101
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Oikonomopoulos A, Kitani T, Wu JC. Pluripotent Stem Cell-Derived Cardiomyocytes as a Platform for Cell Therapy Applications: Progress and Hurdles for Clinical Translation. Mol Ther 2018; 26:1624-1634. [PMID: 29699941 PMCID: PMC6035734 DOI: 10.1016/j.ymthe.2018.02.026] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/26/2018] [Accepted: 02/26/2018] [Indexed: 12/17/2022] Open
Abstract
Cardiovascular diseases are the leading cause of morbidity and mortality worldwide. Regenerative therapy has been applied to restore lost cardiac muscle and cardiac performance. Induced pluripotent stem cells (iPSCs) can provide an unlimited source of cardiomyocytes and therefore play a key role in cardiac regeneration. Despite initial encouraging results from pre-clinical studies, progress toward clinical applications has been hampered by issues such as tumorigenesis, arrhythmogenesis, immune rejection, scalability, low graft-cell survival, and poor engraftment. Here, we review recent developments in iPSC research on regenerating injured heart tissue, including novel advances in cell therapy and potential strategies to overcome current obstacles in the field.
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Affiliation(s)
- Angelos Oikonomopoulos
- Stanford Cardiovascular Institute, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomoya Kitani
- Stanford Cardiovascular Institute, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA 94305, USA; Division of Cardiology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
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102
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A mixed antagonistic/synergistic miRNA repression model enables accurate predictions of multi-input miRNA sensor activity. Nat Commun 2018; 9:2430. [PMID: 29934631 PMCID: PMC6014984 DOI: 10.1038/s41467-018-04575-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 05/07/2018] [Indexed: 01/07/2023] Open
Abstract
MicroRNAs (miRNAs) regulate a majority of protein-coding genes, affecting nearly all biological pathways. However, the quantitative dimensions of miRNA-based regulation are not fully understood. In particular, the implications of miRNA target site location, composition rules for multiple target sites, and cooperativity limits for genes regulated by many miRNAs have not been quantitatively characterized. We explore these aspects of miRNA biology at a quantitative single-cell level using a library of 620 miRNA sensors and reporters that are regulated by many miRNA target sites at different positions. Interestingly, we find that miRNA target site sets within the same untranslated region exhibit combined miRNA activity described by an antagonistic relationship while those in separate untranslated regions show synergy. The resulting antagonistic/synergistic computational model enables the high-fidelity prediction of miRNA sensor activity for sensors containing many miRNA targets. These findings may help to accelerate the development of sophisticated sensors for clinical and research applications.
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103
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Sedlmayer F, Aubel D, Fussenegger M. Synthetic gene circuits for the detection, elimination and prevention of disease. Nat Biomed Eng 2018; 2:399-415. [PMID: 31011195 DOI: 10.1038/s41551-018-0215-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 03/05/2018] [Indexed: 12/13/2022]
Abstract
In living organisms, naturally evolved sensors that constantly monitor and process environmental cues trigger corrective actions that enable the organisms to cope with changing conditions. Such natural processes have inspired biologists to construct synthetic living sensors and signalling pathways, by repurposing naturally occurring proteins and by designing molecular building blocks de novo, for customized diagnostics and therapeutics. In particular, designer cells that employ user-defined synthetic gene circuits to survey disease biomarkers and to autonomously re-adjust unbalanced pathological states can coordinate the production of therapeutics, with controlled timing and dosage. Furthermore, tailored genetic networks operating in bacterial or human cells have led to cancer remission in experimental animal models, owing to the network's unprecedented specificity. Other applications of designer cells in infectious, metabolic and autoimmune diseases are also being explored. In this Review, we describe the biomedical applications of synthetic gene circuits in major disease areas, and discuss how the first genetically engineered devices developed on the basis of synthetic-biology principles made the leap from the laboratory to the clinic.
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Affiliation(s)
- Ferdinand Sedlmayer
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Dominique Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Lyon, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland. .,Faculty of Science, University of Basel, Basel, Switzerland.
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104
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Salehi SA, Liu X, Riedel MD, Parhi KK. Computing Mathematical Functions using DNA via Fractional Coding. Sci Rep 2018; 8:8312. [PMID: 29844537 PMCID: PMC5974329 DOI: 10.1038/s41598-018-26709-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 05/18/2018] [Indexed: 12/22/2022] Open
Abstract
This paper discusses the implementation of mathematical functions such as exponentials, trigonometric functions, the sigmoid function and the perceptron function with molecular reactions in general, and DNA strand displacement reactions in particular. The molecular constructs for these functions are predicated on a novel representation for input and output values: a fractional encoding, in which values are represented by the relative concentrations of two molecular types, denoted as type-1 and type-0. This representation is inspired by a technique from digital electronic design, termed stochastic logic, in which values are represented by the probability of 1's in a stream of randomly generated 0's and 1's. Research in the electronic realm has shown that a variety of complex functions can be computed with remarkably simple circuitry with this stochastic approach. This paper demonstrates how stochastic electronic designs can be translated to molecular circuits. It presents molecular implementations of mathematical functions that are considerably more complex than any shown to date. All designs are validated using mass-action simulations of the chemical kinetics of DNA strand displacement reactions.
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Affiliation(s)
- Sayed Ahmad Salehi
- Department of Electrical and Computer Engineering, University of Minnesota, 200 Union St. S.E., Minneapolis, MN, 55455, USA
| | - Xingyi Liu
- Department of Electrical and Computer Engineering, University of Minnesota, 200 Union St. S.E., Minneapolis, MN, 55455, USA
| | - Marc D Riedel
- Department of Electrical and Computer Engineering, University of Minnesota, 200 Union St. S.E., Minneapolis, MN, 55455, USA
| | - Keshab K Parhi
- Department of Electrical and Computer Engineering, University of Minnesota, 200 Union St. S.E., Minneapolis, MN, 55455, USA.
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105
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Engineering modular intracellular protein sensor-actuator devices. Nat Commun 2018; 9:1881. [PMID: 29760420 PMCID: PMC5951936 DOI: 10.1038/s41467-018-03984-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/27/2018] [Indexed: 12/17/2022] Open
Abstract
Understanding and reshaping cellular behaviors with synthetic gene networks requires the ability to sense and respond to changes in the intracellular environment. Intracellular proteins are involved in almost all cellular processes, and thus can provide important information about changes in cellular conditions such as infections, mutations, or disease states. Here we report the design of a modular platform for intrabody-based protein sensing-actuation devices with transcriptional output triggered by detection of intracellular proteins in mammalian cells. We demonstrate reporter activation response (fluorescence, apoptotic gene) to proteins involved in hepatitis C virus (HCV) infection, human immunodeficiency virus (HIV) infection, and Huntington’s disease, and show sensor-based interference with HIV-1 downregulation of HLA-I in infected T cells. Our method provides a means to link varying cellular conditions with robust control of cellular behavior for scientific and therapeutic applications. Synthetic biology principles are often used to design circuits that tune gene expression in response to changes in intracellular environments. Here the authors design a modular platform for intracellular protein sensing devices with transcriptional output.
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106
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Omole AE, Fakoya AOJ. Ten years of progress and promise of induced pluripotent stem cells: historical origins, characteristics, mechanisms, limitations, and potential applications. PeerJ 2018; 6:e4370. [PMID: 29770269 PMCID: PMC5951134 DOI: 10.7717/peerj.4370] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/24/2018] [Indexed: 12/11/2022] Open
Abstract
The discovery of induced pluripotent stem cells (iPSCs) by Shinya Yamanaka in 2006 was heralded as a major breakthrough of the decade in stem cell research. The ability to reprogram human somatic cells to a pluripotent embryonic stem cell-like state through the ectopic expression of a combination of embryonic transcription factors was greeted with great excitement by scientists and bioethicists. The reprogramming technology offers the opportunity to generate patient-specific stem cells for modeling human diseases, drug development and screening, and individualized regenerative cell therapy. However, fundamental questions have been raised regarding the molecular mechanism of iPSCs generation, a process still poorly understood by scientists. The efficiency of reprogramming of iPSCs remains low due to the effect of various barriers to reprogramming. There is also the risk of chromosomal instability and oncogenic transformation associated with the use of viral vectors, such as retrovirus and lentivirus, which deliver the reprogramming transcription factors by integration in the host cell genome. These challenges can hinder the therapeutic prospects and promise of iPSCs and their clinical applications. Consequently, extensive studies have been done to elucidate the molecular mechanism of reprogramming and novel strategies have been identified which help to improve the efficiency of reprogramming methods and overcome the safety concerns linked with iPSC generation. Distinct barriers and enhancers of reprogramming have been elucidated, and non-integrating reprogramming methods have been reported. Here, we summarize the progress and the recent advances that have been made over the last 10 years in the iPSC field, with emphasis on the molecular mechanism of reprogramming, strategies to improve the efficiency of reprogramming, characteristics and limitations of iPSCs, and the progress made in the applications of iPSCs in the field of disease modelling, drug discovery and regenerative medicine. Additionally, this study appraises the role of genomic editing technology in the generation of healthy iPSCs.
