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Blanch-Asensio A, Grandela C, Brandão KO, de Korte T, Mei H, Ariyurek Y, Yiangou L, Mol MP, van Meer BJ, Kloet SL, Mummery CL, Davis RP. STRAIGHT-IN enables high-throughput targeting of large DNA payloads in human pluripotent stem cells. CELL REPORTS METHODS 2022; 2:100300. [PMID: 36313798 PMCID: PMC9606106 DOI: 10.1016/j.crmeth.2022.100300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 07/12/2022] [Accepted: 08/31/2022] [Indexed: 04/20/2023]
Abstract
Inserting large DNA payloads (>10 kb) into specific genomic sites of mammalian cells remains challenging. Applications ranging from synthetic biology to evaluating the pathogenicity of disease-associated variants for precision medicine initiatives would greatly benefit from tools that facilitate this process. Here, we merge the strengths of different classes of site-specific recombinases and combine these with CRISPR-Cas9-mediated homologous recombination to develop a strategy for stringent site-specific replacement of genomic fragments at least 50 kb in size in human induced pluripotent stem cells (hiPSCs). We demonstrate the versatility of STRAIGHT-IN (serine and tyrosine recombinase-assisted integration of genes for high-throughput investigation) by (1) inserting various combinations of fluorescent reporters into hiPSCs to assess the excitation-contraction coupling cascade in derivative cardiomyocytes and (2) simultaneously targeting multiple variants associated with inherited cardiac arrhythmic disorders into a pool of hiPSCs. STRAIGHT-IN offers a precise approach to generate genetically matched panels of hiPSC lines efficiently and cost effectively.
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Affiliation(s)
- Albert Blanch-Asensio
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Catarina Grandela
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Karina O. Brandão
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Tessa de Korte
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Yavuz Ariyurek
- Leiden Genome Technology Center, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Loukia Yiangou
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Mervyn P.H. Mol
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Berend J. van Meer
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
| | - Susan L. Kloet
- Leiden Genome Technology Center, Leiden University Medical Center, 2333RC Leiden, the Netherlands
| | - Christine L. Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
- Department of Applied Stem Cell Technologies, University of Twente, 7500AE Enschede, the Netherlands
| | - Richard P. Davis
- Department of Anatomy and Embryology, Leiden University Medical Center, 2300RC Leiden, the Netherlands
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2
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Cre/Lox-based RMCE for Site-specific Integration in CHO Cells. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0332-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Human ESC-derived Neuromesodermal Progenitors (NMPs) Successfully Differentiate into Mesenchymal Stem Cells (MSCs). Stem Cell Rev Rep 2021; 18:278-293. [PMID: 34669151 DOI: 10.1007/s12015-021-10281-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2021] [Indexed: 10/20/2022]
Abstract
Mesenchymal Stem Cells (MSCs), as an adult stem cell type, are used to treat various disorders in clinics. However, derivation of homogenous and adequate amount of MSCs limits the regenerative treatment potential. Although mesoderm is the main source of mesenchymal progenitors during embryonic development, neuromesodermal progenitors (NMPs), reside in the primitive streak during development, is known to differentiate into paraxial mesoderm. In the current study, we generated NMPs from human embryonic stem cells (hESC), subsequently derived MSCs and characterized this cell population in vitro and in vivo. Using a bFGF and CHIR induced NMP formation protocol followed by serum containing culture conditions; here we show that MSCs can be generated from NMPs identified by not only the expression of T/Bra and Sox 2 but also FLK-1/PDGFRα in our study. NMP-derived MSCs were plastic adherent fibroblast like cells with colony forming capacity and trilineage (osteo-, chondro- and adipo-genic) differentiation potential. In the present study, we demonstrate that NMP-derived MSCs have an endothelial tendency which might be related to their FLK-1+/PDGFRα + NMP origin. NMP-derived MSCs displayed a protein expression profile of characterized MSCs. Growth factor and angiogenesis related pathway proteins were similarly expressed in NMP-derived MSCs and characterized MSCs. NMP-derived MSCs keep characteristics after short-term and long-term freeze-thaw cycles and localized into bone marrow followed by tail vein injection into NOD/SCID mice. Together, these data showed that hESC-derived NMPs might be used as a precursor cell population for MSC derivation and could be used for in vitro and in vivo research.
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Oksdath Mansilla M, Salazar-Hernandez C, Perrin SL, Scheer KG, Cildir G, Toubia J, Sedivakova K, Tea MN, Lenin S, Ponthier E, Yeo ECF, Tergaonkar V, Poonnoose S, Ormsby RJ, Pitson SM, Brown MP, Ebert LM, Gomez GA. 3D-printed microplate inserts for long term high-resolution imaging of live brain organoids. BMC Biomed Eng 2021; 3:6. [PMID: 33789767 PMCID: PMC8015192 DOI: 10.1186/s42490-021-00049-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Organoids are a reliable model used in the study of human brain development and under pathological conditions. However, current methods for brain organoid culture generate tissues that range from 0.5 to 2 mm of size, which need to be constantly agitated to allow proper oxygenation. The culture conditions are, therefore, not suitable for whole-brain organoid live imaging, required to study developmental processes and disease progression within physiologically relevant time frames (i.e. days, weeks, months). RESULTS Here we designed 3D-printed microplate inserts adaptable to standard 24 multi-well plates, which allow the growth of multiple organoids in pre-defined and fixed XYZ coordinates. This innovation facilitates high-resolution imaging of whole-cerebral organoids, allowing precise assessment of organoid growth and morphology, as well as cell tracking within the organoids, over long periods. We applied this technology to track neocortex development through neuronal progenitors in brain organoids, as well as the movement of patient-derived glioblastoma stem cells within healthy brain organoids. CONCLUSIONS This new bioengineering platform constitutes a significant advance that permits long term detailed analysis of whole-brain organoids using multimodal inverted fluorescence microscopy.
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Affiliation(s)
- Mariana Oksdath Mansilla
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia.
| | - Camilo Salazar-Hernandez
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Sally L Perrin
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Kaitlin G Scheer
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Gökhan Cildir
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - John Toubia
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Frome Road, Adelaide, SA, 5000, Australia
| | - Kristyna Sedivakova
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Melinda N Tea
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Sakthi Lenin
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Elise Ponthier
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Erica C F Yeo
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
| | - Vinay Tergaonkar
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A-STAR), Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Santosh Poonnoose
- Department of Neurosurgery, Flinders Medical Centre, Adelaide, SA, 5042, Australia
- Flinders Health & Medical Research Institute, College of Medicine & Public Health, Flinders University, Adelaide, SA, 5042, Australia
| | - Rebecca J Ormsby
- Flinders Health & Medical Research Institute, College of Medicine & Public Health, Flinders University, Adelaide, SA, 5042, Australia
| | - Stuart M Pitson
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, 5000, Australia
| | - Michael P Brown
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, 5000, Australia
- Cancer Clinical Trials Unit, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Lisa M Ebert
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, 5000, Australia
- Cancer Clinical Trials Unit, Royal Adelaide Hospital, Adelaide, SA, 5000, Australia
| | - Guillermo A Gomez
- Centre for Cancer Biology, SA Pathology and University of South Australia, Adelaide, SA, 5000, Australia.
