51
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Shi ZD, Soh CL, Zhu Z, Huangfu D. Genome Editing and Directed Differentiation of hPSCs for Interrogating Lineage Determinants in Human Pancreatic Development. J Vis Exp 2017:55267. [PMID: 28287608 PMCID: PMC5408939 DOI: 10.3791/55267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Interrogating gene function in self-renewing or differentiating human pluripotent stem cells (hPSCs) offers a valuable platform towards understanding human development and dissecting disease mechanisms in a dish. To capitalize on this potential application requires efficient genome-editing tools to generate hPSC mutants in disease-associated genes, as well as in vitro hPSC differentiation protocols to produce disease-relevant cell types that closely recapitulate their in vivo counterparts. An efficient genome-editing platform for hPSCs named iCRISPR has been developed through the TALEN-mediated targeting of a Cas9 expression cassette in the AAVS1 locus. Here, the protocols for the generation of inducible Cas9 hPSC lines using cells cultured in a chemically defined medium and a feeder-free condition are described. Detailed procedures for using the iCRISPR system for gene knockout or precise genetic alterations in hPSCs, either through non-homologous end joining (NHEJ) or via precise nucleotide alterations using a homology-directed repair (HDR) template, respectively, are included. These technical procedures include descriptions of the design, production, and transfection of CRISPR guide RNAs (gRNAs); the measurement of the CRISPR mutation rate by T7E1 or RFLP assays; and the establishment and validation of clonal mutant lines. Finally, we chronicle procedures for hPSC differentiation into glucose-responsive pancreatic β-like cells by mimicking in vivo pancreatic embryonic development. Combining iCRISPR technology with directed hPSC differentiation enables the systematic examination of gene function to further our understanding of pancreatic development and diabetes disease mechanisms.
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Affiliation(s)
- Zhong-Dong Shi
- Developmental Biology Program, Sloan Kettering Institute
| | - Chew-Li Soh
- Developmental Biology Program, Sloan Kettering Institute
| | - Zengrong Zhu
- Developmental Biology Program, Sloan Kettering Institute;
| | - Danwei Huangfu
- Developmental Biology Program, Sloan Kettering Institute;
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52
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Genome Editing in hPSCs Reveals GATA6 Haploinsufficiency and a Genetic Interaction with GATA4 in Human Pancreatic Development. Cell Stem Cell 2017; 20:675-688.e6. [PMID: 28196600 DOI: 10.1016/j.stem.2017.01.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/08/2016] [Accepted: 01/03/2017] [Indexed: 01/19/2023]
Abstract
Human disease phenotypes associated with haploinsufficient gene requirements are often not recapitulated well in animal models. Here, we have investigated the association between human GATA6 haploinsufficiency and a wide range of clinical phenotypes that include neonatal and adult-onset diabetes using CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9-mediated genome editing coupled with human pluripotent stem cell (hPSC) directed differentiation. We found that loss of one GATA6 allele specifically affects the differentiation of human pancreatic progenitors from the early PDX1+ stage to the more mature PDX1+NKX6.1+ stage, leading to impaired formation of glucose-responsive β-like cells. In addition to this GATA6 haploinsufficiency, we also identified dosage-sensitive requirements for GATA6 and GATA4 in the formation of both definitive endoderm and pancreatic progenitor cells. Our work expands the application of hPSCs from studying the impact of individual gene loci to investigation of multigenic human traits, and it establishes an approach for identifying genetic modifiers of human disease.
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53
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Ahfeldt T, Litterman NK, Rubin LL. Studying human disease using human neurons. Brain Res 2017; 1656:40-48. [PMID: 27060768 PMCID: PMC5053850 DOI: 10.1016/j.brainres.2016.03.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 03/08/2016] [Accepted: 03/31/2016] [Indexed: 01/25/2023]
Abstract
Utilizing patient derived cells has enormous promise for discovering new drugs for diseases of the nervous system, a goal that has been historically quite challenging. In this review, we will outline the potential of human stem cell derived neuron models for assessing therapeutics and high-throughput screening and compare to more traditional drug discovery strategies. We summarize recent successes of the approach and discuss special considerations for developing human stem cell based assays. New technologies, such as genome editing, offer improvements to help overcome the challenges that remain. Finally, human neurons derived from patient cells have advantages for translational research beyond drug screening as they can also be used to identify individual efficacy and safety prior to clinical testing and for dissecting disease mechanisms. This article is part of a Special Issue entitled SI: Exploiting human neurons.
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Affiliation(s)
- Tim Ahfeldt
- Department of Stem Cells and Regenerative Biology, Harvard University, Cambridge MA , USA, , Fax: 617-495-3961
| | - Nadia K. Litterman
- Department of Stem Cells and Regenerative Biology, Harvard University, Cambridge MA , USA, , Fax: 617-495-3961
| | - Lee L. Rubin
- Department of Stem Cells and Regenerative Biology, Harvard University, Cambridge MA , USA, , Fax: 617-495-3961
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54
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Genome engineering of stem cell organoids for disease modeling. Protein Cell 2017; 8:315-327. [PMID: 28102490 PMCID: PMC5413597 DOI: 10.1007/s13238-016-0368-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 12/28/2016] [Indexed: 12/17/2022] Open
Abstract
Precision medicine emerges as a new approach that takes into account individual variability. Successful realization of precision medicine requires disease models that are able to incorporate personalized disease information and recapitulate disease development processes at the molecular, cellular and organ levels. With recent development in stem cell field, a variety of tissue organoids can be derived from patient specific pluripotent stem cells and adult stem cells. In combination with the state-of-the-art genome editing tools, organoids can be further engineered to mimic disease-relevant genetic and epigenetic status of a patient. This has therefore enabled a rapid expansion of sophisticated in vitro disease models, offering a unique system for fundamental and biomedical research as well as the development of personalized medicine. Here we summarize some of the latest advances and future perspectives in engineering stem cell organoids for human disease modeling.
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55
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Kim EJ, Kang KH, Ju JH. CRISPR-Cas9: a promising tool for gene editing on induced pluripotent stem cells. Korean J Intern Med 2017; 32:42-61. [PMID: 28049282 PMCID: PMC5214730 DOI: 10.3904/kjim.2016.198] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/10/2016] [Indexed: 12/13/2022] Open
Abstract
Recent advances in genome editing with programmable nucleases have opened up new avenues for multiple applications, from basic research to clinical therapy. The ease of use of the technology-and particularly clustered regularly interspaced short palindromic repeats (CRISPR)-will allow us to improve our understanding of genomic variation in disease processes via cellular and animal models. Here, we highlight the progress made in correcting gene mutations in monogenic hereditary disorders and discuss various CRISPR-associated applications, such as cancer research, synthetic biology, and gene therapy using induced pluripotent stem cells. The challenges, ethical issues, and future prospects of CRISPR-based systems for human research are also discussed.
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Affiliation(s)
- Eun Ji Kim
- Division of Rheumatology, Department of Internal Medicine, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul, Korea
| | - Ki Ho Kang
- Division of Rheumatology, Department of Internal Medicine, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul, Korea
| | - Ji Hyeon Ju
- Division of Rheumatology, Department of Internal Medicine, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, Seoul, Korea
- Correspondence to Ji Hyeon Ju, M.D. Division of Rheumatology, Department of Internal Medicine, College of Medicine, Seoul St. Mary’s Hospital, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul 06591, Korea Tel: +82-2-2258-6893 Fax: +82-2-3476-2274 E-mail:
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56
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Requirements for Using iPSC-Based Cell Models for Assay Development in Drug Discovery. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 163:207-220. [PMID: 29071405 DOI: 10.1007/10_2017_23] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A prevalent challenge in drug discovery is the translation of findings from preclinical research into clinical success. Currently, more physiological in vitro systems are being developed to overcome some of these challenges. In particular, induced pluripotent stem cells (iPSCs) have provided the opportunity to generate human cell types that can be utilized for developing more disease-relevant cellular assay models. As the use of these complex models is lengthy and fairly complicated, we lay out our experiences of the cultivation, differentiation, and quality control requirements to successfully utilize pluripotent stem cells in drug discovery.
