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Huang C, Jiang H, Dong J, Jiang L, Li J, Xu J, Cui T, Wang L, Li X, Feng G, Zhang Y, Li T, Li W, Zhou Q. Functional mouse hepatocytes derived from interspecies chimeric livers effectively mitigate chronic liver fibrosis. Stem Cell Reports 2024; 19:877-889. [PMID: 38729156 PMCID: PMC11390683 DOI: 10.1016/j.stemcr.2024.04.006] [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: 03/18/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
Liver disease is a major global health challenge. There is a shortage of liver donors worldwide, and hepatocyte transplantation (HT) may be an effective treatment to overcome this problem. However, the present approaches for generation of hepatocytes are associated with challenges, and interspecies chimera-derived hepatocytes produced by interspecies blastocyst complementation (IBC) may be promising donor hepatocytes because of their more comprehensive hepatic functions. In this study, we isolated mouse hepatocytes from mouse-rat chimeric livers using IBC and found that interspecies chimera-derived hepatocytes exhibited mature hepatic functions in terms of lipid accumulation, glycogen storage, and urea synthesis. Meanwhile, they were more similar to endogenous hepatocytes than hepatocytes derived in vitro. Interspecies chimera-derived hepatocytes could relieve chronic liver fibrosis and reside in the injured liver after transplantation. Our results suggest that interspecies chimera-derived hepatocytes are a potentially reliable source of hepatocytes and can be applied as a therapeutic approach for HT.
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Affiliation(s)
- Cheng Huang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiping Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingxi Dong
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Liyuan Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tongtong Cui
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Leyun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Xin Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Tianda Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing 100101, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Organ Regeneration and Reconstruction, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.
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Nieto-Romero V, García-Torralba A, Molinos-Vicente A, Moya FJ, Rodríguez-Perales S, García-Escudero R, Salido E, Segovia JC, García-Bravo M. Restored glyoxylate metabolism after AGXT gene correction and direct reprogramming of primary hyperoxaluria type 1 fibroblasts. iScience 2024; 27:109530. [PMID: 38577102 PMCID: PMC10993186 DOI: 10.1016/j.isci.2024.109530] [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] [Received: 04/03/2023] [Revised: 01/18/2024] [Accepted: 03/16/2024] [Indexed: 04/06/2024] Open
Abstract
Primary hyperoxaluria type 1 (PH1) is a rare inherited metabolic disorder characterized by oxalate overproduction in the liver, resulting in renal damage. It is caused by mutations in the AGXT gene. Combined liver and kidney transplantation is currently the only permanent curative treatment. We combined locus-specific gene correction and hepatic direct cell reprogramming to generate autologous healthy induced hepatocytes (iHeps) from PH1 patient-derived fibroblasts. First, site-specific AGXT corrected cells were obtained by homology directed repair (HDR) assisted by CRISPR-Cas9, following two different strategies: accurate point mutation (c.731T>C) correction or knockin of an enhanced version of AGXT cDNA. Then, iHeps were generated, by overexpression of hepatic transcription factors. Generated AGXT-corrected iHeps showed hepatic gene expression profile and exhibited in vitro reversion of oxalate accumulation compared to non-edited PH1-derived iHeps. This strategy set up a potential alternative cellular source for liver cell replacement therapy and a personalized PH1 in vitro disease model.
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Affiliation(s)
- Virginia Nieto-Romero
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Aida García-Torralba
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Andrea Molinos-Vicente
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Francisco José Moya
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | - Sandra Rodríguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | - Ramón García-Escudero
- Molecular Oncology Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)-ISCIII, Research Institute Hospital 12 de Octubre (imas12)-University Hospital 12 de Octubre, 28040 Madrid, Spain
| | - Eduardo Salido
- Pathology Department, Hospital Universitario de Canarias, Universidad La Laguna, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, 38320 Tenerife, Spain
| | - José-Carlos Segovia
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - María García-Bravo
- Cell Technology Division, Biomedical Innovation Unit, CIEMAT (Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-ISCIII, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
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3
