151
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Salas-Mckee J, Kong W, Gladney WL, Jadlowsky JK, Plesa G, Davis MM, Fraietta JA. CRISPR/Cas9-based genome editing in the era of CAR T cell immunotherapy. Hum Vaccin Immunother 2019; 15:1126-1132. [PMID: 30735463 DOI: 10.1080/21645515.2019.1571893] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The advent of engineered T cells as a form of immunotherapy marks the beginning of a new era in medicine, providing a transformative way to combat complex diseases such as cancer. Following FDA approval of CAR T cells directed against the CD19 protein for the treatment of acute lymphoblastic leukemia and diffuse large B cell lymphoma, CAR T cells are poised to enter mainstream oncology. Despite this success, a number of patients are unable to receive this therapy due to inadequate T cell numbers or rapid disease progression. Furthermore, lack of response to CAR T cell treatment is due in some cases to intrinsic autologous T cell defects and/or the inability of these cells to function optimally in a strongly immunosuppressive tumor microenvironment. We describe recent efforts to overcome these limitations using CRISPR/Cas9 technology, with the goal of enhancing potency and increasing the availability of CAR-based therapies. We further discuss issues related to the efficiency/scalability of CRISPR/Cas9-mediated genome editing in CAR T cells and safety considerations. By combining the tools of synthetic biology such as CARs and CRISPR/Cas9, we have an unprecedented opportunity to optimally program T cells and improve adoptive immunotherapy for most, if not all future patients.
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Affiliation(s)
- January Salas-Mckee
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA
| | - Weimin Kong
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA
| | - Whitney L Gladney
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA
| | - Julie K Jadlowsky
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA
| | - Gabriela Plesa
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA
| | - Megan M Davis
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA.,b Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Joseph A Fraietta
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA.,b Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA.,c Parker Institute for Cancer Immunotherapy , University of Pennsylvania , Philadelphia , PA , USA.,d Department of Microbiology, Perelman School of Medicine , University of Pennsylvania , Philadelphia, PA , USA
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152
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Sun D, Sun Z, Jiang H, Vaidya AM, Xin R, Ayat NR, Schilb AL, Qiao PL, Han Z, Naderi A, Lu ZR. Synthesis and Evaluation of pH-Sensitive Multifunctional Lipids for Efficient Delivery of CRISPR/Cas9 in Gene Editing. Bioconjug Chem 2019; 30:667-678. [PMID: 30582790 PMCID: PMC6429435 DOI: 10.1021/acs.bioconjchem.8b00856] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/20/2018] [Indexed: 01/06/2023]
Abstract
CRISPR/Cas9 system is a promising approach for gene editing in gene therapy. Effective gene editing requires safe and efficient delivery of CRISPR/Cas9 system in target cells. Several new multifunctional pH-sensitive amino lipids were designed and synthesized with modification of the amino head groups for intracellular delivery of CRISPR/Cas9 system. These multifunctional pH-sensitive amino lipids exhibited structurally dependent formulation of stable nanoparticles with the DNA plasmids of CRISPR/Cas9 system with the sizes ranging from 100 to 200 nm. The amino lipid plasmid DNA nanoparticles showed pH-sensitive hemolysis with minimal hemolytic activity at pH 7.4 and increased hemolysis at acidic pH (pH = 5.5, 6.5). The nanoparticles exhibited low cytotoxicity at an N/P ratio of 10. Expression of both Cas9 and sgRNA of the CRISPR/Cas9 system was in the range from 4.4% to 33%, dependent on the lipid structure in NIH3T3-GFP cells. The amino lipids that formed stable nanoparticles with high expression of both Cas9 and sgRNA mediated high gene editing efficiency. ECO and iECO mediated more efficient gene editing than other tested lipids. ECO mediated up to 50% GFP suppression based on observations with confocal microscopy and nearly 80% reduction of GFP mRNA based on RT-PCR measurement in NIH3T3-GFP cells. The multifunctional pH-sensitive amino lipids have the potential for efficient intracellular delivery of CRISPR/Cas9 for effective gene editing.
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Affiliation(s)
| | | | - Hongfa Jiang
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Amita M. Vaidya
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Rui Xin
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Nadia R. Ayat
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Andrew L. Schilb
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Peter L. Qiao
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Zheng Han
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Amirreza Naderi
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
| | - Zheng-Rong Lu
- Department
of Biomedical
Engineering, School of Engineering, Case
Western Reserve University, Cleveland, Ohio 44106, United States
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153
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Xu H, Wang B, Ono M, Kagita A, Fujii K, Sasakawa N, Ueda T, Gee P, Nishikawa M, Nomura M, Kitaoka F, Takahashi T, Okita K, Yoshida Y, Kaneko S, Hotta A. Targeted Disruption of HLA Genes via CRISPR-Cas9 Generates iPSCs with Enhanced Immune Compatibility. Cell Stem Cell 2019; 24:566-578.e7. [PMID: 30853558 DOI: 10.1016/j.stem.2019.02.005] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 12/18/2018] [Accepted: 02/06/2019] [Indexed: 12/18/2022]
Abstract
Induced pluripotent stem cells (iPSCs) have strong potential in regenerative medicine applications; however, immune rejection caused by HLA mismatching is a concern. B2M gene knockout and HLA-homozygous iPSC stocks can address this issue, but the former approach may induce NK cell activity and fail to present antigens, and it is challenging to recruit rare donors for the latter method. Here, we show two genome-editing strategies for making immunocompatible donor iPSCs. First, we generated HLA pseudo-homozygous iPSCs with allele-specific editing of HLA heterozygous iPSCs. Second, we generated HLA-C-retained iPSCs by disrupting both HLA-A and -B alleles to suppress the NK cell response while maintaining antigen presentation. HLA-C-retained iPSCs could evade T cells and NK cells in vitro and in vivo. We estimated that 12 lines of HLA-C-retained iPSCs combined with HLA-class II knockout are immunologically compatible with >90% of the world's population, greatly facilitating iPSC-based regenerative medicine applications.
