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Chaudhari P, Tian L, Deshmukh A, Jang YY. Expression kinetics of hepatic progenitor markers in cellular models of human liver development recapitulating hepatocyte and biliary cell fate commitment. Exp Biol Med (Maywood) 2016; 241:1653-62. [PMID: 27390263 DOI: 10.1177/1535370216657901] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Due to the limitations of research using human embryos and the lack of a biological model of human liver development, the roles of the various markers associated with liver stem or progenitor cell potential in humans are largely speculative, and based on studies utilizing animal models and certain patient tissues. Human pluripotent stem cell-based in vitro multistage hepatic differentiation systems may serve as good surrogate models for mimicking normal human liver development, pathogenesis and injury/regeneration studies. Here, we describe the implications of various liver stem or progenitor cell markers and their bipotency (i.e. hepatocytic- and biliary-epithelial cell differentiation), based on the pluripotent stem cell-derived model of human liver development. Future studies using the human cellular model(s) of liver and biliary development will provide more human relevant biological and/or pathological roles of distinct markers expressed in heterogeneous liver stem/progenitor cell populations.
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Affiliation(s)
- Pooja Chaudhari
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore 21205, USA Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore 21205, USA Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205, USA
| | - Lipeng Tian
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore 21205, USA
| | - Abhijeet Deshmukh
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore 21205, USA
| | - Yoon-Young Jang
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore 21205, USA Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore 21205, USA Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore 21205, USA
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102
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Site-Specific Genome Engineering in Human Pluripotent Stem Cells. Int J Mol Sci 2016; 17:ijms17071000. [PMID: 27347935 PMCID: PMC4964376 DOI: 10.3390/ijms17071000] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 12/21/2022] Open
Abstract
The possibility to generate patient-specific induced pluripotent stem cells (iPSCs) offers an unprecedented potential of applications in clinical therapy and medical research. Human iPSCs and their differentiated derivatives are tools for diseases modelling, drug discovery, safety pharmacology, and toxicology. Moreover, they allow for the engineering of bioartificial tissue and are promising candidates for cellular therapies. For many of these applications, the ability to genetically modify pluripotent stem cells (PSCs) is indispensable, but efficient site-specific and safe technologies for genetic engineering of PSCs were developed only recently. By now, customized engineered nucleases provide excellent tools for targeted genome editing, opening new perspectives for biomedical research and cellular therapies.
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103
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Gene correction in patient-specific iPSCs for therapy development and disease modeling. Hum Genet 2016; 135:1041-58. [PMID: 27256364 DOI: 10.1007/s00439-016-1691-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 05/18/2016] [Indexed: 12/20/2022]
Abstract
The discovery that mature cells can be reprogrammed to become pluripotent and the development of engineered endonucleases for enhancing genome editing are two of the most exciting and impactful technology advances in modern medicine and science. Human pluripotent stem cells have the potential to establish new model systems for studying human developmental biology and disease mechanisms. Gene correction in patient-specific iPSCs can also provide a novel source for autologous cell therapy. Although historically challenging, precise genome editing in human iPSCs is becoming more feasible with the development of new genome-editing tools, including ZFNs, TALENs, and CRISPR. iPSCs derived from patients of a variety of diseases have been edited to correct disease-associated mutations and to generate isogenic cell lines. After directed differentiation, many of the corrected iPSCs showed restored functionality and demonstrated their potential in cell replacement therapy. Genome-wide analyses of gene-corrected iPSCs have collectively demonstrated a high fidelity of the engineered endonucleases. Remaining challenges in clinical translation of these technologies include maintaining genome integrity of the iPSC clones and the differentiated cells. Given the rapid advances in genome-editing technologies, gene correction is no longer the bottleneck in developing iPSC-based gene and cell therapies; generating functional and transplantable cell types from iPSCs remains the biggest challenge needing to be addressed by the research field.
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104
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Abstract
The Cas9 protein (CRISPR-associated protein 9), derived from type II CRISPR (clustered regularly interspaced short palindromic repeats) bacterial immune systems, is emerging as a powerful tool for engineering the genome in diverse organisms. As an RNA-guided DNA endonuclease, Cas9 can be easily programmed to target new sites by altering its guide RNA sequence, and its development as a tool has made sequence-specific gene editing several magnitudes easier. The nuclease-deactivated form of Cas9 further provides a versatile RNA-guided DNA-targeting platform for regulating and imaging the genome, as well as for rewriting the epigenetic status, all in a sequence-specific manner. With all of these advances, we have just begun to explore the possible applications of Cas9 in biomedical research and therapeutics. In this review, we describe the current models of Cas9 function and the structural and biochemical studies that support it. We focus on the applications of Cas9 for genome editing, regulation, and imaging, discuss other possible applications and some technical considerations, and highlight the many advantages that CRISPR/Cas9 technology offers.
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Affiliation(s)
- Haifeng Wang
- Department of Bioengineering, Stanford University, Stanford, California 94305; , ,
| | - Marie La Russa
- Department of Bioengineering, Stanford University, Stanford, California 94305; , ,
- Biomedical Sciences Graduate Program, University of California, San Francisco, California 94158
| | - Lei S Qi
- Department of Bioengineering, Stanford University, Stanford, California 94305; , ,
- Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305
- Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California 94305
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105
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Hung SSC, McCaughey T, Swann O, Pébay A, Hewitt AW. Genome engineering in ophthalmology: Application of CRISPR/Cas to the treatment of eye disease. Prog Retin Eye Res 2016; 53:1-20. [PMID: 27181583 DOI: 10.1016/j.preteyeres.2016.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 04/30/2016] [Accepted: 05/04/2016] [Indexed: 12/12/2022]
Abstract
The Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) and CRISPR-associated protein (Cas) system has enabled an accurate and efficient means to edit the human genome. Rapid advances in this technology could results in imminent clinical application, and with favourable anatomical and immunological profiles, ophthalmic disease will be at the forefront of such work. There have been a number of breakthroughs improving the specificity and efficacy of CRISPR/Cas-mediated genome editing. Similarly, better methods to identify off-target cleavage sites have also been developed. With the impending clinical utility of CRISPR/Cas technology, complex ethical issues related to the regulation and management of the precise applications of human gene editing must be considered. This review discusses the current progress and recent breakthroughs in CRISPR/Cas-based gene engineering, and outlines some of the technical issues that must be addressed before gene correction, be it in vivo or in vitro, is integrated into ophthalmic care. We outline a clinical pipeline for CRISPR-based treatments of inherited eye diseases and provide an overview of the important ethical implications of gene editing and how these may influence the future of this technology.
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Affiliation(s)
- Sandy S C Hung
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Tristan McCaughey
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia; Department of Surgery, Monash University, Victoria, Australia
| | - Olivia Swann
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Australia
| | - Alice Pébay
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, Melbourne, Australia; Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Australia.
