1
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Tesarova T, Fiala O, Hora M, Vaclavikova R. Non-coding transcriptome profiles in clear-cell renal cell carcinoma. Nat Rev Urol 2024:10.1038/s41585-024-00926-3. [PMID: 39242964 DOI: 10.1038/s41585-024-00926-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 09/09/2024]
Abstract
Clear-cell renal cell carcinoma (ccRCC) is a common urological malignancy with an increasing incidence. The development of molecular biomarkers that can predict the response to treatment and guide personalized therapy selection would substantially improve patient outcomes. Dysregulation of non-coding RNA (ncRNA) has been shown to have a role in the pathogenesis of ccRCC. Thus, an increasing number of studies are being carried out with a focus on the identification of ncRNA biomarkers in ccRCC tissue samples and the connection of these markers with patients' prognosis, pathological stage and grade (including metastatic potential), and therapy outcome. RNA sequencing analysis led to the identification of several ncRNA biomarkers that are dysregulated in ccRCC and might have a role in ccRCC development. These ncRNAs have the potential to be prognostic and predictive biomarkers for ccRCC, with prospective applications in personalized treatment selection. Research on ncRNA biomarkers in ccRCC is advancing, but clinical implementation remains preliminary owing to challenges in validation, standardization and reproducibility. Comprehensive studies and integration of ncRNAs into clinical trials are essential to accelerate the clinical use of these biomarkers.
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Affiliation(s)
- Tereza Tesarova
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic.
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
| | - Ondrej Fiala
- Department of Oncology and Radiotherapeutics, Faculty of Medicine in Pilsen and University Hospital, Charles University, Pilsen, Czech Republic
- Laboratory of Cancer Treatment and Tissue Regeneration, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Milan Hora
- Department of Urology, Faculty of Medicine in Pilsen and University Hospital, Charles University, Pilsen, Czech Republic
| | - Radka Vaclavikova
- Toxicogenomics Unit, National Institute of Public Health, Prague, Czech Republic
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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2
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Jin J, Nguyen LTG, Wassef A, Sadek R, Schmitt TM, Guo GL, Rasmussen TP, Zhong XB. Identification and Functional Characterization of Alternative Transcripts of LncRNA HNF1A-AS1 and Their Impacts on Cell Growth, Differentiation, Liver Diseases, and in Response to Drug Induction. Noncoding RNA 2024; 10:28. [PMID: 38668386 PMCID: PMC11053763 DOI: 10.3390/ncrna10020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/29/2024] Open
Abstract
The long non-coding RNA (lncRNA) hepatocyte nuclear factor-1 alpha (HNF1A) antisense RNA 1 (HNF1A-AS1) is an important lncRNA for liver growth, development, cell differentiation, and drug metabolism. Like many lncRNAs, HNF1A-AS1 has multiple annotated alternative transcripts in the human genome. Several fundamental biological questions are still not solved: (1) How many transcripts really exist in biological samples, such as liver samples and liver cell lines? (2) What are the expression patterns of different alternative HNF1A-AS1 transcripts at different conditions, including during cell growth and development, after exposure to xenobiotics (such as drugs), and in disease conditions, such as metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-associated liver disease (ALD) cirrhosis, and obesity? (3) Does the siRNA used in previous studies knock down one or multiple transcripts? (4) Do different transcripts have the same or different functions for gene regulation? The presented data confirm the existence of several annotated HNF1A-AS1 transcripts in liver samples and cell lines, but also identify some new transcripts, which are not annotated in the Ensembl genome database. Expression patterns of the identified HNF1A-AS1 transcripts are highly correlated with the cell differentiation of matured hepatocyte-like cells from human embryonic stem cells (hESC), growth and differentiation of HepaRG cells, in response to rifampicin induction, and in various liver disease conditions. The expression levels of the HNF1A-AS1 transcripts are also highly correlated to the expression of cytochrome P450 enzymes, such as CYP3A4, during HepaRG growth, differentiation, and in response to rifampicin induction.
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Affiliation(s)
- Jing Jin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Le Tra Giang Nguyen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Andrew Wassef
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08901, USA;
- Center of Excellence for Pharmaceutical Translational Research and Education, Rutgers University, Piscataway, NJ 08901, USA
- Center of Excellence for Metabolic and Bariatric Surgery, Robert Wood Johnson Barnabas University Hospital, New Brunswick, NJ 08901, USA;
| | - Ragui Sadek
- Center of Excellence for Metabolic and Bariatric Surgery, Robert Wood Johnson Barnabas University Hospital, New Brunswick, NJ 08901, USA;
| | - Timothy M. Schmitt
- Department of General Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Grace L. Guo
- Department of Pharmacology and Toxicology, Ernst Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08901, USA;
| | - Theodore P. Rasmussen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
| | - Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (J.J.); (L.T.G.N.); (T.P.R.)
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3
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Ali ES, Yalın AE, Yalın S. Long noncoding RNAs and their possible roles in tumorigenesis and drug resistance in cancer chemotherapy. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-15. [PMID: 38575568 DOI: 10.1080/15257770.2024.2336210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 03/22/2024] [Indexed: 04/06/2024]
Abstract
Cancer is still one of the most important diseases that have a high mortality rate around the world. The management of cancer involves many procedures, which include surgery, radiotherapy, and chemotherapy. Drug resistance in cancer chemotherapy is considered one of the most important problems in clinical oncology. A good understanding of the tumorigenesis process and the mechanisms of developing chemotherapy resistance in cancer cells will help achieve significant advances in cancer treatment protocols. In recent years, there has been an increasing interest in long noncoding RNAs (lncRNAs). LncRNAs are no longer just a transcriptional noise, and many investigations proved their possible roles in regulating mandatory cellular functions. A lot of newly published studies confirmed the implication of lncRNAs in the tumor formation process and the multiple drug resistance in cancer chemotherapy. The main aim of this review is to focus on the lncRNAs' functions in the cell, their possible roles in the tumor formation process, and their roles in the development of chemotherapy resistance in different cancer cells.
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Affiliation(s)
- Ehsan Sayed Ali
- Department of Biochemistry, Faculty of Pharmacy, Mersin University, Mersin, Turkey
| | - Ali Erdinç Yalın
- Department of Biochemistry, Faculty of Pharmacy, Mersin University, Mersin, Turkey
| | - Serap Yalın
- Department of Biochemistry, Faculty of Pharmacy, Mersin University, Mersin, Turkey
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4
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Wang Y, Wang P, Wang Q, Chen S, Wang X, Zhong X, Hu W, Thorne RF, Han S, Wu M, Zhang L. The long noncoding RNA HNF1A-AS1 with dual functions in the regulation of cytochrome P450 3A4. Biochem Pharmacol 2024; 220:116016. [PMID: 38176619 DOI: 10.1016/j.bcp.2023.116016] [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: 10/25/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 01/06/2024]
Abstract
Cytochrome P450 3A4 (CYP3A4) is the most important and abundant drug-metabolizing enzyme in the human liver. Inter-individual differences in the expression and activity of CYP3A4 affect clinical and precision medicine. Increasing evidence indicates that long noncoding RNAs (lncRNAs) play crucial roles in the regulation of CYP3A4 expression. Here, we showed that lncRNA hepatocyte nuclear factor 1 alpha-antisense 1 (HNF1A-AS1) exerted dual functions in regulating CYP3A4 expression in Huh7 and HepG2 cells. Mechanistically, HNF1A-AS1 served as an RNA scaffold to interact with both protein arginine methyltransferase 1 and pregnane X receptor (PXR), thereby facilitating their protein interactions and resulting in the transactivation of PXR and transcriptional alteration of CYP3A4 via histone modifications. Furthermore, HNF1A-AS1 bound to the HNF1A protein, a liver-specific transcription factor, thereby blocking its interaction with the E3 ubiquitin ligase tripartite motif containing 25, ultimately preventing HNF1A ubiquitination and protein degradation, further regulating the expression of CYP3A4. In summary, these results reveal the novel functions of HNF1A-AS1 as the transcriptional and post-translational regulator of CYP3A4; thus, HNF1A-AS1 may serve as a new indicator for establishing or predicting individual differences in CYP3A4 expression.
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Affiliation(s)
- Yiting Wang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China; Department of Clinical Pharmacology, School of Medicine, Henan University of Chinese Medicine, 450046 Zhengzhou, China
| | - Pei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China
| | - Qi Wang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China
| | - Shitong Chen
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China
| | - Xiaofei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China
| | - Xiaobo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, 06269 Storrs, CT, USA
| | - Wanglai Hu
- Translational Research Institute, Zhengzhou University People's Hospital, Academy of Medical Science, Zhengzhou University, 450003 Zhengzhou, China
| | - Rick F Thorne
- Translational Research Institute, Zhengzhou University People's Hospital, Academy of Medical Science, Zhengzhou University, 450003 Zhengzhou, China
| | - Shengna Han
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China.
| | - Mian Wu
- Translational Research Institute, Zhengzhou University People's Hospital, Academy of Medical Science, Zhengzhou University, 450003 Zhengzhou, China.
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450001 Zhengzhou, China.
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5
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Dahal L, Graham TGW, Dailey GM, Heckert A, Tjian R, Darzacq X. Surprising Features of Nuclear Receptor Interaction Networks Revealed by Live Cell Single Molecule Imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.16.558083. [PMID: 37745337 PMCID: PMC10516011 DOI: 10.1101/2023.09.16.558083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Type 2 Nuclear Receptors (T2NRs) require heterodimerization with a common partner, the Retinoid X Receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and over-expression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged retinoid X receptor (RXR) and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.