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Affiliation(s)
- Huaigeng Xu
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Bo Wang
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Miyuki Ono
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Akihiro Kagita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Kaho Fujii
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Noriko Sasakawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Tatsuki Ueda
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Peter Gee
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Misato Nishikawa
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Masaki Nomura
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Fumiyo Kitaoka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Tomoko Takahashi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Keisuke Okita
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yoshinori Yoshida
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Shin Kaneko
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
| | - Akitsu Hotta
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan; Core Center for iPS Cell Research, Research Center Network for Realization of Regenerative Medicine, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
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154
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Dyikanov DT, Vasiluev PA, Rysenkova KD, Aleksandrushkina NA, Tyurin-Kuzmin PA, Kulebyakin KY, Rubtsov YP, Shmakova AA, Evseeva MN, Balatskiy AV, Semina EV, Rostovtseva AI, Makarevich PI, Karagyaur MN. Optimization of CRISPR/Cas9 Technology to Knock Out Genes of Interest in Aneuploid Cell Lines. Tissue Eng Part C Methods 2019; 25:168-175. [DOI: 10.1089/ten.tec.2018.0365] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Daniyar T. Dyikanov
- Institute of Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Petr A. Vasiluev
- FGBI of Science “Institute of Gene Biology” of the Russian Academy of Sciences, Moscow, Russia
- FGBI “Medical Genetics Research Center,” Moscow, Russia
| | - Karina D. Rysenkova
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
- FGBI “National Medical Research Center of Cardiology” of the Ministry of Health of Russia, Moscow, Russia
| | - Natalia A. Aleksandrushkina
- Institute of Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Moscow, Russia
| | | | - Konstantin Y. Kulebyakin
- Institute of Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Yury P. Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
- National Research University Higher School of Economics, Moscow, Russia
| | - Anna A. Shmakova
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Maria N. Evseeva
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander V. Balatskiy
- Institute of Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina V. Semina
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
- FGBI “National Medical Research Center of Cardiology” of the Ministry of Health of Russia, Moscow, Russia
| | | | - Pavel I. Makarevich
- Institute of Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim N. Karagyaur
- Institute of Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
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155
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Rui Y, Wilson DR, Green JJ. Non-Viral Delivery To Enable Genome Editing. Trends Biotechnol 2019; 37:281-293. [PMID: 30278987 PMCID: PMC6378131 DOI: 10.1016/j.tibtech.2018.08.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 12/27/2022]
Abstract
Genome-editing technologies such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENS), and the clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein system have revolutionized biological research. Each biotechnology consists of a DNA-binding protein that can be programmed to recognize and initiate double-strand breaks (DSBs) for site-specific gene modification. These technologies have the potential to be harnessed to cure diseases caused by aberrant gene expression. To be successful therapeutically, their functionality depends on their safe and efficient delivery into the cell nucleus. This review discusses the challenges in the delivery of genome-editing tools, and highlights recent innovations in non-viral delivery that have potential to overcome these limitations and advance the translation of genome editing towards patient care.
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Affiliation(s)
- Yuan Rui
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; These authors contributed equally
| | - David R Wilson
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Institute for Nanobiotechnology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; These authors contributed equally
| | - Jordan J Green
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Institute for Nanobiotechnology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Departments of Materials Science and Engineering and Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA; Departments of Ophthalmology, Oncology, and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA.
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156
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Karimian A, Azizian K, Parsian H, Rafieian S, Shafiei‐Irannejad V, Kheyrollah M, Yousefi M, Majidinia M, Yousefi B. CRISPR/Cas9 technology as a potent molecular tool for gene therapy. J Cell Physiol 2019; 234:12267-12277. [DOI: 10.1002/jcp.27972] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/19/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Ansar Karimian
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences Babol Iran
- Cancer & Immunology Research Center, Kurdistan University of Medical Sciences Sanandaj Iran
- Student Research Committee, Babol University of Medical Sciences Babol Iran
| | - Khalil Azizian
- Liver and Gastrointestinal Diseases Research Center, Tabriz University of Medical Science Tabriz Iran
| | - Hadi Parsian
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences Babol Iran
| | - Sona Rafieian
- Department of Oral and Maxillofacial Pathology School of Dentistry, Zanjan University of Medical Sciences Zanjan Iran
| | | | - Maryam Kheyrollah
- Department of Molecular Medicine National Institue of Genetic Engeneering and Biotechnology Tehran Iran
| | - Mehdi Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences Tabriz Iran
- Immunology Research Center, Tabriz University of Medical Sciences Tabriz Iran
| | - Maryam Majidinia
- Tumor Research Center, Urmia University of Medical Sciences Urmia Iran
| | - Bahman Yousefi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences Tehran Iran
- Department of Biochemistry and Clinical Laboratories Faculty of Medicine, Tabriz University of Medical Science Tabriz Iran
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157
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Xue L, Tang B, Chen W, Luo J. Prediction of CRISPR sgRNA Activity Using a Deep Convolutional Neural Network. J Chem Inf Model 2019; 59:615-624. [PMID: 30485088 DOI: 10.1021/acs.jcim.8b00368] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The CRISPR-Cas9 system derived from adaptive immunity in bacteria and archaea has been developed into a powerful tool for genome engineering with wide-ranging applications. Optimizing single-guide RNA (sgRNA) design to improve efficiency of target cleavage is a key step for successful gene editing using the CRISPR-Cas9 system. Because not all sgRNAs that cognate to a given target gene are equally effective, computational tools have been developed based on experimental data to increase the likelihood of selecting effective sgRNAs. Despite considerable efforts to date, it still remains a big challenge to accurately predict functional sgRNAs directly from large-scale sequence data. We propose DeepCas9, a deep-learning framework based on the convolutional neural network (CNN), to automatically learn the sequence determinants and further enable the identification of functional sgRNAs for the CRISPR-Cas9 system. We show that the CNN method outperforms previous methods in both (i) the ability to correctly identify highly active sgRNAs in experiments not used in the training and (ii) the ability to accurately predict the target efficacies of sgRNAs in different organisms. Besides, we further visualize the convolutional kernels and show the match of identified sequence signatures and known nucleotide preferences. We finally demonstrate the application of our method to the design of next-generation genome-scale CRISPRi and CRISPRa libraries targeting human and mouse genomes. We expect that DeepCas9 will assist in reducing the numbers of sgRNAs that must be experimentally validated to enable more effective and efficient genetic screens and genome engineering. DeepCas9 can be freely accessed via the Internet at https://github.com/lje00006/DeepCas9 .
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Affiliation(s)
- Li Xue
- School of Public Health , Southwest Medical University , Luzhou , Sichuan , China
| | - Bin Tang
- Basic Medical College , Southwest Medical University , Luzhou , Sichuan , China
| | - Wei Chen
- Integrative Genomics Core , City of Hope National Medical Center , Duarte , California 91010 , United States
| | - Jiesi Luo
- Key Laboratory for Aging and Regenerative Medicine, Department of Pharmacology, School of Pharmacy , Southwest Medical University , Luzhou , Sichuan , China
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158
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Jayavaradhan R, Pillis DM, Malik P. A Versatile Tool for the Quantification of CRISPR/Cas9-Induced Genome Editing Events in Human Hematopoietic Cell Lines and Hematopoietic Stem/Progenitor Cells. J Mol Biol 2019; 431:102-110. [PMID: 29751014 DOI: 10.1016/j.jmb.2018.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/03/2018] [Indexed: 11/28/2022]
Abstract
The efficient site-specific DNA double-strand breaks (DSB) created by CRISPR/Cas9 has revolutionized genome engineering and has great potential for editing hematopoietic stem/progenitor cells (HSPCs). However, detailed understanding of the variables that influence choice of DNA-DSB repair (DDR) pathways by HSPC is required for therapeutic levels of editing in these clinically relevant cells. We developed a hematopoietic-reporter system that rapidly quantifies the three major DDR pathways utilized at the individual DSB created by CRISPR/Cas9-NHEJ, MMEJ, and HDR-and show its applicability in evaluating the different DDR outcomes utilized by human hematopoietic cell lines and primary human HSPC.
