251
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Das K, Eisel D, Lenkl C, Goyal A, Diederichs S, Dickes E, Osen W, Eichmüller SB. Generation of murine tumor cell lines deficient in MHC molecule surface expression using the CRISPR/Cas9 system. PLoS One 2017; 12:e0174077. [PMID: 28301575 PMCID: PMC5354463 DOI: 10.1371/journal.pone.0174077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/02/2017] [Indexed: 01/05/2023] Open
Abstract
In this study, the CRISPR/Cas9 technology was used to establish murine tumor cell lines, devoid of MHC I or MHC II surface expression, respectively. The melanoma cell line B16F10 and the murine breast cancer cell line EO-771, the latter stably expressing the tumor antigen NY-BR-1 (EO-NY), were transfected with an expression plasmid encoding a β2m-specific single guide (sg)RNA and Cas9. The resulting MHC I negative cells were sorted by flow cytometry to obtain single cell clones, and loss of susceptibility of peptide pulsed MHC I negative clones to peptide-specific CTL recognition was determined by IFNγ ELISpot assay. The β2m knockout (KO) clones did not give rise to tumors in syngeneic mice (C57BL/6N), unless NK cells were depleted, suggesting that outgrowth of the β2m KO cell lines was controlled by NK cells. Using sgRNAs targeting the β-chain encoding locus of the IAb molecule we also generated several B16F10 MHC II KO clones. Peptide loaded B16F10 MHC II KO cells were insusceptible to recognition by OT-II cells and tumor growth was unaltered compared to parental B16F10 cells. Thus, in our hands the CRISPR/Cas9 system has proven to be an efficient straight forward strategy for the generation of MHC knockout cell lines. Such cell lines could serve as parental cells for co-transfection of compatible HLA alleles together with human tumor antigens of interest, thereby facilitating the generation of HLA matched transplantable tumor models, e.g. in HLAtg mouse strains of the newer generation, lacking cell surface expression of endogenous H2 molecules. In addition, our tumor cell lines established might offer a useful tool to investigate tumor reactive T cell responses that function independently from MHC molecule surface expression by the tumor.
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Affiliation(s)
- Krishna Das
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Eisel
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Clarissa Lenkl
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ashish Goyal
- Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sven Diederichs
- Division of RNA Biology and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Cancer Research, Dept. of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg & German Cancer Consortium (DKTK), Freiburg, Germany
| | - Elke Dickes
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wolfram Osen
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan B. Eichmüller
- GMP & T Cell Therapy Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
- * E-mail:
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252
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Astrocyte pathology in a human neural stem cell model of frontotemporal dementia caused by mutant TAU protein. Sci Rep 2017; 7:42991. [PMID: 28256506 PMCID: PMC5335603 DOI: 10.1038/srep42991] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 01/18/2017] [Indexed: 11/11/2022] Open
Abstract
Astroglial pathology is seen in various neurodegenerative diseases including frontotemporal dementia (FTD), which can be caused by mutations in the gene encoding the microtubule-associated protein TAU (MAPT). Here, we applied a stem cell model of FTD to examine if FTD astrocytes carry an intrinsic propensity to degeneration and to determine if they can induce non-cell-autonomous effects in neighboring neurons. We utilized CRISPR/Cas9 genome editing in human induced pluripotent stem (iPS) cell-derived neural progenitor cells (NPCs) to repair the FTD-associated N279K MAPT mutation. While astrocytic differentiation was not impaired in FTD NPCs derived from one patient carrying the N279K MAPT mutation, FTD astrocytes appeared larger, expressed increased levels of 4R-TAU isoforms, demonstrated increased vulnerability to oxidative stress and elevated protein ubiquitination and exhibited disease-associated changes in transcriptome profiles when compared to astrocytes derived from one control individual and to the isogenic control. Interestingly, co-culture experiments with FTD astrocytes revealed increased oxidative stress and robust changes in whole genome expression in previously healthy neurons. Our study highlights the utility of iPS cell-derived NPCs to elucidate the role of astrocytes in the pathogenesis of FTD.
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253
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Lin L, Petersen TS, Jensen KT, Bolund L, Kühn R, Luo Y. Fusion of SpCas9 to E. coli Rec A protein enhances CRISPR-Cas9 mediated gene knockout in mammalian cells. J Biotechnol 2017; 247:42-49. [PMID: 28259533 DOI: 10.1016/j.jbiotec.2017.02.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/03/2017] [Accepted: 02/25/2017] [Indexed: 01/24/2023]
Abstract
Mammalian cells repair double-strand DNA breaks (DSB) by a range of different pathways following DSB induction by the engineered clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein Cas9. While CRISPR-Cas9 thus enables predesigned modifications of the genome, applications of CRISPR-Cas9-mediated genome-editing are frequently hampered by the unpredictable and varying pathways for DSB repair in mammalian cells. Here we present a strategy of fusing Cas9 to recombinant proteins for fine-tuning of the DSB repair preferences in mammalian cells. By fusing Streptococcus Pyogenes Cas9 (SpCas9) to the recombinant protein A (Rec A, NP_417179.1) from Escherichia coli, we create a recombinant Cas9 protein (rSpCas9) which enhances the generation of indel mutations at DSB sites in mammalian cells, increases the frequency of DSB repair by homology-directed single-strand annealing (SSA), and represses homology-directed gene conversion by approximately 33%. Our study thus proves for the first time that fusing SpCas9 to recombinant proteins can influence the balance between DSB repair pathways in mammalian cells. This approach may form the basis for further investigations of the applications of recombinant Cas9 proteins to fine-tuning DSB repair pathways in eukaryotic cells.
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Affiliation(s)
- Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | | | - Kristopher Torp Jensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; University of Cambridge, UK
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Ralf Kühn
- Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany; Berlin Institute of Health, 10117 Berlin, Germany
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
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254
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Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis. Nat Protoc 2017; 12:581-603. [PMID: 28207001 DOI: 10.1038/nprot.2016.165] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This protocol describes methods for increasing and evaluating the efficiency of genome editing based on the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated 9) system, transcription activator-like effector nucleases (TALENs) or zinc-finger nucleases (ZFNs). First, Indel Detection by Amplicon Analysis (IDAA) determines the size and frequency of insertions and deletions elicited by nucleases in cells, tissues or embryos through analysis of fluorophore-labeled PCR amplicons covering the nuclease target site by capillary electrophoresis in a sequenator. Second, FACS enrichment of cells expressing nucleases linked to fluorescent proteins can be used to maximize knockout or knock-in editing efficiencies or to balance editing efficiency and toxic/off-target effects. The two methods can be combined to form a pipeline for cell-line editing that facilitates the testing of new nuclease reagents and the generation of edited cell pools or clonal cell lines, reducing the number of clones that need to be generated and increasing the ease with which they are screened. The pipeline shortens the time line, but it most prominently reduces the workload of cell-line editing, which may be completed within 4 weeks.
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255
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Moreno AM, Mali P. Therapeutic genome engineering via CRISPR-Cas systems. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [DOI: 10.1002/wsbm.1380] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/15/2016] [Accepted: 12/16/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Ana M. Moreno
- Department of Bioengineering; University of California San Diego; San Diego CA USA
| | - Prashant Mali
- Department of Bioengineering; University of California San Diego; San Diego CA USA
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256
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Han X, Liu Z, Ma Y, Zhang K, Qin L. Cas9 Ribonucleoprotein Delivery via Microfluidic Cell-Deformation Chip for Human T-Cell Genome Editing and Immunotherapy. ACTA ACUST UNITED AC 2017; 1:e1600007. [DOI: 10.1002/adbi.201600007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/09/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Xin Han
- Department of Nanomedicine; Houston Methodist Research Institute; Houston TX 77030 USA
- Department of Cell and Developmental Biology; Weill Medical College of Cornell University; New York NY 10065 USA
| | - Zongbin Liu
- Department of Nanomedicine; Houston Methodist Research Institute; Houston TX 77030 USA
- Department of Cell and Developmental Biology; Weill Medical College of Cornell University; New York NY 10065 USA
| | - Yuan Ma
- Department of Nanomedicine; Houston Methodist Research Institute; Houston TX 77030 USA
- Department of Cell and Developmental Biology; Weill Medical College of Cornell University; New York NY 10065 USA
| | - Kai Zhang
- Department of Nanomedicine; Houston Methodist Research Institute; Houston TX 77030 USA
- Department of Cell and Developmental Biology; Weill Medical College of Cornell University; New York NY 10065 USA
| | - Lidong Qin
- Department of Nanomedicine; Houston Methodist Research Institute; Houston TX 77030 USA
- Department of Cell and Developmental Biology; Weill Medical College of Cornell University; New York NY 10065 USA
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257
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Arya D, Sachithanandan SP, Ross C, Palakodeti D, Li S, Krishna S. MiRNA182 regulates percentage of myeloid and erythroid cells in chronic myeloid leukemia. Cell Death Dis 2017; 8:e2547. [PMID: 28079885 PMCID: PMC5386378 DOI: 10.1038/cddis.2016.471] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 12/20/2022]
Abstract
The deregulation of lineage control programs is often associated with the progression of haematological malignancies. The molecular regulators of lineage choices in the context of tyrosine kinase inhibitor (TKI) resistance remain poorly understood in chronic myeloid leukemia (CML). To find a potential molecular regulator contributing to lineage distribution and TKI resistance, we undertook an RNA-sequencing approach for identifying microRNAs (miRNAs). Following an unbiased screen, elevated miRNA182-5p levels were detected in Bcr-Abl-inhibited K562 cells (CML blast crisis cell line) and in a panel of CML patients. Earlier, miRNA182-5p upregulation was reported in several solid tumours and haematological malignancies. We undertook a strategy involving transient modulation and CRISPR/Cas9 (clustered regularly interspersed short palindromic repeats)-mediated knockout of the MIR182 locus in CML cells. The lineage contribution was assessed by methylcellulose colony formation assay. The transient modulation of miRNA182-5p revealed a biased phenotype. Strikingly, Δ182 cells (homozygous deletion of MIR182 locus) produced a marked shift in lineage distribution. The phenotype was rescued by ectopic expression of miRNA182-5p in Δ182 cells. A bioinformatic analysis and Hes1 modulation data suggested that Hes1 could be a putative target of miRNA182-5p. A reciprocal relationship between miRNA182-5p and Hes1 was seen in the context of TK inhibition. In conclusion, we reveal a key role for miRNA182-5p in restricting the myeloid development of leukemic cells. We propose that the Δ182 cell line will be valuable in designing experiments for next-generation pharmacological interventions.