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Affiliation(s)
- Liza Dahal
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Thomas GW Graham
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Gina M Dailey
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Alec Heckert
- Eikon Therapeutics Inc., Hayward, California, United States
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
- Howard Hughes Medical Institute, University of California, Berkeley, United States
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
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6
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Jackson KD, Achour B, Lee J, Geffert RM, Beers JL, Latham BD. Novel Approaches to Characterize Individual Drug Metabolism and Advance Precision Medicine. Drug Metab Dispos 2023; 51:1238-1253. [PMID: 37419681 PMCID: PMC10506699 DOI: 10.1124/dmd.122.001066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 05/30/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023] Open
Abstract
Interindividual variability in drug metabolism can significantly affect drug concentrations in the body and subsequent drug response. Understanding an individual's drug metabolism capacity is important for predicting drug exposure and developing precision medicine strategies. The goal of precision medicine is to individualize drug treatment for patients to maximize efficacy and minimize drug toxicity. While advances in pharmacogenomics have improved our understanding of how genetic variations in drug-metabolizing enzymes (DMEs) affect drug response, nongenetic factors are also known to influence drug metabolism phenotypes. This minireview discusses approaches beyond pharmacogenetic testing to phenotype DMEs-particularly the cytochrome P450 enzymes-in clinical settings. Several phenotyping approaches have been proposed: traditional approaches include phenotyping with exogenous probe substrates and the use of endogenous biomarkers; newer approaches include evaluating circulating noncoding RNAs and liquid biopsy-derived markers relevant to DME expression and function. The goals of this minireview are to 1) provide a high-level overview of traditional and novel approaches to phenotype individual drug metabolism capacity, 2) describe how these approaches are being applied or can be applied to pharmacokinetic studies, and 3) discuss perspectives on future opportunities to advance precision medicine in diverse populations. SIGNIFICANCE STATEMENT: This minireview provides an overview of recent advances in approaches to characterize individual drug metabolism phenotypes in clinical settings. It highlights the integration of existing pharmacokinetic biomarkers with novel approaches; also discussed are current challenges and existing knowledge gaps. The article concludes with perspectives on the future deployment of a liquid biopsy-informed physiologically based pharmacokinetic strategy for patient characterization and precision dosing.
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Affiliation(s)
- Klarissa D Jackson
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.D.J., J.L., R.M.G., J.L.B., B.D.L.); and Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island (B.A.)
| | - Brahim Achour
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.D.J., J.L., R.M.G., J.L.B., B.D.L.); and Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island (B.A.)
| | - Jonghwa Lee
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.D.J., J.L., R.M.G., J.L.B., B.D.L.); and Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island (B.A.)
| | - Raeanne M Geffert
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.D.J., J.L., R.M.G., J.L.B., B.D.L.); and Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island (B.A.)
| | - Jessica L Beers
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.D.J., J.L., R.M.G., J.L.B., B.D.L.); and Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island (B.A.)
| | - Bethany D Latham
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (K.D.J., J.L., R.M.G., J.L.B., B.D.L.); and Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island (B.A.)
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7
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Jin J, Zhong XB. Epigenetic Mechanisms Contribute to Intraindividual Variations of Drug Metabolism Mediated by Cytochrome P450 Enzymes. Drug Metab Dispos 2023; 51:672-684. [PMID: 36973001 PMCID: PMC10197210 DOI: 10.1124/dmd.122.001007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 02/24/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Significant interindividual and intraindividual variations on cytochrome P450 (CYP)-mediated drug metabolism exist in the general population globally. Genetic polymorphisms are one of the major contribution factors for interindividual variations, but epigenetic mechanisms mainly contribute to intraindividual variations, including DNA methylation, histone modifications, microRNAs, and long non-coding RNAs. The current review provides analysis of advanced knowledge in the last decade on contributions of epigenetic mechanisms to intraindividual variations on CYP-mediated drug metabolism in several situations, including (1) ontogeny, the developmental changes of CYP expression in individuals from neonates to adults; (2) increased activities of CYP enzymes induced by drug treatment; (3) increased activities of CYP enzymes in adult ages induced by drug treatment at neonate ages; and (4) decreased activities of CYP enzymes in individuals with drug-induced liver injury (DILI). Furthermore, current challenges, knowledge gaps, and future perspective of the epigenetic mechanisms in development of CYP pharmacoepigenetics are discussed. In conclusion, epigenetic mechanisms have been proven to contribute to intraindividual variations of drug metabolism mediated by CYP enzymes in age development, drug induction, and DILI conditions. The knowledge has helped understanding how intraindividual variation are generated. Future studies are needed to develop CYP-based pharmacoepigenetics to guide clinical applications for precision medicine with improved therapeutic efficacy and reduced risk of adverse drug reactions and toxicity. SIGNIFICANCE STATEMENT: Understanding epigenetic mechanisms in contribution to intraindividual variations of CYP-mediated drug metabolism may help to develop CYP-based pharmacoepigenetics for precision medicine to improve therapeutic efficacy and reduce adverse drug reactions and toxicity for drugs metabolized by CYP enzymes.
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Affiliation(s)
- Jing Jin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
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8
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Huang H, Zhang S, Wen X, Sadee W, Wang D, Yang S, Li L. Transcription Factors and ncRNAs Associated with CYP3A Expression in Human Liver and Small Intestine Assessed with Weighted Gene Co-Expression Network Analysis. Biomedicines 2022; 10:biomedicines10123061. [PMID: 36551817 PMCID: PMC9775998 DOI: 10.3390/biomedicines10123061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022] Open
Abstract
CYP3A4, CYP3A5, and CYP3A7, which are located in a multigene locus (CYP3A), play crucial roles in drug metabolism. To understand the highly variable hepatic expression of CYP3As, regulatory network analyses have focused on transcription factors (TFs). Since long non-coding RNAs (lncRNAs) likely contribute to such networks, we assessed the regulatory effects of both TFs and lncRNAs on CYP3A expression in the human liver and small intestine, main organs of CYP3A expression. Using weighted gene co-expression network analysis (WGCNA) of GTEx v8 RNA expression data and multiple stepwise regression analysis, we constructed TF-lncRNA-CYP3A co-expression networks. Multiple lncRNAs and TFs displayed robust associations with CYP3A expression that differed between liver and small intestines (LINC02499, HNF4A-AS1, AC027682.6, LOC102724153, and RP11-503C24.6), indicating that lncRNAs contribute to variance in CYP3A expression in both organs. Of these, HNF4A-AS1 had been experimentally demonstrated to affect CYP3A expression. Incorporating ncRNAs into CYP3A expression regulatory network revealed additional candidate TFs associated with CYP3A expression. These results serve as a guide for experimental studies on lncRNA-TF regulation of CYP3A expression in the liver and small intestines.
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Affiliation(s)
- Huina Huang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Siqi Zhang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiaozhen Wen
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wolfgang Sadee
- Center for Pharmacogenomics, Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Danxin Wang
- Center for Pharmacogenomics, Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA
| | - Siyao Yang
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Liang Li
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Experimental Education and Administration Center, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Correspondence:
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9
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Yang J, Bai X, Liu G, Li X. A transcriptional regulatory network of HNF4α and HNF1α involved in human diseases and drug metabolism. Drug Metab Rev 2022; 54:361-385. [PMID: 35892182 DOI: 10.1080/03602532.2022.2103146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
HNF4α and HNF1α are core transcription factors involved in the development and progression of a variety of human diseases and drug metabolism. They play critical roles in maintaining the normal growth and function of multiple organs, mainly the liver, and in the metabolism of endogenous and exogenous substances. The twelve isoforms of HNF4α may exhibit different physiological functions, and HNF4α and HNF1α show varying or even opposing effects in different types of diseases, particularly cancer. Additionally, the regulation of CYP450, phase II drug-metabolizing enzymes, and drug transporters is affected by several factors. This article aims to review the role of HNF4α and HNF1α in human diseases and drug metabolism, including their structures and physiological functions, affected diseases, regulated drug metabolism genes, influencing factors, and related mechanisms. We also propose a transcriptional regulatory network of HNF4α and HNF1α that regulates the expression of target genes related to disease and drug metabolism.
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Affiliation(s)
- Jianxin Yang
- Research Center for High Altitude Medicine, Qinghai University Medical College, Xining, China
| | - Xue Bai
- Research Center for High Altitude Medicine, Qinghai University Medical College, Xining, China
| | - Guiqin Liu
- Research Center for High Altitude Medicine, Qinghai University Medical College, Xining, China
| | - Xiangyang Li
- Research Center for High Altitude Medicine, Qinghai University Medical College, Xining, China.,State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
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10
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Klyushova LS, Perepechaeva ML, Grishanova AY. The Role of CYP3A in Health and Disease. Biomedicines 2022; 10:2686. [PMID: 36359206 PMCID: PMC9687714 DOI: 10.3390/biomedicines10112686] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/16/2022] Open
Abstract
CYP3A is an enzyme subfamily in the cytochrome P450 (CYP) superfamily and includes isoforms CYP3A4, CYP3A5, CYP3A7, and CYP3A43. CYP3A enzymes are indiscriminate toward substrates and are unique in that these enzymes metabolize both endogenous compounds and diverse xenobiotics (including drugs); almost the only common characteristic of these compounds is lipophilicity and a relatively large molecular weight. CYP3A enzymes are widely expressed in human organs and tissues, and consequences of these enzymes' activities play a major role both in normal regulation of physiological levels of endogenous compounds and in various pathological conditions. This review addresses these aspects of regulation of CYP3A enzymes under physiological conditions and their involvement in the initiation and progression of diseases.