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Affiliation(s)
- Rajeswari Jayavaradhan
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute (CBDI), Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA; Pathology and Molecular Medicine Program, University of Cincinnati, Cincinnati, OH, 45229, USA
| | - Devin M Pillis
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute (CBDI), Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA
| | - Punam Malik
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Disease Institute (CBDI), Cincinnati Children's Hospital Medical Center (CCHMC), Cincinnati, OH, 45229, USA; Division of Hematology, CBDI, CCHMC, Cincinnati, OH, 45229, USA.
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159
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Lattanzi A, Meneghini V, Pavani G, Amor F, Ramadier S, Felix T, Antoniani C, Masson C, Alibeu O, Lee C, Porteus MH, Bao G, Amendola M, Mavilio F, Miccio A. Optimization of CRISPR/Cas9 Delivery to Human Hematopoietic Stem and Progenitor Cells for Therapeutic Genomic Rearrangements. Mol Ther 2019; 27:137-150. [PMID: 30424953 PMCID: PMC6318785 DOI: 10.1016/j.ymthe.2018.10.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 12/21/2022] Open
Abstract
Editing the β-globin locus in hematopoietic stem cells is an alternative therapeutic approach for gene therapy of β-thalassemia and sickle cell disease. Using the CRISPR/Cas9 system, we genetically modified human hematopoietic stem and progenitor cells (HSPCs) to mimic the large rearrangements in the β-globin locus associated with hereditary persistence of fetal hemoglobin (HPFH), a condition that mitigates the clinical phenotype of patients with β-hemoglobinopathies. We optimized and compared the efficiency of plasmid-, lentiviral vector (LV)-, RNA-, and ribonucleoprotein complex (RNP)-based methods to deliver the CRISPR/Cas9 system into HSPCs. Plasmid delivery of Cas9 and gRNA pairs targeting two HPFH-like regions led to high frequency of genomic rearrangements and HbF reactivation in erythroblasts derived from sorted, Cas9+ HSPCs but was associated with significant cell toxicity. RNA-mediated delivery of CRISPR/Cas9 was similarly toxic but much less efficient in editing the β-globin locus. Transduction of HSPCs by LVs expressing Cas9 and gRNA pairs was robust and minimally toxic but resulted in poor genome-editing efficiency. Ribonucleoprotein (RNP)-based delivery of CRISPR/Cas9 exhibited a good balance between cytotoxicity and efficiency of genomic rearrangements as compared to the other delivery systems and resulted in HbF upregulation in erythroblasts derived from unselected edited HSPCs.
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Affiliation(s)
| | - Vasco Meneghini
- Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris 75015, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France
| | | | | | - Sophie Ramadier
- Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris 75015, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France
| | - Tristan Felix
- Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris 75015, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France
| | - Chiara Antoniani
- Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris 75015, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France
| | - Cecile Masson
- Paris-Descartes Bioinformatics Platform, Imagine Institute, Paris 75015, France
| | - Olivier Alibeu
- Genomic Platform, Imagine Institute, Paris 75015, France
| | - Ciaran Lee
- Department of Bioengineering, Rice University, Houston, TX 77006, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77006, USA
| | | | - Fulvio Mavilio
- Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France; Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Annarita Miccio
- Genethon, INSERM UMR951, Evry 91000, France; Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris 75015, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France.
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160
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Abbasi SA, Ponni G, Tauseef SM. Potential of joyweed Alternanthera sessilis for rapid treatment of domestic sewage in SHEFROL ® bioreactor. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2019; 21:160-169. [PMID: 30701990 DOI: 10.1080/15226514.2018.1488814] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In a first-ever report on this subject, it is shown that a common amphibious plant joyweed (Alternanthera sessilis) can be used in rapid and efficient treatment of biodegradable wastewaters, typified by domestic sewage. The plant was effective when used indoors under artificial lighting, as well as outdoors. It enabled treatment of sewage, varying widely in strength (from 300 mg/L to 1800 mg/L in chemical oxygen demand), to the extent of 78.9-83.9%. It was also able to remove biological oxygen demand, suspended solids, phosphorous, nitrogen, and the heavy metal copper to the extent of 87%, 93%, 45%, and 43%, respectively. Over 99% of total coliforms, faecal coliforms, and faecal streptococci were also removed. The treatment was very swiftly achieved, at a hydraulic retention time of just 6 h, in the "sheet flow root level" (SHEFROL®) bioreactor developed earlier by us and of which a patent claim has been registered. The findings indicate that A. sessilis has the potential to affect primary, secondary, and tertiary treatment of domestic sewage along with significant pathogen removal in a single process step when used in SHEFROL® bioreactors.
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Affiliation(s)
- S A Abbasi
- a Centre for Pollution Control & Environmental Engineering , Pondicherry University , Puducherry , India
| | - G Ponni
- a Centre for Pollution Control & Environmental Engineering , Pondicherry University , Puducherry , India
| | - S M Tauseef
- b Department of Health, Safety, Environment and Civil Engineering , University of Petroleum and Energy Studies , Dehradun , India
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161
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Hultquist JF, Hiatt J, Schumann K, McGregor MJ, Roth TL, Haas P, Doudna JA, Marson A, Krogan NJ. CRISPR-Cas9 genome engineering of primary CD4 + T cells for the interrogation of HIV-host factor interactions. Nat Protoc 2019; 14:1-27. [PMID: 30559373 PMCID: PMC6637941 DOI: 10.1038/s41596-018-0069-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas9 gene-editing strategies have revolutionized our ability to engineer the human genome for robust functional interrogation of complex biological processes. We have recently adapted this technology for use in primary human CD4+ T cells to create a high-throughput platform for analyzing the role of host factors in HIV infection and pathogenesis. Briefly, CRISPR-Cas9 ribonucleoproteins (crRNPs) are synthesized in vitro and delivered to activated CD4+ T cells by nucleofection. These cells are then assayed for editing efficiency and expanded for use in downstream cellular, genetic, or protein-based assays. This platform supports the rapid, arrayed generation of multiple gene manipulations and is widely adaptable across culture conditions, infection protocols, and downstream applications. Here, we present detailed protocols for crRNP synthesis, primary T-cell culture, 96-well nucleofection, molecular validation, and HIV infection, and discuss additional considerations for guide and screen design, as well as crRNP multiplexing. Taken together, this procedure allows high-throughput identification and mechanistic interrogation of HIV host factors in primary CD4+ T cells by gene knockout, validation, and HIV spreading infection in as little as 2-3 weeks.
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Affiliation(s)
- Judd F Hultquist
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA
- Institute for Virology and Immunology, J. David Gladstone Institutes, San Francisco, CA, USA
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Joseph Hiatt
- Institute for Virology and Immunology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Kathrin Schumann
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Michael J McGregor
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA
- Institute for Virology and Immunology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Theodore L Roth
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Paige Haas
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA
- Institute for Virology and Immunology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Medicine, University of California, San Francisco, CA, USA.
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
- Institute for Virology and Immunology, J. David Gladstone Institutes, San Francisco, CA, USA.