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106
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Osorio MJ, Goldman SA. Glial progenitor cell-based treatment of the childhood leukodystrophies. Exp Neurol 2016; 283:476-88. [PMID: 27170209 DOI: 10.1016/j.expneurol.2016.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 04/19/2016] [Accepted: 05/05/2016] [Indexed: 12/19/2022]
Abstract
The childhood leukodystrophies comprise a group of hereditary disorders characterized by the absence, malformation or destruction of myelin. These disorders share common clinical, radiological and pathological features, despite their diverse molecular and genetic etiologies. Oligodendrocytes and astrocytes are the major affected cell populations, and are either structurally impaired or metabolically compromised through cell-intrinsic pathology, or are the victims of mis-accumulated toxic byproducts of metabolic derangement. In either case, glial cell replacement using implanted tissue or pluripotent stem cell-derived human neural or glial progenitor cells may comprise a promising strategy for both structural remyelination and metabolic rescue. A broad variety of pediatric white matter disorders, including the primary hypomyelinating disorders, the lysosomal storage disorders, and the broader group of non-lysosomal metabolic leukodystrophies, may all be appropriate candidates for glial progenitor cell-based treatment. Nonetheless, a variety of specific challenges remain before this therapeutic strategy can be applied to children. These include timely diagnosis, before irreparable neuronal injury has ensued; understanding the natural history of the targeted disease; defining the optimal cell phenotype for each disorder; achieving safe and scalable cellular compositions; designing age-appropriate controlled clinical trials; and for autologous therapy of genetic disorders, achieving the safe genetic editing of pluripotent stem cells. Yet these challenges notwithstanding, the promise of glial progenitor cell-based treatment of the childhood myelin disorders offers hope to the many victims of this otherwise largely untreatable class of disease.
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Affiliation(s)
- M Joana Osorio
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, United States; Center for Basic and Translational Neuroscience, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen 2200, Denmark.
| | - Steven A Goldman
- Center for Translational Neuromedicine, University of Rochester Medical Center, Rochester, NY 14642, United States; Center for Basic and Translational Neuroscience, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen 2200, Denmark.
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107
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Huang X, Wang Y, Yan W, Smith C, Ye Z, Wang J, Gao Y, Mendelsohn L, Cheng L. Production of Gene-Corrected Adult Beta Globin Protein in Human Erythrocytes Differentiated from Patient iPSCs After Genome Editing of the Sickle Point Mutation. Stem Cells 2016; 33:1470-9. [PMID: 25702619 DOI: 10.1002/stem.1969] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 01/14/2015] [Indexed: 12/11/2022]
Abstract
Human induced pluripotent stem cells (iPSCs) and genome editing provide a precise way to generate gene-corrected cells for disease modeling and cell therapies. Human iPSCs generated from sickle cell disease (SCD) patients have a homozygous missense point mutation in the HBB gene encoding adult β-globin proteins, and are used as a model system to improve strategies of human gene therapy. We demonstrate that the CRISPR/Cas9 system designer nuclease is much more efficient in stimulating gene targeting of the endogenous HBB locus near the SCD point mutation in human iPSCs than zinc finger nucleases and TALENs. Using a specific guide RNA and Cas9, we readily corrected one allele of the SCD HBB gene in human iPSCs by homologous recombination with a donor DNA template containing the wild-type HBB DNA and a selection cassette that was subsequently removed to avoid possible interference of HBB transcription and translation. We chose targeted iPSC clones that have one corrected and one disrupted SCD allele for erythroid differentiation assays, using an improved xeno-free and feeder-free culture condition we recently established. Erythrocytes from either the corrected or its parental (uncorrected) iPSC line were generated with similar efficiencies. Currently ∼6%-10% of these differentiated erythrocytes indeed lacked nuclei, characteristic of further matured erythrocytes called reticulocytes. We also detected the 16-kDa β-globin protein expressed from the corrected HBB allele in the erythrocytes differentiated from genome-edited iPSCs. Our results represent a significant step toward the clinical applications of genome editing using patient-derived iPSCs to generate disease-free cells for cell and gene therapies. Stem Cells 2015;33:1470-1479.
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Affiliation(s)
- Xiaosong Huang
- Division of Hematology, Department of Medicine; Institute for Cell Engineering
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108
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Abstract
PURPOSE OF REVIEW In this review, we summarize the current status of clinical trials using therapeutic cells produced from human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs). We also discuss combined cell and gene therapy via correction of defined mutations in human pluripotent stem cells and provide commentary on key obstacles facing widescale clinical adoption of pluripotent stem cell-based therapy. RECENT FINDINGS Initial data suggest that hESC/hiPSC-derived cell products used for retinal repair and spinal cord injury are safe for human use. Early-stage studies for treatment of cardiac injury and diabetes are also in progress. However, there remain key concerns regarding the safety and efficacy of these cells that need to be addressed in additional well designed clinical trials. Advances using the clustered regulatory interspaced short palindromic repeats (CRISPR)/Cas9 gene-editing system offer an improved tool for more rapid and on-target gene correction of genetic diseases. Combined gene and cell therapy using human pluripotent stem cells may provide an additional curative approach for disabling or lethal genetic and degenerative diseases wherein there are currently limited therapeutic opportunities. SUMMARY Human pluripotent stem cells are emerging as a promising tool to produce cells and tissues suitable for regenerative therapy for a variety of genetic and degenerative diseases.
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109
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Turan S, Farruggio AP, Srifa W, Day JW, Calos MP. Precise Correction of Disease Mutations in Induced Pluripotent Stem Cells Derived From Patients With Limb Girdle Muscular Dystrophy. MOLECULAR THERAPY : THE JOURNAL OF THE AMERICAN SOCIETY OF GENE THERAPY 2016. [PMID: 26916285 DOI: 10.1038/mt.2016.40.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Limb girdle muscular dystrophies types 2B (LGMD2B) and 2D (LGMD2D) are degenerative muscle diseases caused by mutations in the dysferlin and alpha-sarcoglycan genes, respectively. Using patient-derived induced pluripotent stem cells (iPSC), we corrected the dysferlin nonsense mutation c.5713C>T; p.R1905X and the most common alpha-sarcoglycan mutation, missense c.229C>T; p.R77C, by single-stranded oligonucleotide-mediated gene editing, using the CRISPR/Cas9 gene-editing system to enhance the frequency of homology-directed repair. We demonstrated seamless, allele-specific correction at efficiencies of 0.7-1.5%. As an alternative, we also carried out precise gene addition strategies for correction of the LGMD2B iPSC by integration of wild-type dysferlin cDNA into the H11 safe harbor locus on chromosome 22, using dual integrase cassette exchange (DICE) or TALEN-assisted homologous recombination for insertion precise (THRIP). These methods employed TALENs and homologous recombination, and DICE also utilized site-specific recombinases. With DICE and THRIP, we obtained targeting efficiencies after selection of ~20%. We purified iPSC corrected by all methods and verified rescue of appropriate levels of dysferlin and alpha-sarcoglycan protein expression and correct localization, as shown by immunoblot and immunocytochemistry. In summary, we demonstrate for the first time precise correction of LGMD iPSC and validation of expression, opening the possibility of cell therapy utilizing these corrected iPSC.