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Affiliation(s)
| | - Maria L. Perepechaeva
- Institute of Molecular Biology and Biophysics, Federal Research Center of Fundamental and Translational Medicine, Timakova Str. 2, 630117 Novosibirsk, Russia
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11
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Maldonato BJ, Vergara AG, Yadav J, Glass SM, Paragas EM, Li D, Lazarus P, McClay JL, Ning B, Daly AK, Russell LE. Epigenetics in drug disposition & drug therapy: symposium report of the 24 th North American meeting of the International Society for the Study of Xenobiotics (ISSX). Drug Metab Rev 2022; 54:318-330. [PMID: 35876105 PMCID: PMC9970013 DOI: 10.1080/03602532.2022.2101662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/10/2022] [Indexed: 11/03/2022]
Abstract
The 24th North American International Society for the Study of Xenobiotics (ISSX) meeting, held virtually from September 13 to 17, 2021, embraced the theme of "Broadening Our Horizons." This reinforces a key mission of ISSX: striving to share innovative science related to drug discovery and development. Session speakers and the ISSX New Investigators Group, which supports the scientific and professional development of student and early career ISSX members, elected to highlight the scientific content presented during the captivating session titled, "Epigenetics in Drug Disposition & Drug Therapy." The impact genetic variation has on drug response is well established; however, this session underscored the importance of investigating the role of epigenetics in drug disposition and drug discovery. Session speakers, Drs. Ning, McClay, and Lazarus, detailed mechanisms by which epigenetic players including long non-coding RNA (lncRNAs), microRNA (miRNAs), DNA methylation, and histone acetylation can alter the expression of genes involved in pharmacokinetics, pharmacodynamics, and toxicity. Dr. Ning detailed current knowledge about miRNAs and lncRNAs and the mechanisms by which they can affect the expression of drug metabolizing enzymes (DMEs) and nuclear receptors. Dr. Lazarus discussed the potential role of miRNAs on UDP-glucuronosyltransferase (UGT) expression and activity. Dr. McClay provided evidence that aging alters methylation and acetylation of DMEs in the liver, affecting gene expression and activity. These topics, compiled by the symposium organizers, presenters, and the ISSX New Investigators Group, are herein discussed, along with exciting future perspectives for epigenetics in drug disposition and drug discovery research.
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Affiliation(s)
- Benjamin J Maldonato
- Department of Nonclinical Development and Clinical Pharmacology, Revolution Medicines, Inc, Redwood City, CA, United States
| | - Ana G Vergara
- Department of ADME & Discovery Toxicology, Merck & Co., Inc, Rahway, NJ, United States
| | - Jaydeep Yadav
- Department of ADME & Discovery Toxicology, Merck & Co., Inc, Rahway, NJ, United States
| | - Sarah M Glass
- Janssen Research & Development, San Diego, CA, United States
| | | | - Dongying Li
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, United States
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, United States
| | - Joseph L McClay
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, United States
| | - Baitang Ning
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, United States
| | - Ann K Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Laura E Russell
- Drug Metabolism and Pharmacokinetics, AbbVie Inc, North Chicago, Illinois, United States
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12
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Bao Y, Phan M, Zhu J, Ma X, Manautou JE, Zhong XB. Alterations of Cytochrome P450-Mediated Drug Metabolism during Liver Repair and Regeneration after Acetaminophen-Induced Liver Injury in Mice. Drug Metab Dispos 2022; 50:694-703. [PMID: 34348940 PMCID: PMC9132219 DOI: 10.1124/dmd.121.000459] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/28/2021] [Indexed: 11/22/2022] Open
Abstract
Acetaminophen (APAP)-induced liver injury (AILI) is the leading cause of acute liver failure in the United States, but its impact on metabolism, therapeutic efficacy, and adverse drug reactions (ADRs) of co- and/or subsequent administered drugs are not fully investigated. The current work explored this field with a focus on the AILI-mediated alterations of cytochrome P450-mediated drug metabolism. Various levels of liver injury were induced in mice by treatment with APAP at 0, 200, 400, and 600 mg/kg. Severity of liver damage was determined at 24, 48, 72, and 96 hours by plasma levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), microRNA miR122, and tissue staining. The expression and activities of CYP3A11, 1A2, 2B10, 2C29, and 2E1 were measured. Sedation efficacy and ADRs of midazolam, a CYP3A substrate, were monitored after APAP treatment. ALT, AST, and miR122 increased at 24 hours after APAP treatment with all APAP doses, whereas only groups treated with 200 and 400 mg/kg recovered back to normal levels at 72 and 96 hours. The expression and activity of the cytochromes P450 significantly decreased at 24 hours with all APAP doses but only recovered back to normal at 72 and 96 hours with 200 and 400, but not 600, mg/kg of APAP. The alterations of cytochrome P450 activities resulted in altered sedation efficacy and ADRs of midazolam, which were corrected by dose justification of midazolam. Overall, this work illustrated a low cytochrome P450 expression window after AILI, which can decrease drug metabolism and negatively impact drug efficacy and ADRs. SIGNIFICANCE STATEMENT: The data generated in the mouse model demonstrated that expression and activities of cytochrome P450 enzymes and correlated drug efficacy and ADRs are altered during the time course of liver repair and regeneration after liver is injured by treatment with APAP. Dose justifications based on predicted changes of cytochrome P450 activities can achieve desired therapeutic efficacy and avoid ADRs. The generated data provide fundamental knowledge for translational research to drug treatment for patients during liver recovery and regeneration who have experienced AILI.
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Affiliation(s)
- Yifan Bao
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (Y.B., M.P., J.E.M., X.-b.Z.), and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania (J.Z., X.M.)
| | - Mi Phan
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (Y.B., M.P., J.E.M., X.-b.Z.), and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania (J.Z., X.M.)
| | - Junjie Zhu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (Y.B., M.P., J.E.M., X.-b.Z.), and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania (J.Z., X.M.)
| | - Xiaochao Ma
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (Y.B., M.P., J.E.M., X.-b.Z.), and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania (J.Z., X.M.)
| | - José E Manautou
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (Y.B., M.P., J.E.M., X.-b.Z.), and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania (J.Z., X.M.)
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (Y.B., M.P., J.E.M., X.-b.Z.), and Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania (J.Z., X.M.)
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13
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Auwerx C, Sadler MC, Reymond A, Kutalik Z. From pharmacogenetics to pharmaco-omics: Milestones and future directions. HGG ADVANCES 2022; 3:100100. [PMID: 35373152 PMCID: PMC8971318 DOI: 10.1016/j.xhgg.2022.100100] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The origins of pharmacogenetics date back to the 1950s, when it was established that inter-individual differences in drug response are partially determined by genetic factors. Since then, pharmacogenetics has grown into its own field, motivated by the translation of identified gene-drug interactions into therapeutic applications. Despite numerous challenges ahead, our understanding of the human pharmacogenetic landscape has greatly improved thanks to the integration of tools originating from disciplines as diverse as biochemistry, molecular biology, statistics, and computer sciences. In this review, we discuss past, present, and future developments of pharmacogenetics methodology, focusing on three milestones: how early research established the genetic basis of drug responses, how technological progress made it possible to assess the full extent of pharmacological variants, and how multi-dimensional omics datasets can improve the identification, functional validation, and mechanistic understanding of the interplay between genes and drugs. We outline novel strategies to repurpose and integrate molecular and clinical data originating from biobanks to gain insights analogous to those obtained from randomized controlled trials. Emphasizing the importance of increased diversity, we envision future directions for the field that should pave the way to the clinical implementation of pharmacogenetics.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Marie C. Sadler
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University Center for Primary Care and Public Health, Lausanne, Switzerland
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14
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Stanley LA, Wolf CR. Through a glass, darkly? HepaRG and HepG2 cells as models of human phase I drug metabolism. Drug Metab Rev 2022; 54:46-62. [PMID: 35188018 DOI: 10.1080/03602532.2022.2039688] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The pharmacokinetic and safety assessment of drug candidates is becoming increasingly dependent upon in vitro models of hepatic metabolism and toxicity. Predominant among these is the HepG2 cell line, although HepaRG is becoming increasingly popular because of its perceived closer resemblance to human hepatocytes. We review the functionality of these cell lines in terms of Phase I protein expression, basal cytochrome P450-dependent activity, and utility in P450 induction studies. Our analysis indicates that HepG2 cells are severely compromised: proteomic studies show that they express few key proteins in common with hepatocytes and they lack drug-metabolizing capacity. Differentiated HepaRGs are more hepatocyte-like than HepG2s, but they also have limitations, and it is difficult to assess their utility because of the enormous variability in data reported, possibly arising from the complex differentiation protocols required to obtain hepatocyte-like cells. This is exacerbated by the use of DMSO in the induction protocol, together with proprietary supplements whose composition is a commercial secret. We conclude that, while currently available data on the utility of HepaRG generates a confusing picture, this line does have potential utility in drug metabolism studies. However, to allow studies to be compared directly a standardized, reproducible differentiation protocol is essential and the cell line's functionality in terms of known mechanisms of P450 regulation must be demonstrated. We, therefore, support the development of regulatory guidelines for the use of HepaRGs in induction studies as a first step in generating a database of consistent, reliable data.