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57
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Ricq EL, Hooker JM, Haggarty SJ. Toward development of epigenetic drugs for central nervous system disorders: Modulating neuroplasticity via H3K4 methylation. Psychiatry Clin Neurosci 2016; 70:536-550. [PMID: 27485392 PMCID: PMC5764164 DOI: 10.1111/pcn.12426] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/29/2016] [Indexed: 12/19/2022]
Abstract
The mammalian brain dynamically activates or silences gene programs in response to environmental input and developmental cues. This neuroplasticity is controlled by signaling pathways that modify the activity, localization, and/or expression of transcriptional-regulatory enzymes in combination with alterations in chromatin structure in the nucleus. Consistent with this key neurobiological role, disruptions in the fine-tuning of epigenetic and transcriptional regulation have emerged as a recurrent theme in studies of the genetics of neurodevelopmental and neuropsychiatric disorders. Furthermore, environmental factors have been implicated in the increased risk of heterogeneous, multifactorial, neuropsychiatric disorders via epigenetic mechanisms. Aberrant epigenetic regulation of gene expression thus provides an attractive unifying model for understanding the complex risk architecture of mental illness. Here, we review emerging genetic evidence implicating dysregulation of histone lysine methylation in neuropsychiatric disease and outline advancements in small-molecule probes targeting this chromatin modification. The emerging field of neuroepigenetic research is poised to provide insight into the biochemical basis of genetic risk for diverse neuropsychiatric disorders and to develop the highly selective chemical tools and imaging agents necessary to dissect dynamic transcriptional-regulatory mechanisms in the nervous system. On the basis of these findings, continued advances may lead to the validation of novel, disease-modifying therapeutic targets for a range of disorders with aberrant chromatin-mediated neuroplasticity.
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Affiliation(s)
- Emily L. Ricq
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
- Chemical Neurobiology Laboratory, Center for Human Genetic Research, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Jacob M. Hooker
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Stephen J. Haggarty
- Chemical Neurobiology Laboratory, Center for Human Genetic Research, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
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58
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Lee PC, Truong B, Vega-Crespo A, Gilmore WB, Hermann K, Angarita SA, Tang JK, Chang KM, Wininger AE, Lam AK, Schoenberg BE, Cederbaum SD, Pyle AD, Byrne JA, Lipshutz GS. Restoring Ureagenesis in Hepatocytes by CRISPR/Cas9-mediated Genomic Addition to Arginase-deficient Induced Pluripotent Stem Cells. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e394. [PMID: 27898091 PMCID: PMC5155330 DOI: 10.1038/mtna.2016.98] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/26/2016] [Indexed: 12/18/2022]
Abstract
Urea cycle disorders are incurable enzymopathies that affect nitrogen metabolism and typically lead to hyperammonemia. Arginase deficiency results from a mutation in Arg1, the enzyme regulating the final step of ureagenesis and typically results in developmental disabilities, seizures, spastic diplegia, and sometimes death. Current medical treatments for urea cycle disorders are only marginally effective, and for proximal disorders, liver transplantation is effective but limited by graft availability. Advances in human induced pluripotent stem cell research has allowed for the genetic modification of stem cells for potential cellular replacement therapies. In this study, we demonstrate a universally-applicable CRISPR/Cas9-based strategy utilizing exon 1 of the hypoxanthine-guanine phosphoribosyltransferase locus to genetically modify and restore arginase activity, and thus ureagenesis, in genetically distinct patient-specific human induced pluripotent stem cells and hepatocyte-like derivatives. Successful strategies restoring gene function in patient-specific human induced pluripotent stem cells may advance applications of genetically modified cell therapy to treat urea cycle and other inborn errors of metabolism.
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Affiliation(s)
- Patrick C Lee
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Brian Truong
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Agustin Vega-Crespo
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - W Blake Gilmore
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Kip Hermann
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Stephanie Ak Angarita
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Jonathan K Tang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Katherine M Chang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Austin E Wininger
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Alex K Lam
- Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Benjamen E Schoenberg
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Stephen D Cederbaum
- Department of Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Intellectual and Developmental Disabilities Research Center at UCLA, Los Angeles, California, USA.,Semel Institute for Neuroscience, UCLA, Los Angeles, California, USA
| | - April D Pyle
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - James A Byrne
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Gerald S Lipshutz
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Psychiatry, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Intellectual and Developmental Disabilities Research Center at UCLA, Los Angeles, California, USA.,Semel Institute for Neuroscience, UCLA, Los Angeles, California, USA.,Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Urology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
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59
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Rubio A, Luoni M, Giannelli SG, Radice I, Iannielli A, Cancellieri C, Di Berardino C, Regalia G, Lazzari G, Menegon A, Taverna S, Broccoli V. Rapid and efficient CRISPR/Cas9 gene inactivation in human neurons during human pluripotent stem cell differentiation and direct reprogramming. Sci Rep 2016; 6:37540. [PMID: 27857203 PMCID: PMC5114606 DOI: 10.1038/srep37540] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 10/31/2016] [Indexed: 12/15/2022] Open
Abstract
The CRISPR/Cas9 system is a rapid and customizable tool for gene editing in mammalian cells. In particular, this approach has widely opened new opportunities for genetic studies in neurological disease. Human neurons can be differentiated in vitro from hPSC (human Pluripotent Stem Cells), hNPCs (human Neural Precursor Cells) or even directly reprogrammed from fibroblasts. Here, we described a new platform which enables, rapid and efficient CRISPR/Cas9-mediated genome targeting simultaneously with three different paradigms for in vitro generation of neurons. This system was employed to inactivate two genes associated with neurological disorder (TSC2 and KCNQ2) and achieved up to 85% efficiency of gene targeting in the differentiated cells. In particular, we devised a protocol that, combining the expression of the CRISPR components with neurogenic factors, generated functional human neurons highly enriched for the desired genome modification in only 5 weeks. This new approach is easy, fast and that does not require the generation of stable isogenic clones, practice that is time consuming and for some genes not feasible.
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Affiliation(s)
- Alicia Rubio
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Mirko Luoni
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Serena G. Giannelli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Isabella Radice
- Advanced Light and Electron Microscopy Bio-Imaging Centre, Experimental Imaging Centre, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Angelo Iannielli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Cinzia Cancellieri
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Giulia Regalia
- Advanced Light and Electron Microscopy Bio-Imaging Centre, Experimental Imaging Centre, San Raffaele Scientific Institute, 20132 Milan, Italy
- Neuroengineering and medical robotics laboratory, Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
| | - Giovanna Lazzari
- Avantea srl, Laboratory of Reproductive Technologies, Via Porcellasco 7f, 26100 Cremona, Fondazione Avantea, Cremona
| | - Andrea Menegon
- Advanced Light and Electron Microscopy Bio-Imaging Centre, Experimental Imaging Centre, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Stefano Taverna
- Neuroimmunology Unit, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Vania Broccoli
- Division of Neuroscience, San Raffaele Scientific Institute, 20132 Milan, Italy
- National Research Council (CNR), Institute of Neuroscience, Milan, Italy
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60
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Choi H, Song J, Park G, Kim J. Modeling of Autism Using Organoid Technology. Mol Neurobiol 2016; 54:7789-7795. [DOI: 10.1007/s12035-016-0274-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/30/2016] [Indexed: 01/01/2023]
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61
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Horvath P, Aulner N, Bickle M, Davies AM, Nery ED, Ebner D, Montoya MC, Östling P, Pietiäinen V, Price LS, Shorte SL, Turcatti G, von Schantz C, Carragher NO. Screening out irrelevant cell-based models of disease. Nat Rev Drug Discov 2016; 15:751-769. [PMID: 27616293 DOI: 10.1038/nrd.2016.175] [Citation(s) in RCA: 322] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The common and persistent failures to translate promising preclinical drug candidates into clinical success highlight the limited effectiveness of disease models currently used in drug discovery. An apparent reluctance to explore and adopt alternative cell- and tissue-based model systems, coupled with a detachment from clinical practice during assay validation, contributes to ineffective translational research. To help address these issues and stimulate debate, here we propose a set of principles to facilitate the definition and development of disease-relevant assays, and we discuss new opportunities for exploiting the latest advances in cell-based assay technologies in drug discovery, including induced pluripotent stem cells, three-dimensional (3D) co-culture and organ-on-a-chip systems, complemented by advances in single-cell imaging and gene editing technologies. Funding to support precompetitive, multidisciplinary collaborations to develop novel preclinical models and cell-based screening technologies could have a key role in improving their clinical relevance, and ultimately increase clinical success rates.