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162
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Raikwar SP, Thangavel R, Dubova I, Selvakumar GP, Ahmed ME, Kempuraj D, Zaheer SA, Iyer SS, Zaheer A. Targeted Gene Editing of Glia Maturation Factor in Microglia: a Novel Alzheimer's Disease Therapeutic Target. Mol Neurobiol 2019; 56:378-393. [PMID: 29704201 PMCID: PMC6344368 DOI: 10.1007/s12035-018-1068-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/08/2018] [Indexed: 02/07/2023]
Abstract
Alzheimer's disease (AD) is a devastating, progressive neurodegenerative disorder that leads to severe cognitive impairment in elderly patients. Chronic neuroinflammation plays an important role in the AD pathogenesis. Glia maturation factor (GMF), a proinflammatory molecule discovered in our laboratory, is significantly upregulated in various regions of AD brains. We have previously reported that GMF is predominantly expressed in the reactive glial cells surrounding the amyloid plaques (APs) in the mouse and human AD brain. Microglia are the major source of proinflammatory cytokines and chemokines including GMF. Recently clustered regularly interspaced short palindromic repeats (CRISPR) based genome editing has been recognized to study the functions of genes that are implicated in various diseases. Here, we investigated if CRISPR-Cas9-mediated GMF gene editing leads to inhibition of GMF expression and suppression of microglial activation. Confocal microscopy of murine BV2 microglial cell line transduced with an adeno-associated virus (AAV) coexpressing Staphylococcus aureus (Sa) Cas9 and a GMF-specific guide RNA (GMF-sgRNA) revealed few cells expressing SaCas9 while lacking GMF expression, thereby confirming successful GMF gene editing. To further improve GMF gene editing efficiency, we developed lentiviral vectors (LVs) expressing either Streptococcus pyogenes (Sp) Cas9 or GMF-sgRNAs. BV2 cells cotransduced with LVs expressing SpCas9 and GMF-sgRNAs revealed reduced GMF expression and the presence of indels in the exons 2 and 3 of the GMF coding sequence. Lipopolysaccharide (LPS) treatment of GMF-edited cells led to reduced microglial activation as shown by reduced p38 MAPK phosphorylation. We believe that targeted in vivo GMF gene editing has a significant potential for developing a unique and novel AD therapy.
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Affiliation(s)
- Sudhanshu P Raikwar
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- Harry S. Truman Memorial Veteran's Hospital, US Department of Veterans Affairs, Columbia, MO, USA
| | - Ramasamy Thangavel
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- Harry S. Truman Memorial Veteran's Hospital, US Department of Veterans Affairs, Columbia, MO, USA
| | - Iuliia Dubova
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
| | - Govindhasamy Pushpavathi Selvakumar
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- Harry S. Truman Memorial Veteran's Hospital, US Department of Veterans Affairs, Columbia, MO, USA
| | - Mohammad Ejaz Ahmed
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- Harry S. Truman Memorial Veteran's Hospital, US Department of Veterans Affairs, Columbia, MO, USA
| | - Duraisamy Kempuraj
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- Harry S. Truman Memorial Veteran's Hospital, US Department of Veterans Affairs, Columbia, MO, USA
| | - Smita A Zaheer
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
| | - Shankar S Iyer
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA
- Harry S. Truman Memorial Veteran's Hospital, US Department of Veterans Affairs, Columbia, MO, USA
| | - Asgar Zaheer
- Department of Neurology, Center for Translational Neuroscience, School of Medicine, University of Missouri, M741A Medical Science Building, 1 Hospital Drive, Columbia, MO, 65211, USA.
- Harry S. Truman Memorial Veteran's Hospital, US Department of Veterans Affairs, Columbia, MO, USA.
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163
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Laustsen A, Bak RO. Electroporation-Based CRISPR/Cas9 Gene Editing Using Cas9 Protein and Chemically Modified sgRNAs. Methods Mol Biol 2019; 1961:127-134. [PMID: 30912044 DOI: 10.1007/978-1-4939-9170-9_9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
CRISPR/Cas9 is an effective and easy-to-use tool for editing the genome of many human cancer cell lines. However, in some hard-to-transfect cell lines and primary cells, gene editing is more challenging. This protocol details an electroporation-based protocol for the delivery of Cas9 protein from Streptococcus pyogenes complexed with chemically modified sgRNAs. We have found this protocol to work very efficiently in numerous cell lines and primary cells that are difficult to transfect by conventional chemical-based transfection methods.
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Affiliation(s)
- Anders Laustsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus, Denmark.
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164
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Patel S, Athirasala A, Menezes PP, Ashwanikumar N, Zou T, Sahay G, Bertassoni LE. Messenger RNA Delivery for Tissue Engineering and Regenerative Medicine Applications. Tissue Eng Part A 2019; 25:91-112. [PMID: 29661055 PMCID: PMC6352544 DOI: 10.1089/ten.tea.2017.0444] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 04/09/2018] [Indexed: 12/25/2022] Open
Abstract
The ability to control cellular processes and precisely direct cellular reprogramming has revolutionized regenerative medicine. Recent advances in in vitro transcribed (IVT) mRNA technology with chemical modifications have led to development of methods that control spatiotemporal gene expression. Additionally, there is a current thrust toward the development of safe, integration-free approaches to gene therapy for translational purposes. In this review, we describe strategies of synthetic IVT mRNA modifications and nonviral technologies for intracellular delivery. We provide insights into the current tissue engineering approaches that use a hydrogel scaffold with genetic material. Furthermore, we discuss the transformative potential of novel mRNA formulations that when embedded in hydrogels can trigger controlled genetic manipulation to regenerate tissues and organs in vitro and in vivo. The role of mRNA delivery in vascularization, cytoprotection, and Cas9-mediated xenotransplantation is additionally highlighted. Harmonizing mRNA delivery vehicle interactions with polymeric scaffolds can be used to present genetic cues that lead to precise command over cellular reprogramming, differentiation, and secretome activity of stem cells-an ultimate goal for tissue engineering.
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Affiliation(s)
- Siddharth Patel
- Department of Pharmaceutical Sciences, College of Pharmacy, Collaborative Life Science Building, Oregon State University, Portland, Oregon
| | - Avathamsa Athirasala
- Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, Oregon
| | - Paula P. Menezes
- Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, Oregon
- Postgraduate Program in Health Sciences, Department of Pharmacy, Federal University of Sergipe, Aracaju, Sergipe, Brazil
| | - N. Ashwanikumar
- Department of Pharmaceutical Sciences, College of Pharmacy, Collaborative Life Science Building, Oregon State University, Portland, Oregon
| | - Ting Zou
- Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, Oregon
- Endodontology, Faculty of Dentistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Gaurav Sahay
- Department of Pharmaceutical Sciences, College of Pharmacy, Collaborative Life Science Building, Oregon State University, Portland, Oregon
- Department of Biomedical Engineering, Collaborative Life Science Building, Oregon Health and Science University, Portland, Oregon
| | - Luiz E. Bertassoni
- Division of Biomaterials and Biomechanics, Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, Portland, Oregon
- Department of Biomedical Engineering, Collaborative Life Science Building, Oregon Health and Science University, Portland, Oregon
- Center for Regenerative Medicine, Oregon Health and Science University, Portland, Oregon
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165
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Cook PJ, Ventura A. Cancer diagnosis and immunotherapy in the age of CRISPR. Genes Chromosomes Cancer 2018; 58:233-243. [PMID: 30382614 DOI: 10.1002/gcc.22702] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/26/2018] [Accepted: 10/01/2018] [Indexed: 12/19/2022] Open
Abstract
The explosion in genome editing technologies that has occurred in the past decade has revolutionized cancer research and promises to improve cancer diagnosis and therapy. Ongoing efforts include engineering of chimeric antigen receptor-T cells using clustered regularly interspaced short palindromic repeats (CRISPR) to generate a safer, more effective therapy with improved performance in immunologically "cold" tumors, as well as clever adaptations of CRISPR enzymes to allow fast, simple, and sensitive detection of specific nucleotide sequences. While still in their infancy, CRISPR-based cancer therapeutics and diagnostics are developing at an impressive speed and it is likely they will soon impact clinical practice. Here, we summarize their history and the most recent developments.