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Affiliation(s)
- Deepak Arya
- Cellular Organization and Signalling Group, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
- Manipal University, Manipal, India
| | - Sasikala P Sachithanandan
- Cellular Organization and Signalling Group, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Cecil Ross
- Department of Medicine, St Johns Medical College and Hospitals, Bangalore, India
| | - Dasaradhi Palakodeti
- Stem Cells and Regeneration Group, Institute for Stem Cell Biology and Regenerative Medicine, Bangalore, India
| | - Shang Li
- Duke-NUS Graduate Medical School, Singapore
| | - Sudhir Krishna
- Cellular Organization and Signalling Group, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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258
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Serena M, Parolini F, Biswas P, Sironi F, Blanco Miranda A, Zoratti E, Scupoli MT, Ziglio S, Valenzuela-Fernandez A, Gibellini D, Romanelli MG, Siccardi A, Malnati M, Beretta A, Zipeto D. HIV-1 Env associates with HLA-C free-chains at the cell membrane modulating viral infectivity. Sci Rep 2017; 7:40037. [PMID: 28051183 PMCID: PMC5209703 DOI: 10.1038/srep40037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/30/2016] [Indexed: 12/13/2022] Open
Abstract
HLA-C has been demonstrated to associate with HIV-1 envelope glycoprotein (Env). Virions lacking HLA-C have reduced infectivity and increased susceptibility to neutralizing antibodies. Like all others MHC-I molecules, HLA-C requires β2-microglobulin (β2m) for appropriate folding and expression on the cell membrane but this association is weaker, thus generating HLA-C free-chains on the cell surface. In this study, we deepen the understanding of HLA-C and Env association by showing that HIV-1 specifically increases the amount of HLA-C free chains, not bound to β2m, on the membrane of infected cells. The association between Env and HLA-C takes place at the cell membrane requiring β2m to occur. We report that the enhanced infectivity conferred to HIV-1 by HLA-C specifically involves HLA-C free chain molecules that have been correctly assembled with β2m. HIV-1 Env-pseudotyped viruses produced in the absence of β2m are less infectious than those produced in the presence of β2m. We hypothesize that the conformation and surface expression of HLA-C molecules could be a discriminant for the association with Env. Binding stability to β2m may confer to HLA-C the ability to preferentially act either as a conventional immune-competent molecule or as an accessory molecule involved in HIV-1 infectivity.
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Affiliation(s)
- Michela Serena
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Francesca Parolini
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Priscilla Biswas
- IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132, Milan, Italy
| | - Francesca Sironi
- IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132, Milan, Italy
| | - Almudena Blanco Miranda
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Elisa Zoratti
- University Laboratory of Medical Research, Piazzale L. A. Scuro 10, 37134 Verona, Italy
| | - Maria Teresa Scupoli
- University Laboratory of Medical Research, Piazzale L. A. Scuro 10, 37134 Verona, Italy
| | - Serena Ziglio
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134, Verona, Italy.,Laboratorio de Inmunología Celular y Viral, Unidad de Virología IUETSPC, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, Tenerife, Spain
| | - Agustin Valenzuela-Fernandez
- Laboratorio de Inmunología Celular y Viral, Unidad de Virología IUETSPC, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna (ULL), Campus de Ofra s/n, 38071, Tenerife, Spain
| | - Davide Gibellini
- Department of Diagnostics and Public Health, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Maria Grazia Romanelli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
| | - Antonio Siccardi
- IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132, Milan, Italy
| | - Mauro Malnati
- IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132, Milan, Italy
| | - Alberto Beretta
- IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132, Milan, Italy
| | - Donato Zipeto
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada le Grazie 8, 37134, Verona, Italy
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259
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Liu X, Zhang Y, Cheng C, Cheng AW, Zhang X, Li N, Xia C, Wei X, Liu X, Wang H. CRISPR-Cas9-mediated multiplex gene editing in CAR-T cells. Cell Res 2017; 27:154-157. [PMID: 27910851 PMCID: PMC5223227 DOI: 10.1038/cr.2016.142] [Citation(s) in RCA: 254] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Xiaojuan Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China
| | - Yongping Zhang
- Department of Hematology, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Chen Cheng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China
- Graduate School, University of Science and Technology of China, Hefei, China
| | - Albert W Cheng
- The Jackson Laboratory for Genome Medicine, Farmington, CN, USA
| | - Xingying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences
| | - Na Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China
| | - Changqing Xia
- Department of Hematology, Xuanwu Hospital, Capital Medical University, Beijing, China
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, FL, USA
| | | | - Xiang Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, The Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences
- The Jackson Laboratory, Bar Harbor, ME, USA
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260
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Tabebordbar M, Cheng J, Wagers AJ. Therapeutic Gene Editing in Muscles and Muscle Stem Cells. RESEARCH AND PERSPECTIVES IN NEUROSCIENCES 2017. [DOI: 10.1007/978-3-319-60192-2_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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261
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Abstract
The recent development of CRISPR-Cas systems as easily accessible and programmable tools for genome editing and regulation is spurring a revolution in biology. Paired with the rapid expansion of reference and personalized genomic sequence information, technologies based on CRISPR-Cas are enabling nearly unlimited genetic manipulation, even in previously difficult contexts, including human cells. Although much attention has focused on the potential of CRISPR-Cas to cure Mendelian diseases, the technology also holds promise to transform the development of therapies to treat complex heritable and somatic disorders. In this Review, we discuss how CRISPR-Cas can affect the next generation of drugs by accelerating the identification and validation of high-value targets, uncovering high-confidence biomarkers and developing differentiated breakthrough therapies. We focus on the promises, pitfalls and hurdles of this revolutionary gene-editing technology, discuss key aspects of different CRISPR-Cas screening platforms and offer our perspectives on the best practices in genome engineering.
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262
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Bertero A, Pawlowski M, Ortmann D, Snijders K, Yiangou L, Cardoso de Brito M, Brown S, Bernard WG, Cooper JD, Giacomelli E, Gambardella L, Hannan NRF, Iyer D, Sampaziotis F, Serrano F, Zonneveld MCF, Sinha S, Kotter M, Vallier L. Optimized inducible shRNA and CRISPR/Cas9 platforms for in vitro studies of human development using hPSCs. Development 2016; 143:4405-4418. [PMID: 27899508 PMCID: PMC5201041 DOI: 10.1242/dev.138081] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 10/07/2016] [Indexed: 12/22/2022]
Abstract
Inducible loss of gene function experiments are necessary to uncover mechanisms underlying development, physiology and disease. However, current methods are complex, lack robustness and do not work in multiple cell types. Here we address these limitations by developing single-step optimized inducible gene knockdown or knockout (sOPTiKD or sOPTiKO) platforms. These are based on genetic engineering of human genomic safe harbors combined with an improved tetracycline-inducible system and CRISPR/Cas9 technology. We exemplify the efficacy of these methods in human pluripotent stem cells (hPSCs), and show that generation of sOPTiKD/KO hPSCs is simple, rapid and allows tightly controlled individual or multiplexed gene knockdown or knockout in hPSCs and in a wide variety of differentiated cells. Finally, we illustrate the general applicability of this approach by investigating the function of transcription factors (OCT4 and T), cell cycle regulators (cyclin D family members) and epigenetic modifiers (DPY30). Overall, sOPTiKD and sOPTiKO provide a unique opportunity for functional analyses in multiple cell types relevant for the study of human development.
