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Abstract
The regulation of brain cytochrome P450 enzymes (CYPs) is different compared with respective hepatic enzymes. This may result from anatomical bases and physiological functions of the two organs. The brain is composed of a variety of functional structures built of different interconnected cell types endowed with specific receptors that receive various neuronal signals from other brain regions. Those signals activate transcription factors or alter functioning of enzyme proteins. Moreover, the blood-brain barrier (BBB) does not allow free penetration of all substances from the periphery into the brain. Differences in neurotransmitter signaling, availability to endogenous and exogenous active substances, and levels of transcription factors between neuronal and hepatic cells lead to differentiated expression and susceptibility to the regulation of CYP genes in the brain and liver. Herein, we briefly describe the CYP enzymes of CYP1-3 families, their distribution in the brain, and discuss brain-specific regulation of CYP genes. In parallel, a comparison to liver CYP regulation is presented. CYP enzymes play an essential role in maintaining the levels of bioactive molecules within normal ranges. These enzymes modulate the metabolism of endogenous neurochemicals, such as neurosteroids, dopamine, serotonin, melatonin, anandamide, and exogenous substances, including psychotropics, drugs of abuse, neurotoxins, and carcinogens. The role of these enzymes is not restricted to xenobiotic-induced neurotoxicity, but they are also involved in brain physiology. Therefore, it is crucial to recognize the function and regulation of CYP enzymes in the brain to build a foundation for future medicine and neuroprotection and for personalized treatment of brain diseases.
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Affiliation(s)
- Wojciech Kuban
- Department of Pharmacokinetics and Drug Metabolism, Maj Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland
| | - Władysława Anna Daniel
- Department of Pharmacokinetics and Drug Metabolism, Maj Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland
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52
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Deng Y, Wu S, Fan H. Genome-wide pathway-based quantitative multiple phenotypes analysis. PLoS One 2020; 15:e0240910. [PMID: 33175855 PMCID: PMC7657528 DOI: 10.1371/journal.pone.0240910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/06/2020] [Indexed: 11/18/2022] Open
Abstract
For complex diseases, genome-wide pathway association studies have become increasingly promising. Currently, however, pathway-based association analysis mainly focus on a single phenotype, which may insufficient to describe the complex diseases and physiological processes. This work proposes a combination model to evaluate the association between a pathway and multiple phenotypes and to reduce the run time based on asymptotic results. For a single phenotype, we propose a semi-supervised maximum kernel-based U-statistics (mSKU) method to assess the pathway-based association analysis. For multiple phenotypes, we propose the fisher combination function with dependent phenotypes (FC) to transform the p-values between the pathway and each marginal phenotype individually to achieve pathway-based multiple phenotypes analysis. With real data from the Alzheimer Disease Neuroimaging Initiative (ADNI) study and Human Liver Cohort (HLC) study, the FC-mSKU method allows us to specify which pathways are specific to a single phenotype or contribute to common genetic constructions of multiple phenotypes. If we only focus on single-phenotype tests, we may miss some findings for etiology studies. Through extensive simulation studies, the FC-mSKU method demonstrates its advantages compared with its counterparts.
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Affiliation(s)
- Yamin Deng
- Statistics Center, First Hospital of Shanxi Medical University, Taiyuan, China.,Division of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Shiman Wu
- Statistics Center, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Huifang Fan
- Statistics Center, First Hospital of Shanxi Medical University, Taiyuan, China
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53
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Chen YX, Rong Y, Jiang F, Chen JB, Duan YY, Dong SS, Zhu DL, Chen H, Yang TL, Dai Z, Guo Y. An integrative multi-omics network-based approach identifies key regulators for breast cancer. Comput Struct Biotechnol J 2020; 18:2826-2835. [PMID: 33133424 PMCID: PMC7585874 DOI: 10.1016/j.csbj.2020.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 09/13/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Although genome-wide association studies (GWASs) have successfully identified thousands of risk variants for human complex diseases, understanding the biological function and molecular mechanisms of the associated SNPs involved in complex diseases is challenging. Here we developed a framework named integrative multi-omics network-based approach (IMNA), aiming to identify potential key genes in regulatory networks by integrating molecular interactions across multiple biological scales, including GWAS signals, gene expression-based signatures, chromatin interactions and protein interactions from the network topology. We applied this approach to breast cancer, and prioritized key genes involved in regulatory networks. We also developed an abnormal gene expression score (AGES) signature based on the gene expression deviation of the top 20 rank-ordered genes in breast cancer. The AGES values are associated with genetic variants, tumor properties and patient survival outcomes. Among the top 20 genes, RNASEH2A was identified as a new candidate gene for breast cancer. Thus, our integrative network-based approach provides a genetic-driven framework to unveil tissue-specific interactions from multiple biological scales and reveal potential key regulatory genes for breast cancer. This approach can also be applied in other complex diseases such as ovarian cancer to unravel underlying mechanisms and help for developing therapeutic targets.
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Affiliation(s)
- Yi-Xiao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Jia-Bin Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China.,Research Institute of Xi'an Jiaotong University, Zhejiang Province 311215, PR China
| | - Hao Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China.,Research Institute of Xi'an Jiaotong University, Zhejiang Province 311215, PR China
| | - Zhijun Dai
- Department of Breast Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province 310003, PR China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi Province 710049, PR China
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54
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Taylor C, Crosby I, Yip V, Maguire P, Pirmohamed M, Turner RM. A Review of the Important Role of CYP2D6 in Pharmacogenomics. Genes (Basel) 2020; 11:E1295. [PMID: 33143137 PMCID: PMC7692531 DOI: 10.3390/genes11111295] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/25/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022] Open
Abstract
Cytochrome P450 2D6 (CYP2D6) is a critical pharmacogene involved in the metabolism of ~20% of commonly used drugs across a broad spectrum of medical disciplines including psychiatry, pain management, oncology and cardiology. Nevertheless, CYP2D6 is highly polymorphic with single-nucleotide polymorphisms, small insertions/deletions and larger structural variants including multiplications, deletions, tandem arrangements, and hybridisations with non-functional CYP2D7 pseudogenes. The frequency of these variants differs across populations, and they significantly influence the drug-metabolising enzymatic function of CYP2D6. Importantly, altered CYP2D6 function has been associated with both adverse drug reactions and reduced drug efficacy, and there is growing recognition of the clinical and economic burdens associated with suboptimal drug utilisation. To date, pharmacogenomic clinical guidelines for at least 48 CYP2D6-substrate drugs have been developed by prominent pharmacogenomics societies, which contain therapeutic recommendations based on CYP2D6-predicted categories of metaboliser phenotype. Novel algorithms to interpret CYP2D6 function from sequencing data that consider structural variants, and machine learning approaches to characterise the functional impact of novel variants, are being developed. However, CYP2D6 genotyping is yet to be implemented broadly into clinical practice, and so further effort and initiatives are required to overcome the implementation challenges and deliver the potential benefits to the bedside.
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Affiliation(s)
- Christopher Taylor
- Wolfson Centre for Personalised Medicine, University of Liverpool, Liverpool L69 3BX, UK; (V.Y.); (M.P.); (R.M.T.)
- MC Diagnostics, St Asaph Business Park, Saint Asaph LL17 0LJ, UK; (I.C.); (P.M.)
| | - Ian Crosby
- MC Diagnostics, St Asaph Business Park, Saint Asaph LL17 0LJ, UK; (I.C.); (P.M.)
| | - Vincent Yip
- Wolfson Centre for Personalised Medicine, University of Liverpool, Liverpool L69 3BX, UK; (V.Y.); (M.P.); (R.M.T.)
| | - Peter Maguire
- MC Diagnostics, St Asaph Business Park, Saint Asaph LL17 0LJ, UK; (I.C.); (P.M.)
| | - Munir Pirmohamed
- Wolfson Centre for Personalised Medicine, University of Liverpool, Liverpool L69 3BX, UK; (V.Y.); (M.P.); (R.M.T.)
| | - Richard M. Turner
- Wolfson Centre for Personalised Medicine, University of Liverpool, Liverpool L69 3BX, UK; (V.Y.); (M.P.); (R.M.T.)
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55
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Yamasaki C, Ishida Y, Yanagi A, Yoshizane Y, Kojima Y, Ogawa Y, Kageyama Y, Iwasaki Y, Ishida S, Chayama K, Tateno C. Culture density contributes to hepatic functions of fresh human hepatocytes isolated from chimeric mice with humanized livers: Novel, long-term, functional two-dimensional in vitro tool for developing new drugs. PLoS One 2020; 15:e0237809. [PMID: 32915792 PMCID: PMC7485858 DOI: 10.1371/journal.pone.0237809] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/03/2020] [Indexed: 01/25/2023] Open
Abstract
Chimeric mice with humanized livers are considered a useful animal model for predicting human (h-) drug metabolism and toxicity. In this study, the characteristics of fresh h-hepatocytes (cFHHs, PXB-cells®) isolated from chimeric mice (PXB-mice®) were evaluated in vitro to confirm their utility for drug development. cFHHs cultured at high density (2.13 × 105 cells/cm2) displayed stable production of h-albumin and cytochrome P450 (CYP) 3A activities for at least 21 days. The mRNA expression levels of 10 of 13 CYP, UDP-glucuronosyltransferase (UGT), and transporters were maintained at >10% of the levels of freshly isolated cFHHs after 21 days. From 1 week, many bile canaliculi were observed between cFHHs, and the accumulation of the multidrug resistance-associated protein and bile salt export pump substrates in these bile canaliculi was clearly inhibited by cyclosporin A. Microarray analysis of cFHHs cultured at high density and at low density (0.53 × 105 cells/cm2) revealed that high density culture maintained high expressions of some transcription factors (HNF4α, PXR, and FXR) perhaps involved in the high CYP, UGT and transporter gene expressions of cFHHs. These results strongly suggest that cFHHs could be a novel in vitro tool for drug development studies.
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Affiliation(s)
| | - Yuji Ishida
- PhoenixBio Co., Ltd., Higashi-Hiroshima, Hiroshima, Japan
- Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan
| | - Ami Yanagi
- PhoenixBio Co., Ltd., Higashi-Hiroshima, Hiroshima, Japan
| | | | - Yuha Kojima
- PhoenixBio Co., Ltd., Higashi-Hiroshima, Hiroshima, Japan
| | - Yuko Ogawa
- PhoenixBio Co., Ltd., Higashi-Hiroshima, Hiroshima, Japan
| | | | - Yumiko Iwasaki
- PhoenixBio Co., Ltd., Higashi-Hiroshima, Hiroshima, Japan
| | - Seiichi Ishida
- Department of Pharmacology, National Institute of Health Sciences, Kanagawa, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical and Health Sciences, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Chise Tateno
- PhoenixBio Co., Ltd., Higashi-Hiroshima, Hiroshima, Japan
- Research Center for Hepatology and Gastroenterology, Hiroshima University, Hiroshima, Japan
- * E-mail:
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56
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Volpe DA. Interindividual Variability in Drug Metabolizing Enzymes. Curr Drug Metab 2020; 20:1041-1043. [PMID: 30117390 DOI: 10.2174/1389200219666180817144411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/02/2018] [Accepted: 08/02/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Donna A Volpe
- Division of Applied Regulatory Science, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, United States
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57
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Tait S, Carli F, Busani L, Buzzigoli E, Della Latta V, Deodati A, Fabbrizi E, Gaggini M, Maranghi F, Tassinari R, Toffol G, Cianfarani S, Gastaldelli A, La Rocca C. Biomonitoring of Bis(2-ethylhexyl)phthalate (DEHP) in Italian children and adolescents: Data from LIFE PERSUADED project. ENVIRONMENTAL RESEARCH 2020; 185:109428. [PMID: 32251910 DOI: 10.1016/j.envres.2020.109428] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/24/2020] [Accepted: 03/22/2020] [Indexed: 06/11/2023]
Abstract
The Bis(2-ethylhexyl)phthalate (DEHP), a widespread plasticizer, is considered an endocrine disrupting chemical with main toxicological effects on reproductive and metabolic systems. Human biomonitoring (HBM) studies are promoted to evaluate the background exposure levels. In the frame of LIFE PERSUADED project, the HBM study measured DEHP main metabolites (mono-(2-ethylhexyl) phthalate, MEHP; 2-ethyl-5-hydroxy-hexylphthalate, MEHHP; 2-ethyl-5-oxo-hexylphthalate, MEOHP) in Italian children and adolescent (4-14 years old) according to geographical macro-areas and areas, age and sex. Children from the South and the Centre of Italy showed higher median levels of DEHP, as a sum of its metabolites (48.14 and 47.80 μg/L), than those from the North (39.47 μg/L; p = 0.0090 and 0.0004, respectively). Considering the total population, boys are more exposed than girls (only as urinary volume), and children aged 4-6 years have higher median levels than those 7-10 and 11-14 years old. The derived reference values (RV95) for DEHP in children is 168 μg/L. The relative metabolic rates of DEHP, the background levels and, thus, the RV95, vary with the geographical area, age and sex, indicating that all these parameters should be considered in the risk assessment.