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Affiliation(s)
- Soeren Turan
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Alfonso P Farruggio
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Waracharee Srifa
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - John W Day
- Department of Neurology, Stanford University School of Medicine, Stanford, California, USA
| | - Michele P Calos
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
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110
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Turan S, Farruggio AP, Srifa W, Day JW, Calos MP. Precise Correction of Disease Mutations in Induced Pluripotent Stem Cells Derived From Patients With Limb Girdle Muscular Dystrophy. Mol Ther 2016; 24:685-96. [PMID: 26916285 DOI: 10.1038/mt.2016.40] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/09/2016] [Indexed: 12/22/2022] Open
Abstract
Limb girdle muscular dystrophies types 2B (LGMD2B) and 2D (LGMD2D) are degenerative muscle diseases caused by mutations in the dysferlin and alpha-sarcoglycan genes, respectively. Using patient-derived induced pluripotent stem cells (iPSC), we corrected the dysferlin nonsense mutation c.5713C>T; p.R1905X and the most common alpha-sarcoglycan mutation, missense c.229C>T; p.R77C, by single-stranded oligonucleotide-mediated gene editing, using the CRISPR/Cas9 gene-editing system to enhance the frequency of homology-directed repair. We demonstrated seamless, allele-specific correction at efficiencies of 0.7-1.5%. As an alternative, we also carried out precise gene addition strategies for correction of the LGMD2B iPSC by integration of wild-type dysferlin cDNA into the H11 safe harbor locus on chromosome 22, using dual integrase cassette exchange (DICE) or TALEN-assisted homologous recombination for insertion precise (THRIP). These methods employed TALENs and homologous recombination, and DICE also utilized site-specific recombinases. With DICE and THRIP, we obtained targeting efficiencies after selection of ~20%. We purified iPSC corrected by all methods and verified rescue of appropriate levels of dysferlin and alpha-sarcoglycan protein expression and correct localization, as shown by immunoblot and immunocytochemistry. In summary, we demonstrate for the first time precise correction of LGMD iPSC and validation of expression, opening the possibility of cell therapy utilizing these corrected iPSC.
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Affiliation(s)
- Soeren Turan
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Alfonso P Farruggio
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Waracharee Srifa
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - John W Day
- Department of Neurology, Stanford University School of Medicine, Stanford, California, USA
| | - Michele P Calos
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
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111
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Wobma H, Vunjak-Novakovic G. Tissue Engineering and Regenerative Medicine 2015: A Year in Review. TISSUE ENGINEERING PART B-REVIEWS 2016; 22:101-13. [PMID: 26714410 DOI: 10.1089/ten.teb.2015.0535] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This may be the most exciting time ever for the field of tissue engineering and regenerative medicine (TERM). After decades of progress, it has matured, integrated, and diversified into entirely new areas, and it is starting to make the pivotal shift toward translation. The most exciting science and applications continue to emerge at the boundaries of disciplines, through increasingly effective interactions between stem cell biologists, bioengineers, clinicians, and the commercial sector. In this "Year in Review," we highlight some of the major advances reported over the last year (Summer 2014-Fall 2015). Using a methodology similar to that established in previous years, we identified four areas that generated major progress in the field: (i) pluripotent stem cells, (ii) microtissue platforms for drug testing and disease modeling, (iii) tissue models of cancer, and (iv) whole organ engineering. For each area, we used some of the most impactful articles to illustrate the important concepts and results that advanced the state of the art of TERM. We conclude with reflections on emerging areas and perspectives for future development in the field.
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Affiliation(s)
- Holly Wobma
- 1 Department of Biomedical Engineering, Columbia University , New York
| | - Gordana Vunjak-Novakovic
- 1 Department of Biomedical Engineering, Columbia University , New York.,2 Department of Medicine, Columbia University , New York
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112
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Fujita T, Yuno M, Fujii H. Efficient sequence-specific isolation of DNA fragments and chromatin by in vitro enChIP technology using recombinant CRISPR ribonucleoproteins. Genes Cells 2016; 21:370-7. [PMID: 26848818 DOI: 10.1111/gtc.12341] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Accepted: 12/18/2015] [Indexed: 01/08/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) system is widely used for various biological applications, including genome editing. We developed engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR to isolate target genomic regions from cells for their biochemical characterization. In this study, we developed 'in vitro enChIP' using recombinant CRISPR ribonucleoproteins (RNPs) to isolate target genomic regions. in vitro enChIP has the great advantage over conventional enChIP of not requiring expression of CRISPR complexes in cells. We first showed that in vitro enChIP using recombinant CRISPR RNPs can be used to isolate target DNA from mixtures of purified DNA in a sequence-specific manner. In addition, we showed that this technology can be used to efficiently isolate target genomic regions, while retaining their intracellular molecular interactions, with negligible contamination from irrelevant genomic regions. Thus, in vitro enChIP technology is of potential use for sequence-specific isolation of DNA, as well as for identification of molecules interacting with genomic regions of interest in vivo in combination with downstream analysis.