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Affiliation(s)
- Adekunle Ebenezer Omole
- Department of Basic Sciences, American University of Antigua College of Medicine, St. John's, Antigua
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107
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Dunn KK, Palecek SP. Engineering Scalable Manufacturing of High-Quality Stem Cell-Derived Cardiomyocytes for Cardiac Tissue Repair. Front Med (Lausanne) 2018; 5:110. [PMID: 29740580 PMCID: PMC5928319 DOI: 10.3389/fmed.2018.00110] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/03/2018] [Indexed: 12/29/2022] Open
Abstract
Recent advances in the differentiation and production of human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) have stimulated development of strategies to use these cells in human cardiac regenerative therapies. A prerequisite for clinical trials and translational implementation of hPSC-derived CMs is the ability to manufacture safe and potent cells on the scale needed to replace cells lost during heart disease. Current differentiation protocols generate fetal-like CMs that exhibit proarrhythmogenic potential. Sufficient maturation of these hPSC-derived CMs has yet to be achieved to allow these cells to be used as a regenerative medicine therapy. Insights into the native cardiac environment during heart development may enable engineering of strategies that guide hPSC-derived CMs to mature. Specifically, considerations must be made in regard to developing methods to incorporate the native intercellular interactions and biomechanical cues into hPSC-derived CM production that are conducive to scale-up.
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Affiliation(s)
- Kaitlin K Dunn
- University of Wisconsin-Madison, Chemical and Biological Engineering, Madison, WI, United States
| | - Sean P Palecek
- University of Wisconsin-Madison, Chemical and Biological Engineering, Madison, WI, United States
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108
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Valdés-Bango Curell R, Barron N. Exploring the Potential Application of Short Non-Coding RNA-Based Genetic Circuits in Chinese Hamster Ovary Cells. Biotechnol J 2018; 13:e1700220. [PMID: 29377624 DOI: 10.1002/biot.201700220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/15/2018] [Indexed: 12/14/2022]
Abstract
The majority of cell engineering for recombinant protein production to date has relied on traditional genetic engineering strategies, such as gene overexpression and gene knock-outs, to substantially improve the production capabilities of Chinese Hamster Ovary (CHO) cells. However, further improvements in cellular productivity or control over product quality is likely to require more sophisticated rational approaches to coordinate and balance cellular pathways. For these strategies to be implemented, novel molecular tools need to be developed to facilitate more refined control of gene expression. Multiple gene control strategies are developed over the last decades in the field of synthetic biology, including DNA and RNA-based systems, which allows tight and timely control over gene expression. microRNAs has received a lot of attention over the last decade in the CHO field and are used to engineer and improve CHO cells. In this review we focus on microRNA-based gene control systems and discuss their potential use as tools rather than targets in order to gain better control over gene expression.
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Affiliation(s)
| | - Niall Barron
- The National Institute for Bioprocessing Research and Training, Fosters Avenue, Blackrock, Dublin, Ireland.,University College Dublin, Dublin, Ireland
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109
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Park M, Yoon YS. Cardiac Regeneration with Human Pluripotent Stem Cell-Derived Cardiomyocytes. Korean Circ J 2018; 48:974-988. [PMID: 30334384 PMCID: PMC6196153 DOI: 10.4070/kcj.2018.0312] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 09/27/2018] [Indexed: 12/29/2022] Open
Abstract
Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs), which are collectively called pluripotent stem cells (PSCs), have emerged as a promising source for regenerative medicine. Particularly, human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) have shown robust potential for regenerating injured heart. Over the past two decades, protocols to differentiate hPSCs into CMs at high efficiency have been developed, opening the door for clinical application. Studies further demonstrated therapeutic effects of hPSC-CMs in small and large animal models and the underlying mechanisms of cardiac repair. However, gaps remain in explanations of the therapeutic effects of engrafted hPSC-CMs. In addition, bioengineering technologies improved survival and therapeutic effects of hPSC-CMs in vivo. While most of the original concerns associated with the use of hPSCs have been addressed, several issues remain to be resolved such as immaturity of transplanted cells, lack of electrical integration leading to arrhythmogenic risk, and tumorigenicity. Cell therapy with hPSC-CMs has shown great potential for biological therapy of injured heart; however, more studies are needed to ensure the therapeutic effects, underlying mechanisms, and safety, before this technology can be applied clinically.
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Affiliation(s)
- Misun Park
- Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Young Sup Yoon
- Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea.,Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, GA, USA.
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110
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Hatani T, Miki K, Yoshida Y. Induction of Human Induced Pluripotent Stem Cells to Cardiomyocytes Using Embryoid Bodies. Methods Mol Biol 2018; 1816:79-92. [PMID: 29987812 DOI: 10.1007/978-1-4939-8597-5_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Specific cell lineages differentiated from human induced pluripotent stem cells (iPSCs) are promising sources for cell replacement therapy and are useful biomedical research tools for research on disease mechanisms and drug discovery. Among the different lineages, cardiac lineage has been one of the most efficiently differentiated through several established protocols. In this chapter, we describe our reproducible and highly efficient methodology for differentiating iPSCs into cardiomyocytes using embryoid bodies. We also describe methods to dissociate iPSC-derived cardiomyocytes and to evaluate iPSC-derived cardiomyocytes.
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Affiliation(s)
- Takeshi Hatani
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Kenji Miki
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yoshinori Yoshida
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan.
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111
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Velazquez JJ, Su E, Cahan P, Ebrahimkhani MR. Programming Morphogenesis through Systems and Synthetic Biology. Trends Biotechnol 2017; 36:415-429. [PMID: 29229492 DOI: 10.1016/j.tibtech.2017.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 01/07/2023]
Abstract
Mammalian tissue development is an intricate, spatiotemporal process of self-organization that emerges from gene regulatory networks of differentiating stem cells. A major goal in stem cell biology is to gain a sufficient understanding of gene regulatory networks and cell-cell interactions to enable the reliable and robust engineering of morphogenesis. Here, we review advances in synthetic biology, single cell genomics, and multiscale modeling, which, when synthesized, provide a framework to achieve the ambitious goal of programming morphogenesis in complex tissues and organoids.
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Affiliation(s)
- Jeremy J Velazquez
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA; Authors contributed equally
| | - Emily Su
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Authors contributed equally
| | - Patrick Cahan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Mo R Ebrahimkhani
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA; Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Phoenix, AZ, USA.
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112
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Kim CM, Smolke CD. Biomedical applications of RNA-based devices. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017; 4:106-115. [DOI: 10.1016/j.cobme.2017.10.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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113
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miR-600 Acts as a Bimodal Switch that Regulates Breast Cancer Stem Cell Fate through WNT Signaling. Cell Rep 2017; 18:2256-2268. [PMID: 28249169 DOI: 10.1016/j.celrep.2017.02.016] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 12/15/2016] [Accepted: 02/02/2017] [Indexed: 02/07/2023] Open
Abstract
Breast cancer stem cells (bCSCs) have been implicated in tumor progression and therapeutic resistance; however, the molecular mechanisms that define this state are unclear. We have performed two microRNA (miRNA) gain- and loss-of-function screens to identify miRNAs that regulate the choice between bCSC self-renewal and differentiation. We find that micro-RNA (miR)-600 silencing results in bCSC expansion, while its overexpression reduces bCSC self-renewal, leading to decreased in vivo tumorigenicity. miR-600 targets stearoyl desaturase 1 (SCD1), an enzyme required to produce active, lipid-modified WNT proteins. In the absence of miR-600, WNT signaling is active and promotes self-renewal, whereas overexpression of miR-600 inhibits the production of active WNT and promotes bCSC differentiation. In a series of 120 breast tumors, we found that a low level of miR-600 is correlated with active WNT signaling and a poor prognosis. These findings highlight a miR-600-centered signaling network that governs bCSC-fate decisions and influences tumor progression.