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Affiliation(s)
- Peter J Cook
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Washington
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York
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166
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Bayat H, Naderi F, Khan AH, Memarnejadian A, Rahimpour A. The Impact of CRISPR-Cas System on Antiviral Therapy. Adv Pharm Bull 2018; 8:591-597. [PMID: 30607331 PMCID: PMC6311650 DOI: 10.15171/apb.2018.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 09/08/2018] [Accepted: 09/29/2018] [Indexed: 12/16/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein nuclease (Cas) is identified as an adaptive immune system in archaea and bacteria. Type II of this system, CRISPR-Cas9, is the most versatile form that has enabled facile and efficient targeted genome editing. Viral infections have serious impacts on global health and conventional antiviral therapies have not yielded a successful solution hitherto. The CRISPR-Cas9 system represents a promising tool for eliminating viral infections. In this review, we highlight 1) the recent progress of CRISPR-Cas technology in decoding and diagnosis of viral outbreaks, 2) its applications to eliminate viral infections in both pre-integration and provirus stages, and 3) various delivery systems that are employed to introduce the platform into target cells.
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Affiliation(s)
- Hadi Bayat
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Naderi
- Department of Molecular Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Amjad Hayat Khan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | | | - Azam Rahimpour
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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167
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Bolukbasi MF, Liu P, Luk K, Kwok SF, Gupta A, Amrani N, Sontheimer EJ, Zhu LJ, Wolfe SA. Orthogonal Cas9-Cas9 chimeras provide a versatile platform for genome editing. Nat Commun 2018; 9:4856. [PMID: 30451839 PMCID: PMC6242970 DOI: 10.1038/s41467-018-07310-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 10/30/2018] [Indexed: 12/22/2022] Open
Abstract
The development of robust, versatile and accurate toolsets is critical to facilitate therapeutic genome editing applications. Here we establish RNA-programmable Cas9-Cas9 chimeras, in single- and dual-nuclease formats, as versatile genome engineering systems. In both of these formats, Cas9-Cas9 fusions display an expanded targeting repertoire and achieve highly specific genome editing. Dual-nuclease Cas9-Cas9 chimeras have distinct advantages over monomeric Cas9s including higher target site activity and the generation of predictable precise deletion products between their target sites. At a therapeutically relevant site within the BCL11A erythroid enhancer, Cas9-Cas9 nucleases produced precise deletions that comprised up to 97% of all sequence alterations. Thus Cas9-Cas9 chimeras represent an important tool that could be particularly valuable for therapeutic genome editing applications where a precise cleavage position and defined sequence end products are desirable. Therapeutic genome engineering relies on the development of reliable, robust and versatile tools. Here the authors develop Cas9-Cas9 chimeras with high target site activity that generate predictable deletions.
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Affiliation(s)
- Mehmet Fatih Bolukbasi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.,Exonics Therapeutics, Watertown, MA, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Samantha F Kwok
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ankit Gupta
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.,Bluebird Bio., Cambridge, MA, USA
| | - Nadia Amrani
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, USA. .,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
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168
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Yen J, Fiorino M, Liu Y, Paula S, Clarkson S, Quinn L, Tschantz WR, Klock H, Guo N, Russ C, Yu VWC, Mickanin C, Stevenson SC, Lee C, Yang Y. TRIAMF: A New Method for Delivery of Cas9 Ribonucleoprotein Complex to Human Hematopoietic Stem Cells. Sci Rep 2018; 8:16304. [PMID: 30389991 PMCID: PMC6214993 DOI: 10.1038/s41598-018-34601-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/16/2018] [Indexed: 02/07/2023] Open
Abstract
CRISPR/Cas9 mediated gene editing of patient-derived hematopoietic stem and progenitor cells (HSPCs) ex vivo followed by autologous transplantation of the edited HSPCs back to the patient can provide a potential cure for monogenic blood disorders such as β-hemoglobinopathies. One challenge for this strategy is efficient delivery of the ribonucleoprotein (RNP) complex, consisting of purified Cas9 protein and guide RNA, into HSPCs. Because β-hemoglobinopathies are most prevalent in developing countries, it is desirable to have a reliable, efficient, easy-to-use and cost effective delivery method. With this goal in mind, we developed TRansmembrane Internalization Assisted by Membrane Filtration (TRIAMF), a new method to quickly and effectively deliver RNPs into HSPCs by passing a RNP and cell mixture through a filter membrane. We achieved robust gene editing in HSPCs using TRIAMF and demonstrated that the multilineage colony forming capacities and the competence for engraftment in immunocompromised mice of HSPCs were preserved post TRIAMF treatment. TRIAMF is a custom designed system using inexpensive components and has the capacity to process HSPCs at clinical scale.
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Affiliation(s)
- Jonathan Yen
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Michael Fiorino
- NIBR Informatics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Yi Liu
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Steve Paula
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Scott Clarkson
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Lisa Quinn
- Biotherapeutic and Analytical Tech, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - William R Tschantz
- Biotherapeutic and Analytical Tech, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Heath Klock
- Biotherapeutics & Biotechnology, The Genomics Institute of the Novartis Research Foundation, La Jolla, California, USA
| | - Ning Guo
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Carsten Russ
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Vionnie W C Yu
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Craig Mickanin
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Susan C Stevenson
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Cameron Lee
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA
| | - Yi Yang
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, USA.
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169
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Yin L, Hu S, Mei S, Sun H, Xu F, Li J, Zhu W, Liu X, Zhao F, Zhang D, Cen S, Liang C, Guo F. CRISPR/Cas9 Inhibits Multiple Steps of HIV-1 Infection. Hum Gene Ther 2018; 29:1264-1276. [PMID: 29644868 DOI: 10.1089/hum.2018.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CRISPR/Cas9 is an adaptive immune system where bacteria and archaea have evolved to resist the invading viruses and plasmid DNA by creating site-specific double-strand breaks in DNA. This study tested this gene editing system in inhibiting human immunodeficiency virus type 1 (HIV-1) infection by targeting the viral long terminal repeat and the gene coding sequences. Strong inhibition of HIV-1 infection by Cas9/gRNA was observed, which resulted not only from insertions and deletions (indels) that were introduced into viral DNA due to Cas9 cleavage, but also from the marked decrease in the levels of the late viral DNA products and the integrated viral DNA. This latter defect might have reflected the degradation of viral DNA that has not been immediately repaired after Cas9 cleavage. It was further observed that Cas9, when solely located in the cytoplasm, inhibits HIV-1 as strongly as the nuclear Cas9, except that the cytoplasmic Cas9 does not act on the integrated HIV-1 DNA and thus cannot be used to excise the latent provirus. Together, the results suggest that Cas9/gRNA is able to target and edit HIV-1 DNA both in the cytoplasm and in the nucleus. The inhibitory effect of Cas9 on HIV-1 is attributed to both the indels in viral DNA and the reduction in the levels of viral DNA.