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Affiliation(s)
- Peter Horvath
- Synthetic and Systems Biology Unit, Biological Research Centre of the Hungarian Academy of Sciences, Szeged H-6726, Hungary; and at the Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland.,European Cell-Based Assays Interest Group
| | - Nathalie Aulner
- Imagopole-Citech, Institut Pasteur, Paris 75015, France.,European Cell-Based Assays Interest Group
| | - Marc Bickle
- Technology Development Studio, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany.,European Cell-Based Assays Interest Group
| | - Anthony M Davies
- Translational Cell Imaging Queensland (TCIQ), Institute of Health Biomedical Innovation, Queensland University of Technology, Brisbane 4102 QLD, Australia; and The Irish National Centre for High Content Screening and Analysis, Trinity Translational Medicine Institute, Trinity College Dublin, Phase 3 Trinity Health Sciences 1.20, St James Hospital, Dublin D8, Republic of Ireland.,European Cell-Based Assays Interest Group
| | - Elaine Del Nery
- Institut Curie, PSL Research University, Department of Translational Research, The Biophenics High-Content Screening Laboratory, Cell and Tissue Imaging Facility (PICT-IBiSA), F-75005, Paris, France.,European Cell-Based Assays Interest Group
| | - Daniel Ebner
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK.,European Cell-Based Assays Interest Group
| | - Maria C Montoya
- Cellomics Unit, Cell Biology &Physiology Program, Cell &Developmental Biology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain.,European Cell-Based Assays Interest Group
| | - Päivi Östling
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland.,Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, Stockholm 17165, Sweden.,European Cell-Based Assays Interest Group
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland.,European Cell-Based Assays Interest Group
| | - Leo S Price
- Faculty of Science, Leiden Academic Centre for Drug Research, Toxicology, Universiteit Leiden, The Netherlands; and at OcellO, J.H Oortweg 21, 2333 CH, Leiden, The Netherlands.,European Cell-Based Assays Interest Group
| | - Spencer L Shorte
- Imagopole-Citech, Institut Pasteur, Paris 75015, France.,European Cell-Based Assays Interest Group
| | - Gerardo Turcatti
- Biomolecular Screening Facility, Swiss Federal Institute of Technology (EPFL), Lausanne CH-1015, Switzerland.,European Cell-Based Assays Interest Group
| | - Carina von Schantz
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki 00290, Finland.,European Cell-Based Assays Interest Group
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XR, UK.,European Cell-Based Assays Interest Group
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62
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Lee CM, Wu J, Xia Y, Hu J. ESE-1 in Early Development: Approaches for the Future. Front Cell Dev Biol 2016; 4:73. [PMID: 27446923 PMCID: PMC4924247 DOI: 10.3389/fcell.2016.00073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/17/2016] [Indexed: 01/14/2023] Open
Abstract
E26 transformation-specific (Ets) family of transcription factors are characterized by the presence of Ets-DNA binding domain and have been found to be highly involved in hematopoiesis and various tissue differentiation. ESE-1, or Elf3 in mice, is a member of epithelium-specific Ets sub-family which is most prominently expressed in epithelial tissues such as the gut, mammary gland, and lung. The role of ESE-1 during embryogenesis had long been alluded from 30% fetal lethality in homozygous knockout mice and its high expression in preimplantation mouse embryos, but there has been no in-depth of analysis of ESE-1 function in early development. With improved proteomics, gene editing tools and increasing knowledge of ESE-1 function in adult tissues, we hereby propose future research directions for the study of ESE-1 in embryogenesis, including studying its regulation at the protein level and at the protein family level, as well as better defining the developmental phase under investigation. Understanding the role of ESE-1 in early development will provide new insights into its involvement in tissue regeneration and cancer, as well as how it functions with other Ets factors as a protein family.
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Affiliation(s)
- Chan Mi Lee
- Program in Physiology and Experimental Medicine, Peter Gilgan Centre for Research and Learning, SickKids Research Institute, SickKids HospitalToronto, ON, Canada; Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
| | - Jing Wu
- Program in Physiology and Experimental Medicine, Peter Gilgan Centre for Research and Learning, SickKids Research Institute, SickKids Hospital Toronto, ON, Canada
| | - Yi Xia
- Program in Physiology and Experimental Medicine, Peter Gilgan Centre for Research and Learning, SickKids Research Institute, SickKids HospitalToronto, ON, Canada; Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
| | - Jim Hu
- Program in Physiology and Experimental Medicine, Peter Gilgan Centre for Research and Learning, SickKids Research Institute, SickKids HospitalToronto, ON, Canada; Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
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63
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Stillitano F, Turnbull IC, Karakikes I, Nonnenmacher M, Backeris P, Hulot JS, Kranias EG, Hajjar RJ, Costa KD. Genomic correction of familial cardiomyopathy in human engineered cardiac tissues. Eur Heart J 2016; 37:3282-3284. [PMID: 27450564 DOI: 10.1093/eurheartj/ehw307] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 04/22/2016] [Accepted: 06/20/2016] [Indexed: 01/09/2023] Open
Abstract
In this study, we used three-dimensional human engineered cardiac tissue technology to directly show that phospholamban (PLN) R14del mutation impairs cardiac contractility and to demonstrate restoration of contractile properties with targeted genetic correction of this inheritable form of dilated cardiomyopathy.
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Affiliation(s)
- Francesca Stillitano
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, PO Box 1030, New York, NY 10029, USA
| | - Irene C Turnbull
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, PO Box 1030, New York, NY 10029, USA
| | - Ioannis Karakikes
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, PO Box 1030, New York, NY 10029, USA.,Department of Medicine, Division of Cardiovascular Medicine, Stanford Cardiovascular Institute, Stanford, CA 94305, USA
| | - Mathieu Nonnenmacher
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, PO Box 1030, New York, NY 10029, USA
| | - Peter Backeris
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, PO Box 1030, New York, NY 10029, USA
| | - Jean-Sébastien Hulot
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, PO Box 1030, New York, NY 10029, USA.,Sorbonne Universités, UPMC Univ Paris 06, AP-HP, Institute of Cardiometabolism and Nutrition (ICAN), Pitié-Salpêtrière Hospital, Paris F-75013, France
| | - Evangelia G Kranias
- Department of Pharmacology, University of Cincinnati, Cincinnati, OH 45267-0575, USA
| | - Roger J Hajjar
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, PO Box 1030, New York, NY 10029, USA
| | - Kevin D Costa
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, PO Box 1030, New York, NY 10029, USA
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Lin J, Hu Y, Nunez S, Foulkes AS, Cieply B, Xue C, Gerelus M, Li W, Zhang H, Rader DJ, Musunuru K, Li M, Reilly MP. Transcriptome-Wide Analysis Reveals Modulation of Human Macrophage Inflammatory Phenotype Through Alternative Splicing. Arterioscler Thromb Vasc Biol 2016; 36:1434-47. [PMID: 27230130 PMCID: PMC4919157 DOI: 10.1161/atvbaha.116.307573] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/17/2016] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Human macrophages can shift phenotype across the inflammatory M1 and reparative M2 spectrum in response to environmental challenges, but the mechanisms promoting inflammatory and cardiometabolic disease-associated M1 phenotypes remain incompletely understood. Alternative splicing (AS) is emerging as an important regulator of cellular function, yet its role in macrophage activation is largely unknown. We investigated the extent to which AS occurs in M1 activation within the cardiometabolic disease context and validated a functional genomic cell model for studying human macrophage-related AS events. APPROACH AND RESULTS From deep RNA-sequencing of resting, M1, and M2 primary human monocyte-derived macrophages, we found 3860 differentially expressed genes in M1 activation and detected 233 M1-induced AS events; the majority of AS events were cell- and M1-specific with enrichment for pathways relevant to macrophage inflammation. Using genetic variant data for 10 cardiometabolic traits, we identified 28 trait-associated variants within the genomic loci of 21 alternatively spliced genes and 15 variants within 7 differentially expressed regulatory splicing factors in M1 activation. Knockdown of 1 such splicing factor, CELF1, in primary human macrophages led to increased inflammatory response to M1 stimulation, demonstrating CELF1's potential modulation of the M1 phenotype. Finally, we demonstrated that an induced pluripotent stem cell-derived macrophage system recapitulates M1-associated AS events and provides a high-fidelity macrophage AS model. CONCLUSIONS AS plays a role in defining macrophage phenotype in a cell- and stimulus-specific fashion. Alternatively spliced genes and splicing factors with trait-associated variants may reveal novel pathways and targets in cardiometabolic diseases.
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Affiliation(s)
- Jennie Lin
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.).
| | - Yu Hu
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Sara Nunez
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Andrea S Foulkes
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Benjamin Cieply
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Chenyi Xue
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Mark Gerelus
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Wenjun Li
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Hanrui Zhang
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Daniel J Rader
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Kiran Musunuru
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Mingyao Li
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.)
| | - Muredach P Reilly
- From the Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine (J.L.), Department of Biostatistics and Epidemiology (Y.H., M.L.), Department of Genetics, Perelman School of Medicine (B.C., K.M., D.J.R.), and Cardiovascular Institute, Department of Medicine, Perelman School of Medicine (M.G., W.L., K.M.), University of Pennsylvania, Philadelphia; Irving Institute for Clinical and Translational Research (M.P.R.) and Division of Cardiology, Department of Medicine (C.X., H.Z., M.P.R.), Columbia University Medical Center, New York, NY; and Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA (S.N., A.S.F.).
