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Chang TY, Waxman DJ. HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo. RESEARCH SQUARE 2024:rs.3.rs-4559581. [PMID: 38978599 PMCID: PMC11230509 DOI: 10.21203/rs.3.rs-4559581/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background STARR-seq and other massively-parallel reporter assays are widely used to discover functional enhancers in transfected cell models, which can be confounded by plasmid vector-induced type-I interferon immune responses and lack the multicellular environment and endogenous chromatin state of complex mammalian tissues. Results Here, we describe HDI-STARR-seq, which combines STARR-seq plasmid library delivery to the liver, by hydrodynamic tail vein injection (HDI), with reporter RNA transcriptional initiation driven by a minimal Albumin promoter, which we show is essential for mouse liver STARR-seq enhancer activity assayed 7 days after HDI. Importantly, little or no vector-induced innate type-I interferon responses were observed. Comparisons of HDI-STARR-seq activity between male and female mouse livers and in livers from males treated with an activating ligand of the transcription factor CAR (Nr1i3) identified many condition-dependent enhancers linked to condition-specific gene expression. Further, thousands of active liver enhancers were identified using a high complexity STARR-seq library comprised of ~ 50,000 genomic regions released by DNase-I digestion of mouse liver nuclei. When compared to stringently inactive library sequences, the active enhancer sequences identified were highly enriched for liver open chromatin regions with activating histone marks (H3K27ac, H3K4me1, H3K4me3), were significantly closer to gene transcriptional start sites, and were significantly depleted of repressive (H3K27me3, H3K9me3) and transcribed region histone marks (H3K36me3). Conclusions HDI-STARR-seq offers substantial improvements over current methodologies for large scale, functional profiling of enhancers, including condition-dependent enhancers, in liver tissue in vivo, and can be adapted to characterize enhancer activities in a variety of species and tissues by selecting suitable tissue- and species-specific promoter sequences.
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Chang TY, Waxman DJ. HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598329. [PMID: 38915578 PMCID: PMC11195054 DOI: 10.1101/2024.06.10.598329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
STARR-seq and other massively-parallel reporter assays are widely used to discover functional enhancers in transfected cell models, which can be confounded by plasmid vector-induced type-I interferon immune responses and lack the multicellular environment and endogenous chromatin state of complex mammalian tissues. Here, we describe HDI-STARR-seq, which combines STARR-seq plasmid library delivery to the liver, by hydrodynamic tail vein injection (HDI), with reporter RNA transcriptional initiation driven by a minimal Albumin promoter, which we show is essential for mouse liver STARR-seq enhancer activity assayed 7 days after HDI. Importantly, little or no vector-induced innate type-I interferon responses were observed. Comparisons of HDI-STARR-seq activity between male and female mouse livers and in livers from males treated with an activating ligand of the transcription factor CAR (Nr1i3) identified many condition-dependent enhancers linked to condition-specific gene expression. Further, thousands of active liver enhancers were identified using a high complexity STARR-seq library comprised of ~50,000 genomic regions released by DNase-I digestion of mouse liver nuclei. When compared to stringently inactive library sequences, the active enhancer sequences identified were highly enriched for liver open chromatin regions with activating histone marks (H3K27ac, H3K4me1, H3K4me3), were significantly closer to gene transcriptional start sites, and were significantly depleted of repressive (H3K27me3, H3K9me3) and transcribed region histone marks (H3K36me3). HDI-STARR-seq offers substantial improvements over current methodologies for large scale, functional profiling of enhancers, including condition-dependent enhancers, in liver tissue in vivo, and can be adapted to characterize enhancer activities in a variety of species and tissues by selecting suitable tissue- and species-specific promoter sequences.
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Affiliation(s)
- Ting-Ya Chang
- Departments of Biology and Biomedical Engineering, and Bioinformatics program, Boston University, Boston, MA 02215
| | - David J Waxman
- Departments of Biology and Biomedical Engineering, and Bioinformatics program, Boston University, Boston, MA 02215
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Ali AS, Wu D, Bannach-Brown A, Dhamrait D, Berg J, Tolksdorf B, Lichtenstein D, Dressler C, Braeuning A, Kurreck J, Hülsemann M. 3D bioprinting of liver models: A systematic scoping review of methods, bioinks, and reporting quality. Mater Today Bio 2024; 26:100991. [PMID: 38558773 PMCID: PMC10978534 DOI: 10.1016/j.mtbio.2024.100991] [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: 11/08/2023] [Revised: 01/19/2024] [Accepted: 02/03/2024] [Indexed: 04/04/2024] Open
Abstract
Background Effective communication is crucial for broad acceptance and applicability of alternative methods in 3R biomedical research and preclinical testing. 3D bioprinting is used to construct intricate biological structures towards functional liver models, specifically engineered for deployment as alternative models in drug screening, toxicological investigations, and tissue engineering. Despite a growing number of reviews in this emerging field, a comprehensive study, systematically assessing practices and reporting quality for bioprinted liver models is missing. Methods In this systematic scoping review we systematically searched MEDLINE (Ovid), EMBASE (Ovid) and BioRxiv for studies published prior to June 2nd, 2022. We extracted data on methodological conduct, applied bioinks, the composition of the printed model, performed experiments and model applications. Records were screened for eligibility and data were extracted from included articles by two independent reviewers from a panel of seven domain experts specializing in bioprinting and liver biology. We used RAYYAN for the screening process and SyRF for data extraction. We used R for data analysis, and R and Graphpad PRISM for visualization. Results Through our systematic database search we identified 1042 records, from which 63 met the eligibility criteria for inclusion in this systematic scoping review. Our findings revealed that extrusion-based printing, in conjunction with bioinks composed of natural components, emerged as the predominant printing technique in the bioprinting of liver models. Notably, the HepG2 hepatoma cell line was the most frequently employed liver cell type, despite acknowledged limitations. Furthermore, 51% of the printed models featured co-cultures with non-parenchymal cells to enhance their complexity. The included studies offered a variety of techniques for characterizing these liver models, with their primary application predominantly focused on toxicity testing. Among the frequently analyzed liver markers, albumin and urea stood out. Additionally, Cytochrome P450 (CYP) isoforms, primarily CYP3A and CYP1A, were assessed, and select studies employed nuclear receptor agonists to induce CYP activity. Conclusion Our systematic scoping review offers an evidence-based overview and evaluation of the current state of research on bioprinted liver models, representing a promising and innovative technology for creating alternative organ models. We conducted a thorough examination of both the methodological and technical facets of model development and scrutinized the reporting quality within the realm of bioprinted liver models. This systematic scoping review can serve as a valuable template for systematically evaluating the progress of organ model development in various other domains. The transparently derived evidence presented here can provide essential support to the research community, facilitating the adaptation of technological advancements, the establishment of standards, and the enhancement of model robustness. This is particularly crucial as we work toward the long-term objective of establishing new approach methods as reliable alternatives to animal testing, with extensive and versatile applications.
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Affiliation(s)
- Ahmed S.M. Ali
- Department of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Germany
| | - Dongwei Wu
- Department of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Germany
| | - Alexandra Bannach-Brown
- Berlin Institute of Health (BIH) @Charité, QUEST Center for Responsible Research, Berlin, Germany
| | - Diyal Dhamrait
- Berlin Institute of Health (BIH) @Charité, QUEST Center for Responsible Research, Berlin, Germany
| | - Johanna Berg
- Department of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Germany
| | - Beatrice Tolksdorf
- Department of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Germany
| | - Dajana Lichtenstein
- German Federal Institute for Risk Assessment (BfR), Department Food Safety, Berlin, Germany
| | - Corinna Dressler
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt Universität zu Berlin, Medical Library, Germany
| | - Albert Braeuning
- German Federal Institute for Risk Assessment (BfR), Department Food Safety, Berlin, Germany
| | - Jens Kurreck
- Department of Applied Biochemistry, Institute of Biotechnology, Technische Universität Berlin, Germany
| | - Maren Hülsemann
- Berlin Institute of Health (BIH) @Charité, QUEST Center for Responsible Research, Berlin, Germany
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4
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Afonso MB, Marques V, van Mil SW, Rodrigues CM. Human liver organoids: From generation to applications. Hepatology 2024; 79:1432-1451. [PMID: 36815360 PMCID: PMC11095893 DOI: 10.1097/hep.0000000000000343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 02/24/2023]
Abstract
In the last decade, research into human hepatology has been revolutionized by the development of mini human livers in a dish. These liver organoids are formed by self-organizing stem cells and resemble their native counterparts in cellular content, multicellular architecture, and functional features. Liver organoids can be derived from the liver tissue or pluripotent stem cells generated from a skin biopsy, blood cells, or renal epithelial cells present in urine. With the development of liver organoids, a large part of previous hurdles in modeling the human liver is likely to be solved, enabling possibilities to better model liver disease, improve (personalized) drug testing, and advance bioengineering options. In this review, we address strategies to generate and use organoids in human liver disease modeling, followed by a discussion of their potential application in drug development and therapeutics, as well as their strengths and limitations.
