1
|
Mm Yahya S, Elsayed GH. The role of MiRNA-34 family in different signaling pathways and its therapeutic options. Gene 2024; 931:148829. [PMID: 39154971 DOI: 10.1016/j.gene.2024.148829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 08/20/2024]
Abstract
MiRNAs are short non-coding RNA molecules that have been shown to affect a vast number of genes at the post-transcriptional level, hence regulating several signaling pathways. Because the miRNA-34 family regulates a number of different signaling pathways, including those linked to cancer, the immune system, metabolism, cellular structure, and neurological disorders, it has garnered a great deal of attention from researchers. Members of the miRNA-34 family have been shown to inhibit tumors in a variety of cancer types. This family is also important for obesity, the cardiovascular system, and glycolysis. It's interesting to note that the miRNA-34 family is known to play a role in major depressive disorder, schizophrenia, Parkinson's disease (PD), adverse childhood experiences or trauma, regulation of stress responses, Alzheimer's disease (AD), and stress-related psychatric conditions. In this review, the expected targets of the miRNA-34 family are presented alongside the well-established targets identified by pathway analysis. Furthermore, the therapeutic potential of this miRNA family will be discussed.
Collapse
Affiliation(s)
- Shaymaa Mm Yahya
- Hormones Department, Medical Research and Clinical Studies Institute, and Stem Cell Lab, Centre of Excellence for Advanced SciencesNational Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt.
| | - Ghada H Elsayed
- Hormones Department, Medical Research and Clinical Studies Institute, and Stem Cell Lab, Centre of Excellence for Advanced SciencesNational Research Centre, 33 El-Bohouth St., Dokki, Giza 12622, Egypt
| |
Collapse
|
2
|
Abdel Halim AS, Rudayni HA, Chaudhary AA, Ali MAM. MicroRNAs: Small molecules with big impacts in liver injury. J Cell Physiol 2023; 238:32-69. [PMID: 36317692 DOI: 10.1002/jcp.30908] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022]
Abstract
A type of small noncoding RNAs known as microRNAs (miRNAs) fine-tune gene expression posttranscriptionally by binding to certain messenger RNA targets. Numerous physiological processes in the liver, such as differentiation, proliferation, and apoptosis, are regulated by miRNAs. Additionally, there is growing evidence that miRNAs contribute to liver pathology. Extracellular vesicles like exosomes, which contain secreted miRNAs, may facilitate paracrine and endocrine communication between various tissues by changing the gene expression and function of distal cells. The use of stable miRNAs as noninvasive biomarkers was made possible by the discovery of these molecules in body fluids. Circulating miRNAs reflect the conditions of the liver that are abnormal and may serve as new biomarkers for the early detection, prognosis, and evaluation of liver pathological states. miRNAs are appealing therapeutic targets for a range of liver disease states because altered miRNA expression is associated with deregulation of the liver's metabolism, liver damage, liver fibrosis, and tumor formation. This review provides a comprehensive review and update on miRNAs biogenesis pathways and mechanisms of miRNA-mediated gene silencing. It also outlines how miRNAs affect hepatic cell proliferation, death, and regeneration as well as hepatic detoxification. Additionally, it highlights the diverse functions that miRNAs play in the onset and progression of various liver diseases, including nonalcoholic fatty liver disease, alcoholic liver disease, fibrosis, hepatitis C virus infection, and hepatocellular carcinoma. Further, it summarizes the diverse liver-specific miRNAs, illustrating the potential merits and possible caveats of their utilization as noninvasive biomarkers and appealing therapeutic targets for liver illnesses.
Collapse
Affiliation(s)
- Alyaa S Abdel Halim
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Hassan Ahmed Rudayni
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Mohamed A M Ali
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt.,Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| |
Collapse
|
3
|
Abstract
Non-alcoholic fatty liver disease (NAFLD) is emerging as the most common chronic liver disease worldwide. It refers to a range of liver conditions affecting people who drink little or no alcohol. NAFLD comprises non-alcoholic fatty liver and non-alcoholic steatohepatitis (NASH), the more aggressive form of NAFLD. NASH is featured by steatosis, lobular inflammation, hepatocyte injury, and various degrees of fibrosis. Although much progress has been made over the past decades, the pathogenic mechanism of NAFLD remains to be fully elucidated. Hepatocyte nuclear factor 4α (HNF4α) is a nuclear hormone receptor that is highly expressed in hepatocytes. Hepatic HNF4α expression is markedly reduced in NAFLD patients and mouse models of NASH. HNF4α has been shown to regulate bile acid, lipid, glucose, and drug metabolism. In this review, we summarize the recent advances in the understanding of the pathogenesis of NAFLD with a focus on the regulation of HNF4α and the role of hepatic HNF4α in NAFLD. Several lines of evidence have shown that hepatic HNF4α plays a key role in the initiation and progression of NAFLD. Recent data suggest that hepatic HNF4α may be a promising target for treatment of NAFLD.
Collapse
|
4
|
Role of miR-653 and miR-29c in downregulation of CYP1A2 expression in hepatocellular carcinoma. Pharmacol Rep 2021; 74:148-158. [PMID: 34780054 DOI: 10.1007/s43440-021-00338-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/21/2021] [Accepted: 10/27/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a major contributor to the worldwide cancer burden. Recent studies on HCC have demonstrated dramatic alterations in expression of several cytochrome P450 (CYP) family members that play a crucial role in biotransformation of many drugs and other xenobiotics; however, the mechanisms responsible for their deregulation remain unclear. METHODS We investigated a potential involvement of miRNAs in downregulation of expression of CYPs observed in HCC tumors. We compared miRNA expression profiles (TaqMan Array Human MicroRNA v3.0 TLDA qPCR) between HCC human patient tumors with strong (CYP-) and weak/no (CYP+) downregulation of drug-metabolizing CYPs. The role of significantly deregulated miRNAs in modulation of expression of the CYPs and associated xenobiotic receptors was then investigated in human liver HepaRG cells transfected with relevant miRNA mimics or inhibitors. RESULTS We identified five differentially expressed miRNAs in CYP- versus CYP+ tumors, namely miR-29c, miR-125b1, miR-505, miR-653 and miR-675. The two most-upregulated miRNAs found in CYP- tumor samples, miR-29c and miR-653, were found to act as efficient suppressors of CYP1A2 or AHR expression. CONCLUSIONS Our results revealed a novel role of miR-653 and miR-29c in regulation of expresion of CYPs involved in crucial biotransformation processes in liver, which are often deregulated during liver cancer progression.
Collapse
|
5
|
Skandalaki A, Sarantis P, Theocharis S. Pregnane X Receptor (PXR) Polymorphisms and Cancer Treatment. Biomolecules 2021; 11:1142. [PMID: 34439808 PMCID: PMC8394562 DOI: 10.3390/biom11081142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/20/2022] Open
Abstract
Pregnane X Receptor (PXR) belongs to the nuclear receptors' superfamily and mainly functions as a xenobiotic sensor activated by a variety of ligands. PXR is widely expressed in normal and malignant tissues. Drug metabolizing enzymes and transporters are also under PXR's regulation. Antineoplastic agents are of particular interest since cancer patients are characterized by significant intra-variability to treatment response and severe toxicities. Various PXR polymorphisms may alter the function of the protein and are linked with significant effects on the pharmacokinetics of chemotherapeutic agents and clinical outcome variability. The purpose of this review is to summarize the roles of PXR polymorphisms in the metabolism and pharmacokinetics of chemotherapeutic drugs. It is also expected that this review will highlight the importance of PXR polymorphisms in selection of chemotherapy, prediction of adverse effects and personalized medicine.
Collapse
Affiliation(s)
| | | | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (A.S.); (P.S.)
| |
Collapse
|
6
|
Wang Z, Zhang Y, Zhang J, Deng Q, Liang H. Controversial roles of hepatocyte nuclear receptor 4 α on tumorigenesis. Oncol Lett 2021; 21:356. [PMID: 33747213 PMCID: PMC7968000 DOI: 10.3892/ol.2021.12617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocyte nuclear receptor 4 α (HNF4α) is known to be a master transcription regulator of gene expression in multiple biological processes, particularly in liver development and liver function. To date, the function of HNF4α in human cancers has been widely investigated; however, the critical roles of HNF4α in tumorigenesis remain unclear. Numerous controversies exist, even in studies from different research groups but on the same type of cancer. In the present review, the critical roles of HNF4α in tumorigenesis will be summarized and discussed. Furthermore, HNF4α expression profile and alterations will be examined by pan-cancer analysis through bioinformatics, in order to provide a better understanding of the functional roles of this gene in human cancers.
Collapse
Affiliation(s)
- Zhu Wang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Ying Zhang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Jianwen Zhang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Qiong Deng
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Hui Liang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| |
Collapse
|
7
|
Gu XQ, Tang D, Wan P, Qin T, Yang TH, Wu J, Ji H, Liu JC, Xue F, Tang YJ, Xia Q. Multiple microRNAs regulate tacrolimus metabolism through CYP3A5. Pharmacol Res 2020; 164:105382. [PMID: 33348024 DOI: 10.1016/j.phrs.2020.105382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 01/19/2023]
Abstract
The CYP3A5 gene polymorphism accounts for the majority of inter-individual variability in tacrolimus pharmacokinetics. We found that the basal expression of CYP3A5 in donor grafts also played a significant role in tacrolimus metabolism under the same genetic conditions after pediatric liver transplantation. Thus, we hypothesized that some potential epigenetic factors could affect CYP3A5 expression and contributed to the variability. We used a high-throughput functional screening for miRNAs to identify miRNAs that had the most abundant expression in normal human liver and could regulate tacrolimus metabolism in HepaRG cells and HepLPCs. Four of these miRNAs (miR-29a-3p, miR-99a-5p, miR-532-5p, and miR-26-5p) were selected for testing. We found that these miRNAs inhibited tacrolimus metabolism that was dependent on CYP3A5. Putative miRNAs targeting key drug-metabolizing enzymes and transporters (DMETs) were selected using an in silico prediction algorithm. Luciferase reporter assays and functional studies showed that miR-26b-5p inhibited tacrolimus metabolism by directly regulating CYP3A5, while miR-29a-5p, miR-99a-5p, and miR-532-5p targeted HNF4α, NR1I3, and NR1I2, respectively, in turn regulating the downstream expression of CYP3A5; the corresponding target gene siRNAs markedly abolished the effects caused by miRNA inhibitors. Also, the expression of miR-29a-3p, miR-99a-5p, miR-532-5p, and miR-26b-5p in donor grafts were negatively correlated with tacrolimus C/D following pediatric liver transplantation. Taken together, our findings identify these miRNAs as novel regulators of tacrolimus metabolism.
Collapse
Affiliation(s)
- Xiang-Qian Gu
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Dan Tang
- Department of Anesthesiology and Critical Care Medicine, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ping Wan
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Tian Qin
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, EA 11, 9713 GZ, Groningen, The Netherlands
| | - Tai-Hua Yang
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Ji Wu
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Hao Ji
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Jin-Chuan Liu
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| | - Feng Xue
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China.
| | - Yuan-Jia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200127, China
| |
Collapse
|
8
|
Smutny T, Hyrsova L, Braeuning A, Ingelman-Sundberg M, Pavek P. Transcriptional and post-transcriptional regulation of the pregnane X receptor: a rationale for interindividual variability in drug metabolism. Arch Toxicol 2020; 95:11-25. [PMID: 33164107 DOI: 10.1007/s00204-020-02916-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/17/2020] [Indexed: 12/15/2022]
Abstract
The pregnane X receptor (PXR, encoded by the NR1I2 gene) is a ligand-regulated transcription factor originally described as a master regulator of xenobiotic detoxification. Later, however, PXR was also shown to interact with endogenous metabolism and to be further associated with various pathological states. This review focuses predominantly on such aspects, currently less covered in literature, as the control of PXR expression per se in the context of inter-individual differences in drug metabolism. There is growing evidence that non-coding RNAs post-transcriptionally regulate PXR. Effects on PXR have especially been reported for microRNAs (miRNAs), which include miR-148a, miR-18a-5p, miR-140-3p, miR-30c-1-3p and miR-877-5p. Likewise, miRNAs control the expression of both transcription factors involved in PXR expression and regulators of PXR function. The impact of NR1I2 genetic polymorphisms on miRNA-mediated PXR regulation is also discussed. As revealed recently, long non-coding RNAs (lncRNAs) appear to interfere with PXR expression. Reciprocally, PXR activation regulates non-coding RNA expression, thus comprising another level of PXR action in addition to the direct transactivation of protein-coding genes. PXR expression is further controlled by several transcription factors (cross-regulation) giving rise to different PXR transcript variants. Controversies remain regarding the suggested role of feedback regulation (auto-regulation) of PXR expression. In this review, we comprehensively summarize the miRNA-mediated, lncRNA-mediated and transcriptional regulation of PXR expression, and we propose that deciphering the precise mechanisms of PXR expression may bridge our knowledge gap in inter-individual differences in drug metabolism and toxicity.
