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Smutny T, Bernhauerova V, Smutna L, Tebbens JD, Pavek P. Expression dynamics of pregnane X receptor-controlled genes in 3D primary human hepatocyte spheroids. Arch Toxicol 2021; 96:195-210. [PMID: 34689256 DOI: 10.1007/s00204-021-03177-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/06/2021] [Indexed: 02/07/2023]
Abstract
The pregnane X receptor (PXR) is a ligand-activated nuclear receptor controlling hepatocyte expression of numerous genes. Although expression changes in xenobiotic-metabolizing, lipogenic, gluconeogenic and bile acid synthetic genes have been described after PXR activation, the temporal dynamics of their expression is largely unknown. Recently, 3D spheroids of primary human hepatocytes (PHHs) have been characterized as the most phenotypically relevant hepatocyte model. We used 3D PHHs to assess time-dependent expression profiles of 12 prototypic PXR-controlled genes in the time course of 168 h of rifampicin treatment (1 or 10 µM). We observed a similar bell-shaped time-induction pattern for xenobiotic-handling genes (CYP3A4, CYP2C9, CYP2B6, and MDR1). However, we observed either biphasic profiles for genes involved in endogenous metabolism (FASN, GLUT2, G6PC, PCK1, and CYP7A1), a decrease for SHP or oscillation for PDK4 and PXR. The rifampicin concentration determined the expression profiles for some genes. Moreover, we calculated half-lives of CYP3A4 and CYP2C9 mRNA under induced or basal conditions and we used a mathematical model to describe PXR-mediated regulation of CYP3A4 expression employing 3D PHHs. The study shows the importance of long-term time-expression profiling of PXR target genes in phenotypically stable 3D PHHs and provides insight into PXR function in liver beyond our knowledge from conventional 2D in vitro models.
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Affiliation(s)
- Tomas Smutny
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic.
| | - Veronika Bernhauerova
- Department of Biophysics and Physical Chemistry, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Lucie Smutna
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Jurjen Duintjer Tebbens
- Department of Biophysics and Physical Chemistry, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
| | - Petr Pavek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, Hradec Kralove, 500 05, Czech Republic
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van Groen BD, Bi C, Gaedigk R, Staggs VS, Tibboel D, de Wildt SN, Leeder JS. Alternative Splicing of the SLCO1B1 Gene: An Exploratory Analysis of Isoform Diversity in Pediatric Liver. Clin Transl Sci 2020; 13:509-519. [PMID: 31917523 PMCID: PMC7214651 DOI: 10.1111/cts.12733] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/26/2019] [Indexed: 11/30/2022] Open
Abstract
The hepatic influx transporter OATP1B1 (SLCO1B1) plays an important role in the disposition of endogenous substrates and drugs prescribed to children. Alternative splicing increases the diversity of protein products from > 90% of human genes and may be triggered by developmental signals. As concentrations of several endogenous OATP1B1 substrates change during growth and development, with this exploratory study we investigated age-dependent alternative splicing of SLCO1B1 mRNA in 97 postmortem livers (fetus-adolescents). Twenty-seven splice variants were detected; 10 were confirmed by additional bioinformatic analyses and verified by quantitative polymerase chain reaction, and selected for detailed analysis based on relative abundance, association with age, and overlap with an adjacent gene. Two splice variants code for reference OATP1B1 protein, and eight code for truncated proteins. The expression of eight isoforms was associated with age. We conclude that alternative splicing of SLCO1B1 occurs frequently in children; although the functional consequences remain unknown, the data raise the possibility of a regulatory role for alternative splicing in mediating developmental changes in drug disposition.