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Affiliation(s)
- Marta B. Afonso
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - Vanda Marques
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - Saskia W.C. van Mil
- Center for Molecular Medicine, University Medical Center Utrecht and Utrecht University, The Netherlands
| | - Cecilia M.P. Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
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Woo Y, Ma M, Okawa M, Saito T. Hepatocyte Intrinsic Innate Antiviral Immunity against Hepatitis Delta Virus Infection: The Voices of Bona Fide Human Hepatocytes. Viruses 2024; 16:740. [PMID: 38793622 PMCID: PMC11126147 DOI: 10.3390/v16050740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 04/24/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
The pathogenesis of viral infection is attributed to two folds: intrinsic cell death pathway activation due to the viral cytopathic effect, and immune-mediated extrinsic cellular injuries. The immune system, encompassing both innate and adaptive immunity, therefore acts as a double-edged sword in viral infection. Insufficient potency permits pathogens to establish lifelong persistent infection and its consequences, while excessive activation leads to organ damage beyond its mission to control viral pathogens. The innate immune response serves as the front line of defense against viral infection, which is triggered through the recognition of viral products, referred to as pathogen-associated molecular patterns (PAMPs), by host cell pattern recognition receptors (PRRs). The PRRs-PAMPs interaction results in the induction of interferon-stimulated genes (ISGs) in infected cells, as well as the secretion of interferons (IFNs), to establish a tissue-wide antiviral state in an autocrine and paracrine manner. Cumulative evidence suggests significant variability in the expression patterns of PRRs, the induction potency of ISGs and IFNs, and the IFN response across different cell types and species. Hence, in our understanding of viral hepatitis pathogenesis, insights gained through hepatoma cell lines or murine-based experimental systems are uncertain in precisely recapitulating the innate antiviral response of genuine human hepatocytes. Accordingly, this review article aims to extract and summarize evidence made possible with bona fide human hepatocytes-based study tools, along with their clinical relevance and implications, as well as to identify the remaining gaps in knowledge for future investigations.
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Affiliation(s)
- Yein Woo
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Muyuan Ma
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Masashi Okawa
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- R&D Department, PhoenixBio USA Corporation, New York, NY 10006, USA
| | - Takeshi Saito
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- USC Research Center for Liver Diseases, Los Angeles, CA 90033, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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6
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Sen Zhao, Wang Y, Zhong C, Chen J, Meng L. Biotransformation of 5-methoxy-N-isopropyl-N-methyltryptamine by zebrafish and human liver microsome with high-resolution mass spectrometry. J Pharm Biomed Anal 2024; 241:115987. [PMID: 38280235 DOI: 10.1016/j.jpba.2024.115987] [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: 11/26/2023] [Revised: 01/07/2024] [Accepted: 01/15/2024] [Indexed: 01/29/2024]
Abstract
To explore the metabolites of 5-Methoxy-N-isopropyl-N-methyltryptamine (5-MeO-MiPT) and unveil its toxicological effects, we examined its metabolic profiles using zebrafish and human liver microsome models. Employing ultra-high-performance liquid chromatography Q Exactive hybrid quadrupole-Orbitrap high-resolution mass spectrometry (UPLC-QE-HRMS), we analyzed samples from intoxicated zebrafish and human liver microsomes. In the zebrafish model, we identified a total of six metabolites. Primary phase I metabolic pathways involved N-Demethylation and Indole-hydroxylation reactions, while phase II metabolism included Glucoside conjugation directly, Glucoside conjugation after Indole-hydroxylation, and Sulfonation following Indole-hydroxylation. In the human liver microsome model, nine metabolites were generated. Major phase I metabolic pathways encompassed N-Demethylation, 5-O-Demethylation, and N-Depropylation, N-Oxidation, Indole-hydroxylation, N-Demethylation combined with Indole-hydroxylation, and 5-O-Methylation-carboxylation. Phase II metabolism involved Glucoside conjugation after Indole-hydroxylation, as well as Glucoside conjugation after 5-O-Demethylation. Proposed phase I metabolites, such as 5-MeO-MiPT-N-Demethylation (5-MeO-NiPT) and 5-MeO-MiPT-Indole-hydroxylation, alongside the phase II metabolite OH&Glucoside conjugation-5-MeO-MiPT, were identified as effective markers for screening 5-MeO-MiPT intake. This study systematically delineates the phase I and II metabolites of 5-MeO-MiPT, confirming their pathways through in vivo and in vitro extrapolation. Additionally, inclusion of the parent drug itself and OH&Glucoside conjugation-5-MeO-MiPT could serve as valuable confirmation tools.
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Affiliation(s)
- Sen Zhao
- Zhejiang Police College, Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, Hangzhou 310053, PR China; College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yanjiao Wang
- Binjiang Institute of Zhejiang University, Hangzhou 310053, PR China
| | - Chenhao Zhong
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Jinyuan Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Liang Meng
- Department of Forensic Science, Fujian Police College, Fuzhou 350007, PR China.
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Recoules C, Mirey G, Audebert M. Effect of cell treatment procedures on in vitro genotoxicity assessment. Arch Toxicol 2024; 98:1225-1236. [PMID: 38427119 DOI: 10.1007/s00204-024-03690-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/23/2024] [Indexed: 03/02/2024]
Abstract
So far, the majority of in vitro toxicological experiments are conducted after an acute 24 h treatment that does not represent a realistic human chemical exposure. Recently, new in vitro approaches have been proposed to study the chemical toxicological effect over several days in order to be more predictive of a representative exposure scenario. In this study, we investigated the genotoxic potential of chemicals (direct or bioactived clastogen, aneugen and apoptotic inducer) with the γH2AX and pH3 biomarkers, in the human liver-derived HepaRP cell line. We used different treatment durations, with or without a three-day recovery stage (release period), before genotoxicity measurement. Data were analysed with the Benchmark Dose approach. We observed that the detection of clastogenic compounds (notably for DNA damaging agents) was more sensitive after three days of repeated treatment compared to one or three treatments over 24 h. In contrast, aneugenic chemicals were detected as genotoxic in a similar manner whether after a 24 h exposure or a three-day repeated treatment. Globally, the release period decreases the genotoxicity measurement substantially. For DNA damaging agents, after high concentration treatments, γH2AX induction was always observed after a three-day release period. In contrast, for DNA topoisomerase inhibitors, no effect could be observed after the release period. In conclusion, in the HepaRP cell line, there are some important differences between a one-day acute and a three-day repeated treatment protocol, indicating that different cell treatment procedures may differentiate chemical genotoxic mechanisms of action more efficiently.
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Affiliation(s)
- Cynthia Recoules
- Toxalim, INRAE-UMR1331, INP-ENVT, INP-EI-Purpan, Université de Toulouse 3 Paul Sabatier, 180 Chemin de Tournefeuille, BP 93173, 31027, Toulouse Cedex 3, France
| | - Gladys Mirey
- Toxalim, INRAE-UMR1331, INP-ENVT, INP-EI-Purpan, Université de Toulouse 3 Paul Sabatier, 180 Chemin de Tournefeuille, BP 93173, 31027, Toulouse Cedex 3, France
| | - Marc Audebert
- Toxalim, INRAE-UMR1331, INP-ENVT, INP-EI-Purpan, Université de Toulouse 3 Paul Sabatier, 180 Chemin de Tournefeuille, BP 93173, 31027, Toulouse Cedex 3, France.
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Gandhi N, Wills L, Akers K, Su Y, Niccum P, Murali TM, Rajagopalan P. Comparative transcriptomic and phenotypic analysis of induced pluripotent stem cell hepatocyte-like cells and primary human hepatocytes. Cell Tissue Res 2024; 396:119-139. [PMID: 38369646 DOI: 10.1007/s00441-024-03868-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Primary human hepatocytes (PHHs) are used extensively for in vitro liver cultures to study hepatic functions. However, limited availability and invasive retrieval prevent their widespread use. Induced pluripotent stem cells exhibit significant potential since they can be obtained non-invasively and differentiated into hepatic lineages, such as hepatocyte-like cells (iHLCs). However, there are concerns about their fetal phenotypic characteristics and their hepatic functions compared to PHHs in culture. Therefore, we performed an RNA-sequencing (RNA-seq) analysis to understand pathways that are either up- or downregulated in each cell type. Analysis of the RNA-seq data showed an upregulation in the bile secretion pathway where genes such as AQP9 and UGT1A1 were higher expressed in PHHs compared to iHLCs by 455- and 15-fold, respectively. Upon immunostaining, bile canaliculi were shown to be present in PHHs. The TCA cycle in PHHs was upregulated compared to iHLCs. Cellular analysis showed a 2-2.5-fold increase in normalized urea production in PHHs compared to iHLCs. In addition, drug metabolism pathways, including cytochrome P450 (CYP450) and UDP-glucuronosyltransferase enzymes, were upregulated in PHHs compared to iHLCs. Of note, CYP2E1 gene expression was significantly higher (21,810-fold) in PHHs. Acetaminophen and ethanol were administered to PHH and iHLC cultures to investigate differences in biotransformation. CYP450 activity of baseline and toxicant-treated samples was significantly higher in PHHs compared to iHLCs. Our analysis revealed that iHLCs have substantial differences from PHHs in critical hepatic functions. These results have highlighted the differences in gene expression and hepatic functions between PHHs and iHLCs to motivate future investigation.
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Affiliation(s)
- Neeti Gandhi
- Department of Chemical Engineering, Virginia Tech, 333 Kelly Hall, Blacksburg, VA, 24061, USA
| | - Lauren Wills
- School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, USA
| | - Kyle Akers
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA, USA
| | - Yiqi Su
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Parker Niccum
- Genetics, Bioinformatics, and Computational Biology Ph.D. Program, Virginia Tech, Blacksburg, VA, USA
| | - T M Murali
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Padmavathy Rajagopalan
- Department of Chemical Engineering, Virginia Tech, 333 Kelly Hall, Blacksburg, VA, 24061, USA.
- School of Biomedical Engineering and Sciences, Virginia Tech, Blacksburg, USA.