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Affiliation(s)
- Lijuan Yin
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Siqi Hu
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Shan Mei
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Hong Sun
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Fengwen Xu
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Jian Li
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Weijun Zhu
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Xiaoman Liu
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Fei Zhao
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Di Zhang
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Shan Cen
- 2 Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Chen Liang
- 3 McGill University AIDS Centre , Lady Davis Institute, Jewish General Hospital, Montreal, Canada
| | - Fei Guo
- 1 MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Center for AIDS Research, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
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170
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Dampier W, Sullivan NT, Mell JC, Pirrone V, Ehrlich GD, Chung CH, Allen AG, DeSimone M, Zhong W, Kercher K, Passic S, Williams JW, Szep Z, Khalili K, Jacobson JM, Nonnemacher MR, Wigdahl B. Broad-Spectrum and Personalized Guide RNAs for CRISPR/Cas9 HIV-1 Therapeutics. AIDS Res Hum Retroviruses 2018; 34:950-960. [PMID: 29968495 PMCID: PMC6238604 DOI: 10.1089/aid.2017.0274] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas9 system has been used to excise the HIV-1 proviral genome from latently infected cells, potentially offering a cure for HIV-infected patients. Recent studies have shown that most published HIV-1 guide RNAs (gRNAs) do not account for the diverse viral quasispecies within or among patients, which continue to diversify with time even in long-term antiretroviral therapy (ART)-suppressed patients. Given this observation, proviral genomes were deep sequenced from 23 HIV-1-infected patients in the Drexel Medicine CNS AIDS Research and Eradication Study cohort at two different visits. Based on the spectrum of integrated proviral DNA polymorphisms observed, three gRNA design strategies were explored: based on the patient's own HIV-1 sequences (personalized), based on consensus sequences from a large sample of patients [broad-spectrum (BS)], or a combination of both approaches. Using a bioinformatic algorithm, the personalized gRNA design was predicted to cut 46 of 48 patient samples at 90% efficiency, whereas the top 4 BS gRNAs (BS4) were predicted to excise provirus from 44 of 48 patient samples with 90% efficiency. Using a mixed design with the top three BS gRNAs plus one personalized gRNA (BS3 + PS1) resulted in predicted excision of provirus from 45 of 48 patient samples with 90% efficiency. In summary, these studies used an algorithmic design strategy to identify potential BS gRNAs to target a spectrum of HIV-1 long teriminal repeat (LTR) quasispecies for use with a small HIV-1-infected population. This approach should advance CRISPR/Cas9 excision technology taking into account the extensive molecular heterogeneity of HIV-1 that persists in situ after prolonged ART.
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Affiliation(s)
- Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, Pennsylvania
| | - Neil T. Sullivan
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Joshua Chang Mell
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Vanessa Pirrone
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Garth D. Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Otolaryngology—Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Cheng-Han Chung
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Alexander G. Allen
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Mathew DeSimone
- School of Biomedical Engineering, Science, and Health Systems, Drexel University, Philadelphia, Pennsylvania
| | - Wen Zhong
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Katherine Kercher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Shendra Passic
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Jean W. Williams
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Zsofia Szep
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Clinical and Translational Medicine, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Kamel Khalili
- Department of Neuroscience, Center for Neurovirology, and Comprehensive NeuroAIDS Center, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
- Center for Translational AIDS Research, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Jeffrey M. Jacobson
- Department of Neuroscience, Center for Neurovirology, and Comprehensive NeuroAIDS Center, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
- Center for Translational AIDS Research, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
- Section of Infectious Disease, Department of Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania
| | - Michael R. Nonnemacher
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Center for Molecular Virology and Translational Neuroscience, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
- Center for Clinical and Translational Medicine, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, Pennsylvania
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171
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Guo T, Feng YL, Xiao JJ, Liu Q, Sun XN, Xiang JF, Kong N, Liu SC, Chen GQ, Wang Y, Dong MM, Cai Z, Lin H, Cai XJ, Xie AY. Harnessing accurate non-homologous end joining for efficient precise deletion in CRISPR/Cas9-mediated genome editing. Genome Biol 2018; 19:170. [PMID: 30340517 PMCID: PMC6195759 DOI: 10.1186/s13059-018-1518-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/25/2018] [Indexed: 11/25/2022] Open
Abstract
Background Many applications of CRISPR/Cas9-mediated genome editing require Cas9-induced non-homologous end joining (NHEJ), which was thought to be error prone. However, with directly ligatable ends, Cas9-induced DNA double strand breaks may be repaired preferentially by accurate NHEJ. Results In the repair of two adjacent double strand breaks induced by paired Cas9-gRNAs at 71 genome sites, accurate NHEJ accounts for about 50% of NHEJ events. This paired Cas9-gRNA approach underestimates the level of accurate NHEJ due to frequent + 1 templated insertions, which can be avoided by the predefined Watson/Crick orientation of protospacer adjacent motifs (PAMs). The paired Cas9-gRNA strategy also provides a flexible, reporter-less approach for analyzing both accurate and mutagenic NHEJ in cells and in vivo, and it has been validated in cells deficient for XRCC4 and in mouse liver. Due to high frequencies of precise deletions of defined “3n”-, “3n + 1”-, or “3n + 2”-bp length, accurate NHEJ is used to improve the efficiency and homogeneity of gene knockouts and targeted in-frame deletions. Compared to “3n + 1”-bp, “3n + 2”-bp can overcome + 1 templated insertions to increase the frequency of out-of-frame mutations. By applying paired Cas9-gRNAs to edit MDC1 and key 53BP1 domains, we are able to generate predicted, precise deletions for functional analysis. Lastly, a Plk3 inhibitor promotes NHEJ with bias towards accurate NHEJ, providing a chemical approach to improve genome editing requiring precise deletions. Conclusions NHEJ is inherently accurate in repair of Cas9-induced DNA double strand breaks and can be harnessed to improve CRISPR/Cas9 genome editing requiring precise deletion of a defined length. Electronic supplementary material The online version of this article (10.1186/s13059-018-1518-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tao Guo
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Yi-Li Feng
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Jing-Jing Xiao
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Qian Liu
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Xiu-Na Sun
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Ji-Feng Xiang
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China.,Department of General Surgery, Chongqing General Hospital, Chongqing, 400013, China
| | - Na Kong
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Si-Cheng Liu
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Guo-Qiao Chen
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Yue Wang
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China
| | - Meng-Meng Dong
- Multiple Myeloma Treatment Center & Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310003, Hangzhou, China
| | - Zhen Cai
- Multiple Myeloma Treatment Center & Bone Marrow Transplantation Center, The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, 310003, Hangzhou, China
| | - Hui Lin
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China
| | - Xiu-Jun Cai
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China.
| | - An-Yong Xie
- Department of General Surgery, Innovation Center for Minimally Invasive Techniques and Devices, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Zhejiang, 310019, Hangzhou, China. .,Institute of Translational Medicine, Zhejiang University School of Medicine, Zhejiang, 310029, Hangzhou, China.