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Generation of Isogenic Human iPS Cell Line Precisely Corrected by Genome Editing Using the CRISPR/Cas9 System. Stem Cell Rev Rep 2016; 11:774-87. [PMID: 26059412 DOI: 10.1007/s12015-015-9600-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome engineering and human iPS cells are two powerful technologies, which can be combined to highlight phenotypic differences and identify pathological mechanisms of complex diseases by providing isogenic cellular material. However, very few data are available regarding precise gene correction in human iPS cells. Here, we describe an optimized stepwise protocol to deliver CRISPR/Cas9 plasmids in human iPS cells. We highlight technical issues especially those associated to human stem cell culture and to the correction of a point mutation to obtain isogenic iPS cell line, without inserting any resistance cassette. Based on a two-steps clonal isolation protocol (mechanical picking followed by enzymatic dissociation), we succeed to select and expand corrected human iPS cell line with a great efficiency (more than 2% of the sequenced colonies). This protocol can also be used to obtain knock-out cell line from healthy iPS cell line by the NHEJ pathway (with about 15% efficiency) and reproduce disease phenotype. In addition, we also provide protocols for functional validation tests after every critical step.
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Takata N, Sakakura E, Kasukawa T, Sakuma T, Yamamoto T, Sasai Y. Establishment of Functional Genomics Pipeline in Mouse Epiblast-Like Tissue by Combining Transcriptomic Analysis and Gene Knockdown/Knockin/Knockout, Using RNA Interference and CRISPR/Cas9. Hum Gene Ther 2016; 27:436-50. [PMID: 26839115 DOI: 10.1089/hum.2015.148] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The epiblast (foremost embryonic ectoderm) generates all three germ layers and therefore has crucial roles in the formation of all mammalian body cells. However, regulation of epiblast gene expression is poorly understood because of the difficulty of manipulating epiblast tissues in vivo. In the present study, using the self-organizing properties of mouse embryonic stem cell (ESC), we generated and characterized epiblast-like tissue in three-dimensional culture. We identified significant genome-wide gene expression changes in this epiblast-like tissue by transcriptomic analysis. In addition, we identified the particular significance of the Erk/Mapk and integrin-linked kinase pathways, and genes related to ectoderm/epithelial formation, using the bioinformatics resources IPA and DAVID. Here, we focused on Fgf5, which ranked in the top 10 among the discovered genes. To develop a functional analysis of Fgf5, we created an efficient method combining CRISPR/Cas9-mediated genome engineering and RNA interference (RNAi). Notably, we show one-step generation of various Fgf5 reporter lines including heterozygous and homozygous knockins (the GET method). For time- and dose-dependent depletion of fgf5 over the course of development, we generated an ESC line harboring Tol2 transposon-mediated integration of an inducible short hairpin RNA interference system (pdiRNAi). Our findings raised the possibility that Fgf/Erk signaling and apicobasal epithelial integrity are important factors in epiblast development. In addition, our methods provide a framework for a broad array of applications in the areas of mammalian genetics and molecular biology to understand development and to improve future therapeutics.
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Affiliation(s)
- Nozomu Takata
- 1 Laboratory for In Vitro Histogenesis, RIKEN Center for Developmental Biology , Hyogo, Japan
| | - Eriko Sakakura
- 1 Laboratory for In Vitro Histogenesis, RIKEN Center for Developmental Biology , Hyogo, Japan
| | - Takeya Kasukawa
- 2 Large Scale Data Managing Unit, RIKEN Center for Life Science Technologies , Kanagawa, Japan
| | - Tetsushi Sakuma
- 3 Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University , Hiroshima, Japan
| | - Takashi Yamamoto
- 3 Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University , Hiroshima, Japan
| | - Yoshiki Sasai
- 4 Laboratory for Organogenesis and Neurogenesis, RIKEN Center for Developmental Biology , Hyogo, Japan
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Zhu H, Behr B, Reddy VV, Hughes M, Pan Y, Baker J. Human Embryonic Stem Cell Lines with Lesions in FOXP3 and NF1. PLoS One 2016; 11:e0151836. [PMID: 26990425 PMCID: PMC4798423 DOI: 10.1371/journal.pone.0151836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/05/2016] [Indexed: 11/18/2022] Open
Abstract
Human embryonic stem cells (hESCs) are derived from the inner cell mass (ICM) of blastocyst staged embryos. Spare blastocyst staged embryos were obtained by in vitro fertilization (IVF) and donated for research purposes. hESCs carrying specific mutations can be used as a powerful cell system in modeling human genetic disorders. We obtained preimplantation genetic diagnosed (PGD) blastocyst staged embryos with genetic mutations that cause human disorders and derived hESCs from these embryos. We applied laser assisted micromanipulation to isolate the inner cell mass from the blastocysts and plated the ICM onto the mouse embryonic fibroblast cells. Two hESC lines with lesions in FOXP3 and NF1 were established. Both lines maintain a typical undifferentiated hESCs phenotype and present a normal karyotype. The two lines express a panel of pluripotency markers and have the potential to differentiate to the three germ layers in vitro and in vivo. The hESC lines with lesions in FOXP3 and NF1 are available for the scientific community and may serve as an important resource for research into these disease states.
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Affiliation(s)
- Hui Zhu
- Department of Genetics, Stanford University, Stanford, California, 94305, United States of America
| | - Barry Behr
- Stanford IVF Laboratory, Stanford Fertility and Reproductive Health, Lucile Packard Childrens Hospital Stanford, Palo Alto, California, 94304, United States of America
- Department of Obstetrics/Gynecology, Stanford University School of Medicine, Stanford, California, 94305, United States of America
| | - Vikrant V. Reddy
- Stanford IVF Laboratory, Stanford Fertility and Reproductive Health, Lucile Packard Childrens Hospital Stanford, Palo Alto, California, 94304, United States of America
| | - Mark Hughes
- Genesis Genetics Institute, Plymouth, Michigan, 48170, United States of America
| | - Yuqiong Pan
- Department of Medicine, Division of Blood and Marrow Transplantation, Stanford University, Stanford, California, 94305, United States of America
| | - Julie Baker
- Department of Genetics, Stanford University, Stanford, California, 94305, United States of America
- * E-mail:
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Abstract
Cardiovascular and neurodegenerative diseases are major health threats in many
developed countries. Recently, target tissues derived from human embryonic stem
(hES) cells and induced pluripotent stem cells (iPSCs), such as cardiomyocytes
(CMs) or neurons, have been actively mobilized for drug screening. Knowledge of
drug toxicity and efficacy obtained using stem cell-derived tissues could
parallel that obtained from human trials. Furthermore, iPSC disease models could
be advantageous in the development of personalized medicine in various parts of
disease sectors. To obtain the maximum benefit from iPSCs in disease modeling,
researchers are now focusing on aging, maturation, and metabolism to
recapitulate the pathological features seen in patients. Compared to pediatric
disease modeling, adult-onset disease modeling with iPSCs requires proper
maturation for full manifestation of pathological features. Herein, the success
of iPSC technology, focusing on patient-specific drug treatment,
maturation-based disease modeling, and alternative approaches to compensate for
the current limitations of patient iPSC modeling, will be further discussed.
[BMB Reports 2015; 48(5): 256-265]
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Affiliation(s)
- Changsung Kim
- Department of Bioscience and Biotechnology, Sejong University, Seoul 143-747, Korea
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Sackett SD, Brown ME, Tremmel DM, Ellis T, Burlingham WJ, Odorico JS. Modulation of human allogeneic and syngeneic pluripotent stem cells and immunological implications for transplantation. Transplant Rev (Orlando) 2016; 30:61-70. [PMID: 26970668 DOI: 10.1016/j.trre.2016.02.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/05/2016] [Indexed: 01/20/2023]
Abstract
Tissues derived from induced pluripotent stem cells (iPSCs) are a promising source of cells for building various regenerative medicine therapies; from simply transplanting cells to reseeding decellularized organs to reconstructing multicellular tissues. Although reprogramming strategies for producing iPSCs have improved, the clinical use of iPSCs is limited by the presence of unique human leukocyte antigen (HLA) genes, the main immunologic barrier to transplantation. In order to overcome the immunological hurdles associated with allogeneic tissues and organs, the generation of patient-histocompatible iPSCs (autologous or HLA-matched cells) provides an attractive platform for personalized medicine. However, concerns have been raised as to the fitness, safety and immunogenicity of iPSC derivatives because of variable differentiation potential of different lines and the identification of genetic and epigenetic aberrations that can occur during the reprogramming process. In addition, significant cost and regulatory barriers may deter commercialization of patient specific therapies in the short-term. Nonetheless, recent studies provide some evidence of immunological benefit for using autologous iPSCs. Yet, more studies are needed to evaluate the immunogenicity of various autologous and allogeneic human iPSC-derived cell types as well as test various methods to abrogate rejection. Here, we present perspectives of using allogeneic vs. autologous iPSCs for transplantation therapies and the advantages and disadvantages of each related to differentiation potential, immunogenicity, genetic stability and tumorigenicity. We also review the current literature on the immunogenicity of syngeneic iPSCs and discuss evidence that questions the feasibility of HLA-matched iPSC banks. Finally, we will discuss emerging methods of abrogating or reducing host immune responses to PSC derivatives.