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Niemeijer M, Więcek W, Fu S, Huppelschoten S, Bouwman P, Baze A, Parmentier C, Richert L, Paules RS, Bois FY, van de Water B. Mapping Interindividual Variability of Toxicodynamics Using High-Throughput Transcriptomics and Primary Human Hepatocytes from Fifty Donors. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:37005. [PMID: 38498338 PMCID: PMC10947137 DOI: 10.1289/ehp11891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024]
Abstract
BACKGROUND Understanding the variability across the human population with respect to toxicodynamic responses after exposure to chemicals, such as environmental toxicants or drugs, is essential to define safety factors for risk assessment to protect the entire population. Activation of cellular stress response pathways are early adverse outcome pathway (AOP) key events of chemical-induced toxicity and would elucidate the estimation of population variability of toxicodynamic responses. OBJECTIVES We aimed to map the variability in cellular stress response activation in a large panel of primary human hepatocyte (PHH) donors to aid in the quantification of toxicodynamic interindividual variability to derive safety uncertainty factors. METHODS High-throughput transcriptomics of over 8,000 samples in total was performed covering a panel of 50 individual PHH donors upon 8 to 24 h exposure to broad concentration ranges of four different toxicological relevant stimuli: tunicamycin for the unfolded protein response (UPR), diethyl maleate for the oxidative stress response (OSR), cisplatin for the DNA damage response (DDR), and tumor necrosis factor alpha (TNF α ) for NF- κ B signaling. Using a population mixed-effect framework, the distribution of benchmark concentrations (BMCs) and maximum fold change were modeled to evaluate the influence of PHH donor panel size on the correct estimation of interindividual variability for the various stimuli. RESULTS Transcriptome mapping allowed the investigation of the interindividual variability in concentration-dependent stress response activation, where the average of BMCs had a maximum difference of 864-, 13-, 13-, and 259-fold between different PHHs for UPR, OSR, DDR, and NF- κ B signaling-related genes, respectively. Population modeling revealed that small PHH panel sizes systematically underestimated the variance and gave low probabilities in estimating the correct human population variance. Estimated toxicodynamic variability factors of stress response activation in PHHs based on this dataset ranged between 1.6 and 6.3. DISCUSSION Overall, by combining high-throughput transcriptomics and population modeling, improved understanding of interindividual variability in chemical-induced activation of toxicity relevant stress pathways across the human population using a large panel of plated cryopreserved PHHs was established, thereby contributing toward increasing the confidence of in vitro-based prediction of adverse responses, in particular hepatotoxicity. https://doi.org/10.1289/EHP11891.
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Affiliation(s)
- Marije Niemeijer
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, The Netherlands
| | | | - Shuai Fu
- Simcyp Division, CERTARA, Sheffield, UK
| | - Suzanna Huppelschoten
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, The Netherlands
| | - Peter Bouwman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, The Netherlands
| | | | | | | | - Richard S. Paules
- Division of the National Toxicology Program, NIEHS, NIH, Research Triangle Park, North Carolina, USA
| | | | - Bob van de Water
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, The Netherlands
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10
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Liu Y, Ge Y, Wu Y, Feng Y, Liu H, Cao W, Xie J, Zhang J. High-Voltage Electrostatic Field Hydrogel Microsphere 3D Culture System Improves Viability and Liver-like Properties of HepG2 Cells. Int J Mol Sci 2024; 25:1081. [PMID: 38256154 PMCID: PMC10816196 DOI: 10.3390/ijms25021081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
Three-dimensional (3D) hepatocyte models have become a research hotspot for evaluating drug metabolism and hepatotoxicity. Compared to two-dimensional (2D) cultures, 3D cultures are better at mimicking the morphology and microenvironment of hepatocytes in vivo. However, commonly used 3D culture techniques are not suitable for high-throughput drug screening (HTS) due to their high cost, complex handling, and inability to simulate cell-extracellular matrix (ECM) interactions. This article describes a method for rapid and reproducible 3D cell cultures with ECM-cell interactions based on 3D culture instrumentation to provide more efficient HTS. We developed a microsphere preparation based on a high-voltage electrostatic (HVE) field and used sodium alginate- and collagen-based hydrogels as scaffolds for 3D cultures of HepG2 cells. The microsphere-generating device enables the rapid and reproducible preparation of bioactive hydrogel microspheres. This 3D culture system exhibited better cell viability, heterogeneity, and drug-metabolizing activity than 2D and other 3D culture models, and the long-term culture characteristics of this system make it suitable for predicting long-term liver toxicity. This system improves the overall applicability of HepG2 spheroids in safety assessment studies, and this simple and controllable high-throughput-compatible method shows potential for use in drug toxicity screening assays and mechanistic studies.
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Affiliation(s)
- Yi Liu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (Y.L.); (Y.W.)
- The CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; (Y.G.); (Y.F.); (H.L.); (W.C.); (J.X.)
| | - Yang Ge
- The CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; (Y.G.); (Y.F.); (H.L.); (W.C.); (J.X.)
| | - Yanfan Wu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (Y.L.); (Y.W.)
- The CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; (Y.G.); (Y.F.); (H.L.); (W.C.); (J.X.)
| | - Yongtong Feng
- The CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; (Y.G.); (Y.F.); (H.L.); (W.C.); (J.X.)
| | - Han Liu
- The CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; (Y.G.); (Y.F.); (H.L.); (W.C.); (J.X.)
| | - Wei Cao
- The CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; (Y.G.); (Y.F.); (H.L.); (W.C.); (J.X.)
| | - Jinsong Xie
- The CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; (Y.G.); (Y.F.); (H.L.); (W.C.); (J.X.)
| | - Jingzhong Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (Y.L.); (Y.W.)
- The CAS Key Laboratory of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China; (Y.G.); (Y.F.); (H.L.); (W.C.); (J.X.)
- School of Medical Imaging, Xuzhou Medical University, Xuzhou 221004, China
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11
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Smiriglia A, Lorito N, Serra M, Perra A, Morandi A, Kowalik MA. Sex difference in liver diseases: How preclinical models help to dissect the sex-related mechanisms sustaining NAFLD and hepatocellular carcinoma. iScience 2023; 26:108363. [PMID: 38034347 PMCID: PMC10682354 DOI: 10.1016/j.isci.2023.108363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Abstract
Only a few preclinical findings are confirmed in the clinic, posing a critical issue for clinical development. Therefore, identifying the best preclinical models can help to dissect molecular and mechanistic insights into liver disease pathogenesis while being clinically relevant. In this context, the sex relevance of most preclinical models has been only partially considered. This is particularly significant in NAFLD and HCC, which have a higher prevalence in men when compared to pre-menopause women but not to those in post-menopausal status, suggesting a role for sex hormones in the pathogenesis of the diseases. This review gathers the sex-relevant findings and the available preclinical models focusing on both in vitro and in vivo studies and discusses the potential implications and perspectives of introducing the sex effect in the selection of the best preclinical model. This is a critical aspect that would help to tailor personalized therapies based on sex.
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Affiliation(s)
- Alfredo Smiriglia
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134 Florence, Italy
| | - Nicla Lorito
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134 Florence, Italy
| | - Marina Serra
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Andrea Perra
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Andrea Morandi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134 Florence, Italy
| | - Marta Anna Kowalik
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, Italy
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12
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Kozlova A, Sarygina E, Deinichenko K, Radko S, Ptitsyn K, Khmeleva S, Kurbatov L, Spirin P, Prassolov V, Ilgisonis E, Lisitsa A, Ponomarenko E. Comparison of Alternative Splicing Landscapes Revealed by Long-Read Sequencing in Hepatocyte-Derived HepG2 and Huh7 Cultured Cells and Human Liver Tissue. BIOLOGY 2023; 12:1494. [PMID: 38132320 PMCID: PMC10740679 DOI: 10.3390/biology12121494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/17/2023] [Accepted: 11/25/2023] [Indexed: 12/23/2023]
Abstract
The long-read RNA sequencing developed by Oxford Nanopore Technologies provides a direct quantification of transcript isoforms, thereby making it possible to present alternative splicing (AS) profiles as arrays of single splice variants with different abundances. Additionally, AS profiles can be presented as arrays of genes characterized by the degree of alternative splicing (the DAS-the number of detected splice variants per gene). Here, we successfully utilized the DAS to reveal biological pathways influenced by the alterations in AS in human liver tissue and the hepatocyte-derived malignant cell lines HepG2 and Huh7, thus employing the mathematical algorithm of gene set enrichment analysis. Furthermore, analysis of the AS profiles as abundances of single splice variants by using the graded tissue specificity index τ provided the selection of the groups of genes expressing particular splice variants specifically in liver tissue, HepG2 cells, and Huh7 cells. The majority of these splice variants were translated into proteins products and appeal to be in focus regarding further insights into the mechanisms underlying cell malignization. The used metrics are intrinsically suitable for transcriptome-wide AS profiling using long-read sequencing.
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Affiliation(s)
- Anna Kozlova
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Elizaveta Sarygina
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Kseniia Deinichenko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Sergey Radko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Konstantin Ptitsyn
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Svetlana Khmeleva
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Leonid Kurbatov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Pavel Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia; (P.S.); (V.P.)
| | - Vladimir Prassolov
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia; (P.S.); (V.P.)
| | - Ekaterina Ilgisonis
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Andrey Lisitsa
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
| | - Elena Ponomarenko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia (S.R.)
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13
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Sarygina E, Kozlova A, Deinichenko K, Radko S, Ptitsyn K, Khmeleva S, Kurbatov LK, Spirin P, Prassolov VS, Ilgisonis E, Lisitsa A, Ponomarenko E. Principal Component Analysis of Alternative Splicing Profiles Revealed by Long-Read ONT Sequencing in Human Liver Tissue and Hepatocyte-Derived HepG2 and Huh7 Cell Lines. Int J Mol Sci 2023; 24:15502. [PMID: 37958484 PMCID: PMC10648607 DOI: 10.3390/ijms242115502] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/12/2023] [Accepted: 10/14/2023] [Indexed: 11/15/2023] Open
Abstract
The long-read RNA sequencing developed by Oxford Nanopore Technology provides a direct quantification of transcript isoforms. That makes the number of transcript isoforms per gene an intrinsically suitable metric for alternative splicing (AS) profiling in the application to this particular type of RNA sequencing. By using this simple metric and recruiting principal component analysis (PCA) as a tool to visualize the high-dimensional transcriptomic data, we were able to group biospecimens of normal human liver tissue and hepatocyte-derived malignant HepG2 and Huh7 cells into clear clusters in a 2D space. For the transcriptome-wide analysis, the clustering was observed regardless whether all genes were included in analysis or only those expressed in all biospecimens tested. However, in the application to a particular set of genes known as pharmacogenes, which are involved in drug metabolism, the clustering worsened dramatically in the latter case. Based on PCA data, the subsets of genes most contributing to biospecimens' grouping into clusters were selected and subjected to gene ontology analysis that allowed us to determine the top 20 biological processes among which translation and processes related to its regulation dominate. The suggested metrics can be a useful addition to the existing metrics for describing AS profiles, especially in application to transcriptome studies with long-read sequencing.
