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Moreno-Torres M, Kumar M, García-Llorens G, Quintás G, Tricot T, Boon R, Tolosa L, Toprakhisar B, Chesnais F, Verfaillie C, Castell JV. A Novel UPLC-MS Metabolomic Analysis-Based Strategy to Monitor the Course and Extent of iPSC Differentiation to Hepatocytes. J Proteome Res 2022; 21:702-712. [PMID: 34982937 DOI: 10.1021/acs.jproteome.1c00779] [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: 01/04/2023]
Abstract
Typical protocols to differentiate induced pluripotent stem cells (iPSCs) from hepatocyte-like cells (HLCs) imply complex strategies that include transfection with key hepatic transcription factors and the addition to culture media of nutrients, growth factors, and cytokines. A main constraint to evaluate the hepatic phenotype achieved arises from the way the grade of differentiation is determined. Currently, it relies on the assessment of the expression of a limited number of hepatic gene transcripts, less frequently by assessing certain hepatic metabolic functions, and rarely by the global metabolic performance of differentiated cells. We envisaged a new strategy to assess the extent of differentiation achieved, based on the analysis of the cellular metabolome along the differentiation process and its quantitative comparison with that of primary human hepatocytes (PHHs). To validate our approach, we examined the changes in the metabolome of three iPSC progenies (transfected with/without key transcription factors), cultured in three differentiation media, and compared them to PHHs. Results revealed consistent metabolome changes along differentiation and evidenced the factors that more strongly promote changes in the metabolome. The integrated dissimilarities between the PHHs and HLCs retrieved metabolomes were used as a numerical reference for quantifying the degree of iPSCs differentiation. This newly developed metabolome-analysis approach evidenced its utility in assisting us to select a cell's source, culture conditions, and differentiation media, to achieve better-differentiated HLCs.
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Affiliation(s)
- Marta Moreno-Torres
- Unidad de Hepatología Experimental, Health Research Institute La Fe, Valencia 46026, Spain
| | - Manoj Kumar
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven 3000, Belgium
| | - Guillem García-Llorens
- Unidad de Hepatología Experimental, Health Research Institute La Fe, Valencia 46026, Spain.,Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Valencia 46010, Spain
| | - Guillermo Quintás
- Health and Biomedicine, LEITAT Technological Center, Valencia 46026, Spain.,Analytical Unit, Health Research Institute La Fe, Valencia 46026, Spain
| | - Tine Tricot
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven 3000, Belgium
| | - Ruben Boon
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven 3000, Belgium.,Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston 02114, Massachusetts, United States.,The Broad Institute, Harvard & MIT, Cambridge 02142, Massachusetts, United States
| | - Laia Tolosa
- Unidad de Hepatología Experimental, Health Research Institute La Fe, Valencia 46026, Spain
| | - Burak Toprakhisar
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven 3000, Belgium
| | - Francois Chesnais
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven 3000, Belgium.,Academic Center of Reconstructive Science, King's College London, London SE1 9RT, U.K
| | - Catherine Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven 3000, Belgium
| | - José V Castell
- Unidad de Hepatología Experimental, Health Research Institute La Fe, Valencia 46026, Spain.,Analytical Unit, Health Research Institute La Fe, Valencia 46026, Spain.,Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Valencia 46010, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas, Instituto de Salud Carlos III, Madrid 28029, Spain
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2
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Huang D, Gibeley SB, Xu C, Xiao Y, Celik O, Ginsberg HN, Leong KW. Engineering liver microtissues for disease modeling and regenerative medicine. ADVANCED FUNCTIONAL MATERIALS 2020; 30:1909553. [PMID: 33390875 PMCID: PMC7774671 DOI: 10.1002/adfm.201909553] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Indexed: 05/08/2023]
Abstract
The burden of liver diseases is increasing worldwide, accounting for two million deaths annually. In the past decade, tremendous progress has been made in the basic and translational research of liver tissue engineering. Liver microtissues are small, three-dimensional hepatocyte cultures that recapitulate liver physiology and have been used in biomedical research and regenerative medicine. This review summarizes recent advances, challenges, and future directions in liver microtissue research. Cellular engineering approaches are used to sustain primary hepatocytes or produce hepatocytes derived from pluripotent stem cells and other adult tissues. Three-dimensional microtissues are generated by scaffold-free assembly or scaffold-assisted methods such as macroencapsulation, droplet microfluidics, and bioprinting. Optimization of the hepatic microenvironment entails incorporating the appropriate cell composition for enhanced cell-cell interactions and niche-specific signals, and creating scaffolds with desired chemical, mechanical and physical properties. Perfusion-based culture systems such as bioreactors and microfluidic systems are used to achieve efficient exchange of nutrients and soluble factors. Taken together, systematic optimization of liver microtissues is a multidisciplinary effort focused on creating liver cultures and on-chip models with greater structural complexity and physiological relevance for use in liver disease research, therapeutic development, and regenerative medicine.