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Affiliation(s)
- Alessandro Bertero
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Matthias Pawlowski
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Daniel Ortmann
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Kirsten Snijders
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Loukia Yiangou
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Miguel Cardoso de Brito
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Stephanie Brown
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - William G Bernard
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - James D Cooper
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Elisa Giacomelli
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Laure Gambardella
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Nicholas R F Hannan
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Dharini Iyer
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Fotios Sampaziotis
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Felipe Serrano
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Mariëlle C F Zonneveld
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Sanjay Sinha
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Mark Kotter
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Ludovic Vallier
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, CB2 0SZ, UK
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
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263
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The potential application and challenge of powerful CRISPR/Cas9 system in cardiovascular research. Int J Cardiol 2016; 227:191-193. [PMID: 27847153 DOI: 10.1016/j.ijcard.2016.11.177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 11/06/2016] [Indexed: 11/23/2022]
Abstract
CRISPR/Cas9 is a precision-guided munition found in bacteria to fight against invading viruses. This technology has enormous potential applications, including altering genes in both somatic and germ cells, as well as generating knockout animals. Compared to other gene editing techniques such as zinc finger nucleases and TALENS, CRISPR/Cas9 is much easier to use and highly efficient. Importantly, the multiplex capacity of this technology allows multiple genes to be edited simultaneously. CRISPR/Cas9 also has the potential to prevent and cure human diseases. In this review, we wish to highlight some key points regarding the future prospect of using CRISPR/Cas9 as a powerful tool for cardiovascular research, and as a novel therapeutic strategy to treat cardiovascular diseases.
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264
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Ren J, Liu X, Fang C, Jiang S, June CH, Zhao Y. Multiplex Genome Editing to Generate Universal CAR T Cells Resistant to PD1 Inhibition. Clin Cancer Res 2016; 23:2255-2266. [PMID: 27815355 DOI: 10.1158/1078-0432.ccr-16-1300] [Citation(s) in RCA: 647] [Impact Index Per Article: 80.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/27/2016] [Accepted: 10/23/2016] [Indexed: 11/16/2022]
Abstract
Purpose: Using gene-disrupted allogeneic T cells as universal effector cells provides an alternative and potentially improves current chimeric antigen receptor (CAR) T-cell therapy against cancers and infectious diseases.Experimental Design: The CRISPR/Cas9 system has recently emerged as a simple and efficient way for multiplex genome engineering. By combining lentiviral delivery of CAR and electro-transfer of Cas9 mRNA and gRNAs targeting endogenous TCR, β-2 microglobulin (B2M) and PD1 simultaneously, to generate gene-disrupted allogeneic CAR T cells deficient of TCR, HLA class I molecule and PD1.Results: The CRISPR gene-edited CAR T cells showed potent antitumor activities, both in vitro and in animal models and were as potent as non-gene-edited CAR T cells. In addition, the TCR and HLA class I double deficient T cells had reduced alloreactivity and did not cause graft-versus-host disease. Finally, simultaneous triple genome editing by adding the disruption of PD1 led to enhanced in vivo antitumor activity of the gene-disrupted CAR T cells.Conclusions: Gene-disrupted allogeneic CAR and TCR T cells could provide an alternative as a universal donor to autologous T cells, which carry difficulties and high production costs. Gene-disrupted CAR and TCR T cells with disabled checkpoint molecules may be potent effector cells against cancers and infectious diseases. Clin Cancer Res; 23(9); 2255-66. ©2016 AACR.
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Affiliation(s)
- Jiangtao Ren
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Xiaojun Liu
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Chongyun Fang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Shuguang Jiang
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Carl H June
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yangbing Zhao
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania. .,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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265
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Vad-Nielsen J, Lin L, Bolund L, Nielsen AL, Luo Y. Golden Gate Assembly of CRISPR gRNA expression array for simultaneously targeting multiple genes. Cell Mol Life Sci 2016; 73:4315-4325. [PMID: 27178736 PMCID: PMC11108369 DOI: 10.1007/s00018-016-2271-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 04/29/2016] [Accepted: 05/06/2016] [Indexed: 12/12/2022]
Abstract
The engineered CRISPR/Cas9 technology has developed as the most efficient and broadly used genome editing tool. However, simultaneously targeting multiple genes (or genomic loci) in the same individual cells using CRISPR/Cas9 remain one technical challenge. In this article, we have developed a Golden Gate Assembly method for the generation of CRISPR gRNA expression arrays, thus enabling simultaneous gene targeting. Using this method, the generation of CRISPR gRNA expression array can be accomplished in 2 weeks, and contains up to 30 gRNA expression cassettes. We demonstrated in the study that simultaneously targeting 10 genomic loci or simultaneously inhibition of multiple endogenous genes could be achieved using the multiplexed gRNA expression array vector in human cells. The complete set of plasmids is available through the non-profit plasmid repository Addgene.
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Affiliation(s)
- Johan Vad-Nielsen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, Building 1242, 8000, Aarhus C, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, Building 1242, 8000, Aarhus C, Denmark
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, Building 1242, 8000, Aarhus C, Denmark
| | - Anders Lade Nielsen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, Building 1242, 8000, Aarhus C, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, Building 1242, 8000, Aarhus C, Denmark.
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266
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Ludwig LS, Khajuria RK, Sankaran VG. Emerging cellular and gene therapies for congenital anemias. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2016; 172:332-348. [PMID: 27792859 DOI: 10.1002/ajmg.c.31529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Congenital anemias comprise a group of blood disorders characterized by a reduction in the number of peripherally circulating erythrocytes. Various genetic etiologies have been identified that affect diverse aspects of erythroid physiology and broadly fall into two main categories: impaired production or increased destruction of mature erythrocytes. Current therapies are largely focused on symptomatic treatment and are often based on transfusion of donor-derived erythrocytes and management of complications. Hematopoietic stem cell transplantation represents the only curative option currently available for the majority of congenital anemias. Recent advances in gene therapy and genome editing hold promise for the development of additional curative strategies for these blood disorders. The relative ease of access to the hematopoietic stem cell compartment, as well as the possibility of genetic manipulation ex vivo and subsequent transplantation in an autologous manner, make blood disorders among the most amenable to cellular therapies. Here we review cell-based and gene therapy approaches, and discuss the limitations and prospects of emerging avenues, including genome editing tools and the use of pluripotent stem cells, for the treatment of congenital forms of anemia. © 2016 Wiley Periodicals, Inc.
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267
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Hendriks WT, Warren CR, Cowan CA. Genome Editing in Human Pluripotent Stem Cells: Approaches, Pitfalls, and Solutions. Cell Stem Cell 2016; 18:53-65. [PMID: 26748756 DOI: 10.1016/j.stem.2015.12.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human pluripotent stem cells (hPSCs) with knockout or mutant alleles can be generated using custom-engineered nucleases. Transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 nucleases are the most commonly employed technologies for editing hPSC genomes. In this Protocol Review, we provide a brief overview of custom-engineered nucleases in the context of gene editing in hPSCs with a focus on the application of TALENs and CRISPR/Cas9. We will highlight the advantages and disadvantages of each method and discuss theoretical and technical considerations for experimental design.
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Affiliation(s)
- William T Hendriks
- The Collaborative Center for X-Linked Dystonia Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Brain Science Initiative, Harvard Medical School, Boston, MA 02114, USA
| | - Curtis R Warren
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Chad A Cowan
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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268
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Hu X. CRISPR/Cas9 system and its applications in human hematopoietic cells. Blood Cells Mol Dis 2016; 62:6-12. [PMID: 27736664 DOI: 10.1016/j.bcmd.2016.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/19/2016] [Accepted: 09/23/2016] [Indexed: 12/26/2022]
Abstract
Since 2012, the CRISPR-Cas9 system has been quickly and successfully tested in a broad range of organisms and cells including hematopoietic cells. The application of CRISPR-Cas9 in human hematopoietic cells mainly involves the genes responsible for HIV infection, β-thalassemia and sickle cell disease (SCD). The successful disruption of CCR5 and CXCR4 genes in T cells by CRISPR-Cas9 promotes the prospect of the technology in the functional cure of HIV. More recently, eliminating CCR5 and CXCR4 in induced pluripotent stem cells (iPSCs) derived from patients and targeting the HIV genome have been successfully carried out in several laboratories. The outcome from these approaches bring us closer to the goal of eradicating HIV infection. For hemoglobinopathies the ability to produce iPSC-derived from patients with the correction of hemoglobin (HBB) mutations by CRISPR-Cas9 has been tested in a number of laboratories. These corrected iPSCs also show the potential to differentiate into mature erythrocytes expressing high-level and normal HBB. In light of the initial success of CRESPR-Cas9 in target mutated gene(s) in the iPSCs, a combination of genomic editing and autogenetic stem cell transplantation would be the best strategy for root treatment of the diseases, which could replace traditional allogeneic stem cell transplantation.
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Affiliation(s)
- Xiaotang Hu
- Department of Biology, College of Arts & Sciences, Barry University, 11300 Northeast Second Avenue, Miami Shores, FL 33161, United States.