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5
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Chang Y, Hellwarth PB, Randolph LN, Sun Y, Xing Y, Zhu W, Lian XL, Bao X. Fluorescent indicators for continuous and lineage-specific reporting of cell-cycle phases in human pluripotent stem cells. Biotechnol Bioeng 2020; 117:2177-2186. [PMID: 32277708 DOI: 10.1002/bit.27352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/22/2022]
Abstract
Proper cell-cycle progression is essential for the self-renewal and differentiation of human pluripotent stem cells (hPSCs). The fluorescent ubiquitination-based cell-cycle indicator (FUCCI) has allowed the dual-color visualization of the G1 and S/G2 /M phases in various dynamic models, but its application in hPSCs is not widely reported. In addition, lineage-specific FUCCI reporters have not yet been developed to analyze complex tissue-specific cell-cycle progression during hPSC differentiation. Desiring a robust tool for spatiotemporal reporting of cell-cycle events in hPSCs, we employed the CRISPR/Cas9 genome editing tool and successfully knocked the FUCCI reporter into the AAVS1 safe harbor locus of hPSCs for stable and constitutive FUCCI expression, exhibiting reliable cell-cycle-dependent fluorescence in both hPSCs and their differentiated progeny. We also established a cardiac-specific TNNT2-FUCCI reporter for lineage-specific cell-cycle monitoring of cardiomyocyte differentiation from hPSCs. This powerful and modular FUCCI system should provide numerous opportunities for studying human cell-cycle activity, and enable the identification and investigation of novel regulators for adult tissue regeneration.
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Affiliation(s)
- Yun Chang
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana
| | - Peter B Hellwarth
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana
| | - Lauren N Randolph
- Department of Biomedical Engineering, Huck institutes of the Life Sciences, Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Yufei Sun
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana
| | - Yuxian Xing
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana
| | - Wuqiang Zhu
- Department of Cardiovascular Medicine, Physiology and Biomedical Engineering, Mayo Clinic, Scottsdale, Arizona
| | - Xiaojun Lance Lian
- Department of Biomedical Engineering, Huck institutes of the Life Sciences, Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Xiaoping Bao
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana
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6
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Bao X, Adil MM, Muckom R, Zimmermann JA, Tran A, Suhy N, Xu Y, Sampayo RG, Clark DS, Schaffer DV. Gene Editing to Generate Versatile Human Pluripotent Stem Cell Reporter Lines for Analysis of Differentiation and Lineage Tracing. Stem Cells 2019; 37:1556-1566. [DOI: 10.1002/stem.3096] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 07/22/2019] [Accepted: 08/23/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Xiaoping Bao
- Department of Bioengineering; University of California; Berkeley California USA
- Department of Chemical and Biomolecular Engineering; University of California; Berkeley California USA
- Davidson School of Chemical Engineering; Purdue University; West Lafayette Indiana USA
| | - Maroof M. Adil
- Department of Bioengineering; University of California; Berkeley California USA
- Department of Chemical and Biomolecular Engineering; University of California; Berkeley California USA
| | - Riya Muckom
- Department of Bioengineering; University of California; Berkeley California USA
- Department of Chemical and Biomolecular Engineering; University of California; Berkeley California USA
| | - Joshua A. Zimmermann
- Department of Bioengineering; University of California; Berkeley California USA
- Department of Chemical and Biomolecular Engineering; University of California; Berkeley California USA
| | - Aurelie Tran
- Department of Molecular and Cell Biology; University of California; Berkeley California USA
| | - Natalie Suhy
- Department of Molecular and Cell Biology; University of California; Berkeley California USA
| | - Yibo Xu
- Davidson School of Chemical Engineering; Purdue University; West Lafayette Indiana USA
| | - Rocío G. Sampayo
- Department of Bioengineering; University of California; Berkeley California USA
- Department of Chemical and Biomolecular Engineering; University of California; Berkeley California USA
| | - Douglas S. Clark
- Department of Chemical and Biomolecular Engineering; University of California; Berkeley California USA
- Department of Chemistry; University of California; Berkeley California USA
| | - David V. Schaffer
- Department of Bioengineering; University of California; Berkeley California USA
- Department of Chemical and Biomolecular Engineering; University of California; Berkeley California USA
- Davidson School of Chemical Engineering; Purdue University; West Lafayette Indiana USA
- Department of Molecular and Cell Biology; University of California; Berkeley California USA
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7
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Panepucci RA, de Souza Lima IM. Arrayed functional genetic screenings in pluripotency reprogramming and differentiation. Stem Cell Res Ther 2019; 10:24. [PMID: 30635073 PMCID: PMC6330485 DOI: 10.1186/s13287-018-1124-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Thoroughly understanding the molecular mechanisms responsible for the biological properties of pluripotent stem cells, as well as for the processes involved in reprograming, differentiation, and transition between Naïve and Primed pluripotent states, is of great interest in basic and applied research. Although pluripotent cells have been extensively characterized in terms of their transcriptome and miRNome, a comprehensive understanding of how these gene products specifically impact their biology, depends on gain- or loss-of-function experimental approaches capable to systematically interrogate their function. We review all studies carried up to date that used arrayed screening approaches to explore the function of these genetic elements on those biological contexts, using focused or genome-wide genetic libraries. We further discuss the limitations and advantages of approaches based on assays with population-level primary readouts, derived from single-parameter plate readers, or cell-level primary readouts, obtained using multiparametric flow cytometry or quantitative fluorescence microscopy (i.e., high-content screening). Finally, we discuss technical limitation and future perspectives, highlighting how the integration of screening data may lead to major advances in the field of stem cell research and therapy.
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Affiliation(s)
- Rodrigo Alexandre Panepucci
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP CEP: 14051-140 Brazil
- Department of Genetics, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP Brazil
| | - Ildercílio Mota de Souza Lima
- Laboratory of Functional Biology (LFBio), Center for Cell-Based Therapy (CTC), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP CEP: 14051-140 Brazil
- Department of Genetics, Ribeirao Preto Medical School, University of São Paulo (FMRP-USP), Ribeirão Preto, SP Brazil
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8
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Luo J, Arbely E, Zhang J, Chou C, Uprety R, Chin JW, Deiters A. Genetically encoded optical activation of DNA recombination in human cells. Chem Commun (Camb) 2018; 52:8529-32. [PMID: 27277957 PMCID: PMC5048445 DOI: 10.1039/c6cc03934k] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We developed two tightly regulated, light-activated Cre recombinase enzymes through site-specific incorporation of two genetically-encoded photocaged amino acids in human cells. Excellent optical off to on switching of DNA recombination was achieved. Furthermore, we demonstrated precise spatial control of Cre recombinase through patterned illumination.