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Affiliation(s)
- Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Miyuki Yuno
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
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113
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Hansel MC, Davila JC, Vosough M, Gramignoli R, Skvorak KJ, Dorko K, Marongiu F, Blake W, Strom SC. The Use of Induced Pluripotent Stem Cells for the Study and Treatment of Liver Diseases. ACTA ACUST UNITED AC 2016; 67:14.13.1-14.13.27. [PMID: 26828329 DOI: 10.1002/0471140856.tx1413s67] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Liver disease is a major global health concern. Liver cirrhosis is one of the leading causes of death in the world and currently the only therapeutic option for end-stage liver disease (e.g., acute liver failure, cirrhosis, chronic hepatitis, cholestatic diseases, metabolic diseases, and malignant neoplasms) is orthotropic liver transplantation. Transplantation of hepatocytes has been proposed and used as an alternative to whole organ transplant to stabilize and prolong the lives of patients in some clinical cases. Although these experimental therapies have demonstrated promising and beneficial results, their routine use remains a challenge due to the shortage of donor livers available for cell isolation, variable quality of those tissues, the potential need for lifelong immunosuppression in the transplant recipient, and high costs. Therefore, new therapeutic strategies and more reliable clinical treatments are urgently needed. Recent and continuous technological advances in the development of stem cells suggest they may be beneficial in this respect. In this review, we summarize the history of stem cell and induced pluripotent stem cell (iPSC) technology in the context of hepatic differentiation and discuss the potential applications the technology may offer for human liver disease modeling and treatment. This includes developing safer drugs and cell-based therapies to improve the outcomes of patients with currently incurable health illnesses. We also review promising advances in other disease areas to highlight how the stem cell technology could be applied to liver diseases in the future. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Marc C Hansel
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.,McGowan Institute for Regenerative Medicine, Pittsburgh, Pennsylvania
| | - Julio C Davila
- Department of Biochemistry, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
| | - Massoud Vosough
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Roberto Gramignoli
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Kristen J Skvorak
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kenneth Dorko
- Department of Pharmacology, Toxicology and Therapeutics, Kansas University Medical Center, Kansas City, Kansas
| | - Fabio Marongiu
- Department of Biomedical Sciences, Section of Experimental Pathology, Unit of Experimental Medicine, University of Cagliari, Cagliari, Italy
| | - William Blake
- Genetically Modified Models Center of Emphasis, Pfizer, Groton, Connecticut
| | - Stephen C Strom
- McGowan Institute for Regenerative Medicine, Pittsburgh, Pennsylvania.,Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden
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114
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Golas MM, Sander B. Use of human stem cells in Huntington disease modeling and translational research. Exp Neurol 2016; 278:76-90. [PMID: 26826449 DOI: 10.1016/j.expneurol.2016.01.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 02/08/2023]
Abstract
Huntington disease (HD) is a devastating neurological disorder caused by an extended CAG repeat in exon 1 of the gene that encodes the huntingtin (HTT) protein. HD pathology involves a loss of striatal medium spiny neurons (MSNs) and progressive neurodegeneration affects the striatum and other brain regions. Because HTT is involved in multiple cellular processes, the molecular mechanisms of HD pathogenesis should be investigated on multiple levels. On the cellular level, in vitro stem cell models, such as induced pluripotent stem cells (iPSCs) derived from HD patients and HD embryonic stem cells (ESCs), have yielded progress. Approaches to differentiate functional MSNs from ESCs, iPSCs, and neural stem/progenitor cells (NSCs/NPCs) have been established, enabling MSN differentiation to be studied and disease phenotypes to be recapitulated. Isolation of target stem cells and precursor cells may also provide a resource for grafting. In animal models, transplantation of striatal precursors differentiated in vitro to the striatum has been reported to improve disease phenotype. Initial clinical trials examining intrastriatal transplantation of fetal neural tissue suggest a more favorable clinical course in a subset of HD patients, though shortcomings persist. Here, we review recent advances in the development of cellular HD models and approaches aimed at cell regeneration with human stem cells. We also describe how genome editing tools could be used to correct the HTT mutation in patient-specific stem cells. Finally, we discuss the potential and the remaining challenges of stem cell-based approaches in HD research and therapy development.
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Affiliation(s)
- Monika M Golas
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark.
| | - Bjoern Sander
- Stereology and Electron Microscopy Laboratory, Department of Clinical Medicine, Aarhus University, Aarhus C, Denmark
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115
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Mitochondrial resetting and metabolic reprogramming in induced pluripotent stem cells and mitochondrial disease modeling. Biochim Biophys Acta Gen Subj 2016; 1860:686-93. [PMID: 26779594 DOI: 10.1016/j.bbagen.2016.01.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 01/19/2023]
Abstract
BACKGROUND Nuclear reprogramming with pluripotency factors enables somatic cells to gain the properties of embryonic stem cells. Mitochondrial resetting and metabolic reprogramming are suggested to be key early events in the induction of human skin fibroblasts to induced pluripotent stem cells (iPSCs). SCOPE OF REVIEW We review recent advances in the study of the molecular basis for mitochondrial resetting and metabolic reprogramming in the regulation of the formation of iPSCs. In particular, the recent progress in using iPSCs for mitochondrial disease modeling was discussed. MAJOR CONCLUSIONS iPSCs rely on glycolysis rather than oxidative phosphorylation as a major supply of energy. Mitochondrial resetting and metabolic reprogramming thus play crucial roles in the process of generation of iPSCs from somatic cells. GENERAL SIGNIFICANCE Neurons, myocytes, and cardiomyocytes are cells containing abundant mitochondria in the human body, which can be differentiated from iPSCs or trans-differentiated from fibroblasts. Generating these cells from iPSCs derived from skin fibroblasts of patients with mitochondrial diseases or by trans-differentiation with cell-specific transcription factors will provide valuable insights into the role of mitochondrial DNA heteroplasmy in mitochondrial disease modeling and serves as a novel platform for screening of drugs to treat patients with mitochondrial diseases.
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Wojtal D, Kemaladewi DU, Malam Z, Abdullah S, Wong TWY, Hyatt E, Baghestani Z, Pereira S, Stavropoulos J, Mouly V, Mamchaoui K, Muntoni F, Voit T, Gonorazky HD, Dowling JJ, Wilson MD, Mendoza-Londono R, Ivakine EA, Cohn RD. Spell Checking Nature: Versatility of CRISPR/Cas9 for Developing Treatments for Inherited Disorders. Am J Hum Genet 2016; 98:90-101. [PMID: 26686765 DOI: 10.1016/j.ajhg.2015.11.012] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/13/2015] [Indexed: 12/26/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) has arisen as a frontrunner for efficient genome engineering. However, the potentially broad therapeutic implications are largely unexplored. Here, to investigate the therapeutic potential of CRISPR/Cas9 in a diverse set of genetic disorders, we establish a pipeline that uses readily obtainable cells from affected individuals. We show that an adapted version of CRISPR/Cas9 increases the amount of utrophin, a known disease modifier in Duchenne muscular dystrophy (DMD). Furthermore, we demonstrate preferential elimination of the dominant-negative FGFR3 c.1138G>A allele in fibroblasts of an individual affected by achondroplasia. Using a previously undescribed approach involving single guide RNA, we successfully removed large genome rearrangement in primary cells of an individual with an X chromosome duplication including MECP2. Moreover, removal of a duplication of DMD exons 18-30 in myotubes of an individual affected by DMD produced full-length dystrophin. Our findings establish the far-reaching therapeutic utility of CRISPR/Cas9, which can be tailored to target numerous inherited disorders.