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269
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Yi L, Li J. CRISPR-Cas9 therapeutics in cancer: promising strategies and present challenges. Biochim Biophys Acta Rev Cancer 2016; 1866:197-207. [PMID: 27641687 DOI: 10.1016/j.bbcan.2016.09.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 01/05/2023]
Abstract
Cancer is characterized by multiple genetic and epigenetic alterations that drive malignant cell proliferation and confer chemoresistance. The ability to correct or ablate such mutations holds immense promise for combating cancer. Recently, because of its high efficiency and accuracy, the CRISPR-Cas9 genome editing technique has been widely used in cancer therapeutic explorations. Several studies used CRISPR-Cas9 to directly target cancer cell genomic DNA in cellular and animal cancer models which have shown therapeutic potential in expanding our anticancer protocols. Moreover, CRISPR-Cas9 can also be employed to fight oncogenic infections, explore anticancer drugs, and engineer immune cells and oncolytic viruses for cancer immunotherapeutic applications. Here, we summarize these preclinical CRISPR-Cas9-based therapeutic strategies against cancer, and discuss the challenges and improvements in translating therapeutic CRISPR-Cas9 into clinical use, which will facilitate better application of this technique in cancer research. Further, we propose potential directions of the CRISPR-Cas9 system in cancer therapy.
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Affiliation(s)
- Lang Yi
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China.
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270
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Liu Z, Hui Y, Shi L, Chen Z, Xu X, Chi L, Fan B, Fang Y, Liu Y, Ma L, Wang Y, Xiao L, Zhang Q, Jin G, Liu L, Zhang X. Efficient CRISPR/Cas9-Mediated Versatile, Predictable, and Donor-Free Gene Knockout in Human Pluripotent Stem Cells. Stem Cell Reports 2016; 7:496-507. [PMID: 27594587 PMCID: PMC5032288 DOI: 10.1016/j.stemcr.2016.07.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 07/28/2016] [Accepted: 07/28/2016] [Indexed: 11/17/2022] Open
Abstract
Loss-of-function studies in human pluripotent stem cells (hPSCs) require efficient methodologies for lesion of genes of interest. Here, we introduce a donor-free paired gRNA-guided CRISPR/Cas9 knockout strategy (paired-KO) for efficient and rapid gene ablation in hPSCs. Through paired-KO, we succeeded in targeting all genes of interest with high biallelic targeting efficiencies. More importantly, during paired-KO, the cleaved DNA was repaired mostly through direct end joining without insertions/deletions (precise ligation), and thus makes the lesion product predictable. The paired-KO remained highly efficient for one-step targeting of multiple genes and was also efficient for targeting of microRNA, while for long non-coding RNA over 8 kb, cleavage of a short fragment of the core promoter region was sufficient to eradicate downstream gene transcription. This work suggests that the paired-KO strategy is a simple and robust system for loss-of-function studies for both coding and non-coding genes in hPSCs.
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Affiliation(s)
- Zhongliang Liu
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Yi Hui
- Department of Anatomy and Neurobiology, the Jiangsu Key Laboratory of Neuroregeneration, Nantong University, 19 Qixiu Road, Nantong, Jiangsu 226001, China
| | - Lei Shi
- College of Animal Science and Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhenyu Chen
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Xiangjie Xu
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Liankai Chi
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Beibei Fan
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Yujiang Fang
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Yang Liu
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Lin Ma
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Yiran Wang
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Lei Xiao
- College of Animal Science and Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Quanbin Zhang
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China
| | - Guohua Jin
- Department of Anatomy and Neurobiology, the Jiangsu Key Laboratory of Neuroregeneration, Nantong University, 19 Qixiu Road, Nantong, Jiangsu 226001, China.
| | - Ling Liu
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China; Tongji University Advanced Institute of Translational Medicine, Tongji University School of Medicine, 1239 Siping Road, Shanghai 200092, China.
| | - Xiaoqing Zhang
- Shanghai Tenth People's Hospital, and Neuroregeneration Key Laboratory of Shanghai Universities, Tongji University School of Medicine, Shanghai 200092, China; Tongji University Advanced Institute of Translational Medicine, Tongji University School of Medicine, 1239 Siping Road, Shanghai 200092, China; The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China.
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271
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Garcia-Beltran WF, Hölzemer A, Martrus G, Chung AW, Pacheco Y, Simoneau CR, Rucevic M, Lamothe-Molina PA, Pertel T, Kim TE, Dugan H, Alter G, Dechanet-Merville J, Jost S, Carrington M, Altfeld M. Open conformers of HLA-F are high-affinity ligands of the activating NK-cell receptor KIR3DS1. Nat Immunol 2016; 17:1067-74. [PMID: 27455421 PMCID: PMC4992421 DOI: 10.1038/ni.3513] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 06/13/2016] [Indexed: 12/23/2022]
Abstract
The activating natural killer (NK)-cell receptor KIR3DS1 has been linked to the outcome of various human diseases, including delayed progression of disease caused by human immunodeficiency virus type 1 (HIV-1), yet a ligand that would account for its biological effects has remained unknown. We screened 100 HLA class I proteins and found that KIR3DS1 bound to HLA-F, a result we confirmed biochemically and functionally. Primary human KIR3DS1(+) NK cells degranulated and produced antiviral cytokines after encountering HLA-F and inhibited HIV-1 replication in vitro. Activation of CD4(+) T cells triggered the transcription and surface expression of HLA-F mRNA and HLA-F protein, respectively, and induced binding of KIR3DS1. HIV-1 infection further increased the transcription of HLA-F mRNA but decreased the binding of KIR3DS1, indicative of a mechanism for evading recognition by KIR3DS1(+) NK cells. Thus, we have established HLA-F as a ligand of KIR3DS1 and have demonstrated cell-context-dependent expression of HLA-F that might explain the widespread influence of KIR3DS1 in human disease.
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Affiliation(s)
| | - Angelique Hölzemer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
- Heinrich-Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- First Department of Internal Medicine, University Medical Centre Eppendorf, Hamburg, Germany
| | - Gloria Martrus
- Heinrich-Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Amy W. Chung
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | - Yovana Pacheco
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
- Departamento de Matemáticas, Facultad de Ciencias, Universidad Nuestra Señora del Rosario, Bogotá, Colombia
| | | | | | | | - Thomas Pertel
- Center for Neurologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Tae-Eun Kim
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | - Haley Dugan
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
| | | | | | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Marcus Altfeld
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
- Heinrich-Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
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272
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Abstract
The rapid development of programmable nuclease-based genome editing technologies has enabled targeted gene disruption and correction both in vitro and in vivo This revolution opens up the possibility of precise genome editing at target genomic sites to modulate gene function in animals and plants. Among several programmable nucleases, the type II clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated nuclease 9 (Cas9) system has progressed remarkably in recent years, leading to its widespread use in research, medicine and biotechnology. In particular, CRISPR-Cas9 shows highly efficient gene editing activity for therapeutic purposes in systems ranging from patient stem cells to animal models. However, the development of therapeutic approaches and delivery methods remains a great challenge for biomedical applications. Herein, we review therapeutic applications that use the CRISPR-Cas9 system and discuss the possibilities and challenges ahead.
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273
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Park A, Hong P, Won ST, Thibault PA, Vigant F, Oguntuyo KY, Taft JD, Lee B. Sendai virus, an RNA virus with no risk of genomic integration, delivers CRISPR/Cas9 for efficient gene editing. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016; 3:16057. [PMID: 27606350 PMCID: PMC4996130 DOI: 10.1038/mtm.2016.57] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/01/2016] [Accepted: 07/03/2016] [Indexed: 12/19/2022]
Abstract
The advent of RNA-guided endonuclease (RGEN)-mediated gene editing, specifically via CRISPR/Cas9, has spurred intensive efforts to improve the efficiency of both RGEN delivery and targeted mutagenesis. The major viral vectors in use for delivery of Cas9 and its associated guide RNA, lentiviral and adeno-associated viral systems, have the potential for undesired random integration into the host genome. Here, we repurpose Sendai virus, an RNA virus with no viral DNA phase and that replicates solely in the cytoplasm, as a delivery system for efficient Cas9-mediated gene editing. The high efficiency of Sendai virus infection resulted in high rates of on-target mutagenesis in cell lines (75–98% at various endogenous and transgenic loci) and primary human monocytes (88% at the ccr5 locus) in the absence of any selection. In conjunction with extensive former work on Sendai virus as a promising gene therapy vector that can infect a wide range of cell types including hematopoietic stem cells, this proof-of-concept study opens the door to using Sendai virus as well as other related paramyxoviruses as versatile and efficient tools for gene editing.
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Affiliation(s)
- Arnold Park
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Patrick Hong
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Sohui T Won
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Patricia A Thibault
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Frederic Vigant
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Kasopefoluwa Y Oguntuyo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Justin D Taft
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai , New York, New York, USA
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274
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Kushwaha M, Rostain W, Prakash S, Duncan JN, Jaramillo A. Using RNA as Molecular Code for Programming Cellular Function. ACS Synth Biol 2016; 5:795-809. [PMID: 26999422 DOI: 10.1021/acssynbio.5b00297] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA is involved in a wide-range of important molecular processes in the cell, serving diverse functions: regulatory, enzymatic, and structural. Together with its ease and predictability of design, these properties can lead RNA to become a useful handle for biological engineers with which to control the cellular machinery. By modifying the many RNA links in cellular processes, it is possible to reprogram cells toward specific design goals. We propose that RNA can be viewed as a molecular programming language that, together with protein-based execution platforms, can be used to rewrite wide ranging aspects of cellular function. In this review, we catalogue developments in the use of RNA parts, methods, and associated computational models that have contributed to the programmability of biology. We discuss how RNA part repertoires have been combined to build complex genetic circuits, and review recent applications of RNA-based parts and circuitry. We explore the future potential of RNA engineering and posit that RNA programmability is an important resource for firmly establishing an era of rationally designed synthetic biology.