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Affiliation(s)
- Bianca D. van Groen
- Intensive Care and Department of Pediatric SurgeryErasmus MC‐Sophia Children’s HospitalRotterdamThe Netherlands
| | - Chengpeng Bi
- Division of Clinical Pharmacology, Toxicology, & Therapeutic InnovationDepartment of PediatricsChildren's Mercy Kansas CityKansas CityMissouriUSA
| | - Roger Gaedigk
- Division of Clinical Pharmacology, Toxicology, & Therapeutic InnovationDepartment of PediatricsChildren's Mercy Kansas CityKansas CityMissouriUSA
| | - Vincent S. Staggs
- Health Services and Outcomes ResearchChildren's Mercy Kansas CitySchool of MedicineUniversity of Missouri‐KansasKansas CityMissouriUSA
| | - Dick Tibboel
- Intensive Care and Department of Pediatric SurgeryErasmus MC‐Sophia Children’s HospitalRotterdamThe Netherlands
| | - Saskia N. de Wildt
- Intensive Care and Department of Pediatric SurgeryErasmus MC‐Sophia Children’s HospitalRotterdamThe Netherlands
- Department of Pharmacology and ToxicologyRadboud Institute for Health SciencesRadboud University Medical CenterNijmegenThe Netherlands
| | - J. Steven Leeder
- Division of Clinical Pharmacology, Toxicology, & Therapeutic InnovationDepartment of PediatricsChildren's Mercy Kansas CityKansas CityMissouriUSA
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Ding W, Cao C, Gao Y, Zhou X, Lai Y. Inhibition of CYP3A4 and CYP3A5 expression by scutellarin is not mediated via the regulation of hsa-miR-27a, 27b, 148a, 298 and 451a levels. Xenobiotica 2018; 50:1267-1274. [PMID: 30501535 DOI: 10.1080/00498254.2018.1555344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
1. Scutellarin is a flavonoid glycoside widely used in the treatment of cardio-cerebrovascular diseases in China. In this study, we investigated the effect of scutellarin on cytochrome P450 3A4 (CYP3A4) and CYP3A5 expression. Furthermore, we studied the expression of hsa-miR-27a, hsa-miR-27b, hsa-miR-148a, hsa-miR-298 and hsa-miR-451a in humans to determine whether scutellarin regulated CYP3A4 and CYP3A5 expression by altering levels of those micro-ribonucleic acids (miRNAs). 2. In vitro CYP3A4 and CYP3A5 expression was measured in Chang liver cells via quantitative real-time polymerase chain reaction (qPCR) and western blot. In vivo CYP3A4 and CYP3A5 expression was evaluated through the metabolism of their substrate midazolam (MID), and detected via ultra-performance liquid chromatography-mass spectrometry. The relative miRNA levels in the plasma of study participants were investigated via qPCR. 3. Results showed that scutellarin significantly inhibited the CYP3A4 and CYP3A5 expression both in vitro and in vivo. However, the levels of hsa-miR-27a, hsa-miR-27b, hsa-miR-148a, hsa-miR-298 and hsa-miR-451a in scutellarin group did not show significant changes when compared with those of the placebo group (p > 0.05), suggesting that the expression of these miRNAs is not relevant to the scutellarin-induced down-regulation of CYP3A4 and CYP3A5.
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Affiliation(s)
- Weiyao Ding
- Institute of Pharmacy and Chemistry, Dali University, Yunnan, China
| | - Change Cao
- Institute of Pharmacy and Chemistry, Dali University, Yunnan, China.,Central Laboratory, Qujing hospital of traditional Chinese medicine, Yunnan, China
| | - Yangyang Gao
- Institute of Pharmacy and Chemistry, Dali University, Yunnan, China
| | - Xuan Zhou
- Institute of Pharmacy and Chemistry, Dali University, Yunnan, China
| | - Yong Lai
- Institute of Pharmacy and Chemistry, Dali University, Yunnan, China.,Yunnan Provincial Key Laboratory of Entomological Biopharmaceutical R&D, Yunnan, China
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Abstract
Cytochrome P450 3A4 (CYP3A4) metabolizes 30-50% of clinically used drugs. Large interperson variability in CYP3A4 activity affects response to CYP3A4 substrate drugs. We had demonstrated that an intronic single nucleotide polymorphism rs35599367 (CYP3A4*22, located in intron 6) reduces mRNA/protein expression; however, the underlying mechanism remained unknown. Here we show that CYP3A4*22 is associated with a two-fold or greater increase in formation of a nonfunctional CYP3A4 alternative splice variant with partial intron 6 retention in human liver (P=0.006), but not in small intestines. Consistent with this observation, in-vitro transfection experiments with a CYP3A4 minigene (spanning from intron 5 to intron 7) demonstrated that plasmids carrying the rs35599367 minor T allele caused significantly greater intron 6 retention than the C allele in liver derived HepG2 cells, but not in intestine-derived LS-174T cells. These results indicate that tissue-specific increased formation of nonfunctional alternative splice variant causes reduced CYP3A4 mRNA/protein expression in CYP3A4*22 carriers.