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172
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Oh SA, Seki A, Rutz S. Ribonucleoprotein Transfection for CRISPR/Cas9-Mediated Gene Knockout in Primary T Cells. ACTA ACUST UNITED AC 2018; 124:e69. [PMID: 30334617 DOI: 10.1002/cpim.69] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
CRISPR/Cas9 has enabled the rapid and efficient generation of gene knockouts across various cell types of several species. T cells are central players in adaptive immune responses. Gene editing in primary T cells not only represents a valuable research tool, but is also critical for next generation immunotherapies, such as CAR T cells. Broad application of CRIPSR/Cas9 for gene editing in primary T cells has been hampered by limitations in transfection efficiency and the requirement for TCR stimulation. In this article, we provide a detailed protocol for Cas9/gRNA ribonucleoprotein (RNP) transfection of primary mouse and human T cells without the need for TCR stimulation that achieves near complete loss of target gene expression at the population level. This approach enables rapid target discovery and validation in both mouse and human primary T cells. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Soyoung A Oh
- Department of Cancer Immunology, Genentech, South San Francisco, California
| | - Akiko Seki
- Department of Cancer Immunology, Genentech, South San Francisco, California
| | - Sascha Rutz
- Department of Cancer Immunology, Genentech, South San Francisco, California
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173
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Gilani U, Shaukat M, Rasheed A, Shahid M, Tasneem F, Arshad M, Rashid N, Shahzad N. The implication of CRISPR/Cas9 genome editing technology in combating human oncoviruses. J Med Virol 2018; 91:1-13. [PMID: 30133783 DOI: 10.1002/jmv.25292] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/31/2018] [Indexed: 12/23/2022]
Abstract
It is evidenced that 20% of all tumors in humans are caused by oncoviruses, including human papilloma viruses, Epstein-Barr virus, Kaposi sarcoma virus, human polyomaviruses, human T-lymphotrophic virus-1, and hepatitis B and C viruses. Human immunodeficiency virus is also involved in carcinogenesis, although not directly, but by facilitating the infection of many oncoviruses through compromising the immune system. Being intracellular parasites with the property of establishing latency and integrating into the host genome, these viruses are a therapeutic challenge for biomedical researchers. Therefore, strategies able to target nucleotide sequences within episomal or integrated viral genomes are of prime importance in antiviral or anticancerous armamentarium. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) has emerged as a powerful genome editing tool. Standing out as a precise and efficient oncoviruses method, it has been extensively applied in recent experimental ventures in the field of molecular medicine, particularly in combating infections including tumor inducing viruses. This review is aimed at collating the experimental and clinical advances in CRISPR/Cas9 technology in terms of its applications against oncoviruses. Primarily, it will focus on the application of CRISPR/Cas9 in combating tumor viruses, types of mechanisms targeted, and the significant outcomes till date. The technical pitfalls of the CRISPR/Cas9 and the comparative approaches in evaluating this technique with respect to other available alternatives are also described briefly. Furthermore, the review also discussed the clinical aspects and the ethical, legal, and social issues associated with the use of CRISPR/Cas9.
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Affiliation(s)
- Usman Gilani
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Memoona Shaukat
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Arisha Rasheed
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Mehak Shahid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Fareeda Tasneem
- Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Arshad
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Naveed Shahzad
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
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174
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Tsai YT, Wu WH, Lee TT, Wu WP, Xu CL, Park KS, Cui X, Justus S, Lin CS, Jauregui R, Su PY, Tsang SH. Clustered Regularly Interspaced Short Palindromic Repeats-Based Genome Surgery for the Treatment of Autosomal Dominant Retinitis Pigmentosa. Ophthalmology 2018; 125:1421-1430. [PMID: 29759820 PMCID: PMC6109419 DOI: 10.1016/j.ophtha.2018.04.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 03/29/2018] [Accepted: 04/02/2018] [Indexed: 01/02/2023] Open
Abstract
PURPOSE To develop a universal gene therapy to overcome the genetic heterogeneity in retinitis pigmentosa (RP) resulting from mutations in rhodopsin (RHO). DESIGN Experimental study for a combination gene therapy that uses both gene ablation and gene replacement. PARTICIPANTS This study included 2 kinds of human RHO mutation knock-in mouse models: RhoP23H and RhoD190N. In total, 23 RhoP23H/P23H, 43 RhoP23H/+, and 31 RhoD190N/+ mice were used for analysis. METHODS This study involved gene therapy using dual adeno-associated viruses (AAVs) that (1) destroy expression of the endogenous Rho gene in a mutation-independent manner via an improved clustered regularly interspaced short palindromic repeats-based gene deletion and (2) enable expression of wild-type protein via exogenous cDNA. MAIN OUTCOME MEASURES Electroretinographic and histologic analysis. RESULTS The thickness of the outer nuclear layer (ONL) after the subretinal injection of combination ablate-and-replace gene therapy was approximately 17% to 36% more than the ONL thickness resulting from gene replacement-only therapy at 3 months after AAV injection. Furthermore, electroretinography results demonstrated that the a and b waves of both RhoP23H and RhoD190N disease models were preserved more significantly using ablate-and-replace gene therapy (P < 0.001), but not by gene replacement monotherapy. CONCLUSIONS As a proof of concept, our results suggest that the ablate-and-replace strategy can ameliorate disease progression as measured by photoreceptor structure and function for both of the human mutation knock-in models. These results demonstrate the potency of the ablate-and-replace strategy to treat RP caused by different Rho mutations. Furthermore, because ablate-and-replace treatment is mutation independent, this strategy may be used to treat a wide array of dominant diseases in ophthalmology and other fields. Clinical trials using ablate-and-replace gene therapy would allow researchers to determine if this strategy provides any benefits for patients with diseases of interest.
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Affiliation(s)
- Yi-Ting Tsai
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, New York; Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Wen-Hsuan Wu
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, New York
| | - Ting-Ting Lee
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, New York
| | - Wei-Pu Wu
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, New York
| | - Christine L Xu
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, New York
| | - Karen S Park
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, New York
| | - Xuan Cui
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, New York
| | - Sally Justus
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, New York
| | - Chyuan-Sheng Lin
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York
| | - Ruben Jauregui
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, New York; Weill Cornell Medical College, New York, New York
| | - Pei-Yin Su
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, New York
| | - Stephen H Tsang
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Departments of Ophthalmology, Pathology and Cell Biology, Columbia University, New York, New York; Institute of Human Nutrition, College of Physicians and Surgeons, Columbia University, New York, New York; Department of Ophthalmology, Edward S. Harkness Eye Institute, New York Presbyterian Hospital, New York, New York.
