not only with genetic variation but also with methylation levels. The tissue-specificities of these associations were analyzed in muscle, subcutaneous adipose tissue and visceral adipose tissue. We observed that meQTL were more stable between tissues than eQTL and a very strong tissue-specificity for the identified associations between CpG methylation and gene expression. Conclusions Our analyses generated a comprehensive resource of factors involved in the regulation of hepatic gene expression, and allowed us to estimate the proportion of variation in gene expression that could be attributed to genetic and epigenetic variation, both crucial to understanding differences in drug response and the etiology of liver diseases. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-860) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Hanzeplein 1, 9700 RB Groningen, the Netherlands.
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Tang J, Xiong Y, Zhou HH, Chen XP. DNA methylation and personalized medicine. J Clin Pharm Ther 2014; 39:621-7. [PMID: 25230364 DOI: 10.1111/jcpt.12206] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 08/17/2014] [Indexed: 12/12/2022]
Affiliation(s)
- J. Tang
- Department of Clinical Pharmacology; Xiangya Hospital; Central South University; Changsha China
- Pharmacogenetics Research Institute; Institute of Clinical Pharmacology; Hunan Key laboratory of Pharmacogenetics; Central South University; Changsha China
| | - Y. Xiong
- Department of Clinical Pharmacology; Xiangya Hospital; Central South University; Changsha China
- Pharmacogenetics Research Institute; Institute of Clinical Pharmacology; Hunan Key laboratory of Pharmacogenetics; Central South University; Changsha China
| | - H.-H. Zhou
- Department of Clinical Pharmacology; Xiangya Hospital; Central South University; Changsha China
- Pharmacogenetics Research Institute; Institute of Clinical Pharmacology; Hunan Key laboratory of Pharmacogenetics; Central South University; Changsha China
| | - X.-P. Chen
- Department of Clinical Pharmacology; Xiangya Hospital; Central South University; Changsha China
- Pharmacogenetics Research Institute; Institute of Clinical Pharmacology; Hunan Key laboratory of Pharmacogenetics; Central South University; Changsha China
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38
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Ivanov M, Barragan I, Ingelman-Sundberg M. Epigenetic mechanisms of importance for drug treatment. Trends Pharmacol Sci 2014; 35:384-96. [PMID: 24993164 DOI: 10.1016/j.tips.2014.05.004] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 05/13/2014] [Accepted: 05/23/2014] [Indexed: 12/15/2022]
Abstract
There are pronounced interindividual variations in drug metabolism, drug responses, and the incidence of adverse drug reactions. To a certain extent such variability can be explained by genetic factors, but epigenetic modifications, which are relatively scarcely described so far, also contribute. It is known that a novel class of drugs termed epidrugs intervene in the epigenetic control of gene expression, and many of these are now in clinical trials for disease treatment. In addition, disease prognosis and drug treatment success can be monitored using epigenetic biomarkers. Here we review these novel aspects in pharmacology and address intriguing future opportunities for gene-specific epigenetic editing.
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Affiliation(s)
- Maxim Ivanov
- Pharmacogenetics Section, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Isabel Barragan
- Pharmacogenetics Section, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Ingelman-Sundberg
- Pharmacogenetics Section, Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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Mooij MG, Schwarz UI, de Koning BAE, Leeder JS, Gaedigk R, Samsom JN, Spaans E, van Goudoever JB, Tibboel D, Kim RB, de Wildt SN. Ontogeny of human hepatic and intestinal transporter gene expression during childhood: age matters. Drug Metab Dispos 2014; 42:1268-74. [PMID: 24829289 DOI: 10.1124/dmd.114.056929] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Many drugs prescribed to children are drug transporter substrates. Drug transporters are membrane-bound proteins that mediate the cellular uptake or efflux of drugs and are important to drug absorption and elimination. Very limited data are available on the effect of age on transporter expression. Our study assessed age-related gene expression of hepatic and intestinal drug transporters. Multidrug resistance protein 2 (MRP2), organic anion transporting polypeptide 1B1 (OATP1B1), and OATP1B3 expression was determined in postmortem liver samples (fetal n = 6, neonatal n = 19, infant n = 7, child n = 2, adult n = 11) and multidrug resistance 1 (MDR1) expression in 61 pediatric liver samples. Intestinal expression of MDR1, MRP2, and OATP2B1 was determined in surgical small bowel samples (neonates n = 15, infants n = 3, adults n = 14). Using real-time reverse-transcription polymerase chain reaction, we measured fetal and pediatric gene expression relative to 18S rRNA (liver) and villin (intestines), and we compared it with adults using the 2(-∆∆Ct) method. Hepatic expression of MRP2, OATP1B1, and OATP1B3 in all pediatric age groups was significantly lower than in adults. Hepatic MDR1 mRNA expression in fetuses, neonates, and infants was significantly lower than in adults. Neonatal intestinal expressions of MDR1 and MRP2 were comparable to those in adults. Intestinal OATP2B1 expression in neonates was significantly higher than in adults. We provide new data that show organ- and transporter-dependent differences in hepatic and intestinal drug transporter expression in an age-dependent fashion. This suggests that substrate drug absorption mediated by these transporters may be subject to age-related variation in a transporter dependent pattern.