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Misiewicz-Krzeminska I, Sarasquete ME, Vicente-Dueñas C, Krzeminski P, Wiktorska K, Corchete LA, Quwaider D, Rojas EA, Corral R, Martín AA, Escalante F, Bárez A, García JL, Sánchez-García I, García-Sanz R, San Miguel JF, Gutiérrez NC. Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma. Clin Cancer Res 2015; 22:207-17. [PMID: 26341922 DOI: 10.1158/1078-0432.ccr-14-2796] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 08/14/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Dysregulation of one of the three D-cyclin genes has been observed in virtually all multiple myeloma tumors. The mechanisms by which CCND2 is upregulated in a set of multiple myeloma are not completely deciphered. We investigated the role of post-transcriptional regulation through the interaction between miRNAs and their binding sites at 3'UTR in CCND2 overexpression in multiple myeloma. EXPERIMENTAL DESIGN Eleven myeloma cell lines and 45 primary myeloma samples were included in the study. Interactions between miRNAs deregulated in multiple myeloma and mRNA targets were analyzed by 3'UTR-luciferase plasmid assay. The presence of CCND2 mRNA isoforms different in length was explored using qRT-PCR, Northern blot, mRNA FISH, and 3' rapid amplification of cDNA ends (RACE)-PCR. RESULTS We detected the presence of short CCND2 mRNA, both in the multiple myeloma cell lines and primary cells. The results obtained by 3'RACE experiments revealed that changes in CCND2 3'UTR length are explained by alternative polyadenylation. The luciferase assays using plasmids harboring the truncated CCND2 mRNA strongly confirmed the loss of miRNA sites in the shorter CCND2 mRNA isoform. Those multiple myelomas with greater abundance of the shorter 3'UTR isoform were associated with significant higher level of total CCND2 mRNA expression. Furthermore, functional analysis showed significant CCND2 mRNA shortening after CCND1 silencing and an increased relative expression of longer isoform after CCND1 and CCND3 overexpression, suggesting that cyclin D1 and D3 could regulate CCND2 levels through modifications in polyadenylation-cleavage reaction. CONCLUSIONS Overall, these results highlight the impact of CCND2 3'UTR shortening on miRNA-dependent regulation of CCND2 in multiple myeloma.
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Affiliation(s)
- Irena Misiewicz-Krzeminska
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. National Medicines Institute, Warsaw, Poland
| | - María E Sarasquete
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Carolina Vicente-Dueñas
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. Experimental Therapeutics and Translational Oncology Program, Instituto de Biologia Molecular y Celular del Cancer, CSIC/Universidad de Salamanca, Salamanca, Spain
| | - Patryk Krzeminski
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | | | - Luis Antonio Corchete
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Dalia Quwaider
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Elizabeta A Rojas
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Rocío Corral
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. Servicio de Hematología, Hospital Universitario, Salamanca, Spain
| | - Ana A Martín
- Servicio de Hematología, Hospital Universitario, Salamanca, Spain
| | | | | | - Juan Luis García
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain
| | - Isidro Sánchez-García
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. Experimental Therapeutics and Translational Oncology Program, Instituto de Biologia Molecular y Celular del Cancer, CSIC/Universidad de Salamanca, Salamanca, Spain
| | - Ramón García-Sanz
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. Servicio de Hematología, Hospital Universitario, Salamanca, Spain
| | - Jesús F San Miguel
- Clinica Universidad de Navarra, Centro de Investigaciones Medicas Aplicadas (CIMA), Pamplona, Spain
| | - Norma C Gutiérrez
- Centro de Investigacion del Cancer-IBMCC (USAL-CSIC), Salamanca, Spain. Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain. Servicio de Hematología, Hospital Universitario, Salamanca, Spain.
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Genome-wide binding and transcriptome analysis of human farnesoid X receptor in primary human hepatocytes. PLoS One 2014; 9:e105930. [PMID: 25198545 PMCID: PMC4157742 DOI: 10.1371/journal.pone.0105930] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/20/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND & AIMS Farnesoid X receptor (FXR, NR1H4) is a ligand-activated transcription factor, belonging to the nuclear receptor superfamily. FXR is highly expressed in the liver and is essential in regulating bile acid homeostasis. FXR deficiency is implicated in numerous liver diseases and mice with modulation of FXR have been used as animal models to study liver physiology and pathology. We have reported genome-wide binding of FXR in mice by chromatin immunoprecipitation - deep sequencing (ChIP-seq), with results indicating that FXR may be involved in regulating diverse pathways in liver. However, limited information exists for the functions of human FXR and the suitability of using murine models to study human FXR functions. METHODS In the current study, we performed ChIP-seq in primary human hepatocytes (PHHs) treated with a synthetic FXR agonist, GW4064 or DMSO control. In parallel, RNA deep sequencing (RNA-seq) and RNA microarray were performed for GW4064 or control treated PHHs and wild type mouse livers, respectively. RESULTS ChIP-seq showed similar profiles of genome-wide FXR binding in humans and mice in terms of motif analysis and pathway prediction. However, RNA-seq and microarray showed more different transcriptome profiles between PHHs and mouse livers upon GW4064 treatment. CONCLUSIONS In summary, we have established genome-wide human FXR binding and transcriptome profiles. These results will aid in determining the human FXR functions, as well as judging to what level the mouse models could be used to study human FXR functions.