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Affiliation(s)
- J Luo
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania 15260, USA.
| | - E Arbely
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB20QH, UK and Department of Chemistry and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
| | - J Zhang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - C Chou
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - R Uprety
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - J W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB20QH, UK
| | - A Deiters
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania 15260, USA.
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9
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Zaccagnini G, Maimone B, Fuschi P, Maselli D, Spinetti G, Gaetano C, Martelli F. Overexpression of miR-210 and its significance in ischemic tissue damage. Sci Rep 2017; 7:9563. [PMID: 28842599 PMCID: PMC5573334 DOI: 10.1038/s41598-017-09763-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 07/28/2017] [Indexed: 02/07/2023] Open
Abstract
Hypoxia-induced miR-210 displays a pro-survival, cytoprotective and pro-angiogenic role in several in vitro systems. In vivo, we previously found that miR-210 inhibition increases ischemic damage. Here we describe the generation of a versatile transgenic mouse model allowing the evaluation of miR-210 therapeutic potential in ischemic cardiovascular diseases. We generated a Tet-On miR-210 transgenic mouse strain (TG-210) by targeted transgenesis in the ROSA26 locus. To functionally validate miR-210 transgenic mice, hindlimb ischemia was induced by femoral artery dissection. Blood perfusion was evaluated by power Doppler while tissue damage and inflammation were assessed by histological evaluation. We found that miR-210 levels were rapidly increased in TG-210 mice upon doxycycline administration. miR-210 overexpression was maintained over time and remained within physiological levels in multiple tissues. When hindlimb ischemia was induced, miR-210 overexpression protected from both muscular and vascular ischemic damage, decreased inflammatory cells density and allowed to maintain a better calf perfusion. In conclusion, we generated and functionally validated a miR-210 transgenic mouse model. Albeit validated in the context of a specific cardiovascular ischemic disease, miR-210 transgenic mice may also represent a useful model to assess the function of miR-210 in other physio-pathological conditions.
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Affiliation(s)
- G Zaccagnini
- Laboratory of Molecular Cardiology, Policlinico San Donato-IRCCS, 20097 San Donato Milanese, Milan, Italy
| | - B Maimone
- Laboratory of Molecular Cardiology, Policlinico San Donato-IRCCS, 20097 San Donato Milanese, Milan, Italy
| | - P Fuschi
- Laboratory of Molecular Cardiology, Policlinico San Donato-IRCCS, 20097 San Donato Milanese, Milan, Italy
| | - D Maselli
- Laboratory of Cardiovascular Research, MultiMedica-IRCCS, 20138, Milan, Italy
| | - G Spinetti
- Laboratory of Cardiovascular Research, MultiMedica-IRCCS, 20138, Milan, Italy
| | - C Gaetano
- Division of Cardiovascular Epigenetics, Department of Cardiology, Internal Medicine Clinic III, Goethe University, Frankfurt am Main, Germany
| | - F Martelli
- Laboratory of Molecular Cardiology, Policlinico San Donato-IRCCS, 20097 San Donato Milanese, Milan, Italy.
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10
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Ordovás L, Boon R, Pistoni M, Chen Y, Sambathkumar R, Helsen N, Vanhove J, Berckmans P, Cai Q, Vanuytsel K, Raitano S, Verfaillie CM. Rapid and Efficient Generation of Recombinant Human Pluripotent Stem Cells by Recombinase-mediated Cassette Exchange in the AAVS1 Locus. J Vis Exp 2016. [PMID: 27911376 PMCID: PMC5226264 DOI: 10.3791/54718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Even with the revolution of gene-targeting technologies led by CRISPR-Cas9, genetic modification of human pluripotent stem cells (hPSCs) is still time consuming. Comparative studies that use recombinant lines with transgenes integrated into safe harbor loci could benefit from approaches that use site-specific targeted recombinases, like Cre or FLPe, which are more rapid and less prone to off-target effects. Such methods have been described, although they do not significantly outperform gene targeting in most aspects. Using Zinc-finger nucleases, we previously created a master cell line in the AAVS1 locus of hPSCs that contains a GFP-Hygromycin-tk expressing cassette, flanked by heterotypic FRT sequences. Here, we describe the procedures to perform FLPe recombinase-mediated cassette exchange (RMCE) using this line. The master cell line is transfected with a RMCE donor vector, which contains a promoterless Puromycin resistance, and with FLPe recombinase. Application of both a positive (Puromycin) and negative (FIAU) selection program leads to the selection of RMCE without random integrations. RMCE generates fully characterized pluripotent polyclonal transgenic lines in 15 d with 100% efficiency. Despite the recently described limitations of the AAVS1 locus, the ease of the system paves the way for hPSC transgenesis in isogenic settings, is necessary for comparative studies, and enables semi-high-throughput genetic screens for gain/loss of function analysis that would otherwise be highly time consuming.
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Affiliation(s)
- Laura Ordovás
- Stem Cell Institute, Katholieke Universiteit Leuven;
| | - Ruben Boon
- Stem Cell Institute, Katholieke Universiteit Leuven
| | | | - Yemiao Chen
- Stem Cell Institute, Katholieke Universiteit Leuven
| | | | - Nicky Helsen
- Stem Cell Institute, Katholieke Universiteit Leuven
| | | | | | - Qing Cai
- Stem Cell Institute, Katholieke Universiteit Leuven
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11
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Lent-On-Plus Lentiviral vectors for conditional expression in human stem cells. Sci Rep 2016; 6:37289. [PMID: 27853296 PMCID: PMC5112523 DOI: 10.1038/srep37289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 10/28/2016] [Indexed: 12/25/2022] Open
Abstract
Conditional transgene expression in human stem cells has been difficult to achieve due to the low efficiency of existing delivery methods, the strong silencing of the transgenes and the toxicity of the regulators. Most of the existing technologies are based on stem cells clones expressing appropriate levels of tTA or rtTA transactivators (based on the TetR-VP16 chimeras). In the present study, we aim the generation of Tet-On all-in-one lentiviral vectors (LVs) that tightly regulate transgene expression in human stem cells using the original TetR repressor. By using appropriate promoter combinations and shielding the LVs with the Is2 insulator, we have constructed the Lent-On-Plus Tet-On system that achieved efficient transgene regulation in human multipotent and pluripotent stem cells. The generation of inducible stem cell lines with the Lent-ON-Plus LVs did not require selection or cloning, and transgene regulation was maintained after long-term cultured and upon differentiation toward different lineages. To our knowledge, Lent-On-Plus is the first all-in-one vector system that tightly regulates transgene expression in bulk populations of human pluripotent stem cells and its progeny.