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Affiliation(s)
- Elizaveta Sarygina
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; (E.S.); (A.K.); (S.R.)
| | - Anna Kozlova
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; (E.S.); (A.K.); (S.R.)
| | - Kseniia Deinichenko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; (E.S.); (A.K.); (S.R.)
| | - Sergey Radko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; (E.S.); (A.K.); (S.R.)
| | - Konstantin Ptitsyn
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; (E.S.); (A.K.); (S.R.)
| | - Svetlana Khmeleva
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; (E.S.); (A.K.); (S.R.)
| | - Leonid K. Kurbatov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; (E.S.); (A.K.); (S.R.)
| | - Pavel Spirin
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
| | - Vladimir S. Prassolov
- Department of Cancer Cell Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, 119991 Moscow, Russia
| | - Ekaterina Ilgisonis
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; (E.S.); (A.K.); (S.R.)
| | - Andrey Lisitsa
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; (E.S.); (A.K.); (S.R.)
| | - Elena Ponomarenko
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, 119121 Moscow, Russia; (E.S.); (A.K.); (S.R.)
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14
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Suominen S, Hyypijev T, Venäläinen M, Yrjänäinen A, Vuorenpää H, Lehti-Polojärvi M, Räsänen M, Seppänen A, Hyttinen J, Miettinen S, Aalto-Setälä K, Viiri LE. Improvements in Maturity and Stability of 3D iPSC-Derived Hepatocyte-like Cell Cultures. Cells 2023; 12:2368. [PMID: 37830581 PMCID: PMC10571736 DOI: 10.3390/cells12192368] [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: 08/31/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023] Open
Abstract
Induced pluripotent stem cell (iPSC) technology enables differentiation of human hepatocytes or hepatocyte-like cells (iPSC-HLCs). Advances in 3D culturing platforms enable the development of more in vivo-like liver models that recapitulate the complex liver architecture and functionality better than traditional 2D monocultures. Moreover, within the liver, non-parenchymal cells (NPCs) are critically involved in the regulation and maintenance of hepatocyte metabolic function. Thus, models combining 3D culture and co-culturing of various cell types potentially create more functional in vitro liver models than 2D monocultures. Here, we report the establishment of 3D cultures of iPSC-HLCs alone and in co-culture with human umbilical vein endothelial cells (HUVECs) and adipose tissue-derived mesenchymal stem/stromal cells (hASCs). The 3D cultures were performed as spheroids or on microfluidic chips utilizing various biomaterials. Our results show that both 3D spheroid and on-chip culture enhance the expression of mature liver marker genes and proteins compared to 2D. Among the spheroid models, we saw the best functionality in iPSC-HLC monoculture spheroids. On the contrary, in the chip system, the multilineage model outperformed the monoculture chip model. Additionally, the optical projection tomography (OPT) and electrical impedance tomography (EIT) system revealed changes in spheroid size and electrical conductivity during spheroid culture, suggesting changes in cell-cell connections. Altogether, the present study demonstrates that iPSC-HLCs can successfully be cultured in 3D as spheroids and on microfluidic chips, and co-culturing iPSC-HLCs with NPCs enhances their functionality. These 3D in vitro liver systems are promising human-derived platforms usable in various liver-related studies, specifically when using patient-specific iPSCs.
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Affiliation(s)
- Siiri Suominen
- Heart Group, Finnish Cardiovascular Research Center and Science Mimicking Life Research Center, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland (L.E.V.)
| | - Tinja Hyypijev
- Heart Group, Finnish Cardiovascular Research Center and Science Mimicking Life Research Center, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland (L.E.V.)
| | - Mari Venäläinen
- Heart Group, Finnish Cardiovascular Research Center and Science Mimicking Life Research Center, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland (L.E.V.)
| | - Alma Yrjänäinen
- Adult Stem Cell Group, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
- Research, Development and Innovation Centre, Tampere University Hospital, 33520 Tampere, Finland
| | - Hanna Vuorenpää
- Adult Stem Cell Group, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
- Research, Development and Innovation Centre, Tampere University Hospital, 33520 Tampere, Finland
| | - Mari Lehti-Polojärvi
- Computational Biophysics and Imaging Group, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
| | - Mikko Räsänen
- Department of Technical Physics, University of Eastern Finland, 70210 Kuopio, Finland
| | - Aku Seppänen
- Department of Technical Physics, University of Eastern Finland, 70210 Kuopio, Finland
| | - Jari Hyttinen
- Computational Biophysics and Imaging Group, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
| | - Susanna Miettinen
- Adult Stem Cell Group, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
- Research, Development and Innovation Centre, Tampere University Hospital, 33520 Tampere, Finland
| | - Katriina Aalto-Setälä
- Heart Group, Finnish Cardiovascular Research Center and Science Mimicking Life Research Center, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland (L.E.V.)
- Heart Hospital, Tampere University Hospital, 33520 Tampere, Finland
| | - Leena E. Viiri
- Heart Group, Finnish Cardiovascular Research Center and Science Mimicking Life Research Center, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland (L.E.V.)
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15
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Sun L, Wang Y, Zhang S, Yang H, Mao Y. 3D bioprinted liver tissue and disease models: Current advances and future perspectives. BIOMATERIALS ADVANCES 2023; 152:213499. [PMID: 37295133 DOI: 10.1016/j.bioadv.2023.213499] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/23/2023] [Accepted: 06/02/2023] [Indexed: 06/12/2023]
Abstract
Three-dimensional (3D) bioprinting is a promising technology for fabricating complex tissue constructs with biomimetic biological functions and stable mechanical properties. In this review, the characteristics of different bioprinting technologies and materials are compared, and development in strategies for bioprinting normal and diseased hepatic tissue are summarized. In particular, features of bioprinting and other bio-fabrication strategies, such as organoids and spheroids are compared to demonstrate the strengths and weaknesses of 3D printing technology. Directions and suggestions, such as vascularization and primary human hepatocyte culture, are provided for the future development of 3D bioprinting.
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Affiliation(s)
- Lejia Sun
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Dongcheng, Beijing, 100730, China; Department of General Surgery, The First affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yinhan Wang
- Peking Union Medical College (PUMC), Chinese Academy of Medical Sciences & PUMC, Dongcheng, Beijing 100730, China
| | - Shuquan Zhang
- Peking Union Medical College (PUMC), Chinese Academy of Medical Sciences & PUMC, Dongcheng, Beijing 100730, China
| | - Huayu Yang
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Dongcheng, Beijing, 100730, China.
| | - Yilei Mao
- Department of Liver Surgery, Peking Union Medical College (PUMC) Hospital, PUMC & Chinese Academy of Medical Sciences, Dongcheng, Beijing, 100730, China.
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16
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Recio-Vega R, Facio-Campos RA, Hernández-González SI, Olivas-Calderón E. State of the Art of Genomic Technology in Toxicology: A Review. Int J Mol Sci 2023; 24:ijms24119618. [PMID: 37298568 DOI: 10.3390/ijms24119618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/23/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
The rapid growth of genomics techniques has revolutionized and impacted, greatly and positively, the knowledge of toxicology, ushering it into a "new era": the era of genomic technology (GT). This great advance permits us to analyze the whole genome, to know the gene response to toxicants and environmental stressors, and to determine the specific profiles of gene expression, among many other approaches. The aim of this work was to compile and narrate the recent research on GT during the last 2 years (2020-2022). A literature search was managed using the PubMed and Medscape interfaces on the Medline database. Relevant articles published in peer-reviewed journals were retrieved and their main results and conclusions are mentioned briefly. It is quite important to form a multidisciplinary taskforce on GT with the aim of designing and implementing a comprehensive, collaborative, and a strategic work plan, prioritizing and assessing the most relevant diseases, so as to decrease human morbimortality due to exposure to environmental chemicals and stressors.
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Affiliation(s)
| | - Rolando Adair Facio-Campos
- Laboratory of Environmental Health, School of Chemical Sciences, Juarez University of Durango State, Gomez Palacio 35010, Mexico
| | - Sandra Isabel Hernández-González
- Laboratory of Environmental Health, School of Chemical Sciences, Juarez University of Durango State, Gomez Palacio 35010, Mexico
| | - Edgar Olivas-Calderón
- Laboratory of Environmental Health, School of Chemical Sciences, Juarez University of Durango State, Gomez Palacio 35010, Mexico
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17
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Stern S, Wang H, Sadrieh N. Microphysiological Models for Mechanistic-Based Prediction of Idiosyncratic DILI. Cells 2023; 12:1476. [PMID: 37296597 PMCID: PMC10253021 DOI: 10.3390/cells12111476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Drug-induced liver injury (DILI) is a major contributor to high attrition rates among candidate and market drugs and a key regulatory, industry, and global health concern. While acute and dose-dependent DILI, namely, intrinsic DILI, is predictable and often reproducible in preclinical models, the nature of idiosyncratic DILI (iDILI) limits its mechanistic understanding due to the complex disease pathogenesis, and recapitulation using in vitro and in vivo models is extremely challenging. However, hepatic inflammation is a key feature of iDILI primarily orchestrated by the innate and adaptive immune system. This review summarizes the in vitro co-culture models that exploit the role of the immune system to investigate iDILI. Particularly, this review focuses on advancements in human-based 3D multicellular models attempting to supplement in vivo models that often lack predictability and display interspecies variations. Exploiting the immune-mediated mechanisms of iDILI, the inclusion of non-parenchymal cells in these hepatoxicity models, namely, Kupffer cells, stellate cells, dendritic cells, and liver sinusoidal endothelial cells, introduces heterotypic cell-cell interactions and mimics the hepatic microenvironment. Additionally, drugs recalled from the market in the US between 1996-2010 that were studies in these various models highlight the necessity for further harmonization and comparison of model characteristics. Challenges regarding disease-related endpoints, mimicking 3D architecture with different cell-cell contact, cell source, and the underlying multi-cellular and multi-stage mechanisms are described. It is our belief that progressing our understanding of the underlying pathogenesis of iDILI will provide mechanistic clues and a method for drug safety screening to better predict liver injury in clinical trials and post-marketing.