Collapse
Affiliation(s)
- Tomas Smutny
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 500 05, Hradec Kralove, Czech Republic.
| | - Lucie Hyrsova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 500 05, Hradec Kralove, Czech Republic
| | - Albert Braeuning
- Department Food Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589, Berlin, Germany
| | - Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institutet, Solna vägen 9, 17165, Stockholm, Sweden
| | - Petr Pavek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Akademika Heyrovskeho 1203, 500 05, Hradec Kralove, Czech Republic
| |
Collapse
|
9
|
Daujat-Chavanieu M, Gerbal-Chaloin S. Regulation of CAR and PXR Expression in Health and Disease. Cells 2020; 9:E2395. [PMID: 33142929 PMCID: PMC7692647 DOI: 10.3390/cells9112395] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/22/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Pregnane X receptor (PXR, NR1I2) and constitutive androstane receptor (CAR, NR1I3) are members of the nuclear receptor superfamily that mainly act as ligand-activated transcription factors. Their functions have long been associated with the regulation of drug metabolism and disposition, and it is now well established that they are implicated in physiological and pathological conditions. Considerable efforts have been made to understand the regulation of their activity by their cognate ligand; however, additional regulatory mechanisms, among which the regulation of their expression, modulate their pleiotropic effects. This review summarizes the current knowledge on CAR and PXR expression during development and adult life; tissue distribution; spatial, temporal, and metabolic regulations; as well as in pathological situations, including chronic diseases and cancers. The expression of CAR and PXR is modulated by complex regulatory mechanisms that involve the interplay of transcription factors and also post-transcriptional and epigenetic modifications. Moreover, many environmental stimuli affect CAR and PXR expression through mechanisms that have not been elucidated.
Collapse
Affiliation(s)
| | - Sabine Gerbal-Chaloin
- IRMB, University of Montpellier, INSERM, CHU Montpellier, 34295 Montpellier, France;
| |
Collapse
|
10
|
Ipe J, Li R, Metzger IF, Bo Li Lu J, Gufford BT, Desta Z, Liu Y, Skaar TC. Circulating miRNAs as Biomarkers for CYP2B6 Enzyme Activity. Clin Pharmacol Ther 2020; 109:485-493. [PMID: 32772362 DOI: 10.1002/cpt.2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/16/2020] [Indexed: 01/08/2023]
Abstract
The CYP2B6 gene is highly polymorphic and its activity shows wide interindividual variability. However, substantial variability in CYP2B6 activity remains unexplained by the known CYP2B6 genetic variations. Circulating, cell-free micro RNAs (miRNAs) may serve as biomarkers of hepatic enzyme activity. CYP2B6 activity in 72 healthy volunteers was determined using the disposition of efavirenz as a probe drug. Circulating miRNA expression was quantified from baseline plasma samples. A linear model consisting of the effects of miRNA expression, genotype-determined metabolizer status, and demographic information was developed to predict CYP2B6 activity. Expression of 2,510 miRNAs were quantified out of which 7 miRNAs, together with the CYP2B6-genotypic metabolizer status and demographics, was shown to be predictive markers for CYP2B6 activity. The reproducibility of the model was evaluated by cross-validation. The average Pearson's correlation (R) between the predicted and observed maximum plasma concentration (Cmax ) ratios of efavirenz and its metabolite-8-OH efavirenz using the linear model with all features (7 miRNA + metabolizer status + age + sex + race) was 0.6702. Similar results were also observed using area under the curve (AUC) ratios (Pearson correlation's R = 0.6035). Thus, at least 36% (R2 ) of the variability of in vivo CYP2B6 activity was explained using this model. This is a significant improvement over the models using only the genotype-based metabolizer status or the demographic information, which explained only 6% or less of the variability of in vivo CYP2B6 activity. Our results, therefore, demonstrate that circulating plasma miRNAs can be valuable biomarkers for in vivo CYP2B6 activity.
Collapse
Affiliation(s)
- Joseph Ipe
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Rudong Li
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Ingrid F Metzger
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Jessica Bo Li Lu
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Brandon T Gufford
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Zeruesenay Desta
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Todd C Skaar
- Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| |
Collapse
|
11
|
Bolleyn J, Rombaut M, Nair N, Branson S, Heymans A, Chuah M, VandenDriessche T, Rogiers V, De Kock J, Vanhaecke T. Genetic and Epigenetic Modification of Rat Liver Progenitor Cells via HNF4α Transduction and 5' Azacytidine Treatment: An Integrated miRNA and mRNA Expression Profile Analysis. Genes (Basel) 2020; 11:E486. [PMID: 32365562 PMCID: PMC7291069 DOI: 10.3390/genes11050486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/17/2022] Open
Abstract
Neonatal liver-derived rat epithelial cells (rLEC) from biliary origin are liver progenitor cells that acquire a hepatocyte-like phenotype upon sequential exposure to hepatogenic growth factors and cytokines. Undifferentiated rLEC express several liver-enriched transcription factors, including the hepatocyte nuclear factors (HNF) 3β and HNF6, but not the hepatic master regulator HNF4α. In this study, we first investigated the impact of the ectopic expression of HNF4α in rLEC on both mRNA and microRNA (miR) level by means of microarray technology. We found that HNF4α transduction did not induce major changes to the rLEC phenotype. However, we next investigated the influence of DNA methyl transferase (DNMT) inhibition on the phenotype of undifferentiated naïve rLEC by exposure to 5' azacytidine (AZA), which was found to have a significant impact on rLEC gene expression. The transduction of HNF4α or AZA treatment resulted both in significantly downregulated C/EBPα expression levels, while the exposure of the cells to AZA had a significant effect on the expression of HNF3β. Computationally, dysregulated miRNAs were linked to target mRNAs using the microRNA Target Filter function of Ingenuity Pathway Analysis. We found that differentially regulated miRNA-mRNA target associations predict ectopic HNF4α expression in naïve rLEC to interfere with cell viability and cellular maturation (miR-19b-3p/NR4A2, miR30C-5p/P4HA2, miR328-3p/CD44) while it predicts AZA exposure to modulate epithelial/hepatic cell proliferation, apoptosis, cell cycle progression and the differentiation of stem cells (miR-18a-5p/ESR1, miR-503-5p/CCND1). Finally, our computational analysis predicts that the combination of HNF4α transduction with subsequent AZA treatment might cause changes in hepatic cell proliferation and maturation (miR-18a-5p/ESR1, miR-503-5p/CCND1, miR-328-3p/CD44) as well as the apoptosis (miR-16-5p/BCL2, miR-17-5p/BCL2, miR-34a-5p/BCL2 and miR-494-3p/HMOX1) of naïve rLEC.
Collapse
Affiliation(s)
- Jennifer Bolleyn
- Department of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium; (J.B.); (M.R.); (S.B.); (A.H.); (V.R.); (T.V.)
| | - Matthias Rombaut
- Department of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium; (J.B.); (M.R.); (S.B.); (A.H.); (V.R.); (T.V.)
| | - Nisha Nair
- Department of Gene Therapy and Regenerative Medicine (GTRM), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium; (N.N.); (M.C.); (T.V.)
| | - Steven Branson
- Department of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium; (J.B.); (M.R.); (S.B.); (A.H.); (V.R.); (T.V.)
| | - Anja Heymans
- Department of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium; (J.B.); (M.R.); (S.B.); (A.H.); (V.R.); (T.V.)
| | - Marinee Chuah
- Department of Gene Therapy and Regenerative Medicine (GTRM), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium; (N.N.); (M.C.); (T.V.)
| | - Thierry VandenDriessche
- Department of Gene Therapy and Regenerative Medicine (GTRM), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium; (N.N.); (M.C.); (T.V.)
| | - Vera Rogiers
- Department of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium; (J.B.); (M.R.); (S.B.); (A.H.); (V.R.); (T.V.)
| | - Joery De Kock
- Department of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium; (J.B.); (M.R.); (S.B.); (A.H.); (V.R.); (T.V.)
| | - Tamara Vanhaecke
- Department of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, Belgium; (J.B.); (M.R.); (S.B.); (A.H.); (V.R.); (T.V.)
| |
Collapse
|
12
|
Xing Y, Yan J, Niu Y. PXR: a center of transcriptional regulation in cancer. Acta Pharm Sin B 2020; 10:197-206. [PMID: 32082968 PMCID: PMC7016272 DOI: 10.1016/j.apsb.2019.06.012] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/10/2019] [Accepted: 06/20/2019] [Indexed: 02/05/2023] Open
Abstract
Pregnane X receptor (PXR, NR1I2) is a prototypical member of the nuclear receptor superfamily. PXR can be activated by both endobiotics and xenobiotics. As a key xenobiotic receptor, the cellular function of PXR is mostly exerted by its binding to the regulatory gene sequences in a ligand-dependent manner. Classical downstream target genes of PXR participate in xenobiotic responses, such as detoxification, metabolism and inflammation. Emerging evidence also implicates PXR signaling in the processes of apoptosis, cell cycle arrest, proliferation, angiogenesis and oxidative stress, which are closely related to cancer. Here, we discussed, in addition to the characterization of PXR per se, the biological function and regulatory mechanism of PXR signaling in cancer, and its potential for the targeted prevention and therapeutics.
Collapse
Affiliation(s)
- Yaqi Xing
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China
| | - Jiong Yan
- Center for Pharmacogenetics, University of Pittsburgh, PA 15261, USA
| | - Yongdong Niu
- Department of Pharmacology, Shantou University Medical College, Shantou 515041, China
- Corresponding author.
| |
Collapse
|
13
|
Smutny T, Dusek J, Hyrsova L, Nekvindova J, Horvatova A, Micuda S, Gerbal-Chaloin S, Pavek P. The 3'-untranslated region contributes to the pregnane X receptor (PXR) expression down-regulation by PXR ligands and up-regulation by glucocorticoids. Acta Pharm Sin B 2020; 10:136-152. [PMID: 31998607 PMCID: PMC6976988 DOI: 10.1016/j.apsb.2019.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 12/16/2022] Open
Abstract
Pregnane X receptor (PXR) is the major regulator of xenobiotic metabolism. PXR itself is controlled by various signaling molecules including glucocorticoids. Moreover, negative feed-back regulation has been proposed at the transcriptional level. We examined the involvement of the 3'-untranslated region (3'-UTR) of NR1I2 mRNA and microRNAs in PXR- and glucocorticoid receptor (GR)-mediated regulation of NR1I2 gene expression. PXR ligands were found to significantly downregulate NR1I2 mRNA expression in a set of 14 human hepatocyte cultures. Similarly, PXR was downregulated by PCN in the C57/BL6 mice liver. In mechanistic studies with the full-length 3'-UTR cloned into luciferase reporter or expression vectors, we showed that the 3'-UTR reduces PXR expression. From the miRNAs tested, miR-18a-5p inhibited both NR1I2 expression and CYP3A4 gene induction. Importantly, we observed significant upregulation of miR-18a-5p expression 6 h after treatment with the PXR ligand rifampicin, which indicates a putative mechanism underlying NR1I2 negative feed-back regulation in hepatic cells. Additionally, glucocorticoids upregulated NR1I2 expression not only through the promoter region but also via 3'-UTR regulation, which likely involves downregulation of miR-18a-5p. We conclude that miR-18a-5p is involved in the down-regulation of NR1I2 expression by its ligands and in the upregulation of NR1I2 mRNA expression by glucocorticoids in hepatic cells.