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12
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Kaus A, Sareen D. ALS Patient Stem Cells for Unveiling Disease Signatures of Motoneuron Susceptibility: Perspectives on the Deadly Mitochondria, ER Stress and Calcium Triad. Front Cell Neurosci 2015; 9:448. [PMID: 26635528 PMCID: PMC4652136 DOI: 10.3389/fncel.2015.00448] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a largely sporadic progressive neurodegenerative disease affecting upper and lower motoneurons (MNs) whose specific etiology is incompletely understood. Mutations in superoxide dismutase-1 (SOD1), TAR DNA-binding protein 43 (TARDBP/TDP-43) and C9orf72, have been identified in subsets of familial and sporadic patients. Key associated molecular and neuropathological features include ubiquitinated TDP-43 inclusions, stress granules, aggregated dipeptide proteins from mutant C9orf72 transcripts, altered mitochondrial ultrastructure, dysregulated calcium homeostasis, oxidative and endoplasmic reticulum (ER) stress, and an unfolded protein response (UPR). Such impairments have been documented in ALS animal models; however, whether these mechanisms are initiating factors or later consequential events leading to MN vulnerability in ALS patients is debatable. Human induced pluripotent stem cells (iPSCs) are a valuable tool that could resolve this “chicken or egg” causality dilemma. Relevant systems for probing pathophysiologically affected cells from large numbers of ALS patients and discovering phenotypic disease signatures of early MN susceptibility are described. Performing unbiased ‘OMICS and high-throughput screening in relevant neural cells from a cohort of ALS patient iPSCs, and rescuing mitochondrial and ER stress impairments, can identify targeted therapeutics for increasing MN longevity in ALS.
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Affiliation(s)
- Anjoscha Kaus
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center Los Angeles, CA, USA ; Department of Biomedical Sciences, Cedars-Sinai Medical Center Los Angeles, CA, USA
| | - Dhruv Sareen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center Los Angeles, CA, USA ; Department of Biomedical Sciences, Cedars-Sinai Medical Center Los Angeles, CA, USA ; iPSC Core, The David and Janet Polak Stem Cell Laboratory, Cedars-Sinai Medical Center Los Angeles, CA, USA
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13
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Ordovás L, Boon R, Pistoni M, Chen Y, Wolfs E, Guo W, Sambathkumar R, Bobis-Wozowicz S, Helsen N, Vanhove J, Berckmans P, Cai Q, Vanuytsel K, Eggermont K, Vanslembrouck V, Schmidt BZ, Raitano S, Van Den Bosch L, Nahmias Y, Cathomen T, Struys T, Verfaillie CM. Efficient Recombinase-Mediated Cassette Exchange in hPSCs to Study the Hepatocyte Lineage Reveals AAVS1 Locus-Mediated Transgene Inhibition. Stem Cell Reports 2015; 5:918-931. [PMID: 26455413 PMCID: PMC4649136 DOI: 10.1016/j.stemcr.2015.09.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 09/07/2015] [Accepted: 09/07/2015] [Indexed: 01/08/2023] Open
Abstract
Tools for rapid and efficient transgenesis in "safe harbor" loci in an isogenic context remain important to exploit the possibilities of human pluripotent stem cells (hPSCs). We created hPSC master cell lines suitable for FLPe recombinase-mediated cassette exchange (RMCE) in the AAVS1 locus that allow generation of transgenic lines within 15 days with 100% efficiency and without random integrations. Using RMCE, we successfully incorporated several transgenes useful for lineage identification, cell toxicity studies, and gene overexpression to study the hepatocyte lineage. However, we observed unexpected and variable transgene expression inhibition in vitro, due to DNA methylation and other unknown mechanisms, both in undifferentiated hESC and differentiating hepatocytes. Therefore, the AAVS1 locus cannot be considered a universally safe harbor locus for reliable transgene expression in vitro, and using it for transgenesis in hPSC will require careful assessment of the function of individual transgenes.
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Affiliation(s)
- Laura Ordovás
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium.
| | - Ruben Boon
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium
| | - Mariaelena Pistoni
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium
| | - Yemiao Chen
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium
| | - Esther Wolfs
- Group of Morphology, Biomedical Research Institute, Hasselt University, Diepenbeek 3590, Belgium
| | - Wenting Guo
- Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium; Department of Neurosciences, Experimental Neurology, KU Leuven, Leuven 3000, Belgium; Laboratory for Neurobiology, VIB-Vesalius Research Center, Leuven 3000, Belgium
| | - Rangarajan Sambathkumar
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium
| | - Sylwia Bobis-Wozowicz
- Institute for Cell and Gene Therapy, University Medical Center Freiburg, Freiburg 79108, Germany; Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg 79108, Germany
| | - Nicky Helsen
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium
| | - Jolien Vanhove
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium
| | - Pieter Berckmans
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium
| | - Qing Cai
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium
| | - Kim Vanuytsel
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium
| | - Kristel Eggermont
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium
| | - Veerle Vanslembrouck
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium
| | - Béla Z Schmidt
- Switch Laboratory, VIB, Leuven 3000, Belgium; Department of Cellular and Molecular Medicine, Switch Laboratory, KU Leuven, Leuven 300, Belgium
| | - Susanna Raitano
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium
| | - Ludo Van Den Bosch
- Leuven Research Institute for Neuroscience and Disease (LIND), Leuven 3000, Belgium; Department of Neurosciences, Experimental Neurology, KU Leuven, Leuven 3000, Belgium; Laboratory for Neurobiology, VIB-Vesalius Research Center, Leuven 3000, Belgium
| | - Yaakov Nahmias
- Department of Cell and Developmental Biology, Hebrew University of Jerusalem, Jerusalem 91904, Israel; Grass Center for Bioengineering, Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Toni Cathomen
- Institute for Cell and Gene Therapy, University Medical Center Freiburg, Freiburg 79108, Germany; Center for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg 79108, Germany
| | - Tom Struys
- Group of Morphology, Biomedical Research Institute, Hasselt University, Diepenbeek 3590, Belgium
| | - Catherine M Verfaillie
- Stem Cell Institute, KU Leuven, Leuven 3000, Belgium; Department of Development and Regeneration, Stem Cell Biology and Embryology, KU Leuven, Leuven 3000, Belgium.