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Affiliation(s)
- S D Sackett
- Division of Transplantation, Department of Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - M E Brown
- Division of Transplantation, Department of Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - D M Tremmel
- Division of Transplantation, Department of Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - T Ellis
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - W J Burlingham
- Division of Transplantation, Department of Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
| | - J S Odorico
- Division of Transplantation, Department of Surgery, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA.
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Advancing drug discovery for neuropsychiatric disorders using patient-specific stem cell models. Mol Cell Neurosci 2016; 73:104-15. [PMID: 26826498 DOI: 10.1016/j.mcn.2016.01.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 12/17/2022] Open
Abstract
Compelling clinical, social, and economic reasons exist to innovate in the process of drug discovery for neuropsychiatric disorders. The use of patient-specific, induced pluripotent stem cells (iPSCs) now affords the ability to generate neuronal cell-based models that recapitulate key aspects of human disease. In the context of neuropsychiatric disorders, where access to physiologically active and relevant cell types of the central nervous system for research is extremely limiting, iPSC-derived in vitro culture of human neurons and glial cells is transformative. Potential applications relevant to early stage drug discovery, include support of quantitative biochemistry, functional genomics, proteomics, and perhaps most notably, high-throughput and high-content chemical screening. While many phenotypes in human iPSC-derived culture systems may prove adaptable to screening formats, addressing the question of which in vitro phenotypes are ultimately relevant to disease pathophysiology and therefore more likely to yield effective pharmacological agents that are disease-modifying treatments requires careful consideration. Here, we review recent examples of studies of neuropsychiatric disorders using human stem cell models where cellular phenotypes linked to disease and functional assays have been reported. We also highlight technical advances using genome-editing technologies in iPSCs to support drug discovery efforts, including the interpretation of the functional significance of rare genetic variants of unknown significance and for the purpose of creating cell type- and pathway-selective functional reporter assays. Additionally, we evaluate the potential of in vitro stem cell models to investigate early events of disease pathogenesis, in an effort to understand the underlying molecular mechanism, including the basis of selective cell-type vulnerability, and the potential to create new cell-based diagnostics to aid in the classification of patients and subsequent selection for clinical trials. A number of key challenges remain, including the scaling of iPSC models to larger cohorts and integration with rich clinicopathological information and translation of phenotypes. Still, the overall use of iPSC-based human cell models with functional cellular and biochemical assays holds promise for supporting the discovery of next-generation neuropharmacological agents for the treatment and ultimately prevention of a range of severe mental illnesses.
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iPSCs: A Minireview from Bench to Bed, including Organoids and the CRISPR System. Stem Cells Int 2016; 2016:5934782. [PMID: 26880972 PMCID: PMC4736429 DOI: 10.1155/2016/5934782] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 10/19/2015] [Accepted: 10/25/2015] [Indexed: 12/22/2022] Open
Abstract
When Dolly the sheep was born, the first probe into an adult mammalian genome traveling back in time and generating a whole new animal appeared. Ten years later, the reprogramming process became a defined method of producing induced pluripotent stem cells (iPSCs) through the overexpression of four transcription factors. iPSCs are capable of originating virtually all types of cells and tissues, including a whole new animal. The reprogramming strategies based on patient-derived cells should make the development of clinical applications of cell based therapy much more straightforward. Here, we analyze the current state, opportunities, and challenges of iPSCs from bench to bed, including organoids and the CRISPR system.
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Castrillo JI, Oliver SG. Alzheimer's as a Systems-Level Disease Involving the Interplay of Multiple Cellular Networks. Methods Mol Biol 2016; 1303:3-48. [PMID: 26235058 DOI: 10.1007/978-1-4939-2627-5_1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease (AD), and many neurodegenerative disorders, are multifactorial in nature. They involve a combination of genomic, epigenomic, interactomic and environmental factors. Progress is being made, and these complex diseases are beginning to be understood as having their origin in altered states of biological networks at the cellular level. In the case of AD, genomic susceptibility and mechanisms leading to (or accompanying) the impairment of the central Amyloid Precursor Protein (APP) processing and tau networks are widely accepted as major contributors to the diseased state. The derangement of these networks may result in both the gain and loss of functions, increased generation of toxic species (e.g., toxic soluble oligomers and aggregates) and imbalances, whose effects can propagate to supra-cellular levels. Although well sustained by empirical data and widely accepted, this global perspective often overlooks the essential roles played by the main counteracting homeostatic networks (e.g., protein quality control/proteostasis, unfolded protein response, protein folding chaperone networks, disaggregases, ER-associated degradation/ubiquitin proteasome system, endolysosomal network, autophagy, and other stress-protective and clearance networks), whose relevance to AD is just beginning to be fully realized. In this chapter, an integrative perspective is presented. Alzheimer's disease is characterized to be a result of: (a) intrinsic genomic/epigenomic susceptibility and, (b) a continued dynamic interplay between the deranged networks and the central homeostatic networks of nerve cells. This interplay of networks will underlie both the onset and rate of progression of the disease in each individual. Integrative Systems Biology approaches are required to effect its elucidation. Comprehensive Systems Biology experiments at different 'omics levels in simple model organisms, engineered to recapitulate the basic features of AD may illuminate the onset and sequence of events underlying AD. Indeed, studies of models of AD in simple organisms, differentiated cells in culture and rodents are beginning to offer hope that the onset and progression of AD, if detected at an early stage, may be stopped, delayed, or even reversed, by activating or modulating networks involved in proteostasis and the clearance of toxic species. In practice, the incorporation of next-generation neuroimaging, high-throughput and computational approaches are opening the way towards early diagnosis well before irreversible cell death. Thus, the presence or co-occurrence of: (a) accumulation of toxic Aβ oligomers and tau species; (b) altered splicing and transcriptome patterns; (c) impaired redox, proteostatic, and metabolic networks together with, (d) compromised homeostatic capacities may constitute relevant 'AD hallmarks at the cellular level' towards reliable and early diagnosis. From here, preventive lifestyle changes and tailored therapies may be investigated, such as combined strategies aimed at both lowering the production of toxic species and potentiating homeostatic responses, in order to prevent or delay the onset, and arrest, alleviate, or even reverse the progression of the disease.
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Affiliation(s)
- Juan I Castrillo
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK,
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Freedman BS. Modeling Kidney Disease with iPS Cells. Biomark Insights 2015; 10:153-69. [PMID: 26740740 PMCID: PMC4689367 DOI: 10.4137/bmi.s20054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 07/19/2015] [Accepted: 07/21/2015] [Indexed: 12/14/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are somatic cells that have been transcriptionally reprogrammed to an embryonic stem cell (ESC)-like state. iPSCs are a renewable source of diverse somatic cell types and tissues matching the original patient, including nephron-like kidney organoids. iPSCs have been derived representing several kidney disorders, such as ADPKD, ARPKD, Alport syndrome, and lupus nephritis, with the goals of generating replacement tissue and ‘disease in a dish’ laboratory models. Cellular defects in iPSCs and derived kidney organoids provide functional, personalized biomarkers, which can be correlated with genetic and clinical information. In proof of principle, disease-specific phenotypes have been described in iPSCs and ESCs with mutations linked to polycystic kidney disease or focal segmental glomerulosclerosis. In addition, these cells can be used to model nephrotoxic chemical injury. Recent advances in directed differentiation and CRISPR genome editing enable more specific iPSC models and present new possibilities for diagnostics, disease modeling, therapeutic screens, and tissue regeneration using human cells. This review outlines growth opportunities and design strategies for this rapidly expanding and evolving field.