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114
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Lin X, Chen W, Wei F, Zhou BP, Hung MC, Xie X. Nanoparticle Delivery of miR-34a Eradicates Long-term-cultured Breast Cancer Stem Cells via Targeting C22ORF28 Directly. Theranostics 2017; 7:4805-4824. [PMID: 29187905 PMCID: PMC5706101 DOI: 10.7150/thno.20771] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/16/2017] [Indexed: 12/28/2022] Open
Abstract
Rationale: Cancer stem cells (CSCs) have been implicated as the seeds of therapeutic resistance and metastasis, due to their unique abilities of self-renew, wide differentiation potentials and resistance to most conventional therapies. It is a proactive strategy for cancer therapy to eradicate CSCs. Methods: Tumor tissue-derived breast CSCs (BCSC), including XM322 and XM607, were isolated by fluorescence-activated cell sorting (FACS); while cell line-derived BCSC, including MDA-MB-231.SC and MCF-7.SC, were purified by magnetic-activated cell sorting (MACS). Analyses of microRNA and mRNA expression array profiles were performed in multiple breast cell lines. The mentioned nanoparticles were constructed following the standard molecular cloning protocol. Tissue microarray analysis has been used to study 217 cases of clinical breast cancer specimens. Results: Here, we have successfully established four long-term maintenance BCSC that retain their tumor-initiating biological properties. Our analyses of microarray and qRT-PCR explored that miR-34a is the most pronounced microRNA for investigation of BCSC. We establish hTERT promoter-driven VISA delivery of miR-34a (TV-miR-34a) plasmid that can induce high throughput of miR-34a expression in BCSC. TV-miR-34a significantly inhibited the tumor-initiating properties of long-term-cultured BCSC in vitro and reduced the proliferation of BCSC in vivo by an efficient and safe way. TV-miR-34a synergizes with docetaxel, a standard therapy for invasive breast cancer, to act as a BCSC inhibitor. Further mechanistic investigation indicates that TV-miR-34a directly prevents C22ORF28 accumulation, which abrogates clonogenicity and tumor growth and correlates with low miR-34 and high C22ORF28 levels in breast cancer patients. Conclusion: Taken together, we generated four long-term maintenance BCSC derived from either clinical specimens or cell lines, which would be greatly beneficial to the research progress in breast cancer patients. We further developed the non-viral TV-miR-34a plasmid, which has a great potential to be applied as a clinical application for breast cancer therapy.
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115
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Kawasaki S, Fujita Y, Nagaike T, Tomita K, Saito H. Synthetic mRNA devices that detect endogenous proteins and distinguish mammalian cells. Nucleic Acids Res 2017; 45:e117. [PMID: 28525643 PMCID: PMC5499560 DOI: 10.1093/nar/gkx298] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 04/13/2017] [Indexed: 01/04/2023] Open
Abstract
Synthetic biology has great potential for future therapeutic applications including autonomous cell programming through the detection of protein signals and the production of desired outputs. Synthetic RNA devices are promising for this purpose. However, the number of available devices is limited due to the difficulty in the detection of endogenous proteins within a cell. Here, we show a strategy to construct synthetic mRNA devices that detect endogenous proteins in living cells, control translation and distinguish cell types. We engineered protein-binding aptamers that have increased stability in the secondary structures of their active conformation. The designed devices can efficiently respond to target proteins including human LIN28A and U1A proteins, while the original aptamers failed to do so. Moreover, mRNA delivery of an LIN28A-responsive device into human induced pluripotent stem cells (hiPSCs) revealed that we can distinguish living hiPSCs and differentiated cells by quantifying endogenous LIN28A protein expression level. Thus, our endogenous protein-driven RNA devices determine live-cell states and program mammalian cells based on intracellular protein information.
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Affiliation(s)
- Shunsuke Kawasaki
- Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan.,Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yoshihiko Fujita
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takashi Nagaike
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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116
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Sano M, Ohtaka M, Iijima M, Nakasu A, Kato Y, Nakanishi M. Sensitive and long-term monitoring of intracellular microRNAs using a non-integrating cytoplasmic RNA vector. Sci Rep 2017; 7:12673. [PMID: 28978921 PMCID: PMC5627244 DOI: 10.1038/s41598-017-12847-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/14/2017] [Indexed: 01/01/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that modulate gene expression at the post-transcriptional level. Different types of cells express unique sets of miRNAs that can be exploited as potential molecular markers to identify specific cell types. Among the variety of miRNA detection methods, a fluorescence-based imaging system that utilises a fluorescent-reporter gene regulated by a target miRNA offers a major advantage for long-term tracking of the miRNA in living cells. In this study, we developed a novel fluorescence-based miRNA-monitoring system using a non-integrating cytoplasmic RNA vector based on a replication-defective and persistent Sendai virus (SeVdp). Because SeVdp vectors robustly and stably express transgenes, this system enabled sensitive monitoring of miRNAs by fluorescence microscopy. By applying this system for cellular reprogramming, we found that miR-124, but not miR-9, was significantly upregulated during direct neuronal conversion. Additionally, we were able to isolate integration-free human induced pluripotent stem cells by long-term tracking of let-7 expression. Notably, this system was easily expandable to allow detection of multiple miRNAs separately and simultaneously. Our findings provide insight into a powerful tool for evaluating miRNA expression during the cellular reprogramming process and for isolating reprogrammed cells potentially useful for medical applications.
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Affiliation(s)
- Masayuki Sano
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan.
| | - Manami Ohtaka
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Minoru Iijima
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Asako Nakasu
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
| | - Yoshio Kato
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Mahito Nakanishi
- Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8565, Japan
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117
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Protein-driven RNA nanostructured devices that function in vitro and control mammalian cell fate. Nat Commun 2017; 8:540. [PMID: 28912471 PMCID: PMC5599586 DOI: 10.1038/s41467-017-00459-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 06/29/2017] [Indexed: 11/22/2022] Open
Abstract
Nucleic acid nanotechnology has great potential for future therapeutic applications. However, the construction of nanostructured devices that control cell fate by detecting and amplifying protein signals has remained a challenge. Here we design and build protein-driven RNA-nanostructured devices that actuate in vitro by RNA-binding-protein-inducible conformational change and regulate mammalian cell fate by RNA–protein interaction-mediated protein assembly. The conformation and function of the RNA nanostructures are dynamically controlled by RNA-binding protein signals. The protein-responsive RNA nanodevices are constructed inside cells using RNA-only delivery, which may provide a safe tool for building functional RNA–protein nanostructures. Moreover, the designed RNA scaffolds that control the assembly and oligomerization of apoptosis-regulatory proteins on a nanometre scale selectively kill target cells via specific RNA–protein interactions. These findings suggest that synthetic RNA nanodevices could function as molecular robots that detect signals and localize target proteins, induce RNA conformational changes, and programme mammalian cellular behaviour. Nucleic acid nanotechnology has great potential for future therapeutic applications. Here the authors build protein-driven RNA nanostructures that can function within mammalian cells and regulate the cell fate.
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118
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MicroRNA Profiling Reveals Distinct Profiles for Tissue-Derived and Cultured Endothelial Cells. Sci Rep 2017; 7:10943. [PMID: 28887500 PMCID: PMC5591252 DOI: 10.1038/s41598-017-11487-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/25/2017] [Indexed: 12/19/2022] Open
Abstract
Endothelial plasticity enables the cells to switch their phenotype according to the surrounding vascular microenvironment. MicroRNAs (miRNAs) are small noncoding RNAs that control endothelial plasticity. The objective of this study was to investigate the differences in miRNA profiles of tissue-derived cells and cultured endothelial cells. To this end, miRNA expression was profiled from freshly isolated tissue-derived human vascular endothelial cells and endothelial cells cultured until cellular senescence using miRNA sequencing. In addition, the data was searched for putative novel endothelial miRNAs and miRNA isoforms. The data analysis revealed a striking change in endothelial miRNA profile as the cells adapted from tissue to cell culture environment and the overall miRNA expression decreased significantly in cultured compared to tissue-derived endothelial cells. In addition to changes in mechanosensitive miRNA expression, alterations in senescence-associated and endothelial-to-mesenchymal-transition-associated miRNAs were observed in aging cells. Collectively, the data illustrates the adaptability of endothelial cell miRNA expression that mirrors prevailing cellular environment.