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Garcia-Llorens G, Martínez-Sena T, Pareja E, Tolosa L, Castell JV, Bort R. A robust reprogramming strategy for generating hepatocyte-like cells usable in pharmaco-toxicological studies. Stem Cell Res Ther 2023; 14:94. [PMID: 37072803 PMCID: PMC10114490 DOI: 10.1186/s13287-023-03311-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/28/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND High-throughput pharmaco-toxicological testing frequently relies on the use of established liver-derived cell lines, such as HepG2 cells. However, these cells often display limited hepatic phenotype and features of neoplastic transformation that may bias the interpretation of the results. Alternate models based on primary cultures or differentiated pluripotent stem cells are costly to handle and difficult to implement in high-throughput screening platforms. Thus, cells without malignant traits, optimal differentiation pattern, producible in large and homogeneous amounts and with patient-specific phenotypes would be desirable. METHODS We have designed and implemented a novel and robust approach to obtain hepatocytes from individuals by direct reprogramming, which is based on a combination of a single doxycycline-inducible polycistronic vector system expressing HNF4A, HNF1A and FOXA3, introduced in human fibroblasts previously transduced with human telomerase reverse transcriptase (hTERT). These cells can be maintained in fibroblast culture media, under standard cell culture conditions. RESULTS Clonal hTERT-transduced human fibroblast cell lines can be expanded at least to 110 population doublings without signs of transformation or senescence. They can be easily differentiated at any cell passage number to hepatocyte-like cells with the simple addition of doxycycline to culture media. Acquisition of a hepatocyte phenotype is achieved in just 10 days and requires a simple and non-expensive cell culture media and standard 2D culture conditions. Hepatocytes reprogrammed from low and high passage hTERT-transduced fibroblasts display very similar transcriptomic profiles, biotransformation activities and show analogous pattern behavior in toxicometabolomic studies. Results indicate that this cell model outperforms HepG2 in toxicological screening. The procedure also allows generation of hepatocyte-like cells from patients with given pathological phenotypes. In fact, we succeeded in generating hepatocyte-like cells from a patient with alpha-1 antitrypsin deficiency, which recapitulated accumulation of intracellular alpha-1 antitrypsin polymers and deregulation of unfolded protein response and inflammatory networks. CONCLUSION Our strategy allows the generation of an unlimited source of clonal, homogeneous, non-transformed induced hepatocyte-like cells, capable of performing typical hepatic functions and suitable for pharmaco-toxicological high-throughput testing. Moreover, as far as hepatocyte-like cells derived from fibroblasts isolated from patients suffering hepatic dysfunctions, retain the disease traits, as demonstrated for alpha-1-antitrypsin deficiency, this strategy can be applied to the study of other cases of anomalous hepatocyte functionality.
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Affiliation(s)
- Guillem Garcia-Llorens
- Unidad de Hepatología Experimental y Trasplante Hepático, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politecnico La Fe, Torre A. Lab 6.08, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Valencia, Spain
| | - Teresa Martínez-Sena
- Unidad de Hepatología Experimental y Trasplante Hepático, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politecnico La Fe, Torre A. Lab 6.08, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
| | - Eugenia Pareja
- Unidad de Hepatología Experimental y Trasplante Hepático, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politecnico La Fe, Torre A. Lab 6.08, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Cirugía General y Aparato Digestivo, Hospital Universitario Dr. Peset, Valencia, Spain
| | - Laia Tolosa
- Unidad de Hepatología Experimental y Trasplante Hepático, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politecnico La Fe, Torre A. Lab 6.08, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
- Centro de Investigación Biomédica en Red de Bioingenieria, Biomateriales y Nanomedicina (CIBER-Bbn), Instituto de Salud Carlos III, Madrid, Spain
| | - José V Castell
- Unidad de Hepatología Experimental y Trasplante Hepático, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politecnico La Fe, Torre A. Lab 6.08, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Valencia, Spain
| | - Roque Bort
- Unidad de Hepatología Experimental y Trasplante Hepático, Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politecnico La Fe, Torre A. Lab 6.08, Avda. Fernando Abril Martorell 106, 46026, Valencia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.
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Abstract
Embryonic development and cell specification have been viewed as an epigenetically rigid process. Through accumulation of irreversible epigenetic marks, the differentiation process has been considered unidirectional, and once completed cell specification would be permanent and stable. However, somatic cell nuclear transfer that involved the implantation of a somatic nucleus into a previously enucleated oocyte accomplished in amphibians in the 1950s and in mammals in the late 1990s-resulting in the birth of "Dolly the sheep"-clearly showed that "terminal" differentiation is reversible. In parallel, work on lineage-determining factors like MyoD revealed surprising potential to modulate lineage identity in somatic cells. This work culminated in the discovery that a set of four defined factors can reprogram fibroblasts into induced pluripotent stem (iPS) cells, which were shown to be molecularly and functionally equivalent to blastocyst-derived embryonic stem (ES) cells, thus essentially showing that defined factors can induce authentic reprogramming without the need of oocytes. This concept was further extended when it was shown that fibroblasts can be directly converted into neurons, showing induced lineage conversion is possible even between cells representing two different germ layers. These findings suggest that "everything is possible" (i.e., once key lineage reprogramming factors are identified, cells should be able to convert into any desired lineage).