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Affiliation(s)
- Sydney Stern
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, USA;
| | - Hongbing Wang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, USA;
| | - Nakissa Sadrieh
- Office of New Drugs, Center of Drug Evaluation and Research, FDA, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA
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18
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Hou YT, Wu CC, Wang WT, Yang WT, Liao YH, Chen CY. Monitoring Cultured Rat Hepatocytes Using RNA-Seq In Vitro. Int J Mol Sci 2023; 24:ijms24087534. [PMID: 37108701 PMCID: PMC10139060 DOI: 10.3390/ijms24087534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Compared to other techniques, RNA sequencing (RNA-Seq) has the advantage of having details of the expression abundance of all transcripts in a single run. In this study, we used RNA-Seq to monitor the maturity and dynamic characteristics of in vitro hepatocyte cultures. Hepatocytes, including mature hepatocytes and small hepatocytes, were analyzed in vitro using RNA-Seq and quantitative polymerase chain reaction (qPCR). The results demonstrated that the gene expression profiles measured by RNA-Seq showed a similar trend to the expression profiles measured by qPCR, and can be used to infer the success of in vitro hepatocyte cultures. The results of the differential analysis, which compared mature hepatocytes against small hepatocytes, revealed 836 downregulated and 137 upregulated genes. In addition, the success of the hepatocyte cultures could be explained by the gene list screened from the adopted gene enrichment test. In summary, we demonstrated that RNA-Seq could become an effective method for monitoring the whole transcriptome of hepatocyte cultures and provide a more comprehensive list of factors related to the differentiation of small hepatocytes into mature hepatocytes. This monitoring system not only shows high potential in medical applications but may also be a novel method for the clinical diagnosis of liver-related diseases.
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Affiliation(s)
- Yung-Te Hou
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Chia-Chun Wu
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Wen-Ting Wang
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Wen-Tse Yang
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Ying-Hsiu Liao
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Chien-Yu Chen
- Department of Biomechatronics Engineering, National Taiwan University, Taipei 106, Taiwan
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19
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Pognan F, Beilmann M, Boonen HCM, Czich A, Dear G, Hewitt P, Mow T, Oinonen T, Roth A, Steger-Hartmann T, Valentin JP, Van Goethem F, Weaver RJ, Newham P. The evolving role of investigative toxicology in the pharmaceutical industry. Nat Rev Drug Discov 2023; 22:317-335. [PMID: 36781957 PMCID: PMC9924869 DOI: 10.1038/s41573-022-00633-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 02/15/2023]
Abstract
For decades, preclinical toxicology was essentially a descriptive discipline in which treatment-related effects were carefully reported and used as a basis to calculate safety margins for drug candidates. In recent years, however, technological advances have increasingly enabled researchers to gain insights into toxicity mechanisms, supporting greater understanding of species relevance and translatability to humans, prediction of safety events, mitigation of side effects and development of safety biomarkers. Consequently, investigative (or mechanistic) toxicology has been gaining momentum and is now a key capability in the pharmaceutical industry. Here, we provide an overview of the current status of the field using case studies and discuss the potential impact of ongoing technological developments, based on a survey of investigative toxicologists from 14 European-based medium-sized to large pharmaceutical companies.
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Affiliation(s)
- Francois Pognan
- Discovery and Investigative Safety, Novartis Pharma AG, Basel, Switzerland.
| | - Mario Beilmann
- Nonclinical Drug Safety Germany, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Harrie C M Boonen
- Drug Safety, Dept of Exploratory Toxicology, Lundbeck A/S, Valby, Denmark
| | | | - Gordon Dear
- In Vitro In Vivo Translation, GlaxoSmithKline David Jack Centre for Research, Ware, UK
| | - Philip Hewitt
- Chemical and Preclinical Safety, Merck Healthcare KGaA, Darmstadt, Germany
| | - Tomas Mow
- Safety Pharmacology and Early Toxicology, Novo Nordisk A/S, Maaloev, Denmark
| | - Teija Oinonen
- Preclinical Safety, Orion Corporation, Espoo, Finland
| | - Adrian Roth
- Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | | | - Freddy Van Goethem
- Predictive, Investigative & Translational Toxicology, Nonclinical Safety, Janssen Research & Development, Beerse, Belgium
| | - Richard J Weaver
- Innovation Life Cycle Management, Institut de Recherches Internationales Servier, Suresnes, France
| | - Peter Newham
- Clinical Pharmacology and Safety Sciences, AstraZeneca R&D, Cambridge, UK.
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20
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Carpentier N, Urbani L, Dubruel P, Van Vlierberghe S. The native liver as inspiration to create superior in vitro hepatic models. Biomater Sci 2023; 11:1091-1115. [PMID: 36594602 DOI: 10.1039/d2bm01646j] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Drug induced liver injury (DILI) is one of the major reasons of drug withdrawal during the different phases of drug development. The later in the drug development a drug is discovered to be toxic, the higher the economical as well as the ethical impact will be. In vitro models for early detection of drug liver toxicity are under constant development, however to date a superior model of the liver is still lacking. Ideally, a highly reliable model should be established to maintain the different hepatic cell functionalities to the greatest extent possible, during a period of time long enough to allow for tracking of the toxicity of compounds. In the case of DILI, toxicity can appear even after months of exposure. To reach this goal, an in vitro model should be developed that mimics the in vivo liver environment, function and response to external stimuli. The different approaches for the development of liver models currently used in the field of tissue engineering will be described in this review. Combining different technologies, leading to optimal materials, cells and 3D-constructs will ultimately lead to an ideal superior model that fully recapitulates the liver.
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Affiliation(s)
- Nathan Carpentier
- Polymer Chemistry & Biomaterials Group, Centre of Macromolecular Chemistry, Ghent University, Ghent, Belgium.
| | - Luca Urbani
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London SE5 9NT, UK.,Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Peter Dubruel
- Polymer Chemistry & Biomaterials Group, Centre of Macromolecular Chemistry, Ghent University, Ghent, Belgium.
| | - Sandra Van Vlierberghe
- Polymer Chemistry & Biomaterials Group, Centre of Macromolecular Chemistry, Ghent University, Ghent, Belgium.
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21
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Shuoxin Y, Shuping W, Xinyue Z, Tao Z, Yuanneng C. Progress of research on tumor organoids: A bibliometric analysis of relevant publications from 2011 to 2021. Front Oncol 2023; 13:1092870. [PMID: 36776331 PMCID: PMC9909405 DOI: 10.3389/fonc.2023.1092870] [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: 11/08/2022] [Accepted: 01/04/2023] [Indexed: 01/27/2023] Open
Abstract
Background Research on tumor organoids has developed rapidly over the past 20 years, but a systematic analysis of current research trends is lacking. Researchers in the field need relevant references and knowledge of current research hot spots. Bibliometric analysis and visualization is a systematic method of acquiring an in-depth understanding of the status of research on tumor organoids. Methods CiteSpace, VOSviewer and the Bibliometric Online Analysis Platform from the Web of Science Core Collection were used to analyze and predict publishing trends and research hot spots worldwide in the field of tumor organoids. Results A total of 3,666 publications on tumor organoids were retrieved, and 2,939 eligible articles were included in the final analysis. The number of publications has grown significantly, with the United States of America as the leading country for research on tumor organoids. Among journals, Cancers published the largest number of articles. Harvard Medical School published the highest number of articles among all institutions. The Chinese Academy of Sciences was ranked highest among all contributing institutions on the importance of their publications. A trend in multi-disciplinary collaboration was observed in studies on tumor organoids. Keywords indicated that the current research largely concentrated on optimizing the construction of organoid models to use for medication development and screening in the clinical setting, and to provide patients with individualized treatment for gastric cancer and colorectal cancer, which are newly emerging research hotspots. Gastric and colorectal cancers were the top two tumors that have received increasing attention and have become the focal points of recent studies. Conclusion This study analyzed 2,939 publications covering the topic of tumor organoids. Although optimizing the construction of organoid models has always been a hot topic in this field, the application of tumor organoids to the development of medications and screenings will foster individualized treatment for patients, which is another emerging hot spot in this field of research.
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Affiliation(s)
- Yin Shuoxin
- Graduate School of Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Wang Shuping
- Graduate School of Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Zhang Xinyue
- Department of Gastroenterology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Zhang Tao
- Department of Gastroenterology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, Guangxi, China,*Correspondence: Chen Yuanneng, ; Zhang Tao,
| | - Chen Yuanneng
- Department of Gastroenterology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, Guangxi, China,*Correspondence: Chen Yuanneng, ; Zhang Tao,
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22
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Deynichenko KA, Ptitsyn KG, Radko SP, Kurbatov LK, Vakhrushev IV, Buromski IV, Markin SS, Archakov AI, Lisitsa AV, Ponomarenko EA. Splice Variants of mRNA of Cytochrome P450 Genes: Analysis by the Nanopore Sequencing Method in Human Liver Tissue and HepG2 Cell Line. BIOCHEMISTRY (MOSCOW), SUPPLEMENT SERIES B: BIOMEDICAL CHEMISTRY 2022. [DOI: 10.1134/s1990750822040047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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23
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A comprehensive transcriptomic comparison of hepatocyte model systems improves selection of models for experimental use. Commun Biol 2022; 5:1094. [PMID: 36241695 PMCID: PMC9568534 DOI: 10.1038/s42003-022-04046-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022] Open
Abstract
The myriad of available hepatocyte in vitro models provides researchers the possibility to select hepatocyte-like cells (HLCs) for specific research goals. However, direct comparison of hepatocyte models is currently challenging. We systematically searched the literature and compared different HLCs, but reported functions were limited to a small subset of hepatic functions. To enable a more comprehensive comparison, we developed an algorithm to compare transcriptomic data across studies that tested HLCs derived from hepatocytes, biliary cells, fibroblasts, and pluripotent stem cells, alongside primary human hepatocytes (PHHs). This revealed that no HLC covered the complete hepatic transcriptome, highlighting the importance of HLC selection. HLCs derived from hepatocytes had the highest transcriptional resemblance to PHHs regardless of the protocol, whereas the quality of fibroblasts and PSC derived HLCs varied depending on the protocol used. Finally, we developed and validated a web application (HLCompR) enabling comparison for specific pathways and addition of new HLCs. In conclusion, our comprehensive transcriptomic comparison of HLCs allows selection of HLCs for specific research questions and can guide improvements in culturing conditions.
