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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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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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Ji C. Molecular Factors and Pathways of Hepatotoxicity Associated with HIV/SARS-CoV-2 Protease Inhibitors. Int J Mol Sci 2023; 24:ijms24097938. [PMID: 37175645 PMCID: PMC10178330 DOI: 10.3390/ijms24097938] [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: 03/26/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Antiviral protease inhibitors are peptidomimetic molecules that block the active catalytic center of viral proteases and, thereby, prevent the cleavage of viral polyprotein precursors into maturation. They continue to be a key class of antiviral drugs that can be used either as boosters for other classes of antivirals or as major components of current regimens in therapies for the treatment of infections with human immunodeficiency virus (HIV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, sustained/lifelong treatment with the drugs or drugs combined with other substance(s) often leads to severe hepatic side effects such as lipid abnormalities, insulin resistance, and hepatotoxicity. The underlying pathogenic mechanisms are not fully known and are under continuous investigation. This review focuses on the general as well as specific molecular mechanisms of the protease inhibitor-induced hepatotoxicity involving transporter proteins, apolipoprotein B, cytochrome P450 isozymes, insulin-receptor substrate 1, Akt/PKB signaling, lipogenic factors, UDP-glucuronosyltransferase, pregnane X receptor, hepatocyte nuclear factor 4α, reactive oxygen species, inflammatory cytokines, off-target proteases, and small GTPase Rab proteins related to ER-Golgi trafficking, organelle stress, and liver injury. Potential pharmaceutical/therapeutic solutions to antiviral drug-induced hepatic side effects are also discussed.
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Affiliation(s)
- Cheng Ji
- Research Center for Liver Disease, GI/Liver Division, Department of Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90089, USA
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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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Zhang Y, Shi J, Luo J, Liu C, Zhu L. Regulatory mechanisms and potential medical applications of HNF1A-AS1 in cancers. Am J Transl Res 2022; 14:4154-4168. [PMID: 35836869 PMCID: PMC9274608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Long noncoding RNAs (lncRNAs) are defined as a class of non-protein-coding RNAs that are longer than 200 nucleotides. Previous studies have shown that lncRNAs play a vital role in the progression of multiple diseases, which highlights their potential for medical applications. The lncRNA hepatocyte nuclear factor 1 homeobox A (HNF1A) antisense RNA 1 (HNF1A-AS1) is known to be abnormally expressed in multiple cancers. HNF1A-AS1 exerts its oncogenic roles through a variety of molecular mechanisms. Moreover, aberrant HNF1A-AS1 expression is associated with diverse clinical features in cancer patients. Therefore, HNF1A-AS1 is a promising biomarker for tumor diagnosis and prognosis and thus a potential candidate for tumor therapy. This review summarizes current studies on the role and the underlying mechanisms of HNF1A-AS1 various cancer types, including gastric cancer, liver cancer, glioma, lung cancer, colorectal cancer, breast cancer, bladder cancer, osteosarcoma, esophageal adenocarcinoma, hemangioma, oral squamous cell carcinoma, laryngeal squamous cell carcinoma, cervical cancer, as well as gastroenteropancreatic neuroendocrine neoplasms. We also describe the diagnostic, prognostic, and therapeutic value of HNF1A-AS1 for multiple cancer patients.
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Affiliation(s)
- Yang Zhang
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Jiang Shi
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Junfang Luo
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Cong Liu
- Department of Geriatric Respiratory and Sleep, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
| | - Lixu Zhu
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, China
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