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Affiliation(s)
- Daria Wojtal
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Dwi U Kemaladewi
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Zeenat Malam
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sarah Abdullah
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Tatianna W Y Wong
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Elzbieta Hyatt
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Zahra Baghestani
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Sergio Pereira
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - James Stavropoulos
- Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Vincent Mouly
- INSERM UMRS974, Centre National de la Recherche Scientifique FRE3617, Center for Research in Myology, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 47 Boulevard de l'Hôpital, 75013 Paris, France
| | - Kamel Mamchaoui
- INSERM UMRS974, Centre National de la Recherche Scientifique FRE3617, Center for Research in Myology, Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, 47 Boulevard de l'Hôpital, 75013 Paris, France
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, Institute of Child Health and Great Ormond Street Hospital, London WC1N 1EH, UK
| | - Thomas Voit
- NIHR Biomedical Research Centre, Institute of Child Health, University College London, 30 Guilford Street, London WC1N 1EH, UK
| | - Hernan D Gonorazky
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - James J Dowling
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Michael D Wilson
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Roberto Mendoza-Londono
- Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Evgueni A Ivakine
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ronald D Cohn
- Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Centre for Genetic Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
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117
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Sun N, Tischfield JA, King RA, Heiman GA. Functional Evaluations of Genes Disrupted in Patients with Tourette's Disorder. Front Psychiatry 2016; 7:11. [PMID: 26903887 PMCID: PMC4746269 DOI: 10.3389/fpsyt.2016.00011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/18/2016] [Indexed: 01/04/2023] Open
Abstract
Tourette's disorder (TD) is a highly heritable neurodevelopmental disorder with complex genetic architecture and unclear neuropathology. Disruptions of particular genes have been identified in subsets of TD patients. However, none of the findings have been replicated, probably due to the complex and heterogeneous genetic architecture of TD that involves both common and rare variants. To understand the etiology of TD, functional analyses are required to characterize the molecular and cellular consequences caused by mutations in candidate genes. Such molecular and cellular alterations may converge into common biological pathways underlying the heterogeneous genetic etiology of TD patients. Herein, we review specific genes implicated in TD etiology, discuss the functions of these genes in the mammalian central nervous system and the corresponding behavioral anomalies exhibited in animal models, and importantly, review functional analyses that can be performed to evaluate the role(s) that the genetic disruptions might play in TD. Specifically, the functional assays include novel cell culture systems, genome editing techniques, bioinformatics approaches, transcriptomic analyses, and genetically modified animal models applied or developed to study genes associated with TD or with other neurodevelopmental and neuropsychiatric disorders. By describing methods used to study diseases with genetic architecture similar to TD, we hope to develop a systematic framework for investigating the etiology of TD and related disorders.
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Affiliation(s)
- Nawei Sun
- Department of Genetics, Rutgers University, Piscataway, NJ, USA; Human Genetics Institute of New Jersey, Piscataway, NJ, USA
| | - Jay A Tischfield
- Department of Genetics, Rutgers University, Piscataway, NJ, USA; Human Genetics Institute of New Jersey, Piscataway, NJ, USA
| | - Robert A King
- Child Study Center, Yale School of Medicine , New Haven, CT , USA
| | - Gary A Heiman
- Department of Genetics, Rutgers University, Piscataway, NJ, USA; Human Genetics Institute of New Jersey, Piscataway, NJ, USA
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118
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Off-target Effects in CRISPR/Cas9-mediated Genome Engineering. MOLECULAR THERAPY. NUCLEIC ACIDS 2015; 4:e264. [PMID: 26575098 PMCID: PMC4877446 DOI: 10.1038/mtna.2015.37] [Citation(s) in RCA: 739] [Impact Index Per Article: 82.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/05/2015] [Indexed: 12/26/2022]
Abstract
CRISPR/Cas9 is a versatile genome-editing technology that is widely used for studying the functionality of genetic elements, creating genetically modified organisms as well as preclinical research of genetic disorders. However, the high frequency of off-target activity (≥50%)—RGEN (RNA-guided endonuclease)-induced mutations at sites other than the intended on-target site—is one major concern, especially for therapeutic and clinical applications. Here, we review the basic mechanisms underlying off-target cutting in the CRISPR/Cas9 system, methods for detecting off-target mutations, and strategies for minimizing off-target cleavage. The improvement off-target specificity in the CRISPR/Cas9 system will provide solid genotype–phenotype correlations, and thus enable faithful interpretation of genome-editing data, which will certainly facilitate the basic and clinical application of this technology.
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119
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Čermák T, Baltes NJ, Čegan R, Zhang Y, Voytas DF. High-frequency, precise modification of the tomato genome. Genome Biol 2015; 16:232. [PMID: 26541286 PMCID: PMC4635538 DOI: 10.1186/s13059-015-0796-9] [Citation(s) in RCA: 341] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 10/02/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The use of homologous recombination to precisely modify plant genomes has been challenging, due to the lack of efficient methods for delivering DNA repair templates to plant cells. Even with the advent of sequence-specific nucleases, which stimulate homologous recombination at predefined genomic sites by creating targeted DNA double-strand breaks, there are only a handful of studies that report precise editing of endogenous genes in crop plants. More efficient methods are needed to modify plant genomes through homologous recombination, ideally without randomly integrating foreign DNA. RESULTS Here, we use geminivirus replicons to create heritable modifications to the tomato genome at frequencies tenfold higher than traditional methods of DNA delivery (i.e., Agrobacterium). A strong promoter was inserted upstream of a gene controlling anthocyanin biosynthesis, resulting in overexpression and ectopic accumulation of pigments in tomato tissues. More than two-thirds of the insertions were precise, and had no unanticipated sequence modifications. Both TALENs and CRISPR/Cas9 achieved gene targeting at similar efficiencies. Further, the targeted modification was transmitted to progeny in a Mendelian fashion. Even though donor molecules were replicated in the vectors, no evidence was found of persistent extra-chromosomal replicons or off-target integration of T-DNA or replicon sequences. CONCLUSIONS High-frequency, precise modification of the tomato genome was achieved using geminivirus replicons, suggesting that these vectors can overcome the efficiency barrier that has made gene targeting in plants challenging. This work provides a foundation for efficient genome editing of crop genomes without the random integration of foreign DNA.
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Affiliation(s)
- Tomáš Čermák
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, 55455, USA.
| | - Nicholas J Baltes
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, 55455, USA.
| | - Radim Čegan
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, CZ-612 65, Brno, Czech Republic.
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, University of Electronic Science and Technology of China, 216 Main Building No. 4, Section 2, North Jianshe Road, Chengdu, 610054, P.R. China.
| | - Daniel F Voytas
- Department of Genetics, Cell Biology & Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, 55455, USA.