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119
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Hirosawa M, Fujita Y, Parr C, Hayashi K, Kashida S, Hotta A, Woltjen K, Saito H. Cell-type-specific genome editing with a microRNA-responsive CRISPR-Cas9 switch. Nucleic Acids Res 2017; 45:e118. [PMID: 28525578 PMCID: PMC5570128 DOI: 10.1093/nar/gkx309] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/05/2017] [Accepted: 05/09/2017] [Indexed: 12/17/2022] Open
Abstract
The CRISPR-Cas9 system is a powerful genome-editing tool useful in a variety of biotechnology and biomedical applications. Here we developed a synthetic RNA-based, microRNA (miRNA)-responsive CRISPR-Cas9 system (miR-Cas9 switch) in which the genome editing activity of Cas9 can be modulated through endogenous miRNA signatures in mammalian cells. We created miR-Cas9 switches by using a miRNA-complementary sequence in the 5΄-UTR of mRNA encoding Streptococcus pyogenes Cas9. The miR-21-Cas9 or miR-302-Cas9 switches selectively and efficiently responded to miR-21-5p in HeLa cells or miR-302a-5p in human induced pluripotent stem cells, and post-transcriptionally attenuated the Cas9 activity only in the target cells. Moreover, the miR-Cas9 switches could differentially control the genome editing by sensing endogenous miRNA activities within a heterogeneous cell population. Our miR-Cas9 switch system provides a promising framework for cell-type selective genome editing and cell engineering based on intracellular miRNA information.
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Affiliation(s)
- Moe Hirosawa
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihiko Fujita
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Callum J. C. Parr
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Karin Hayashi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shunnichi Kashida
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Akitsu Hotta
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Knut Woltjen
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
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120
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Achieving Efficient Manufacturing and Quality Assurance through Synthetic Cell Therapy Design. Cell Stem Cell 2017; 20:13-17. [PMID: 28061350 DOI: 10.1016/j.stem.2016.12.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
New methods to manipulate gene and cell state can be used to engineer cell functionality, simplify quality assessment, and enhance manufacturability. These strategies could help overcome unresolved cell therapy manufacturing challenges and complement frameworks to design quality into these complex cellular systems, ultimately increasing patient access to living therapeutics.
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121
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Jeong HC, Cho SJ, Lee MO, Cha HJ. Technical approaches to induce selective cell death of pluripotent stem cells. Cell Mol Life Sci 2017; 74:2601-2611. [PMID: 28246701 PMCID: PMC11107638 DOI: 10.1007/s00018-017-2486-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 01/24/2017] [Accepted: 02/06/2017] [Indexed: 01/24/2023]
Abstract
Despite the recent promising results of clinical trials using human pluripotent stem cell (hPSC)-based cell therapies for age-related macular degeneration (AMD), the risk of teratoma formation resulting from residual undifferentiated hPSCs remains a serious and critical hurdle for broader clinical implementation. To mitigate the tumorigenic risk of hPSC-based cell therapy, a variety of approaches have been examined to ablate the undifferentiated hPSCs based on the unique molecular properties of hPSCs. In the present review, we offer a brief overview of recent attempts at selective elimination of undifferentiated hPSCs to decrease the risk of teratoma formation in hPSC-based cell therapy.
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Affiliation(s)
- Ho-Chang Jeong
- Dept. of Life Sciences, College of Natural Sciences, Sogang University, #1 Sinsu-dong, Mapo-gu, Seoul,, 121-742, Republic of Korea
| | - Seung-Ju Cho
- Dept. of Life Sciences, College of Natural Sciences, Sogang University, #1 Sinsu-dong, Mapo-gu, Seoul,, 121-742, Republic of Korea
| | - Mi-Ok Lee
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon,, 305-806, Republic of Korea
| | - Hyuk-Jin Cha
- Dept. of Life Sciences, College of Natural Sciences, Sogang University, #1 Sinsu-dong, Mapo-gu, Seoul,, 121-742, Republic of Korea.
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122
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Ho P, Chen YY. Mammalian synthetic biology in the age of genome editing and personalized medicine. Curr Opin Chem Biol 2017. [PMID: 28628856 DOI: 10.1016/j.cbpa.2017.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The recent expansion of molecular tool kits has propelled synthetic biology toward the design of increasingly sophisticated mammalian systems. Specifically, advances in genome editing, protein engineering, and circuitry design have enabled the programming of cells for diverse applications, including regenerative medicine and cancer immunotherapy. The ease with which molecular and cellular interactions can be harnessed promises to yield novel approaches to elucidate genetic interactions, program cellular functions, and design therapeutic interventions. Here, we review recent advancements in the development of enabling technologies and the practical applications of mammalian synthetic biology.
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Affiliation(s)
- Patrick Ho
- Department of Chemical and Biomolecular Engineering, University of California-Los Angeles, 420 Westwood Plaza, Boelter Hall 5531, Los Angeles, CA 90095, USA
| | - Yvonne Y Chen
- Department of Chemical and Biomolecular Engineering, University of California-Los Angeles, 420 Westwood Plaza, Boelter Hall 5531, Los Angeles, CA 90095, USA.
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123
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Affiliation(s)
- Yoshinori Yoshida
- From the Center for iPS Cell Research and Application, Kyoto University, Japan (Y.Y., S.Y.); and Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA (S.Y.)
| | - Shinya Yamanaka
- From the Center for iPS Cell Research and Application, Kyoto University, Japan (Y.Y., S.Y.); and Gladstone Institute of Cardiovascular Disease, Gladstone Institutes, San Francisco, CA (S.Y.)
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124
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An update on stem cell biology and engineering for brain development. Mol Psychiatry 2017; 22:808-819. [PMID: 28373686 DOI: 10.1038/mp.2017.66] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 02/16/2017] [Indexed: 02/07/2023]
Abstract
Two recent technologies, induced-pluripotent stem cells (iPSCs) and direct somatic reprogramming, have shown enormous potential for cell-based therapies against intractable diseases such as those that affect the central nervous system. Already, methods that generate most major cell types of the human brain exist. Whether the cell types are directly reprogrammed from human somatic cells or differentiated from an iPSC intermediate, the overview presented here demonstrates how these protocols vary greatly in their efficiencies, purity and maturation of the resulting cells. Possible solutions including micro-RNA switch technologies that purify target cell types are also outlined. Further, an update on the transition from 2D to 3D cultures and current organoid (mini-brain) cultures are reviewed to give the stem cell and developmental engineering communities an up-to-date account of the progress and future perspectives for modeling of central nervous system disease and brain development in vitro.
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125
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Efficient, Selective Removal of Human Pluripotent Stem Cells via Ecto-Alkaline Phosphatase-Mediated Aggregation of Synthetic Peptides. Cell Chem Biol 2017; 24:685-694.e4. [DOI: 10.1016/j.chembiol.2017.04.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 12/30/2016] [Accepted: 04/17/2017] [Indexed: 01/17/2023]
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126
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Monitoring and visualizing microRNA dynamics during live cell differentiation using microRNA-responsive non-viral reporter vectors. Biomaterials 2017; 128:121-135. [DOI: 10.1016/j.biomaterials.2017.02.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/25/2017] [Accepted: 02/26/2017] [Indexed: 01/17/2023]
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127
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Ban K, Bae S, Yoon YS. Current Strategies and Challenges for Purification of Cardiomyocytes Derived from Human Pluripotent Stem Cells. Theranostics 2017. [PMID: 28638487 PMCID: PMC5479288 DOI: 10.7150/thno.19427] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Cardiomyocytes (CMs) derived from human pluripotent stem cells (hPSCs) are considered a most promising option for cell-based cardiac repair. Hence, various protocols have been developed for differentiating hPSCs into CMs. Despite remarkable improvement in the generation of hPSC-CMs, without purification, these protocols can only generate mixed cell populations including undifferentiated hPSCs or non-CMs, which may elicit adverse outcomes. Therefore, one of the major challenges for clinical use of hPSC-CMs is the development of efficient isolation techniques that allow enrichment of hPSC-CMs. In this review, we will discuss diverse strategies that have been developed to enrich hPSC-CMs. We will describe major characteristics of individual hPSC-CM purification methods including their scientific principles, advantages, limitations, and needed improvements. Development of a comprehensive system which can enrich hPSC-CMs will be ultimately useful for cell therapy for diseased hearts, human cardiac disease modeling, cardiac toxicity screening, and cardiac tissue engineering.