Collapse
Key Words
- 3′-UTR, 3′-untranslated region
- CAR, constitutive androstane receptor
- CYP3A4, cytochrome P450 3A4
- Cytochrome P450 3A4
- DEX, dexamethasone
- DMEs, drug metabolizing enzymes
- DMSO, dimethyl sulfoxide
- ER, estrogen receptor
- GRα, glucocorticoid receptor α
- Gene expression
- Gluc, Gaussia luciferase
- Glucocorticoid
- LBD, ligand binding domain
- MRE, miRNA-response element
- MicroRNA
- NR, nuclear receptor
- PB, phenobarbital
- PCN, pregnenolone 16α-carbonitrile
- PHHs, primary human hepatocytes
- PPARα, peroxisome proliferator-activated receptor α
- PXR, pregnane X receptor
- Pregnane X receptor
- RXRα, retinoid X receptor α
- Regulation
- Rif, rifampicin
- SEAP, secreted alkaline phosphatase
- miRNA, microRNA
Collapse
Affiliation(s)
- Tomas Smutny
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove CZ-500 05, Czech Republic
| | - Jan Dusek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove CZ-500 05, Czech Republic
| | - Lucie Hyrsova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove CZ-500 05, Czech Republic
| | - Jana Nekvindova
- Institute of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Hradec Kralove CZ-500 05, Czech Republic
| | - Alzbeta Horvatova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove CZ-500 05, Czech Republic
| | - Stanislav Micuda
- Department of Pharmacology, Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove CZ-500 03, Czech Republic
| | | | - Petr Pavek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove CZ-500 05, Czech Republic
| |
Collapse
|
14
|
Wang Y, Tatham MH, Schmidt-Heck W, Swann C, Singh-Dolt K, Meseguer-Ripolles J, Lucendo-Villarin B, Kunath T, Rudd TR, Smith AJH, Hengstler JG, Godoy P, Hay RT, Hay DC. Multiomics Analyses of HNF4α Protein Domain Function during Human Pluripotent Stem Cell Differentiation. iScience 2019; 16:206-217. [PMID: 31185456 PMCID: PMC6556878 DOI: 10.1016/j.isci.2019.05.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/08/2019] [Accepted: 05/21/2019] [Indexed: 02/06/2023] Open
Abstract
During mammalian development, liver differentiation is driven by signals that converge on multiple transcription factor networks. The hepatocyte nuclear factor signaling network is known to be essential for hepatocyte specification and maintenance. In this study, we have generated deletion and point mutants of hepatocyte nuclear factor-4alpha (HNF4α) to precisely evaluate the function of protein domains during hepatocyte specification from human pluripotent stem cells. We demonstrate that nuclear HNF4α is essential for hepatic progenitor specification, and the introduction of point mutations in HNF4α's Small Ubiquitin-like Modifier (SUMO) consensus motif leads to disrupted hepatocyte differentiation. Taking a multiomics approach, we identified key deficiencies in cell biology, which included dysfunctional metabolism, substrate adhesion, tricarboxylic acid cycle flux, microRNA transport, and mRNA processing. In summary, the combination of genome editing and multiomics analyses has provided valuable insight into the diverse functions of HNF4α during pluripotent stem cell entry into the hepatic lineage and during hepatocellular differentiation.
Collapse
Affiliation(s)
- Yu Wang
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK
| | - Michael H Tatham
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Wolfgang Schmidt-Heck
- Leibniz Institute for Natural Product Research and Infection Biology eV-Hans-Knoll Institute, Jena, Germany
| | - Carolyn Swann
- National Institute for Biological Standards and Control (MHRA), Blanche Lane, South Mimms, Hertfordshire EN6 3QG, UK
| | - Karamjit Singh-Dolt
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK
| | - Jose Meseguer-Ripolles
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK
| | - Baltasar Lucendo-Villarin
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK
| | - Tilo Kunath
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK
| | - Timothy R Rudd
- National Institute for Biological Standards and Control (MHRA), Blanche Lane, South Mimms, Hertfordshire EN6 3QG, UK
| | - Andrew J H Smith
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK
| | - Jan G Hengstler
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Patricio Godoy
- IfADo-Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - David C Hay
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, Scotland EH16 4UU, UK.
| |
Collapse
|
15
|
Nozaki K, Nakano M, Iwakami C, Fukami T, Nakajima M. RNA Editing Enzymes Modulate the Expression of Hepatic CYP2B6, CYP2C8, and Other Cytochrome P450 Isoforms. Drug Metab Dispos 2019; 47:639-647. [DOI: 10.1124/dmd.119.086702] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 04/08/2019] [Indexed: 11/22/2022] Open
|
16
|
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: 4] [Impact Index Per Article: 0.8] [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.
Collapse
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
| |
Collapse
|
17
|
Burgess KS, Ipe J, Swart M, Metzger IF, Lu J, Gufford BT, Thong N, Desta Z, Gaedigk R, Pearce RE, Gaedigk A, Liu Y, Skaar TC. Variants in the CYP2B6 3'UTR Alter In Vitro and In Vivo CYP2B6 Activity: Potential Role of MicroRNAs. Clin Pharmacol Ther 2018; 104:130-138. [PMID: 28960269 PMCID: PMC5871545 DOI: 10.1002/cpt.892] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 01/07/2023]
Abstract
CYP2B6*6 and CYP2B6*18 are the most clinically important variants causing reduced CYP2B6 protein expression and activity. However, these variants do not account for all variability in CYP2B6 activity. Emerging evidence has shown that genetic variants in the 3'UTR may explain variable drug response by altering microRNA regulation. Five 3'UTR variants were associated with significantly altered efavirenz AUC0-48 (8-OH-EFV/EFV) ratios in healthy human volunteers. The rs70950385 (AG>CA) variant, predicted to create a microRNA binding site for miR-1275, was associated with a 33% decreased CYP2B6 activity among normal metabolizers (AG/AG vs. CA/CA (P < 0.05)). In vitro luciferase assays were used to confirm that the CA on the variant allele created a microRNA binding site causing an 11.3% decrease in activity compared to the AG allele when treated with miR-1275 (P = 0.0035). Our results show that a 3'UTR variant contributes to variability in CYP2B6 activity.
Collapse
Affiliation(s)
- Kimberly S. Burgess
- Department of Pharmacology & Toxicology, Indiana University School of Medicine, Indianapolis, IN
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN
| | - Joseph Ipe
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN
| | - Marelize Swart
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN
| | - Ingrid F. Metzger
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN
| | - Jessica Lu
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN
| | - Brandon T. Gufford
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN
| | - Nancy Thong
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN
| | - Zeruesenay Desta
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN
| | - Roger Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children’s Mercy Kansas City, Kansas City, MO
| | - Robin E. Pearce
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children’s Mercy Kansas City, Kansas City, MO
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children’s Mercy Kansas City, Kansas City, MO
| | - Yunlong Liu
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN
| | - Todd C. Skaar
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, IN
| |
Collapse
|
18
|
Ipe J, Collins KS, Hao Y, Gao H, Bhatia P, Gaedigk A, Liu Y, Skaar TC. PASSPORT-seq: A Novel High-Throughput Bioassay to Functionally Test Polymorphisms in Micro-RNA Target Sites. Front Genet 2018; 9:219. [PMID: 29963077 PMCID: PMC6013768 DOI: 10.3389/fgene.2018.00219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/29/2018] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing (NGS) studies have identified large numbers of genetic variants that are predicted to alter miRNA–mRNA interactions. We developed a novel high-throughput bioassay, PASSPORT-seq, that can functionally test in parallel 100s of these variants in miRNA binding sites (mirSNPs). The results are highly reproducible across both technical and biological replicates. The utility of the bioassay was demonstrated by testing 100 mirSNPs in HEK293, HepG2, and HeLa cells. The results of several of the variants were validated in all three cell lines using traditional individual luciferase assays. Fifty-five mirSNPs were functional in at least one of three cell lines (FDR ≤ 0.05); 11, 36, and 27 of them were functional in HEK293, HepG2, and HeLa cells, respectively. Only four of the variants were functional in all three cell lines, which demonstrates the cell-type specific effects of mirSNPs and the importance of testing the mirSNPs in multiple cell lines. Using PASSPORT-seq, we functionally tested 111 variants in the 3′ UTR of 17 pharmacogenes that are predicted to alter miRNA regulation. Thirty-three of the variants tested were functional in at least one cell line.
Collapse
Affiliation(s)
- Joseph Ipe
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kimberly S Collins
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yangyang Hao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Puja Bhatia
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, Kansas City, MO, United States
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Todd C Skaar
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| |
Collapse
|
19
|
Bandi S, Gupta S, Tchaikovskaya T, Gupta S. Differentiation in stem/progenitor cells along fetal or adult hepatic stages requires transcriptional regulators independently of oscillations in microRNA expression. Exp Cell Res 2018; 370:1-12. [PMID: 29883712 DOI: 10.1016/j.yexcr.2018.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 06/03/2018] [Accepted: 06/04/2018] [Indexed: 01/09/2023]
Abstract
Understanding mechanisms in lineage differentiation is critical for organ development, pathophysiology and oncogenesis. To determine whether microRNAs (miRNA) may serve as drivers or adjuncts in hepatic differentiation, we studied human embryonic stem cell-derived hepatocytes and primary hepatocytes representing fetal or adult stages. Model systems were used for hepatic lineage advancement or regression under culture conditions with molecular assays. Profiles of miRNA in primary fetal and adult hepatocytes shared similarities and distinctions from pluripotent stem cells or stem cell-derived early fetal-like hepatocytes. During phenotypic regression in fetal or adult hepatocytes, miRNA profiles oscillated to regain stemness-associated features that had not been extinguished in stem cell-derived fetal-like hepatocytes. These oscillations in stemness-associated features were not altered in fetal-like hepatocytes by inhibitory mimics for dominantly-expressed miRNA, such as hsa-miR-99b, -100, -214 and -221/222. The stem cell-derived fetal-like hepatocytes were permissive for miRNA characterizing mature hepatocytes, including mimics for hsa-miR-122, -126, -192, -194 and -26b, although transfections of the latter did not advance hepatic differentiation. Examination of genome-wide mRNA expression profiles in stem cell-derived or primary fetal hepatocytes indicated targets of highly abundant miRNA regulated general processes, e.g., cell survival, growth and proliferation, functional maintenance, etc., without directing cell differentiation. Among upstream regulators of gene networks in stem cell-derived hepatocytes included HNF4A, SNAI1, and others, which affect transcriptional circuits directing lineage development or maintenance. Therefore, miRNA expression oscillated in response to microenvironmental conditions, whereas lineage-specific transcriptional regulators, such as HNF4A, were necessary for directing hepatic differentiation. This knowledge will be helpful for understanding the contribution of stem cells in pathophysiological states and oncogenesis, as well as for applications of stem cell-derived hepatocytes.
Collapse
Affiliation(s)
- Sriram Bandi
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States; Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, United States.
| | - Sanchit Gupta
- Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, United States.
| | - Tatyana Tchaikovskaya
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States; Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, United States.
| | - Sanjeev Gupta
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, United States; Marion Bessin Liver Research Center, Albert Einstein College of Medicine, Bronx, NY, United States; Diabetes Center, Albert Einstein College of Medicine, Bronx, NY, United States; The Irwin S. and Sylvia Chanin Institute for Cancer Research, Albert Einstein College of Medicine, Bronx, NY, United States; The Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, NY, United States.
| |
Collapse
|
20
|
Zanger UM, Klein K, Kugler N, Petrikat T, Ryu CS. Epigenetics and MicroRNAs in Pharmacogenetics. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2018; 83:33-64. [PMID: 29801581 DOI: 10.1016/bs.apha.2018.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Germline pharmacogenetics has so far mainly studied common variants in "pharmacogenes," i.e., genes encoding drug metabolizing enzymes and transporters (DMET genes), certain auxiliary and regulatory genes, and drug target genes. Despite remarkable progress in understanding genetically determined differences in pharmacokinetics and pharmacodynamics of drugs, currently known common variants even in important pharmacogenes explain genetic variability only partially. This suggests "missing heritability" that may in part be due to rare variants in the classical pharmacogenes, but current evidence suggests that largely unexplored resources with potential for pharmacogenetics exist, both within already known pharmacogenes and in entirely new areas. In particular, recent studies suggest that epigenetic processes and noncoding RNAs, including mostly microRNAs (miRNAs), represent important and largely unexplored layers of DMET gene regulation that may fill some of the gaps in understanding interindividual variability and lead to new biomarkers. In this chapter we summarize recent advances in the understanding of genetic variability in epigenetic and miRNA-mediated processes with focus on their significance for DMET regulation and pharmacokinetic or pharmacological endpoints.