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Affiliation(s)
- Manish Kushwaha
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - William Rostain
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
| | - Satya Prakash
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - John N. Duncan
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - Alfonso Jaramillo
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
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275
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van Overbeek M, Capurso D, Carter MM, Thompson MS, Frias E, Russ C, Reece-Hoyes JS, Nye C, Gradia S, Vidal B, Zheng J, Hoffman GR, Fuller CK, May AP. DNA Repair Profiling Reveals Nonrandom Outcomes at Cas9-Mediated Breaks. Mol Cell 2016; 63:633-646. [PMID: 27499295 DOI: 10.1016/j.molcel.2016.06.037] [Citation(s) in RCA: 288] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/11/2016] [Accepted: 06/27/2016] [Indexed: 12/16/2022]
Abstract
The repair outcomes at site-specific DNA double-strand breaks (DSBs) generated by the RNA-guided DNA endonuclease Cas9 determine how gene function is altered. Despite the widespread adoption of CRISPR-Cas9 technology to induce DSBs for genome engineering, the resulting repair products have not been examined in depth. Here, the DNA repair profiles of 223 sites in the human genome demonstrate that the pattern of DNA repair following Cas9 cutting at each site is nonrandom and consistent across experimental replicates, cell lines, and reagent delivery methods. Furthermore, the repair outcomes are determined by the protospacer sequence rather than genomic context, indicating that DNA repair profiling in cell lines can be used to anticipate repair outcomes in primary cells. Chemical inhibition of DNA-PK enabled dissection of the DNA repair profiles into contributions from c-NHEJ and MMEJ. Finally, this work elucidates a strategy for using "error-prone" DNA-repair machinery to generate precise edits.
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Affiliation(s)
| | | | | | | | - Elizabeth Frias
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Carsten Russ
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - John S Reece-Hoyes
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | - Scott Gradia
- Caribou Biosciences, Inc., Berkeley, CA 94710, USA
| | | | | | - Gregory R Hoffman
- Development and Molecular Pathways Department, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | - Andrew P May
- Caribou Biosciences, Inc., Berkeley, CA 94710, USA.
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276
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Jin X, Wu RM, Zhao MF. [Donor- derived CD19 chimeric antigen receptor T cells for relapsed B cell malignancies after allogeneic hematopoietic stem cell transplantations]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2016; 37:725-8. [PMID: 27587261 PMCID: PMC7348526 DOI: 10.3760/cma.j.issn.0253-2727.2016.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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277
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Tristetraprolin as a Therapeutic Target in Inflammatory Disease. Trends Pharmacol Sci 2016; 37:811-821. [PMID: 27503556 DOI: 10.1016/j.tips.2016.07.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 11/22/2022]
Abstract
Members of the tristetraprolin (TTP) family of RNA-binding proteins are found in all major eukaryotic groups. TTP family members, from plants through humans, can bind adenosine-uridine rich elements in target mRNAs with high affinity. In mammalian cells, these proteins then promote deadenylation and decay of target transcripts. Four such proteins are found in mice, of which the best studied is TTP. When the gene encoding TTP is disrupted in mice, the animals develop a severe syndrome of arthritis, autoimmunity, cachexia, dermatitis, and myeloid hyperplasia. Conversely, recent overexpression studies have demonstrated protection against several experimental models of immune inflammatory disease. This endogenous anti-inflammatory protein could serve as the basis for novel approaches to therapy of similar conditions in humans.
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278
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Yu KR, Natanson H, Dunbar CE. Gene Editing of Human Hematopoietic Stem and Progenitor Cells: Promise and Potential Hurdles. Hum Gene Ther 2016; 27:729-740. [PMID: 27483988 DOI: 10.1089/hum.2016.107] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) have great therapeutic potential because of their ability to both self-renew and differentiate. It has been proposed that, given their unique properties, a small number of genetically modified HSPCs could accomplish lifelong, corrective reconstitution of the entire hematopoietic system in patients with various hematologic disorders. Scientists have demonstrated that gene addition therapies-targeted to HSPCs and using integrating retroviral vectors-possess clear clinical benefits in multiple diseases, among them immunodeficiencies, storage disorders, and hemoglobinopathies. Scientists attempting to develop clinically relevant gene therapy protocols have, however, encountered a number of unexpected hurdles because of their incomplete knowledge of target cells, genomic control, and gene transfer technologies. Targeted gene-editing technologies using engineered nucleases such as ZFN, TALEN, and/or CRISPR/Cas9 RGEN show great clinical promise, allowing for the site-specific correction of disease-causing mutations-a process with important applications in autosomal dominant or dominant-negative genetic disorders. The relative simplicity of the CRISPR/Cas9 system, in particular, has sparked an exponential increase in the scientific community's interest in and use of these gene-editing technologies. In this minireview, we discuss the specific applications of gene-editing technologies in human HSPCs, as informed by prior experience with gene addition strategies. HSPCs are desirable but challenging targets; the specific mechanisms these cells evolved to protect themselves from DNA damage render them potentially more susceptible to oncogenesis, especially given their ability to self-renew and their long-term proliferative potential. We further review scientists' experience with gene-editing technologies to date, focusing on strategies to move these techniques toward implementation in safe and effective clinical trials.
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Affiliation(s)
- Kyung-Rok Yu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland
| | - Hannah Natanson
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland
| | - Cynthia E Dunbar
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland
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279
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Pernet O, Yadav SS, An DS. Stem cell-based therapies for HIV/AIDS. Adv Drug Deliv Rev 2016; 103:187-201. [PMID: 27151309 PMCID: PMC4935568 DOI: 10.1016/j.addr.2016.04.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 12/26/2022]
Abstract
One of the current focuses in HIV/AIDS research is to develop a novel therapeutic strategy that can provide a life-long remission of HIV/AIDS without daily drug treatment and, ultimately, a cure for HIV/AIDS. Hematopoietic stem cell-based anti-HIV gene therapy aims to reconstitute the patient immune system by transplantation of genetically engineered hematopoietic stem cells with anti-HIV genes. Hematopoietic stem cells can self-renew, proliferate and differentiate into mature immune cells. In theory, anti-HIV gene-modified hematopoietic stem cells can continuously provide HIV-resistant immune cells throughout the life of a patient. Therefore, hematopoietic stem cell-based anti-HIV gene therapy has a great potential to provide a life-long remission of HIV/AIDS by a single treatment. Here, we provide a comprehensive review of the recent progress of developing anti-HIV genes, genetic modification of hematopoietic stem progenitor cells, engraftment and reconstitution of anti-HIV gene-modified immune cells, HIV inhibition in in vitro and in vivo animal models, and in human clinical trials.
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Affiliation(s)
- Olivier Pernet
- School of Nursing, University of California Los Angeles, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA; UCLA AIDS Institute, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA.
| | - Swati Seth Yadav
- School of Nursing, University of California Los Angeles, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA; UCLA AIDS Institute, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA.
| | - Dong Sung An
- School of Nursing, University of California Los Angeles, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA; UCLA AIDS Institute, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA; Hematology-Oncology, The Department of Medicine, David Geffen School of Medicine at UCLA, 188 BSRB, 615 Charles E. Young Dr. South, Los Angeles, CA 90095, USA.
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280
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Müller AM, Huppertz S, Henschler R. Hematopoietic Stem Cells in Regenerative Medicine: Astray or on the Path? Transfus Med Hemother 2016; 43:247-254. [PMID: 27721700 DOI: 10.1159/000447748] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/20/2016] [Indexed: 12/12/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are the best characterized adult stem cells and the only stem cell type in routine clinical use. The concept of stem cell transplantation laid the foundations for the development of novel cell therapies within, and even outside, the hematopoietic system. Here, we report on the history of hematopoietic cell transplantation (HCT) and of HSC isolation, we briefly summarize the capabilities of HSCs to reconstitute the entire hemato/lymphoid cell system, and we assess current indications for HCT. We aim to draw the lines between areas where HCT has been firmly established, areas where HCT can in the future be expected to be of clinical benefit using their regenerative functions, and areas where doubts persist. We further review clinical trials for diverse approaches that are based on HCT. Finally, we highlight the advent of genome editing in HSCs and critically view the use of HSCs in non-hematopoietic tissue regeneration.