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128
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Doppler SA, Lange R, Laugwitz KL, Krane M. Cardiac development: from current understanding to new regenerative concepts. J Thorac Dis 2017; 9:S1-S4. [PMID: 28446962 DOI: 10.21037/jtd.2017.03.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stefanie A Doppler
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich, Germany
| | - Rüdiger Lange
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich, Germany.,DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Karl-Ludwig Laugwitz
- DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany.,I. Department of Medicine (Cardiology), Klinikum rechts der Isar der Technischen Universität München, Munich, Germany
| | - Markus Krane
- Department of Cardiovascular Surgery, Division of Experimental Surgery, German Heart Center Munich, Technische Universität München, Munich, Germany.,DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
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129
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Shi Y, Inoue H, Wu JC, Yamanaka S. Induced pluripotent stem cell technology: a decade of progress. Nat Rev Drug Discov 2017; 16:115-130. [PMID: 27980341 PMCID: PMC6416143 DOI: 10.1038/nrd.2016.245] [Citation(s) in RCA: 896] [Impact Index Per Article: 128.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Since the advent of induced pluripotent stem cell (iPSC) technology a decade ago, enormous progress has been made in stem cell biology and regenerative medicine. Human iPSCs have been widely used for disease modelling, drug discovery and cell therapy development. Novel pathological mechanisms have been elucidated, new drugs originating from iPSC screens are in the pipeline and the first clinical trial using human iPSC-derived products has been initiated. In particular, the combination of human iPSC technology with recent developments in gene editing and 3D organoids makes iPSC-based platforms even more powerful in each area of their application, including precision medicine. In this Review, we discuss the progress in applications of iPSC technology that are particularly relevant to drug discovery and regenerative medicine, and consider the remaining challenges and the emerging opportunities in the field.
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Affiliation(s)
- Yanhong Shi
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, California 91010, USA
| | - Haruhisa Inoue
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Joseph C Wu
- Stanford Cardiovascular Institute, 265 Campus Drive, Room G1120B, Stanford, California 94305-5454, USA
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
- Gladstone Institute of Cardiovascular Disease, San Francisco, California 94158, USA
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130
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Mohammadi P, Beerenwinkel N, Benenson Y. Automated Design of Synthetic Cell Classifier Circuits Using a Two-Step Optimization Strategy. Cell Syst 2017; 4:207-218.e14. [DOI: 10.1016/j.cels.2017.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 10/25/2016] [Accepted: 01/06/2017] [Indexed: 10/20/2022]
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131
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Schreiber J, Arter M, Lapique N, Haefliger B, Benenson Y. Model-guided combinatorial optimization of complex synthetic gene networks. Mol Syst Biol 2016; 12:899. [PMID: 28031353 PMCID: PMC5199127 DOI: 10.15252/msb.20167265] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/18/2016] [Accepted: 11/25/2016] [Indexed: 01/25/2023] Open
Abstract
Constructing gene circuits that satisfy quantitative performance criteria has been a long-standing challenge in synthetic biology. Here, we show a strategy for optimizing a complex three-gene circuit, a novel proportional miRNA biosensor, using predictive modeling to initiate a search in the phase space of sensor genetic composition. We generate a library of sensor circuits using diverse genetic building blocks in order to access favorable parameter combinations and uncover specific genetic compositions with greatly improved dynamic range. The combination of high-throughput screening data and the data obtained from detailed mechanistic interrogation of a small number of sensors was used to validate the model. The validated model facilitated further experimentation, including biosensor reprogramming and biosensor integration into larger networks, enabling in principle arbitrary logic with miRNA inputs using normal form circuits. The study reveals how model-guided generation of genetic diversity followed by screening and model validation can be successfully applied to optimize performance of complex gene networks without extensive prior knowledge.
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Affiliation(s)
- Joerg Schreiber
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zürich), Basel, Switzerland
| | - Meret Arter
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zürich), Basel, Switzerland
| | - Nicolas Lapique
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zürich), Basel, Switzerland
| | - Benjamin Haefliger
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zürich), Basel, Switzerland
| | - Yaakov Benenson
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology (ETH Zürich), Basel, Switzerland
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132
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Hosoya M, Czysz K. Translational Prospects and Challenges in Human Induced Pluripotent Stem Cell Research in Drug Discovery. Cells 2016; 5:cells5040046. [PMID: 28009813 PMCID: PMC5187530 DOI: 10.3390/cells5040046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/27/2016] [Accepted: 12/15/2016] [Indexed: 02/07/2023] Open
Abstract
Despite continuous efforts to improve the process of drug discovery and development, achieving success at the clinical stage remains challenging because of a persistent translational gap between the preclinical and clinical settings. Under these circumstances, the discovery of human induced pluripotent stem (iPS) cells has brought new hope to the drug discovery field because they enable scientists to humanize a variety of pharmacological and toxicological models in vitro. The availability of human iPS cell-derived cells, particularly as an alternative for difficult-to-access tissues and organs, is increasing steadily; however, their use in the field of translational medicine remains challenging. Biomarkers are an essential part of the translational effort to shift new discoveries from bench to bedside as they provide a measurable indicator with which to evaluate pharmacological and toxicological effects in both the preclinical and clinical settings. In general, during the preclinical stage of the drug development process, in vitro models that are established to recapitulate human diseases are validated by using a set of biomarkers; however, their translatability to a clinical setting remains problematic. This review provides an overview of current strategies for human iPS cell-based drug discovery from the perspective of translational research, and discusses the importance of early consideration of clinically relevant biomarkers.
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Affiliation(s)
- Masaki Hosoya
- Integrated Technology Research Laboratories, Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
| | - Katherine Czysz
- Integrated Technology Research Laboratories, Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan.
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133
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Mathur M, Xiang JS, Smolke CD. Mammalian synthetic biology for studying the cell. J Cell Biol 2016; 216:73-82. [PMID: 27932576 PMCID: PMC5223614 DOI: 10.1083/jcb.201611002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/25/2022] Open
Abstract
Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology.
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Affiliation(s)
- Melina Mathur
- Department of Bioengineering, Stanford University, Stanford, CA 94305
| | - Joy S Xiang
- Department of Bioengineering, Stanford University, Stanford, CA 94305
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134
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Parr CJC, Katayama S, Miki K, Kuang Y, Yoshida Y, Morizane A, Takahashi J, Yamanaka S, Saito H. MicroRNA-302 switch to identify and eliminate undifferentiated human pluripotent stem cells. Sci Rep 2016; 6:32532. [PMID: 27608814 PMCID: PMC5016789 DOI: 10.1038/srep32532] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/05/2016] [Indexed: 01/28/2023] Open
Abstract
The efficiency of pluripotent stem cell differentiation is highly variable, often resulting in heterogeneous populations that contain undifferentiated cells. Here we developed a sensitive, target-specific, and general method for removing undesired cells before transplantation. MicroRNA-302a-5p (miR-302a) is highly and specifically expressed in human pluripotent stem cells and gradually decreases to basal levels during differentiation. We synthesized a new RNA tool, miR-switch, as a live-cell reporter mRNA for miR-302a activity that can specifically detect human induced pluripotent stem cells (hiPSCs) down to a spiked level of 0.05% of hiPSCs in a heterogeneous population and can prevent teratoma formation in an in vivo tumorigenicity assay. Automated and selective hiPSC-elimination was achieved by controlling puromycin resistance using the miR-302a switch. Our system uniquely provides sensitive detection of pluripotent stem cells and partially differentiated cells. In addition to its ability to eliminate undifferentiated cells, miR-302a switch also holds great potential in investigating the dynamics of differentiation and/or reprograming of live-cells based on intracellular information.
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Affiliation(s)
- Callum J C Parr
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shota Katayama
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kenji Miki
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yi Kuang
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yoshinori Yoshida
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Asuka Morizane
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Jun Takahashi
- Department of Clinical Application, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shinya Yamanaka
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.,Gladstone Institute of Cardiovascular Disease, San Francisco, CA 94158, USA
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
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135
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Points to consider for a validation study of iPS cell-derived cardiomyocytes using a multi-electrode array system. J Pharmacol Toxicol Methods 2016; 81:196-200. [DOI: 10.1016/j.vascn.2016.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 06/25/2016] [Accepted: 06/27/2016] [Indexed: 12/16/2022]
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136
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Abstract
Throughout biology, function is intimately linked with form. Across scales ranging from subcellular to multiorganismal, the identity and organization of a biological structure's subunits dictate its properties. The field of molecular morphogenesis has traditionally been concerned with describing these links, decoding the molecular mechanisms that give rise to the shape and structure of cells, tissues, organs, and organisms. Recent advances in synthetic biology promise unprecedented control over these molecular mechanisms; this opens the path to not just probing morphogenesis but directing it. This review explores several frontiers in the nascent field of synthetic morphogenesis, including programmable tissues and organs, synthetic biomaterials and programmable matter, and engineering complex morphogenic systems de novo. We will discuss each frontier's objectives, current approaches, constraints and challenges, and future potential.