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14
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Cerbini T, Funahashi R, Luo Y, Liu C, Park K, Rao M, Malik N, Zou J. Transcription activator-like effector nuclease (TALEN)-mediated CLYBL targeting enables enhanced transgene expression and one-step generation of dual reporter human induced pluripotent stem cell (iPSC) and neural stem cell (NSC) lines. PLoS One 2015; 10:e0116032. [PMID: 25587899 PMCID: PMC4294658 DOI: 10.1371/journal.pone.0116032] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/30/2014] [Indexed: 01/28/2023] Open
Abstract
Targeted genome engineering to robustly express transgenes is an essential methodology for stem cell-based research and therapy. Although designer nucleases have been used to drastically enhance gene editing efficiency, targeted addition and stable expression of transgenes to date is limited at single gene/locus and mostly PPP1R12C/AAVS1 in human stem cells. Here we constructed transcription activator-like effector nucleases (TALENs) targeting the safe-harbor like gene CLYBL to mediate reporter gene integration at 38%–58% efficiency, and used both AAVS1-TALENs and CLYBL-TALENs to simultaneously knock-in multiple reporter genes at dual safe-harbor loci in human induced pluripotent stem cells (iPSCs) and neural stem cells (NSCs). The CLYBL-TALEN engineered cell lines maintained robust reporter expression during self-renewal and differentiation, and revealed that CLYBL targeting resulted in stronger transgene expression and less perturbation on local gene expression than PPP1R12C/AAVS1. TALEN-mediated CLYBL engineering provides improved transgene expression and options for multiple genetic modification in human stem cells.
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Affiliation(s)
- Trevor Cerbini
- NIH Center for Regenerative Medicine, Laboratory of Stem Cell Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, Maryland, United States of America
| | - Ray Funahashi
- NIH Center for Regenerative Medicine, Laboratory of Stem Cell Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, Maryland, United States of America
| | - Yongquan Luo
- NIH Center for Regenerative Medicine, Laboratory of Stem Cell Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, Maryland, United States of America
| | - Chengyu Liu
- Center for Molecular Medicine, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - Kyeyoon Park
- Stem Cell Unit, National Institute of Neurological Disorders and Stroke, Bethesda, Maryland, United States of America
| | - Mahendra Rao
- NIH Center for Regenerative Medicine, Laboratory of Stem Cell Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, Maryland, United States of America
| | - Nasir Malik
- NIH Center for Regenerative Medicine, Laboratory of Stem Cell Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, Maryland, United States of America
| | - Jizhong Zou
- NIH Center for Regenerative Medicine, Laboratory of Stem Cell Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, Maryland, United States of America
- Center for Molecular Medicine, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
- * E-mail:
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15
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Qian K, Huang CTL, Huang CL, Chen H, Blackbourn LW, Chen Y, Cao J, Yao L, Sauvey C, Du Z, Zhang SC. A simple and efficient system for regulating gene expression in human pluripotent stem cells and derivatives. Stem Cells 2014; 32:1230-8. [PMID: 24497442 DOI: 10.1002/stem.1653] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 01/06/2014] [Indexed: 12/19/2022]
Abstract
Regulatable transgene expression in human pluripotent stem cells (hPSCs) and their progenies is often necessary to dissect gene function in a temporal and spatial manner. However, hPSC lines with inducible transgene expression, especially in differentiated progenies, have not been established due to silencing of randomly inserted genes during stem cell expansion and/or differentiation. Here, we report the use of transcription activator-like effector nucleases-mediated targeting to AAVS1 site to generate versatile conditional hPSC lines. Transgene (both green fluorescent protein and a functional gene) expression in hPSCs and their derivatives was not only sustained but also tightly regulated in response to doxycycline both in vitro and in vivo. We modified the donor construct so that any gene of interest can be readily inserted to produce hPSC lines with conditional transgene expression. This technology will substantially improve the way we study human stem cells.
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Affiliation(s)
- Kun Qian
- Reproductive Medicine Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China; Waisman Center, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
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16
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Kim HS, Bernitz JM, Lee DF, Lemischka IR. Genomic editing tools to model human diseases with isogenic pluripotent stem cells. Stem Cells Dev 2014; 23:2673-86. [PMID: 25075441 PMCID: PMC4216528 DOI: 10.1089/scd.2014.0167] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/30/2014] [Indexed: 12/21/2022] Open
Abstract
Patient-specific induced pluripotent stem cells (iPSCs) are considered a versatile resource in the field of biomedicine. As iPSCs are generated on an individual basis, iPSCs may be the optimal cellular material to use for disease modeling, drug discovery, and the development of patient-specific cellular therapies. Recently, to gain an in-depth understanding of human pathologies, patient-specific iPSCs have been used to model human diseases with some iPSC-derived cells recapitulating pathological phenotypes in vitro. However, complex multigenic diseases generally have not resulted in concise conclusions regarding the underlying mechanisms of disease, in large part due to genetic variations between disease-state and control iPSCs. To circumvent this, the use of genomic editing tools to generate perfect isogenic controls is gaining momentum. To date, DNA binding domain-based zinc finger nucleases and transcription activator-like effector nucleases have been utilized to create genetically defined conditions in patient-specific iPSCs, with some examples leading to the successful identification of novel mechanisms of disease. As the feasibility and utility of genomic editing tools in iPSCs improve, along with the introduction of the clustered regularly interspaced short palindromic repeat system, understanding the features and limitations of genomic editing tools and their applications to iPSC technology is critical to expending the field of human disease modeling.
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Affiliation(s)
- Huen Suk Kim
- Department of Developmental and Regenerative Biology, The Black Family Stem Cell Institute , Icahn School of Medicine at Mount Sinai, New York, New York
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17
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Substratum-induced differentiation of human pluripotent stem cells reveals the coactivator YAP is a potent regulator of neuronal specification. Proc Natl Acad Sci U S A 2014; 111:13805-10. [PMID: 25201954 DOI: 10.1073/pnas.1415330111] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Physical stimuli can act in either a synergistic or antagonistic manner to regulate cell fate decisions, but it is less clear whether insoluble signals alone can direct human pluripotent stem (hPS) cell differentiation into specialized cell types. We previously reported that stiff materials promote nuclear localization of the Yes-associated protein (YAP) transcriptional coactivator and support long-term self-renewal of hPS cells. Here, we show that even in the presence of soluble pluripotency factors, compliant substrata inhibit the nuclear localization of YAP and promote highly efficient differentiation of hPS cells into postmitotic neurons. In the absence of neurogenic factors, the effective substrata produce neurons rapidly (2 wk) and more efficiently (>75%) than conventional differentiation methods. The neurons derived from substrate induction express mature markers and possess action potentials. The hPS differentiation observed on compliant surfaces could be recapitulated on stiff surfaces by adding small-molecule inhibitors of F-actin polymerization or by depleting YAP. These studies reveal that the matrix alone can mediate differentiation of hPS cells into a mature cell type, independent of soluble inductive factors. That mechanical cues can override soluble signals suggests that their contributions to early tissue development and lineage commitment are profound.