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Affiliation(s)
- Miriam G Mooij
- Intensive Care and Department of Pediatric Surgery (M.G.M., S.N.W., B.A.E.K., E.S., D.T.), and Laboratory of Pediatrics, Division of Gastroenterology and Nutrition (J.N.S.), Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands; Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London, Ontario, Canada (U.I.S., R.B.K.); Division of Clinical Pharmacology and Therapeutic Innovation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (J.S.L., R.G.); Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, and Department of Pediatrics, VU University Medical Center, Amsterdam, the Netherlands (J.B.G.)
| | - Ute I Schwarz
- Intensive Care and Department of Pediatric Surgery (M.G.M., S.N.W., B.A.E.K., E.S., D.T.), and Laboratory of Pediatrics, Division of Gastroenterology and Nutrition (J.N.S.), Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands; Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London, Ontario, Canada (U.I.S., R.B.K.); Division of Clinical Pharmacology and Therapeutic Innovation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (J.S.L., R.G.); Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, and Department of Pediatrics, VU University Medical Center, Amsterdam, the Netherlands (J.B.G.)
| | - Barbara A E de Koning
- Intensive Care and Department of Pediatric Surgery (M.G.M., S.N.W., B.A.E.K., E.S., D.T.), and Laboratory of Pediatrics, Division of Gastroenterology and Nutrition (J.N.S.), Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands; Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London, Ontario, Canada (U.I.S., R.B.K.); Division of Clinical Pharmacology and Therapeutic Innovation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (J.S.L., R.G.); Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, and Department of Pediatrics, VU University Medical Center, Amsterdam, the Netherlands (J.B.G.)
| | - J Steven Leeder
- Intensive Care and Department of Pediatric Surgery (M.G.M., S.N.W., B.A.E.K., E.S., D.T.), and Laboratory of Pediatrics, Division of Gastroenterology and Nutrition (J.N.S.), Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands; Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London, Ontario, Canada (U.I.S., R.B.K.); Division of Clinical Pharmacology and Therapeutic Innovation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (J.S.L., R.G.); Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, and Department of Pediatrics, VU University Medical Center, Amsterdam, the Netherlands (J.B.G.)
| | - Roger Gaedigk
- Intensive Care and Department of Pediatric Surgery (M.G.M., S.N.W., B.A.E.K., E.S., D.T.), and Laboratory of Pediatrics, Division of Gastroenterology and Nutrition (J.N.S.), Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands; Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London, Ontario, Canada (U.I.S., R.B.K.); Division of Clinical Pharmacology and Therapeutic Innovation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (J.S.L., R.G.); Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, and Department of Pediatrics, VU University Medical Center, Amsterdam, the Netherlands (J.B.G.)
| | - Janneke N Samsom
- Intensive Care and Department of Pediatric Surgery (M.G.M., S.N.W., B.A.E.K., E.S., D.T.), and Laboratory of Pediatrics, Division of Gastroenterology and Nutrition (J.N.S.), Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands; Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London, Ontario, Canada (U.I.S., R.B.K.); Division of Clinical Pharmacology and Therapeutic Innovation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (J.S.L., R.G.); Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, and Department of Pediatrics, VU University Medical Center, Amsterdam, the Netherlands (J.B.G.)