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Affiliation(s)
- Hannah Shelby
- Departments of Pathology and Chemical and Systems Biology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Tara Shelby
- Departments of Pathology and Chemical and Systems Biology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Marius Wernig
- Departments of Pathology and Chemical and Systems Biology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
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5
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Li R, Zhao Y, Yourick JJ, Sprando RL, Gao X. Phenotypical, functional and transcriptomic comparison of two modified methods of hepatocyte differentiation from human induced pluripotent stem cells. Biomed Rep 2022; 16:43. [PMID: 35371477 PMCID: PMC8972237 DOI: 10.3892/br.2022.1526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Directed differentiation of human induced pluripotent stem cells (iPSCs) into hepatocytes could provide an unlimited source of liver cells, and therefore holds great promise for regenerative medicine, disease modeling, drug screening and toxicology studies. Various methods have been established during the past decade to differentiate human iPSCs into hepatocyte-like cells (HLCs) using growth factors and/or small molecules. However, direct comparison of the differentiation efficiency and the quality of the final HLCs between different methods has rarely been reported. In the current study, two hepatocyte differentiation methods were devised, termed Method 1 and 2, through modifying existing well-known hepatocyte differentiation strategies, and the resultant cells were compared phenotypically and functionally at different stages of hepatocyte differentiation. Compared to Method 1, higher differentiation efficiency and reproducibility were observed in Method 2, which generated highly homogeneous functional HLCs at the end of the differentiation process. The cells exhibited morphology closely resembling primary human hepatocytes and expressed high levels of hepatic protein markers. More importantly, these HLCs demonstrated several essential characteristics of mature hepatocytes, including major serum protein (albumin, fibronectin and α-1 antitrypsin) secretion, urea release, glycogen storage and inducible cytochrome P450 activity. Further transcriptomic comparison of the HLCs derived from the two methods identified 1,481 differentially expressed genes (DEGs); 290 Gene Ontology terms in the biological process category were enriched by these genes, which were further categorized into 34 functional classes. Pathway analysis of the DEGs identified several signaling pathways closely involved in hepatocyte differentiation of pluripotent stem cells, including 'signaling pathways regulating pluripotency of stem cells', 'Wnt signaling pathway', 'TGF-beta signaling pathway' and 'PI3K-Akt signaling pathway'. These results may provide a molecular basis for the differences observed between the two differentiation methods and suggest ways to further improve hepatocyte differentiation in order to obtain more mature HLCs for biomedical applications.
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Affiliation(s)
- Rong Li
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Yang Zhao
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Jeffrey J Yourick
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Robert L Sprando
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
| | - Xiugong Gao
- Division of Toxicology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
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6
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Kuusisto F, Ng D, Steill J, Ross I, Livny M, Thomson J, Page D, Stewart R. KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications. F1000Res 2021; 9:832. [PMID: 35083039 PMCID: PMC8756297 DOI: 10.12688/f1000research.25523.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 11/21/2022] Open
Abstract
Many important scientific discoveries require lengthy experimental processes of trial and error and could benefit from intelligent prioritization based on deep domain understanding. While exponential growth in the scientific literature makes it difficult to keep current in even a single domain, that same rapid growth in literature also presents an opportunity for automated extraction of knowledge via text mining. We have developed a web application implementation of the KinderMiner algorithm for proposing ranked associations between a list of target terms and a key phrase. Any key phrase and target term list can be used for biomedical inquiry. We built the web application around a text index derived from PubMed. It is the first publicly available implementation of the algorithm, is fast and easy to use, and includes an interactive analysis tool. The KinderMiner web application is a public resource offering scientists a cohesive summary of what is currently known about a particular topic within the literature, and helping them to prioritize experiments around that topic. It performs comparably or better to similar state-of-the-art text mining tools, is more flexible, and can be applied to any biomedical topic of interest. It is also continually improving with quarterly updates to the underlying text index and through response to suggestions from the community. The web application is available at
https://www.kinderminer.org.
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Affiliation(s)
- Finn Kuusisto
- Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Daniel Ng
- Computer Sciences Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John Steill
- Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Ian Ross
- Computer Sciences Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Miron Livny
- Morgridge Institute for Research, Madison, WI, 53715, USA
- Computer Sciences Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - James Thomson
- Morgridge Institute for Research, Madison, WI, 53715, USA
- Department of Molecular and Cellular Biology, University of California, Santa Barbara, Santa Barbara, CA, 93117, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - David Page
- Department of Biostatistics & Bioinformatics, Duke University, Durham, NC, 27710, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI, 53715, USA
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Rombaut M, Boeckmans J, Rodrigues RM, van Grunsven LA, Vanhaecke T, De Kock J. Direct reprogramming of somatic cells into induced hepatocytes: Cracking the Enigma code. J Hepatol 2021; 75:690-705. [PMID: 33989701 DOI: 10.1016/j.jhep.2021.04.048] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 01/10/2023]
Abstract
There is an unmet need for functional primary human hepatocytes to support the pharmaceutical and (bio)medical demand. The unique discovery, a decade ago, that somatic cells can be drawn out of their apparent biological lockdown to reacquire a pluripotent state has revealed a completely new avenue of possibilities for generating surrogate human hepatocytes. Since then, the number of papers reporting the direct conversion of somatic cells into induced hepatocytes (iHeps) has burgeoned. A hepatic cell fate can be established via the ectopic expression of native liver-enriched transcription factors in somatic cells, thereby bypassing the need for an intermediate (pluripotent) stem cell state. That said, understanding and eventually controlling the processes that give rise to functional iHeps remains challenging. In this review, we provide an overview of the state-of-the-art reprogramming cocktails and techniques, as well as their corresponding conversion efficiencies. Special attention is paid to the role of liver-enriched transcription factors as hepatogenic reprogramming tools and small molecules as facilitators of hepatic transdifferentiation. To conclude, we formulate recommendations to optimise, standardise and enrich the in vitro production of iHeps to reach clinical standards, and propose minimal criteria for their characterisation.
