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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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Rampersaud A, Lodato NJ, Shin A, Waxman DJ. Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR. Toxicol Sci 2019; 171:315-338. [PMID: 31236583 PMCID: PMC6760311 DOI: 10.1093/toxsci/kfz148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
CAR (Nr1i3), a liver nuclear receptor and xenobiotic sensor, induces drug, steroid and lipid metabolism and dysregulates genes linked to hepatocellular carcinogenesis, but its impact on the liver epigenome is poorly understood. TCPOBOP, a halogenated xenochemical and highly specific CAR agonist ligand, induces localized chromatin opening or closing at several thousand mouse liver genomic regions, discovered as differential DNase-hypersensitive sites (ΔDHS). Active enhancer and promoter histone marks induced by TCPOBOP were enriched at opening DHS and TCPOBOP-inducible genes. Enrichment of CAR binding and CAR motifs was seen at opening DHS and their inducible drug/lipid metabolism gene targets, and at many constitutively open DHS located nearby. TCPOBOP-responsive cell cycle and DNA replication genes co-dependent on MET/EGFR signaling for induction were also enriched for CAR binding. A subset of opening DHS and many closing DHS mapping to TCPOBOP-responsive target genes did not bind CAR, indicating an indirect mechanism for their changes in chromatin accessibility. TCPOBOP-responsive DHS were also enriched for induced binding of RXRA, CEBPA and CEBPB, and for motifs for liver-enriched factors that may contribute to liver-specific transcriptional responses to TCPOBOP exposure. These studies elucidate the enhancer landscape of TCPOBOP-exposed liver and the widespread epigenetic changes that are induced by both direct and indirect mechanisms linked to CAR activation. The global maps of thousands of environmental chemical-induced epigenetic changes described here constitute a rich resource for further research on xenochemical effects on liver chromatin states and the epigenome.
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Affiliation(s)
- Andy Rampersaud
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA USA
| | - Nicholas J Lodato
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA USA
| | - Aram Shin
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA USA
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Banaeiyan AA, Theobald J, Paukštyte J, Wölfl S, Adiels CB, Goksör M. Design and fabrication of a scalable liver-lobule-on-a-chip microphysiological platform. Biofabrication 2017; 9:015014. [DOI: 10.1088/1758-5090/9/1/015014] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Liang Q, Wang C, Li B. Metabolomic Analysis Using Liquid Chromatography/Mass Spectrometry for Gastric Cancer. Appl Biochem Biotechnol 2015; 176:2170-84. [PMID: 26088916 DOI: 10.1007/s12010-015-1706-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 06/08/2015] [Indexed: 12/15/2022]
Abstract
Metabolomics is a post-genomics research field for analysis of low molecular weight compounds in biological samples and has shown great potentials for elucidating complex mechanisms associated with diseases. However, metabolomics studies on gastric cancer (GC), which is the second leading cause of cancer death worldwide, remain scarce, and the molecular mechanisms to metabolomics phenotypes are also still not fully understood. This study reports that the metabolic pathways can be exploited as biomarkers for diagnosis and treatment of GC progression as a case study. Importantly, the urinary metabolites and metabolic patterns were analyzed by high-throughput liquid chromatography mass spectrometry (LC-MS) metabolomics strategy coupled with chemometric evaluation. Sixteen metabolites (nine upregulated and seven downregulated) were differentially expressed and may thus serve as potential urinary biomarkers for human GC. These metabolites were mainly involved in multiple metabolic pathways, including citrate cycle (malic acid, succinic acid, 2-oxoglutarate, citric acid), cyanoamino acid metabolism (glycine, alanine), primary bile acid biosynthesis (glycine, taurine, glycocholic acid), arginine and proline metabolism (urea, L-proline), and fatty acid metabolism (hexadecanoic acid), among others. Network analysis validated close association between these identified metabolites and altered metabolic pathways in a variety of biological processes. These results suggest that urine metabolic profiles have great potential in detecting GC and may aid in understanding its underlying mechanisms. It provides insight into disease pathophysiology and can serve as the basis for developing disease biomarkers and therapeutic interventions for GC diseases.
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Affiliation(s)
- Qun Liang
- First Affiliated Hospital, Heilongjiang University of Chinese Medicine, Heping Road 24, Xiangfang District, Harbin, 150040, China,
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