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Affiliation(s)
- Sabrina Tait
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Fabrizia Carli
- Institute of Clinical Physiology, National Research Council, Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.
| | - Luca Busani
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Emma Buzzigoli
- Institute of Clinical Physiology, National Research Council, Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.
| | - Veronica Della Latta
- Institute of Clinical Physiology, National Research Council, Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.
| | - Annalisa Deodati
- Dipartimento Pediatrico Universitario Ospedaliero "Bambino Gesù" Children's Hospital, Piazza di Sant'Onofrio 4, 00165, Rome, Italy.
| | - Enrica Fabbrizi
- Unità Operativa Complessa Pediatria e Neonatologia, Augusto Murri Hospital, Via Augusto Murri 21, 63900, Fermo, Italy.
| | - Melania Gaggini
- Institute of Clinical Physiology, National Research Council, Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.
| | - Francesca Maranghi
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Roberta Tassinari
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
| | - Giacomo Toffol
- Associazione Culturale Pediatri, Via Montiferru 6, 09070, Narbolia (OR), Italy.
| | - Stefano Cianfarani
- Dipartimento Pediatrico Universitario Ospedaliero "Bambino Gesù" Children's Hospital, Piazza di Sant'Onofrio 4, 00165, Rome, Italy; University of Rome Tor Vergata, Via Cracovia, 50, 00133, Rome, Italy; Department of Women's and Children's Health, Karolinska Institutet and University Hospital, Solnavägen 1, 171 77, Solna, Stockholm, Sweden.
| | - Amalia Gastaldelli
- Institute of Clinical Physiology, National Research Council, Via Giuseppe Moruzzi 1, 56124, Pisa, Italy.
| | - Cinzia La Rocca
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
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58
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Darst BF, Koscik RL, Hogan KJ, Johnson SC, Engelman CD. Longitudinal plasma metabolomics of aging and sex. Aging (Albany NY) 2020; 11:1262-1282. [PMID: 30799310 PMCID: PMC6402508 DOI: 10.18632/aging.101837] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/17/2019] [Indexed: 12/18/2022]
Abstract
Understanding how metabolites are longitudinally influenced by age and sex could facilitate the identification of metabolomic profiles and trajectories that indicate disease risk. We investigated the metabolomics of age and sex using longitudinal plasma samples from the Wisconsin Registry for Alzheimer’s Prevention (WRAP), a cohort of participants who were dementia free at enrollment. Metabolomic profiles were quantified for 2,344 fasting plasma samples among 1,212 participants, each with up to three study visits. Of 1,097 metabolites tested, 623 (56.8%) were associated with age and 695 (63.4%) with sex after correcting for multiple testing. Approximately twice as many metabolites were associated with age in stratified analyses of women versus men, and 68 metabolite trajectories significantly differed by sex, most notably including sphingolipids, which tended to increase in women and decrease in men with age. Using genome-wide genotyping, we also report the heritabilities of metabolites investigated, which ranged dramatically (0.2–99.2%); however, the median heritability of 36.2% suggests that many metabolites are highly influenced by a complex combination of genomic and environmental influences. These findings offer a more profound description of the aging process and may inform many new hypotheses regarding the role metabolites play in healthy and accelerated aging.
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Affiliation(s)
- Burcu F Darst
- Department of Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA
| | - Rebecca L Koscik
- Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, Madison, WI 53726, USA
| | - Kirk J Hogan
- Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, Madison, WI 53726, USA.,Department of Anesthesiology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Sterling C Johnson
- Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, Madison, WI 53726, USA.,Geriatric Research Education and Clinical Center, Wm. S. Middleton Memorial VA Hospital, Madison, WI 53705, USA.,Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
| | - Corinne D Engelman
- Department of Population Health Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI 53726, USA.,Wisconsin Alzheimer's Institute, University of Wisconsin School of Medicine and Public Health, Madison, Madison, WI 53726, USA.,Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792, USA
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59
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Guengerich FP. Cytochrome P450 2E1 and its roles in disease. Chem Biol Interact 2020; 322:109056. [PMID: 32198084 PMCID: PMC7217708 DOI: 10.1016/j.cbi.2020.109056] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/12/2019] [Accepted: 03/10/2020] [Indexed: 12/27/2022]
Abstract
Cytochrome P450 (P450) 2E1 is the major P450 enzyme involved in ethanol metabolism. That role is shared with two other enzymes that oxidize ethanol, alcohol dehydrogenase and catalase. P450 2E1 is also involved in the bioactivation of a number of low molecular weight cancer suspects, as validated in vivo in mouse models where cancers could be attenuated by deletion of Cyp2e1. P450 2E1 does not have a role in global production of reactive oxygen species but localized roles are possible, e.g. in mitochondria. The structures, conformations, and catalytic mechanisms of P450 2E1 have some unusual features among P450s. The concentration of hepatic P450 varies ≥10-fold among humans, possibly in part due to single nucleotide variants. The level of P450 2E1 may have relevance in the rates of oxidation of drugs, particularly acetaminophen and anesthetics.
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Affiliation(s)
- F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, 638 Robinson Research Building, 2200 Pierce Avenue, Nashville, TN, 37232-0146, USA.
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60
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Integrative analysis of proteomic and metabonomics data for identification of pathways related to Rhizoma Paridis-induced hepatotoxicity. Sci Rep 2020; 10:6540. [PMID: 32300172 PMCID: PMC7162872 DOI: 10.1038/s41598-020-63632-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/03/2020] [Indexed: 12/21/2022] Open
Abstract
Clinical reports on hepatotoxicity that arise from Rhizoma Paridis have recently received widespread attention. Because the hepatotoxicity mechanism is little understood, this research strived to investigate the hepatotoxicity mechanism of Rhizoma Paridis extracts based on iTRAQ quantitative proteomics and metabonomics. The extraction solutions were administrated to rats for 7 days by gavage, and the hepatotoxicity was assessed through quantification of biochemical indexes and Oil red O staining. Additionally, the mechanism of hepatotoxicity was investigated by metabonomics based upon GC-MS and iTRAQ quantitative proteomics. The biochemical and histopathological analysis stood out that Rhizoma Paridis extract could induce liver injury, which was proved by the formation of fat droplets, the changes of mitochondrial structure, and biochemical parameters. The iTRAQ proteomics and metabonomics revealed that Rhizoma Paridis-induced hepatotoxicity was chiefly connected with the abnormal activity of mitochondrion function, which brought about oxidative stress injuries and inflammation, finally causing cell apoptosis. Collectively, we have provided previously uncharacterized hepatotoxic mechanism induced by Rhizoma Paridis and a reference to ensure its safe use in the future.
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61
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Yuan X, Lu H, Zhao A, Ding Y, Min Q, Wang R. Transcriptional regulation of CYP3A4 by nuclear receptors in human hepatocytes under hypoxia. Drug Metab Rev 2020; 52:225-234. [PMID: 32270716 DOI: 10.1080/03602532.2020.1733004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The human hepatic cytochrome P-450 3A4 (CYP3A4), recognized as a multifunctional enzyme, has a wide range of substrates including commonly used drugs. Previous investigations demonstrated that the expression of CYP3A4 in human hepatocytes could be regulated by some nuclear receptors (NRs) at transcriptional level under diverse situations. The significance of oxygen on CYP3A4-mediated metabolism seems notable while the regulatory mode of CYP3A4 in the particular case still remains elusive. Recently, striking evidence has emerged that both CYP3A4 and its regulator NR could be inhibited by exposure to hypoxia. Therefore, it is of great importance to elucidate whether and how these NRs act in the transcriptional regulation of CYP3A4 in human hepatocytes under hypoxic conditions. In this review, we mainly summarized transcriptional regulation of the pivotal enzyme CYP3A4 by NRs and explored the possible regulatory pathways of CYP3A4 via these major NRs under hypoxia, expecting to provide favorable evidence for further clinical guidance under such pathological situations.
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Affiliation(s)
- Xuechun Yuan
- Key Laboratory of the Plateau Environmental Damage Control, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou, China.,College of Pharmacy, Lanzhou University, Lanzhou, China
| | - Hui Lu
- Key Laboratory of the Plateau Environmental Damage Control, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou, China
| | - Anpeng Zhao
- Key Laboratory of the Plateau Environmental Damage Control, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou, China
| | - Yidan Ding
- Key Laboratory of the Plateau Environmental Damage Control, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou, China.,College of Pharmacy, Lanzhou University, Lanzhou, China
| | - Qiong Min
- Pharmacy department, Gansu Provincial Cancer Hospital, Lanzhou, China
| | - Rong Wang
- Key Laboratory of the Plateau Environmental Damage Control, The 940th Hospital of Joint Logistics Support Force of Chinese People's Liberation Army, Lanzhou, China.,College of Pharmacy, Lanzhou University, Lanzhou, China
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62
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Nakamura T, Fukuda M, Matsukane R, Suetsugu K, Harada N, Yoshizumi T, Egashira N, Mori M, Masuda S. Influence of POR*28 Polymorphisms on CYP3A5*3-Associated Variations in Tacrolimus Blood Levels at an Early Stage after Liver Transplantation. Int J Mol Sci 2020; 21:ijms21072287. [PMID: 32225074 PMCID: PMC7178010 DOI: 10.3390/ijms21072287] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/22/2020] [Accepted: 03/24/2020] [Indexed: 12/19/2022] Open
Abstract
It is well known that the CYP3A5*3 polymorphism is an important marker that correlates with the tacrolimus dose requirement after organ transplantation. Recently, it has been revealed that the POR*28 polymorphism affects the pharmacokinetics of tacrolimus in renal transplant patients. In this study, we examined whether POR*28 as well as CYP3A5*3 polymorphism in Japanese recipients and donors would be another biomarker for the variation of tacrolimus blood levels in the recipients during the first month after living-donor liver transplantation. We enrolled 65 patients treated with tacrolimus, who underwent liver transplantation between July 2016 and January 2019. Genomic DNA was extracted from whole-blood samples, and genotyping was performed to examine the presence of CYP3A5*3 and POR*28 polymorphisms in the recipients and donors. The CYP3A5*3/*3 genotype (defective CYP3A5) of the recipient (standard partial regression coefficient [median C/D ratio of CYP3A5 expressor vs. CYP3A5 non-expressor, p value]: Pod 1–7, β= −0.389 [1.76 vs. 2.73, p < 0.001]; Pod 8–14, β = −0.345 [2.03 vs. 2.83, p < 0.001]; Pod 15–21, β= −0.417 [1.75 vs. 2.94, p < 0.001]; Pod 22–28, β = −0.627 [1.55 vs. 2.90, p < 0.001]) rather than donor (Pod 1–7, β = n/a [1.88 vs. 2.76]; Pod 8–14, β = n/a [1.99 vs. 2.93]; Pod 15–21, β = −0.175 [1.91 vs. 2.94, p = 0.004]; Pod 22–28, β = n/a [1.61 vs. 2.67]) significantly contributed to the increase in the concentration/dose (C/D) ratio of tacrolimus for at least one month after surgery. We found that the tacrolimus C/D ratio significantly decreased from the third week after transplantation when the recipient carried both CYP3A5*1 (functional CYP3A5) and POR*28 (n = 19 [29.2%], median C/D ratio [inter quartile range] = 1.58 [1.39–2.17]), compared with that in the recipients carrying CYP3A5*1 and POR*1/*1 (n = 8 [12.3%], median C/D ratio [inter quartile range] = 2.23 [2.05–3.06]) (p < 0.001). In conclusion, to our knowledge, this is the first report suggesting that the POR*28 polymorphism is another biomarker for the tacrolimus oral dosage after liver transplantation in patients carrying CYP3A5*1 rather than CYP3A5*3/*3.
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Affiliation(s)
- Takahiro Nakamura
- Department of Clinical Pharmacology and Biopharmaceutics, The Pharmaceutical College, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan;
| | - Mio Fukuda
- Department of Pharmacy, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (M.F.); (R.M.); (K.S.); (N.E.)
| | - Ryosuke Matsukane
- Department of Pharmacy, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (M.F.); (R.M.); (K.S.); (N.E.)
| | - Kimitaka Suetsugu
- Department of Pharmacy, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (M.F.); (R.M.); (K.S.); (N.E.)
| | - Noboru Harada
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (N.H.); (T.Y.); (M.M.)
| | - Tomoharu Yoshizumi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (N.H.); (T.Y.); (M.M.)
| | - Nobuaki Egashira
- Department of Pharmacy, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (M.F.); (R.M.); (K.S.); (N.E.)
| | - Masaki Mori
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (N.H.); (T.Y.); (M.M.)
| | - Satohiro Masuda
- Department of Pharmacy, Kyushu University Hospital, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (M.F.); (R.M.); (K.S.); (N.E.)