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Affiliation(s)
- Matthias Rombaut
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium.
| | - Joost Boeckmans
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Robim M Rodrigues
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Leo A van Grunsven
- Liver Cell Biology Research Group, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Tamara Vanhaecke
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium
| | - Joery De Kock
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, B-1090 Brussels, Belgium.
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8
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Kulkeaw K, Pengsart W. Progress and Challenges in the Use of a Liver-on-a-Chip for Hepatotropic Infectious Diseases. MICROMACHINES 2021; 12:mi12070842. [PMID: 34357252 PMCID: PMC8306537 DOI: 10.3390/mi12070842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/13/2021] [Accepted: 07/17/2021] [Indexed: 12/16/2022]
Abstract
The liver is a target organ of life-threatening pathogens and prominently contributes to the variation in drug responses and drug-induced liver injury among patients. Currently available drugs significantly decrease the morbidity and mortality of liver-dwelling pathogens worldwide; however, emerging clinical evidence reveals the importance of host factors in the design of safe and effective therapies for individuals, known as personalized medicine. Given the primary adherence of cells in conventional two-dimensional culture, the use of these one-size-fit-to-all models in preclinical drug development can lead to substantial failures in assessing therapeutic safety and efficacy. Advances in stem cell biology, bioengineering and material sciences allow us to develop a more physiologically relevant model that is capable of recapitulating the human liver. This report reviews the current use of liver-on-a-chip models of hepatotropic infectious diseases in the context of precision medicine including hepatitis virus and malaria parasites, assesses patient-specific responses to antiviral drugs, and designs personalized therapeutic treatments to address the need for a personalized liver-like model. Second, most organs-on-chips lack a monitoring system for cell functions in real time; thus, the review discusses recent advances and challenges in combining liver-on-a-chip technology with biosensors for assessing hepatocyte viability and functions. Prospectively, the biosensor-integrated liver-on-a-chip device would provide novel biological insights that could accelerate the development of novel therapeutic compounds.
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Affiliation(s)
- Kasem Kulkeaw
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Correspondence: ; Tel.: +66-2-419-6468 (ext. 96484)
| | - Worakamol Pengsart
- Faculty of Graduate Studies, Mahidol University, Nakhon Pathom 73170, Thailand;
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9
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Kuusisto F, Ng D, Steill J, Ross I, Livny M, Thomson J, Page D, Stewart R. KinderMiner Web: a simple web tool for ranking pairwise associations in biomedical applications. F1000Res 2020; 9:832. [PMID: 35083039 PMCID: PMC8756297 DOI: 10.12688/f1000research.25523.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 11/03/2023] Open
Abstract
Many important scientific discoveries require lengthy experimental processes of trial and error and could benefit from intelligent prioritization based on deep domain understanding. While exponential growth in the scientific literature makes it difficult to keep current in even a single domain, that same rapid growth in literature also presents an opportunity for automated extraction of knowledge via text mining. We have developed a web application implementation of the KinderMiner algorithm for proposing ranked associations between a list of target terms and a key phrase. Any key phrase and target term list can be used for biomedical inquiry. We built the web application around a text index derived from PubMed. It is the first publicly available implementation of the algorithm, is fast and easy to use, and includes an interactive analysis tool. The KinderMiner web application is a public resource offering scientists a cohesive summary of what is currently known about a particular topic within the literature, and helping them to prioritize experiments around that topic. It performs comparably or better to similar state-of-the-art text mining tools, is more flexible, and can be applied to any biomedical topic of interest. It is also continually improving with quarterly updates to the underlying text index and through response to suggestions from the community. The web application is available at https://www.kinderminer.org.
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Affiliation(s)
- Finn Kuusisto
- Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Daniel Ng
- Computer Sciences Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - John Steill
- Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Ian Ross
- Computer Sciences Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Miron Livny
- Morgridge Institute for Research, Madison, WI, 53715, USA
- Computer Sciences Department, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - James Thomson
- Morgridge Institute for Research, Madison, WI, 53715, USA
- Department of Molecular and Cellular Biology, University of California, Santa Barbara, Santa Barbara, CA, 93117, USA
- School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - David Page
- Department of Biostatistics & Bioinformatics, Duke University, Durham, NC, 27710, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI, 53715, USA
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10
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Kunst RF, Niemeijer M, van der Laan LJW, Spee B, van de Graaf SFJ. From fatty hepatocytes to impaired bile flow: Matching model systems for liver biology and disease. Biochem Pharmacol 2020; 180:114173. [PMID: 32717228 DOI: 10.1016/j.bcp.2020.114173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 02/08/2023]
Abstract
A large variety of model systems are used in hepatobiliary research. In this review, we aim to provide an overview of established and emerging models for specific research questions. We specifically discuss the value and limitations of these models for research on metabolic associated fatty liver disease (MAFLD), (previously named non-alcoholic fatty liver diseases/non-alcoholic steatohepatitis (NAFLD/NASH)) and cholestasis-related diseases such as primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC). The entire range of models is discussed varying from immortalized cell lines, mature or pluripotent stem cell-based models including organoids/spheroids, to animal models and human ex vivo models such as normothermic machine perfusion of livers and living liver slices. Finally, the pros and cons of each model are discussed as well as the need in the scientific community for continuous innovation in model development to better mimic the human (patho)physiology.