| | - Edwin Spaans
- Intensive Care and Department of Pediatric Surgery (M.G.M., S.N.W., B.A.E.K., E.S., D.T.), and Laboratory of Pediatrics, Division of Gastroenterology and Nutrition (J.N.S.), Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands; Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London, Ontario, Canada (U.I.S., R.B.K.); Division of Clinical Pharmacology and Therapeutic Innovation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (J.S.L., R.G.); Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, and Department of Pediatrics, VU University Medical Center, Amsterdam, the Netherlands (J.B.G.)
| | - Johannes B van Goudoever
- Intensive Care and Department of Pediatric Surgery (M.G.M., S.N.W., B.A.E.K., E.S., D.T.), and Laboratory of Pediatrics, Division of Gastroenterology and Nutrition (J.N.S.), Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands; Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London, Ontario, Canada (U.I.S., R.B.K.); Division of Clinical Pharmacology and Therapeutic Innovation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (J.S.L., R.G.); Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, and Department of Pediatrics, VU University Medical Center, Amsterdam, the Netherlands (J.B.G.)
| | - Dick Tibboel
- Intensive Care and Department of Pediatric Surgery (M.G.M., S.N.W., B.A.E.K., E.S., D.T.), and Laboratory of Pediatrics, Division of Gastroenterology and Nutrition (J.N.S.), Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands; Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London, Ontario, Canada (U.I.S., R.B.K.); Division of Clinical Pharmacology and Therapeutic Innovation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (J.S.L., R.G.); Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, and Department of Pediatrics, VU University Medical Center, Amsterdam, the Netherlands (J.B.G.)
| | - Richard B Kim
- Intensive Care and Department of Pediatric Surgery (M.G.M., S.N.W., B.A.E.K., E.S., D.T.), and Laboratory of Pediatrics, Division of Gastroenterology and Nutrition (J.N.S.), Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands; Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London, Ontario, Canada (U.I.S., R.B.K.); Division of Clinical Pharmacology and Therapeutic Innovation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (J.S.L., R.G.); Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, and Department of Pediatrics, VU University Medical Center, Amsterdam, the Netherlands (J.B.G.)
| | - Saskia N de Wildt
- Intensive Care and Department of Pediatric Surgery (M.G.M., S.N.W., B.A.E.K., E.S., D.T.), and Laboratory of Pediatrics, Division of Gastroenterology and Nutrition (J.N.S.), Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands; Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London, Ontario, Canada (U.I.S., R.B.K.); Division of Clinical Pharmacology and Therapeutic Innovation, Children's Mercy Hospitals and Clinics, Kansas City, Missouri (J.S.L., R.G.); Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, and Department of Pediatrics, VU University Medical Center, Amsterdam, the Netherlands (J.B.G.)
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Chiang TS, Yang KC, Chiou LL, Huang GT, Lee HS. Enhancement of CYP3A4 activity in Hep G2 cells by lentiviral transfection of hepatocyte nuclear factor-1 alpha. PLoS One 2014; 9:e94885. [PMID: 24733486 PMCID: PMC3986372 DOI: 10.1371/journal.pone.0094885] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 03/20/2014] [Indexed: 01/06/2023] Open
Abstract
Human hepatoma cell lines are commonly used as alternatives to primary hepatocytes for the study of drug metabolism in vitro. However, the phase I cytochrome P450 (CYP) enzyme activities in these cell lines occur at a much lower level than their corresponding activities in primary hepatocytes, and thus these cell lines may not accurately predict drug metabolism. In the present study, we selected hepatocyte nuclear factor-1 alpha (HNF1α) from six transcriptional regulators for lentiviral transfection into Hep G2 cells to optimally increase their expression of the CYP3A4 enzyme, which is the major CYP enzyme in the human body. We subsequently found that HNF1α-transfected Hep G2 enhanced the CYP3A4 expression in a time- and dose-dependent manner and the activity was noted to increase with time and peaked 7 days. With a multiplicity of infection (MOI) of 100, CYP3A4 expression increased 19-fold and enzyme activity more than doubled at day 7. With higher MOI (1,000 to 3,000), the activity increased 8- to 10-fold; however, it was noted the higher MOI, the higher cell death rate and lower cell survival. Furthermore, the CYP3A4 activity in the HNF1α-transfected cells could be induced by CYP3A4-specific inducer, rifampicin, and metabolized nifedipine in a dose-dependent manner. With an MOI of 3,000, nifedipine-metabolizing activity was 6-fold of control and as high as 66% of primary hepatocytes. In conclusion, forceful delivery of selected transcriptional regulators into human hepatoma cells might be a valuable method to enhance the CYP activity for a more accurate determination of drug metabolism in vitro.