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Affiliation(s)
- Lesley A Stanley
- Consultant in Investigative Toxicology, Linlithgow, UK.,School of Applied Sciences, Edinburgh Napier University, Edinburgh, UK
| | - C Roland Wolf
- Systems Medicine, School of Medicine, University of Dundee, Jacqui Wood Cancer Centre, Ninewells Hospital, Dundee, UK
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15
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Nakano M, Nakajima M. A-to-I RNA editing and m6A modification modulating expression of drug-metabolizing enzymes. Drug Metab Dispos 2022; 50:624-633. [DOI: 10.1124/dmd.121.000390] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 02/02/2022] [Indexed: 11/22/2022] Open
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16
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Wang X, Yu Y, Wang P, Yang K, Wang Y, Yan L, Zhong XB, Zhang L. Long Noncoding RNAs Hepatocyte Nuclear Factor 4A Antisense RNA 1 and Hepatocyte Nuclear Factor 1A Antisense RNA 1 are Involved in Ritonavir-induced Cytotoxicity in Hepatoma Cells. Drug Metab Dispos 2021; 50:704-715. [PMID: 34949673 PMCID: PMC9132102 DOI: 10.1124/dmd.121.000693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022] Open
Abstract
Ritonavir (RTV), a pharmacoenhancer used in anti-HIV regimens, can induce liver damage. RTV is primarily metabolized by cytochrome P450 3A4 (CYP3A4) in the liver. HNF4A antisense RNA 1 (HNF4A-AS1) and HNF1A antisense RNA 1 (HNF1A-AS1) are long noncoding RNAs (lncRNAs) that regulate the expression of pregnane X receptor (PXR) and CYP3A4. This study investigated the role and underlying mechanisms of HNF4A-AS1 and HNF1A-AS1 in RTV-induced hepatotoxicity. HNF4A-AS1 and HNF1A-AS1 were knocked down by small hairpin RNAs in Huh7 and HepG2 cells. Lactate dehydrogenase and reactive oxygen species assays were performed to assess RTV-induced hepatotoxicity. Chromatin immunoprecipitation qPCR was used to detect PXR enrichment and histone modifications in the CYP3A4 promoter. HNF4A-AS1 knockdown increased PXR and CYP3A4 expression and exacerbated RTV-induced cytotoxicity, whereas HNF1A-AS1 knockdown generated the opposite phenotype. Mechanistically, enrichment of PXR and trimethylation of histone 3 lysine 4 (H3K4me3) in the CYP3A4 promoter was increased, and trimethylation of histone 3 lysine 27 (H3K27me3) was decreased after HNF4A-AS1 knockdown. However, PXR and H3K4me3 enrichment decreased after HNF1A-AS1 knockdown. Alterations in RTV-induced hepatotoxicity caused by decreasing HNF4A-AS1 or HNF1A-AS1 were reversed by knockdown or overexpression of PXR. Increased susceptibility to RTV-induced liver injury caused by the PXR activator rifampicin was attenuated by HNF4A-AS1 overexpression or HNF1A-AS1 knockdown. Taken together, these results revealed that HNF4A-AS1 and HNF1A-AS1 modulated RTV-induced hepatotoxicity by regulating CYP3A4 expression, primarily by affecting the binding of PXR and histone modification status in the CYP3A4 promoter. Significance Statement HNF4A-AS1 and HNF1A-AS1, transcribed separately from neighboring antisense genes of the human transcription factor genes HNF4A and HNF1A, were identified as lncRNAs that can affect RTV-induced hepatotoxicity and susceptibility to RTV-induced hepatotoxicity caused by rifampicin exposure, mainly by affecting the expression of CY3A4 via alterations in PXR enrichment and histone modification status in the CYP3A4 promoter. This discovery provides directions for further research on the mechanisms of RTV-induced liver injury.
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Affiliation(s)
- Xiaofei Wang
- School of Basic Medical Sciences, Zhengzhou University, China
| | - Yihang Yu
- School of Basic Medical Sciences, Zhengzhou University, China
| | | | - Kun Yang
- School of Basic Medical Sciences, Zhengzhou University, China
| | - Yiting Wang
- School of Basic Medical Sciences, Zhengzhou University, China
| | - Liang Yan
- The First Affiliated Hospital of Zhengzhou University, China
| | - Xiao-Bo Zhong
- Pharmaceutical Sciences, University of Connecticut, United States
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, China
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17
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Wang P, Chen S, Wang Y, Wang X, Yan L, Yang K, Zhong XB, Han S, Zhang L. The Long Noncoding RNA Hepatocyte Nuclear Factor 4 α Antisense RNA 1 Negatively Regulates Cytochrome P450 Enzymes in Huh7 Cells via Histone Modifications. Drug Metab Dispos 2021; 49:361-368. [PMID: 33674270 DOI: 10.1124/dmd.120.000316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/02/2021] [Indexed: 01/22/2023] Open
Abstract
The maintenance of homeostasis of cytochromes P450 enzymes (P450s) under both physiologic and xenobiotic exposure conditions is ensured by the action of positive and negative regulators. In the current study, the hepatocyte nuclear factor 4α (HNF4A) antisense RNA 1 (HNF4A-AS1), an antisense long noncoding RNA of HNF4A, was found to be a negative regulator of the basal and rifampicin (RIF)-induced expression of nuclear receptors and downstream P450s. In Huh7 cells, knockdown of HNF4A-AS1 resulted in elevated expression of HNF4A, pregnane X receptor (PXR), and P450s (including CYP3A4) under both basal and RIF-induced conditions. Conversely, overexpression of HNF4A-AS1 led to decreased basal expression of constitutive androstane receptor, aryl hydrocarbon receptor, PXR, and all studied P450s. Of note, significantly diminished induction levels of PXR and CYP1A2, 2C8, 2C19, and 3A4 by RIF were also observed in HNF4A-AS1 plasmid-transfected Huh7 cells. Moreover, the negative feedback of HNF4A on HNF4A-AS1-mediated gene expression was validated using a loss-of-function experiment in this study. Strikingly, our data showed that increased enrichment levels of histone 3 lysine 4 trimethylation and HNF4A in the CYP3A4 promoter contribute to the elevated CYP3A4 expression after HNF4A-AS1 knockdown. Overall, the current study reveals that histone modifications contribute to the negative regulation of nuclear receptors and P450s by HNF4A-AS1 in basal and drug-induced levels. SIGNIFICANCE STATEMENT: Utilizing loss-of-function and gain-of-function experiments, the current study systematically investigated the negative regulation of HNF4A-AS1 on the expression of nuclear receptors (including HNF4A, constitutive androstane receptor, aryl hydrocarbon receptor, and pregnane X receptor) and P450s (including CYP1A2, 2E1, 2B6, 2D6, 2C8, 2C9, 2C19, and 3A4) in both basal and rifampicin-induced levels in Huh7 cells. Notably, this study is the first to reveal the contribution of histone modification to the HNF4A-AS1-mediated expression of CYP3A4 in Huh7 cells.
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Affiliation(s)
- Pei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China (P.W., S.C., Y.W., X.W., K.Y., S.H., L.Z.); Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (X.-b.Z.)
| | - Shitong Chen
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China (P.W., S.C., Y.W., X.W., K.Y., S.H., L.Z.); Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (X.-b.Z.)
| | - Yiting Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China (P.W., S.C., Y.W., X.W., K.Y., S.H., L.Z.); Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (X.-b.Z.)
| | - Xiaofei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China (P.W., S.C., Y.W., X.W., K.Y., S.H., L.Z.); Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (X.-b.Z.)
| | - Liang Yan
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China (P.W., S.C., Y.W., X.W., K.Y., S.H., L.Z.); Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (X.-b.Z.)
| | - Kun Yang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China (P.W., S.C., Y.W., X.W., K.Y., S.H., L.Z.); Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (X.-b.Z.)
| | - Xiao-Bo Zhong
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China (P.W., S.C., Y.W., X.W., K.Y., S.H., L.Z.); Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (X.-b.Z.)
| | - Shengna Han
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China (P.W., S.C., Y.W., X.W., K.Y., S.H., L.Z.); Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (X.-b.Z.)
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China (P.W., S.C., Y.W., X.W., K.Y., S.H., L.Z.); Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (X.-b.Z.)
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18
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Yin J, Li F, Zhou Y, Mou M, Lu Y, Chen K, Xue J, Luo Y, Fu J, He X, Gao J, Zeng S, Yu L, Zhu F. INTEDE: interactome of drug-metabolizing enzymes. Nucleic Acids Res 2021; 49:D1233-D1243. [PMID: 33045737 PMCID: PMC7779056 DOI: 10.1093/nar/gkaa755] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/19/2020] [Accepted: 09/22/2020] [Indexed: 12/15/2022] Open
Abstract
Drug-metabolizing enzymes (DMEs) are critical determinant of drug safety and efficacy, and the interactome of DMEs has attracted extensive attention. There are 3 major interaction types in an interactome: microbiome-DME interaction (MICBIO), xenobiotics-DME interaction (XEOTIC) and host protein-DME interaction (HOSPPI). The interaction data of each type are essential for drug metabolism, and the collective consideration of multiple types has implication for the future practice of precision medicine. However, no database was designed to systematically provide the data of all types of DME interactions. Here, a database of the Interactome of Drug-Metabolizing Enzymes (INTEDE) was therefore constructed to offer these interaction data. First, 1047 unique DMEs (448 host and 599 microbial) were confirmed, for the first time, using their metabolizing drugs. Second, for these newly confirmed DMEs, all types of their interactions (3359 MICBIOs between 225 microbial species and 185 DMEs; 47 778 XEOTICs between 4150 xenobiotics and 501 DMEs; 7849 HOSPPIs between 565 human proteins and 566 DMEs) were comprehensively collected and then provided, which enabled the crosstalk analysis among multiple types. Because of the huge amount of accumulated data, the INTEDE made it possible to generalize key features for revealing disease etiology and optimizing clinical treatment. INTEDE is freely accessible at: https://idrblab.org/intede/.