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Affiliation(s)
- Roni F Kunst
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Marije Niemeijer
- Department of Surgery, Erasmus MC-University Medical Center, Rotterdam, the Netherlands; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC-University Medical Center, Rotterdam, the Netherlands
| | - Bart Spee
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Stan F J van de Graaf
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands.
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11
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Tricot T, De Boeck J, Verfaillie C. Alternative Cell Sources for Liver Parenchyma Repopulation: Where Do We Stand? Cells 2020; 9:E566. [PMID: 32121068 PMCID: PMC7140465 DOI: 10.3390/cells9030566] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/20/2020] [Accepted: 02/22/2020] [Indexed: 12/28/2022] Open
Abstract
Acute and chronic liver failure is a highly prevalent medical condition with high morbidity and mortality. Currently, the therapy is orthotopic liver transplantation. However, in some instances, chiefly in the setting of metabolic diseases, transplantation of individual cells, specifically functional hepatocytes, can be an acceptable alternative. The gold standard for this therapy is the use of primary human hepatocytes, isolated from livers that are not suitable for whole organ transplantations. Unfortunately, primary human hepatocytes are scarcely available, which has led to the evaluation of alternative sources of functional hepatocytes. In this review, we will compare the ability of most of these candidate alternative cell sources to engraft and repopulate the liver of preclinical animal models with the repopulation ability found with primary human hepatocytes. We will discuss the current shortcomings of the different cell types, and some of the next steps that we believe need to be taken to create alternative hepatocyte progeny capable of regenerating the failing liver.
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12
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Grath A, Dai G. Direct cell reprogramming for tissue engineering and regenerative medicine. J Biol Eng 2019; 13:14. [PMID: 30805026 PMCID: PMC6373087 DOI: 10.1186/s13036-019-0144-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 01/27/2019] [Indexed: 02/06/2023] Open
Abstract
Direct cell reprogramming, also called transdifferentiation, allows for the reprogramming of one somatic cell type directly into another, without the need to transition through an induced pluripotent state. Thus, it is an attractive approach to develop novel tissue engineering applications to treat diseases and injuries where there is a shortage of proliferating cells for tissue repair. In certain tissue damage, terminally differentiated somatic cells lose their ability to proliferate, as a result, damaged tissues cannot heal by themselves. Examples of these scenarios include myocardial infarctions, neurodegenerative diseases, and cartilage injuries. Transdifferentiation is capable of reprogramming cells that are abundant in the body into desired cell phenotypes that are able to restore tissue function in damaged areas. Therefore, direct cell reprogramming is a promising direction in the cell and tissue engineering and regenerative medicine fields. In recent years, several methods for transdifferentiation have been developed, ranging from the overexpression of transcription factors via viral vectors, to small molecules, to clustered regularly interspaced short palindromic repeats (CRISPR) and its associated protein (Cas9) for both genetic and epigenetic reprogramming. Overexpressing transcription factors by use of a lentivirus is currently the most prevalent technique, however it lacks high reprogramming efficiencies and can pose problems when transitioning to human subjects and clinical trials. CRISPR/Cas9, fused with proteins that modulate transcription, has been shown to improve efficiencies greatly. Transdifferentiation has successfully generated many cell phenotypes, including endothelial cells, skeletal myocytes, neuronal cells, and more. These cells have been shown to emulate mature adult cells such that they are able to mimic major functions, and some are capable of promoting regeneration of damaged tissue in vivo. While transdifferentiated cells have not yet seen clinical use, they have had promise in mice models, showing success in treating liver disease and several brain-related diseases, while also being utilized as a cell source for tissue engineered vascular grafts to treat damaged blood vessels. Recently, localized transdifferentiated cells have been generated in situ, allowing for treatments without invasive surgeries and more complete transdifferentiation. In this review, we summarized the recent development in various cell reprogramming techniques, their applications in converting various somatic cells, their uses in tissue regeneration, and the challenges of transitioning to a clinical setting, accompanied with potential solutions.