- Department of Pharmacy, International University of Health and Welfare Narita Hospital, 852 Hatakeda, Narita 286-0124, Japan
- Correspondence: ; Tel.: +81-476-28-1401
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Neyshaburinezhad N, Rouini M, Shirzad N, Esteghamati A, Nakhjavani M, Namazi S, Ardakani YH. Evaluating the effect of type 2 diabetes mellitus on CYP450 enzymes and P-gp activities, before and after glycemic control: A protocol for a case-control pharmacokinetic study. MethodsX 2020; 7:100853. [PMID: 32337164 PMCID: PMC7176986 DOI: 10.1016/j.mex.2020.100853] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 02/29/2020] [Indexed: 12/18/2022] Open
Abstract
Cytochrome P450s (CYP450) family is one of the most critical factors in the metabolism process. Hence, the present study aims to characterize the activity of CYP1A2, CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A4/5, and P-glycoprotein (P-gp) pump in patients with type 2 diabetes (T2DM). This characterization was performed before and after good glycemic control versus non-diabetic subjects following the administration of a substrate probe drug cocktail. This single-center clinical study proposes the characterization of T2DM impacts on major CYP450 drug-metabolizing enzyme and P-glycoprotein (P-gp) activities. The main propose of the present study is evaluating any alternation in major CYP450 enzymes and P-gp activities in patients with T2DM, before (A1C>7%) and after (A1C≤7%) good glycemic control along with comparing the activities versus non-diabetic subjects. The phenotypes will be assessed following the oral administration of a drug cocktail containing caffeine (CYP1A2), bupropion (CYP2B6), flurbiprofen (CYP2C9), omeprazole (CYP2C19), dextromethorphan (CYP2D6), midazolam (CYP3A4/5), and fexofenadine (P-gp) as probe substrates. Furthermore, the influence of variables such as glycemia, genetic polymorphisms, and inflammation on the metabolism process will be evaluated. The first patient has entered the study in Dec 2018.
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Affiliation(s)
- Navid Neyshaburinezhad
- Biopharmaceutics and Pharmacokinetic Division, Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Rouini
- Biopharmaceutics and Pharmacokinetic Division, Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Nooshin Shirzad
- Endocrinology and Metabolism Research Center (EMRC), Vali-Asr Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Esteghamati
- Endocrinology and Metabolism Research Center (EMRC), Vali-Asr Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Manouchehr Nakhjavani
- Endocrinology and Metabolism Research Center (EMRC), Vali-Asr Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Soha Namazi
- Department of Clinical Pharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Yalda H. Ardakani
- Biopharmaceutics and Pharmacokinetic Division, Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
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Gao N, Tang H, Gao L, Tu G, Luo H, Xia Y. CYP3A4 and CYP11A1 variants are risk factors for ischemic stroke: a case control study. BMC Neurol 2020; 20:77. [PMID: 32126981 PMCID: PMC7055027 DOI: 10.1186/s12883-020-1628-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 01/23/2020] [Indexed: 01/11/2023] Open
Abstract
Background This study aimed to investigate the roles of CYP3A4 and CYP11A1 variants in ischemic stroke (IS) susceptibility among the Han Chinese population. Methods Four hundred seventy-seven patients with IS and 493 healthy controls were enrolled. Seven single-nucleotide polymorphisms (SNPs) of CYP3A4 and CYP11A1 were genotyped by Agena MassARRAY. Odds ratio (OR) and 95% confidence intervals (CI) were calculated by logistic regression adjusted for age and gender. Results We found that CYP3A4 rs3735451 (OR = 0.81, p = 0.039) and rs4646440 (OR = 0.72, p = 0.021) polymorphisms decreased the risk of IS. CYP3A4 rs4646440 (OR = 0.74, p = 0.038) and CYP11A1 rs12912592 (OR = 1.58, p = 0.034) polymorphisms were correlated with IS risk in males. CYP3A4 rs3735451 (OR = 0.63, p = 0.031) and rs4646440 (OR = 0.57, p = 0.012) possibly weaken the IS susceptibility at age > 61 years. Besides, CYP3A4 rs4646437 (OR = 0.59, p = 0.029), CYP11A1 rs12912592 (OR = 1.84, p = 0.017) and rs28681535 (OR = 0.66, p = 0.038) were associated with IS risk at age ≤ 61 years. CYP11A1 rs28681535 TT genotype was higher high-density lipoprotein cholesterol level than the GT and GG genotype (p = 0.027). Conclusions Our findings indicated that rs3735451, rs4646440, rs4646437 in CYP3A4 and rs28681535 in CYP11A1 might be protective factors for IS, while CYP11A1 rs12912592 polymorphism be a risk factor for IS in Chinese Han population.
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Affiliation(s)
- Ning Gao
- Department of Neurosurgery, Affiliated Haikou Hospital of Xiangya Medical College of Central South University, Haikou People's Hospital, #43, People's Avenue, Haidian Island, Haikou, 570208, Hainan, China
| | - Hong Tang
- Department of Neurosurgery, Affiliated Haikou Hospital of Xiangya Medical College of Central South University, Haikou People's Hospital, #43, People's Avenue, Haidian Island, Haikou, 570208, Hainan, China
| | - Ling Gao
- Department of Neurosurgery, Affiliated Haikou Hospital of Xiangya Medical College of Central South University, Haikou People's Hospital, #43, People's Avenue, Haidian Island, Haikou, 570208, Hainan, China
| | - Guolong Tu
- Department of Neurosurgery, Affiliated Haikou Hospital of Xiangya Medical College of Central South University, Haikou People's Hospital, #43, People's Avenue, Haidian Island, Haikou, 570208, Hainan, China
| | - Han Luo
- Department of Neurosurgery, Affiliated Haikou Hospital of Xiangya Medical College of Central South University, Haikou People's Hospital, #43, People's Avenue, Haidian Island, Haikou, 570208, Hainan, China
| | - Ying Xia
- Department of Neurosurgery, Affiliated Haikou Hospital of Xiangya Medical College of Central South University, Haikou People's Hospital, #43, People's Avenue, Haidian Island, Haikou, 570208, Hainan, China.
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Gao B, Liu X, Li H, Cui Y. Integrative analysis of genetical genomics data incorporating network structures. Biometrics 2019; 75:1063-1075. [PMID: 31009063 PMCID: PMC6810723 DOI: 10.1111/biom.13072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/15/2019] [Accepted: 03/28/2019] [Indexed: 12/18/2022]
Abstract
In a living organism, tens of thousands of genes are expressed and interact with each other to achieve necessary cellular functions. Gene regulatory networks contain information on regulatory mechanisms and the functions of gene expressions. Thus, incorporating network structures, discerned either through biological experiments or statistical estimations, could potentially increase the selection and estimation accuracy of genes associated with a phenotype of interest. Here, we considered a gene selection problem using gene expression data and the graphical structures found in gene networks. Because gene expression measurements are intermediate phenotypes between a trait and its associated genes, we adopted an instrumental variable regression approach. We treated genetic variants as instrumental variables to address the endogeneity issue. We proposed a two-step estimation procedure. In the first step, we applied the LASSO algorithm to estimate the effects of genetic variants on gene expression measurements. In the second step, the projected expression measurements obtained from the first step were treated as input variables. A graph-constrained regularization method was adopted to improve the efficiency of gene selection and estimation. We theoretically showed the selection consistency of the estimation method and derived the L ∞ bound of the estimates. Simulation and real data analyses were conducted to demonstrate the effectiveness of our method and to compare it with its counterparts.
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Affiliation(s)
- Bin Gao
- Department of Statistics and Probability, Michigan State University, East Lansing, Michigan
- Quantitative Sciences, Janssen Research & Development, LLC, Spring House, Pennsylvania
| | - Xu Liu
- School of Statistics and Management, Shanghai University of Finance and Economics, Shanghai, China
| | - Hongzhe Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yuehua Cui
- Department of Statistics and Probability, Michigan State University, East Lansing, Michigan
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Blencowe M, Karunanayake T, Wier J, Hsu N, Yang X. Network Modeling Approaches and Applications to Unravelling Non-Alcoholic Fatty Liver Disease. Genes (Basel) 2019; 10:E966. [PMID: 31771247 PMCID: PMC6947017 DOI: 10.3390/genes10120966] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/18/2019] [Accepted: 11/22/2019] [Indexed: 12/12/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a progressive condition of the liver encompassing a range of pathologies including steatosis, non-alcoholic steatohepatitis (NASH), cirrhosis, and hepatocellular carcinoma. Research into this disease is imperative due to its rapid growth in prevalence, economic burden, and current lack of FDA approved therapies. NAFLD involves a highly complex etiology that calls for multi-tissue multi-omics network approaches to uncover the pathogenic genes and processes, diagnostic biomarkers, and potential therapeutic strategies. In this review, we first present a basic overview of disease pathogenesis, risk factors, and remaining knowledge gaps, followed by discussions of the need and concepts of multi-tissue multi-omics approaches, various network methodologies and application examples in NAFLD research. We highlight the findings that have been uncovered thus far including novel biomarkers, genes, and biological pathways involved in different stages of NAFLD, molecular connections between NAFLD and its comorbidities, mechanisms underpinning sex differences, and druggable targets. Lastly, we outline the future directions of implementing network approaches to further improve our understanding of NAFLD in order to guide diagnosis and therapeutics.
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Affiliation(s)
- Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Tilan Karunanayake
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
| | - Julian Wier
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
| | - Neil Hsu
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA; (M.B.); (T.K.); (J.W.); (N.H.)
- Molecular, Cellular, and Integrative Physiology Interdepartmental Program, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
- Interdepartmental Program of Bioinformatics, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
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Krogstad V, Peric A, Robertsen I, Kringen MK, Wegler C, Angeles PC, Hjelmesæth J, Karlsson C, Andersson S, Artursson P, Åsberg A, Andersson TB, Christensen H. A Comparative Analysis of Cytochrome P450 Activities in Paired Liver and Small Intestinal Samples from Patients with Obesity. Drug Metab Dispos 2019; 48:8-17. [DOI: 10.1124/dmd.119.087940] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 10/28/2019] [Indexed: 12/28/2022] Open
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Wang D, Lu R, Rempala G, Sadee W. Ligand-Free Estrogen Receptor α (ESR1) as Master Regulator for the Expression of CYP3A4 and Other Cytochrome P450 Enzymes in the Human Liver. Mol Pharmacol 2019; 96:430-440. [PMID: 31399483 PMCID: PMC6724575 DOI: 10.1124/mol.119.116897] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 08/01/2019] [Indexed: 12/25/2022] Open
Abstract
Cytochrome P450 3A4 isoform (CYP3A4) transcription is controlled by hepatic transcription factors (TFs), but how TFs dynamically interact remains uncertain. We hypothesize that several TFs form a regulatory network with nonlinear, dynamic, and hierarchical interactions. To resolve complex interactions, we have applied a computational approach for estimating Sobol's sensitivity indices (SSI) under generalized linear models to existing liver RNA expression microarray data (GSE9588) and RNA-seq data from genotype-tissue expression (GTEx), generating robust importance ranking of TF effects and interactions. The SSI-based analysis identified TFs and interacting TF pairs, triplets, and quadruplets involved in CYP3A4 expression. In addition to known CYP3A4 TFs, estrogen receptor α (ESR1) emerges as key TF with the strongest main effect and as the most frequently included TF interacting partner. Model predictions were validated using small interfering RNA (siRNA)/short hairpin RNA (shRNA) gene knockdown and clustered regularly interspaced short palindromic repeats (CRISPR)-mediated transcriptional activation of ESR1 in biliary epithelial Huh7 cells and human hepatocytes in the absence of estrogen. Moreover, ESR1 and known CYP3A4 TFs mutually regulate each other. Detectable in both male and female hepatocytes without added estrogen, the results demonstrate a role for unliganded ESR1 in CYP3A4 expression consistent with unliganded ESR1 signaling reported in other cell types. Added estrogen further enhances ESR1 effects. We propose a hierarchical regulatory network for CYP3A4 expression directed by ESR1 through self-regulation, cross regulation, and TF-TF interactions. We also demonstrate that ESR1 regulates the expression of other P450 enzymes, suggesting broad influence of ESR1 on xenobiotics metabolism in human liver. Further studies are required to understand the mechanisms underlying role of ESR1 in P450 regulation. SIGNIFICANCE STATEMENT: This study focuses on identifying key transcription factors and regulatory networks for CYP3A4, the main drug metabolizing enzymes in liver. We applied a new computational approach (Sobol's sensitivity analysis) to existing hepatic gene expression data to determine the role of transcription factors in regulating CYP3A4 expression, and used molecular genetics methods (siRNA/shRNA gene knockdown and CRISPR-mediated transcriptional activation) to test these interactions in life cells. This approach reveals a robust network of TFs, including their putative interactions and the relative impact of each interaction. We find that ESR1 serves as a key transcription factor function in regulating CYP3A4, and it appears to be acting at least in part in a ligand-free fashion.