Collapse
Affiliation(s)
- Ulrich M Zanger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany; University Hospital Tübingen, Tübingen, Germany.
| | - Kathrin Klein
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Nicole Kugler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Tamara Petrikat
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Chang S Ryu
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| |
Collapse
|
21
|
Wang P, Nie YL, Wang SJ, Yang LL, Yang WH, Li JF, Li XT, Zhang LR. Regulation of UGT1A expression by miR-298 in human livers from the Han Chinese population and in human cell lines. Epigenomics 2018; 10:43-57. [DOI: 10.2217/epi-2017-0068] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: This study aimed to investigate the role of miRNAs in UGT1A regulation. Materials & methods: Based on bioinformatic prediction results, luciferase reporter assay and cell-transfection experiments were performed to study effects of miR-298 on UGT1A expression. Correlation study was conducted in human livers. Results: miR-298 overexpression reduced mRNA level of UGT1A1 and UGT1A4 in HepG2 and LS174T cells, and that of UGT1A3 and UGT1A9 in LS174T cells. miR-298 repression increased mRNA level of UGT1A4 in HepG2 and LS174T cells, and that of UGT1A1 and UGT1A3 in LS174T cells. Inverse correlations between miR-298, as well as miR-491–3p, and UGT1A3 and 1A4 mRNA levels were observed in livers. Conclusion: The study demonstrates that miR-298 and miR-491–3p downregulates UGT1A expression.
Collapse
Affiliation(s)
- Pei Wang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Ya-li Nie
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Shu-jie Wang
- Department of Pharmacology, School of Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Lin-lin Yang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Wei-hong Yang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Jiang-feng Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Xiao-tian Li
- Department of Pharmacology, School of Pharmacy, Zhengzhou University, Zhengzhou, China
| | - Li-rong Zhang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| |
Collapse
|
22
|
Victoria B, Nunez Lopez YO, Masternak MM. MicroRNAs and the metabolic hallmarks of aging. Mol Cell Endocrinol 2017; 455:131-147. [PMID: 28062199 PMCID: PMC5724961 DOI: 10.1016/j.mce.2016.12.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 10/10/2016] [Accepted: 12/16/2016] [Indexed: 12/12/2022]
Abstract
Aging, the natural process of growing older, is characterized by a progressive deterioration of physiological homeostasis at the cellular, tissue, and organismal level. Metabolically, the aging process is characterized by extensive changes in body composition, multi-tissue/multi-organ insulin resistance, and physiological declines in multiple signaling pathways including growth hormone, insulin/insulin-like growth factor 1, and sex steroids regulation. With this review, we intend to consolidate published information about microRNAs that regulate critical metabolic processes relevant to aging. In certain occasions we uncover relationships likely relevant to aging, which has not been directly described before, such as the miR-451/AMPK axis. We have also included a provocative section highlighting the potential role in aging of a new designation of miRNAs, namely fecal miRNAs, recently discovered to regulate intestinal microbiota in mammals.
Collapse
Affiliation(s)
- Berta Victoria
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL 32827, USA.
| | - Yury O Nunez Lopez
- Translational Research Institute for Metabolism & Diabetes. Florida Hospital, 301 East Princeton St, Orlando, FL 32804, USA.
| | - Michal M Masternak
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL 32827, USA; Department of Head and Neck Surgery, The Greater Poland Cancer Centre, 15 Garbary St., 61-866, Poznan, Poland.
| |
Collapse
|
23
|
Sharma D, Turkistani AA, Chang W, Hu C, Xu Z, Chang TKH. Negative Regulation of Human Pregnane X Receptor by MicroRNA-18a-5p: Evidence for Suppression of MicroRNA-18a-5p Expression by Rifampin and Rilpivirine. Mol Pharmacol 2017; 92:48-56. [DOI: 10.1124/mol.116.107003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
|
24
|
MicroRNA hsa-miR-370-3p suppresses the expression and induction of CYP2D6 by facilitating mRNA degradation. Biochem Pharmacol 2017; 140:139-149. [PMID: 28552654 DOI: 10.1016/j.bcp.2017.05.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 05/24/2017] [Indexed: 11/21/2022]
Abstract
Cytochrome P450 2D6 (CYP2D6) participates in the metabolism of approximately 20-25% of prescribed drugs. Genetic polymorphisms influence the expression and/or activity of CYP2D6, and inter-individual differences in drug activation and elimination caused by CYP2D6 genetic variants were reported. However, little is known about the potential modulation of CYP2D6 expression by microRNAs (miRNAs). In the current study, by using in silico prediction of the stabilities of miRNA/mRNA complexes, we screened 38 miRNA candidates that may interact with the transcript of CYP2D6. An inverse correlation between the expression of miRNA hsa-miR-370-3p and the expression of CYP2D6 was observed in human liver tissue samples. Electrophoretic mobility shift assays confirmed that hsa-miR-370-3p was able to directly bind to its cognate target within the coding region of the CYP2D6 transcript. The transfection of hsa-miR-370-3p mimics into the HepG2CYP2D6 cell line, a genetically modified cell line that overexpresses exogenous CYP2D6, was able to suppress the expression of CYP2D6 significantly at both mRNA and protein levels. The transfection of hsa-miR-370-3p mimics was also able to inhibit endogenous mRNA expression and/or protein production of CYP2D6 in HepaRG cells. Furthermore, in HepaRG, HepG2, and Huh7 cells, dexamethasone-induced expression of CYP2D6 was inhibited by hsa-miR-370-3p mimics. To investigate whether the miRNA mediated suppression is caused by inhibiting protein translation or promoting mRNA degradation, an actinomycin D assay was used to measure the stability of CYP2D6 transcripts. The results indicated that hsa-miR-370-3p mimics facilitated significantly the degradation of CYP2D6 mRNA. In addition, proteomics analyses of proteins isolated from the miRNA/mRNA/protein complex suggested that a group of multifunctional proteins facilitated the interaction between hsa-miR-370-3p and CYP2D6, thereby promoting mRNA degradation.
Collapse
|
25
|
Ipe J, Swart M, Burgess KS, Skaar TC. High-Throughput Assays to Assess the Functional Impact of Genetic Variants: A Road Towards Genomic-Driven Medicine. Clin Transl Sci 2017; 10:67-77. [PMID: 28213901 PMCID: PMC5355973 DOI: 10.1111/cts.12440] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/03/2017] [Indexed: 01/08/2023] Open
Affiliation(s)
- J Ipe
- Indiana University School of MedicineDepartment of MedicineDivision of Clinical PharmacologyIndianapolisIndianaUSA
| | - M Swart
- Indiana University School of MedicineDepartment of MedicineDivision of Clinical PharmacologyIndianapolisIndianaUSA
| | - KS Burgess
- Indiana University School of MedicineDepartment of MedicineDivision of Clinical PharmacologyIndianapolisIndianaUSA
- Indiana University School of MedicineDepartment of Pharmacology and ToxicologyIndianapolisIndianaUSA
| | - TC Skaar
- Indiana University School of MedicineDepartment of MedicineDivision of Clinical PharmacologyIndianapolisIndianaUSA
| |
Collapse
|
26
|
Dorado P, González I, Naranjo MEG, de Andrés F, Peñas-Lledó EM, Calzadilla LR, LLerena A. Lessons from Cuba for Global Precision Medicine: CYP2D6 Genotype Is Not a Robust Predictor of CYP2D6 Ultrarapid Metabolism. ACTA ACUST UNITED AC 2017; 21:17-26. [DOI: 10.1089/omi.2016.0166] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Pedro Dorado
- CICAB, Clinical Research Centre, Extremadura University Hospital and Medical School, Badajoz, Spain
| | - Idilio González
- Centro de Salud Mental, Área de Salud Zafra-Llerena, Servicio Extremeño de Salud, Llerena, Spain
| | - María Eugenia G. Naranjo
- CICAB, Clinical Research Centre, Extremadura University Hospital and Medical School, Badajoz, Spain
| | - Fernando de Andrés
- CICAB, Clinical Research Centre, Extremadura University Hospital and Medical School, Badajoz, Spain
- Department of Analytical Chemistry and Food Technology, Faculty of Pharmacy, University of Castilla-La Mancha, Albacete, Spain
| | - Eva María Peñas-Lledó
- CICAB, Clinical Research Centre, Extremadura University Hospital and Medical School, Badajoz, Spain
| | | | - Adrián LLerena
- CICAB, Clinical Research Centre, Extremadura University Hospital and Medical School, Badajoz, Spain
| |
Collapse
|
27
|
Li MP, Hu YD, Hu XL, Zhang YJ, Yang YL, Jiang C, Tang J, Chen XP. MiRNAs and miRNA Polymorphisms Modify Drug Response. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2016; 13:ijerph13111096. [PMID: 27834829 PMCID: PMC5129306 DOI: 10.3390/ijerph13111096] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/17/2016] [Accepted: 10/31/2016] [Indexed: 12/13/2022]
Abstract
Differences in expression of drug response-related genes contribute to inter-individual variation in drugs’ biological effects. MicroRNAs (miRNAs) are small noncoding RNAs emerging as new players in epigenetic regulation of gene expression at post-transcriptional level. MiRNAs regulate the expression of genes involved in drug metabolism, drug transportation, drug targets and downstream signal molecules directly or indirectly. MiRNA polymorphisms, the genetic variations affecting miRNA expression and/or miRNA-mRNA interaction, provide a new insight into the understanding of inter-individual difference in drug response. Here, we provide an overview of the recent progress in miRNAs mediated regulation of biotransformation enzymes, drug transporters, and nuclear receptors. We also describe the implications of miRNA polymorphisms in cancer chemotherapy response.
Collapse
Affiliation(s)
- Mu-Peng Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Yao-Dong Hu
- Department of Cardiology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi 046000, China.
| | - Xiao-Lei Hu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Yan-Jiao Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Yong-Long Yang
- Haikou People's Hospital and Affiliated Haikou Hospital of Xiangya Medical School, Central South University, Haikou 570311, China.
| | - Chun Jiang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Jie Tang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| | - Xiao-Ping Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.
- Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha 410078, China.
| |
Collapse
|
28
|
Lauschke VM, Mkrtchian S, Ingelman-Sundberg M. The role of microRNAs in liver injury at the crossroad between hepatic cell death and regeneration. Biochem Biophys Res Commun 2016; 482:399-407. [PMID: 27789285 DOI: 10.1016/j.bbrc.2016.10.084] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/19/2016] [Accepted: 10/23/2016] [Indexed: 02/07/2023]
Abstract
The liver fulfills critical metabolic functions, such as controlling blood sugar and ammonia levels, and is of central importance for lipid metabolism and detoxification of environmental and chemical agents, including drugs. Liver injuries of different etiology can elicit a spectrum of responses. Some hepatocytes initiate molecular programs resulting in cell death, whereas others undergo cellular divisions to regenerate the damaged organ. Interestingly, recent research indicates that microRNAs serve as very rapid as well as long-term regulators in these processes. In this review, we discuss their importance in liver disease etiology and progression as well as for therapy with particular focus on metabolic and inflammatory conditions. Furthermore, we highlight the central role of microRNAs in controlling hepatocyte differentiation and plasticity, which are required for successful regeneration, but under certain conditions, such as chronic liver insults, can result in the formation of hepatocellular carcinoma.
Collapse
Affiliation(s)
- Volker M Lauschke
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institute, Stockholm, Sweden.
| | - Souren Mkrtchian
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institute, Stockholm, Sweden
| | - Magnus Ingelman-Sundberg
- Department of Physiology and Pharmacology, Section of Pharmacogenetics, Karolinska Institute, Stockholm, Sweden
| |
Collapse
|
29
|
Pan X, Ning M, Jeong H. Transcriptional Regulation of CYP2D6 Expression. Drug Metab Dispos 2016; 45:42-48. [PMID: 27698228 DOI: 10.1124/dmd.116.072249] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 09/29/2016] [Indexed: 01/04/2023] Open
Abstract
CYP2D6-mediated drug metabolism exhibits large interindividual variability. Although genetic variations in the CYP2D6 gene are well known contributors to the variability, the sources of CYP2D6 variability in individuals of the same genotype remain unexplained. Accumulating data indicate that transcriptional regulation of CYP2D6 may account for part of CYP2D6 variability. Yet, our understanding of factors governing transcriptional regulation of CYP2D6 is limited. Recently, mechanistic studies of increased CYP2D6-mediated drug metabolism in pregnancy revealed two transcription factors, small heterodimer partner (SHP) and Krüppel-like factor 9, as a transcriptional repressor and an activator, respectively, of CYP2D6. Chemicals that increase SHP expression (e.g., retinoids and activators of farnesoid X receptor) were shown to downregulate CYP2D6 expression in the humanized mice as well as in human hepatocytes. This review summarizes the series of studies on the transcriptional regulation of CYP2D6 expression, potentially providing a basis to better understand the large interindividual variability in CYP2D6-mediated drug metabolism.