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Affiliation(s)
- Alexander Grath
- Department of Bioengineering, Northeastern University, Lake Hall 214A, 360 Huntington Avenue, Boston, MA 02115 USA
| | - Guohao Dai
- Department of Bioengineering, Northeastern University, Lake Hall 214A, 360 Huntington Avenue, Boston, MA 02115 USA
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13
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A serum-free medium suitable for maintaining cell morphology and liver-specific function in induced human hepatocytes. Cytotechnology 2019; 71:329-344. [PMID: 30603919 DOI: 10.1007/s10616-018-0289-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 12/05/2018] [Indexed: 12/15/2022] Open
Abstract
hiHep is a new type of hepatocyte-like cell that is predicted to be a potential unlimited source of hepatocytes for a bioartificial liver. However, hiHep cannot currently be used in clinical settings because serum must be added during the culture process. Thus, a defined medium is required. Because serum is complex, an efficient statistical approach based on the Plackett-Burman design was used. In this manner, an original medium and several significant cell growth factors were identified. These factors include insulin, VH, and VE, and the original medium was optimized based on these significant factors. Additionally, hiHep liver-specific functions and metabolism in the optimized serum-free medium were measured. Results showed that hiHep functions, such as glycogen storage, albumin secretion, and urea production, were well maintained in our optimized serum-free medium. In summary, we created a chemically defined, serum-free medium in which cell growth, proliferation, metabolism, and function were well maintained. This medium has the potential to support the clinical use of hiHep.
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14
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Katayama H, Yasuchika K, Miyauchi Y, Kojima H, Yamaoka R, Kawai T, Yukie Yoshitoshi E, Ogiso S, Kita S, Yasuda K, Sasaki N, Fukumitsu K, Komori J, Ishii T, Uemoto S. Generation of non-viral, transgene-free hepatocyte like cells with piggyBac transposon. Sci Rep 2017; 7:44498. [PMID: 28295042 PMCID: PMC5353749 DOI: 10.1038/srep44498] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/08/2017] [Indexed: 12/12/2022] Open
Abstract
Somatic cells can be reprogrammed to induced hepatocyte-like cells (iHeps) by overexpressing certain defined factors in direct reprogramming techniques. Of the various methods to deliver genes into cells, typically used genome-integrating viral vectors are associated with integration-related adverse events such as mutagenesis, whereas non-integrating viral vectors have low efficiency, making viral vectors unsuitable for clinical application. Therefore, we focused on developing a transposon system to establish a non-viral reprogramming method. Transposons are unique DNA elements that can be integrated into and removed from chromosomes. PiggyBac, a type of transposon, has high transduction efficiency and cargo capacity, and the integrated transgene can be precisely excised in the presence of transposase. This feature enables the piggyBac vector to achieve efficient transgene expression and a transgene-free state, thus making it a promising method for cell reprogramming. Here, we attempted to utilize the piggyBac transposon system to generate iHeps by integrating a transgene consisting of Hnf4a and Foxa3, and successfully obtained functional iHeps. We then demonstrated removal of the transgene to obtain transgene-free iHeps, which still maintained hepatocyte functions. This non-viral, transgene-free reprogramming method using the piggyBac vector may facilitate clinical applications of iHeps in upcoming cell therapy.
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Affiliation(s)
- Hokahiro Katayama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kentaro Yasuchika
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuya Miyauchi
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hidenobu Kojima
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryoya Yamaoka
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takayuki Kawai
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Elena Yukie Yoshitoshi
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Satoshi Ogiso
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Sadahiko Kita
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsutaro Yasuda
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Naoya Sasaki
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Fukumitsu
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junji Komori
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takamichi Ishii
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinji Uemoto
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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15
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Kamaraj US, Gough J, Polo JM, Petretto E, Rackham OJL. Computational methods for direct cell conversion. Cell Cycle 2016; 15:3343-3354. [PMID: 27736295 PMCID: PMC5224461 DOI: 10.1080/15384101.2016.1238119] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 09/08/2016] [Indexed: 12/19/2022] Open
Abstract
Directed cell conversion (or transdifferentiation) of one somatic cell-type to another can be achieved by ectopic expression of a set of transcription factors. Since the experimental identification of transcription factors for transdifferentiation is extremely time-consuming and expensive, there are still relatively few transdifferentiations achieved in comparison to the number of human cell-types. However, the growing volume of transcriptional data available and the recent introduction of data-driven algorithmic approaches that predict factors for transdifferentiation holds great promise for accelerating this field. Here we review those computational methods whose in-silico predictions have been experimentally validated, highlighting differences and similarities. Our analysis reveals that the factors predicted by each method tend to be different due to varying source cells used, gene expression quantification and algorithmic steps. We show these differences have an impact on the regulatory influences downstream, with some methods favoring transcription factors regulating developmental progression and others favoring factors regulating mature cell processes. These computational approaches offer a starting point to predict and test novel factors for transdifferentiation. We argue that collecting high-quality gene expression data from single-cells or pure cell-populations across a broader set of cell-types would be necessary to improve the quality and consistency of the in-silico predictions.