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18
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Phang RZ, Tay FC, Goh SL, Lau CH, Zhu H, Tan WK, Liang Q, Chen C, Du S, Li Z, Tay JCK, Wu C, Zeng J, Fan W, Toh HC, Wang S. Zinc finger nuclease-expressing baculoviral vectors mediate targeted genome integration of reprogramming factor genes to facilitate the generation of human induced pluripotent stem cells. Stem Cells Transl Med 2013; 2:935-45. [PMID: 24167318 DOI: 10.5966/sctm.2013-0043] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Integrative gene transfer using retroviruses to express reprogramming factors displays high efficiency in generating induced pluripotent stem cells (iPSCs), but the value of the method is limited because of the concern over mutagenesis associated with random insertion of transgenes. Site-specific integration into a preselected locus by engineered zinc-finger nuclease (ZFN) technology provides a potential way to overcome the problem. Here, we report the successful reprogramming of human fibroblasts into a state of pluripotency by baculoviral transduction-mediated, site-specific integration of OKSM (Oct3/4, Klf4, Sox2, and c-myc) transcription factor genes into the AAVS1 locus in human chromosome 19. Two nonintegrative baculoviral vectors were used for cotransduction, one expressing ZFNs and another as a donor vector encoding the four transcription factors. iPSC colonies were obtained at a high efficiency of 12% (the mean value of eight individual experiments). All characterized iPSC clones carried the transgenic cassette only at the ZFN-specified AAVS1 locus. We further demonstrated that when the donor cassette was flanked by heterospecific loxP sequences, the reprogramming genes in iPSCs could be replaced by another transgene using a baculoviral vector-based Cre recombinase-mediated cassette exchange system, thereby producing iPSCs free of exogenous reprogramming factors. Although the use of nonintegrating methods to generate iPSCs is rapidly becoming a standard approach, methods based on site-specific integration of reprogramming factor genes as reported here hold the potential for efficient generation of genetically amenable iPSCs suitable for future gene therapy applications.
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Affiliation(s)
- Rui-Zhe Phang
- Department of Biological Sciences, National University of Singapore, Singapore
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19
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Zhu H, Lau CH, Goh SL, Liang Q, Chen C, Du S, Phang RZ, Tay FC, Tan WK, Li Z, Tay JCK, Fan W, Wang S. Baculoviral transduction facilitates TALEN-mediated targeted transgene integration and Cre/LoxP cassette exchange in human-induced pluripotent stem cells. Nucleic Acids Res 2013; 41:e180. [PMID: 23945944 PMCID: PMC3799456 DOI: 10.1093/nar/gkt721] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Safety and reliability of transgene integration in human genome continue to pose challenges for stem cell-based gene therapy. Here, we report a baculovirus-transcription activator-like effector nuclease system for AAVS1 locus-directed homologous recombination in human induced pluripotent stem cells (iPSCs). This viral system, when optimized in human U87 cells, provided a targeted integration efficiency of 95.21% in incorporating a Neo-eGFP cassette and was able to mediate integration of DNA insert up to 13.5 kb. In iPSCs, targeted integration with persistent transgene expression was achieved without compromising genomic stability. The modified iPSCs continued to express stem cell pluripotency markers and maintained the ability to differentiate into three germ lineages in derived embryoid bodies. Using a baculovirus-Cre/LoxP system in the iPSCs, the Neo-eGFP cassette at the AAVS1 locus could be replaced by a Hygro-mCherry cassette, demonstrating the feasibility of cassette exchange. Moreover, as assessed by measuring γ-H2AX expression levels, genome toxicity associated with chromosomal double-strand breaks was not detectable after transduction with moderate doses of baculoviral vectors expressing transcription activator-like effector nucleases. Given high targeted integration efficiency, flexibility in transgene exchange and low genome toxicity, our baculoviral transduction-based approach offers great potential and attractive option for precise genetic manipulation in human pluripotent stem cells.
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Affiliation(s)
- Haibao Zhu
- Department of Biological Sciences, National University of Singapore, 117543 Singapore, Department of Surgery, Program of Innovative Cancer Therapeutics, First Affiliated Hospital of Zhejiang University College of Medicine, 310009 Hangzhou, China and Institute of Bioengineering and Nanotechnology, 138669 Singapore
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20
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Du ZW, Ma LX, Phillips C, Zhang SC. miR-200 and miR-96 families repress neural induction from human embryonic stem cells. Development 2013; 140:2611-8. [PMID: 23637338 DOI: 10.1242/dev.092809] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The role of miRNAs in neuroectoderm specification is largely unknown. We screened miRNA profiles that are differentially changed when human embryonic stem cells (hESCs) were differentiated to neuroectodermal precursors (NEP), but not to epidermal (EPI) cells and found that two miRNA families, miR-200 and miR-96, were uniquely downregulated in the NEP cells. We confirmed zinc-finger E-box-binding homeobox (ZEB) transcription factors as a target of the miR-200 family members and identified paired box 6 (PAX6) transcription factor as the new target of miR-96 family members via gain- and loss-of-function analyses. Given the essential roles of ZEBs and PAX6 in neural induction, we propose a model by which miR-200 and miR-96 families coordinate to regulate neural induction.
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Affiliation(s)
- Zhong-Wei Du
- Department of Neuroscience and Department of Neurology, School of Medicine and Public Health, Waisman Center, University of Wisconsin, Madison, WI 53705, USA
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21
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Liu Y, Weick JP, Liu H, Krencik R, Zhang X, Ma L, Zhou GM, Ayala M, Zhang SC. Medial ganglionic eminence-like cells derived from human embryonic stem cells correct learning and memory deficits. Nat Biotechnol 2013; 31:440-7. [PMID: 23604284 DOI: 10.1038/nbt.2565] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 03/27/2013] [Indexed: 02/07/2023]
Abstract
Dysfunction of basal forebrain cholinergic neurons (BFCNs) and γ-aminobutyric acid (GABA) interneurons, derived from medial ganglionic eminence (MGE), is implicated in disorders of learning and memory. Here we present a method for differentiating human embryonic stem cells (hESCs) to a nearly uniform population of NKX2.1(+) MGE-like progenitor cells. After transplantation into the hippocampus of mice in which BFCNs and some GABA neurons in the medial septum had been destroyed by mu P75-saporin, human MGE-like progenitors, but not ventral spinal progenitors, produced BFCNs that synaptically connected with endogenous neurons, whereas both progenitors generated similar populations of GABA neurons. Mice transplanted with MGE-like but not spinal progenitors showed improvements in learning and memory deficits. These results suggest that progeny of the MGE-like progenitors, particularly BFCNs, contributed to learning and memory. Our findings support the prospect of using human stem cell-derived MGE-like progenitors in developing therapies for neurological disorders of learning and memory.