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Affiliation(s)
- Danxin Wang
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Clinical Sciences, Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, Texas (R.L.); and Mathematical Bioscience Institute, (G.R.) and Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine (W.S.), Ohio State University, Columbus, Ohio
| | - Rong Lu
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Clinical Sciences, Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, Texas (R.L.); and Mathematical Bioscience Institute, (G.R.) and Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine (W.S.), Ohio State University, Columbus, Ohio
| | - Grzegorz Rempala
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Clinical Sciences, Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, Texas (R.L.); and Mathematical Bioscience Institute, (G.R.) and Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine (W.S.), Ohio State University, Columbus, Ohio
| | - Wolfgang Sadee
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida (D.W.); Department of Clinical Sciences, Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, Texas (R.L.); and Mathematical Bioscience Institute, (G.R.) and Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine (W.S.), Ohio State University, Columbus, Ohio
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Feltrin C, Oliveira Simões CM. Reviewing the mechanisms of natural product-drug interactions involving efflux transporters and metabolic enzymes. Chem Biol Interact 2019; 314:108825. [PMID: 31553897 DOI: 10.1016/j.cbi.2019.108825] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/28/2019] [Accepted: 09/19/2019] [Indexed: 12/20/2022]
Abstract
The World Health Organization (WHO) and other worldwide health agencies have recently taken initiatives to encourage the use of traditional medicine and/or complementary/alternative medicine in order to promote well-being and public health. In this way, one of the WHO's concerns is the safe use of these therapies. Phytotherapy is a strategy consisting of the use of medicinal plants (MP) and/or herbal medicinal products (HMP) for medicinal purposes. The use of phytotherapy concomitantly with drugs may cause interactions compromising the expected pharmacological action or generating toxic effects. These interactions are complex processes that may occur with multiple medications targeting different metabolic pathways, and involving different compounds present in MP and HMP. Thus, the aim of this review was to summarize the main MP- and HMP-drug interactions that involve specific transporters (P-glycoprotein and BCRP) and CYP450 enzymes (CYP3A4 and CYP2D6), which play relevant roles in the mechanisms of interactions. Firstly, multiple databases were used to search studies describing in vitro or in vivo MP and HMP-drug interactions and, after that, a systematic note-taking and appraisal of the literature was conducted. It was observed that several MP and HMP, metabolic pathways and transcription factors are involved in the transporters and enzymes expression or in the modulation of their activity having the potential to provide such interactions. Thus, the knowledge of MP- and HMP-drug interaction mechanisms could contribute to prevent harmful interactions and can ensure the safe use of these products to help the establishment of the therapeutic planning in order to certify the best treatment strategy to be used.
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Affiliation(s)
- Clarissa Feltrin
- Programa de Pós-Graduação em Farmácia, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Cláudia Maria Oliveira Simões
- Programa de Pós-Graduação em Farmácia, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil.
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Integrating physiologically based kinetic (PBK) and Monte Carlo modelling to predict inter-individual and inter-ethnic variation in bioactivation and liver toxicity of lasiocarpine. Arch Toxicol 2019; 93:2943-2960. [PMID: 31511935 DOI: 10.1007/s00204-019-02563-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/02/2019] [Indexed: 10/26/2022]
Abstract
The aim of the present study was to predict the effect of inter-individual and inter-ethnic human kinetic variation on the sensitivity towards acute liver toxicity of lasiocarpine in the Chinese and the Caucasian population, and to derive chemical specific adjustment factors (CSAFs) by integrating variation in the in vitro kinetic constants Vmax and Km, physiologically based kinetic (PBK) modelling and Monte Carlo simulation. CSAFs were derived covering the 90th and 99th percentile of the population distribution of pyrrole glutathione adduct (7-GS-DHP) formation, reflecting bioactivation. The results revealed that in the Chinese population, as compared to the Caucasian population, the predicted 7-GS-DHP formation at the geometric mean, the 90th and the 99th percentile were 2.1-, 3.3- and 4.3-fold lower respectively. The CSAFs obtained using the 99th percentile values were 8.3, 17.0 and 19.5 in the Chinese, the Caucasian population and the two populations combined, respectively, while the CSAFs were generally 3.0-fold lower at the 90th percentile. These results indicate that when considering the formation of 7-GS-DHP the Caucasian population may be more sensitive towards acute liver toxicity of lasiocarpine, and further point out that the default safety factor of 3.16 for inter-individual human kinetic differences may not be sufficiently protective. Altogether, the results obtained demonstrate that integrating PBK modelling with Monte Carlo simulations using human in vitro data is a powerful strategy to quantify inter-individual variations in kinetics, and can be used to refine the human risk assessment of pyrrolizidine alkaloids.
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Bissada JE, Truong V, Abouda AA, Wines KJ, Crouch RD, Jackson KD. Interindividual Variation in CYP3A Activity Influences Lapatinib Bioactivation. Drug Metab Dispos 2019; 47:1257-1269. [PMID: 31492693 DOI: 10.1124/dmd.119.088823] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/03/2019] [Indexed: 12/14/2022] Open
Abstract
Lapatinib is a dual tyrosine kinase inhibitor associated with rare but potentially severe idiosyncratic hepatotoxicity. We have previously shown that cytochromes P450 CYP3A4 and CYP3A5 quantitatively contribute to lapatinib bioactivation, leading to formation of a reactive, potentially toxic quinone imine. CYP3A5 is highly polymorphic; however, the impact of CYP3A5 polymorphism on lapatinib metabolism has not been fully established. The goal of this study was to determine the effect of CYP3A5 genotype and individual variation in CYP3A activity on the metabolic activation of lapatinib using human-relevant in vitro systems. Lapatinib metabolism was examined using CYP3A5-genotyped human liver microsomes and cryopreserved human hepatocytes. CYP3A and CYP3A5-selective activities were measured in liver tissues using probe substrates midazolam and T-5 (T-1032), respectively, to evaluate the correlation between enzymatic activity and lapatinib metabolite formation. Drug metabolites were measured by high-performance liquid chromatography-tandem mass spectrometry. Further, the relative contributions of CYP3A4 and CYP3A5 to lapatinib O-debenzylation were estimated using selective chemical inhibitors of CYP3A. The results from this study demonstrated that lapatinib O-debenzylation and quinone imine-GSH conjugate formation were highly correlated with hepatic CYP3A activity, as measured by midazolam 1'-hydroxylation. CYP3A4 played a dominant role in lapatinib bioactivation in all liver tissues evaluated. The CYP3A5 contribution to lapatinib bioactivation varied by individual donor and was dependent on CYP3A5 genotype and activity. CYP3A5 contributed approximately 20%-42% to lapatinib O-debenzylation in livers from CYP3A5 expressers. These findings indicate that individual CYP3A activity, not CYP3A5 genotype alone, is a key determinant of lapatinib bioactivation and likely influences exposure to reactive metabolites. SIGNIFICANCE STATEMENT: This study is the first to examine the effect of CYP3A5 genotype, total CYP3A activity, and CYP3A5-selective activity on lapatinib bioactivation in individual human liver tissues. The results of this investigation indicate that lapatinib bioactivation via oxidative O-debenzylation is highly correlated with total hepatic CYP3A activity, and not CYP3A5 genotype alone. These findings provide insight into the individual factors, namely, CYP3A activity, that may affect individual exposure to reactive, potentially toxic metabolites of lapatinib.
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Affiliation(s)
- Jennifer E Bissada
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy and Health Sciences, Nashville, Tennessee (J.E.B., V.T., A.A.A., K.J.W., R.D.C., K.D.J.); Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee (R.D.C., K.D.J.); and 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.)
| | - Vivian Truong
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy and Health Sciences, Nashville, Tennessee (J.E.B., V.T., A.A.A., K.J.W., R.D.C., K.D.J.); Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee (R.D.C., K.D.J.); and 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.)
| | - Arsany A Abouda
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy and Health Sciences, Nashville, Tennessee (J.E.B., V.T., A.A.A., K.J.W., R.D.C., K.D.J.); Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee (R.D.C., K.D.J.); and 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.)
| | - Kahari J Wines
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy and Health Sciences, Nashville, Tennessee (J.E.B., V.T., A.A.A., K.J.W., R.D.C., K.D.J.); Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee (R.D.C., K.D.J.); and 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.)
| | - Rachel D Crouch
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy and Health Sciences, Nashville, Tennessee (J.E.B., V.T., A.A.A., K.J.W., R.D.C., K.D.J.); Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee (R.D.C., K.D.J.); and 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.)
| | - Klarissa D Jackson
- Department of Pharmaceutical Sciences, Lipscomb University College of Pharmacy and Health Sciences, Nashville, Tennessee (J.E.B., V.T., A.A.A., K.J.W., R.D.C., K.D.J.); Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee (R.D.C., K.D.J.); and 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.)
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72
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Shaffo FC, Grodzki AC, Schelegle ES, Lein PJ. The Organophosphorus Pesticide Chlorpyrifos Induces Sex-Specific Airway Hyperreactivity in Adult Rats. Toxicol Sci 2019; 165:244-253. [PMID: 29939342 DOI: 10.1093/toxsci/kfy158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Occupational and environmental exposures to organophosphorus pesticides (OPs) are associated with increased incidence of asthma and other pulmonary diseases. Although the canonical mechanism of OP neurotoxicity is inhibition of acetylcholinesterase (AChE), it was previously reported that the OP chlorpyrifos (CPF) causes airway hyperreactivity (AHR) in guinea pigs at levels that do not inhibit lung or brain AChE. The guinea pig is considered to have inherently hyperresponsive airways, thus, cross-species validation is needed to confirm relevance to humans. Additionally, sex differences in asthma incidence have been demonstrated in the human population, but whether OP-induced AHR is sex-dependent has not been systematically studied in a preclinical model. In this study, 8-week old male and female Sprague Dawley rats were administered CPF at doses causing comparable AChE inhibition in whole lung homogenate (30 mg/kg in males, 7 mg/kg in females, sc) prior to assessing pulmonary mechanics in response to electrical stimulation of the vagus nerves at 24 h, 48 h, 72 h, 7 d or 14 d post-exposure in males, and 24 h or 7 d post-exposure in females. CPF significantly potentiated vagally induced airway resistance and tissue elastance at 7 d post-exposure in males, and at 24 h and 7 d post-exposure in females. These effects occurred independent of significant AChE inhibition in cerebellum, blood, trachealis, or isolated airway, suggesting that AChE independent OP-induced airway hyperreactivity is a cross-species phenomenon. These findings have significant implications for assessing the risk posed by CPF, and potentially other OPs, to human health and safety.
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Affiliation(s)
| | | | - Edward S Schelegle
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, California 95616
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73
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Development and validation of a UPLC-MS/MS method for quantification of doxofylline and its metabolites in human plasma. J Pharm Biomed Anal 2019; 174:220-225. [DOI: 10.1016/j.jpba.2019.05.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/18/2019] [Accepted: 05/20/2019] [Indexed: 02/06/2023]
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74
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Zhou M, Shao J, Wu CY, Shu L, Dong W, Liu Y, Chen M, Wynn RM, Wang J, Wang J, Gui WJ, Qi X, Lusis AJ, Li Z, Wang W, Ning G, Yang X, Chuang DT, Wang Y, Sun H. Targeting BCAA Catabolism to Treat Obesity-Associated Insulin Resistance. Diabetes 2019; 68:1730-1746. [PMID: 31167878 PMCID: PMC6702639 DOI: 10.2337/db18-0927] [Citation(s) in RCA: 179] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 05/29/2019] [Indexed: 12/12/2022]
Abstract
Recent studies implicate a strong association between elevated plasma branched-chain amino acids (BCAAs) and insulin resistance (IR). However, a causal relationship and whether interrupted BCAA homeostasis can serve as a therapeutic target for diabetes remain to be established experimentally. In this study, unbiased integrative pathway analyses identified a unique genetic link between obesity-associated IR and BCAA catabolic gene expression at the pathway level in human and mouse populations. In genetically obese (ob/ob) mice, rate-limiting branched-chain α-keto acid (BCKA) dehydrogenase deficiency (i.e., BCAA and BCKA accumulation), a metabolic feature, accompanied the systemic suppression of BCAA catabolic genes. Restoring BCAA catabolic flux with a pharmacological inhibitor of BCKA dehydrogenase kinase (BCKDK) ( a suppressor of BCKA dehydrogenase) reduced the abundance of BCAA and BCKA and markedly attenuated IR in ob/ob mice. Similar outcomes were achieved by reducing protein (and thus BCAA) intake, whereas increasing BCAA intake did the opposite; this corroborates the pathogenic roles of BCAAs and BCKAs in IR in ob/ob mice. Like BCAAs, BCKAs also suppressed insulin signaling via activation of mammalian target of rapamycin complex 1. Finally, the small-molecule BCKDK inhibitor significantly attenuated IR in high-fat diet-induced obese mice. Collectively, these data demonstrate a pivotal causal role of a BCAA catabolic defect and elevated abundance of BCAAs and BCKAs in obesity-associated IR and provide proof-of-concept evidence for the therapeutic validity of manipulating BCAA metabolism for treating diabetes.