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120
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Mussolino C, Mlambo T, Cathomen T. Proven and novel strategies for efficient editing of the human genome. Curr Opin Pharmacol 2015; 24:105-12. [DOI: 10.1016/j.coph.2015.08.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/12/2015] [Accepted: 08/18/2015] [Indexed: 12/18/2022]
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121
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Lim CS, Yang JE, Lee YK, Lee K, Lee JA, Kaang BK. Understanding the molecular basis of autism in a dish using hiPSCs-derived neurons from ASD patients. Mol Brain 2015; 8:57. [PMID: 26419846 PMCID: PMC4589208 DOI: 10.1186/s13041-015-0146-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 09/11/2015] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder characterized by deficits in social cognition, language development, and repetitive/restricted behaviors. Due to the complexity and heterogeneity of ASD and lack of a proper human cellular model system, the pathophysiological mechanism of ASD during the developmental process is largely unknown. However, recent progress in induced pluripotent stem cell (iPSC) technology as well as in vitro neural differentiation techniques have allowed us to functionally characterize neurons and analyze cortical development during neural differentiation. These technical advances will increase our understanding of the pathogenic mechanisms of heterogeneous ASD and help identify molecular biomarkers for patient stratification as well as personalized medicine. In this review, we summarize our current knowledge of iPSC generation, differentiation of specific neuronal subtypes from iPSCs, and phenotypic characterizations of human ASD patient-derived iPSC models. Finally, we discuss the current limitations of iPSC technology and future directions of ASD pathophysiology studies using iPSCs.
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Affiliation(s)
- Chae-Seok Lim
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanangno 599, Seoul, Gwanak-gu, 151-747, Korea
| | - Jung-Eun Yang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanangno 599, Seoul, Gwanak-gu, 151-747, Korea
| | - You-Kyung Lee
- Department of Biological Sciences and Biotechnology, College of Life Science and NanoTechnology, Hannam University, Jeonmin-dong 461-6, Daejeon, Yuseong-gu, 305-811, Korea
| | - Kyungmin Lee
- Department of Anatomy, Kyungpook National University Graduate School of Medicine, Dongin-dong 2-101, Daegu, Jung-gu, 700-422, Korea
| | - Jin-A Lee
- Department of Biological Sciences and Biotechnology, College of Life Science and NanoTechnology, Hannam University, Jeonmin-dong 461-6, Daejeon, Yuseong-gu, 305-811, Korea.
| | - Bong-Kiun Kaang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Gwanangno 599, Seoul, Gwanak-gu, 151-747, Korea.
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122
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Pellagatti A, Dolatshad H, Yip BH, Valletta S, Boultwood J. Application of genome editing technologies to the study and treatment of hematological disease. Adv Biol Regul 2015; 60:122-134. [PMID: 26433620 DOI: 10.1016/j.jbior.2015.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/07/2015] [Accepted: 09/09/2015] [Indexed: 11/29/2022]
Abstract
Genome editing technologies have advanced significantly over the past few years, providing a fast and effective tool to precisely manipulate the genome at specific locations. The three commonly used genome editing technologies are Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs), and the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Cas9 (CRISPR/Cas9) system. ZFNs and TALENs consist of endonucleases fused to a DNA-binding domain, while the CRISPR/Cas9 system uses guide RNAs to target the bacterial Cas9 endonuclease to the desired genomic location. The double-strand breaks made by these endonucleases are repaired in the cells either by non-homologous end joining, resulting in the introduction of insertions/deletions, or, if a repair template is provided, by homology directed repair. The ZFNs, TALENs and CRISPR/Cas9 systems take advantage of these repair mechanisms for targeted genome modification and have been successfully used to manipulate the genome in human cells. These genome editing tools can be used to investigate gene function, to discover new therapeutic targets, and to develop disease models. Moreover, these genome editing technologies have great potential in gene therapy. Here, we review the latest advances in the application of genome editing technology to the study and treatment of hematological disorders.
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Affiliation(s)
- Andrea Pellagatti
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and NIHR Biomedical Research Centre, Oxford, UK.
| | - Hamid Dolatshad
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and NIHR Biomedical Research Centre, Oxford, UK
| | - Bon Ham Yip
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and NIHR Biomedical Research Centre, Oxford, UK
| | - Simona Valletta
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and NIHR Biomedical Research Centre, Oxford, UK
| | - Jacqueline Boultwood
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and NIHR Biomedical Research Centre, Oxford, UK.
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123
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The pros and cons of vertebrate animal models for functional and therapeutic research on inherited retinal dystrophies. Prog Retin Eye Res 2015; 48:137-59. [DOI: 10.1016/j.preteyeres.2015.04.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/12/2015] [Accepted: 04/16/2015] [Indexed: 01/19/2023]
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124
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CRISPR/Cas9 DNA cleavage at SNP-derived PAM enables both in vitro and in vivo KRT12 mutation-specific targeting. Gene Ther 2015; 23:108-12. [PMID: 26289666 PMCID: PMC4705418 DOI: 10.1038/gt.2015.82] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/16/2015] [Accepted: 07/09/2015] [Indexed: 12/13/2022]
Abstract
CRISPR/Cas9-based therapeutics hold the possibility for permanent treatment of genetic disease. The potency and specificity of this system has been used to target dominantly inherited conditions caused by heterozygous missense mutations through inclusion of the mutated base in the short-guide RNA (sgRNA) sequence. This research evaluates a novel approach for targeting heterozygous single-nucleotide polymorphisms (SNPs) using CRISPR/Cas9. We determined that a mutation within KRT12, which causes Meesmann's epithelial corneal dystrophy (MECD), leads to the occurrence of a novel protospacer adjacent motif (PAM). We designed an sgRNA complementary to the sequence adjacent to this SNP-derived PAM and evaluated its potency and allele specificity both in vitro and in vivo. This sgRNA was found to be highly effective at reducing the expression of mutant KRT12 mRNA and protein in vitro. To assess its activity in vivo we injected a combined Cas9/sgRNA expression construct into the corneal stroma of a humanized MECD mouse model. Sequence analysis of corneal genomic DNA revealed non-homologous end-joining repair resulting in frame-shifting deletions within the mutant KRT12 allele. This study is the first to demonstrate in vivo gene editing of a heterozygous disease-causing SNP that results in a novel PAM, further highlighting the potential for CRISPR/Cas9-based therapeutics.
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125
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LaFountaine JS, Fathe K, Smyth HDC. Delivery and therapeutic applications of gene editing technologies ZFNs, TALENs, and CRISPR/Cas9. Int J Pharm 2015; 494:180-94. [PMID: 26278489 DOI: 10.1016/j.ijpharm.2015.08.029] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/05/2015] [Accepted: 08/09/2015] [Indexed: 12/24/2022]
Abstract
In recent years, several new genome editing technologies have been developed. Of these the zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the CRISPR/Cas9 RNA-guided endonuclease system are the most widely described. Each of these technologies utilizes restriction enzymes to introduce a DNA double stranded break at a targeted location with the guide of homologous binding proteins or RNA. Such targeting is viewed as a significant advancement compared to current gene therapy methods that lack such specificity. Proof-of-concept studies have been performed to treat multiple disorders, including in vivo experiments in mammals and even early phase human trials. Careful consideration and investigation of delivery strategies will be required so that the therapeutic potential for gene editing is achieved. In this review, the mechanisms of each of these gene editing technologies and evidence of therapeutic potential will be briefly described and a comprehensive list of past studies will be provided. The pharmaceutical approaches of each of these technologies are discussed along with the current delivery obstacles. The topics and information reviewed herein provide an outline of the groundbreaking research that is being performed, but also highlights the potential for progress yet to be made using these gene editing technologies.