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Affiliation(s)
- Yan Liu
- Waisman Center, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
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22
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23
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Leavitt AD, Hamlett I. Homologous recombination in human embryonic stem cells: a tool for advancing cell therapy and understanding and treating human disease. Clin Transl Sci 2011; 4:298-305. [PMID: 21884519 DOI: 10.1111/j.1752-8062.2011.00281.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Human embryonic stem cells (hESCs) hold great promise for ushering in an era of novel cell therapies to treat a wide range of rare and common diseases, yet they also provide an unprecedented opportunity for basic research to yield clinical benefit. HESCs can be used to better understand human development, to model human diseases, to understand the contribution of specific mutations to the pathogenesis of disease, and to develop human cell-based screening systems to identify novel therapeutic agents and evaluate potential toxicity of therapeutic agents under development. Such basic research will benefit greatly from efficient methods to perform targeted gene modification, an area of hESC investigation that is currently in its infancy. Moreover, the reality of hESC-based cellular therapies will require improved methods for generating the specific cells of interest, and reporter cell lines generated through targeted gene modifications are expected to play an important role in developing optimal cell-specific differentiation protocols. Herein, we review the current status of homologous recombination in hESCs, a gene targeting technique that is sure to continue to improve, and to play an important role in realizing the maximal human benefit from hESCs.
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Affiliation(s)
- Andrew D Leavitt
- Laboratory Medicine, University of California, San Francisco, California, USA.
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24
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Macarthur CC, Xue H, Van Hoof D, Lieu PT, Dudas M, Fontes A, Swistowski A, Touboul T, Seerke R, Laurent LC, Loring JF, German MS, Zeng X, Rao MS, Lakshmipathy U, Chesnut JD, Liu Y. Chromatin insulator elements block transgene silencing in engineered human embryonic stem cell lines at a defined chromosome 13 locus. Stem Cells Dev 2011; 21:191-205. [PMID: 21699412 DOI: 10.1089/scd.2011.0163] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Lineage reporters of human embryonic stem cell (hESC) lines are useful for differentiation studies and drug screening. Previously, we created reporter lines driven by an elongation factor 1 alpha (EF1α) promoter at a chromosome 13q32.3 locus in the hESC line WA09 and an abnormal hESC line BG01V in a site-specific manner. Expression of reporters in these lines was maintained in long-term culture at undifferentiated state. However, when these cells were differentiated into specific lineages, reduction in reporter expression was observed, indicating transgene silencing. To develop an efficient and reliable genetic engineering strategy in hESCs, we used chromatin insulator elements to flank single-copy transgenes and integrated the combined expression constructs via PhiC31/R4 integrase-mediated recombination technology to the chromosome 13 locus precisely. Two copies of cHS4 double-insulator sequences were placed adjacent to both 5' and 3' of the promoter reporter constructs. The green fluorescent protein (GFP) gene was driven by EF1α or CMV early enhancer/chicken β actin (CAG) promoter. In the engineered hESC lines, for both insulated CAG-GFP and EF1α-GFP, constitutive expression at the chromosome 13 locus was maintained during prolonged culture and in directed differentiation assays toward diverse types of neurons, pancreatic endoderm, and mesodermal progeny. In particular, described here is the first normal hESC fluorescent reporter line that robustly expresses GFP in both the undifferentiated state and throughout dopaminergic lineage differentiation. The dual strategy of utilizing insulator sequences and integration at the constitutive chromosome 13 locus ensures appropriate transgene expression. This is a valuable tool for lineage development study, gain- and loss-of-function experiments, and human disease modeling using hESCs.
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Affiliation(s)
- Chad C Macarthur
- Primary and Stem Cell Systems, Life Technologies Corporation, Carlsbad, California, USA
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25
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Ramachandra CJA, Shahbazi M, Kwang TWX, Choudhury Y, Bak XY, Yang J, Wang S. Efficient recombinase-mediated cassette exchange at the AAVS1 locus in human embryonic stem cells using baculoviral vectors. Nucleic Acids Res 2011; 39:e107. [PMID: 21685448 PMCID: PMC3167641 DOI: 10.1093/nar/gkr409] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insertion of a transgene into a defined genomic locus in human embryonic stem cells (hESCs) is crucial in preventing random integration-induced insertional mutagenesis, and can possibly enable persistent transgene expression during hESC expansion and in their differentiated progenies. Here, we employed homologous recombination in hESCs to introduce heterospecific loxP sites into the AAVS1 locus, a site with an open chromatin structure that allows averting transgene silencing phenomena. We then performed Cre recombinase mediated cassette exchange using baculoviral vectors to insert a transgene into the modified AAVS1 locus. Targeting efficiency in the master hESC line with the loxP-docking sites was up to 100%. Expression of the inserted transgene lasted for at least 20 passages during hESC expansion and was retained in differentiated cells derived from the genetically modified hESCs. Thus, this study demonstrates the feasibility of genetic manipulation at the AAVS1 locus with homologous recombination and using viral transduction in hESCs to facilitate recombinase-mediated cassette exchange. The method developed will be useful for repeated gene targeting at a defined locus of the hESC genome.
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Affiliation(s)
- Chrishan J A Ramachandra
- Institute of Bioengineering and Nanotechnology and Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
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26
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Maury JJP, Choo ABH, Chan KKK. Technical advances to genetically engineering human embryonic stem cells. Integr Biol (Camb) 2011; 3:717-23. [DOI: 10.1039/c1ib00019e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Julien Jean Pierre Maury
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668. Fax: (65) 64789561; Tel: (65) 64070898
| | - Andre Boon-Hwa Choo
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668. Fax: (65) 64789561; Tel: (65) 64070898
| | - Ken Kwok-Keung Chan
- Stem Cell Group, Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore 138668. Fax: (65) 64789561; Tel: (65) 64070898
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Shiozawa S, Kawai K, Okada Y, Tomioka I, Maeda T, Kanda A, Shinohara H, Suemizu H, James Okano H, Sotomaru Y, Sasaki E, Okano H. Gene targeting and subsequent site-specific transgenesis at the β-actin (ACTB) locus in common marmoset embryonic stem cells. Stem Cells Dev 2011; 20:1587-99. [PMID: 21126169 DOI: 10.1089/scd.2010.0351] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Nonhuman primate embryonic stem (ES) cells have vast promise for preclinical studies. Genetic modification in nonhuman primate ES cells is an essential technique for maximizing the potential of these cells. The common marmoset (Callithrix jacchus), a nonhuman primate, is expected to be a useful transgenic model for preclinical studies. However, genetic modification in common marmoset ES (cmES) cells has not yet been adequately developed. To establish efficient and stable genetic modifications in cmES cells, we inserted the enhanced green fluorescent protein (EGFP) gene with heterotypic lox sites into the β-actin (ACTB) locus of the cmES cells using gene targeting. The resulting knock-in ES cells expressed EGFP ubiquitously under the control of the endogenous ACTB promoter. Using inserted heterotypic lox sites, we demonstrated Cre recombinase-mediated cassette exchange (RMCE) and successfully established a monomeric red fluorescent protein (mRFP) knock-in cmES cell line. Further, a herpes simplex virus-thymidine kinase (HSV-tk) knock-in cmES cell line was established using RMCE. The growth of tumor cells originating from the cell line was significantly suppressed by the administration of ganciclovir. Therefore, the HSV-tk/ganciclovir system is promising as a safeguard for stem cell therapy. The stable and ubiquitous expression of EGFP before RMCE enables cell fate to be tracked when the cells are transplanted into an animal. Moreover, the creation of a transgene acceptor locus for site-specific transgenesis will be a powerful tool, similar to the ROSA26 locus in mice.