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Affiliation(s)
- Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Zhou
- The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yinjing Lu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Kangli Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jia Xue
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianbo Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xu He
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
| | - Lushan Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Hangzhou 310018, China
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19
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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.
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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
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20
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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.
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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
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Pande P, Zhong XB, Ku WW. Histone Methyltransferase G9a Regulates Expression of Nuclear Receptors and Cytochrome P450 Enzymes in HepaRG Cells at Basal Level and in Fatty Acid Induced Steatosis. Drug Metab Dispos 2020; 48:1321-1329. [DOI: 10.1124/dmd.120.000195] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/11/2020] [Indexed: 12/17/2022] Open
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22
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Zhou Y, Sun W, Qin Z, Guo S, Kang Y, Zeng S, Yu L. LncRNA regulation: New frontiers in epigenetic solutions to drug chemoresistance. Biochem Pharmacol 2020; 189:114228. [PMID: 32976832 DOI: 10.1016/j.bcp.2020.114228] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 02/09/2023]
Abstract
Long-noncoding RNAs (lncRNAs) have been shown to participate in sensitizing or de-sensitizing cancer cells to chemical drugs during cancer therapeutics. Notably, a plethora of lncRNAs have been confirmed to be associated with epigenetic controllers and regulate histone protein modification or DNA methylation states in the process of gene transcription. This correlation between lncRNAs and epigenetic regulators can induce the expression of core genes to trigger drug resistance. In addition, epigenetic signatures are considered to be effective and attractive biomarkers for monitoring drug therapeutic effects because they are inheritable, dynamic, and reversible. Therefore, the regulatory mechanism between lncRNAs and epigenetic machinery can serve as a novel indicator and target to overcome or reverse drug resistance in cancer therapy. In this review, we also presented a curated selection of computational tools (including online databases and network analysis) in the area of epigenetics. A classic workflow for lncRNA expression network analysis is presented, providing guidance for non-bioinformaticians to identify significant correlation between lncRNAs and other biomolecules.
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Affiliation(s)
- Ying Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Wen Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Zhiyuan Qin
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Suhang Guo
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yu Kang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lushan Yu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
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23
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Hlaváč V, Holý P, Souček P. Pharmacogenomics to Predict Tumor Therapy Response: A Focus on ATP-Binding Cassette Transporters and Cytochromes P450. J Pers Med 2020; 10:jpm10030108. [PMID: 32872162 PMCID: PMC7565825 DOI: 10.3390/jpm10030108] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 02/06/2023] Open
Abstract
Pharmacogenomics is an evolving tool of precision medicine. Recently, due to the introduction of next-generation sequencing and projects generating "Big Data", a plethora of new genetic variants in pharmacogenes have been discovered. Cancer resistance is a major complication often preventing successful anticancer treatments. Pharmacogenomics of both somatic mutations in tumor cells and germline variants may help optimize targeted treatments and improve the response to conventional oncological therapy. In addition, integrative approaches combining copy number variations and long noncoding RNA profiling with germline and somatic variations seem to be a promising approach as well. In pharmacology, expression and enzyme activity are traditionally the more studied aspects of ATP-binding cassette transporters and cytochromes P450. In this review, we briefly introduce the field of pharmacogenomics and the advancements driven by next-generation sequencing and outline the possible roles of genetic variation in the two large pharmacogene superfamilies. Although the evidence needs further substantiation, somatic and copy number variants as well as rare variants and common polymorphisms in these genes could all affect response to cancer therapy. Regulation by long noncoding RNAs has also been shown to play a role. However, in all these areas, more comprehensive studies on larger sets of patients are needed.
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Affiliation(s)
- Viktor Hlaváč
- Toxicogenomics Unit, National Institute of Public Health, 100 00 Prague, Czech Republic; (P.H.); (P.S.)
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
- Correspondence: ; Tel.: +420-267082681; Fax: +420-267311236
| | - Petr Holý
- Toxicogenomics Unit, National Institute of Public Health, 100 00 Prague, Czech Republic; (P.H.); (P.S.)
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
- Third Faculty of Medicine, Charles University, 100 00 Prague, Czech Republic
| | - Pavel Souček
- Toxicogenomics Unit, National Institute of Public Health, 100 00 Prague, Czech Republic; (P.H.); (P.S.)
- Laboratory of Pharmacogenomics, Biomedical Center, Faculty of Medicine in Pilsen, Charles University, 306 05 Pilsen, Czech Republic
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24
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Chen L, Bao Y, Jiang S, Zhong XB. The Roles of Long Noncoding RNAs HNF1α-AS1 and HNF4α-AS1 in Drug Metabolism and Human Diseases. Noncoding RNA 2020; 6:ncrna6020024. [PMID: 32599764 PMCID: PMC7345002 DOI: 10.3390/ncrna6020024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNAs with a length of over 200 nucleotides that do not have protein-coding abilities. Recent studies suggest that lncRNAs are highly involved in physiological functions and diseases. lncRNAs HNF1α-AS1 and HNF4α-AS1 are transcripts of lncRNA genes HNF1α-AS1 and HNF4α-AS1, which are antisense lncRNA genes located in the neighborhood regions of the transcription factor (TF) genes HNF1α and HNF4α, respectively. HNF1α-AS1 and HNF4α-AS1 have been reported to be involved in several important functions in human physiological activities and diseases. In the liver, HNF1α-AS1 and HNF4α-AS1 regulate the expression and function of several drug-metabolizing cytochrome P450 (P450) enzymes, which also further impact P450-mediated drug metabolism and drug toxicity. In addition, HNF1α-AS1 and HNF4α-AS1 also play important roles in the tumorigenesis, progression, invasion, and treatment outcome of several cancers. Through interacting with different molecules, including miRNAs and proteins, HNF1α-AS1 and HNF4α-AS1 can regulate their target genes in several different mechanisms including miRNA sponge, decoy, or scaffold. The purpose of the current review is to summarize the identified functions and mechanisms of HNF1α-AS1 and HNF4α-AS1 and to discuss the future directions of research of these two lncRNAs.
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Affiliation(s)
- Liming Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
| | - Yifan Bao
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
| | - Suzhen Jiang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 51006, China
| | - Xiao-bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269, USA; (L.C.); (Y.B.); (S.J.)
- Correspondence: ; Tel.: +01-860-486-3697
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25
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Adam AAA, Jongejan A, Moerland PD, van der Mark VA, Oude Elferink RP, Chamuleau RAFM, Hoekstra R. Genome-wide expression profiling reveals increased stability and mitochondrial energy metabolism of the human liver cell line HepaRG-CAR. Cytotechnology 2020; 72:377-395. [PMID: 32130581 PMCID: PMC7225227 DOI: 10.1007/s10616-020-00384-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/24/2020] [Indexed: 02/06/2023] Open
Abstract
Human liver cell line HepaRG is a well-known source of human hepatocyte-like cells which, however, displays limited biotransformation and a tendency to transform after 20 passages. The new HepaRG-CAR cell line overexpressing constitutive androstane receptor (CAR, NR1I3), a regulator of detoxification and energy metabolism outperforms the parental HepaRG cell line in various liver functions. To further characterize this cell line and assess its stability we compared HepaRG-CAR with HepaRG cells at different passages for their expression profile, ammonia and lactate metabolism, bile acid and reactive oxygen species (ROS) production. Transcriptomic profiling of HepaRG-CAR vs. HepaRG early-passage revealed downregulation of hypoxia, glycolysis and proliferation and upregulation of oxidative phosphorylation genesets. In addition CAR overexpression downregulated the mTORC1 signaling pathway, which, as mediator of proliferation and metabolic reprogramming, may play an important role in the establishment of the HepaRG-CAR phenotype. The ammonia and lactate metabolism and bile acid production of HepaRG-CAR cells was stable for 10 additional passages compared to HepaRG cells. Interestingly, bile acid production was 4.5-fold higher in HepaRG-CAR vs. HepaRG cells, whereas lactate and ROS production were 2.7- and 2.0-fold lower, respectively. Principal component analysis showed clustering of HepaRG-CAR (early- and late-passage) and HepaRG early-passage and not with HepaRG late-passage indicating that passaging exerted larger effect on the transcriptional profile of HepaRG than HepaRG-CAR cells. In conclusion, overexpression of CAR in HepaRG cells improves their bile acid production, mitochondrial energy metabolism, and stability, with the latter possibly due to reduced ROS production, resulting in an optimized source of human hepatocytes.