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24
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Duff C, Baruteau J. Modelling urea cycle disorders using iPSCs. NPJ Regen Med 2022; 7:56. [PMID: 36163209 PMCID: PMC9513077 DOI: 10.1038/s41536-022-00252-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 08/10/2022] [Indexed: 11/23/2022] Open
Abstract
The urea cycle is a liver-based pathway enabling disposal of nitrogen waste. Urea cycle disorders (UCDs) are inherited metabolic diseases caused by deficiency of enzymes or transporters involved in the urea cycle and have a prevalence of 1:35,000 live births. Patients present recurrent acute hyperammonaemia, which causes high rate of death and neurological sequelae. Long-term therapy relies on a protein-restricted diet and ammonia scavenger drugs. Currently, liver transplantation is the only cure. Hence, high unmet needs require the identification of effective methods to model these diseases to generate innovative therapeutics. Advances in both induced pluripotent stem cells (iPSCs) and genome editing technologies have provided an invaluable opportunity to model patient-specific phenotypes in vitro by creating patients’ avatar models, to investigate the pathophysiology, uncover novel therapeutic targets and provide a platform for drug discovery. This review summarises the progress made thus far in generating 2- and 3-dimensional iPSCs models for UCDs, the challenges encountered and how iPSCs offer future avenues for innovation in developing the next-generation of therapies for UCDs.
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Affiliation(s)
- Claire Duff
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Julien Baruteau
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK. .,National Institute of Health Research Great Ormond Street Biomedical Research Centre, London, UK. .,Metabolic Medicine Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
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25
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Colchicine overdose impairs the capacity of Kupffer cells to clear foreign particles and endotoxins. Arch Toxicol 2022; 96:3067-3076. [PMID: 36102954 PMCID: PMC9525399 DOI: 10.1007/s00204-022-03353-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 02/07/2023]
Abstract
AbstractColchicine is an anti-inflammatory drug with a narrow therapeutic index. Its binding to tubulin prevents microtubule polymerization; however, little is known about how depolymerization of microtubules interferes with the phagocytosis function of Kupffer cells (KC). Here, we applied functional intravital imaging techniques to investigate the influence of microtubule disruption by colchicine on KC morphology, as well as its capacity to clear foreign particles and bacterial lipopolysaccharide (LPS) in anesthetized mice. Intravital imaging of KC in healthy mice showed the typical elongated morphology, localization at the luminal side of the sinusoidal endothelial cells, and moving cell protrusions. In contrast, at colchicine doses of 1 mg/kg and higher (intraperitoneal), KC appeared roundish with strongly reduced protrusions and motility. To study the functional consequences of these alterations, we analyzed the capacity of KC to phagocytose fluorescent nanospheres (100 nm-size) and LPS. After tail vein injection, the nanospheres formed aggregates of up to ~ 5 µm moving along the sinusoidal bloodstream. In controls, the nanosphere aggregates were rapidly captured by the Kupffer cell protrusions, followed by an internalization process that lasted up to 10 min. Similar capture events and internalization processes were observed after the administration of fluorescently labeled LPS. In contrast, capture and internalization of both nanospheres and LPS by KC were strongly reduced in colchicine-treated mice. Reduced phagocytosis of LPS was accompanied by aggravated production of inflammatory cytokines. Since 0.4 mg/kg colchicine in mice has been reported to be bio-equivalent to human therapeutic doses, the here-observed adverse effects on KC occurred at doses only slightly above those used clinically, and may be critical for patients with endotoxemia due to a leaky gut–blood barrier.
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26
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Urbanczyk M, Zbinden A, Schenke-Layland K. Organ-specific endothelial cell heterogenicity and its impact on regenerative medicine and biomedical engineering applications. Adv Drug Deliv Rev 2022; 186:114323. [PMID: 35568103 DOI: 10.1016/j.addr.2022.114323] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/23/2022] [Accepted: 05/05/2022] [Indexed: 02/08/2023]
Abstract
Endothelial cells (ECs) are a key cellular component of the vascular system as they form the inner lining of the blood vessels. Recent findings highlight that ECs express extensive phenotypic heterogenicity when following the vascular tree from the major vasculature down to the organ capillaries. However, in vitro models, used for drug development and testing, or to study the role of ECs in health and disease, rarely acknowledge this EC heterogenicity. In this review, we highlight the main differences between different EC types, briefly summarize their different characteristics and focus on the use of ECs in in vitro models. We introduce different approaches on how ECs can be utilized in co-culture test systems in the field of brain, pancreas, and liver research to study the role of the endothelium in health and disease. Finally, we discuss potential improvements to current state-of-the-art in vitro models and future directions.
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27
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Mirahmad M, Sabourian R, Mahdavi M, Larijani B, Safavi M. In vitro cell-based models of drug-induced hepatotoxicity screening: progress and limitation. Drug Metab Rev 2022; 54:161-193. [PMID: 35403528 DOI: 10.1080/03602532.2022.2064487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Drug-induced liver injury (DILI) is one of the major causes of post-approval withdrawal of therapeutics. As a result, there is an increasing need for accurate predictive in vitro assays that reliably detect hepatotoxic drug candidates while reducing drug discovery time, costs, and the number of animal experiments. In vitro hepatocyte-based research has led to an improved comprehension of the underlying mechanisms of chemical toxicity and can assist the prioritization of therapeutic choices with low hepatotoxicity risk. Therefore, several in vitro systems have been generated over the last few decades. This review aims to comprehensively present the development and validation of 2D (two-dimensional) and 3D (three-dimensional) culture approaches on hepatotoxicity screening of compounds and highlight the main factors affecting predictive power of experiments. To this end, we first summarize some of the recognized hepatotoxicity mechanisms and related assays used to appraise DILI mechanisms and then discuss the challenges and limitations of in vitro models.
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Affiliation(s)
- Maryam Mirahmad
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reyhaneh Sabourian
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Maliheh Safavi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
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28
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Deynichenko KA, Ptitsyn KG, Radko SP, Kurbatov LK, Vakhrushev IV, Buromski IV, Markin SS, Archakov AI, Lisitsa AV, Ponomarenko EA. [Splice variants of mRNA of cytochrome P450 genes: analysis by the nanopore sequencing method in human liver tissue and HepG2 cell line]. BIOMEDITSINSKAIA KHIMIIA 2022; 68:117-125. [PMID: 35485485 DOI: 10.18097/pbmc20226802117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The analysis of cytochrome P450 transcripts was carried out by the nanopore sequencing in liver tissue samples of three donors and HepG2 line cells. It has been demonstrated that direct mRNA sequencing with a MinION nanopore sequencer (Oxford Nanopore Technologies) allows one to obtained quantitative profiles for transcripts (and their splice variants) of cytochrome P450 superfamily genes encoding isoforms involved in metabolism of the large (~80%) part of drugs. The splice variant profiles substantially differ for donors. The cytochrome P450 gene expression at the transcript level is significantly weaker in cells of the HepG2 line compared with that in the normal liver tissue. This limits the capability of the direct mRNA nanopore sequencing for studying alternative splicing of cytochrome P450 transcripts in HepG2 cells. Both quantitative and qualitative profiles of the cytochrome P450 gene expression at the transcript level are notably differ in human liver tissue and HepG2 cells.
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Affiliation(s)
| | - K G Ptitsyn
- Institute of Biomedical Chemistry, Moscow, Russia
| | - S P Radko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - L K Kurbatov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - I V Buromski
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - S S Markin
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A V Lisitsa
- Institute of Biomedical Chemistry, Moscow, Russia
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29
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HepG2-Based Designer Cells with Heat-Inducible Enhanced Liver Functions. Cells 2022; 11:cells11071194. [PMID: 35406758 PMCID: PMC8997820 DOI: 10.3390/cells11071194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Functional human hepatocytes have been a pivotal tool in pharmacological studies such as those investigating drug metabolism and hepatotoxicity. However, primary human hepatocytes are difficult to obtain in large quantities and may cause ethical problems, necessitating the development of a new cell source to replace human primary hepatocytes. We previously developed genetically modified murine hepatoma cell lines with inducible enhanced liver functions, in which eight liver-enriched transcription factor (LETF) genes were introduced into hepatoma cells as inducible transgene expression cassettes. Here, we establish a human hepatoma cell line with heat-inducible liver functions using HepG2 cells. The genetically modified hepatoma cells, designated HepG2/8F_HS, actively proliferated under normal culture conditions and, therefore, can be easily prepared in large quantities. When the expression of LETFs was induced by heat treatment at 43 °C for 30 min, cells ceased proliferation and demonstrated enhanced liver functions. Furthermore, three-dimensional spheroid cultures of HepG2/8F_HS cells showed a further increase in liver functions upon heat treatment. Comprehensive transcriptome analysis using DNA microarrays revealed that HepG2/8F_HS cells had enhanced overall expression of many liver function-related genes following heat treatment. HepG2/8F_HS cells could be useful as a new cell source for pharmacological studies and for constructing bioartificial liver systems.