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Affiliation(s)
- Benjamin S Freedman
- Division of Nephrology, Kidney Research Institute, and Institute for Stem Cell and Regenerative Medicine, Department of Medicine, University of Washington School of Medicine, Seattle, WA, USA
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75
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Wang J, Li T, Zhou M, Hu Z, Zhou X, Zhou S, Wang N, Huang L, Zhao L, Cao Y, Xiao M, Ma D, Zhou P, Shang Z, Zhou J. TALENs-mediated gene disruption of FLT3 in leukemia cells: Using genome-editing approach for exploring the molecular basis of gene abnormality. Sci Rep 2015; 5:18454. [PMID: 26669855 PMCID: PMC4680874 DOI: 10.1038/srep18454] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 11/17/2015] [Indexed: 12/11/2022] Open
Abstract
Novel analytic tools are needed to elucidate the molecular basis of leukemia-relevant gene mutations in the post-genome era. We generated isogenic leukemia cell clones in which the FLT3 gene was disrupted in a single allele using TALENs. Isogenic clones with mono-allelic disrupted FLT3 were compared to an isogenic wild-type control clone and parental leukemia cells for transcriptional expression, downstream FLT3 signaling and proliferation capacity. The global gene expression profiles of mutant K562 clones and corresponding wild-type controls were compared using RNA-seq. The transcriptional levels and the ligand-dependent autophosphorylation of FLT3 were decreased in the mutant clones. TALENs-mediated FLT3 haplo-insufficiency impaired cell proliferation and colony formation in vitro. These inhibitory effects were maintained in vivo, improving the survival of NOD/SCID mice transplanted with mutant K562 clones. Cluster analysis revealed that the gene expression pattern of isogenic clones was determined by the FLT3 mutant status rather than the deviation among individual isogenic clones. Differentially expressed genes between the mutant and wild-type clones revealed an activation of nonsense-mediated decay pathway in mutant K562 clones as well as an inhibited FLT3 signaling. Our data support that this genome-editing approach is a robust and generally applicable platform to explore the molecular bases of gene mutations.
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Affiliation(s)
- Jue Wang
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tongjuan Li
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mi Zhou
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zheng Hu
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoxi Zhou
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shiqiu Zhou
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Na Wang
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liang Huang
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lei Zhao
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yang Cao
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Min Xiao
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ding Ma
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Pengfei Zhou
- Wuhan YZY Bio-Pharma Co., Ltd., Wuhan, Hubei, China
| | - Zhen Shang
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jianfeng Zhou
- Department of hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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76
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Gupta RM, Meissner TB, Cowan CA, Musunuru K. Genome-Edited Human Pluripotent Stem Cell-Derived Macrophages as a Model of Reverse Cholesterol Transport--Brief Report. Arterioscler Thromb Vasc Biol 2015; 36:15-8. [PMID: 26543098 DOI: 10.1161/atvbaha.115.305956] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 10/22/2015] [Indexed: 01/26/2023]
Abstract
OBJECTIVE To create isogenic human pluripotent stem cell-derived macrophages with and without ABCA1 expression as a model for reverse cholesterol transport. APPROACH AND RESULTS The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) genome-editing system was used to introduce frameshift mutations into the coding sequence of ATP-binding cassette, subfamily A, member 1. Individual human pluripotent stem cell clones with deleterious mutations were identified, expanded, and differentiated into mature macrophages with a cytokine-based, feeder-free differentiation protocol. Wild-type cells demonstrated effective cholesterol efflux to apoAI acceptor, whereas ABCA1(-/-) cells displayed significantly reduced efflux ability and increased expression of proinflammatory cytokines. CONCLUSIONS Human pluripotent stem cell-derived macrophages capable of reverse cholesterol transport can be rapidly generated and genetically edited with CRISPR/Cas9. Introduction of homozygous frameshift mutations results in loss of ABCA1 expression in differentiated macrophages and subsequent reduction of cholesterol efflux capability. This facile genome-editing approach and differentiation protocol pave the way for future studies of the molecular determinants of reverse cholesterol transport and other macrophage properties.
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Affiliation(s)
- Rajat M Gupta
- From the Department of Stem Cell and Regenerative Biology, Harvard University, and Harvard Stem Cell Institute, Cambridge, MA (R.M.G., T.B.M., C.A.C., K.M.); and Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA (R.M.G., K.M.)
| | - Torsten B Meissner
- From the Department of Stem Cell and Regenerative Biology, Harvard University, and Harvard Stem Cell Institute, Cambridge, MA (R.M.G., T.B.M., C.A.C., K.M.); and Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA (R.M.G., K.M.)
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77
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Tang S, Xie M, Cao N, Ding S. Patient-Specific Induced Pluripotent Stem Cells for Disease Modeling and Phenotypic Drug Discovery. J Med Chem 2015; 59:2-15. [PMID: 26322868 DOI: 10.1021/acs.jmedchem.5b00789] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In vitro cell models are invaluable tools for studying diseases and discovering drugs. Human induced pluripotent stem cells, particularly derived from patients, are an advantageous resource for generating ample supplies of cells to create unique platforms that model disease. This manuscript will review recent developments in modeling a variety of diseases (including their cellular phenotypes) with induced pluripotent stem cells derived from patients. It will also describe how researchers have exploited these models to validate drugs as potential therapeutics for these devastating diseases.
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Affiliation(s)
- Shibing Tang
- Gladstone Institutes , 1650 Owens Street, San Francisco, California 94158, United States
| | - Min Xie
- Gladstone Institutes , 1650 Owens Street, San Francisco, California 94158, United States
| | - Nan Cao
- Gladstone Institutes , 1650 Owens Street, San Francisco, California 94158, United States
| | - Sheng Ding
- Gladstone Institutes , 1650 Owens Street, San Francisco, California 94158, United States
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78
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Lee HJ, Lee HC, Han JY. Germline Modification and Engineering in Avian Species. Mol Cells 2015; 38:743-9. [PMID: 26333275 PMCID: PMC4588716 DOI: 10.14348/molcells.2015.0225] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 08/26/2015] [Accepted: 08/27/2015] [Indexed: 12/21/2022] Open
Abstract
Production of genome-edited animals using germline-competent cells and genetic modification tools has provided opportunities for investigation of biological mechanisms in various organisms. The recently reported programmed genome editing technology that can induce gene modification at a target locus in an efficient and precise manner facilitates establishment of animal models. In this regard, the demand for genome-edited avian species, which are some of the most suitable model animals due to their unique embryonic development, has also increased. Furthermore, germline chimera production through long-term culture of chicken primordial germ cells (PGCs) has facilitated research on production of genome-edited chickens. Thus, use of avian germline modification is promising for development of novel avian models for research of disease control and various biological mechanisms. Here, we discuss recent progress in genome modification technology in avian species and its applications and future strategies.
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Affiliation(s)
- Hong Jo Lee
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Hyung Chul Lee
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT,
UK
| | - Jae Yong Han
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
- Institute for Biomedical Sciences, Shinshu University, 8304 Minamiminowa, Kamiina, Nagano 399-4598,
Japan
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79
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Lee CT, Freed WJ, Mash DC. CNVs in neurodevelopmental disorders. Oncotarget 2015; 6:18238-9. [PMID: 26285833 PMCID: PMC4621882 DOI: 10.18632/oncotarget.4853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 07/10/2015] [Indexed: 11/25/2022] Open
Affiliation(s)
- Chun-Ting Lee
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - William J Freed
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Deborah C Mash
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, USA
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80
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Kim JJ. Applications of iPSCs in Cancer Research. Biomark Insights 2015; 10:125-31. [PMID: 26279620 PMCID: PMC4521640 DOI: 10.4137/bmi.s20065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/10/2015] [Accepted: 06/11/2015] [Indexed: 12/11/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) derived from reprogrammed somatic cells are emerging as one of the most versatile tools in biomedical research and pharmacological studies. Oncogenic transformation and somatic cell reprogramming are multistep processes that share some common features, and iPSCs generated from cancerous cells can help us better understand the molecular mechanisms underlying the initiation and progression of human cancers and overcome them. Aside from the mechanistic modeling of human tumorigenesis, immediate applications of this technology in cancer research include high-throughput drug screening, toxicological testing, early biomarker identification, and bioengineering of replacement tissues. Here, we review the current advances in generating iPSCs from cancer cell lines and patient-derived primary cancer tissues, and discuss their potential applications.
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Affiliation(s)
- Jean J Kim
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
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81
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Veres A, Gosis BS, Ding Q, Collins R, Ragavendran A, Brand H, Erdin S, Cowan CA, Talkowski ME, Musunuru K. Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. Cell Stem Cell 2015; 15:27-30. [PMID: 24996167 DOI: 10.1016/j.stem.2014.04.020] [Citation(s) in RCA: 384] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 03/13/2014] [Accepted: 04/24/2014] [Indexed: 12/26/2022]
Abstract
Genome editing has attracted wide interest for the generation of cellular models of disease using human pluripotent stem cells and other cell types. CRISPR-Cas systems and TALENs can target desired genomic sites with high efficiency in human cells, but recent publications have led to concern about the extent to which these tools may cause off-target mutagenic effects that could potentially confound disease-modeling studies. Using CRISPR-Cas9 and TALEN targeted human pluripotent stem cell clones, we performed whole-genome sequencing at high coverage in order to assess the degree of mutagenesis across the entire genome. In both types of clones, we found that off-target mutations attributable to the nucleases were very rare. From this analysis, we suggest that, although some cell types may be at risk for off-target mutations, the incidence of such effects in human pluripotent stem cells may be sufficiently low and thus not a significant concern for disease modeling and other applications.