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Affiliation(s)
- Aziza A. A. Adam
- Tytgat Institute for Liver and Intestinal Research, AG&M, Amsterdam UMC, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
| | - Aldo Jongejan
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Perry D. Moerland
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Vincent A. van der Mark
- Tytgat Institute for Liver and Intestinal Research, AG&M, Amsterdam UMC, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
- Surgical Laboratory, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Ronald P. Oude Elferink
- Tytgat Institute for Liver and Intestinal Research, AG&M, Amsterdam UMC, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
| | - Robert A. F. M. Chamuleau
- Tytgat Institute for Liver and Intestinal Research, AG&M, Amsterdam UMC, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
| | - Ruurdtje Hoekstra
- Tytgat Institute for Liver and Intestinal Research, AG&M, Amsterdam UMC, University of Amsterdam, Meibergdreef 69-71, 1105 BK Amsterdam, The Netherlands
- Surgical Laboratory, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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26
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Li D, Wu L, Knox B, Chen S, Tolleson WH, Liu F, Yu D, Guo L, Tong W, Ning B. Long noncoding RNA LINC00844-mediated molecular network regulates expression of drug metabolizing enzymes and nuclear receptors in human liver cells. Arch Toxicol 2020; 94:1637-1653. [PMID: 32222775 DOI: 10.1007/s00204-020-02706-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/09/2020] [Indexed: 12/21/2022]
Abstract
Noncoding RNAs, such as long noncoding RNAs (lncRNAs) and microRNAs (miRNAs), regulate gene expression in many physiological and pathological processes, including drug metabolism. Drug metabolizing enzymes (DMEs) are critical components in drug-induced liver toxicity. In this study, we used human hepatic HepaRG cells treated with 5 or 10 mM acetaminophen (APAP) as a model system and identified LINC00844 as a toxicity-responsive lncRNA. We analyzed the expression profiles of LINC00844 in different human tissues. In addition, we examined the correlations between the levels of LINC00844 and those of key DMEs and nuclear receptors (NRs) for APAP metabolism in humans. Our results showed that lncRNA LINC00844 is enriched in the liver and its expression correlates positively with mRNA levels of CYP3A4, CYP2E1, SULT2A1, pregnane X receptor (PXR), and hepatocyte nuclear factor (HNF) 4α. We demonstrated that LINC00844 regulates the expression of these five genes in HepaRG cells using gain- and loss-of-function assays. Further, we discovered that LINC00844 is localized predominantly in the cytoplasm and acts as an hsa-miR-486-5p sponge, via direct binding, to protect SULT2A1 from miRNA-mediated gene silencing. Our data also demonstrated a functional interaction between LINC00844 and hsa-miR-486-5p in regulating DME and NR expression in HepaRG cells and primary human hepatocytes. We depicted a LINC00844-mediated regulatory network that involves miRNA and NRs and influences DME expression in response to APAP toxicity.
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Affiliation(s)
- Dongying Li
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), 3900 NCTR Road, HFT100, Jefferson, AR, 72079, USA
| | - Leihong Wu
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), 3900 NCTR Road, HFT100, Jefferson, AR, 72079, USA
| | - Bridgett Knox
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), 3900 NCTR Road, HFT100, Jefferson, AR, 72079, USA
| | - Si Chen
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), 3900 NCTR Road, HFT100, Jefferson, AR, 72079, USA
| | - William H Tolleson
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), 3900 NCTR Road, HFT100, Jefferson, AR, 72079, USA
| | - Fang Liu
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), 3900 NCTR Road, HFT100, Jefferson, AR, 72079, USA
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China
| | - Lei Guo
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), 3900 NCTR Road, HFT100, Jefferson, AR, 72079, USA
| | - Weida Tong
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), 3900 NCTR Road, HFT100, Jefferson, AR, 72079, USA
| | - Baitang Ning
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), 3900 NCTR Road, HFT100, Jefferson, AR, 72079, USA.
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Nekvindova J, Mrkvicova A, Zubanova V, Hyrslova Vaculova A, Anzenbacher P, Soucek P, Radova L, Slaby O, Kiss I, Vondracek J, Spicakova A, Bohovicova L, Fabian P, Kala Z, Palicka V. Hepatocellular carcinoma: Gene expression profiling and regulation of xenobiotic-metabolizing cytochromes P450. Biochem Pharmacol 2020; 177:113912. [PMID: 32173367 DOI: 10.1016/j.bcp.2020.113912] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 03/10/2020] [Indexed: 12/18/2022]
Abstract
Hepatocellular carcinoma (HCC) remains a highly prevalent and deadly disease, being among the top causes of cancer-related deaths worldwide. Despite the fact that the liver is the major site of biotransformation, studies on drug metabolizing enzymes in HCC are scarce. It is known that malignant transformation of hepatocytes leads to a significant alteration of their metabolic functions and overall deregulation of gene expression. Advanced stages of the disease are thus frequently associated with liver failure, and severe alteration of drug metabolism. However, the impact of dysregulation of metabolic enzymes on therapeutic efficacy and toxicity in HCC patients is largely unknown. Here we demonstrate a significant down-regulation in European Caucasian patients of cytochromes P450 (CYPs), the major xenobiotic-metabolizing enzymes, in HCC tumour samples as compared to their surrounding non-cancerous (reference) tissue. Moreover, we report for the first time the association of the unique CYP profiles with specific transcriptome changes, and interesting correlations with expression levels of nuclear receptors and with the histological grade of the tumours. Integrated analysis has suggested certain co-expression profiles of CYPs with lncRNAs that need to be further characterized. Patients with large tumours with down-regulated CYPs could be more vulnerable to drug toxicity; on the other hand, such tumours would eliminate drugs more slowly and should be more sensitive to pharmacotherapy (except in the case of pro-drugs where activation is necessary).
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Affiliation(s)
- Jana Nekvindova
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Czech Republic.
| | - Alena Mrkvicova
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Czech Republic; Department of Medical Biochemistry, Charles University, Faculty of Medicine in Hradec Kralove, Czech Republic.
| | - Veronika Zubanova
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Czech Republic.
| | - Alena Hyrslova Vaculova
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
| | - Pavel Anzenbacher
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.
| | - Pavel Soucek
- Center for Toxicology and Health Safety, National Institute of Public Health, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic.
| | - Lenka Radova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Biology, Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic.
| | - Igor Kiss
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute and Masaryk University, Brno, Czech Republic.
| | - Jan Vondracek
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
| | - Alena Spicakova
- Department of Pharmacology, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic.
| | - Lucia Bohovicova
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute and Masaryk University, Brno, Czech Republic.
| | - Pavel Fabian
- Department of Oncological and Experimental Pathology, Cancer Institute, Brno, Czech Republic.
| | - Zdenek Kala
- Department of Surgery, University Hospital Brno, Czech Republic.
| | - Vladimir Palicka
- Department of Clinical Biochemistry and Diagnostics, University Hospital Hradec Kralove, Czech Republic.
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Chen L, Wang P, Manautou JE, Zhong XB. Knockdown of Long Noncoding RNAs Hepatocyte Nuclear Factor 1 α Antisense RNA 1 and Hepatocyte Nuclear Factor 4 α Antisense RNA 1 Alters Susceptibility of Acetaminophen-Induced Cytotoxicity in HepaRG Cells. Mol Pharmacol 2020; 97:278-286. [PMID: 32029527 DOI: 10.1124/mol.119.118778] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/27/2020] [Indexed: 01/08/2023] Open
Abstract
Acetaminophen (APAP) is a commonly used over-the-counter drug for its analgesic and antipyretic effects. However, APAP overdose leads to severe APAP-induced liver injury (AILI) and even death as a result of the accumulation of N-acetyl-p-benzoquinone imine, the toxic metabolite of APAP generated by cytochrome P450s (P450s). Long noncoding RNAs HNF1α antisense RNA 1 (HNF1α-AS1) and HNF4α antisense RNA 1 (HNF4α-AS1) are regulatory RNAs involved in the regulation of P450 expression in both mRNA and protein levels. This study aims to determine the impact of HNF1α-AS1 and HNF4α-AS1 on AILI. Small hairpin RNAs were used to knock down HNF1α-AS1 and HNF4α-AS1 in HepaRG cells. Knockdown of these lncRNAs altered APAP-induced cytotoxicity, indicated by MTT and LDH assays. Specifically, HNF1α-AS1 knockdown decreased APAP toxicity with increased cell viability and decreased LDH release, whereas HNF4α-AS1 knockdown exacerbated APAP toxicity, with opposite effects in the MTT and LDH assays. Alterations on gene expression by knockdown of HNF1α-AS1 and HNF4α-AS1 were examined in several APAP metabolic pathways, including CYP1A2, CYP2E1, CYP3A4, UGT1A1, UGT1A9, SULT1A1, GSTP1, and GSTT1. Knockdown of HNF1α-AS1 decreased mRNA expression of CYP1A2, 2E1, and 3A4 by 0.71-fold, 0.35-fold, and 0.31-fold, respectively, whereas knockdown of HNF4α-AS1 induced mRNAs of CYP1A2, 2E1, and 3A4 by 1.3-fold, 1.95-fold, and 1.9-fold, respectively. These changes were also observed in protein levels. Knockdown of HNF1α-AS1 and HNF4α-AS1 had limited effects on the mRNA expression of UGT1A1, UGT1A9, SULT1A1, GSTP1, and GSTT1. Altogether, our study suggests that HNF1α-AS1 and HNF4α-AS1 affected AILI mainly through alterations of P450-mediated APAP biotransformation in HepaRG cells, indicating an important role of the lncRNAs in AILI. SIGNIFICANCE STATEMENT: The current research identified two lncRNAs, hepatocyte nuclear factor 1α antisense RNA 1 and hepatocyte nuclear factor 4α antisense RNA 1, which were able to affect susceptibility of acetaminophen (APAP)-induced liver injury in HepaRG cells, possibly through regulating the expression of APAP-metabolizing cytochrome P450 enzymes. This discovery added new factors, lncRNAs, which can be used to predict cytochrome P450-mediated drug metabolism and drug-induced toxicity.
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Affiliation(s)
- Liming Chen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., P.W., J.E.M., X.-b.Z.) and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (P.W.)
| | - Pei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., P.W., J.E.M., X.-b.Z.) and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (P.W.)
| | - José E Manautou
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., P.W., J.E.M., X.-b.Z.) and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (P.W.)