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Affiliation(s)
- Seiji Shiozawa
- Department of Physiology, School of Medicine, Keio University, Tokyo, Japan
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Chen YT, Furushima K, Hou PS, Ku AT, Deng JM, Jang CW, Fang H, Adams HP, Kuo ML, Ho HN, Chien CL, Behringer RR. PiggyBac transposon-mediated, reversible gene transfer in human embryonic stem cells. Stem Cells Dev 2010; 19:763-71. [PMID: 19740021 DOI: 10.1089/scd.2009.0118] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Permanent and reversible genetic modifications are important approaches to study gene function in different cell types. They are also important for stem cell researchers to explore and test the therapeutic potential of stem cells. The piggyBac transposon from insects is a rising nonviral system that efficiently mutagenizes and mediates gene transfer into the mammalian genome. It is also characterized by its precise excision, leaving no trace sequence behind so that the genomic integrity of the mutated cell can be restored. Here, we use an optimized piggyBac transposon system to mediate gene transfer and expression of a bifunctional fluorescent reporter in human embryonic stem (ES) cells. We provide molecular evidence for transposase-mediated piggyBac integration events and functional evidence for successful expression of a transferred fluorescent protein genes in human ES cells and their in vitro differentiated derivatives. We also demonstrate that the integrated piggyBac transposon can be removed and an undisrupted insertion site can be restored, which implies potential applications for its use in gene therapy and genetics studies.
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Affiliation(s)
- You-Tzung Chen
- Graduate Institute of Clinical Genomics and Graduate Institute of Clinical Medicine, Stem Cell Core Laboratory, NTU Research Center for Medical Excellence, Taipei, Taiwan.
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29
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Abstract
Human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) possess the potential to become all cell and tissue types of the human body. Under chemically defined culture systems, hESCs and hiPSCs have been efficiently directed to functional spinal motoneurons and astrocytes. The differentiation process faithfully recapitulates the developmental process predicted from studies in vertebrate animals and human specimens, suggesting the usefulness of stem cell differentiation systems in understanding human cellular development. Motoneurons and astrocytes differentiated from genetically altered hESCs or disease hiPSCs exhibit predicted phenotypes. They thus offer a simplified dynamic model for analyzing pathological processes that lead to human motoneuron degeneration, which in turn may serve as a template for pharmaceutical screening. In addition, the human stem cell-derived motoneurons and astrocytes, including those specifically derived from a patient, may become a source for cell therapy.
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Affiliation(s)
- Yan Liu
- Department of Human Anatomy and Histology, Institute of Stem Cells and Regenerative Medicine, Fudan University Shanghai Medical School, Shanghai, China
- Department of Anatomy and Department of Neurology, School of Medicine and Public Health; Waisman Center; University of Wisconsin, Madison, WI, USA
| | - Su-Chun Zhang
- Department of Anatomy and Department of Neurology, School of Medicine and Public Health; Waisman Center; University of Wisconsin, Madison, WI, USA
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30
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Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency. Proc Natl Acad Sci U S A 2010. [PMID: 20160098 DOI: 10.1073/pnas.01910012107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
For the promise of human induced pluripotent stem cells (iPSCs) to be realized, it is necessary to ask if and how efficiently they may be differentiated to functional cells of various lineages. Here, we have directly compared the neural-differentiation capacity of human iPSCs and embryonic stem cells (ESCs). We have shown that human iPSCs use the same transcriptional network to generate neuroepithelia and functionally appropriate neuronal types over the same developmental time course as hESCs in response to the same set of morphogens; however, they do it with significantly reduced efficiency and increased variability. These results were consistent across iPSC lines and independent of the set of reprogramming transgenes used to derive iPSCs as well as the presence or absence of reprogramming transgenes in iPSCs. These findings, which show a need for improving differentiation potency of iPSCs, suggest the possibility of employing human iPSCs in pathological studies, therapeutic screening, and autologous cell transplantation.
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31
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Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency. Proc Natl Acad Sci U S A 2010; 107:4335-40. [PMID: 20160098 DOI: 10.1073/pnas.0910012107] [Citation(s) in RCA: 735] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
For the promise of human induced pluripotent stem cells (iPSCs) to be realized, it is necessary to ask if and how efficiently they may be differentiated to functional cells of various lineages. Here, we have directly compared the neural-differentiation capacity of human iPSCs and embryonic stem cells (ESCs). We have shown that human iPSCs use the same transcriptional network to generate neuroepithelia and functionally appropriate neuronal types over the same developmental time course as hESCs in response to the same set of morphogens; however, they do it with significantly reduced efficiency and increased variability. These results were consistent across iPSC lines and independent of the set of reprogramming transgenes used to derive iPSCs as well as the presence or absence of reprogramming transgenes in iPSCs. These findings, which show a need for improving differentiation potency of iPSCs, suggest the possibility of employing human iPSCs in pathological studies, therapeutic screening, and autologous cell transplantation.
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32
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Kameyama Y, Kawabe Y, Ito A, Kamihira M. An accumulative site-specific gene integration system using cre recombinase-mediated cassette exchange. Biotechnol Bioeng 2010; 105:1106-14. [DOI: 10.1002/bit.22619] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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33
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Patsch C, Peitz M, Otte DM, Kesseler D, Jungverdorben J, Wunderlich FT, Brüstle O, Zimmer A, Edenhofer F. Engineering Cell-Permeant FLP Recombinase for Tightly Controlled Inducible and Reversible Overexpression in Embryonic Stem Cells. Stem Cells 2010; 28:894-902. [DOI: 10.1002/stem.417] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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