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Affiliation(s)
- Brian P Teague
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Patrick Guye
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Ron Weiss
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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137
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Mallanna SK, Cayo MA, Twaroski K, Gundry RL, Duncan SA. Mapping the Cell-Surface N-Glycoproteome of Human Hepatocytes Reveals Markers for Selecting a Homogeneous Population of iPSC-Derived Hepatocytes. Stem Cell Reports 2016; 7:543-556. [PMID: 27569060 PMCID: PMC5032032 DOI: 10.1016/j.stemcr.2016.07.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/18/2016] [Accepted: 07/20/2016] [Indexed: 02/07/2023] Open
Abstract
When comparing hepatic phenotypes between iPSC-derived hepatocyte-like cells from different liver disease patients, cell heterogeneity can confound interpretation. We proposed that homogeneous cell populations could be generated by fluorescence-activated cell sorting (FACS). Using cell-surface capture proteomics, we identified a total of 300 glycoproteins on hepatocytes. Analyses of the expression profiles during the differentiation of iPSCs revealed that SLC10A1, CLRN3, and AADAC were highly enriched during the final stages of hepatocyte differentiation. FACS purification of hepatocyte-like cells expressing SLC10A1, CLRN3, or AADAC demonstrated enrichment of cells with hepatocyte characteristics. Moreover, transcriptome analyses revealed that cells expressing the liver gene regulatory network were enriched while cells expressing a pluripotent stem cell network were depleted. In conclusion, we report an extensive catalog of cell-surface N-linked glycoproteins expressed in primary hepatocytes and identify cell-surface proteins that facilitate the purification of homogeneous populations of iPSC-derived hepatocyte-like cells. Identified N-linked glycoproteins occupying surface of primary human hepatocytes SLC10A1, CLRN3, and AADAC are expressed on ∼25% of iPSC-derived hepatocytes FACS with these markers enriches hepatic character in iPSC-derived hepatocytes SLC10A1 sorted cells provide homogeneous populations of hepatocyte-like cells
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Affiliation(s)
- Sunil K Mallanna
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Max A Cayo
- Department of Cell Biology, Neurobiology and Anatomy, Program in Regenerative Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Kirk Twaroski
- Department of Cell Biology, Neurobiology and Anatomy, Program in Regenerative Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454, USA
| | - Rebekah L Gundry
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Stephen A Duncan
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA.
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138
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Karagiannis P, Eto K. Ten years of induced pluripotency: from basic mechanisms to therapeutic applications. Development 2016; 143:2039-43. [DOI: 10.1242/dev.138172] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Ten years ago, the discovery that mature somatic cells could be reprogrammed into induced pluripotent stem cells (iPSCs) redefined the stem cell field and brought about a wealth of opportunities for both basic research and clinical applications. To celebrate the tenth anniversary of the discovery, the International Society for Stem Cell Research (ISSCR) and Center for iPS Cell Research and Application (CiRA), Kyoto University, together held the symposium ‘Pluripotency: From Basic Science to Therapeutic Applications’ in Kyoto, Japan. The three days of lectures examined both the mechanisms and therapeutic applications of iPSC reprogramming. Here we summarize the main findings reported, which are testament to how far the field has come in only a decade, as well as the enormous potential that iPSCs hold for the future.
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Affiliation(s)
- Peter Karagiannis
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Koji Eto
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
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139
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Saragusty J, Diecke S, Drukker M, Durrant B, Friedrich Ben-Nun I, Galli C, Göritz F, Hayashi K, Hermes R, Holtze S, Johnson S, Lazzari G, Loi P, Loring JF, Okita K, Renfree MB, Seet S, Voracek T, Stejskal J, Ryder OA, Hildebrandt TB. Rewinding the process of mammalian extinction. Zoo Biol 2016; 35:280-92. [PMID: 27142508 DOI: 10.1002/zoo.21284] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/11/2016] [Indexed: 12/15/2022]
Abstract
With only three living individuals left on this planet, the northern white rhinoceros (Ceratotherium simum cottoni) could be considered doomed for extinction. It might still be possible, however, to rescue the (sub)species by combining novel stem cell and assisted reproductive technologies. To discuss the various practical options available to us, we convened a multidisciplinary meeting under the name "Conservation by Cellular Technologies." The outcome of this meeting and the proposed road map that, if successfully implemented, would ultimately lead to a self-sustaining population of an extremely endangered species are outlined here. The ideas discussed here, while centered on the northern white rhinoceros, are equally applicable, after proper adjustments, to other mammals on the brink of extinction. Through implementation of these ideas we hope to establish the foundation for reversal of some of the effects of what has been termed the sixth mass extinction event in the history of Earth, and the first anthropogenic one. Zoo Biol. 35:280-292, 2016. © 2016 The Authors. Zoo Biology published by Wiley Periodicals, Inc.
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Affiliation(s)
- Joseph Saragusty
- The Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | - Micha Drukker
- Institute of Stem Cell Research, German Research Center for Environmental Health, Helmholtz Center Munich, Neuherberg, Germany
| | - Barbara Durrant
- San Diego Zoo Institute for Conservation Research, Escondido, California
| | - Inbar Friedrich Ben-Nun
- Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, California
| | - Cesare Galli
- Avantea srl, Laboratorio di Tecnologie della Riproduzione, Cremona, Italy.,Dipartimento Scienze Mediche Veterinarie, Università di Bologna, Ozzano dell'Emilia, Italy.,Fondazione Avantea, Cremona, Italy
| | - Frank Göritz
- The Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Katsuhiko Hayashi
- Faculty of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Robert Hermes
- The Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Susanne Holtze
- The Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | - Giovanna Lazzari
- Avantea srl, Laboratorio di Tecnologie della Riproduzione, Cremona, Italy.,Fondazione Avantea, Cremona, Italy
| | - Pasqualino Loi
- Faculty of Veterinary Medicine, Univeristy of Teramo, Campus Coste San Agostino, Teramo, Italy
| | - Jeanne F Loring
- Department of Chemical Physiology, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, California
| | - Keisuke Okita
- Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Steven Seet
- The Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | - Jan Stejskal
- ZOO Dvůr Králové, Dvůr Králové nad Labem, Czech Republic
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, California
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140
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Morgado AL, Rodrigues CMP, Solá S. MicroRNA-145 Regulates Neural Stem Cell Differentiation Through the Sox2-Lin28/let-7 Signaling Pathway. Stem Cells 2016; 34:1386-95. [PMID: 26849971 DOI: 10.1002/stem.2309] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 12/05/2015] [Accepted: 12/16/2015] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs or miRs) regulate several biological functions, including cell fate determination and differentiation. Although miR-145 has already been described to regulate glioma development, its precise role in neurogenesis has never been addressed. miR-145 represses sex-determining region Y-box 2 (Sox2), a core transcription factor of embryonic stem cells (ESCs), to inhibit pluripotency and self-renewal in human ESCs. In addition, the Sox2-Lin28/let-7 signaling pathway regulates proliferation and neurogenesis of neural precursors. In this study, we aimed to investigate the precise role of miR-145 in neural stem cell (NSC) fate decision, and the possible involvement of the Sox2-Lin28/let-7 signaling pathway in miR-145 regulatory network. Our results show for the first time that miR-145 expression significantly increased after induction of mouse NSC differentiation, remaining elevated throughout this process. Forced miR-145 downregulation decreased neuronal markers, namely βIII-tubulin, NeuN, and MAP2. Interestingly, throughout NSC differentiation, protein levels of Sox2 and Lin28, a well-known suppressor of let-7 biogenesis, decreased. Of note, neuronal differentiation also resulted in let-7a and let-7b upregulation. Transfection of NSCs with anti-miR-145, in turn, increased both Sox2 and Lin28 protein levels, while decreasing both let-7a and let-7b. More importantly, Sox2 and Lin28 silencing partially rescued the impairment of neuronal differentiation induced by miR-145 downregulation. In conclusion, our results demonstrate a novel role for miR-145 during NSC differentiation, where miR-145 modulation of Sox2-Lin28/let-7 network is crucial for neurogenesis progression. Stem Cells 2016;34:1386-1395.