Collapse
Affiliation(s)
- Xian Pan
- Department of Biopharmaceutical Sciences (X.P., M.N., H.J.), and Department of Pharmacy Practice (H.J.), College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Miaoran Ning
- Department of Biopharmaceutical Sciences (X.P., M.N., H.J.), and Department of Pharmacy Practice (H.J.), College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Hyunyoung Jeong
- Department of Biopharmaceutical Sciences (X.P., M.N., H.J.), and Department of Pharmacy Practice (H.J.), College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| |
Collapse
|
30
|
Sun Z, Zhang Z, Ji M, Yang H, Cromie M, Gu J, Wang C, Yang L, Yu Y, Gao W, Wang SL. BDE47 induces rat CYP3A1 by targeting the transcriptional regulation of miR-23b. Sci Rep 2016; 6:31958. [PMID: 27546062 PMCID: PMC4992956 DOI: 10.1038/srep31958] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 08/01/2016] [Indexed: 01/17/2023] Open
Abstract
Cytochrome P450 3A (CYP3A) is the most abundant CYP450 enzyme in the liver and is involved in the metabolism of over 50% of xenobiotics. Our previous studies revealed that 2,2′,4,4′-tetrabromodiphenyl ether (BDE47) could induce rat CYP3A1 expression, but the molecular basis remains unclear. Using in silico analysis, we identified a potential miR-23b recognition element (MRE23b) in the 3′-UTR region of CYP3A1 mRNA, which was verified by the luciferase assay. The miR-23b mimic and inhibitor significantly down- and up-regulated the expression of CYP3A1, respectively. Additionally, BDE47 significantly down-regulated the expression of miR-23b in rats and in hepatic H4IIE cells. Induction or blockage of CYP3A1 by a miR-23b inhibitor or mimic could correspondingly alter BDE47-induced expression of CYP3A1 and cytotoxicity in H4IIE cells. Furthermore, LV-anti-miR-23b significantly decreased endogenous levels of miR-23b and increased the expression and activity of CYP3A1 in rat liver. LV-anti-miR-23b also significantly increased the hydroxylated metabolites of BDE47 (3-OH-BDE47, 4-OH-BDE42, and 4′-OH-BDE49) in rat serum. In conclusion, we first found that BDE47 induced rat CYP3A1 expression by targeting the transcriptional regulation of miR-23b. This study helps provide a better understanding of CYP3A regulation and offers novel clues for the role of miRNAs in the metabolism and distribution of environmental pollutants.
Collapse
Affiliation(s)
- Zhenzhen Sun
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, P. R. China.,Key Laboratory of Pediatrics, Nanjing Children's Hospital Affiliated to Nanjing Medical University, 72 Guangzhou Road, Nanjing 210008, P. R. China
| | - Zhan Zhang
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, P. R. China.,State Key Lab of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, 140 Hanzhong Rd., Nanjing 210029, P. R. China
| | - Minghui Ji
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, P. R. China
| | - Hongbao Yang
- Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211166, P. R. China
| | - Meghan Cromie
- Department of Environmental Toxicology, The Institute of Environmental and Human Health, Texas Tech University, 1207 Gilbert Drive, Lubbock, TX 79416, USA
| | - Jun Gu
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, P. R. China
| | - Chao Wang
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, P. R. China.,State Key Lab of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, 140 Hanzhong Rd., Nanjing 210029, P. R. China
| | - Lu Yang
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, P. R. China.,State Key Lab of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, 140 Hanzhong Rd., Nanjing 210029, P. R. China
| | - Yongquan Yu
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, P. R. China.,State Key Lab of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, 140 Hanzhong Rd., Nanjing 210029, P. R. China
| | - Weimin Gao
- Department of Environmental Toxicology, The Institute of Environmental and Human Health, Texas Tech University, 1207 Gilbert Drive, Lubbock, TX 79416, USA
| | - Shou-Lin Wang
- Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing 211166, P. R. China.,State Key Lab of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, 140 Hanzhong Rd., Nanjing 210029, P. R. China
| |
Collapse
|
31
|
MicroRNAs as key mediators of hepatic detoxification. Toxicology 2016; 368-369:80-90. [PMID: 27501766 DOI: 10.1016/j.tox.2016.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 08/01/2016] [Accepted: 08/04/2016] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are a class of short noncoding RNAs that modulate gene expression at both transcriptional and post-transcriptional levels. Many studies have extensively revealed the significance of miRNAs in mediating liver development and diseases. However, their role in hepatic detoxification processes has been explored only recently. In this review, we summarized the up-to-date knowledge about miRNA dependent regulation of enzymes involved in all three phases of the drugs and xenobiotics detoxification process. We also discussed the role of miRNA in regulating some upstream nuclear receptors involving gene expression of enzymes for detoxification process in liver. The toxicological significance of miRNAs in liver diseases and future research perspectives are finally presented.
Collapse
|
32
|
Gaedigk A, Sangkuhl K, Whirl-Carrillo M, Klein T, Leeder JS. Prediction of CYP2D6 phenotype from genotype across world populations. Genet Med 2016; 19:69-76. [PMID: 27388693 PMCID: PMC5292679 DOI: 10.1038/gim.2016.80] [Citation(s) in RCA: 328] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/11/2016] [Indexed: 12/15/2022] Open
Abstract
Purpose: Owing to its highly polymorphic nature and major contribution to the metabolism and bioactivation of numerous clinically used drugs, CYP2D6 is one of the most extensively studied drug-metabolizing enzymes and pharmacogenes. CYP2D6 alleles confer no, decreased, normal, or increased activity and cause a wide range of activity among individuals and between populations. However, there is no standard approach to translate diplotypes into predicted phenotype. Methods: We exploited CYP2D6 allele-frequency data that have been compiled for Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines (>60,000 subjects, 173 reports) in order to estimate genotype-predicted phenotype status across major world populations based on activity score (AS) assignments. Results: Allele frequencies vary considerably across the major ethnic groups predicting poor metabolizer status (AS = 0) between 0.4 and 5.4% across world populations. The prevalence of genotypic intermediate (AS = 0.5) and normal (AS = 1, 1.5, or 2) metabolizers ranges between 0.4 and 11% and between 67 and 90%, respectively. Finally, 1 to 21% of subjects (AS >2) are predicted to have ultrarapid metabolizer status. Conclusions: This comprehensive study summarizes allele frequencies, diplotypes, and predicted phenotype across major populations, providing a rich data resource for clinicians and researchers. Challenges of phenotype prediction from genotype data are highlighted and discussed. Genet Med19 1, 69–76.
Collapse
Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy-Kansas City, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - Katrin Sangkuhl
- Department of Genetics, Stanford University, Stanford, California, USA
| | | | - Teri Klein
- Department of Genetics, Stanford University, Stanford, California, USA
| | - J Steven Leeder
- Division of Clinical Pharmacology, Toxicology & Therapeutic Innovation, Children's Mercy-Kansas City, Kansas City, Missouri, USA.,School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| |
Collapse
|
33
|
Moriya N, Kataoka H, Nishikawa JI, Kugawa F. Identification of Candidate Target Cyp Genes for microRNAs Whose Expression Is Altered by PCN and TCPOBOP, Representative Ligands of PXR and CAR. Biol Pharm Bull 2016; 39:1381-6. [PMID: 27237601 DOI: 10.1248/bpb.b16-00279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are involved in mRNA post-transcriptional regulation. The deregulation of miRNAs affects the expression of drug-metabolizing enzymes, drug transporters, and nuclear receptors, all of which are important in regulating drug metabolism. miRNA expression can be altered by several endogenous or exogenous agents, such as steroid hormones, carcinogens, and therapeutic drugs. However, it is unclear whether hepatic miRNA expression is regulated by nuclear receptors, such as pregnane X receptor (PXR) and constitutive androstane receptor (CAR), which are indispensable for the expression of the CYPs. Here we investigated the effects of the mouse PXR and CAR ligands pregnenolone-16α-carbonitrile (PCN) and 1,4-bis[(3,5-dichloropyridin-2-yl)oxy]benzene (TCPOBOP) on hepatic miRNA expression in mice. We found that the expression of 9 miRNAs was increased (>2-fold) and of 4 miRNAs was decreased (>50%) in response to PCN, while TCPOBOP treatment led to the up-regulation of 8 miRNAs and down-regulation of 6 miRNAs. Using several miRNA target prediction algorithms, we found that the predicted target genes included several lesser known Cyp genes (Cyp1a1, Cyp1b1, Cyp2b10, Cyp2c38, Cyp2u1, Cyp4a12a/b, Cyp4v3, Cyp17a1, Cyp39a1, and Cyp51). We analyzed the expression of these genes in response to PCN and TCPOBOP and found changes in their mRNA levels, some of which were negatively correlated with the expression of their corresponding miRNAs, suggesting that miRNAs may play a role in regulating Cyp enzyme expression. Further studies will be required to fully elucidate the miRNA regulatory mechanisms that contribute to modulating CYP expression.
Collapse
Affiliation(s)
- Nozomu Moriya
- Department of Biopharmaceutics, Hyogo University of Health Sciences
| | | | | | | |
Collapse
|
34
|
Yu AM, Tian Y, Tu MJ, Ho PY, Jilek JL. MicroRNA Pharmacoepigenetics: Posttranscriptional Regulation Mechanisms behind Variable Drug Disposition and Strategy to Develop More Effective Therapy. Drug Metab Dispos 2016; 44:308-19. [PMID: 26566807 PMCID: PMC4767381 DOI: 10.1124/dmd.115.067470] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/12/2015] [Indexed: 12/11/2022] Open
Abstract
Knowledge of drug absorption, distribution, metabolism, and excretion (ADME) or pharmacokinetics properties is essential for drug development and safe use of medicine. Varied or altered ADME may lead to a loss of efficacy or adverse drug effects. Understanding the causes of variations in drug disposition and response has proven critical for the practice of personalized or precision medicine. The rise of noncoding microRNA (miRNA) pharmacoepigenetics and pharmacoepigenomics has come with accumulating evidence supporting the role of miRNAs in the modulation of ADME gene expression and then drug disposition and response. In this article, we review the advances in miRNA pharmacoepigenetics including the mechanistic actions of miRNAs in the modulation of Phase I and II drug-metabolizing enzymes, efflux and uptake transporters, and xenobiotic receptors or transcription factors after briefly introducing the characteristics of miRNA-mediated posttranscriptional gene regulation. Consequently, miRNAs may have significant influence on drug disposition and response. Therefore, research on miRNA pharmacoepigenetics shall not only improve mechanistic understanding of variations in pharmacotherapy but also provide novel insights into developing more effective therapeutic strategies.
Collapse
Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry & Molecular Medicine, University of California Davis School of Medicine, Sacramento, California
| | - Ye Tian
- Department of Biochemistry & Molecular Medicine, University of California Davis School of Medicine, Sacramento, California
| | - Mei-Juan Tu
- Department of Biochemistry & Molecular Medicine, University of California Davis School of Medicine, Sacramento, California
| | - Pui Yan Ho
- Department of Biochemistry & Molecular Medicine, University of California Davis School of Medicine, Sacramento, California
| | - Joseph L Jilek
- Department of Biochemistry & Molecular Medicine, University of California Davis School of Medicine, Sacramento, California
| |
Collapse
|
35
|
Nakauchi A, Wong JH, Mahasirimongkol S, Yanai H, Yuliwulandari R, Mabuchi A, Liu X, Mushiroda T, Wattanapokayakit S, Miyagawa T, Keicho N, Tokunaga K. Identification of ITPA on chromosome 20 as a susceptibility gene for young-onset tuberculosis. Hum Genome Var 2016; 3:15067. [PMID: 27081565 PMCID: PMC4760120 DOI: 10.1038/hgv.2015.67] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/30/2015] [Accepted: 11/04/2015] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) is a complex disease, and both genetic and environmental factors contribute to disease progression. A previous genome-wide linkage study in Thailand determined that chromosome 20p13-12.3 may contain risk factors for young-onset disease. The present study aimed to identify novel susceptibility genes for young-onset TB within a 1-Mbp target region adjacent to the top-ranking risk marker in Chr.20p13-12.3. We performed next-generation sequencing (NGS) of the region in 13 young patients from multi-case families in Thailand. We then selected the functionally interesting single-nucleotide polymorphisms as candidates for subsequent analyses. The detected candidates rs13830 and rs1127354 in ITPA showed an association with young (<45 years old) TB patients. However, there was no association in old (⩾45 years old) patients. These findings confirm that stratifying patients based on age of TB onset can be important for identifying genetic risk factors for TB susceptibility. In addition, in silico expression quantitative trait loci analyses indicated that ITPA expression was associated with rs13830 genotype. This is the first study to use NGS resequencing to gain insight into host genetic factors associated with TB and to report a significant association for ITPA with host susceptibility in young-onset TB. The study also demonstrated the effectiveness of NGS in identifying susceptibility genes in common diseases.