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30
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Dolicka D, Zahoran S, Correia de Sousa M, Gjorgjieva M, Sempoux C, Fournier M, Maeder C, Collart MA, Foti M, Sobolewski C. TIA1 Loss Exacerbates Fatty Liver Disease but Exerts a Dual Role in Hepatocarcinogenesis. Cancers (Basel) 2022; 14:cancers14071704. [PMID: 35406476 PMCID: PMC8997004 DOI: 10.3390/cancers14071704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
Alterations in specific RNA-binding protein expression/activity importantly contribute to the development of fatty liver disease (FLD) and hepatocellular carcinoma (HCC). In particular, adenylate–uridylate-rich element binding proteins (AUBPs) were reported to control the post-transcriptional regulation of genes involved in both metabolic and cancerous processes. Herein, we investigated the pathophysiological functions of the AUBP, T-cell-restricted intracellular antigen-1 (TIA1) in the development of FLD and HCC. Analysis of TIA1 expression in mouse and human models of FLD and HCC indicated that TIA1 is downregulated in human HCC. In vivo silencing of TIA1 using AAV8-delivered shRNAs in mice worsens hepatic steatosis and fibrosis induced by a methionine and choline-deficient diet and increases the hepatic tumor burden in liver-specific PTEN knockout (LPTENKO) mice. In contrast, our in vitro data indicated that TIA1 expression promoted proliferation and migration in HCC cell lines, thus suggesting a dual and context-dependent role for TIA1 in tumor initiation versus progression. Consistent with a dual function of TIA1 in tumorigenesis, translatome analysis revealed that TIA1 appears to control the expression of both pro- and anti-tumorigenic factors in hepatic cancer cells. This duality of TIA1′s function in hepatocarcinogenesis calls for cautiousness when considering TIA1 as a therapeutic target or biomarker in HCC.
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Affiliation(s)
- Dobrochna Dolicka
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Szabolcs Zahoran
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (S.Z.); (M.A.C.)
| | - Marta Correia de Sousa
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Monika Gjorgjieva
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Christine Sempoux
- Service of Clinical Pathology, Institute of Pathology, Lausanne University Hospital and University of Lausanne, CH-1007 Lausanne, Switzerland;
| | - Margot Fournier
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Christine Maeder
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Martine A. Collart
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (S.Z.); (M.A.C.)
| | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
| | - Cyril Sobolewski
- Department of Cell Physiology and Metabolism, Translational Research Centre in Onco-Hematology (CRTOH), Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (D.D.); (M.C.d.S.); (M.G.); (M.F.); (C.M.); (M.F.)
- Correspondence: or
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Blaszkiewicz J, Duncan SA. Advancements in Disease Modeling and Drug Discovery Using iPSC-Derived Hepatocyte-like Cells. Genes (Basel) 2022; 13:573. [PMID: 35456379 PMCID: PMC9030659 DOI: 10.3390/genes13040573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/05/2023] Open
Abstract
Serving as the metabolic hub of the human body, the liver is a vital organ that performs a variety of important physiological functions. Although known for its regenerative potential, it remains vulnerable to a variety of diseases. Despite decades of research, liver disease remains a leading cause of mortality in the United States with a multibillion-dollar-per-year economic burden. Prior research with model systems, such as primary hepatocytes and murine models, has provided many important discoveries. However, progress has been impaired by numerous obstacles associated with these models. In recent years, induced pluripotent stem cell (iPSC)-based systems have emerged as advantageous platforms for studying liver disease. Benefits, including preserved differentiation and physiological function, amenability to genetic manipulation via tools such as CRISPR/Cas9, and availability for high-throughput screening, make these systems increasingly attractive for both mechanistic studies of disease and the identification of novel therapeutics. Although limitations exist, recent studies have made progress in ameliorating these issues. In this review, we discuss recent advancements in iPSC-based models of liver disease, including improvements in model system construction as well as the use of high-throughput screens for genetic studies and drug discovery.
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Affiliation(s)
| | - Stephen A. Duncan
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA;
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Ishida S. Research and Development of Microphysiological Systems in Japan Supported by the AMED-MPS Project. FRONTIERS IN TOXICOLOGY 2022; 3:657765. [PMID: 35295097 PMCID: PMC8915811 DOI: 10.3389/ftox.2021.657765] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/22/2021] [Indexed: 12/31/2022] Open
Abstract
Microphysiological systems (MPS) have been actively developed as a new technology for in vitro toxicity testing platforms in recent years. MPS are culture techniques for the reconstruction of the specific functions of human organs or tissues in a limited space to create miniaturized human test systems. MPS have great promise as next-generation in vitro toxicity assessment systems. Here, I will review the current status of MPS and discuss the requirements that must be met in order for MPS to be implemented in the field of drug discovery, presenting the example of an in vitro cell assay system for drug-induced liver injury, which is the research subject in our laboratory. Projects aimed at the development of MPS were implemented early in Europe and the United States, and the AMED-MPS project was launched in Japan in 2017. The AMED-MPS project involves industry, government, and academia. Researchers in the field of drug discovery in the pharmaceutical industry also participate in the project. Based on the discussions made in the project, I will introduce the requirements that need to be met by liver-MPS as in vitro toxicity test platforms.
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Affiliation(s)
- Seiichi Ishida
- Division of Applied Life Science, Graduate School of Engineering, Sojo University, Kumamoto, Japan.,Biological Safety Research Center, National Institute of Health Sciences, Kawasaki, Japan
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Rapid Detection of Direct Compound Toxicity and Trailing Detection of Indirect Cell Metabolite Toxicity in a 96-Well Fluidic Culture Device for Cell-Based Screening Environments: Tactics in Six Sigma Quality Control Charts. APPLIED SCIENCES-BASEL 2022. [PMID: 37502123 PMCID: PMC10374175 DOI: 10.3390/app12062786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Microfluidic screening tools, in vitro, evolve amid varied scientific disciplines. One emergent technique, simultaneously assessing cell toxicity from a primary compound and ensuing cell-generated metabolites (dual-toxicity screening), entails in-line systems having sequentially aligned culture chambers. To explore dual-tox screens, we probe the dissemination of nutrients involving 1-way transport with upstream compound dosing, midstream cascading flows, and downstream cessation. Distribution of flow gives rise to broad concentration ranges of dosing compound (0→ICcompound100) and wide-ranging concentration ranges of generated cell metabolites (0→ICmetabolites100). Innately, single-pass unidirectional flow retains 1st pass informative traits across the network, composed of nine interconnected culture wells, preserving both compound and cell-secreted byproducts as data indicators in each adjacent culture chamber. Thereafter, to assess effective compound hepatotoxicity (0→ECcompound100) and simultaneously classify for cell-metabolite toxicity (0→ECmetabolite100), we reveal utility by analyzing culture viability against ramping exposures of acetaminophen (APAP) and nefazodone (NEF), compounds of hepatic significance. We then discern metabolite generation with an emphasis on amplification across µchannel multiwell sites. Lastly, using conventional cell functions as indicator tools to assess dual toxicity, we investigate a non-drug induced liver injury (non-DILI) compound and DILI compound. The technology is for predictive evaluations of new compound formulations, new chemical entities (NCE), or drugs that have previously failed testing for unresolved reasons.
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Graffmann N, Scherer B, Adjaye J. In vitro differentiation of pluripotent stem cells into hepatocyte like cells - basic principles and current progress. Stem Cell Res 2022; 61:102763. [DOI: 10.1016/j.scr.2022.102763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/08/2022] [Accepted: 03/22/2022] [Indexed: 12/11/2022] Open
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Youhanna S, Kemas AM, Preiss L, Zhou Y, Shen JX, Cakal SD, Paqualini FS, Goparaju SK, Shafagh RZ, Lind JU, Sellgren CM, Lauschke VM. Organotypic and Microphysiological Human Tissue Models for Drug Discovery and Development-Current State-of-the-Art and Future Perspectives. Pharmacol Rev 2022; 74:141-206. [PMID: 35017176 DOI: 10.1124/pharmrev.120.000238] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
The number of successful drug development projects has been stagnant for decades despite major breakthroughs in chemistry, molecular biology, and genetics. Unreliable target identification and poor translatability of preclinical models have been identified as major causes of failure. To improve predictions of clinical efficacy and safety, interest has shifted to three-dimensional culture methods in which human cells can retain many physiologically and functionally relevant phenotypes for extended periods of time. Here, we review the state of the art of available organotypic culture techniques and critically review emerging models of human tissues with key importance for pharmacokinetics, pharmacodynamics, and toxicity. In addition, developments in bioprinting and microfluidic multiorgan cultures to emulate systemic drug disposition are summarized. We close by highlighting important trends regarding the fabrication of organotypic culture platforms and the choice of platform material to limit drug absorption and polymer leaching while supporting the phenotypic maintenance of cultured cells and allowing for scalable device fabrication. We conclude that organotypic and microphysiological human tissue models constitute promising systems to promote drug discovery and development by facilitating drug target identification and improving the preclinical evaluation of drug toxicity and pharmacokinetics. There is, however, a critical need for further validation, benchmarking, and consolidation efforts ideally conducted in intersectoral multicenter settings to accelerate acceptance of these novel models as reliable tools for translational pharmacology and toxicology. SIGNIFICANCE STATEMENT: Organotypic and microphysiological culture of human cells has emerged as a promising tool for preclinical drug discovery and development that might be able to narrow the translation gap. This review discusses recent technological and methodological advancements and the use of these systems for hit discovery and the evaluation of toxicity, clearance, and absorption of lead compounds.