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Affiliation(s)
- Meiyi Zhou
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jing Shao
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cheng-Yang Wu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Le Shu
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA
| | - Weibing Dong
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunxia Liu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mengping Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - R Max Wynn
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jiqiu Wang
- Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ji Wang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wen-Jun Gui
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xiangbing Qi
- Chemistry Center, National Institute of Biological Science, Beijing, China
| | - Aldons J Lusis
- Departments of Medicine, Microbiology, and Human Genetics, University of California at Los Angeles, Los Angeles, CA
| | - Zhaoping Li
- Department of Clinical Nutrition, University of California at Los Angeles, Los Angeles, CA
| | - Weiqing Wang
- Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guang Ning
- Department of Endocrinology and Metabolism, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA
| | - David T Chuang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX
| | - Yibin Wang
- Departments of Anesthesiology, Medicine, and Physiology, University of California at Los Angeles, Los Angeles, CA
| | - Haipeng Sun
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Departments of Anesthesiology, Medicine, and Physiology, University of California at Los Angeles, Los Angeles, CA
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75
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Hennig EE, Piątkowska M, Goryca K, Pośpiech E, Paziewska A, Karczmarski J, Kluska A, Brewczyńska E, Ostrowski J. Non- CYP2D6 Variants Selected by a GWAS Improve the Prediction of Impaired Tamoxifen Metabolism in Patients with Breast Cancer. J Clin Med 2019; 8:jcm8081087. [PMID: 31344832 PMCID: PMC6722498 DOI: 10.3390/jcm8081087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/28/2019] [Accepted: 07/10/2019] [Indexed: 12/25/2022] Open
Abstract
A certain minimum plasma concentration of (Z)-endoxifen is presumably required for breast cancer patients to benefit from tamoxifen therapy. In this study, we searched for DNA variants that could aid in the prediction of risk for insufficient (Z)-endoxifen exposure. A metabolic ratio (MR) corresponding to the (Z)-endoxifen efficacy threshold level was adopted as a cutoff value for a genome-wide association study comprised of 287 breast cancer patients. Multivariate regression was used to preselect variables exhibiting an independent impact on the MR and develop models to predict below-threshold MR values. In total, 15 single-nucleotide polymorphisms (SNPs) were significantly associated with below-threshold MR values. The strongest association was with rs8138080 (WBP2NL). Two alternative models for MR prediction were developed. The predictive accuracy of Model 1, including rs7245, rs6950784, rs1320308, and the CYP2D6 genotype, was considerably higher than that of the CYP2D6 genotype alone (AUC 0.879 vs 0.758). Model 2, which was developed using the same three SNPs as for Model 1 plus rs8138080, appeared as an interesting alternative to the full CYP2D6 genotype testing. In conclusion, the four novel SNPs, tested alone or in combination with the CYP2D6 genotype, improved the prediction of impaired tamoxifen-to-endoxifen metabolism, potentially allowing for treatment optimization.
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Affiliation(s)
- Ewa E Hennig
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland.
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland.
| | - Magdalena Piątkowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Kraków, Poland
| | - Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
| | - Elżbieta Brewczyńska
- Department of Breast Cancer and Reconstructive Surgery, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre of Postgraduate Medical Education, 01-813 Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland
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76
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A Pilot Study towards the Impact of Type 2 Diabetes on the Expression and Activities of Drug Metabolizing Enzymes and Transporters in Human Duodenum. Int J Mol Sci 2019; 20:ijms20133257. [PMID: 31269743 PMCID: PMC6651059 DOI: 10.3390/ijms20133257] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/13/2019] [Accepted: 06/21/2019] [Indexed: 12/24/2022] Open
Abstract
To characterize effects of type 2 diabetes (T2D) on mRNA expression levels for 10 Cytochromes P450 (CYP450s), two carboxylesterases, and three drug transporters (ABCB1, ABCG2, SLCO2B1) in human duodenal biopsies. To compare drug metabolizing enzyme activities of four CYP450 isoenzymes in duodenal biopsies from patients with or without T2D. mRNA levels were quantified (RT-qPCR) in human duodenal biopsies obtained from patients with (n = 20) or without (n = 16) T2D undergoing a scheduled gastro-intestinal endoscopy. CYP450 activities were determined following incubation of biopsy homogenates with probe substrates for CYP2B6 (bupropion), CYP2C9 (tolbutamide), CYP2J2 (ebastine), and CYP3A4/5 (midazolam). Covariables related to inflammation, T2D, demographic, and genetics were investigated. T2D had no major effects on mRNA levels of all enzymes and transporters assessed. Formation rates of metabolites (pmoles mg protein−1 min−1) determined by LC-MS/MS for CYP2C9 (0.48 ± 0.26 vs. 0.41 ± 0.12), CYP2J2 (2.16 ± 1.70 vs. 1.69 ± 0.93), and CYP3A (5.25 ± 3.72 vs. 5.02 ± 4.76) were not different between biopsies obtained from individuals with or without T2D (p > 0.05). No CYP2B6 specific activity was measured. TNF-α levels were higher in T2D patients but did not correlate with any changes in mRNA expression levels for drug metabolizing enzymes or transporters in the duodenum. T2D did not modulate expression or activity of tested drug metabolizing enzymes and transporters in the human duodenum. Previously reported changes in drug oral clearances in patients with T2D could be due to a tissue-specific disease modulation occurring in the liver and/or in other parts of the intestines.
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77
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Ning M, Duarte JD, Stevison F, Isoherranen N, Rubin LH, Jeong H. Determinants of Cytochrome P450 2D6 mRNA Levels in Healthy Human Liver Tissue. Clin Transl Sci 2019; 12:416-423. [PMID: 30821899 PMCID: PMC6618095 DOI: 10.1111/cts.12632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 02/07/2019] [Indexed: 12/28/2022] Open
Abstract
Cytochrome P450 2D6 (CYP2D6) is a major drug‐metabolizing enzyme that exhibits large interindividual variability. Recent studies suggest that differential transcriptional regulation of CYP2D6 in part may be responsible for the variability. In this study, we characterized potential determinants of CYP 2D6 transcript levels in healthy human liver tissue samples (n = 115), including genetic polymorphisms in CYP2D6 and the genes encoding transcription regulators for CYP2D6 expression; mRNA expression of the transcription factors and their known target genes; and hepatic levels of bile acids and retinoids, agents that modulate the expression/activity of the transcription factors. Their associations with CYP2D6 mRNA levels in the tissues were examined. Results from multivariable linear regression analysis revealed CYP8B1 mRNA level and rs3892097, the single‐ nucleotide polymorphism defining the nonfunctional CYP2D6*4 allele, as the two most significant predictors of CYP2D6 mRNA levels in the liver tissue samples, explaining 30% of the variability.
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Affiliation(s)
- Miaoran Ning
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Julio D Duarte
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, Center for Pharmacogenomics, University of Florida, Gainesville, Florida, USA
| | - Faith Stevison
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Nina Isoherranen
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Leah H Rubin
- Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA.,Department of Neurology, Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Hyunyoung Jeong
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA.,Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
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78
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Sun JW, Collins JM, Ling D, Wang D. Highly Variable Expression of ESR1 Splice Variants in Human Liver: Implication in the Liver Gene Expression Regulation and Inter-Person Variability in Drug Metabolism and Liver Related Diseases. J Mol Genet Med 2019; 13:434. [PMID: 32457812 PMCID: PMC7249510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Estrogen receptor alpha (ESR1) plays an important role in many tissues including the liver. Numerous alternative splice variants of ESR1 exist that encode ESR1 proteins with varying functions. We aim to study ESR1 genomic organization and its mRNA expression profile in human liver by incorporating information from literature and genomic databases (Ensembl, NCBI and GTEx), and employing a quantitative method to measure all known ESR1 mRNA splice variants in 36 human livers. We re-constructed ESR1 genomic organization map that contains 29 exons. ESR1 mRNA splice variants with varying 5' untranslated region (5'UTR) and/or missing each of eight coding exons are readily detectable in liver and other tissues. Moreover, we found extensive inter-individual variability in splice variant pattern of ESR1 transcripts. Specifically, ESR1 transcripts lacking first coding exon are the main transcripts in liver, which encode ESR1 proteins missing N-terminal 173 amino acids (for example, ERα46), reported previously to have either constitutive activity or dominant negative effects depending on cellular context. Moreover, some livers predominantly express ESR1 transcripts missing exon 10 or 16, encoding C-terminal truncated ESR1 proteins with varying ESR1 activities. Inter-person variability in ESR1 expression profile may contribute to inter-person variability in drug metabolism and susceptibility to liver related diseases.
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Affiliation(s)
- JW Sun
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - JM Collins
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - D Ling
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - D Wang
- Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida, USA,Corresponding author: Dr. Danxin Wang, Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy, University of Florida, Gainesville, Florida-32610, USA, Tel: 352-273-7673;
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79
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Li Z, Chen G, Cai Z, Dong X, Qiu L, Xu H, Zeng Y, Liu X, Liu J. Genomic and transcriptional Profiling of tumor infiltrated CD8 + T cells revealed functional heterogeneity of antitumor immunity in hepatocellular carcinoma. Oncoimmunology 2018; 8:e1538436. [PMID: 30713796 DOI: 10.1080/2162402x.2018.1538436] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023] Open
Abstract
As key players in HCC antitumor response, the functions of tumor infiltrated CD8+ T cells are significantly affected by surrounding microenvironment. A detailed profiling of their genomic and transcriptional changes could provide valuable insights for both future immunotherapy development and prognosis evaluation. We performed whole exome and transcriptome sequencing on tumor infiltrated CD8+ T cells and CD8+ T cells isolated from other tissue origins (peritumor tissues and corresponding PBMCs) in eight treatment-naive HCC patients. The results demonstrated that transcriptional changes, rather than genomic alterations were the main contributors to the functional alterations of CD8+ T cells in the process of tumor progression. The origins of CD8+ T cells defined their transcriptional landscape, while the tumor infiltrated CD8+ T cells shared more similarity with peritumor-derived CD8+ T cells compared with those CD8+ T cells in blood. In addition, tumor infiltrated CD8+ T cells also showed larger transcriptional heterogeneity among individuals, which was modulated by clinical features such as HBV levels, preoperative anti-viral treatment and the degree of T cell infiltration. We also identified multiple inter-connected pathways involved in the activation and exhaustion of tumor infiltrated CD8+ T cells, among which IL-12 mediated pathway could dynamically reflect the functional status of CD8+ TILs and activation of this pathway indicated a better prognosis. Our results presented an overview picture of CD8+ TILs' genomic and transcriptional landscape and features, as well as how the functional status of CD8+ TILs correlated with patients' clinical course.
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Affiliation(s)
- Zhenli Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Geng Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China.,School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Zhixiong Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China.,School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xiuqing Dong
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Liman Qiu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Haipo Xu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Yongyi Zeng
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China.,Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
| | - Jingfeng Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou, China.,Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.,The Liver Center of Fujian Province, Fujian Medical University, Fuzhou, China
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80
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Ning M, Duarte JD, Rubin LH, Jeong H. CYP2D6 Protein Level Is the Major Contributor to Interindividual Variability in CYP2D6-Mediated Drug Metabolism in Healthy Human Liver Tissue. Clin Pharmacol Ther 2018; 104:974-982. [PMID: 29349771 PMCID: PMC6053340 DOI: 10.1002/cpt.1032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 11/12/2022]
Abstract
CYP2D6 genetic polymorphisms are considered a major contributor to the large interindividual variability in CYP2D6-mediated drug metabolism, but fail to explain a significant portion of the variability. The aim of this study was to assess the ability of the CYP2D6 activity score (AS) estimated from CYP2D6 genotype to predict CYP2D6 expression and enzyme activity. The CYP2D6 gene region was sequenced in 115 healthy human liver tissue samples to determine their CYP2D6 AS. Additionally, CYP2D6 enzyme activity, protein, and mRNA levels were estimated. CYP2D6 AS explained 23% of the interindividual variability in CYP2D6 activity, but only 7.5% in tissues assigned AS 1-2. The CYP2D6 protein level was found to be the major determinant of CYP2D6 activity, explaining 59% of variability. These findings suggest that while CYP2D6 AS is a good predictor of poor metabolizer phenotype, additional nongenetic factors may govern the rate of CYP2D6-mediated metabolism in those without the poor metabolizer phenotype.