Collapse
Affiliation(s)
- Ayaka Nakauchi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Jing Hao Wong
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Surakameth Mahasirimongkol
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health , Nonthaburi, Thailand
| | - Hideki Yanai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Fukujuji Hospital, Japan Anti-Tuberculosis Association (JATA), Tokyo, Japan
| | - Rika Yuliwulandari
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Genomic Medicine Research Group, YARSI Research Institute, YARSI University, Jakarta, Indonesia
| | - Akihiko Mabuchi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Xiaoxi Liu
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; RIKEN Brain Science Institute, Saitama, Japan
| | - Taisei Mushiroda
- Research Group for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences , Kanagawa, Japan
| | - Sukanya Wattanapokayakit
- Medical Genetics Center, Medical Life Sciences Institute, Department of Medical Sciences, Ministry of Public Health , Nonthaburi, Thailand
| | - Taku Miyagawa
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| | - Naoto Keicho
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association (JATA) , Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo , Tokyo, Japan
| |
Collapse
|
36
|
Shah RR, Gaedigk A, LLerena A, Eichelbaum M, Stingl J, Smith RL. CYP450 genotype and pharmacogenetic association studies: a critical appraisal. Pharmacogenomics 2016; 17:259-75. [DOI: 10.2217/pgs.15.172] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Despite strong pharmacological support, association studies using genotype-predicted phenotype as a variable have yielded conflicting or inconclusive evidence to promote personalized pharmacotherapy. Unless the patient is a genotypic poor metabolizer, imputation of patient's metabolic capacity (or metabolic phenotype), a major factor in drug exposure-related clinical response, is a complex and highly challenging task because of limited number of alleles interrogated, population-specific differences in allele frequencies, allele-specific substrate-selectivity and importantly, phenoconversion mediated by co-medications and inflammatory co-morbidities that modulate the functional activity of drug metabolizing enzymes. Furthermore, metabolic phenotype and clinical outcomes are not binary functions; there is large intragenotypic and intraindividual variability. Therefore, the ability of association studies to identify relationships between genotype and clinical outcomes can be greatly enhanced by determining phenotype measures of study participants and/or by therapeutic drug monitoring to correlate drug concentrations with genotype and actual metabolic phenotype. To facilitate improved analysis and reporting of association studies, we propose acronyms with the prefixes ‘g’ (genotype-predicted phenotype) and ‘m’ (measured metabolic phenotype) to better describe this important variable of the study subjects. Inclusion of actually measured metabolic phenotype, and when appropriate therapeutic drug monitoring, promises to reveal relationships that may not be detected by using genotype alone as the variable.
Collapse
Affiliation(s)
| | - Andrea Gaedigk
- Clinical Pharmacology, Toxicology &, Therapeutic Innovation, Children's Mercy-Kansas City, 2401 Gillham Rd, Kansas City, MO 64108, USA
- School of Medicine, University of Missouri-Kansas City, MO, USA
| | - Adrián LLerena
- CICAB Clinical Research Centre, Extremadura University Hospital & Medical School, Badajoz, Spain
| | - Michel Eichelbaum
- Dr. Margarete Fischer-Bosch – Institut für Klinische Pharmakologie, 70376 Stuttgart Auerbachstr., 112 Germany
| | - Julia Stingl
- Centre for Translational Medicine, University of Bonn Medical School, Bonn, Germany
| | - Robert L Smith
- Department of Surgery & Cancer, Faculty of Medicine, Imperial College, South Kensington Campus, London, UK
| |
Collapse
|
37
|
Burgess KS, Philips S, Benson EA, Desta Z, Gaedigk A, Gaedigk R, Segar MW, Liu Y, Skaar TC. Age-Related Changes in MicroRNA Expression and Pharmacogenes in Human Liver. Clin Pharmacol Ther 2015; 98:205-15. [PMID: 25968989 PMCID: PMC4512918 DOI: 10.1002/cpt.145] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 05/07/2015] [Accepted: 05/07/2015] [Indexed: 11/10/2022]
Abstract
Developmental changes in the liver can significantly impact drug disposition. Due to the emergence of microRNAs (miRNAs) as important regulators of drug disposition gene expression, we studied age-dependent changes in miRNA expression. Expression of 533 miRNAs was measured in 90 human liver tissues (fetal, pediatric [1-17 years], and adult [28-80 years]; n = 30 each). In all, 114 miRNAs were upregulated and 72 were downregulated from fetal to pediatric, and 2 and 3, respectively, from pediatric to adult. Among the developmentally changing miRNAs, 99 miRNA-mRNA interactions were predicted or experimentally validated (e.g., hsa-miR-125b-5p-CYP1A1; hsa-miR-34a-5p-HNF4A). In human liver samples (n = 10 each), analyzed by RNA-sequencing, significant negative correlations were observed between the expression of >1,000 miRNAs and mRNAs of drug disposition and regulatory genes. Our data suggest a mechanism for the marked changes in hepatic gene expression between the fetal and pediatric developmental periods, and support a role for these age-dependent miRNAs in regulating drug disposition.
Collapse
Affiliation(s)
- K S Burgess
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - S Philips
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - E A Benson
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Z Desta
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - A Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Hospital, Kansas City, and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - R Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Hospital, Kansas City, and School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
| | - M W Segar
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Y Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - T C Skaar
- Department of Medicine, Division of Clinical Pharmacology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| |
Collapse
|
38
|
Smutny T, Duintjer Tebbens J, Pavek P. Bioinformatic analysis of miRNAs targeting the key nuclear receptors regulating CYP3A4 gene expression: The challenge of the CYP3A4 "missing heritability" enigma. J Appl Biomed 2015. [DOI: 10.1016/j.jab.2015.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
39
|
MicroRNAs as key regulators of xenobiotic biotransformation and drug response. Arch Toxicol 2014; 89:1523-41. [PMID: 25079447 DOI: 10.1007/s00204-014-1314-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/08/2014] [Indexed: 12/11/2022]
Abstract
In the last decade, microRNAs have emerged as key factors that negatively regulate mRNA expression. It has been estimated that more than 50% of protein-coding genes are under microRNA control and each microRNA is predicted to repress several mRNA targets. In this respect, it is recognized that microRNAs play a vital role in various cellular and molecular processes and that, depending on the biological pathways in which they intervene, distorted expression of microRNAs can have serious consequences. It has recently been shown that specific microRNA species are also correlated with toxic responses induced by xenobiotics. Since the latter are primarily linked to the extent of detoxification in the liver by phase I and phase II biotransformation enzymes and influx and efflux drug transporters, the regulation of the mRNA levels of this particular set of genes through microRNAs is of great importance for the overall toxicological outcome. Consequently, in this paper, an overview of the current knowledge with respect to the complex interplay between microRNAs and the expression of biotransformation enzymes and drug transporters in the liver is provided. Nuclear receptors and transcription factors, known to be involved in the transcriptional regulation of these genes, are also discussed.
Collapse
|
40
|
Gaedigk A, Leeder JS. CYP2D6 and pharmacogenomics: where does future research need to focus? Part 1: technical aspects. Pharmacogenomics 2014; 15:407-10. [DOI: 10.2217/pgs.14.28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Andrea Gaedigk
- Division of Clinical Pharmacology & Therapeutic Innovation, Children‘s Mercy Hospital & Clinics & Department of Pediatrics, University of Missouri-Kansas City, 2401 Gillham Road, Kansas City, MO 64108, USA
| | - J Steven Leeder
- Division of Clinical Pharmacology & Therapeutic Innovation, Children‘s Mercy Hospital & Clinics & Department of Pediatrics, University of Missouri-Kansas City, 2401 Gillham Road, Kansas City, MO 64108, USA
| |
Collapse
|
41
|
microRNA-34a is associated with expression of key hepatic transcription factors and cytochromes P450. Biochem Biophys Res Commun 2014; 445:404-11. [PMID: 24530915 DOI: 10.1016/j.bbrc.2014.02.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/05/2014] [Indexed: 01/10/2023]
Abstract
microRNA (miRNA) mediated regulation of gene expression has emerged as a significant mechanism contributing to variation in gene expression. In this study, we evaluated the potential role of miRNAs in regulating expression of hepatic cytochromes P450 and their transcriptional regulatory genes. We screened the Targetscan database for high scoring miRNA binding site predictions in selected hepatic DMEs and transcription factors. Expression profiling for candidate miRNAs (n=22) and their target genes (n=20) was performed in 50 human liver samples (25 female, 25 male). Significant negative correlations were observed between expression levels of several CYPs/hepatic transcription factors and the hepatic miRNAs studied. Interestingly, hepatic miR-34a demonstrated significant negative correlation with expression levels of multiple hepatic transcription factors (including NR1I2 and HNF4α) and DMEs (CYP3A4, CYP2C19). miR-34a expression was also significantly higher in males than in females in congruence with previous observations of higher CYP3A4 expression in females versus males. A mediation analysis revealed that miR-34a was involved in significant mediation of the association observed between CYP2C19 and several hepatic transcription factors (HNF4α, NR1I2). miR-34a may thus play a key regulatory role and be a key contributory factor to the inter-individual variability observed in expression of key drug metabolizing genes in humans.
Collapse
|
42
|
Babeu JP, Boudreau F. Hepatocyte nuclear factor 4-alpha involvement in liver and intestinal inflammatory networks. World J Gastroenterol 2014; 20:22-30. [PMID: 24415854 PMCID: PMC3886012 DOI: 10.3748/wjg.v20.i1.22] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/12/2013] [Accepted: 09/29/2013] [Indexed: 02/06/2023] Open
Abstract
Hepatocyte nuclear factor 4-alpha (HNF4-α) is a nuclear receptor regulating metabolism, cell junctions, differentiation and proliferation in liver and intestinal epithelial cells. Mutations within the HNF4A gene are associated with human diseases such as maturity-onset diabetes of the young. Recently, HNF4A has also been described as a susceptibility gene for ulcerative colitis in genome-wide association studies. In addition, specific HNF4A genetic variants have been identified in pediatric cohorts of Crohn’s disease. Results obtained from knockout mice supported that HNF4-α can protect the intestinal mucosae against inflammation. However, the exact molecular links behind HNF4-α and inflammatory bowel diseases remains elusive. In this review, we will summarize the current knowledge about the role of HNF4-α and its isoforms in inflammation. Specific nature of HNF4-α P1 and P2 classes of isoforms will be summarized. HNF4-α role as a hepatocyte mediator for cytokines relays during liver inflammation will be integrated based on documented examples of the literature. Conclusions that can be made from these earlier liver studies will serve as a basis to extrapolate correlations and divergences applicable to intestinal inflammation. Finally, potential functional roles for HNF4-α isoforms in protecting the intestinal mucosae from chronic and pathological inflammation will be presented.