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Affiliation(s)
- Dantong Huang
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Sarah B. Gibeley
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Cong Xu
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Ozgenur Celik
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Henry N. Ginsberg
- Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
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3
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Yoshimoto K, Minier N, Yang J, Imamura S, Stocking K, Patel J, Terada S, Hirai Y, Kamei KI. Recapitulation of Human Embryonic Heartbeat to Promote Differentiation of Hepatic Endoderm to Hepatoblasts. Front Bioeng Biotechnol 2020; 8:568092. [PMID: 33015019 PMCID: PMC7506096 DOI: 10.3389/fbioe.2020.568092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/19/2020] [Indexed: 11/13/2022] Open
Abstract
Hepatic development requires multiple sequential physicochemical environmental changes in an embryo, and human pluripotent stem cells (hPSCs) allow for the elucidation of this embryonic developmental process. However, the current in vitro methods for hPSC-hepatic differentiation, which employ various biochemical substances, produce hPSC-derived hepatocytes with less functionality than primary hepatocytes, due to a lack of physical stimuli, such as heart beating. Here, we developed a microfluidic platform that recapitulates the beating of a human embryonic heart to improve the functionality of hepatoblasts derived from hepatic endoderm (HE) in vitro. This microfluidic platform facilitates the application of multiple mechanical stretching forces, to mimic heart beating, to cultured hepatic endoderm cells to identify the optimal stimuli. Results show that stimulated HE-derived hepatoblasts increased cytochrome P450 3A (CYP3A) metabolic activity, as well as the expression of hepatoblast functional markers (albumin, cytokeratin 19 and CYP3A7), compared to unstimulated hepatoblasts. This approach of hepatic differentiation from hPSCs with the application of mechanical stimuli will facilitate improved methods for studying human embryonic liver development, as well as accurate pharmacological testing with functional liver cells.
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Affiliation(s)
- Koki Yoshimoto
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.,Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Laboratory of Cellular and Molecular Biomechanics, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Nicolas Minier
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Jiandong Yang
- Department of Micro Engineering, Kyoto University, Kyoto, Japan
| | - Satoshi Imamura
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Kaylene Stocking
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.,Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States
| | - Janmesh Patel
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Shiho Terada
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Yoshikazu Hirai
- Department of Micro Engineering, Kyoto University, Kyoto, Japan
| | - Ken-Ichiro Kamei
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan.,Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, China.,Department of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
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4
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iPSC-Derived Liver Organoids: A Journey from Drug Screening, to Disease Modeling, Arriving to Regenerative Medicine. Int J Mol Sci 2020; 21:ijms21176215. [PMID: 32867371 PMCID: PMC7503935 DOI: 10.3390/ijms21176215] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/20/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022] Open
Abstract
Liver transplantation is the most common treatment for patients suffering from liver failure that is caused by congenital diseases, infectious agents, and environmental factors. Despite a high rate of patient survival following transplantation, organ availability remains the key limiting factor. As such, research has focused on the transplantation of different cell types that are capable of repopulating and restoring liver function. The best cellular mix capable of engrafting and proliferating over the long-term, as well as the optimal immunosuppression regimens, remain to be clearly well-defined. Hence, alternative strategies in the field of regenerative medicine have been explored. Since the discovery of induced pluripotent stem cells (iPSC) that have the potential of differentiating into a broad spectrum of cell types, many studies have reported the achievement of iPSCs differentiation into liver cells, such as hepatocytes, cholangiocytes, endothelial cells, and Kupffer cells. In parallel, an increasing interest in the study of self-assemble or matrix-guided three-dimensional (3D) organoids have paved the way for functional bioartificial livers. In this review, we will focus on the recent breakthroughs in the development of iPSCs-based liver organoids and the major drawbacks and challenges that need to be overcome for the development of future applications.