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Affiliation(s)
- Adrian Veres
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Bridget S Gosis
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Qiurong Ding
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Ryan Collins
- Molecular Neurogenetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ashok Ragavendran
- Molecular Neurogenetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Harrison Brand
- Molecular Neurogenetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Serkan Erdin
- Molecular Neurogenetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Michael E Talkowski
- Molecular Neurogenetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Kiran Musunuru
- Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA 02142, USA; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
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82
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Veerman CC, Kosmidis G, Mummery CL, Casini S, Verkerk AO, Bellin M. Immaturity of Human Stem-Cell-Derived Cardiomyocytes in Culture: Fatal Flaw or Soluble Problem? Stem Cells Dev 2015; 24:1035-52. [DOI: 10.1089/scd.2014.0533] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Christiaan C. Veerman
- Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Georgios Kosmidis
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands
| | - Christine L. Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands
| | - Simona Casini
- Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arie O. Verkerk
- Department of Anatomy, Embryology and Physiology, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Milena Bellin
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands
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83
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O'Geen H, Henry IM, Bhakta MS, Meckler JF, Segal DJ. A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture. Nucleic Acids Res 2015; 43:3389-404. [PMID: 25712100 PMCID: PMC4381059 DOI: 10.1093/nar/gkv137] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 02/07/2015] [Accepted: 02/09/2015] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) RNA-guided nucleases have gathered considerable excitement as a tool for genome engineering. However, questions remain about the specificity of target site recognition. Cleavage specificity is typically evaluated by low throughput assays (T7 endonuclease I assay, target amplification followed by high-throughput sequencing), which are limited to a subset of potential off-target sites. Here, we used ChIP-seq to examine genome-wide CRISPR binding specificity at gRNA-specific and gRNA-independent sites for two guide RNAs. RNA-guided Cas9 binding was highly specific to the target site while off-target binding occurred at much lower intensities. Cas9-bound regions were highly enriched in NGG sites, a sequence required for target site recognition by Streptococcus pyogenes Cas9. To determine the relationship between Cas9 binding and endonuclease activity, we applied targeted sequence capture, which allowed us to survey 1200 genomic loci simultaneously including potential off-target sites identified by ChIP-seq and by computational prediction. A high frequency of indels was observed at both target sites and one off-target site, while no cleavage activity could be detected at other ChIP-bound regions. Our results confirm the high-specificity of CRISPR endonucleases and demonstrate that sequence capture can be used as a high-throughput genome-wide approach to identify off-target activity.
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Affiliation(s)
- Henriette O'Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA
| | - Mital S Bhakta
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - Joshua F Meckler
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
| | - David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
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84
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Genome Editing in Stem Cells. CURRENT STEM CELL REPORTS 2015. [DOI: 10.1007/s40778-014-0009-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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85
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Musunuru K, Hickey KT, Al-Khatib SM, Delles C, Fornage M, Fox CS, Frazier L, Gelb BD, Herrington DM, Lanfear DE, Rosand J. Basic concepts and potential applications of genetics and genomics for cardiovascular and stroke clinicians: a scientific statement from the American Heart Association. ACTA ACUST UNITED AC 2015; 8:216-42. [PMID: 25561044 DOI: 10.1161/hcg.0000000000000020] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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86
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Khera AV, Mehta NN. Single-cell transcriptomics: an emerging tool in the study of cardiometabolic disease. J Transl Med 2014; 12:312. [PMID: 25377125 PMCID: PMC4228185 DOI: 10.1186/s12967-014-0312-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/27/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Amit V Khera
- Cardiology Division, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA.
| | - Nehal N Mehta
- Section of Inflammation and Cardiometabolic Diseases, National Heart, Lung and Blood Institute, Bethesda, MD, 20892, USA.
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87
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Morris JH, Knudsen GM, Verschueren E, Johnson JR, Cimermancic P, Greninger AL, Pico AR. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc 2014; 9:2539-54. [PMID: 25275790 PMCID: PMC4332878 DOI: 10.1038/nprot.2014.164] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
By determining protein-protein interactions in normal, diseased and infected cells, we can improve our understanding of cellular systems and their reaction to various perturbations. In this protocol, we discuss how to use data obtained in affinity purification-mass spectrometry (AP-MS) experiments to generate meaningful interaction networks and effective figures. We begin with an overview of common epitope tagging, expression and AP practices, followed by liquid chromatography-MS (LC-MS) data collection. We then provide a detailed procedure covering a pipeline approach to (i) pre-processing the data by filtering against contaminant lists such as the Contaminant Repository for Affinity Purification (CRAPome) and normalization using the spectral index (SIN) or normalized spectral abundance factor (NSAF); (ii) scoring via methods such as MiST, SAInt and CompPASS; and (iii) testing the resulting scores. Data formats familiar to MS practitioners are then transformed to those most useful for network-based analyses. The protocol also explores methods available in Cytoscape to visualize and analyze these types of interaction data. The scoring pipeline can take anywhere from 1 d to 1 week, depending on one's familiarity with the tools and data peculiarities. Similarly, the network analysis and visualization protocol in Cytoscape takes 2-4 h to complete with the provided sample data, but we recommend taking days or even weeks to explore one's data and find the right questions.
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Affiliation(s)
- John H Morris
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Giselle M Knudsen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA
| | - Erik Verschueren
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Jeffrey R Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Peter Cimermancic
- 1] Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California, USA. [2] Graduate Group in Bioinformatics, University of California, San Francisco, San Francisco, California, USA
| | - Alexander L Greninger
- School of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Alexander R Pico
- Gladstone Institutes, University of California, San Francisco, San Francisco, California, USA
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88
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Wang Y, Liang P, Lan F, Wu H, Lisowski L, Gu M, Hu S, Kay MA, Urnov FD, Shinnawi R, Gold JD, Gepstein L, Wu JC. Genome editing of isogenic human induced pluripotent stem cells recapitulates long QT phenotype for drug testing. J Am Coll Cardiol 2014; 64:451-9. [PMID: 25082577 DOI: 10.1016/j.jacc.2014.04.057] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 04/07/2014] [Accepted: 04/30/2014] [Indexed: 12/22/2022]
Abstract
BACKGROUND Human induced pluripotent stem cells (iPSCs) play an important role in disease modeling and drug testing. However, the current methods are time-consuming and lack an isogenic control. OBJECTIVES This study sought to establish an efficient technology to generate human PSC-based disease models with isogenic control. METHODS The ion channel genes KCNQ1 and KCNH2 with dominant negative mutations causing long QT syndrome types 1 and 2, respectively, were stably integrated into a safe harbor AAVS1 locus using zinc finger nuclease technology. RESULTS Patch-clamp recording revealed that the edited iPSC-derived cardiomyocytes (iPSC-CMs) displayed characteristic long QT syndrome phenotype and significant prolongation of the action potential duration compared with the unedited control cells. Finally, addition of nifedipine (L-type calcium channel blocker) or pinacidil (KATP-channel opener) shortened the action potential duration of iPSC-CMs, confirming the validity of isogenic iPSC lines for drug testing in the future. CONCLUSIONS Our study demonstrates that iPSC-CM-based disease models can be rapidly generated by overexpression of dominant negative gene mutants.
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Affiliation(s)
- Yongming Wang
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California; Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California; State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China
| | - Ping Liang
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California; Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Feng Lan
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California; Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Haodi Wu
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California; Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Leszek Lisowski
- Departments of Pediatrics and Genetics, Stanford University School of Medicine, Stanford, California
| | - Mingxia Gu
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California; Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Shijun Hu
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California; Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Mark A Kay
- Departments of Pediatrics and Genetics, Stanford University School of Medicine, Stanford, California
| | | | - Rami Shinnawi
- Rambam Medical Center, Technion, Israel Institute of Technology, Haifa, Israel
| | - Joseph D Gold
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California; Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California
| | - Lior Gepstein
- Rambam Medical Center, Technion, Israel Institute of Technology, Haifa, Israel
| | - Joseph C Wu
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, California; Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, California; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California.