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Affiliation(s)
- Sonia Youhanna
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Aurino M Kemas
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Lena Preiss
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Joanne X Shen
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Selgin D Cakal
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Francesco S Paqualini
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Sravan K Goparaju
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Reza Zandi Shafagh
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Johan Ulrik Lind
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Carl M Sellgren
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden (S.Y., A.M.K., L.P., Y.Z., J.X.S., S.K.G., R.Z.S., C.M.S., V.M.L.); Department of Drug Metabolism and Pharmacokinetics (DMPK), Merck KGaA, Darmstadt, Germany (L.P.); Department of Health Technology, Technical University of Denmark, Lyngby, Denmark (S.D.C., J.U.L.); Synthetic Physiology Laboratory, Department of Civil Engineering and Architecture, University of Pavia, Pavia, Italy (F.S.P.); Division of Micro- and Nanosystems, KTH Royal Institute of Technology, Stockholm, Sweden (Z.S.); and Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany (V.M.L.)
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Suleman S, Payne A, Bowden J, Haque SA, Zahn M, Fawaz S, Khalifa MS, Jobling S, Hay D, Franco M, Fronza R, Wang W, Strobel-Freidekind O, Deichmann A, Takeuchi Y, Waddington SN, Gil-Farina I, Schmidt M, Themis M. HIV- 1 lentivirus tethering to the genome is associated with transcription factor binding sites found in genes that favour virus survival. Gene Ther 2022; 29:720-729. [PMID: 35513551 PMCID: PMC9750860 DOI: 10.1038/s41434-022-00335-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 01/09/2023]
Abstract
Lentiviral vectors (LV) are attractive for permanent and effective gene therapy. However, integration into the host genome can cause insertional mutagenesis highlighting the importance of understanding of LV integration. Insertion site (IS) tethering is believed to involve cellular proteins such as PSIP1/LEDGF/p75, which binds to the virus pre-integration complexes (PICs) helping to target the virus genome. Transcription factors (TF) that bind both the vector LTR and host genome are also suspected influential to this. To determine the role of TF in the tethering process, we mapped predicted transcription factor binding sites (pTFBS) near to IS chosen by HIV-1 LV using a narrow 20 bp window in infected human induced pluripotent stem cells (iPSCs) and their hepatocyte-like cell (HLC) derivatives. We then aligned the pTFBS with these sequences found in the LTRs of native and self-inactivated LTRs. We found significant enrichment of these sequences for pTFBS essential to HIV-1 life cycle and virus survival. These same sites also appear in HIV-1 patient IS and in mice infected with HIV-1 based LV. This in silco data analysis suggests pTFBS present in the virus LTR and IS sites selected by HIV-1 LV are important to virus survival and propagation.
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Affiliation(s)
- Saqlain Suleman
- grid.7728.a0000 0001 0724 6933Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK ,Testavec Ltd, Queensgate House, Maidenhead, UK
| | - Annette Payne
- Testavec Ltd, Queensgate House, Maidenhead, UK ,grid.7728.a0000 0001 0724 6933Department of Computer Science, College of Engineering Design and Physical Sciences, Brunel University London, Uxbridge, UK
| | - Johnathan Bowden
- grid.7728.a0000 0001 0724 6933Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
| | - Sharmin Al Haque
- grid.7728.a0000 0001 0724 6933Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
| | - Marco Zahn
- Genewerk GmbH, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373University Heidelberg, Medical Faculty, Heidelberg, Germany
| | - Serena Fawaz
- grid.7728.a0000 0001 0724 6933Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
| | - Mohammad S. Khalifa
- grid.7728.a0000 0001 0724 6933Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK
| | - Susan Jobling
- Testavec Ltd, Queensgate House, Maidenhead, UK ,grid.7728.a0000 0001 0724 6933Institute of Environment, Health and Societies, College of Business, Arts and Social Sciences, Brunel University London, Uxbridge, UK
| | - David Hay
- grid.4305.20000 0004 1936 7988Centre for Regenerative Medicine, The University of Edinburgh, Edinburgh, UK
| | | | | | - Wei Wang
- Genewerk GmbH, Heidelberg, Germany
| | | | | | - Yasuhiro Takeuchi
- grid.83440.3b0000000121901201Division of Infection and Immunity, University College London, London, UK ,grid.70909.370000 0001 2199 6511Division of Advanced Therapies, National Institute for Biological Standards and Control, Potters Bar, UK
| | - Simon N. Waddington
- grid.83440.3b0000000121901201Gene Transfer Technology, EGA Institute for Women’s Health, University College London, London, UK ,grid.11951.3d0000 0004 1937 1135MRC Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg, South Africa
| | | | - Manfred Schmidt
- Genewerk GmbH, Heidelberg, Germany ,grid.461742.20000 0000 8855 0365Department of Translational Oncology, NCT and DKFZ, Heidelberg, Germany
| | - Michael Themis
- grid.7728.a0000 0001 0724 6933Department of Life Sciences, College of Health, Medicine & Life Sciences, Brunel University London, Uxbridge, UK ,grid.7445.20000 0001 2113 8111Division of Ecology and Evolution, Department of Life Sciences, Imperial College London, London, UK
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Hu H, Zhao M, Li Z, Nie H, He J, Chen Z, Yuan J, Guo H, Zhang X, Yang H, Wu T, He M. Plasma miR-193b-3p Is Elevated in Type 2 Diabetes and Could Impair Glucose Metabolism. Front Endocrinol (Lausanne) 2022; 13:814347. [PMID: 35712251 PMCID: PMC9197112 DOI: 10.3389/fendo.2022.814347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 04/12/2022] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To explore differentially expressed miRNAs in type 2 diabetes and their potential cellular functions. METHODS We screened plasma miRNAs by miRNA array analysis and validated them by TaqMan real-time PCR in 113 newly diagnosed, untreated type 2 diabetes cases and 113 healthy controls. Low-abundance plasma proteins encoded by miR-193b-3p target genes were explored in this study population. We further investigated the potential cellular functions of the differentially expressed miRNAs in HepG2 cells. RESULTS miR-193b-3p was differentially expressed in type 2 diabetes cases compared to healthy controls (fold change = 2.01, P = 0.006). Plasma levels of triosephosphate isomerase (TPI1, a protein involved in the glycolytic pathway) decreased in type 2 diabetes cases (fold change = 1.37, P = 0.002). The effect of miR-193b-3p on TPI1 was verified by transfection of miR-193b-3p into HepG2 cells. miR-193b-3p inhibited the expression of YWHAZ/14-3-3ζ in the PI3K-AKT pathway, subsequently altering the expression of FOXO1 and PCK1. After transfection, cells were incubated in glucose-free medium for another 4 h. Glucose levels in medium from cells with elevated miR-193b-3p levels were significantly higher than those in medium from negative control cells (P = 0.016). In addition, elevated miR-193b-3p reduced glucose uptake by inhibiting insulin receptor (IR) and GLUT2 expression. CONCLUSION Plasma miR-193b-3p levels increased in type 2 diabetes cases, and TPI1 levels decreased in both plasma and HepG2 cells with increased miR-193b-3p levels, while extracellular lactate levels did not significantly changed. Moreover, miR-193b-3p may affect glucose metabolism by directly targeting YWHAZ/14-3-3ζ and upregulating the transcription factor FOXO1 downstream of the PI3K-AKT pathway.
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Affiliation(s)
- Hua Hu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Meng Zhao
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Zhaoyang Li
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Hongli Nie
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Jia He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Zhuo Chen
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Yuan
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Huan Guo
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Handong Yang
- Dongfeng Central Hospital, Dongfeng Motor Corporation and Hubei University of Medicine, Shiyan, China
| | - Tangchun Wu
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
| | - Meian He
- Department of Occupational and Environmental Health and State Key Laboratory of Environmental Health for Incubating, School of Public Health, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Meian He,
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select null#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select null,null,null,null,null,null#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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40
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Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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41
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select null,null,null,null,null,null,null-- lvco] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select null,null,null,null,null,null,null,null,null-- foap] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select 16,16,16,16,16,concat(0x716b6a7071,0x53626858706e68556454,0x7178767871),16,16,16,16#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select 16,16,16,concat(0x716b6a7071,0x6d73444b675570455555,0x7178767871),16,16,16,16,16,16#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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45
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select null,null,null,null,null,null,null,null,concat(0x716b6a7071,0x4676717248704b675778,0x7178767871),null#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select 16,16,16,concat(0x716b6a7071,0x6b6e754f54436f795551654a677441695869687a63736c685366707253435553414b554651546c6a,0x7178767871),16,16,16,16,16,16#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select null,null,null,null,null,concat(0x716b6a7071,0x6661577761656e567a64,0x7178767871),null,null,null,null#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 union all select 16,16,16,16,16,16,16,16,concat(0x716b6a7071,0x5a4d42416955786c58706f624a676258746b5a59706f726442475877545a4a657652577a766c4d62,0x7178767871),16#] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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The Curious Case of the HepG2 Cell Line: 40 Years of Expertise. Int J Mol Sci 2021. [DOI: 10.3390/ijms222313135 waitfor delay '0:0:5'-- oive] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is the third leading cause of cancer death worldwide. Representing such a dramatic impact on our lives, liver cancer is a significant public health concern. Sustainable and reliable methods for preventing and treating liver cancer require fundamental research on its molecular mechanisms. Cell lines are treated as in vitro equivalents of tumor tissues, making them a must-have for basic research on the nature of cancer. According to recent discoveries, certified cell lines retain most genetic properties of the original tumor and mimic its microenvironment. On the other hand, modern technologies allowing the deepest level of detail in omics landscapes have shown significant differences even between samples of the same cell line due to cross- and mycoplasma infection. This and other observations suggest that, in some cases, cell cultures are not suitable as cancer models, with limited predictive value for the effectiveness of new treatments. HepG2 is a popular hepatic cell line. It is used in a wide range of studies, from the oncogenesis to the cytotoxicity of substances on the liver. In this regard, we set out to collect up-to-date information on the HepG2 cell line to assess whether the level of heterogeneity of the cell line allows in vitro biomedical studies as a model with guaranteed production and quality.
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