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A two-step lineage reprogramming strategy to generate functionally competent human hepatocytes from fibroblasts. Cell Res 2019; 29:696-710. [PMID: 31270412 PMCID: PMC6796870 DOI: 10.1038/s41422-019-0196-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 06/04/2019] [Indexed: 01/05/2023] Open
Abstract
Terminally differentiated cells can be generated by lineage reprogramming, which is, however, hindered by incomplete conversion with residual initial cell identity and partial functionality. Here, we demonstrate a new reprogramming strategy by mimicking the natural regeneration route, which permits generating expandable hepatic progenitor cells and functionally competent human hepatocytes. Fibroblasts were first induced into human hepatic progenitor-like cells (hHPLCs), which could robustly expand in vitro and efficiently engraft in vivo. Moreover, hHPLCs could be efficiently induced into mature human hepatocytes (hiHeps) in vitro, whose molecular identity highly resembles primary human hepatocytes (PHHs). Most importantly, hiHeps could be generated in large quantity and were functionally competent to replace PHHs for drug-metabolism estimation, toxicity prediction and hepatitis B virus infection modeling. Our results highlight the advantages of the progenitor stage for successful lineage reprogramming. This strategy is promising for generating other mature human cell types by lineage reprogramming.
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6
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Wang J, Qu B, Zhang F, Zhang C, Deng W, Dao Thi VL, Xia Y. Stem Cell-Derived Hepatocyte-Like Cells as Model for Viral Hepatitis Research. Stem Cells Int 2019; 2019:9605252. [PMID: 31281392 PMCID: PMC6594266 DOI: 10.1155/2019/9605252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/09/2019] [Indexed: 02/06/2023] Open
Abstract
Viral hepatitis, the leading cause of liver diseases worldwide, is induced upon infection with hepatotropic viruses, including hepatitis A, B, C, D, and E virus. Due to their obligate intracellular lifestyles, culture systems for efficient viral replication are vital. Although basic and translational research on viral hepatitis has been performed for many years, conventional hepatocellular culture systems are not optimal. These studies have greatly benefited from recent efforts on improving cell culture models for virus replication and infection studies. Here we summarize the use of human stem cell-derived hepatocyte-like cells for hepatotropic virus infection studies, including the dissection of virus-host interactions and virus-induced pathogenesis as well as the identification and validation of novel antiviral agents.
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Affiliation(s)
- Jingjing Wang
- State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Bingqian Qu
- Department of Infectious Diseases, Molecular Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Fang Zhang
- Department of Translational Medicine, Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Cindy Zhang
- Schaller Research Group at Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany
- BioQuant Center, University of Heidelberg, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg, Germany
| | - Wanyan Deng
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Viet Loan Dao Thi
- Schaller Research Group at Department of Infectious Diseases, Molecular Virology, Heidelberg University Hospital, Cluster of Excellence CellNetworks, Heidelberg, Germany
| | - Yuchen Xia
- State Key Laboratory of Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
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Viiri LE, Rantapero T, Kiamehr M, Alexanova A, Oittinen M, Viiri K, Niskanen H, Nykter M, Kaikkonen MU, Aalto-Setälä K. Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation. Sci Rep 2019; 9:3562. [PMID: 30837492 PMCID: PMC6401154 DOI: 10.1038/s41598-019-39215-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/17/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatocyte-like cells (HLCs) derived from induced pluripotent stem cells (iPSCs) provide a renewable source of cells for drug discovery, disease modelling and cell-based therapies. Here, by using GRO-Seq we provide the first genome-wide analysis of the nascent RNAs in iPSCs, HLCs and primary hepatocytes to extend our understanding of the transcriptional changes occurring during hepatic differentiation process. We demonstrate that a large fraction of hepatocyte-specific genes are regulated at transcriptional level and identify hundreds of differentially expressed non-coding RNAs (ncRNAs), including primary miRNAs (pri-miRNAs) and long non-coding RNAs (lncRNAs). Differentiation induced alternative transcription start site (TSS) usage between the cell types as evidenced for miR-221/222 and miR-3613/15a/16-1 clusters. We demonstrate that lncRNAs and coding genes are tightly co-expressed and could thus be co-regulated. Finally, we identified sets of transcriptional regulators that might drive transcriptional changes during hepatocyte differentiation. These included RARG, E2F1, SP1 and FOXH1, which were associated with the down-regulated transcripts, and hepatocyte-specific TFs such as FOXA1, FOXA2, HNF1B, HNF4A and CEBPA, as well as RXR, PPAR, AP-1, JUNB, JUND and BATF, which were associated with up-regulated transcripts. In summary, this study clarifies the role of regulatory ncRNAs and TFs in differentiation of HLCs from iPSCs.
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Affiliation(s)
- Leena E Viiri
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland.
| | - Tommi Rantapero
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Mostafa Kiamehr
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Anna Alexanova
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Mikko Oittinen
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Keijo Viiri
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Katriina Aalto-Setälä
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
- Heart Center, Tampere University Hospital, Tampere, 33520, Finland
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