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Zhang J, Pan Z, Moloney S, Sheppard A. RNA-Seq analysis implicates detoxification pathways in ovine mycotoxin resistance. PLoS One 2014; 9:e99975. [PMID: 24936865 PMCID: PMC4061066 DOI: 10.1371/journal.pone.0099975] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 05/21/2014] [Indexed: 11/19/2022] Open
Abstract
Mycotoxin induced hepatoxocity has been linked to oxidative stress, resulting from either an increase in levels of reactive oxygen species (ROS) above normal levels and/or the suppression of antioxidant protective pathways. However, few detailed molecular studies of mycotoxicoses in animals have been carried out. This study use current RNA-seq based approaches to investigate the effects of mycotoxin exposure in a ruminant model. Having first assembled a de novo reference transcriptome, we use RNA-Seq technology to define in vivo hepatic gene expression changes resulting from mycotoxin exposure in relationship to pathological effect. As expected, characteristic oxidative stress related gene expression is markedly different in animals exhibiting poorer outcomes. However, expression of multiple genes critical for detoxification, particularly members of the cytochrome P450 gene family, was significantly higher in animals exhibiting mycotoxin tolerance ('resistance'). Further, we present novel evidence for the amplification of Wnt signalling pathway activity in 'resistant' animals, resulting from the marked suppression of multiple key Wnt inhibitor genes. Notably, 'resistance' may be determined primarily by the ability of an individual to detoxify secondary metabolites generated by the metabolism of mycotoxins and the potentiation of Wnt signalling may be pivotal to achieving a favourable outcome upon challenge.
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Affiliation(s)
- Jinbi Zhang
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Zengxiang Pan
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | | | - Allan Sheppard
- Liggins Institute, University of Auckland, Auckland, New Zealand
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Elens L, van Gelder T, Hesselink DA, Haufroid V, van Schaik RHN. CYP3A4*22: promising newly identified CYP3A4 variant allele for personalizing pharmacotherapy. Pharmacogenomics 2013; 14:47-62. [PMID: 23252948 DOI: 10.2217/pgs.12.187] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Many studies have attempted to explain the interindividual variability observed in drug metabolism by assessing the impact of SNPs in genes implicated in drug absorption, distribution, metabolism and excretion pathways. Particular attention has been paid to the CYP450s. CYP3A4 is the main CYP isoform in human liver and intestine and is involved in the metabolism of many drugs. Its activity, however, is characterized by widespread variation in the general population, which is thought to have a genetic basis. A new CYP3A4 allele (CYP3A4*22; rs35599367 C>T in intron 6) with a frequency of 5-7% in the Caucasian population was recently discovered through its association with low hepatic CYP3A4 expression and CYP3A4 activity, and showing effects on statin, tacrolimus and cyclosporine metabolism. This review will summarize the current literature on phenotypes linked to this new promising CYP3A4 genetic marker SNP and discusses the potential clinical relevance.
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Affiliation(s)
- Laure Elens
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, Rotterdam, The Netherlands
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Peng L, Yoo B, Gunewardena SS, Lu H, Klaassen CD, Zhong XB. RNA sequencing reveals dynamic changes of mRNA abundance of cytochromes P450 and their alternative transcripts during mouse liver development. Drug Metab Dispos 2012; 40:1198-209. [PMID: 22434873 DOI: 10.1124/dmd.112.045088] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Cytochromes P450 (P450s) are a superfamily of enzymes that have critical functions in liver to catalyze the biotransformation of numerous drugs. However, the functions of most P450s are not mature at birth, which can markedly affect the metabolism of drugs in newborns. Therefore, characterization of the developmental profiles and regulatory mechanisms of P450 expression is needed for more rational drug therapy of pediatric patients. An animal model is indispensable for studying the mechanisms of postnatal development of the P450s. Hence we used RNA sequencing (RNA-Seq) to provide a "true quantification" of mRNA expression of all P450s in mouse liver during development. Liver samples of male C57BL/6 mice at 12 different ages from prenatal to adulthood were used. Total mRNAs of the 103 mouse P450s displayed two rapid increasing stages after birth, reflecting critical functional transition of liver during development. Four ontogenic expression patterns were identified among the 71 significantly expressed P450s, which categorized genes into neonatal-, adolescent-, adolescent/adult-, and adult-enriched groups. The 10 most highly expressed subfamilies of mouse P450s in livers of adult mice were CYP2E, -2C, -2D, -3A, -4A, -2F, -2A, -1A, -4F, and -2B, which showed diverse expression profiles during development. The expression patterns of multiple members within a P450 subfamily were often classified to different groups. RNA-Seq also enabled the quantification of known transcript variants of CYP2C44, CYP2C50, CYP2D22, CYP3A25, and CYP26B1 and identification of novel transcripts for CYP2B10, CYP2D26, and CYP3A13. In conclusion, this study reveals the mRNA abundance of all the P450s in mouse liver during development and provides a foundation for mechanistic studies in the future.
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Affiliation(s)
- Lai Peng
- Department of Pharmacology, Toxicology, and Therapeutics, University of Kansas Medical Center, 3901 Rainbow Blvd., Kansas City, KS 66160, USA
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