Collapse
|
43
|
Kato R, Shigemoto K, Akiyama H, Ieda A, Ijiri Y, Hayashi T. Human Hepatocarcinoma Functional Liver Cell-4 Cell Line Exhibits High Expression of Drug-Metabolizing Enzymes in Three-Dimensional Culture. Biol Pharm Bull 2014; 37:1782-7. [DOI: 10.1248/bpb.b14-00438] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Ryuji Kato
- Laboratory of Cardiovascular Pharmacotherapy and Toxicology, Osaka University of Pharmaceutical Sciences
| | - Kota Shigemoto
- Laboratory of Cardiovascular Pharmacotherapy and Toxicology, Osaka University of Pharmaceutical Sciences
| | - Hiromasa Akiyama
- Laboratory of Cardiovascular Pharmacotherapy and Toxicology, Osaka University of Pharmaceutical Sciences
| | - Asaka Ieda
- Laboratory of Cardiovascular Pharmacotherapy and Toxicology, Osaka University of Pharmaceutical Sciences
| | - Yoshio Ijiri
- Laboratory of Cardiovascular Pharmacotherapy and Toxicology, Osaka University of Pharmaceutical Sciences
| | - Tetsuya Hayashi
- Laboratory of Cardiovascular Pharmacotherapy and Toxicology, Osaka University of Pharmaceutical Sciences
| |
Collapse
|
44
|
De Mattia E, Dreussi E, Cecchin E, Toffoli G. Pharmacogenetics of the nuclear hormone receptors: the missing link between environment and drug effects? Pharmacogenomics 2013; 14:2035-54. [DOI: 10.2217/pgs.13.214] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
In the last decade, genetic variations in ABC/SLC transporters and phase I/II enzymes have raised pharmacogenetic markers as being predictive to the attention of researchers in the field of personalized medicine in oncology. However, it is becoming evident that the sequence variations in these genes cannot address by themselves the sharp interindividual variability in drug effects. Recently, nuclear receptors (NRs), including pregnane X receptor, constitutive androstane receptor, retinoid X receptor, farnesoid X receptor, liver X receptor, vitamin D receptor, peroxisome proliferator-activated receptors and HNF4A, have demonstrated key roles in regulating transporter and metabolic gene expression in response to xeno/endobiotics, as well as antineoplastic drugs. These findings attracted interest to the genetics of the NRs for their possible role in influencing the metabolism and pharmacological profiles of chemotherapeutics. In this review, we aim to summarize the most recent findings in the innovative field of NR pharmacogenetics and findings in how they could integrate with more traditional markers in order to improve drug treatment personalization.
Collapse
Affiliation(s)
- Elena De Mattia
- Experimental & Clinical Pharmacology Unit, Centro di Riferimento Oncologico–National Cancer Institute, Via Franco Gallini, 2, 33081, Aviano, Italy
| | - Eva Dreussi
- Experimental & Clinical Pharmacology Unit, Centro di Riferimento Oncologico–National Cancer Institute, Via Franco Gallini, 2, 33081, Aviano, Italy
| | - Erika Cecchin
- Experimental & Clinical Pharmacology Unit, Centro di Riferimento Oncologico–National Cancer Institute, Via Franco Gallini, 2, 33081, Aviano, Italy
| | - Giuseppe Toffoli
- Experimental & Clinical Pharmacology Unit, Centro di Riferimento Oncologico–National Cancer Institute, Via Franco Gallini, 2, 33081, Aviano, Italy
| |
Collapse
|
45
|
Nidadavolu LS, Niedernhofer LJ, Khan SA. Identification of microRNAs dysregulated in cellular senescence driven by endogenous genotoxic stress. Aging (Albany NY) 2013; 5:460-73. [PMID: 23852002 PMCID: PMC3824412 DOI: 10.18632/aging.100571] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
XFE progeroid syndrome, a disease of accelerated aging caused by deficiency in the DNA repair endonuclease XPF-ERCC1, is modeled by Ercc1 knockout and hypomorphic mice. Tissues and primary cells from these mice senesce prematurely, offering a unique opportunity to identify factors that regulate senescence and aging. We compared microRNA (miRNA) expression in Ercc1−/− primary mouse embryonic fibroblasts (MEFs) and wild-type (WT) MEFs in different growth conditions to identify miRNAs that drive cellular senescence. Microarray analysis showed three differentially expressed miRNAs in passage 7 (P7) Ercc1−/− MEFs grown at 20% O2 compared to Ercc1−/− MEFs grown at 3% O2. Thirty-six differentially expressed miRNAs were identified in Ercc1−/− MEFs at P7 compared to early passage (P3) in 3% O2. Eight of these miRNAs (miR-449a, miR-455*, miR-128, miR-497, miR-543, miR-450b-3p, miR-872 and miR-10b) were similarly downregulated in the liver of progeroid Ercc1−/Δ and old WT mice compared to adult WT mice, a tissue that senesces with aging. Three miRNAs (miR-449a, miR-455* and miR-128) were also downregulated in Ercc1−/Δ and WT old mice kidneys compared to young WT mice. We also discovered that the miRNA expression regulator Dicer is significantly downregulated in tissues of old mice and late passage cells compared to young controls. Collectively these results support the conclusion that the miRNAs identified may play an important role in staving off cellular senescence and their altered expression could be indicative of aging.
Collapse
Affiliation(s)
- Lolita S Nidadavolu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | | | | |
Collapse
|
46
|
Chew SC, Lim J, Singh O, Chen X, Tan EH, Lee EJD, Chowbay B. Pharmacogenetic effects of regulatory nuclear receptors (PXR, CAR, RXRα and HNF4α) on docetaxel disposition in Chinese nasopharyngeal cancer patients. Eur J Clin Pharmacol 2013; 70:155-66. [PMID: 24193570 DOI: 10.1007/s00228-013-1596-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 09/30/2013] [Indexed: 11/28/2022]
Abstract
PURPOSE This exploratory study was aimed at elucidating the pharmacogenetics of regulatory nuclear receptors (PXR, CAR, RXRα and HNF4α) and their implications on docetaxel pharmacokinetics and pharmacodynamics in local Chinese nasopharyngeal cancer patients. METHODS A total of 59 single nucleotide polymorphisms (SNPs), including tag-SNPs and functionally relevant SNPs of the genes encoding these regulatory nuclear receptors (PXR/NR1I2, CAR/NR1I3, RXRα/NR2B1 and HNF4α/NR2A1), were profiled in the patients enrolled in our study by direct sequencing (N = 50). The generalized linear model was employed to estimate the haplotypic effects on the pharmacokinetics and pharmacodynamics of the patients. RESULTS The pharmacokinetic profiles of docetaxel in these patients were characterized by marked interindividual variability, with approximately four- to sixfold variations observed in Cmax, AUC0-∞ and CL. Individual SNP association tests revealed that polymorphisms in NR2B1 and NR2A1 were significantly correlated with altered docetaxel pharmacokinetics. Subsequent haplotype association analysis identified the NR2B1 LD block 2 AG haplotype [*+4458G>A(rs3132291) and *+4988A>G(rs4842198)] to be significantly associated with altered pharmacokinetics, in which patients carrying two copies of the AG haplotype had approximately a 20 % decreased Cmax and AUC0-∞ and a 21 % increased CL compared to those who carried only one copy or no copies of the haplotype. A number of SNPs in NR1I2, NR1I3, NR2B1 and NR2A1 were also associated with a significant decrease in blood counts from baseline. No haplotype was found to exert any effects on the pharmacodynamics parameters. CONCLUSIONS The present exploratory study identified several SNPs in the genes encoding regulatory nuclear receptors which may account for the interpatient variability in docetaxel pharmacokinetics and pharmacodynamics. These findings highlight the important role of regulatory nuclear receptors on the disposition of docetaxel.
Collapse
Affiliation(s)
- Sin-Chi Chew
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, Singapore, 117597
| | | | | | | | | | | | | |
Collapse
|
47
|
Relationship between differential hepatic microRNA expression and decreased hepatic cytochrome P450 3A activity in cirrhosis. PLoS One 2013; 8:e74471. [PMID: 24058572 PMCID: PMC3772944 DOI: 10.1371/journal.pone.0074471] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 07/31/2013] [Indexed: 12/17/2022] Open
Abstract
Background and Aim Liver cirrhosis is associated with decreased hepatic cytochrome P4503A (CYP3A) activity but the pathogenesis of this phenomenon is not well elucidated. In this study, we examined if certain microRNAs (miRNA) are associated with decreased hepatic CYP3A activity in cirrhosis. Methods Hepatic CYP3A activity and miRNA microarray expression profiles were measured in cirrhotic (n=28) and normal (n=12) liver tissue. Hepatic CYP3A activity was measured via midazolam hydroxylation in human liver microsomes. Additionally, hepatic CYP3A4 protein concentration and the expression of CYP3A4 mRNA were measured. Analyses were conducted to identify miRNAs which were differentially expressed between two groups but also were significantly associated with lower hepatic CYP3A activity. Results Hepatic CYP3A activity in cirrhotic livers was 1.7-fold lower than in the normal livers (0.28 ± 0.06 vs. 0.47 ± 0.07mL* min-1*mg protein-1 (mean ± SEM), P=0.02). Six microRNAs (miR-155, miR-454, miR-582-5p, let-7f-1*, miR-181d, and miR-500) had >1.2-fold increase in cirrhotic livers and also had significant negative correlation with hepatic CYP3A activity (range of r = -0.44 to -0.52, P <0.05). Notably, miR-155, a known regulator of liver inflammation, had the highest fold increase in cirrhotic livers (2.2-fold, P=4.16E-08) and significantly correlated with hepatic CYP3A activity (r=-0.50, P=0.017). The relative expression (2-ΔΔCt mean ± SEM) of hepatic CYP3A4 mRNA was significantly higher in cirrhotic livers (21.76 ± 2.65 vs. 5.91 ± 1.29, P=2.04E-07) but their levels did not significantly correlate with hepatic CYP3A activity (r=-0.43, P=0.08). Conclusion The strong association between certain miRNAs, notably miR-155, and lower hepatic CYP3A activity suggest that altered miRNA expression may regulate hepatic CYP3A activity.
Collapse
|
48
|
Ramamoorthy A, Liu Y, Philips S, Desta Z, Lin H, Goswami C, Gaedigk A, Li L, Flockhart DA, Skaar TC. Regulation of microRNA expression by rifampin in human hepatocytes. Drug Metab Dispos 2013; 41:1763-8. [PMID: 23935064 DOI: 10.1124/dmd.113.052886] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rifampin causes drug interactions by altering hepatic drug metabolism. Because microRNAs (miRNAs) have been shown to regulate genes involved in drug metabolism, we determined the effect of rifampin on the expression of hepatic miRNAs. Primary human hepatocytes from seven subjects were treated with rifampin, and the expression of miRNA and cytochrome P450 (P450) mRNAs was measured by TaqMan assays and RNA-seq, respectively. Rifampin induced the expression of 10 clinically important and 13 additional P450 genes and repressed the expression of 9 other P450 genes (P < 0.05). Rifampin induced the expression of 33 miRNAs and repressed the expression of 35 miRNAs (P < 0.05). Several of these changes were highly negatively correlated with the rifampin-induced changes in the expression of their predicted target P450 mRNAs, supporting the possibility of miRNA-induced regulation of P450 mRNA expression. In addition, several other miRNA changes were positively correlated with the changes in P450 mRNA expression, suggesting similar regulatory mechanisms. Despite the interindividual variability in the rifampin effects on miRNA expression, principal components analysis clearly separated the rifampin-treated samples from the controls. In conclusion, rifampin treatment alters miRNA expression patterns in human hepatocytes, and some of the changes were correlated with the rifampin-induced changes in expression of the P450 mRNAs they are predicted to target.
Collapse
Affiliation(s)
- Anuradha Ramamoorthy
- Department of Medicine, Division of Clinical Pharmacology (A.R., S.P., Z.D., D.A.F., T.C.S.), and Department of Medical and Molecular Genetics (A.R., Y.L., H.L., C.G., L.L.), Indiana University School of Medicine, Indianapolis, Indiana; and Division of Clinical Pharmacology and Innovative Therapeutics, the Children's Mercy Hospital and Clinics, Kansas City, Missouri (A.G.)