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Affiliation(s)
- Miaoran Ning
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Julio D Duarte
- Center for Pharmacogenomics, Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, Florida, USA
| | - Leah H Rubin
- Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Hyunyoung Jeong
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Pharmacy Practice, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, USA
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81
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Liu X, Huang X, Zhang S, Niu F, Ouyang Y, Shou Z, Liu J. Correlations between CYP3A4 polymorphism and susceptibility to breast cancer in Chinese Han population. Int J Clin Oncol 2018; 24:179-188. [PMID: 30218411 DOI: 10.1007/s10147-018-1346-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/06/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND CYP3A4 is a major enzyme catalyzing the metabolism of endogenous steroids that play an important role in the etiology of carcinogenesis. This study was designed to investigate the contribution of CYP3A4 polymorphism to breast cancer in Chinese Han female population. METHODS To examine whether variants of CYP3A4 contribute to breast cancer, 5 single-nucleotide polymorphisms (SNPs) of CYP3A4 were genotyped by Sequenom MassARRAY in 267 breast cancer patients and 302 healthy controls. Odds ratio (OR) and 95% confidence intervals (CIs) were calculated by unconditional logistic regression adjusted for age. RESULTS We found that the TT genotype of CYP3A4*1G (rs2242480) polymorphism was associated with increased risk of breast cancer using the fixed effects model (recessive model: OR = 2.34, p = 0.018). Stratified according to age, CYP3A4*1G increased the risk of breast cancer especially in less than 50-year-old group (codominant model OR = 3.68, p = 0.041; recessive model: OR = 3.55, p = 0.012). Furthermore, TT genotype of rs2242480 was associated with Cerb-B2 positive (recessive model: OR = 2.47, p = 0.025) and stage I/II (recessive model: OR = 2.32, p = 0.041). However, no statistically significant associations in other polymorphisms and haploview analysis were observed. CONCLUSIONS This study provides an evidence for polymorphism of CYP3A4 gene associated with the development of breast cancer, also a new insight into etiology of breast cancer. However, the underlying mechanism of the CYP3A4 gene in breast cancer is necessary for further study.
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Affiliation(s)
- Xu Liu
- Department of Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, #1120, Lianhua Road, Futian District, Shenzhen, 518036, Guangdong, China
| | - Xi Huang
- Department of Thyroid and Breast Surgery, Peking University Shenzhen Hospital, Shenzhen, 518036, Guangdong, China
| | - Shanshan Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, 710069, Shaanxi, China
| | - Fanglin Niu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, 710069, Shaanxi, China
| | - Yongri Ouyang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, Xi'an, 710069, Shaanxi, China
| | - Zhexing Shou
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, #1277, Jiefang Avenue, Jianghan District, Wuhan, 430022, Hubei, China.
| | - Jikui Liu
- Department of Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, #1120, Lianhua Road, Futian District, Shenzhen, 518036, Guangdong, China.
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82
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Sausville LN, Gangadhariah MH, Chiusa M, Mei S, Wei S, Zent R, Luther JM, Shuey MM, Capdevila JH, Falck JR, Guengerich FP, Williams SM, Pozzi A. The Cytochrome P450 Slow Metabolizers CYP2C9*2 and CYP2C9*3 Directly Regulate Tumorigenesis via Reduced Epoxyeicosatrienoic Acid Production. Cancer Res 2018; 78:4865-4877. [PMID: 30012669 PMCID: PMC6125168 DOI: 10.1158/0008-5472.can-17-3977] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/31/2018] [Accepted: 07/11/2018] [Indexed: 01/02/2023]
Abstract
Increased expression of cytochrome P450 CYP2C9, together with elevated levels of its products epoxyeicosatrienoic acids (EET), is associated with aggressiveness in cancer. Cytochrome P450 variants CYP2C9*2 and CYP2C9*3 encode proteins with reduced enzymatic activity, and individuals carrying these variants metabolize drugs more slowly than individuals with wild-type CYP2C9*1, potentially affecting their response to drugs and altering their risk of disease. Although genetic differences in CYP2C9-dependent oxidation of arachidonic acid (AA) have been reported, the roles of CYP2C9*2 and CYP2C9*3 in EET biosynthesis and their relevance to disease are unknown. Here, we report that CYP2C9*2 and CYP2C9*3 metabolize AA less efficiently than CYP2C9*1 and that they play a role in the progression of non-small cell lung cancer (NSCLC) via impaired EET biosynthesis. When injected into mice, NSCLC cells expressing CYP2C9*2 and CYP2C9*3 produced lower levels of EETs and developed fewer, smaller, and less vascularized tumors than cells expressing CYP2C9*1. Moreover, endothelial cells expressing these two variants proliferated and migrated less than cells expressing CYP2C*1. Purified CYP2C9*2 and CYP2C9*3 exhibited attenuated catalytic efficiency in producing EETs, primarily due to impaired reduction of these two variants by NADPH-P450 reductase. Loss-of-function SNPs within CYP2C9*2 and CYP2C9*3 were associated with improved survival in female cases of NSCLC. Thus, decreased EET biosynthesis represents a novel mechanism whereby CYPC29*2 and CYP2C9*3 exert a direct protective role in NSCLC development.Significance: These findings report single nucleotide polymorphisms in the human CYP2C9 genes, CYP2C9*2 and CYP2C9*3, exert a direct protective role in tumorigenesis by impairing EET biosynthesis. Cancer Res; 78(17); 4865-77. ©2018 AACR.
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Affiliation(s)
- Lindsay N Sausville
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Mahesha H Gangadhariah
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Pathobiology, Cleveland Clinic, Cleveland, Ohio
| | - Manuel Chiusa
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Shaojun Mei
- Diabetes Research and Training Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Shouzuo Wei
- Division of Clinical Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Roy Zent
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Veterans Affairs Hospital, Nashville, Tennessee
| | - James M Luther
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
- Division of Clinical Pharmacology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Megan M Shuey
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jorge H Capdevila
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - John R Falck
- Division of Chemistry, University of Texas Southwestern Medical Center, Dallas, Texas
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Scott M Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Ambra Pozzi
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee.
- Veterans Affairs Hospital, Nashville, Tennessee
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83
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Plubell DL, Fenton AM, Wilmarth PA, Bergstrom P, Zhao Y, Minnier J, Heinecke JW, Yang X, Pamir N. GM-CSF driven myeloid cells in adipose tissue link weight gain and insulin resistance via formation of 2-aminoadipate. Sci Rep 2018; 8:11485. [PMID: 30065264 PMCID: PMC6068153 DOI: 10.1038/s41598-018-29250-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/03/2018] [Indexed: 02/07/2023] Open
Abstract
In a GM-CSF driven myeloid cell deficient mouse model (Csf2−/−) that has preserved insulin sensitivity despite increased adiposity, we used unbiased three-dimensional integration of proteome profiles, metabolic profiles, and gene regulatory networks to understand adipose tissue proteome-wide changes and their metabolic implications. Multi-dimensional liquid chromatography mass spectrometry and extended multiplex mass labeling was used to analyze proteomes of epididymal adipose tissues isolated from Csf2+/+ and Csf2−/− mice that were fed low fat, high fat, or high fat plus cholesterol diets for 8 weeks. The metabolic health (as measured by body weight, adiposity, plasma fasting glucose, insulin, triglycerides, phospholipids, total cholesterol levels, and glucose and insulin tolerance tests) deteriorated with diet for both genotypes, while mice lacking Csf2 were protected from insulin resistance. Regardless of diet, 30 mostly mitochondrial, branch chain amino acids (BCAA), and lysine metabolism proteins were altered between Csf2−/− and Csf2+/+ mice (FDR < 0.05). Lack of GM-CSF driven myeloid cells lead to reduced adipose tissue 2-oxoglutarate dehydrogenase complex (DHTKD1) levels and subsequent increase in plasma 2-aminoadipate (2-AA) levels, both of which are reported to correlate with insulin resistance. Tissue DHTKD1 levels were >4-fold upregulated and plasma 2-AA levels were >2 fold reduced in Csf2−/− mice (p < 0.05). GM-CSF driven myeloid cells link peripheral insulin sensitivity to adiposity via lysine metabolism involving DHTKD1/2-AA axis in a diet independent manner.
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Affiliation(s)
- Deanna L Plubell
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alexandra M Fenton
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
| | - Phillip A Wilmarth
- Proteomics Shared Resource, Oregon Health & Science University, Portland, OR, USA
| | - Paige Bergstrom
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
| | - Yuqi Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Jessica Minnier
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA
| | - Jay W Heinecke
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, USA
| | - Nathalie Pamir
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA.
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84
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Atwine D, Bonnet M, Taburet AM. Pharmacokinetics of efavirenz in patients on antituberculosis treatment in high human immunodeficiency virus and tuberculosis burden countries: A systematic review. Br J Clin Pharmacol 2018; 84:1641-1658. [PMID: 29624706 DOI: 10.1111/bcp.13600] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/07/2018] [Accepted: 03/26/2018] [Indexed: 12/12/2022] Open
Abstract
AIMS Efavirenz (EFV) and rifampicin-isoniazid (RH) are cornerstone drugs in human immunodeficiency virus (HIV)-tuberculosis (TB) coinfection treatment but with complex drug interactions, efficacy and safety challenges. We reviewed recent data on EFV and RH interaction in TB/HIV high-burden countries. METHODS We conducted a systematic review of studies conducted in the high TB/HIV-burden countries between 1990 and 2016 on EFV pharmacokinetics during RH coadministration in coinfected patients. Two reviewers conducted article screening and data collection. RESULTS Of 119 records retrieved, 22 were included (two conducted in children), reporting either EFV mid-dose or pre-dose concentrations. In 19 studies, median or mean concentrations of RH range between 1000 and 4000 ng ml-1 , the so-called therapeutic range. The proportion of patients with subtherapeutic concentration of RH ranged between 3.1 and 72.2%, in 12 studies including one conducted in children. The proportion of patients with supratherapeutic concentration ranged from 19.6 to 48.0% in six adult studies and one child study. Five of eight studies reported virological suppression >80%. The association between any grade hepatic and central nervous system adverse effects with EFV/RH interaction was demonstrated in two and three studies, respectively. The frequency of the CYP2B6 516G > T polymorphism ranged from 10 to 28% and was associated with higher plasma EFV concentrations, irrespective of ethnicity. CONCLUSIONS Anti-TB drug coadministration minimally affect the EFV exposure, efficacy and safety among TB-HIV coinfected African and Asian patients. This supports the current 600 mg EFV dosing when coadministered with anti-TB drugs.
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Affiliation(s)
- Daniel Atwine
- Epicentre Mbarara Research Centre, Mbarara, Uganda.,Mbarara University of Science and Technology, Mbarara, Uganda.,University of Montpellier, Montpellier, France
| | - Maryline Bonnet
- Epicentre Mbarara Research Centre, Mbarara, Uganda.,IRD UMI233 TransVIHMI-INSERM U1175, Montpellier, France.,University of Montpellier, Montpellier, France
| | - Anne-Marie Taburet
- Bicetre hospital, Paris, France.,UMR 1184, INSERM, CEA, Université Paris-Sud
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85
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Ten Years' Experience with the CYP2D6 Activity Score: A Perspective on Future Investigations to Improve Clinical Predictions for Precision Therapeutics. J Pers Med 2018; 8:jpm8020015. [PMID: 29673183 PMCID: PMC6023391 DOI: 10.3390/jpm8020015] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 12/20/2022] Open
Abstract
The seminal paper on the CYP2D6 Activity Score (AS) was first published ten years ago and, since its introduction in 2008, it has been widely accepted in the field of pharmacogenetics. This scoring system facilitates the translation of highly complex CYP2D6 diplotype data into a patient’s phenotype to guide drug therapy and is at the core of all CYP2D6 gene/drug pair guidelines issued by the Clinical Pharmacogenetics Implementation Consortium (CPIC). The AS, however, only explains a portion of the variability observed among individuals and ethnicities. In this review, we provide an overview of sources in addition to CYP2D6 genotype that contribute to the variability in CYP2D6-mediated drug metabolism and discuss other factors, genetic and non-genetic, that likely contribute to the observed variability in CYP2D6 enzymatic activity.