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Affiliation(s)
- Albrecht M Müller
- Institute of Medical Radiology and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, Würzburg, Germany
| | - Sascha Huppertz
- Institute of Medical Radiology and Cell Research (MSZ) in the Center for Experimental Molecular Medicine (ZEMM), University of Würzburg, Würzburg, Germany
| | - Reinhard Henschler
- Blood Center Zürich, Swiss Red Cross, Schlieren, Switzerland; Red Cross Blood Service Graubünden, Chur, Switzerland
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281
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Sather BD, Romano Ibarra GS, Sommer K, Curinga G, Hale M, Khan IF, Singh S, Song Y, Gwiazda K, Sahni J, Jarjour J, Astrakhan A, Wagner TA, Scharenberg AM, Rawlings DJ. Efficient modification of CCR5 in primary human hematopoietic cells using a megaTAL nuclease and AAV donor template. Sci Transl Med 2016; 7:307ra156. [PMID: 26424571 DOI: 10.1126/scitranslmed.aac5530] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Genetic mutations or engineered nucleases that disrupt the HIV co-receptor CCR5 block HIV infection of CD4(+) T cells. These findings have motivated the engineering of CCR5-specific nucleases for application as HIV therapies. The efficacy of this approach relies on efficient biallelic disruption of CCR5, and the ability to efficiently target sequences that confer HIV resistance to the CCR5 locus has the potential to further improve clinical outcomes. We used RNA-based nuclease expression paired with adeno-associated virus (AAV)-mediated delivery of a CCR5-targeting donor template to achieve highly efficient targeted recombination in primary human T cells. This method consistently achieved 8 to 60% rates of homology-directed recombination into the CCR5 locus in T cells, with over 80% of cells modified with an MND-GFP expression cassette exhibiting biallelic modification. MND-GFP-modified T cells maintained a diverse repertoire and engrafted in immune-deficient mice as efficiently as unmodified cells. Using this method, we integrated sequences coding chimeric antigen receptors (CARs) into the CCR5 locus, and the resulting targeted CAR T cells exhibited antitumor or anti-HIV activity. Alternatively, we introduced the C46 HIV fusion inhibitor, generating T cell populations with high rates of biallelic CCR5 disruption paired with potential protection from HIV with CXCR4 co-receptor tropism. Finally, this protocol was applied to adult human mobilized CD34(+) cells, resulting in 15 to 20% homologous gene targeting. Our results demonstrate that high-efficiency targeted integration is feasible in primary human hematopoietic cells and highlight the potential of gene editing to engineer T cell products with myriad functional properties.
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Affiliation(s)
- Blythe D Sather
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Guillermo S Romano Ibarra
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Karen Sommer
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Gabrielle Curinga
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Malika Hale
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Iram F Khan
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Swati Singh
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Yumei Song
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Kamila Gwiazda
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jaya Sahni
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | | | | | - Thor A Wagner
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98101, USA. Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
| | - Andrew M Scharenberg
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA. Department of Pediatrics, University of Washington, Seattle, WA 98101, USA. Department of Immunology, University of Washington, Seattle, WA 98101, USA
| | - David J Rawlings
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, Seattle, WA 98101, USA. Department of Pediatrics, University of Washington, Seattle, WA 98101, USA. Department of Immunology, University of Washington, Seattle, WA 98101, USA
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282
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Zhou Y, Liu Y, Hussmann D, Brøgger P, Al-Saaidi RA, Tan S, Lin L, Petersen TS, Zhou GQ, Bross P, Aagaard L, Klein T, Rønn SG, Pedersen HD, Bolund L, Nielsen AL, Sørensen CB, Luo Y. Enhanced genome editing in mammalian cells with a modified dual-fluorescent surrogate system. Cell Mol Life Sci 2016; 73:2543-63. [PMID: 26755436 PMCID: PMC11108510 DOI: 10.1007/s00018-015-2128-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 12/09/2015] [Accepted: 12/29/2015] [Indexed: 12/15/2022]
Abstract
Programmable DNA nucleases such as TALENs and CRISPR/Cas9 are emerging as powerful tools for genome editing. Dual-fluorescent surrogate systems have been demonstrated by several studies to recapitulate DNA nuclease activity and enrich for genetically edited cells. In this study, we created a single-strand annealing-directed, dual-fluorescent surrogate reporter system, referred to as C-Check. We opted for the Golden Gate Cloning strategy to simplify C-Check construction. To demonstrate the utility of the C-Check system, we used the C-Check in combination with TALENs or CRISPR/Cas9 in different scenarios of gene editing experiments. First, we disrupted the endogenous pIAPP gene (3.0 % efficiency) by C-Check-validated TALENs in primary porcine fibroblasts (PPFs). Next, we achieved gene-editing efficiencies of 9.0-20.3 and 4.9 % when performing single- and double-gene targeting (MAPT and SORL1), respectively, in PPFs using C-Check-validated CRISPR/Cas9 vectors. Third, fluorescent tagging of endogenous genes (MYH6 and COL2A1, up to 10.0 % frequency) was achieved in human fibroblasts with C-Check-validated CRISPR/Cas9 vectors. We further demonstrated that the C-Check system could be applied to enrich for IGF1R null HEK293T cells and CBX5 null MCF-7 cells with frequencies of nearly 100.0 and 86.9 %, respectively. Most importantly, we further showed that the C-Check system is compatible with multiplexing and for studying CRISPR/Cas9 sgRNA specificity. The C-Check system may serve as an alternative dual-fluorescent surrogate tool for measuring DNA nuclease activity and enrichment of gene-edited cells, and may thereby aid in streamlining programmable DNA nuclease-mediated genome editing and biological research.
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Affiliation(s)
- Yan Zhou
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Yong Liu
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Dianna Hussmann
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Peter Brøgger
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Rasha Abdelkadhem Al-Saaidi
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and University Hospital, 8200, Aarhus N, Denmark
| | - Shuang Tan
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
- Shenzhen Key Laboratory for Anti-aging and Regenerative Medicine, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Trine Skov Petersen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Guang Qian Zhou
- Shenzhen Key Laboratory for Anti-aging and Regenerative Medicine, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Peter Bross
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and University Hospital, 8200, Aarhus N, Denmark
| | - Lars Aagaard
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Tino Klein
- Department of Histology, Gubra A/S, 2970, Hørsholm, Denmark
| | - Sif Groth Rønn
- Department of Incretin and Obesity Research, Novo Nordisk A/S, 2760, Måløv, Denmark
| | | | - Lars Bolund
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
- BGI-Shenzhen, Shenzhen, 518083, China
- The Danish Regenerative Engineering Alliance for Medicine (DREAM), Aarhus University, Aarhus, Denmark
| | - Anders Lade Nielsen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark
| | - Charlotte Brandt Sørensen
- Research Unit for Molecular Medicine, Department of Clinical Medicine, Aarhus University and University Hospital, 8200, Aarhus N, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000, Aarhus C, Denmark.
- Department of Incretin and Obesity Research, Novo Nordisk A/S, 2760, Måløv, Denmark.
- The Danish Regenerative Engineering Alliance for Medicine (DREAM), Aarhus University, Aarhus, Denmark.
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283
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van Diemen FR, Kruse EM, Hooykaas MJG, Bruggeling CE, Schürch AC, van Ham PM, Imhof SM, Nijhuis M, Wiertz EJHJ, Lebbink RJ. CRISPR/Cas9-Mediated Genome Editing of Herpesviruses Limits Productive and Latent Infections. PLoS Pathog 2016; 12:e1005701. [PMID: 27362483 PMCID: PMC4928872 DOI: 10.1371/journal.ppat.1005701] [Citation(s) in RCA: 190] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/23/2016] [Indexed: 12/15/2022] Open
Abstract
Herpesviruses infect the majority of the human population and can cause significant morbidity and mortality. Herpes simplex virus (HSV) type 1 causes cold sores and herpes simplex keratitis, whereas HSV-2 is responsible for genital herpes. Human cytomegalovirus (HCMV) is the most common viral cause of congenital defects and is responsible for serious disease in immuno-compromised individuals. Epstein-Barr virus (EBV) is associated with infectious mononucleosis and a broad range of malignancies, including Burkitt’s lymphoma, nasopharyngeal carcinoma, Hodgkin’s disease, and post-transplant lymphomas. Herpesviruses persist in their host for life by establishing a latent infection that is interrupted by periodic reactivation events during which replication occurs. Current antiviral drug treatments target the clinical manifestations of this productive stage, but they are ineffective at eliminating these viruses from the infected host. Here, we set out to combat both productive and latent herpesvirus infections by exploiting the CRISPR/Cas9 system to target viral genetic elements important for virus fitness. We show effective abrogation of HCMV and HSV-1 replication by targeting gRNAs to essential viral genes. Simultaneous targeting of HSV-1 with multiple gRNAs completely abolished the production of infectious particles from human cells. Using the same approach, EBV can be almost completely cleared from latently infected EBV-transformed human tumor cells. Our studies indicate that the CRISPR/Cas9 system can be effectively targeted to herpesvirus genomes as a potent prophylactic and therapeutic anti-viral strategy that may be used to impair viral replication and clear latent virus infection. Herpesviruses are large DNA viruses that are carried by almost 100% of the adult human population. Herpesviruses include several important human pathogens, such as herpes simplex viruses (HSV) type 1 and 2 (causing cold sores and genital herpes, respectively), human cytomegalovirus (HCMV; the most common viral cause of congenital defects, and responsible for serious disease in immuno-compromised individuals), and Epstein-Barr virus (EBV; associated with infectious mononucleosis and a wide range of malignancies). Current antiviral drug treatments are not effective in clearing herpesviruses from infected individuals. Therefore, there is a need for alternative strategies to combat these pathogenic viruses and prevent or cure herpesvirus-associated diseases. Here, we have assessed whether a direct attack of herpesvirus genomes within virus-infected cells can inactivate these viruses. For this, we have made use of the recently developed CRISPR/Cas9 genome-engineering system to target and alter specific regions within the genome of these viruses. By targeting sites in the genomes of three different herpesviruses (HSV-1, HCMV, and EBV), we show complete inhibition of viral replication and in some cases even eradication of the viral genomes from infected cells. The findings presented in this study open new avenues for the development of therapeutic strategies to combat pathogenic human herpesviruses using novel genome-engineering technologies.