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Godoy P, Hewitt NJ, Albrecht U, Andersen ME, Ansari N, Bhattacharya S, Bode JG, Bolleyn J, Borner C, Böttger J, Braeuning A, Budinsky RA, Burkhardt B, Cameron NR, Camussi G, Cho CS, Choi YJ, Craig Rowlands J, Dahmen U, Damm G, Dirsch O, Donato MT, Dong J, Dooley S, Drasdo D, Eakins R, Ferreira KS, Fonsato V, Fraczek J, Gebhardt R, Gibson A, Glanemann M, Goldring CEP, Gómez-Lechón MJ, Groothuis GMM, Gustavsson L, Guyot C, Hallifax D, Hammad S, Hayward A, Häussinger D, Hellerbrand C, Hewitt P, Hoehme S, Holzhütter HG, Houston JB, Hrach J, Ito K, Jaeschke H, Keitel V, Kelm JM, Kevin Park B, Kordes C, Kullak-Ublick GA, LeCluyse EL, Lu P, Luebke-Wheeler J, Lutz A, Maltman DJ, Matz-Soja M, McMullen P, Merfort I, Messner S, Meyer C, Mwinyi J, Naisbitt DJ, Nussler AK, Olinga P, Pampaloni F, Pi J, Pluta L, Przyborski SA, Ramachandran A, Rogiers V, Rowe C, Schelcher C, Schmich K, Schwarz M, Singh B, Stelzer EHK, Stieger B, Stöber R, Sugiyama Y, Tetta C, Thasler WE, Vanhaecke T, Vinken M, Weiss TS, Widera A, Woods CG, Xu JJ, Yarborough KM, Hengstler JG. Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME. Arch Toxicol 2013; 87:1315-530. [PMID: 23974980 PMCID: PMC3753504 DOI: 10.1007/s00204-013-1078-5] [Citation(s) in RCA: 1062] [Impact Index Per Article: 96.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 05/06/2013] [Indexed: 12/15/2022]
Abstract
This review encompasses the most important advances in liver functions and hepatotoxicity and analyzes which mechanisms can be studied in vitro. In a complex architecture of nested, zonated lobules, the liver consists of approximately 80 % hepatocytes and 20 % non-parenchymal cells, the latter being involved in a secondary phase that may dramatically aggravate the initial damage. Hepatotoxicity, as well as hepatic metabolism, is controlled by a set of nuclear receptors (including PXR, CAR, HNF-4α, FXR, LXR, SHP, VDR and PPAR) and signaling pathways. When isolating liver cells, some pathways are activated, e.g., the RAS/MEK/ERK pathway, whereas others are silenced (e.g. HNF-4α), resulting in up- and downregulation of hundreds of genes. An understanding of these changes is crucial for a correct interpretation of in vitro data. The possibilities and limitations of the most useful liver in vitro systems are summarized, including three-dimensional culture techniques, co-cultures with non-parenchymal cells, hepatospheres, precision cut liver slices and the isolated perfused liver. Also discussed is how closely hepatoma, stem cell and iPS cell-derived hepatocyte-like-cells resemble real hepatocytes. Finally, a summary is given of the state of the art of liver in vitro and mathematical modeling systems that are currently used in the pharmaceutical industry with an emphasis on drug metabolism, prediction of clearance, drug interaction, transporter studies and hepatotoxicity. One key message is that despite our enthusiasm for in vitro systems, we must never lose sight of the in vivo situation. Although hepatocytes have been isolated for decades, the hunt for relevant alternative systems has only just begun.
Collapse
Affiliation(s)
- Patricio Godoy
- Leibniz Research Centre for Working Environment and Human Factors (IFADO), 44139 Dortmund, Germany
| | | | - Ute Albrecht
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Melvin E. Andersen
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Nariman Ansari
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Sudin Bhattacharya
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Johannes Georg Bode
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Jennifer Bolleyn
- Department of Toxicology, Centre for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Christoph Borner
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Jan Böttger
- Institute of Biochemistry, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Albert Braeuning
- Department of Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Wilhelmstr. 56, 72074 Tübingen, Germany
| | - Robert A. Budinsky
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, Midland, MI USA
| | - Britta Burkhardt
- BG Trauma Center, Siegfried Weller Institut, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Neil R. Cameron
- Department of Chemistry, Durham University, Durham, DH1 3LE UK
| | - Giovanni Camussi
- Department of Medical Sciences, University of Torino, 10126 Turin, Italy
| | - Chong-Su Cho
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921 Korea
| | - Yun-Jaie Choi
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921 Korea
| | - J. Craig Rowlands
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, Midland, MI USA
| | - Uta Dahmen
- Experimental Transplantation Surgery, Department of General Visceral, and Vascular Surgery, Friedrich-Schiller-University Jena, 07745 Jena, Germany
| | - Georg Damm
- Department of General-, Visceral- and Transplantation Surgery, Charité University Medicine Berlin, 13353 Berlin, Germany
| | - Olaf Dirsch
- Institute of Pathology, Friedrich-Schiller-University Jena, 07745 Jena, Germany
| | - María Teresa Donato
- Unidad de Hepatología Experimental, IIS Hospital La Fe Avda Campanar 21, 46009 Valencia, Spain
- CIBERehd, Fondo de Investigaciones Sanitarias, Barcelona, Spain
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad de Valencia, Valencia, Spain
| | - Jian Dong
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Steven Dooley
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Dirk Drasdo
- Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, 04107 Leipzig, Germany
- INRIA (French National Institute for Research in Computer Science and Control), Domaine de Voluceau-Rocquencourt, B.P. 105, 78153 Le Chesnay Cedex, France
- UPMC University of Paris 06, CNRS UMR 7598, Laboratoire Jacques-Louis Lions, 4, pl. Jussieu, 75252 Paris cedex 05, France
| | - Rowena Eakins
- Department of Molecular and Clinical Pharmacology, Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Karine Sá Ferreira
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
- GRK 1104 From Cells to Organs, Molecular Mechanisms of Organogenesis, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Valentina Fonsato
- Department of Medical Sciences, University of Torino, 10126 Turin, Italy
| | - Joanna Fraczek
- Department of Toxicology, Centre for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Rolf Gebhardt
- Institute of Biochemistry, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Andrew Gibson
- Department of Molecular and Clinical Pharmacology, Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Matthias Glanemann
- Department of General-, Visceral- and Transplantation Surgery, Charité University Medicine Berlin, 13353 Berlin, Germany
| | - Chris E. P. Goldring
- Department of Molecular and Clinical Pharmacology, Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - María José Gómez-Lechón
- Unidad de Hepatología Experimental, IIS Hospital La Fe Avda Campanar 21, 46009 Valencia, Spain
- CIBERehd, Fondo de Investigaciones Sanitarias, Barcelona, Spain
| | - Geny M. M. Groothuis
- Department of Pharmacy, Pharmacokinetics Toxicology and Targeting, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Lena Gustavsson
- Department of Laboratory Medicine (Malmö), Center for Molecular Pathology, Lund University, Jan Waldenströms gata 59, 205 02 Malmö, Sweden
| | - Christelle Guyot
- Department of Clinical Pharmacology and Toxicology, University Hospital, 8091 Zurich, Switzerland
| | - David Hallifax
- Centre for Applied Pharmacokinetic Research (CAPKR), School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT UK
| | - Seddik Hammad
- Department of Forensic Medicine and Veterinary Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Adam Hayward
- Biological and Biomedical Sciences, Durham University, Durham, DH13LE UK
| | - Dieter Häussinger
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Claus Hellerbrand
- Department of Medicine I, University Hospital Regensburg, 93053 Regensburg, Germany
| | | | - Stefan Hoehme
- Interdisciplinary Center for Bioinformatics (IZBI), University of Leipzig, 04107 Leipzig, Germany
| | - Hermann-Georg Holzhütter
- Institut für Biochemie Abteilung Mathematische Systembiochemie, Universitätsmedizin Berlin (Charité), Charitéplatz 1, 10117 Berlin, Germany
| | - J. Brian Houston
- Centre for Applied Pharmacokinetic Research (CAPKR), School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT UK
| | | | - Kiyomi Ito
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishitokyo-shi, Tokyo, 202-8585 Japan
| | - Hartmut Jaeschke
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160 USA
| | - Verena Keitel
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | | | - B. Kevin Park
- Department of Molecular and Clinical Pharmacology, Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Claus Kordes
- Clinic for Gastroenterology, Hepatology and Infectious Diseases, Heinrich-Heine-University, Moorenstrasse 5, 40225 Düsseldorf, Germany
| | - Gerd A. Kullak-Ublick
- Department of Clinical Pharmacology and Toxicology, University Hospital, 8091 Zurich, Switzerland
| | - Edward L. LeCluyse
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Peng Lu
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | | | - Anna Lutz
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
| | - Daniel J. Maltman
- Reinnervate Limited, NETPark Incubator, Thomas Wright Way, Sedgefield, TS21 3FD UK
| | - Madlen Matz-Soja
- Institute of Biochemistry, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Patrick McMullen
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Irmgard Merfort
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
| | | | - Christoph Meyer
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jessica Mwinyi
- Department of Clinical Pharmacology and Toxicology, University Hospital, 8091 Zurich, Switzerland
| | - Dean J. Naisbitt
- Department of Molecular and Clinical Pharmacology, Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Andreas K. Nussler
- BG Trauma Center, Siegfried Weller Institut, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Peter Olinga
- Division of Pharmaceutical Technology and Biopharmacy, Department of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Francesco Pampaloni
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Jingbo Pi
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Linda Pluta
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | - Stefan A. Przyborski
- Reinnervate Limited, NETPark Incubator, Thomas Wright Way, Sedgefield, TS21 3FD UK
- Biological and Biomedical Sciences, Durham University, Durham, DH13LE UK
| | - Anup Ramachandran
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160 USA
| | - Vera Rogiers
- Department of Toxicology, Centre for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Cliff Rowe
- Department of Molecular and Clinical Pharmacology, Centre for Drug Safety Science, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Celine Schelcher
- Department of Surgery, Liver Regeneration, Core Facility, Human in Vitro Models of the Liver, Ludwig Maximilians University of Munich, Munich, Germany
| | - Kathrin Schmich
- Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Freiburg, Germany
| | - Michael Schwarz
- Department of Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Wilhelmstr. 56, 72074 Tübingen, Germany
| | - Bijay Singh
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921 Korea
| | - Ernst H. K. Stelzer
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Bruno Stieger
- Department of Clinical Pharmacology and Toxicology, University Hospital, 8091 Zurich, Switzerland
| | - Regina Stöber
- Leibniz Research Centre for Working Environment and Human Factors (IFADO), 44139 Dortmund, Germany
| | - Yuichi Sugiyama
- Sugiyama Laboratory, RIKEN Innovation Center, RIKEN, Yokohama Biopharmaceutical R&D Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Ciro Tetta
- Fresenius Medical Care, Bad Homburg, Germany
| | - Wolfgang E. Thasler
- Department of Surgery, Ludwig-Maximilians-University of Munich Hospital Grosshadern, Munich, Germany
| | - Tamara Vanhaecke
- Department of Toxicology, Centre for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Mathieu Vinken
- Department of Toxicology, Centre for Pharmaceutical Research, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, 1090 Brussels, Belgium
| | - Thomas S. Weiss
- Department of Pediatrics and Juvenile Medicine, University of Regensburg Hospital, Regensburg, Germany
| | - Agata Widera
- Leibniz Research Centre for Working Environment and Human Factors (IFADO), 44139 Dortmund, Germany
| | - Courtney G. Woods
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC USA
| | | | | | - Jan G. Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IFADO), 44139 Dortmund, Germany
| |
Collapse
|
50
|
Benson EA, Skaar TC. Incubation of whole blood at room temperature does not alter the plasma concentrations of microRNA-16 and -223. Drug Metab Dispos 2013; 41:1778-81. [PMID: 23886700 DOI: 10.1124/dmd.113.052357] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Plasma-derived microRNAs (miRNAs) are being used as biomarkers, and have been associated with human liver disease and function including fibrosis, inflammation, and drug-induced liver injury. They may also be biomarkers of the drug metabolism function of the liver. In order for plasma miRNA to function as a clinical biomarker, predictable variability is necessary during processing from whole blood to plasma. The current study evaluated the variability of miRNA in whole blood stored for 0.5, 1, 2, 4, 8, and 12 hours following the blood draw under clinical conditions (room temperature) prior to the separation of the plasma. Four healthy volunteers were recruited. Blood from all subjects was collected twice. MicroRNA-16 (miR-16) and miR-223 were evaluated because many studies have shown them to be reliably present in plasma and useful for normalization. miRNA concentrations were measured by real-time polymerase chain reaction. The coefficient of variability of the cycle threshold values for subjects for miR-223 and miR-16 ranged from ∼3.6 to 6.8% and ∼1.48 to 4.1%, respectively, over the 12-hour incubation. A second blood collection was performed to determine interday variability. The coefficient of variance from the initial blood draw compared with the final blood draw for each subject ranged from 0.42 to 7.9% for miR-16 and 1.7 to 8.3% for miR-223, indicating that these miRNAs have limited interday variability. We conclude that plasma miR-16 or miR-223 concentrations are stable in whole blood at room temperature for up to 12 hours.
Collapse
Affiliation(s)
- Eric A Benson
- Indiana University School of Medicine, Division of Clinical Pharmacology, Indianapolis, Indiana
| | | |
Collapse
|