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86
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Butler MG. Pharmacogenetics and Psychiatric Care: A Review and Commentary. JOURNAL OF MENTAL HEALTH & CLINICAL PSYCHOLOGY 2018; 2:17-24. [PMID: 30556062 PMCID: PMC6291002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Merlin G. Butler
- Departments of Psychiatry & Behavioral Sciences and Pediatrics, University of Kansas Medical Center, Kansas City, Kansas, USA
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87
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The role of hepatic cytochrome P450s in the cytotoxicity of dronedarone. Arch Toxicol 2018; 92:1969-1981. [PMID: 29616291 DOI: 10.1007/s00204-018-2196-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/21/2018] [Indexed: 02/06/2023]
Abstract
Dronedarone is used to treat patients with cardiac arrhythmias and has been reported to be associated with liver injury. Our previous mechanistic work demonstrated that DNA damage-induced apoptosis contributes to the cytotoxicity of dronedarone. In this study, we examined further the underlying mechanisms and found that after a 24-h treatment of HepG2 cells, dronedarone caused cytotoxicity, G1-phase cell cycle arrest, suppression of topoisomerase II, and DNA damage in a concentration-dependent manner. We also investigated the role of cytochrome P450s (CYPs)-mediated metabolism in the dronedarone-induced toxicity using our previously established HepG2 cell lines expressing individually 14 human CYPs (1A1, 1A2, 1B1, 2A6, 2B6, 2C8, 2C9, 2C18, 2C19, 2D6, 2E1, 3A4, 3A5, and 3A7). We demonstrated that CYP3A4, 3A5, and 2D6 were the major enzymes that metabolize dronedarone, and that CYP3A7, 2E1, 2C19, 2C18, 1A1, and 2B6 also metabolize dronedarone, but to a lesser extent. Our data showed that the cytotoxicity of dronedarone was decreased in CYP3A4-, 3A5-, or 2D6-overexpressing cells compared to the control HepG2 cells, indicating that the parent dronedarone has higher potency than the metabolites to induce cytotoxicity in these cells. In contrast, cytotoxicity was increased in CYP1A1-overexpressing cells, demonstrating that CYP1A1 exerts an opposite effect in dronedarone's toxicity, comparing to CYP3A4, 3A5, or 2D6. We also studied the involvement of topoisomerase II in dronedarone-induced toxicity, and demonstrated that the overexpression of topoisomerase II caused an increase in cell viability and a decrease in γ-H2A.X induction, suggesting that suppression of topoisomerase II may be one of the mechanisms involved in dronedarone-induced liver toxicity.
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88
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Dücker CM, Brockmöller J. Genomic Variation and Pharmacokinetics in Old Age: A Quantitative Review of Age- vs. Genotype-Related Differences. Clin Pharmacol Ther 2018; 105:625-640. [PMID: 29498032 PMCID: PMC6585622 DOI: 10.1002/cpt.1057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/20/2018] [Indexed: 01/01/2023]
Abstract
Older persons may particularly benefit from pharmacogenetic diagnostics, but there is little clinical evidence on that question. We quantitatively analyzed the effects of age and genotype in drugs with consensus on a therapeutically relevant impact of a genotype. Assuming additive effects of age and genotype, drugs may be classified in groups with different priorities to consider either age, or genotype, or both, in therapy. Particularly interesting were those studies specifically analyzing the age‐by‐genotype interaction.
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Affiliation(s)
- Christof M Dücker
- Institute for Clinical Pharmacology, University Medical Center, Georg-August University, Göttingen, Germany
| | - Jürgen Brockmöller
- Institute for Clinical Pharmacology, University Medical Center, Georg-August University, Göttingen, Germany
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89
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Tanner JA, Tyndale RF. Variation in CYP2A6 Activity and Personalized Medicine. J Pers Med 2017; 7:jpm7040018. [PMID: 29194389 PMCID: PMC5748630 DOI: 10.3390/jpm7040018] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 11/17/2017] [Accepted: 11/27/2017] [Indexed: 12/16/2022] Open
Abstract
The cytochrome P450 2A6 (CYP2A6) enzyme metabolizes several clinically relevant substrates, including nicotine-the primary psychoactive component in cigarette smoke. The gene that encodes the CYP2A6 enzyme is highly polymorphic, resulting in extensive interindividual variation in CYP2A6 enzyme activity and the rate of metabolism of nicotine and other CYP2A6 substrates including cotinine, tegafur, letrozole, efavirenz, valproic acid, pilocarpine, artemisinin, artesunate, SM-12502, caffeine, and tyrosol. CYP2A6 expression and activity are also impacted by non-genetic factors, including induction or inhibition by pharmacological, endogenous, and dietary substances, as well as age-related changes, or interactions with other hepatic enzymes, co-enzymes, and co-factors. As variation in CYP2A6 activity is associated with smoking behavior, smoking cessation, tobacco-related lung cancer risk, and with altered metabolism and resulting clinical responses for several therapeutics, CYP2A6 expression and enzyme activity is an important clinical consideration. This review will discuss sources of variation in CYP2A6 enzyme activity, with a focus on the impact of CYP2A6 genetic variation on metabolism of the CYP2A6 substrates.
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Affiliation(s)
- Julie-Anne Tanner
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, ON M5T 1R8, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, ON M5T 1R8, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada.
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90
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Jia B, Xu S, Xiao G, Lamba V, Liang F. Learning gene regulatory networks from next generation sequencing data. Biometrics 2017; 73:1221-1230. [PMID: 28294287 PMCID: PMC6258556 DOI: 10.1111/biom.12682] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 02/01/2017] [Accepted: 02/01/2017] [Indexed: 12/19/2022]
Abstract
In recent years, next generation sequencing (NGS) has gradually replaced microarray as the major platform in measuring gene expressions. Compared to microarray, NGS has many advantages, such as less noise and higher throughput. However, the discreteness of NGS data also challenges the existing statistical methodology. In particular, there still lacks an appropriate statistical method for reconstructing gene regulatory networks using NGS data in the literature. The existing local Poisson graphical model method is not consistent and can only infer certain local structures of the network. In this article, we propose a random effect model-based transformation to continuize NGS data and then we transform the continuized data to Gaussian via a semiparametric transformation and apply an equivalent partial correlation selection method to reconstruct gene regulatory networks. The proposed method is consistent. The numerical results indicate that the proposed method can lead to much more accurate inference of gene regulatory networks than the local Poisson graphical model and other existing methods. The proposed data-continuized transformation fills the theoretical gap for how to transform discrete data to continuous data and facilitates NGS data analysis. The proposed data-continuized transformation also makes it feasible to integrate different types of data, such as microarray and RNA-seq data, in reconstruction of gene regulatory networks.
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Affiliation(s)
- Bochao Jia
- Department of Biostatistics, University of Florida, Gainesville, Florida, U.S.A
| | - Suwa Xu
- Department of Biostatistics, University of Florida, Gainesville, Florida, U.S.A
| | - Guanghua Xiao
- Department of Clinical Sciences, University of Texas, Southwestern Medical Center, Dallas, Taxes, U.S.A
| | - Vishal Lamba
- Department of Pharmacotherapy and Translational Research, University of Florida, Gainesville, Florida, U.S.A
| | - Faming Liang
- Department of Biostatistics, University of Florida, Gainesville, Florida, U.S.A
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91
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Prediction of cytochrome P450-mediated drug clearance in humans based on the measured activities of selected CYPs. Biosci Rep 2017; 37:BSR20171161. [PMID: 29054967 PMCID: PMC5696450 DOI: 10.1042/bsr20171161] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/14/2017] [Accepted: 10/17/2017] [Indexed: 02/07/2023] Open
Abstract
Determining drug-metabolizing enzyme activities on an individual basis is an important component of personalized medicine, and cytochrome P450 enzymes (CYPs) play a principal role in hepatic drug metabolism. Herein, a simple method for predicting the major CYP-mediated drug clearance in vitro and in vivo is presented. Ten CYP-mediated drug metabolic activities in human liver microsomes (HLMs) from 105 normal liver samples were determined. The descriptive models for predicting the activities of these CYPs in HLMs were developed solely on the basis of the measured activities of a smaller number of more readily assayed CYPs. The descriptive models then were combined with the Conventional Bias Corrected in vitro–in vivo extrapolation method to extrapolate drug clearance in vivo. The Vmax, Km, and CLint of six CYPs (CYP2A6, 2C8, 2D6, 2E1, and 3A4/5) could be predicted by measuring the activities of four CYPs (CYP1A2, 2B6, 2C9, and 2C19) in HLMs. Based on the predicted CLint, the values of CYP2A6-, 2C8-, 2D6-, 2E1-, and 3A4/5-mediated drug clearance in vivo were extrapolated and found that the values for all five drugs were close to the observed clearance in vivo. The percentage of extrapolated values of clearance in vivo which fell within 2-fold of the observed clearance ranged from 75.2% to 98.1%. These findings suggest that measuring the activity of CYP1A2, 2B6, 2C9, and 2C19 allowed us to accurately predict CYP2A6-, 2C8-, 2D6-, 2E1-, and 3A4/5-mediated activities in vitro and in vivo and may possibly be helpful for the assessment of an individual’s drug metabolic profile.
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92
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Lu R, Wang D, Wang M, Rempala GA. Estimation of Sobol's Sensitivity Indices under Generalized Linear Models. COMMUN STAT-THEOR M 2017; 47:5163-5195. [PMID: 30237653 DOI: 10.1080/03610926.2017.1388397] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We derive explicit formulas for Sobol's sensitivity indices (SSIs) under the generalized linear models (GLMs) with independent or multivariate normal inputs. We argue that the main-effect SSIs provide a powerful tool for variable selection under GLMs with identity links under polynomial regressions. We also show via examples that the SSI-based variable selection results are similar to the ones obtained by the random forest algorithm but without the computational burden of data permutation. Finally, applying our results to the problem of gene network discovery, we identify though the SSI analysis of a public microarray dataset several novel higher-order gene-gene interactions missed out by the more standard inference methods. The relevant functions for SSI analysis derived here under GLMs with identity, log, and logit links are implemented and made available in the R package SobolSensitivity.
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Affiliation(s)
- Rong Lu
- Bioinformatics Core Facility, Department of Clinical Sciences, University of Texas, Southwestern Medical Center, 5323 Harry Hines Blvd. Dallas, TX 75390
| | - Danxin Wang
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, 333 W. 10th Avenue, Columbus, OH 43210
| | - Min Wang
- Mathematical Bioscience Institute, The Ohio State University, 1735 Neil Ave., Columbus, OH 43210
| | - Grzegorz A Rempala
- Mathematical Bioscience Institute, The Ohio State University, 1735 Neil Ave., Columbus, OH 43210.,Biostatistics Division, College of Public Health, The Ohio State University, 1841 Neil Ave., Columbus, OH, 43210
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93
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Burns KE, Shepherd P, Finlay G, Tingle MD, Helsby NA. Indirect regulation of CYP2C19 gene expression via DNA methylation. Xenobiotica 2017; 48:781-792. [DOI: 10.1080/00498254.2017.1372648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Kathryn Elisa Burns
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand,
| | - Phillip Shepherd
- School of Medical Sciences, University of Auckland, Auckland, New Zealand, and
| | - Graeme Finlay
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand,
| | - Malcolm Drummond Tingle
- Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
| | - Nuala Ann Helsby
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand,
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94
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Raut A, Khanna A. High-throughput sequencing to identify microRNA signatures during hepatic differentiation of human umbilical cord Wharton's jelly-derived mesenchymal stem cells. Hepatol Res 2017; 47:910-927. [PMID: 27653181 DOI: 10.1111/hepr.12820] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/10/2016] [Accepted: 09/17/2016] [Indexed: 12/27/2022]
Abstract
AIM MicroRNAs (miRNAs) constitute a class of small non-coding RNAs involved in regulation of cognate mRNAs post-transcriptionally. MicroRNAs have been implicated in regulating the stem cell differentiation process. Limited regulatory miRNAs have been reported to date during hepatic differentiation of stem cells. The present study was designed to identify the signature miRNAs implicated in hepatic differentiation of stem cells using next-generation sequencing methods. METHODS We undertook sequencing of miRNAs isolated from three different time points during hepatic differentiation of human umbilical cord Wharton's jelly-derived mesenchymal stem cells (hUC-MSCs) from two biological replicates. RESULTS Out of a total known 2588 miRNAs (according to miRBase version 21), 880 miRNAs were identified in our study. A total of 63 significantly expressed miRNAs during hepatic differentiation, with at least 2-fold change and a false discovery rate value <0.05, were considered for further analysis. The putative target genes of significantly downregulated miRNAs during hepatic differentiation appeared to be mostly associated with biological processes that are essential for hepatic differentiation and maintenance of mature hepatic phenotype-like liver development, stem cell differentiation, Wnt receptor signaling pathway, and drug and cholesterol metabolic processes. Putative target genes of significantly upregulated miRNAs are highly enriched in regulating processes that block hepatic differentiation of hUC-MSCs like epithelial-mesenchymal transition, transforming growth factor-β receptor signaling pathway, and stem cell maintenance. CONCLUSION The study provides a new insight for investigation of miRNA-regulated pathways during the differentiation process.