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Affiliation(s)
- Tsai-Shin Chiang
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Kai-Chiang Yang
- School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Ling-Ling Chiou
- Liver Disease Prevention and Treatment Research Foundation, Taipei, Taiwan
| | - Guan-Tarn Huang
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
- * E-mail: (GTH); (HSL)
| | - Hsuan-Shu Lee
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- * E-mail: (GTH); (HSL)
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Ingelman-Sundberg M, Zhong XB, Hankinson O, Beedanagari S, Yu AM, Peng L, Osawa Y. Potential role of epigenetic mechanisms in the regulation of drug metabolism and transport. Drug Metab Dispos 2013; 41:1725-31. [PMID: 23918665 PMCID: PMC3781370 DOI: 10.1124/dmd.113.053157] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/05/2013] [Indexed: 01/28/2023] Open
Abstract
This is a report of a symposium on the potential role of epigenetic mechanisms in the control of drug disposition sponsored by the American Society for Pharmacology and Experimental Therapeutics and held at the Experimental Biology 2013 meeting in Boston, MA, April 21, 2013. Epigenetics is a rapidly evolving area, and recent studies have revealed that expression of drug-metabolizing enzymes and transporters is regulated by epigenetic factors, including histone modification, DNA methylation, and noncoding RNAs. The symposium speakers provided an overview of genetic and epigenetic mechanisms underlying variable drug metabolism and drug response, as well as the implications for personalized medicine. Considerable insight into the epigenetic mechanisms in differential regulation of the dioxin-inducible drug and carcinogen-metabolizing enzymes CYP1A1 and 1B1 was provided. The role of noncoding microRNAs in the control of drug metabolism and disposition through targeting of cytochrome P450 (P450) enzymes and ATP-binding cassette membrane transporters was discussed. In addition, potential effects of xenobiotics on chromatin interactions and epigenomics, as well as the possible role of long noncoding RNAs in regulation of P450s during liver maturation were presented.
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Affiliation(s)
- Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Stockholm, Sweden (M.I.-S.); Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut (X.-B.Z., L.P.); Interdepartmental Molecular Toxicology Program and the Department of Pathology and Laboratory Medicine, University of California, Los Angeles, California (O.H., S.B.); Department of Biochemistry and Molecular Medicine, University of California at Davis School of Medicine, Sacramento, California (A.-M.Y.); and Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan (Y.O.)
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Relationship between differential hepatic microRNA expression and decreased hepatic cytochrome P450 3A activity in cirrhosis. PLoS One 2013; 8:e74471. [PMID: 24058572 PMCID: PMC3772944 DOI: 10.1371/journal.pone.0074471] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 07/31/2013] [Indexed: 12/17/2022] Open
Abstract
Background and Aim Liver cirrhosis is associated with decreased hepatic cytochrome P4503A (CYP3A) activity but the pathogenesis of this phenomenon is not well elucidated. In this study, we examined if certain microRNAs (miRNA) are associated with decreased hepatic CYP3A activity in cirrhosis. Methods Hepatic CYP3A activity and miRNA microarray expression profiles were measured in cirrhotic (n=28) and normal (n=12) liver tissue. Hepatic CYP3A activity was measured via midazolam hydroxylation in human liver microsomes. Additionally, hepatic CYP3A4 protein concentration and the expression of CYP3A4 mRNA were measured. Analyses were conducted to identify miRNAs which were differentially expressed between two groups but also were significantly associated with lower hepatic CYP3A activity. Results Hepatic CYP3A activity in cirrhotic livers was 1.7-fold lower than in the normal livers (0.28 ± 0.06 vs. 0.47 ± 0.07mL* min-1*mg protein-1 (mean ± SEM), P=0.02). Six microRNAs (miR-155, miR-454, miR-582-5p, let-7f-1*, miR-181d, and miR-500) had >1.2-fold increase in cirrhotic livers and also had significant negative correlation with hepatic CYP3A activity (range of r = -0.44 to -0.52, P <0.05). Notably, miR-155, a known regulator of liver inflammation, had the highest fold increase in cirrhotic livers (2.2-fold, P=4.16E-08) and significantly correlated with hepatic CYP3A activity (r=-0.50, P=0.017). The relative expression (2-ΔΔCt mean ± SEM) of hepatic CYP3A4 mRNA was significantly higher in cirrhotic livers (21.76 ± 2.65 vs. 5.91 ± 1.29, P=2.04E-07) but their levels did not significantly correlate with hepatic CYP3A activity (r=-0.43, P=0.08). Conclusion The strong association between certain miRNAs, notably miR-155, and lower hepatic CYP3A activity suggest that altered miRNA expression may regulate hepatic CYP3A activity.