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Krueger W, Boelsterli UA, Rasmussen TP. Stem Cell Strategies to Evaluate Idiosyncratic Drug-induced Liver Injury. J Clin Transl Hepatol 2014; 2:143-52. [PMID: 26355943 PMCID: PMC4521249 DOI: 10.14218/jcth.2014.00012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/13/2014] [Accepted: 06/07/2014] [Indexed: 12/14/2022] Open
Abstract
The host-dependent nature of idiosyncratic drug-induced liver injury (iDILI) suggests that rare genetic polymorphisms may contribute to the disease. Indeed, a few mutations in key genes have already been identified using conventional human genetics approaches. Over 50 commonly used drugs can precipitate iDILI, making this a substantial medical problem. Only recently have human induced pluripotent stem cells been used as a research tool to discover novel iDILI genes and to study the mechanisms of iDILI in vitro. Here we review the current state of stem cell use in the investigation of iDILI, with a special focus on genetics. In addition, the concerns and difficulties associated with genetics and animal model research are discussed. We then present the features of patient-specific pluripotent stem cells (which may be derived from iDILI patients themselves), and explain why these cells may be of great utility. A variety of recent approaches to produce hepatocyte-like cells from pluripotent cells and the associated advantages and limitations of such cells are discussed. Future directions for the use of stem cell science to investigate iDILI include novel ways to identify new iDILI genes, a consideration of epigenetic impacts on iDILI, and the development of new and improved strategies for the production of hepatocytes from human pluripotent cells.
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Affiliation(s)
- Winfried Krueger
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Urs A. Boelsterli
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
| | - Theodore P. Rasmussen
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- University of Connecticut Stem Cell Institute, Storrs/Farmington, CT, USA
- Correspondence to: Theodore P. Rasmussen, Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, U-3092, Storrs, CT 06269, USA. Tel: +86-486-8339, Fax: +86-486-5792. E-mail:
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Leyton-Mange JS, Milan DJ. Pluripotent stem cells as a platform for cardiac arrhythmia drug screening. CURRENT TREATMENT OPTIONS IN CARDIOVASCULAR MEDICINE 2014; 16:334. [PMID: 25074263 DOI: 10.1007/s11936-014-0334-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
OPINION STATEMENT Since the first demonstrations of the differentiation of pluripotent stem cells to produce functional human cellular models such as cardiomyocytes, the scientific community has been captivated [1, 2••, 3]. In the time since that seminal work, the field has been catapulted forward by the demonstration that adult somatic cells can be reprogrammed to an induced state of pluripotency [4••], and more recently by the development of efficient and sophisticated genome editing tools [5••, 6••, 7], which together afford a theoretically unlimited supply of relevant genetic disease models. In particular, many of the early successes with induced pluripotent stem cell technology have been realized with cardiac arrhythmia syndromes [8••, 9-15]. There is interest in applying stem cell models in large-scale screens to discover novel therapeutics or drug toxicities. This manuscript aims to discuss the potential role of hPSC-derived cardiomyocyte models in therapeutic arrhythmia screens and review recent advances in the field that bring us closer to this reality.
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91
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Janero DR. The future of drug discovery: enabling technologies for enhancing lead characterization and profiling therapeutic potential. Expert Opin Drug Discov 2014; 9:847-58. [PMID: 24965547 DOI: 10.1517/17460441.2014.925876] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Technology often serves as a handmaiden and catalyst of invention. The discovery of safe, effective medications depends critically upon experimental approaches capable of providing high-impact information on the biological effects of drug candidates early in the discovery pipeline. This information can enable reliable lead identification, pharmacological compound differentiation and successful translation of research output into clinically useful therapeutics. The shallow preclinical profiling of candidate compounds promulgates a minimalistic understanding of their biological effects and undermines the level of value creation necessary for finding quality leads worth moving forward within the development pipeline with efficiency and prognostic reliability sufficient to help remediate the current pharma-industry productivity drought. Three specific technologies discussed herein, in addition to experimental areas intimately associated with contemporary drug discovery, appear to hold particular promise for strengthening the preclinical valuation of drug candidates by deepening lead characterization. These are: i) hydrogen-deuterium exchange mass spectrometry for characterizing structural and ligand-interaction dynamics of disease-relevant proteins; ii) activity-based chemoproteomics for profiling the functional diversity of mammalian proteomes; and iii) nuclease-mediated precision gene editing for developing more translatable cellular and in vivo models of human diseases. When applied in an informed manner congruent with the clinical understanding of disease processes, technologies such as these that span levels of biological organization can serve as valuable enablers of drug discovery and potentially contribute to reducing the current, unacceptably high rates of compound clinical failure.
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Affiliation(s)
- David R Janero
- Northeastern University, Bouvé College of Health Sciences, Center for Drug Discovery, Department of Pharmaceutical Sciences, Health Sciences Entrepreneurs , 360 Huntington Avenue, 116 Mugar Life Sciences Hall, Boston, MA 02115-5000 , USA +1 617 373 2208 ; +1 617 373 7493 ;
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Abstract
We have previously reported the genetic correction of Huntington's disease (HD) patient-derived induced pluripotent stem cells using traditional homologous recombination (HR) approaches. To extend this work, we have adopted a CRISPR-based genome editing approach to improve the efficiency of recombination in order to generate allelic isogenic HD models in human cells. Incorporation of a rapid antibody-based screening approach to measure recombination provides a powerful method to determine relative efficiency of genome editing for modeling polyglutamine diseases or understanding factors that modulate CRISPR/Cas9 HR.
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Menendez JA, Alarcón T, Corominas-Faja B, Cuyàs E, López-Bonet E, Martin AG, Vellon L. Xenopatients 2.0: reprogramming the epigenetic landscapes of patient-derived cancer genomes. Cell Cycle 2014; 13:358-70. [PMID: 24406535 DOI: 10.4161/cc.27770] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In the science-fiction thriller film Minority Report, a specialized police department called "PreCrime" apprehends criminals identified in advance based on foreknowledge provided by 3 genetically altered humans called "PreCogs". We propose that Yamanaka stem cell technology can be similarly used to (epi)genetically reprogram tumor cells obtained directly from cancer patients and create self-evolving personalized translational platforms to foresee the evolutionary trajectory of individual tumors. This strategy yields a large stem cell population and captures the cancer genome of an affected individual, i.e., the PreCog-induced pluripotent stem (iPS) cancer cells, which are immediately available for experimental manipulation, including pharmacological screening for personalized "stemotoxic" cancer drugs. The PreCog-iPS cancer cells will re-differentiate upon orthotopic injection into the corresponding target tissues of immunodeficient mice (i.e., the PreCrime-iPS mouse avatars), and this in vivo model will run through specific cancer stages to directly explore their biological properties for drug screening, diagnosis, and personalized treatment in individual patients. The PreCog/PreCrime-iPS approach can perform sets of comparisons to directly observe changes in the cancer-iPS cell line vs. a normal iPS cell line derived from the same human genetic background. Genome editing of PreCog-iPS cells could create translational platforms to directly investigate the link between genomic expression changes and cellular malignization that is largely free from genetic and epigenetic noise and provide proof-of-principle evidence for cutting-edge "chromosome therapies" aimed against cancer aneuploidy. We might infer the epigenetic marks that correct the tumorigenic nature of the reprogrammed cancer cell population and normalize the malignant phenotype in vivo. Genetically engineered models of conditionally reprogrammable mice to transiently express the Yamanaka stemness factors following the activation of phenotypic copies of specific cancer diseases might crucially evaluate a "reprogramming cure" for cancer. A new era of xenopatients 2.0 generated via nuclear reprogramming of the epigenetic landscapes of patient-derived cancer genomes might revolutionize the current personalized translational platforms in cancer research.
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Affiliation(s)
- Javier A Menendez
- Metabolism & Cancer Group; Translational Research Laboratory; Catalan Institute of Oncology; Girona, Spain; Molecular Oncology Group; Girona Biomedical Research Institute (IDIBGI); Girona, Spain
| | - Tomás Alarcón
- Computational & Mathematical Biology Research Group; Centre de Recerca Matemàtica (CRM); Barcelona, Spain
| | - Bruna Corominas-Faja
- Metabolism & Cancer Group; Translational Research Laboratory; Catalan Institute of Oncology; Girona, Spain; Molecular Oncology Group; Girona Biomedical Research Institute (IDIBGI); Girona, Spain
| | - Elisabet Cuyàs
- Metabolism & Cancer Group; Translational Research Laboratory; Catalan Institute of Oncology; Girona, Spain; Molecular Oncology Group; Girona Biomedical Research Institute (IDIBGI); Girona, Spain
| | - Eugeni López-Bonet
- Department of Anatomical Pathology; Dr. Josep Trueta University Hospital of Girona; Girona, Spain
| | | | - Luciano Vellon
- IBYME; CONICET-Laboratorio de Immunohematología, Laboratorio de Química de Proteoglicanos y Matriz Extracelular; Buenos Aires, Argentina
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