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., P.W., J.E.M., X.-b.Z.) and Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, Henan, China (P.W.)
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29
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Wang Y, Fang Z, Hong M, Yang D, Xie W. Long-noncoding RNAs (lncRNAs) in drug metabolism and disposition, implications in cancer chemo-resistance. Acta Pharm Sin B 2020; 10:105-112. [PMID: 31993309 PMCID: PMC6976993 DOI: 10.1016/j.apsb.2019.09.011] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 01/07/2023] Open
Abstract
Drug metabolism is an orchestrated process in which drugs are metabolized and disposed through a series of specialized enzymes and transporters. Alterations in the expression and/or activity of these enzymes and transporters can affect the bioavailability (pharmacokinetics, or PK) and therapeutic efficacy (pharmacodynamics, or PD) of drugs. Recent studies have suggested that the long non-coding RNAs (lncRNAs) are highly relevant to drug metabolism and drug resistance, including chemo-resistance in cancers, through the regulation of drug metabolism and disposition related genes. This review summarizes the regulation of enzymes, transporters, or regulatory proteins involved in drug metabolism by lncRNAs, with a particular emphasis on drug metabolism and chemo-resistance in cancer patients. The perspective strategies to integrate multi-dimensional pharmacogenomics data for future in-depth analysis of drug metabolism related lncRNAs are also proposed. Understanding the role of lncRNAs in drug metabolism will not only facilitate the identification of novel regulatory mechanisms, but also enable the discovery of lncRNA-based biomarkers and drug targets to personalize and improve the therapeutic outcome of patients, including cancer patients.
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Affiliation(s)
- Yue Wang
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Zihui Fang
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Mei Hong
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Da Yang
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
- University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Corresponding authors.
| | - Wen Xie
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Corresponding authors.
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Li Y, Meng Q, Yang M, Liu D, Hou X, Tang L, Wang X, Lyu Y, Chen X, Liu K, Yu AM, Zuo Z, Bi H. Current trends in drug metabolism and pharmacokinetics. Acta Pharm Sin B 2019; 9:1113-1144. [PMID: 31867160 PMCID: PMC6900561 DOI: 10.1016/j.apsb.2019.10.001] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 08/23/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022] Open
Abstract
Pharmacokinetics (PK) is the study of the absorption, distribution, metabolism, and excretion (ADME) processes of a drug. Understanding PK properties is essential for drug development and precision medication. In this review we provided an overview of recent research on PK with focus on the following aspects: (1) an update on drug-metabolizing enzymes and transporters in the determination of PK, as well as advances in xenobiotic receptors and noncoding RNAs (ncRNAs) in the modulation of PK, providing new understanding of the transcriptional and posttranscriptional regulatory mechanisms that result in inter-individual variations in pharmacotherapy; (2) current status and trends in assessing drug-drug interactions, especially interactions between drugs and herbs, between drugs and therapeutic biologics, and microbiota-mediated interactions; (3) advances in understanding the effects of diseases on PK, particularly changes in metabolizing enzymes and transporters with disease progression; (4) trends in mathematical modeling including physiologically-based PK modeling and novel animal models such as CRISPR/Cas9-based animal models for DMPK studies; (5) emerging non-classical xenobiotic metabolic pathways and the involvement of novel metabolic enzymes, especially non-P450s. Existing challenges and perspectives on future directions are discussed, and may stimulate the development of new research models, technologies, and strategies towards the development of better drugs and improved clinical practice.
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Affiliation(s)
- Yuhua Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510275, China
- The First Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Qiang Meng
- College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Mengbi Yang
- School of Pharmacy, the Chinese University of Hong Kong, Hong Kong, China
| | - Dongyang Liu
- Drug Clinical Trial Center, Peking University Third Hospital, Beijing 100191, China
| | - Xiangyu Hou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lan Tang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xin Wang
- School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yuanfeng Lyu
- School of Pharmacy, the Chinese University of Hong Kong, Hong Kong, China
| | - Xiaoyan Chen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kexin Liu
- College of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Ai-Ming Yu
- UC Davis School of Medicine, Sacramento, CA 95817, USA
| | - Zhong Zuo
- School of Pharmacy, the Chinese University of Hong Kong, Hong Kong, China
| | - Huichang Bi
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510275, China
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Ning B, Yu D, Yu AM. Advances and challenges in studying noncoding RNA regulation of drug metabolism and development of RNA therapeutics. Biochem Pharmacol 2019; 169:113638. [PMID: 31518552 PMCID: PMC6802278 DOI: 10.1016/j.bcp.2019.113638] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/06/2019] [Indexed: 01/13/2023]
Abstract
Accumulating evidence has demonstrated that genome-derived noncoding RNAs (ncRNAs) play important roles in modulating inter-individual variations observed in drug metabolism and disposition by controlling the expression of genes coding drug metabolizing enzymes and transporters (DMETs) and relevant nuclear receptors (NRs). With the understanding of novel ncRNA regulatory mechanisms and significance in the control of disease initiation and progression, RNA-based therapies are under active investigation that may expand the druggable targets from conventional proteins to RNAs and the genome for the treatment of human diseases. Herein we provide an overview of research strategies, approaches and their limitations in biochemical and pharmacological studies pertaining to ncRNA functions in the regulation of drug and nutrient metabolism and disposition, and discussion on the promise and challenges in developing RNA therapeutics.
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Affiliation(s)
- Baitang Ning
- National Center for Toxicological Research (NCTR), US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao, China
| | - Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, CA 95817, USA.
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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
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Dempsey JL, Cui JY. Regulation of Hepatic Long Noncoding RNAs by Pregnane X Receptor and Constitutive Androstane Receptor Agonists in Mouse Liver. Drug Metab Dispos 2019; 47:329-339. [PMID: 30593543 PMCID: PMC6382996 DOI: 10.1124/dmd.118.085142] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/21/2018] [Indexed: 12/28/2022] Open
Abstract
Altered expression of long noncoding RNAs (lncRNAs) by environmental chemicals modulates the expression of xenobiotic biotransformation-related genes and may serve as therapeutic targets and novel biomarkers of exposure. The pregnane X receptor (PXR/NR1I2) is a critical xenobiotic-sensing nuclear receptor that regulates the expression of many drug-processing genes, and it has similar target-gene profiles and DNA-binding motifs with another xenobiotic-sensing nuclear receptor, namely, constitutive andronstrane receptor (CAR/Nr1i3). To test our hypothesis that lncRNAs are regulated by PXR in concert with protein-coding genes (PCGs) and to compare the PXR-targeted lncRNAs with CAR-targeted lncRNAs, RNA-Seq was performed from livers of adult male C57BL/6 mice treated with corn oil, the PXR agonist PCN, or the CAR agonist 1, 4-bis[2-(3,5-dichloropyridyloxy)]benzene (TCPOBOP). Among 125,680 known lncRNAs, 3843 were expressed in liver, and 193 were differentially regulated by PXR (among which 40% were also regulated by CAR). Most PXR- or CAR-regulated lncRNAs were mapped to the introns and 3'-untranslated regions (UTRs) of PCGs, as well as intergenic regions. Combining the RNA-Seq data with a published PXR chromatin immunoprecipitation coupled with high-throughput sequencing; cytochrome P450 (P450; ChIP-Seq) data set, we identified 774 expressed lncRNAs with direct PXR-DNA binding sites, and 26.8% of differentially expressed lncRNAs had changes in PXR-DNA binding after PCN exposure. De novo motif analysis identified colocalization of PXR with liver receptor homolog (LRH-1), which regulates bile acid synthesis after PCN exposure. There was limited overlap of PXR binding with an epigenetic mark for transcriptional activation (histone-H3K4-di-methylation, H3K4me2) but no overlap with epigenetic marks for transcriptional silencing [H3 lysine 27 tri-methylation (H3K27me3) and DNA methylation]. Among differentially expressed lncRNAs, 264 were in proximity of PCGs, and the lncRNA-PCG pairs displayed a high coregulatory pattern by PXR and CAR activation. This study was among the first to demonstrate that lncRNAs are regulated by PXR and CAR activation and that they may be important regulators of PCGs involved in xenobiotic metabolism.
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Affiliation(s)
- Joseph L Dempsey
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
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Wu J, Yao N, Hu Q, Liu M, Zhang H, Xiong Y, Hu J, Xia C. Effect of panaxytriol on cytochrome P450 3A4 via the pregnane X receptor regulatory pathway. Phytother Res 2019; 33:968-975. [PMID: 30653754 DOI: 10.1002/ptr.6290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 11/08/2022]
Abstract
Panaxytriol (PXT) is one of the major effective components of red ginseng and Shenmai injection. The present study aimed to explore the effect of PXT on cytochrome P450 3A4 (CYP3A4) based on the pregnane X receptor (PXR)-CYP3A4 regulatory pathway in HepG2 cells and hPXR-overexpressing HepG2 cells treated with PXT for different time periods using quantitative polymerase chain reaction, Western blot, and dual-luciferase reporter gene assays. PXT could upregulate the levels of PXR and CYP3A4 mRNA in HepG2 cells treated with PXT for 1 hr, with no impact on the expression of their protein levels. The expression levels of both PXR and CYP3A4 mRNA and protein in HepG2 cells treated with PXT for 24 hr increased in a concentration-dependent manner. The effects of PXT on the expression of PXR and CYP3A4 mRNA and protein in hPXR-overexpressing HepG2 cells were similar to those in HepG2 cells. Moreover, the influence trend of PXT on CYP3A4 was consistent with that of PXR in HepG2 cells and hPXR-overexpressing HepG2 cells. The dual-luciferase reporter gene assay in HepG2 cells further demonstrated that PXT treatment for specific time periods could significantly induce the expression of CYP3A4 mediated by the PXR regulatory pathway.