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Zhong XB, Leeder JS. Epigenetic regulation of ADME-related genes: focus on drug metabolism and transport. Drug Metab Dispos 2013; 41:1721-4. [PMID: 23935066 DOI: 10.1124/dmd.113.053942] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Epigenetic regulation of gene expression refers to heritable factors that are functionally relevant genomic modifications but that do not involve changes in DNA sequence. Examples of such modifications include DNA methylation, histone modifications, noncoding RNAs, and chromatin architecture. Epigenetic modifications are crucial for packaging and interpreting the genome, and they have fundamental functions in regulating gene expression and activity under the influence of physiologic and environmental factors. Recently, epigenetics has become one of the fastest-growing areas of science and has now become a central issue in biologic studies of development and disease pathogenesis. The interest in epigenetics is also true for studies of drug metabolism and transport. In this issue of Drug Metabolism and Disposition, a series of articles is presented to demonstrate the role of epigenetic factors in regulating the expression of genes involved in drug absorption, distribution, metabolism, and excretion in organ development, tissue-specific gene expression, sexual dimorphism, and in the adaptive response to xenobiotic exposure, both therapeutic and toxic. The articles also demonstrate that, in addition to genetic polymorphisms, epigenetics may also contribute to wide interindividual variations in drug metabolism and transport. Identification of functionally relevant epigenetic biomarkers in human specimens has the potential to improve prediction of drug responses based on patient's epigenetic profiles.
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Affiliation(s)
- Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (X.B.Z.); and Division of Clinical Pharmacology and Therapeutic Innovation, Department of Pediatrics, Children's Mercy Hospitals and Clinics and University of Missouri-Kansas City, Kansas City, Missouri (J.S.L.)
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Chadwick R, O'Connor A. Epigenetics and personalized medicine: prospects and ethical issues. Per Med 2013; 10:463-471. [PMID: 29758832 DOI: 10.2217/pme.13.35] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
As scientific knowledge about gene-environment interactions and the role of epigenetic factors in gene expression grows, new possibilities for personalized medicine may be opened up. In particular, the associations that have been demonstrated between epigenetic markers and certain diseases are an exciting development for personalized medicine. These advances also create new ethical challenges, regarding causal and moral responsibility, due to unique characteristics of how epigenetic effects regulate gene expression, are established and may change over the course of a person's life. This article examines the ethical implications of integrating epigenetic knowledge into personalized medicine.
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Affiliation(s)
- Ruth Chadwick
- Cardiff University, Park Place, Cardiff, CF10 3AT, UK.
| | - Alan O'Connor
- Cardiff University, Park Place, Cardiff, CF10 3AT, UK
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Rieger JK, Klein K, Winter S, Zanger UM. Expression Variability of Absorption, Distribution, Metabolism, Excretion–Related MicroRNAs in Human Liver: Influence of Nongenetic Factors and Association with Gene Expression. Drug Metab Dispos 2013; 41:1752-62. [DOI: 10.1124/dmd.113.052126] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Developmental Changes in the Expression and Function of Cytochrome P450 3A Isoforms: Evidence from In Vitro and In Vivo Investigations. Clin Pharmacokinet 2013; 52:333-45. [DOI: 10.1007/s40262-013-0041-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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