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Affiliation(s)
- Justin S LaFountaine
- The University of Texas at Austin, 2409 University Avenue, Austin, TX 78712, USA
| | - Kristin Fathe
- The University of Texas at Austin, 2409 University Avenue, Austin, TX 78712, USA
| | - Hugh D C Smyth
- The University of Texas at Austin, 2409 University Avenue, Austin, TX 78712, USA.
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126
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Both TALENs and CRISPR/Cas9 directly target the HBB IVS2-654 (C > T) mutation in β-thalassemia-derived iPSCs. Sci Rep 2015; 5:12065. [PMID: 26156589 PMCID: PMC4496796 DOI: 10.1038/srep12065] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/16/2015] [Indexed: 12/19/2022] Open
Abstract
β-Thalassemia is one of the most common genetic blood diseases and is caused by either point mutations or deletions in the β-globin (HBB) gene. The generation of patient-specific induced pluripotent stem cells (iPSCs) and subsequent correction of the disease-causing mutations may be a potential therapeutic strategy for this disease. Due to the low efficiency of typical homologous recombination, endonucleases, including TALENs and CRISPR/Cas9, have been widely used to enhance the gene correction efficiency in patient-derived iPSCs. Here, we designed TALENs and CRISPR/Cas9 to directly target the intron2 mutation site IVS2-654 in the globin gene. We observed different frequencies of double-strand breaks (DSBs) at IVS2-654 loci using TALENs and CRISPR/Cas9, and TALENs mediated a higher homologous gene targeting efficiency compared to CRISPR/Cas9 when combined with the piggyBac transposon donor. In addition, more obvious off-target events were observed for CRISPR/Cas9 compared to TALENs. Finally, TALENs-corrected iPSC clones were selected for erythroblast differentiation using the OP9 co-culture system and detected relatively higher transcription of HBB than the uncorrected cells. This comparison of using TALENs or CRISPR/Cas9 to correct specific HBB mutations in patient-derived iPSCs will guide future applications of TALENs- or CRISPR/Cas9-based gene therapies in monogenic diseases.
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127
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Davidson MD, Ware BR, Khetani SR. Stem cell-derived liver cells for drug testing and disease modeling. DISCOVERY MEDICINE 2015; 19:349-58. [PMID: 26105698 PMCID: PMC5768200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Differences between animals and humans in liver pathways now necessitate the use of in vitro models of the human liver for several applications such as drug screening. However, isolated primary human hepatocytes (PHHs) are a limited resource for building such models given shortages of donor organs. In contrast, human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) can be propagated nearly indefinitely and differentiated into hepatocyte-like cells in vitro using soluble factors inspired from liver development. Additionally, iPSCs can be generated from patients with specific genetic backgrounds to study genotype-phenotype relationships. While current protocols to differentiate hESCs and iPSCs into human hepatocyte-like cells (hESC-HHs and iPSC-HHs) still need improvement to yield cells functionally similar to the adult liver, proof-of-concept studies have already shown utility of these cells in drug development and modeling liver diseases such as α1-antitrypsin deficiency, hepatitis B/C viral infections, and malaria. Here, we present an overview of hESC-HH and iPSC-HH culture platforms that have been utilized for the aforementioned applications. We also discuss the use of semiconductor-driven microfabrication tools to precisely control the microenvironment around these cells to enable higher and longer-term liver functions in vitro. Finally, we discuss areas for improvement in creating next generation stem cell-derived liver models. In the future, stem cell-derived hepatocyte-like cells could provide a sustainable cell source for high-throughput drug screening, enabling better mechanistic understanding of human liver diseases for the development of more efficacious and safer therapeutics, and personalized cell-based therapies in the clinic.
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Affiliation(s)
- Matthew D. Davidson
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523
| | - Brenton R. Ware
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523
| | - Salman R. Khetani
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523
- Department of Mechanical Engineering, Colorado State University, Fort Collins, CO 80523
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128
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Liang P, Xu Y, Zhang X, Ding C, Huang R, Zhang Z, Lv J, Xie X, Chen Y, Li Y, Sun Y, Bai Y, Songyang Z, Ma W, Zhou C, Huang J. CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell 2015. [PMID: 25894090 DOI: 10.1007/s13238-015-0153-5.] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022] Open
Abstract
Genome editing tools such as the clustered regularly interspaced short palindromic repeat (CRISPR)-associated system (Cas) have been widely used to modify genes in model systems including animal zygotes and human cells, and hold tremendous promise for both basic research and clinical applications. To date, a serious knowledge gap remains in our understanding of DNA repair mechanisms in human early embryos, and in the efficiency and potential off-target effects of using technologies such as CRISPR/Cas9 in human pre-implantation embryos. In this report, we used tripronuclear (3PN) zygotes to further investigate CRISPR/Cas9-mediated gene editing in human cells. We found that CRISPR/Cas9 could effectively cleave the endogenous β-globin gene (HBB). However, the efficiency of homologous recombination directed repair (HDR) of HBB was low and the edited embryos were mosaic. Off-target cleavage was also apparent in these 3PN zygotes as revealed by the T7E1 assay and whole-exome sequencing. Furthermore, the endogenous delta-globin gene (HBD), which is homologous to HBB, competed with exogenous donor oligos to act as the repair template, leading to untoward mutations. Our data also indicated that repair of the HBB locus in these embryos occurred preferentially through the non-crossover HDR pathway. Taken together, our work highlights the pressing need to further improve the fidelity and specificity of the CRISPR/Cas9 platform, a prerequisite for any clinical applications of CRSIPR/Cas9-mediated editing.