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Affiliation(s)
- Uma S. Kamaraj
- Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Julian Gough
- Department of Computer Science, University of Bristol, Bristol, UK
| | - Jose M. Polo
- Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Enrico Petretto
- Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Owen J. L. Rackham
- Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
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16
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Vasconcellos R, Alvarenga ÉC, Parreira RC, Lima SS, Resende RR. Exploring the cell signalling in hepatocyte differentiation. Cell Signal 2016; 28:1773-88. [DOI: 10.1016/j.cellsig.2016.08.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/18/2016] [Accepted: 08/18/2016] [Indexed: 02/08/2023]
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17
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Zakikhan K, Pournasr B, Nassiri-Asl M, Baharvand H. Enhanced direct conversion of fibroblasts into hepatocyte-like cells by Kdm2b. Biochem Biophys Res Commun 2016; 474:97-103. [PMID: 27103435 DOI: 10.1016/j.bbrc.2016.04.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 04/15/2016] [Indexed: 01/30/2023]
Abstract
Cell fate conversion of terminally differentiated cells by defined transcription factors between different lineages is a new approach to produce new cells that have the capability to repair or replace diseased and damaged tissues. Previous studies have demonstrated that this inefficient process can be facilitated by the inclusion of additional factors. Here we report that Kdm2b, a histone demethylase, has the capability to promote conversion of fibroblasts to functional induced hepatocyte-like (iHep) cells in combination with previously reported hepatic lineage transcription factors, Hnf4α and Foxa3. This approach led to increased numbers of epithelial-like colonies, hepatic markers and functionality which included periodic acid-Schiff (PAS) positive colonies, CYP450 activity, low-density lipoprotein and indocyanine green (ICG) uptake, as well as Albumin secretion. Additionally, the transplanted iHep cells were engraftable, expressed Albumin, and contributed to the recovery of a carbon tetrachloride-injured mouse model. These results have not only identified an important epigenetic factor for iHep generation, but also brought new insight into the molecular nature of hepatogenesis and future biomedical applications for liver diseases.
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Affiliation(s)
- Kobra Zakikhan
- Department of Molecular Medicine, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Behshad Pournasr
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Marjan Nassiri-Asl
- Cellular and Molecular Research Center, Department of Pharmacology, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran; Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran.
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18
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Forced expression of Hnf1b/Foxa3 promotes hepatic fate of embryonic stem cells. Biochem Biophys Res Commun 2016; 474:199-205. [DOI: 10.1016/j.bbrc.2016.04.102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 04/19/2016] [Indexed: 01/30/2023]
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19
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Rackham OJL, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS, Suzuki H, Nefzger CM, Daub CO, Shin JW, Petretto E, Forrest ARR, Hayashizaki Y, Polo JM, Gough J. A predictive computational framework for direct reprogramming between human cell types. Nat Genet 2016; 48:331-5. [PMID: 26780608 DOI: 10.1038/ng.3487] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/16/2015] [Indexed: 02/06/2023]
Abstract
Transdifferentiation, the process of converting from one cell type to another without going through a pluripotent state, has great promise for regenerative medicine. The identification of key transcription factors for reprogramming is currently limited by the cost of exhaustive experimental testing of plausible sets of factors, an approach that is inefficient and unscalable. Here we present a predictive system (Mogrify) that combines gene expression data with regulatory network information to predict the reprogramming factors necessary to induce cell conversion. We have applied Mogrify to 173 human cell types and 134 tissues, defining an atlas of cellular reprogramming. Mogrify correctly predicts the transcription factors used in known transdifferentiations. Furthermore, we validated two new transdifferentiations predicted by Mogrify. We provide a practical and efficient mechanism for systematically implementing novel cell conversions, facilitating the generalization of reprogramming of human cells. Predictions are made available to help rapidly further the field of cell conversion.