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Affiliation(s)
- Akshata Raut
- Department of Biological Sciences, Sunandan Divatia School of Science, Narsee Monjee Institute of Management Studies University, Mumbai, India
| | - Aparna Khanna
- Department of Biological Sciences, Sunandan Divatia School of Science, Narsee Monjee Institute of Management Studies University, Mumbai, India
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95
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Park YS, Kwon YJ, Chun YJ. CYP1B1 Activates Wnt/β-Catenin Signaling through Suppression of Herc5-Mediated ISGylation for Protein Degradation on β-Catenin in HeLa Cells. Toxicol Res 2017; 33:211-218. [PMID: 28744352 PMCID: PMC5523555 DOI: 10.5487/tr.2017.33.3.211] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 06/19/2017] [Accepted: 06/19/2017] [Indexed: 12/31/2022] Open
Abstract
Cytochrome P450 1B1 (CYP1B1) acts as a hydroxylase for estrogen and activates potential carcinogens. Moreover, its expression in tumor tissues is much higher than that in normal tissues. Despite this association between CYP1B1 and cancer, the detailed molecular mechanism of CYP1B1 on cancer progression in HeLa cells remains unknown. Previous reports indicated that the mRNA expression level of Herc5, an E3 ligase for ISGylation, is promoted by CYP1B1 suppression using specific small interfering RNA, and that ISGylation may be involved in ubiquitination related to β-catenin degradation. With this background, we investigated the relationships among CYP1B1, Herc5, and β-catenin. RT-PCR and western blot analyses showed that CYP1B1 overexpression induced and CYP1B1 inhibition reduced, respectively, the expression of Wnt/β-catenin signaling target genes including β-catenin and cyclin D1. Moreover, HeLa cells were treated with the CYP1B1 inducer 7,12-dimethylbenz[α]anthracene (DMBA) or the CYP1B1 specific inhibitor, tetramethoxystilbene (TMS) and consequently DMBA increased and TMS decreased β-catenin and cyclin D1 expression, respectively. To determine the correlation between CYP1B1 expression and ISGylation, the expression of ISG15, a ubiquitin-like protein, was detected following CYP1B1 regulation, which revealed that CYP1B1 may inhibit ISGylation through suppression of ISG15 expression. In addition, the mRNA and protein expression levels of Herc5 were strongly suppressed by CYP1B1. Finally, an immunoprecipitation assay revealed a direct physical interaction between Herc5 and β-catenin in HeLa cells. In conclusion, these data suggest that CYP1B1 may activate Wnt/β-catenin signaling through stabilization of β-catenin protein from Herc5-mediated ISGylation for proteosomal degradation.
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Affiliation(s)
| | - Yeo-Jung Kwon
- College of Pharmacy, Chung-Ang University, Seoul, Korea
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96
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Yang Y, Botton MR, Scott ER, Scott SA. Sequencing the CYP2D6 gene: from variant allele discovery to clinical pharmacogenetic testing. Pharmacogenomics 2017; 18:673-685. [PMID: 28470112 DOI: 10.2217/pgs-2017-0033] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
CYP2D6 is one of the most studied enzymes in the field of pharmacogenetics. The CYP2D6 gene is highly polymorphic with over 100 catalogued star (*) alleles, and clinical CYP2D6 testing is increasingly accessible and supported by practice guidelines. However, the degree of variation at the CYP2D6 locus and homology with its pseudogenes make interrogating CYP2D6 by short-read sequencing challenging. Moreover, accurate prediction of CYP2D6 metabolizer status necessitates analysis of duplicated alleles when an increased copy number is detected. These challenges have recently been overcome by long-read CYP2D6 sequencing; however, such platforms are not widely available. This review highlights the genomic complexities of CYP2D6, current sequencing methods and the evolution of CYP2D6 from allele discovery to clinical pharmacogenetic testing.
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Affiliation(s)
- Yao Yang
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Genomics & Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mariana R Botton
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erick R Scott
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Genomics & Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stuart A Scott
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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97
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Fasullo M, Freedland J, St John N, Cera C, Egner P, Hartog M, Ding X. An in vitro system for measuring genotoxicity mediated by human CYP3A4 in Saccharomyces cerevisiae. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:217-227. [PMID: 28436563 PMCID: PMC5479318 DOI: 10.1002/em.22093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 04/06/2017] [Accepted: 04/11/2017] [Indexed: 06/07/2023]
Abstract
P450 activity is required to metabolically activate many chemical carcinogens, rendering them highly genotoxic. CYP3A4 is the most abundantly expressed P450 enzyme in the liver, accounting for most drug metabolism and constituting 50% of all hepatic P450 activity. CYP3A4 is also expressed in extrahepatic tissues, including the intestine. However, the role of CYP3A4 in activating chemical carcinogens into potent genotoxins is unclear. To facilitate efforts to determine whether CYP3A4, per se, can activate carcinogens into potent genotoxins, we expressed human CYP3A4 in the DNA-repair mutant (rad4 rad51) strain of budding yeast Saccharomyces cerevisiae and tested the novel, recombinant yeast strain for ability to report CYP3A4-mediated genotoxicity of a well-known genotoxin, aflatoxin B1 (AFB1 ). Yeast microsomes containing human CYP3A4, but not those that do not contain CYP3A4, were active in hydroxylation of diclofenac, a known CYP3A4 substrate drug, a result confirming CYP3A4 activity in the recombinant yeast strain. In cells exposed to AFB1 , the expression of CYP3A4 supported DNA adduct formation, chromosome rearrangements, cell death, and expression of the large subunit of ribonucleotide reductase, Rnr3, a marker of DNA damage. Expression of CYP3A4 also conferred sensitivity in rad4 rad51 mutants exposed to colon carcinogen, 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx). These data confirm the ability of human CYP3A4 to mediate the genotoxicity of AFB1 , and illustrate the usefulness of the CYP3A4-expressing, DNA-repair mutant yeast strain for screening other chemical compounds that are CYP3A4 substrates, for potential genotoxicity. Environ. Mol. Mutagen. 58:217-227, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Michael Fasullo
- College of Nanoscale Sciences and Engineering, State University of New York Polytechnic Institute, Albany, New York 12205
- Department of Biomedical Sciences, State University of New York at Albany, 150 New Scotland Avenue, Albany, New York 12209
| | - Julian Freedland
- College of Nanoscale Sciences and Engineering, State University of New York Polytechnic Institute, Albany, New York 12205
| | | | - Cinzia Cera
- College of Nanoscale Sciences and Engineering, State University of New York Polytechnic Institute, Albany, New York 12205
| | - Patricia Egner
- Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, Maryland 21205
| | - Matt Hartog
- College of Nanoscale Sciences and Engineering, State University of New York Polytechnic Institute, Albany, New York 12205
| | - Xinxin Ding
- College of Nanoscale Sciences and Engineering, State University of New York Polytechnic Institute, Albany, New York 12205
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98
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Plubell DL, Wilmarth PA, Zhao Y, Fenton AM, Minnier J, Reddy AP, Klimek J, Yang X, David LL, Pamir N. Extended Multiplexing of Tandem Mass Tags (TMT) Labeling Reveals Age and High Fat Diet Specific Proteome Changes in Mouse Epididymal Adipose Tissue. Mol Cell Proteomics 2017; 16:873-890. [PMID: 28325852 DOI: 10.1074/mcp.m116.065524] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/28/2017] [Indexed: 01/17/2023] Open
Abstract
The lack of high-throughput methods to analyze the adipose tissue protein composition limits our understanding of the protein networks responsible for age and diet related metabolic response. We have developed an approach using multiple-dimension liquid chromatography tandem mass spectrometry and extended multiplexing (24 biological samples) with tandem mass tags (TMT) labeling to analyze proteomes of epididymal adipose tissues isolated from mice fed either low or high fat diet for a short or a long-term, and from mice that aged on low versus high fat diets. The peripheral metabolic health (as measured by body weight, adiposity, plasma fasting glucose, insulin, triglycerides, total cholesterol levels, and glucose and insulin tolerance tests) deteriorated with diet and advancing age, with long-term high fat diet exposure being the worst. In response to short-term high fat diet, 43 proteins representing lipid metabolism (e.g. AACS, ACOX1, ACLY) and red-ox pathways (e.g. CPD2, CYP2E, SOD3) were significantly altered (FDR < 10%). Long-term high fat diet significantly altered 55 proteins associated with immune response (e.g. IGTB2, IFIT3, LGALS1) and rennin angiotensin system (e.g. ENPEP, CMA1, CPA3, ANPEP). Age-related changes on low fat diet significantly altered only 18 proteins representing mainly urea cycle (e.g. OTC, ARG1, CPS1), and amino acid biosynthesis (e.g. GMT, AKR1C6). Surprisingly, high fat diet driven age-related changes culminated with alterations in 155 proteins involving primarily the urea cycle (e.g. ARG1, CPS1), immune response/complement activation (e.g. C3, C4b, C8, C9, CFB, CFH, FGA), extracellular remodeling (e.g. EFEMP1, FBN1, FBN2, LTBP4, FERMT2, ECM1, EMILIN2, ITIH3) and apoptosis (e.g. YAP1, HIP1, NDRG1, PRKCD, MUL1) pathways. Using our adipose tissue tailored approach we have identified both age-related and high fat diet specific proteomic signatures highlighting a pronounced involvement of arginine metabolism in response to advancing age, and branched chain amino acid metabolism in early response to high fat feeding. Data are available via ProteomeXchange with identifier PXD005953.
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Affiliation(s)
- Deanna L Plubell
- From the ‡Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Sciences University, Portland, Oregon
| | - Phillip A Wilmarth
- §Proteomics Shared Resources, Oregon Health & Sciences University, Portland, Oregon
| | - Yuqi Zhao
- ¶Department of Integrative Biology and Physiology, University of California, Los Angeles, California
| | - Alexandra M Fenton
- From the ‡Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Sciences University, Portland, Oregon
| | - Jessica Minnier
- From the ‡Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Sciences University, Portland, Oregon
| | - Ashok P Reddy
- §Proteomics Shared Resources, Oregon Health & Sciences University, Portland, Oregon
| | - John Klimek
- §Proteomics Shared Resources, Oregon Health & Sciences University, Portland, Oregon
| | - Xia Yang
- ¶Department of Integrative Biology and Physiology, University of California, Los Angeles, California
| | - Larry L David
- §Proteomics Shared Resources, Oregon Health & Sciences University, Portland, Oregon
| | - Nathalie Pamir
- From the ‡Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Sciences University, Portland, Oregon;
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99
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Uno Y, Takata R, Kito G, Yamazaki H, Nakagawa K, Nakamura Y, Kamataki T, Katagiri T. Sex- and age-dependent gene expression in human liver: An implication for drug-metabolizing enzymes. Drug Metab Pharmacokinet 2017; 32:100-107. [DOI: 10.1016/j.dmpk.2016.10.409] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 01/08/2023]
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100
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Meng Q, Zhuang Y, Ying Z, Agrawal R, Yang X, Gomez-Pinilla F. Traumatic Brain Injury Induces Genome-Wide Transcriptomic, Methylomic, and Network Perturbations in Brain and Blood Predicting Neurological Disorders. EBioMedicine 2017; 16:184-194. [PMID: 28174132 PMCID: PMC5474519 DOI: 10.1016/j.ebiom.2017.01.046] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/31/2017] [Accepted: 01/31/2017] [Indexed: 12/28/2022] Open
Abstract
The complexity of the traumatic brain injury (TBI) pathology, particularly concussive injury, is a serious obstacle for diagnosis, treatment, and long-term prognosis. Here we utilize modern systems biology in a rodent model of concussive injury to gain a thorough view of the impact of TBI on fundamental aspects of gene regulation, which have the potential to drive or alter the course of the TBI pathology. TBI perturbed epigenomic programming, transcriptional activities (expression level and alternative splicing), and the organization of genes in networks centered around genes such as Anax2, Ogn, and Fmod. Transcriptomic signatures in the hippocampus are involved in neuronal signaling, metabolism, inflammation, and blood function, and they overlap with those in leukocytes from peripheral blood. The homology between genomic signatures from blood and brain elicited by TBI provides proof of concept information for development of biomarkers of TBI based on composite genomic patterns. By intersecting with human genome-wide association studies, many TBI signature genes and network regulators identified in our rodent model were causally associated with brain disorders with relevant link to TBI. The overall results show that concussive brain injury reprograms genes which could lead to predisposition to neurological and psychiatric disorders, and that genomic information from peripheral leukocytes has the potential to predict TBI pathogenesis in the brain.
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Affiliation(s)
- Qingying Meng
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yumei Zhuang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zhe Ying
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rahul Agrawal
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Fernando Gomez-Pinilla
- Department of Integrative Biology and Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Neurosurgery, UCLA Brain Injury Research Center, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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