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Affiliation(s)
- Puping Liang
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Yanwen Xu
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Xiya Zhang
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Chenhui Ding
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Rui Huang
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Zhen Zhang
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Jie Lv
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Xiaowei Xie
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Yuxi Chen
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Yujing Li
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Ying Sun
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Yaofu Bai
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Zhou Songyang
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Wenbin Ma
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Canquan Zhou
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
| | - Junjiu Huang
- Guangdong Province Key Laboratory of Reproductive Medicine, the First Affiliated Hospital, and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 China
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CRISPR/Cas9-mediated gene editing in human tripronuclear zygotes. Protein Cell 2015; 6:363-372. [PMID: 25894090 PMCID: PMC4417674 DOI: 10.1007/s13238-015-0153-5] [Citation(s) in RCA: 629] [Impact Index Per Article: 69.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 04/01/2015] [Indexed: 12/13/2022] Open
Abstract
Genome editing tools such as the clustered regularly interspaced short palindromic repeat (CRISPR)-associated system (Cas) have been widely used to modify genes in model systems including animal zygotes and human cells, and hold tremendous promise for both basic research and clinical applications. To date, a serious knowledge gap remains in our understanding of DNA repair mechanisms in human early embryos, and in the efficiency and potential off-target effects of using technologies such as CRISPR/Cas9 in human pre-implantation embryos. In this report, we used tripronuclear (3PN) zygotes to further investigate CRISPR/Cas9-mediated gene editing in human cells. We found that CRISPR/Cas9 could effectively cleave the endogenous β-globin gene (HBB). However, the efficiency of homologous recombination directed repair (HDR) of HBB was low and the edited embryos were mosaic. Off-target cleavage was also apparent in these 3PN zygotes as revealed by the T7E1 assay and whole-exome sequencing. Furthermore, the endogenous delta-globin gene (HBD), which is homologous to HBB, competed with exogenous donor oligos to act as the repair template, leading to untoward mutations. Our data also indicated that repair of the HBB locus in these embryos occurred preferentially through the non-crossover HDR pathway. Taken together, our work highlights the pressing need to further improve the fidelity and specificity of the CRISPR/Cas9 platform, a prerequisite for any clinical applications of CRSIPR/Cas9-mediated editing.
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Abstract
The classical myeloproliferative neoplasms (MPNs) are a group of clonal diseases comprising essential thrombocythaemia (ET), polycythaemia vera (PV) and primary myelofibrosis (PMF). PMF is the rarest disease sub type and has been challenging to address due to the lack of a specific genetic marker, inadequate risk identification models and a highly variable clinical course. Continuous efforts have over time, seen the inclusion of cytogenetic information in prognostic scoring models that have resulted in improved risk stratification models providing further rationale for therapeutic management. Technological advances using single nucleotide polymorphism arrays increased the detection of known and novel MPN related changes and variant detection by massively parallel sequencing provided a large scale screening tool for the multitude of somatic gene mutations that have more recently been described in MPN. Some of these mutations show an association with specific cytogenetic changes or phenotypes. While PMF occurs mainly in adults, it has also been described in paediatric cases and shows distinct histopathological, genetic and clinical features in comparison. This review provides an overview of the genomics landscape of PMF and current developments in MPN therapy.
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Affiliation(s)
- Nisha R Singh
- 1 Department of Genetics, Pathology North-Sydney, St Leonards, NSW, Australia ; 2 Kolling Institute, University of Sydney, NSW, Australia
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131
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Ardhanareeswaran K, Coppola G, Vaccarino F. The use of stem cells to study autism spectrum disorder. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2015; 88:5-16. [PMID: 25745370 PMCID: PMC4345539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Autism spectrum disorder (ASD) affects as many as 1 in 68 children and is said to be the fastest-growing serious developmental disability in the United States. There is currently no medical cure or diagnostic test for ASD. Furthermore, the U.S. Food and Drug Administration has yet to approve a single drug for the treatment of autism's core symptoms. Despite numerous genome studies and the identification of hundreds of genes that may cause or predispose children to ASD, the pathways underlying the pathogenesis of idiopathic ASD still remain elusive. Post-mortem brain samples, apart from being difficult to obtain, offer little insight into a disorder that arises through the course of development. Furthermore, ASD is a disorder of highly complex, human-specific behaviors, making it difficult to model in animals. Stem cell models of ASD can be generated by performing skin biopsies of ASD patients and then dedifferentiating these fibroblasts into human-induced pluripotent stem cells (hiPSCs). iPSCs closely resemble embryonic stem cells and retain the unique genetic signature of the ASD patient from whom they were originally derived. Differentiation of these iPSCs into neurons essentially recapitulates the ASD patient's neuronal development in a dish, allowing for a patient-specific model of ASD. Here we review our current understanding of the underlying neurobiology of ASD and how the use of stem cells can advance this understanding, possibly leading to new therapeutic avenues.
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Affiliation(s)
- Karthikeyan Ardhanareeswaran
- Child Study Center, Yale School of Medicine, New Haven, Connecticut,Program in Neurodevelopment and Regeneration, Yale School of Medicine, New Haven, Connecticut,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut
| | - Gianfilippo Coppola
- Child Study Center, Yale School of Medicine, New Haven, Connecticut,Program in Neurodevelopment and Regeneration, Yale School of Medicine, New Haven, Connecticut
| | - Flora Vaccarino
- Child Study Center, Yale School of Medicine, New Haven, Connecticut,Program in Neurodevelopment and Regeneration, Yale School of Medicine, New Haven, Connecticut,Yale Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut,Department of Neurobiology, Yale School of Medicine, New Haven, Connecticut,To whom all correspondence should be addressed: Flora Vaccarino MD, Yale Child Study Center, 230 South Frontage Rd, New Haven, CT 06520; Tele: 203-737-4147; Fax: 203-737-3524;
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Zheng A, Li Y, Tsang SH. Personalized therapeutic strategies for patients with retinitis pigmentosa. Expert Opin Biol Ther 2015; 15:391-402. [PMID: 25613576 DOI: 10.1517/14712598.2015.1006192] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Retinitis pigmentosa (RP) encompasses many different hereditary retinal degenerations that are caused by a vast array of different gene mutations and have highly variable disease presentations and severities. This heterogeneity poses a significant therapeutic challenge, although an answer may eventually be found through two recent innovations: induced pluripotent stem cells (iPSCs) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas genome editing. AREAS COVERED This review discusses the wide-ranging applications of iPSCs and CRISPR-including disease modelling, diagnostics and therapeutics - with an ultimate view towards understanding how these two technologies can come together to address disease heterogeneity and orphan genes in a novel personalized medicine platform. An extensive literature search was conducted in PubMed and Google Scholar, with a particular focus on high-impact research published within the last 1 - 2 years and centered broadly on the subjects of retinal gene therapy, iPSC-derived outer retina cells, stem cell transplantation and CRISPR/Cas gene editing. EXPERT OPINION For the retinal pigment epithelium, autologous transplantation of gene-corrected grafts derived from iPSCs may well be technically feasible in the near future. Photoreceptor transplantation faces more significant unresolved technical challenges but remains an achievable, if more distant, goal given the rapid pace of advancements in the field.
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Affiliation(s)
- Andrew Zheng
- Columbia University, College of Physicians and Surgeons , 50 Haven Ave, Box #123, Bard Hall, New York, NY 10032 , USA
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