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Affiliation(s)
- Owen J L Rackham
- Department of Computer Science, University of Bristol, Bristol, UK.,Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore
| | - Jaber Firas
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hai Fang
- Department of Computer Science, University of Bristol, Bristol, UK
| | - Matt E Oates
- Department of Computer Science, University of Bristol, Bristol, UK
| | - Melissa L Holmes
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Anja S Knaupp
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | | | - Harukazu Suzuki
- RIKEN Omics Science Center, Yokohama, Japan (ceased to exist as of 1 April 2013 owing to reorganization).,Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Christian M Nefzger
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Carsten O Daub
- RIKEN Omics Science Center, Yokohama, Japan (ceased to exist as of 1 April 2013 owing to reorganization).,Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Jay W Shin
- RIKEN Omics Science Center, Yokohama, Japan (ceased to exist as of 1 April 2013 owing to reorganization).,Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore Medical School, Singapore
| | - Alistair R R Forrest
- RIKEN Omics Science Center, Yokohama, Japan (ceased to exist as of 1 April 2013 owing to reorganization).,Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.,Harry Perkins Institute of Medical Research, Queen Elizabeth II Medical Centre and Centre for Medical Research, University of Western Australia, Nedlands, Western Australia, Australia
| | - Yoshihide Hayashizaki
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.,Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.,Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Julian Gough
- Department of Computer Science, University of Bristol, Bristol, UK
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20
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Transcription factor-mediated reprograming of fibroblasts to hepatocyte-like cells. Eur J Cell Biol 2015; 94:603-10. [PMID: 26561000 DOI: 10.1016/j.ejcb.2015.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 09/04/2015] [Accepted: 10/21/2015] [Indexed: 02/07/2023] Open
Abstract
Direct conversion by overexpression of defined transcription factors (TFs) is a promising new method that can generate desired cell types from abundant, accessible cells. While previous studies have reported hepatic generation from fibroblasts, tremendous interest exists in the understanding of hepatic reprograming and its applicability in regenerative medicine. Here, we show that overexpression of Yamanaka factors can induce reprograming of mouse fibroblasts into cells that closely resemble hepatocytes in vitro in the presence of an optimized hepatic growth medium. By screening the effects of 20 candidate transcription factors, we identified a combination of three TFs (Hnf4a, Cebpa, and Nr1i2) that can convert fibroblasts into a hepatic fate. These factors in conjunction with Yamanaka factors increase the efficiency of hepatic reprograming. The induced hepatocyte-like (iHep) cells have multiple hepatocyte-specific characteristics; express hepatocyte-specific markers, glycogen storage, albumin secretion, urea production, as well as low-density lipoprotein and indocyanin green uptake. Production of iHep cells by these novel approaches may bring new insights into the molecular nature of hepatocyte differentiation and future cell-based therapeutics for liver diseases.
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21
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Sanal MG. Cell therapy from bench to bedside: Hepatocytes from fibroblasts - the truth and myth of transdifferentiation. World J Gastroenterol 2015; 21:6427-6433. [PMID: 26074681 PMCID: PMC4458753 DOI: 10.3748/wjg.v21.i21.6427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/24/2015] [Accepted: 05/07/2015] [Indexed: 02/06/2023] Open
Abstract
Hepatocyte transplantation is an alternative to liver transplantation in certain disorders such as inherited liver diseases and liver failure. It is a relatively less complicated surgical procedure, and has the advantage that it can be repeated several times if unsuccessful. Another advantage is that hepatocytes can be isolated from partly damaged livers which are not suitable for liver transplantation. Despite these advantages hepatocyte transplantation is less popular. Important issues are poor engraftment of the transplanted cells and the scarcity of donor hepatocytes. Generation of "hepatocyte like cells"/iHeps from embryonic stem cells (ES) and induced pluripotent stem cells (iPSCs) by directed differentiation is an emerging solution to the latter issue. Direct conversation or trans-differentiation of fibroblasts to "hepatocyte like cells" is another way which is, being explored. However this method has several inherent and technical disadvantages compared to the directed differentiation from ES or iPSC. There are several methods claiming to be "highly efficient" for generating "highly functional" "hepatocyte like cells". Currently different groups are working independently and coming up with differentiation protocols and each group claiming an advantage for their protocol. Directed differentiation protocols need to be designed, compared, analyzed and tweaked systematically and logically than empirically. There is a need for a well-coordinated global initiative comparable to the Human Genome Project to achieve this goal in the near future.
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22
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Pandian GN, Taniguchi J, Sugiyama H. Cellular reprogramming for pancreatic β-cell regeneration: clinical potential of small molecule control. Clin Transl Med 2014; 3:6. [PMID: 24679123 PMCID: PMC3984496 DOI: 10.1186/2001-1326-3-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 03/17/2014] [Indexed: 12/14/2022] Open
Abstract
Recent scientific breakthroughs in stem cell biology suggest that a sustainable treatment approach to cure diabetes mellitus (DM) can be achieved in the near future. However, the transplantation complexities and the difficulty in obtaining the stem cells from adult cells of pancreas, liver, bone morrow and other cells is a major concern. The epoch-making strategy of transcription-factor based cellular reprogramming suggest that these barriers could be overcome, and it is possible to reprogram any cells into functional β cells. Contemporary biological and analytical techniques help us to predict the key transcription factors needed for β-cell regeneration. These β cell-specific transcription factors could be modulated with diverse reprogramming protocols. Among cellular reprogramming strategies, small molecule approach gets proclaimed to have better clinical prospects because it does not involve genetic manipulation. Several small molecules targeting certain epigenetic enzymes and/or signaling pathways have been successful in helping to induce pancreatic β-cell specification. Recently, a synthetic DNA-based small molecule triggered targeted transcriptional activation of pancreas-related genes to suggest the possibility of achieving desired cellular phenotype in a precise mode. Here, we give a brief overview of treating DM by regenerating pancreatic β-cells from various cell sources. Through a comprehensive overview of the available transcription factors, small molecules and reprogramming strategies available for pancreatic β-cell regeneration, this review compiles the current progress made towards the generation of clinically relevant insulin-producing β-cells.
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Affiliation(s)
| | | | - Hiroshi Sugiyama
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo, Kyoto 606-8502, Japan.
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