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Affiliation(s)
- Ana L Morgado
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Cecília M P Rodrigues
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Susana Solá
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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141
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Chistiakov DA, Orekhov AN, Bobryshev YV. Cardiac-specific miRNA in cardiogenesis, heart function, and cardiac pathology (with focus on myocardial infarction). J Mol Cell Cardiol 2016; 94:107-121. [PMID: 27056419 DOI: 10.1016/j.yjmcc.2016.03.015] [Citation(s) in RCA: 198] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/09/2016] [Accepted: 03/24/2016] [Indexed: 12/21/2022]
Abstract
Cardiac miRNAs (miR-1, miR133a, miR-208a/b, and miR-499) are abundantly expressed in the myocardium. They play a central role in cardiogenesis, heart function and pathology. While miR-1 and miR-133a predominantly control early stages of cardiogenesis supporting commitment of cardiac-specific muscle lineage from embryonic stem cells and mesodermal precursors, miR-208 and miR-499 are involved in the late cardiogenic stages mediating differentiation of cardioblasts to cardiomyocytes and fast/slow muscle fiber specification. In the heart, miR-1/133a control cardiac conductance and automaticity by regulating all phases of the cardiac action potential. miR-208/499 located in introns of the heavy chain myosin genes regulate expression of sarcomeric contractile proteins. In cardiac pathology including myocardial infarction (MI), expression of cardiac miRNAs is markedly altered that leads to deleterious effects associated with heart wounding, arrhythmia, increased apoptosis, fibrosis, hypertrophy, and tissue remodeling. In acute MI, circulating levels of cardiac miRNAs are significantly elevated making them to be a promising diagnostic marker for early diagnosis of acute MI. Great cardiospecific capacity of these miRNAs is very helpful for enhancing regenerative properties and survival of stem cell and cardiac progenitor transplants and for reprogramming of mature non-cardiac cells to cardiomyocytes.
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Affiliation(s)
- Dimitry A Chistiakov
- Department of Molecular Genetic Diagnostics and Cell Biology, Division of Laboratory Medicine, Institute of Pediatrics, Research Center for Children's Health, 119991 Moscow, Russia
| | - Alexander N Orekhov
- Institute of General Pathology and Pathophysiology, Russian Academy of Sciences, Moscow 125315, Russia; Department of Biophysics, Biological Faculty, Moscow State University, Moscow 119991, Russia; Institute for Atherosclerosis Research, Skolkovo Innovative Center, Moscow 121609, Russia
| | - Yuri V Bobryshev
- Institute of General Pathology and Pathophysiology, Russian Academy of Sciences, Moscow 125315, Russia; Faculty of Medicine, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia; School of Medicine, University of Western Sydney, Campbelltown, NSW 2560, Australia.
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142
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Salvador MA, Birnbaum D, Charafe-Jauffret E, Ginestier C. Breast cancer stem cells programs: enter the (non)-code. Brief Funct Genomics 2016; 15:186-99. [PMID: 26955842 DOI: 10.1093/bfgp/elw003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Breast tumors exhibit a hierarchical cellular organization driven by several subpopulations of cancer stem cells (CSCs). These breast CSC subpopulations are able to infinitely self-renew and to differentiate, giving rise to tumor heterogeneity. Accumulating evidence show that breast CSCs resist conventional therapies and i`nitiate tumor relapse. The development of anti-CSCs therapies may therefore greatly improve patient survival. A better elucidation of molecular circuitries involved in stemness would offer new relevant targets. Noncoding RNAs, especially microRNAs and long noncoding RNAs, are regulators of cell identity and are notably found deregulated in breast CSCs. This review will focus on noncoding RNAs involved in CSCs biology during breast cancer initiation, maintenance, therapeutic resistance and metastatic progression. Potential clinical applications using noncoding RNAs as biomarkers or therapies will be discussed.
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143
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Endo K, Hayashi K, Saito H. High-resolution Identification and Separation of Living Cell Types by Multiple microRNA-responsive Synthetic mRNAs. Sci Rep 2016; 6:21991. [PMID: 26902536 PMCID: PMC4763229 DOI: 10.1038/srep21991] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/04/2016] [Indexed: 12/21/2022] Open
Abstract
The precise identification and separation of living cell types is critical to both study cell function and prepare cells for medical applications. However, intracellular information to distinguish live cells remains largely inaccessible. Here, we develop a method for high-resolution identification and separation of cell types by quantifying multiple microRNA (miRNA) activities in live cell populations. We found that a set of miRNA-responsive, in vitro synthesized mRNAs identify a specific cell population as a sharp peak and clearly separate different cell types based on less than two-fold differences in miRNA activities. Increasing the number of miRNA-responsive mRNAs enhanced the capability for cell identification and separation, as we precisely and simultaneously distinguished different cell types with similar miRNA profiles. In addition, the set of synthetic mRNAs separated HeLa cells into subgroups, uncovering heterogeneity of the cells and the level of resolution achievable. Our method could identify target live cells and improve the efficiency of cell purification from heterogeneous populations.
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Affiliation(s)
- Kei Endo
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Karin Hayashi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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144
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Kawamura T, Miyagawa S, Fukushima S, Maeda A, Kashiyama N, Kawamura A, Miki K, Okita K, Yoshida Y, Shiina T, Ogasawara K, Miyagawa S, Toda K, Okuyama H, Sawa Y. Cardiomyocytes Derived from MHC-Homozygous Induced Pluripotent Stem Cells Exhibit Reduced Allogeneic Immunogenicity in MHC-Matched Non-human Primates. Stem Cell Reports 2016; 6:312-20. [PMID: 26905198 PMCID: PMC4788782 DOI: 10.1016/j.stemcr.2016.01.012] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 01/14/2016] [Accepted: 01/15/2016] [Indexed: 11/30/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) can serve as a source of cardiomyocytes (CMs) to treat end-stage heart failure; however, transplantation of genetically dissimilar iPSCs even within species (allogeneic) can induce immune rejection. We hypothesized that this might be limited by matching the major histocompatibility complex (MHC) antigens between the donor and the recipient. We therefore transplanted fluorescence-labeled (GFP) iPSC-CMs donated from a macaque with homozygous MHC haplotypes into the subcutaneous tissue and hearts of macaques having heterozygous MHC haplotypes (MHC-matched; group I) or without identical MHC alleles (group II) in conjunction with immune suppression. Group I displayed a higher GFP intensity and less immune-cell infiltration in the graft than group II. However, MHC-matched transplantation with single or no immune-suppressive drugs still induced a substantial host immune response to the graft. Thus, the immunogenicity of allogeneic iPSC-CMs was reduced by MHC-matched transplantation although a requirement for appropriate immune suppression was retained for successful engraftment. Cardiomyocytes from iPSCs can treat heart disease iPSC-CMs were transplanted into MHC-matched or unmatched cynomolgus macacques Matched iPSC-CM grafts had better survival and less host rejection immune response Immunosuppression was still required for successful allogeneic iPSC-CM engraftment
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Affiliation(s)
- Takuji Kawamura
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Shigeru Miyagawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Satsuki Fukushima
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Akira Maeda
- Department of Pediatric Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Noriyuki Kashiyama
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Ai Kawamura
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Kenji Miki
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Kyoto 606-8507, Japan
| | - Keisuke Okita
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Kyoto 606-8507, Japan
| | - Yoshinori Yoshida
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Kyoto 606-8507, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1143, Japan
| | - Kazumasa Ogasawara
- Department of Pathology, Shiga University of Medical Science, Otsu, Shiga 520-2192, Japan
| | - Shuji Miyagawa
- Department of Pediatric Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Koichi Toda
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Hiroomi Okuyama
- Department of Pediatric Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Yoshiki Sawa
- Department of Cardiovascular Surgery, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan.
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145
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Morita Y, Andersen P, Hotta A, Tsukahara Y, Sasagawa N, Hayashida N, Koga C, Nishikawa M, Saga Y, Evans SM, Koshiba-Takeuchi K, Nishinakamura R, Yoshida Y, Kwon C, Takeuchi JK. Sall1 transiently marks undifferentiated heart precursors and regulates their fate. J Mol Cell Cardiol 2016; 92:158-62. [PMID: 26876450 DOI: 10.1016/j.yjmcc.2016.02.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 02/07/2016] [Accepted: 02/09/2016] [Indexed: 12/15/2022]
Abstract
Cardiac progenitor cells (CPCs) are a crucial source of cells in cardiac development and regeneration. However, reported CPCs are heterogeneous, and no gene has been identified to transiently mark undifferentiated CPCs throughout heart development. Here we show that Spalt-like gene 1 (Sall1), a zing-finger transcription factor, is expressed in undifferentiated CPCs giving rise to both left and right ventricles. Sall1 was transiently expressed in precardiac mesoderm contributing to the first heart field (left ventricle precursors) but not in the field itself. Similarly, Sall1 expression was maintained in the second heart field (outflow tract/right ventricle precursors) but not in cardiac cells. In vitro, high levels of Sall1 at mesodermal stages enhanced cardiomyogenesis, whereas its continued expression suppressed cardiac differentiation. Our study demonstrates that Sall1 marks CPCs in an undifferentiated state and regulates cardiac differentiation. These findings provide fundamental insights into CPC maintenance, which can be instrumental for CPC-based regenerative medicine.