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Affiliation(s)
- Ferdy R. van Diemen
- Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Elisabeth M. Kruse
- Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Anita C. Schürch
- Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Petra M. van Ham
- Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Saskia M. Imhof
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Monique Nijhuis
- Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Robert Jan Lebbink
- Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
- * E-mail:
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284
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Vassena R, Heindryckx B, Peco R, Pennings G, Raya A, Sermon K, Veiga A. Genome engineering through CRISPR/Cas9 technology in the human germline and pluripotent stem cells. Hum Reprod Update 2016; 22:411-9. [PMID: 26932460 DOI: 10.1093/humupd/dmw005] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/08/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND With the recent development of CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 genome editing technology, the possibility to genetically manipulate the human germline (gametes and embryos) has become a distinct technical possibility. Although many technical challenges still need to be overcome in order to achieve adequate efficiency and precision of the technology in human embryos, the path leading to genome editing has never been simpler, more affordable, and widespread. OBJECTIVE AND RATIONALE In this narrative review we seek to understand the possible impact of CRISR/Cas9 technology on human reproduction from the technical and ethical point of view, and suggest a course of action for the scientific community. SEARCH METHODS This non-systematic review was carried out using Medline articles in English, as well as technical documents from the Human Fertilisation and Embryology Authority and reports in the media. The technical possibilities of the CRISPR/Cas9 technology with regard to human reproduction are analysed based on results obtained in model systems such as large animals and laboratory rodents. Further, the possibility of CRISPR/Cas9 use in the context of human reproduction, to modify embryos, germline cells, and pluripotent stem cells is reviewed based on the authors' expert opinion. Finally, the possible uses and consequences of CRISPR/cas9 gene editing in reproduction are analysed from the ethical point of view. OUTCOMES We identify critical technical and ethical issues that should deter from employing CRISPR/Cas9 based technologies in human reproduction until they are clarified. WIDER IMPLICATIONS Overcoming the numerous technical limitations currently associated with CRISPR/Cas9 mediated editing of the human germline will depend on intensive research that needs to be transparent and widely disseminated. Rather than a call to a generalized moratorium, or banning, of this type of research, efforts should be placed on establishing an open, international, collaborative and regulated research framework. Equally important, a societal discussion on the risks, benefits, and preferred applications of the new technology, including all relevant stakeholders, is urgently needed and should be promoted, and ultimately guide research priorities in this area.
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Affiliation(s)
- R Vassena
- Clínica EUGIN, Barcelona 08029, Spain
| | - B Heindryckx
- Ghent Fertility and Stem cell Team (G-FaST), Department for Reproductive Medicine, Ghent University Hospital, Ghent, Belgium
| | - R Peco
- Center for Regenerative Medicine in Barcelona (CMRB), 08003 Barcelona, Spain
| | - G Pennings
- Bioethics Institute Ghent (BIG), Faculty of Arts and Philosophy, Ghent University, Ghent, Belgium
| | - A Raya
- Center for Regenerative Medicine in Barcelona (CMRB), 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - K Sermon
- Research Group Reproduction and Genetics, Vrije Universiteit Brussel, Brussels, Belgium
| | - A Veiga
- Center for Regenerative Medicine in Barcelona (CMRB), 08003 Barcelona, Spain Reproductive Medicine Service, Hospital Universitari Quiron Dexeus, Barcelona, Spain
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285
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Abstract
PURPOSE OF REVIEW As T cells engineered with chimeric antigen receptors (CARs) are entering advanced phases of clinical trial testing with promising results, the potential implications of use in an allogeneic environment are emerging as an important consideration. This review discusses the use of allogeneic CAR therapy, the potential effects of T-cell receptor (TCR) signaling on CAR T-cell efficacy, and the potential for TCR elimination to generate an off-the-shelf product. RECENT FINDINGS The majority of preclinical and clinical data regarding allogeneic T cells are focused on safety of their use given the potential for graft-versus-host disease (GVHD) mediated by the T-cell receptor expressed with the introduced CAR. Recent clinical trials using donor-derived CAR T cells are using either rigorous patient selection or T-cell selection (such as enrichment for virus-specific T cells). Although no GVHD has been reported, the efficacy of the allogeneic CAR treatment needs to be optimized. Several preclinical models limit allogeneic CAR-driven GVHD by utilizing memory T-cell selection, virus-specific T cells, gene-editing techniques, or suicide gene engineering. SUMMARY In the allogeneic environment, the potential effects of TCR signaling on the efficacy of CAR could affect the clinical responses with the use of donor-derived CAR T cells. Better understanding of the functionality of donor-derived T cells for therapy is essential for the development of universal effector cells for CAR therapy.
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286
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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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287
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Bolukbasi MF, Gupta A, Wolfe SA. Creating and evaluating accurate CRISPR-Cas9 scalpels for genomic surgery. Nat Methods 2016; 13:41-50. [PMID: 26716561 DOI: 10.1038/nmeth.3684] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 10/05/2015] [Indexed: 12/12/2022]
Abstract
The simplicity of site-specific genome targeting by type II clustered, regularly interspaced, short palindromic repeat (CRISPR)-Cas9 nucleases, along with their robust activity profile, has changed the landscape of genome editing. These favorable properties have made the CRISPR-Cas9 system the technology of choice for sequence-specific modifications in vertebrate systems. For many applications, whether the focus is on basic science investigations or therapeutic efficacy, activity and precision are important considerations when one is choosing a nuclease platform, target site and delivery method. Here we review recent methods for increasing the activity and accuracy of Cas9 and assessing the extent of off-target cleavage events.
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Affiliation(s)
- Mehmet Fatih Bolukbasi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Ankit Gupta
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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288
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Geisinger JM, Turan S, Hernandez S, Spector LP, Calos MP. In vivo blunt-end cloning through CRISPR/Cas9-facilitated non-homologous end-joining. Nucleic Acids Res 2016; 44:e76. [PMID: 26762978 PMCID: PMC4856974 DOI: 10.1093/nar/gkv1542] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 12/23/2015] [Accepted: 12/28/2015] [Indexed: 12/26/2022] Open
Abstract
The CRISPR/Cas9 system facilitates precise DNA modifications by generating RNA-guided blunt-ended double-strand breaks. We demonstrate that guide RNA pairs generate deletions that are repaired with a high level of precision by non-homologous end-joining in mammalian cells. We present a method called knock-in blunt ligation for exploiting these breaks to insert exogenous PCR-generated sequences in a homology-independent manner without loss of additional nucleotides. This method is useful for making precise additions to the genome such as insertions of marker gene cassettes or functional elements, without the need for homology arms. We successfully utilized this method in human and mouse cells to insert fluorescent protein cassettes into various loci, with efficiencies up to 36% in HEK293 cells without selection. We also created versions of Cas9 fused to the FKBP12-L106P destabilization domain in an effort to improve Cas9 performance. Our in vivo blunt-end cloning method and destabilization-domain-fused Cas9 variant increase the repertoire of precision genome engineering approaches.
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Affiliation(s)
- Jonathan M Geisinger
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sören Turan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sophia Hernandez
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Laura P Spector
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michele P Calos
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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289
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A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface. Proc Natl Acad Sci U S A 2016; 113:5364-9. [PMID: 27078102 DOI: 10.1073/pnas.1602886113] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
HLA-G, a nonclassical HLA molecule uniquely expressed in the placenta, is a central component of fetus-induced immune tolerance during pregnancy. The tissue-specific expression of HLA-G, however, remains poorly understood. Here, systematic interrogation of the HLA-G locus using massively parallel reporter assay (MPRA) uncovered a previously unidentified cis-regulatory element 12 kb upstream of HLA-G with enhancer activity, Enhancer L Strikingly, clustered regularly-interspaced short palindromic repeats (CRISPR)/Cas9-mediated deletion of this enhancer resulted in ablation of HLA-G expression in JEG3 cells and in primary human trophoblasts isolated from placenta. RNA-seq analysis demonstrated that Enhancer L specifically controls HLA-G expression. Moreover, DNase-seq and chromatin conformation capture (3C) defined Enhancer L as a cell type-specific enhancer that loops into the HLA-G promoter. Interestingly, MPRA-based saturation mutagenesis of Enhancer L identified motifs for transcription factors of the CEBP and GATA families essential for placentation. These factors associate with Enhancer L and regulate HLA-G expression. Our findings identify long-range chromatin looping mediated by core trophoblast transcription factors as the mechanism controlling tissue-specific HLA-G expression at the maternal-fetal interface. More broadly, these results establish the combination of MPRA and CRISPR/Cas9 deletion as a powerful strategy to investigate human immune gene regulation.