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Affiliation(s)
- Jie Wu
- Clinical Pharmacology Institute, Nanchang University, Nanchang, China.,School of Pharmaceutical Engineering, Chongqing Chemical Industry Vocational College, Chongqing, China
| | - Na Yao
- Clinical Pharmacology Institute, Nanchang University, Nanchang, China
| | - Qingqing Hu
- Clinical Pharmacology Institute, Nanchang University, Nanchang, China
| | - Mingyi Liu
- Clinical Pharmacology Institute, Nanchang University, Nanchang, China
| | - Hong Zhang
- Clinical Pharmacology Institute, Nanchang University, Nanchang, China
| | - Yuqing Xiong
- Clinical Pharmacology Institute, Nanchang University, Nanchang, China
| | - Jinfang Hu
- Drug Clinical Research Center, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chunhua Xia
- Clinical Pharmacology Institute, Nanchang University, Nanchang, China
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Wang Y, Yan L, Liu J, Chen S, Liu G, Nie Y, Wang P, Yang W, Chen L, Zhong X, Han S, Zhang L. The HNF1 α-Regulated LncRNA HNF1 α-AS1 Is Involved in the Regulation of Cytochrome P450 Expression in Human Liver Tissues and Huh7 Cells. J Pharmacol Exp Ther 2019; 368:353-362. [PMID: 30602592 DOI: 10.1124/jpet.118.252940] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/04/2018] [Indexed: 12/20/2022] Open
Abstract
Expression of cytochrome P450s (P450s) is regulated by epigenetic factors, such as DNA methylation, histone modifications, and noncoding RNAs through different mechanisms. Among these factors, long noncoding RNAs (lncRNAs) have been shown to play important roles in the regulation of gene expression; however, little is known about the effects of lncRNAs on the regulation of P450 expression. The aim of this study was to explore the role of lncRNAs in the regulation of P450 expression by using human liver tissues and hepatoma Huh7 cells. Through lncRNA microarray analysis and quantitative polymerase chain reaction in human liver tissues, we found that the lncRNA hepatocyte nuclear factor 1 alpha antisense 1 (HNF1α-AS1), an antisense RNA of HNF1α, is positively correlated with the mRNA expression of CYP2C8, 2C9, 2C19, 2D6, 2E1, and 3A4 as well as pregnane X receptor (PXR) and constitutive androstane receptor (CAR). Gain- and loss-of-function studies in Huh7 cells transfected with small interfering RNAs or overexpression plasmids showed that HNF1α not only regulated the expression of HNF1α-AS1 and P450s, but also regulated the expression of CAR, PXR, and aryl hydrocarbon receptor (AhR). In turn, HNF1α-AS1 regulated the expression of PXR and most P450s without affecting the expression of HNF1α, AhR, and CAR. Moreover, the rifampicin-induced expression of P450s was also affected by HNF1α and HNF1α-AS1. In summary, the results of this study suggested that HNF1α-AS1 is involved in the HNF1α-mediated regulation of P450s in the liver at both basal and drug-induced levels.
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Affiliation(s)
- Yiting Wang
- Department of Pharmacology (Y.W., L.Y., J.L., S.C., G.L., Y.N., P.W., S.H., L.Z.) and Forensic Medicine (W.Y.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., X.Z.)
| | - Liang Yan
- Department of Pharmacology (Y.W., L.Y., J.L., S.C., G.L., Y.N., P.W., S.H., L.Z.) and Forensic Medicine (W.Y.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., X.Z.)
| | - Jingyang Liu
- Department of Pharmacology (Y.W., L.Y., J.L., S.C., G.L., Y.N., P.W., S.H., L.Z.) and Forensic Medicine (W.Y.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., X.Z.)
| | - Shitong Chen
- Department of Pharmacology (Y.W., L.Y., J.L., S.C., G.L., Y.N., P.W., S.H., L.Z.) and Forensic Medicine (W.Y.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., X.Z.)
| | - Guangming Liu
- Department of Pharmacology (Y.W., L.Y., J.L., S.C., G.L., Y.N., P.W., S.H., L.Z.) and Forensic Medicine (W.Y.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., X.Z.)
| | - Yali Nie
- Department of Pharmacology (Y.W., L.Y., J.L., S.C., G.L., Y.N., P.W., S.H., L.Z.) and Forensic Medicine (W.Y.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., X.Z.)
| | - Pei Wang
- Department of Pharmacology (Y.W., L.Y., J.L., S.C., G.L., Y.N., P.W., S.H., L.Z.) and Forensic Medicine (W.Y.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., X.Z.)
| | - Weihong Yang
- Department of Pharmacology (Y.W., L.Y., J.L., S.C., G.L., Y.N., P.W., S.H., L.Z.) and Forensic Medicine (W.Y.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., X.Z.)
| | - Liming Chen
- Department of Pharmacology (Y.W., L.Y., J.L., S.C., G.L., Y.N., P.W., S.H., L.Z.) and Forensic Medicine (W.Y.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., X.Z.)
| | - Xiaobo Zhong
- Department of Pharmacology (Y.W., L.Y., J.L., S.C., G.L., Y.N., P.W., S.H., L.Z.) and Forensic Medicine (W.Y.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., X.Z.)
| | - Shengna Han
- Department of Pharmacology (Y.W., L.Y., J.L., S.C., G.L., Y.N., P.W., S.H., L.Z.) and Forensic Medicine (W.Y.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., X.Z.)
| | - Lirong Zhang
- Department of Pharmacology (Y.W., L.Y., J.L., S.C., G.L., Y.N., P.W., S.H., L.Z.) and Forensic Medicine (W.Y.), School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China (L.Y.); and Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut (L.C., X.Z.)
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Guo S, Lu H. Novel mechanisms of regulation of the expression and transcriptional activity of hepatocyte nuclear factor 4α. J Cell Biochem 2019; 120:519-532. [PMID: 30191603 PMCID: PMC7745837 DOI: 10.1002/jcb.27407] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/10/2018] [Indexed: 12/13/2022]
Abstract
Hepatocyte nuclear factor 4α (HNF4α) is a master regulator of development and function of digestive tissues. The HNF4A gene uses two separate promoters P1 and P2, with P1 products predominant in adult liver, whereas P2 products prevalent in fetal liver, pancreas, and liver/colon cancer. To date, the mechanisms for the regulation of HNF4A and the dynamic switch of P1-HNF4α and P2-HNF4α during ontogenesis and carcinogenesis are still obscure. Our study validated the previously reported self-stimulation of P1-HNF4α but invalidated the reported synergism between HNF4α and HNF1α. HNF4A-AS1, a long noncoding RNA, is localized between the P2 and P1 promoters of HNF4A. We identified critical roles of P1-HNF4α in regulating the expression of HNF4A-AS1 and its mouse ortholog Hnf4a-os. Paired box 6 (PAX6), a master regulator of pancreas development overexpressed in colon cancer, cooperated with HNF1α to induce P2-HNF4α but antagonized HNF4α in HNF4A-AS1 expression. Thus, PAX6 may be important in determining ontogenic and carcinogenic changes of P2-HNF4α and HNF4A-AS1 in the pancreas and intestine. We also interrogated transactivation activities on multiple gene targets by multiple known and novel HNF4α mutants identified in patients with maturity onset diabetes of the young 1 (MODY1) and liver cancer. Particularly, HNF4α-D78A and HNF4α-G79S, two mutants found in liver cancer with mutations in DNA-binding domain, displayed highly gene-specific transactivation activities. Interestingly, HNF4α-Q277X, a MODY1 truncation mutant, antagonized the transactivation activities of HNF1α and farnesoid X receptor, key regulators of insulin secretion. Taken together, our study provides novel mechanistic insights regarding the transcriptional regulation and transactivation activity of HNF4α in digestive tissues.
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Affiliation(s)
- Shangdong Guo
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY 13210, U.S
| | - Hong Lu
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, NY 13210, U.S
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Li D, Tolleson WH, Yu D, Chen S, Guo L, Xiao W, Tong W, Ning B. Regulation of cytochrome P450 expression by microRNAs and long noncoding RNAs: Epigenetic mechanisms in environmental toxicology and carcinogenesis. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2019; 37:180-214. [PMID: 31305208 PMCID: PMC6737535 DOI: 10.1080/10590501.2019.1639481] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Environmental exposures to hazardous chemicals are associated with a variety of human diseases and disorders, including cancers. Phase I metabolic activation and detoxification reactions catalyzed by cytochrome P450 enzymes (CYPs) affect the toxicities of many xenobiotic compounds. Proper regulation of CYP expression influences their biological effects. Noncoding RNAs (ncRNAs) are involved in regulating CYP expression, and ncRNA expression is regulated in response to environmental chemicals. The mechanistic interactions between ncRNAs and CYPs associated with the toxicity and carcinogenicity of environmental chemicals are described in this review, focusing on microRNA-dependent CYP regulation. The role of long noncoding RNAs in regulating CYP expression is also presented and new avenues of research concerning this regulatory mechanism are described.
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Affiliation(s)
- Dongying Li
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - William H Tolleson
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Dianke Yu
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Si Chen
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Lei Guo
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Wenming Xiao
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Weida Tong
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
| | - Baitang Ning
- a National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA) , Jefferson , AR , USA
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