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Affiliation(s)
- Yuika Morita
- Division of Cardiovascular Regeneration, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo 113-0032, Japan; Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Peter Andersen
- Division of Cardiology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, USA
| | - Akitsu Hotta
- Department of Reprogramming Science, Centre for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; AMED, Research Center Network for Realization of Regenerative Medicine, Projects for Technological Development, Japan; JST PESTO, Understanding Life by iPS Cells Technology, Sanbancho building, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Yuko Tsukahara
- Division of Cardiovascular Regeneration, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Noriko Sasagawa
- Department of Reprogramming Science, Centre for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Naoko Hayashida
- Division of Cardiovascular Regeneration, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Chizuko Koga
- Division of Cardiovascular Regeneration, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Misato Nishikawa
- Department of Reprogramming Science, Centre for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Yumiko Saga
- Mammalian Development Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Sylvia M Evans
- Skaggs School of Pharmacy and Pharmaceutical Sciences, Department of Medicine, School of Medicine, University of California, San Diego, USA
| | - Kazuko Koshiba-Takeuchi
- Division of Cardiovascular Regeneration, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo 113-0032, Japan
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Yoshinori Yoshida
- Department of Reprogramming Science, Centre for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; AMED, Research Center Network for Realization of Regenerative Medicine, Projects for Technological Development, Japan
| | - Chulan Kwon
- Division of Cardiology, Institute for Cell Engineering, Johns Hopkins University School of Medicine, USA
| | - Jun K Takeuchi
- Division of Cardiovascular Regeneration, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo 113-0032, Japan; Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1, Hongo, Bunkyo, Tokyo 113-0033, Japan; AMED, Research Center Network for Realization of Regenerative Medicine, Projects for Technological Development, Japan; JST PESTO, Understanding Life by iPS Cells Technology, Sanbancho building, Sanbancho 5, Chiyoda-ku, Tokyo 102-0075, Japan.
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146
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Karagiannis P, Iriguchi S, Kaneko S. Reprogramming away from the exhausted T cell state. Semin Immunol 2016; 28:35-44. [DOI: 10.1016/j.smim.2015.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/23/2015] [Accepted: 10/29/2015] [Indexed: 02/07/2023]
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147
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Kempf H, Andree B, Zweigerdt R. Large-scale production of human pluripotent stem cell derived cardiomyocytes. Adv Drug Deliv Rev 2016; 96:18-30. [PMID: 26658242 DOI: 10.1016/j.addr.2015.11.016] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 11/19/2015] [Accepted: 11/25/2015] [Indexed: 12/20/2022]
Abstract
Regenerative medicine, including preclinical studies in large animal models and tissue engineering approaches as well as innovative assays for drug discovery, will require the constant supply of hPSC-derived cardiomyocytes and other functional progenies. Respective cell production processes must be robust, economically viable and ultimately GMP-compliant. Recent research has enabled transition of lab scale protocols for hPSC expansion and cardiomyogenic differentiation towards more controlled processing in industry-compatible culture platforms. Here, advanced strategies for the cultivation and differentiation of hPSCs will be reviewed by focusing on stirred bioreactor-based techniques for process upscaling. We will discuss how cardiomyocyte mass production might benefit from recent findings such as cell expansion at the cardiovascular progenitor state. Finally, remaining challenges will be highlighted, specifically regarding three dimensional (3D) hPSC suspension culture and critical safety issues ahead of clinical translation.
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Affiliation(s)
- Henning Kempf
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic-, Transplantation and Vascular Surgery, Hannover Medical School, Germany; REBIRTH-Cluster of Excellence, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
| | - Birgit Andree
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic-, Transplantation and Vascular Surgery, Hannover Medical School, Germany; REBIRTH-Cluster of Excellence, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
| | - Robert Zweigerdt
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic-, Transplantation and Vascular Surgery, Hannover Medical School, Germany; REBIRTH-Cluster of Excellence, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.
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148
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Funakoshi S, Miki K, Takaki T, Okubo C, Hatani T, Chonabayashi K, Nishikawa M, Takei I, Oishi A, Narita M, Hoshijima M, Kimura T, Yamanaka S, Yoshida Y. Enhanced engraftment, proliferation, and therapeutic potential in heart using optimized human iPSC-derived cardiomyocytes. Sci Rep 2016; 6:19111. [PMID: 26743035 PMCID: PMC4705488 DOI: 10.1038/srep19111] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 12/01/2015] [Indexed: 02/07/2023] Open
Abstract
Human pluripotent stem cell-derived cardiomyocytes (CMs) are a promising tool for cardiac cell therapy. Although transplantation of induced pluripotent stem cell (iPSC)-derived CMs have been reported in several animal models, the treatment effect was limited, probably due to poor optimization of the injected cells. To optimize graft cells for cardiac reconstruction, we compared the engraftment efficiency of intramyocardially-injected undifferentiated-iPSCs, day 4 mesodermal cells, and day 8, day 20, and day 30 purified iPSC-CMs after initial differentiation by tracing the engraftment ratio (ER) using in vivo bioluminescence imaging. This analysis revealed the ER of day 20 CMs was significantly higher compared to other cells. Transplantation of day 20 CMs into the infarcted hearts of immunodeficient mice showed good engraftment, and echocardiography showed significant functional improvement by cell therapy. Moreover, the imaging signal and ratio of Ki67-positive CMs at 3 months post injection indicated engrafted CMs proliferated in the host heart. Although this graft growth reached a plateau at 3 months, histological analysis confirmed progressive maturation from 3 to 6 months. These results suggested that day 20 CMs had very high engraftment, proliferation, and therapeutic potential in host mouse hearts. They also demonstrate this model can be used to track the fate of transplanted cells over a long time.
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Affiliation(s)
- Shunsuke Funakoshi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Cardiovascular Medicine, Kyoto University Hospital, Kyoto, Japan
| | - Kenji Miki
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Tadashi Takaki
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Chikako Okubo
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Takeshi Hatani
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Department of Cardiovascular Medicine, Kyoto University Hospital, Kyoto, Japan
| | | | - Misato Nishikawa
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Ikue Takei
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Akiko Oishi
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Megumi Narita
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Masahiko Hoshijima
- Center for Research in Biological Systems and Department of Medicine, University of California at San Diego, La Jolla, California, USA
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Kyoto University Hospital, Kyoto, Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
- Gladstone Institute of Cardiovascular Disease, San Francisco, USA
| | - Yoshinori Yoshida
- Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
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149
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KARAGIANNIS P, FUJITA Y, SAITO H. RNA-based gene circuits for cell regulation. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2016; 92:412-422. [PMID: 27840389 PMCID: PMC5328788 DOI: 10.2183/pjab.92.412] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/24/2016] [Indexed: 05/20/2023]
Abstract
A major goal of synthetic biology is to control cell behavior. RNA-mediated genetic switches (RNA switches) are devices that serve this purpose, as they can control gene expressions in response to input signals. In general, RNA switches consist of two domains: an aptamer domain, which binds to an input molecule, and an actuator domain, which controls the gene expression. An input binding to the aptamer can cause the actuator to alter the RNA structure, thus changing access to translation machinery. The assembly of multiple RNA switches has led to complex gene circuits for cell therapies, including the selective killing of pathological cells and purification of cell populations. The inclusion of RNA binding proteins, such as L7Ae, increases the repertoire and precision of the circuit. In this short review, we discuss synthetic RNA switches for gene regulation and their potential therapeutic applications.
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Affiliation(s)
- Peter KARAGIANNIS
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Yoshihiko FUJITA
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hirohide SAITO
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Sakyo-ku, Kyoto, Japan
- Correspondence should be addressed: H. Saito, Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan (e-mail: )
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150
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Santulli G. MicroRNAs and Endothelial (Dys) Function. J Cell Physiol 2015; 231:1638-44. [PMID: 26627535 DOI: 10.1002/jcp.25276] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 12/01/2015] [Indexed: 12/12/2022]
Abstract
Accumulating evidence indicates that microRNAs (miRs)-non-coding RNAs that can regulate gene expression via translational repression and/or post-transcriptional degradation-are becoming one of the most fascinating areas of physiology, given their fundamental roles in countless pathophysiological processes. The relative roles of different miRs in vascular biology as direct or indirect post-transcriptional regulators of fundamental genes implied in vascular remodeling designate miRs as potential biomarkers and/or promising drug targets. The mechanistic importance of miRs in modulating endothelial cell (EC) function in physiology and in disease is addressed here. Drawbacks of currently available therapeutic options are also discussed, pointing at the challenges and clinical opportunities provided by miR-based treatments. J. Cell. Physiol. 231: 1638-1644, 2016. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Gaetano Santulli
- Columbia University Medical Center, New York Presbyterian Hospital-Manhattan, New York, New York
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