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290
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Raikwar SP, Raikwar AS, Chaurasia SS, Mohan RR. Gene editing for corneal disease management. World J Transl Med 2016; 5:1-13. [PMID: 35757280 PMCID: PMC9221704 DOI: 10.5528/wjtm.v5.i1.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/09/2016] [Indexed: 02/06/2023] Open
Abstract
Gene editing has recently emerged as a promising technology to engineer genetic modifications precisely in the genome to achieve long-term relief from corneal disorders. Recent advances in the molecular biology leading to the development of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and CRISPR-associated systems, zinc finger nucleases and transcription activator like effector nucleases have ushered in a new era for high throughput in vitro and in vivo genome engineering. Genome editing can be successfully used to decipher complex molecular mechanisms underlying disease pathophysiology, develop innovative next generation gene therapy, stem cell-based regenerative therapy, and personalized medicine for corneal and other ocular diseases. In this review we describe latest developments in the field of genome editing, current challenges, and future prospects for the development of personalized gene-based medicine for corneal diseases. The gene editing approach is expected to revolutionize current diagnostic and treatment practices for curing blindness.
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291
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292
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Customizing the genome as therapy for the β-hemoglobinopathies. Blood 2016; 127:2536-45. [PMID: 27053533 DOI: 10.1182/blood-2016-01-678128] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/12/2016] [Indexed: 12/11/2022] Open
Abstract
Despite nearly complete understanding of the genetics of the β-hemoglobinopathies for several decades, definitive treatment options have lagged behind. Recent developments in technologies for facile manipulation of the genome (zinc finger nucleases, transcription activator-like effector nucleases, or clustered regularly interspaced short palindromic repeats-based nucleases) raise prospects for their clinical application. The use of genome-editing technologies in autologous CD34(+) hematopoietic stem and progenitor cells represents a promising therapeutic avenue for the β-globin disorders. Genetic correction strategies relying on the homology-directed repair pathway may repair genetic defects, whereas genetic disruption strategies relying on the nonhomologous end joining pathway may induce compensatory fetal hemoglobin expression. Harnessing the power of genome editing may usher in a second-generation form of gene therapy for the β-globin disorders.
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293
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A genome editing primer for the hematologist. Blood 2016; 127:2525-35. [PMID: 27053532 DOI: 10.1182/blood-2016-01-678151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022] Open
Abstract
Gene editing enables the site-specific modification of the genome. These technologies have rapidly advanced such that they have entered common use in experimental hematology to investigate genetic function. In addition, genome editing is becoming increasingly plausible as a treatment modality to rectify genetic blood disorders and improve cellular therapies. Genome modification typically ensues from site-specific double-strand breaks and may result in a myriad of outcomes. Even single-strand nicks and targeted biochemical modifications that do not permanently alter the DNA sequence (epigenome editing) may be powerful instruments. In this review, we examine the various technologies, describe their advantages and shortcomings for engendering useful genetic alterations, and consider future prospects for genome editing to impact hematology.
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294
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The clinical applications of genome editing in HIV. Blood 2016; 127:2546-52. [PMID: 27053530 DOI: 10.1182/blood-2016-01-678144] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 02/09/2016] [Indexed: 12/13/2022] Open
Abstract
HIV/AIDS has long been at the forefront of the development of gene- and cell-based therapies. Although conventional gene therapy approaches typically involve the addition of anti-HIV genes to cells using semirandomly integrating viral vectors, newer genome editing technologies based on engineered nucleases are now allowing more precise genetic manipulations. The possible outcomes of genome editing include gene disruption, which has been most notably applied to the CCR5 coreceptor gene, or the introduction of small mutations or larger whole gene cassette insertions at a targeted locus. Disruption of CCR5 using zinc finger nucleases was the first-in-human application of genome editing and remains the most clinically advanced platform, with 7 completed or ongoing clinical trials in T cells and hematopoietic stem/progenitor cells (HSPCs). Here we review the laboratory and clinical findings of CCR5 editing in T cells and HSPCs for HIV therapy and summarize other promising genome editing approaches for future clinical development. In particular, recent advances in the delivery of genome editing reagents and the demonstration of highly efficient homology-directed editing in both T cells and HSPCs are expected to spur the development of even more sophisticated applications of this technology for HIV therapy.
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295
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Price AA, Grakoui A, Weiss DS. Harnessing the Prokaryotic Adaptive Immune System as a Eukaryotic Antiviral Defense. Trends Microbiol 2016; 24:294-306. [PMID: 26852268 PMCID: PMC4808413 DOI: 10.1016/j.tim.2016.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 02/07/2023]
Abstract
Clustered, regularly interspaced, short palindromic repeats - CRISPR-associated (CRISPR-Cas) systems - are sequence-specific RNA-directed endonuclease complexes that bind and cleave nucleic acids. These systems evolved within prokaryotes as adaptive immune defenses to target and degrade nucleic acids derived from bacteriophages and other foreign genetic elements. The antiviral function of these systems has now been exploited to combat eukaryotic viruses throughout the viral life cycle. Here we discuss current advances in CRISPR-Cas9 technology as a eukaryotic antiviral defense.
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Affiliation(s)
- Aryn A Price
- Department of Microbiology and Immunology, Microbiology and Molecular Genetics Program, Emory University, Atlanta, GA 30329, USA; Emory Vaccine Center, Emory University, Atlanta, GA 30329, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Arash Grakoui
- Emory Vaccine Center, Emory University, Atlanta, GA 30329, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30329, USA.
| | - David S Weiss
- Emory Vaccine Center, Emory University, Atlanta, GA 30329, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA; Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30329, USA.
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296
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Nalla AK, Trobridge GD. Prospects for Foamy Viral Vector Anti-HIV Gene Therapy. Biomedicines 2016; 4:E8. [PMID: 28536375 PMCID: PMC5344253 DOI: 10.3390/biomedicines4020008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/18/2016] [Accepted: 03/23/2016] [Indexed: 12/22/2022] Open
Abstract
Stem cell gene therapy approaches for Human Immunodeficiency Virus (HIV) infection have been explored in clinical trials and several anti-HIV genes delivered by retroviral vectors were shown to block HIV replication. However, gammaretroviral and lentiviral based retroviral vectors have limitations for delivery of anti-HIV genes into hematopoietic stem cells (HSC). Foamy virus vectors have several advantages including efficient delivery of transgenes into HSC in large animal models, and a potentially safer integration profile. This review focuses on novel anti-HIV transgenes and the potential of foamy virus vectors for HSC gene therapy of HIV.
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Affiliation(s)
- Arun K Nalla
- Pharmaceutical Sciences, College of Pharmacy, Washington State University Spokane, Spokane, WA 99202, USA.
| | - Grant D Trobridge
- Pharmaceutical Sciences, College of Pharmacy, Washington State University Spokane, Spokane, WA 99202, USA.
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA.
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297
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Abstract
Nuclease-based gene editing technologies have opened up opportunities for correcting human genetic diseases. For the first time, scientists achieved targeted gene editing of mitochondrial DNA in mouse oocytes fused with patient cells. This fascinating progression may encourage the development of novel therapy for human maternally inherent mitochondrial diseases.
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298
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Long-term multilineage engraftment of autologous genome-edited hematopoietic stem cells in nonhuman primates. Blood 2016; 127:2416-26. [PMID: 26980728 DOI: 10.1182/blood-2015-09-672337] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 02/26/2016] [Indexed: 12/27/2022] Open
Abstract
Genome editing in hematopoietic stem and progenitor cells (HSPCs) is a promising novel technology for the treatment of many human diseases. Here, we evaluated whether the disruption of the C-C chemokine receptor 5 (CCR5) locus in pigtailed macaque HSPCs by zinc finger nucleases (ZFNs) was feasible. We show that macaque-specific CCR5 ZFNs efficiently induce CCR5 disruption at levels of up to 64% ex vivo, 40% in vivo early posttransplant, and 3% to 5% in long-term repopulating cells over 6 months following HSPC transplant. These genome-edited HSPCs support multilineage engraftment and generate progeny capable of trafficking to secondary tissues including the gut. Using deep sequencing technology, we show that these ZFNs are highly specific for the CCR5 locus in primary cells. Further, we have adapted our clonal tracking methodology to follow individual CCR5 mutant cells over time in vivo, reinforcing that CCR5 gene-edited HSPCs are capable of long-term engraftment. Together, these data demonstrate that genome-edited HSPCs engraft, and contribute to multilineage repopulation after autologous transplantation in a clinically relevant large animal model, an important step toward the development of stem cell-based genome-editing therapies for HIV and potentially other diseases as well.
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299
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Affiliation(s)
- Magdalini Papadaki
- Regenerative Medicine Program, Innovate UK, North Star House, North Star Avenue, Swindon, SN2 1UE, UK
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300
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Martin F, Gutierrez-Guerrero A, Sánchez S, Galvani G, Benabdellah K. Genome editing: An alternative to retroviral vectors for Wiskott-Aldrich Syndrome (WAS) Gene Therapy? Expert Opin Orphan Drugs 2016. [DOI: 10.1517/21678707.2016.1142870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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