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175
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Luther D, Lee Y, Nagaraj H, Scaletti F, Rotello V. Delivery approaches for CRISPR/Cas9 therapeutics in vivo: advances and challenges. Expert Opin Drug Deliv 2018; 15:905-913. [PMID: 30169977 PMCID: PMC6295289 DOI: 10.1080/17425247.2018.1517746] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/24/2018] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Therapeutic gene editing is becoming a viable biomedical tool with the emergence of the CRISPR/Cas9 system. CRISPR-based technologies have promise as a therapeutic platform for many human genetic diseases previously considered untreatable, providing a flexible approach to high-fidelity gene editing. For many diseases, such as sickle-cell disease and beta thalassemia, curative therapy may already be on the horizon, with CRISPR-based clinical trials slated for the next few years. Translation of CRISPR-based therapy to in vivo application however, is no small feat, and major hurdles remain for efficacious use of the CRISPR/Cas9 system in clinical contexts. AREAS COVERED In this topical review, we highlight recent advances to in vivo delivery of the CRISPR/Cas9 system using various packaging formats, including viral, mRNA, plasmid, and protein-based approaches. We also discuss some of the barriers which have yet to be overcome for successful translation of this technology. EXPERT OPINION This review focuses on the challenges to efficacy for various delivery formats, with specific emphasis on overcoming these challenges through the development of carrier vehicles for transient approaches to CRISPR/Cas9 delivery in vivo.
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Affiliation(s)
- D.C. Luther
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - Y.W. Lee
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - H. Nagaraj
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
- School of Chemical and Biotechnology, Sastra Deemed-to-be University, Tirumalaisamudram, Thanjavur 613 401,Tamil Nadu, India
| | - F. Scaletti
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
| | - V.M. Rotello
- Department of Chemistry, University of Massachusetts Amherst, 710 North Pleasant Street, Amherst, Massachusetts 01003, United States
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176
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Abstract
Programmable nucleases including zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein have tremendous potential biological and therapeutic applications as novel genome editing tools. These nucleases enable precise modification of the gene of interest by disruption, insertion, or correction. The application of genome editing technology to pluripotent stem cells or hematopoietic stem cells has the potential to remarkably advance the contribution of this technology to life sciences. Specifically, disease models can be generated and effective therapeutics can be developed with great efficiency and speed. Here we review the characteristics and mechanisms of each programmable nuclease. In addition, we review the applications of these nucleases to stem cells for disease therapies and summarize key studies of interest.
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Affiliation(s)
- Minjung Song
- Department of Food Biotechnology, College of Medical and Life Science, Silla University, Busan, South Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea. .,College of Medicine, Hanyang University, Seoul, South Korea.
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177
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Sürün D, von Melchner H, Schnütgen F. CRISPR/Cas9 genome engineering in hematopoietic cells. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 28:33-39. [PMID: 30205879 DOI: 10.1016/j.ddtec.2018.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/17/2018] [Accepted: 08/08/2018] [Indexed: 12/12/2022]
Abstract
The development of genome editing tools capable of modifying specific genomic sequences with unprecedented accuracy has opened up a wide range of new possibilities in targeted gene manipulation. In particular, the CRISPR/Cas9 system, a repurposed prokaryotic adaptive immune system, has been widely adopted because of its unmatched simplicity and flexibility. In this review we discuss achievements and current limitations of CRISPR/Cas9 genome editing in hematopoietic cells with special emphasis on its potential use in ex vivo gene therapy of monogenic blood disorders, HIV and cancer.
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Affiliation(s)
- Duran Sürün
- Department of Molecular Hematology and LOEWE Center for Cell and Gene Therapy, Goethe University Medical School, 60590 Frankfurt am Main, Germany; Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, Fetscherstr. 74, 01307 Dresden, Germany.
| | - Harald von Melchner
- Department of Molecular Hematology and LOEWE Center for Cell and Gene Therapy, Goethe University Medical School, 60590 Frankfurt am Main, Germany
| | - Frank Schnütgen
- Department of Molecular Hematology and LOEWE Center for Cell and Gene Therapy, Goethe University Medical School, 60590 Frankfurt am Main, Germany.
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178
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Stewart MP, Langer R, Jensen KF. Intracellular Delivery by Membrane Disruption: Mechanisms, Strategies, and Concepts. Chem Rev 2018; 118:7409-7531. [PMID: 30052023 PMCID: PMC6763210 DOI: 10.1021/acs.chemrev.7b00678] [Citation(s) in RCA: 382] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intracellular delivery is a key step in biological research and has enabled decades of biomedical discoveries. It is also becoming increasingly important in industrial and medical applications ranging from biomanufacture to cell-based therapies. Here, we review techniques for membrane disruption-based intracellular delivery from 1911 until the present. These methods achieve rapid, direct, and universal delivery of almost any cargo molecule or material that can be dispersed in solution. We start by covering the motivations for intracellular delivery and the challenges associated with the different cargo types-small molecules, proteins/peptides, nucleic acids, synthetic nanomaterials, and large cargo. The review then presents a broad comparison of delivery strategies followed by an analysis of membrane disruption mechanisms and the biology of the cell response. We cover mechanical, electrical, thermal, optical, and chemical strategies of membrane disruption with a particular emphasis on their applications and challenges to implementation. Throughout, we highlight specific mechanisms of membrane disruption and suggest areas in need of further experimentation. We hope the concepts discussed in our review inspire scientists and engineers with further ideas to improve intracellular delivery.
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Affiliation(s)
- Martin P. Stewart
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Klavs F. Jensen
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
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179
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Lee JK, Jeong E, Lee J, Jung M, Shin E, Kim YH, Lee K, Jung I, Kim D, Kim S, Kim JS. Directed evolution of CRISPR-Cas9 to increase its specificity. Nat Commun 2018; 9:3048. [PMID: 30082838 PMCID: PMC6078992 DOI: 10.1038/s41467-018-05477-x] [Citation(s) in RCA: 296] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/09/2018] [Indexed: 12/26/2022] Open
Abstract
The use of CRISPR-Cas9 as a therapeutic reagent is hampered by its off-target effects. Although rationally designed S. pyogenes Cas9 (SpCas9) variants that display higher specificities than the wild-type SpCas9 protein are available, these attenuated Cas9 variants are often poorly efficient in human cells. Here, we develop a directed evolution approach in E. coli to obtain Sniper-Cas9, which shows high specificities without killing on-target activities in human cells. Unlike other engineered Cas9 variants, Sniper-Cas9 shows WT-level on-target activities with extended or truncated sgRNAs with further reduced off-target activities and works well in a preassembled ribonucleoprotein (RNP) format to allow DNA-free genome editing.
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Affiliation(s)
| | - Euihwan Jeong
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, 34121, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | | | | | - Eunji Shin
- Toolgen, Seoul, 08501, Republic of Korea
| | | | - Kangin Lee
- Toolgen, Seoul, 08501, Republic of Korea
| | | | - Daesik Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | | | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, 34121, Republic of Korea.
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea.
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180
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Ewart DT, Peterson EJ, Steer CJ. Gene editing for inflammatory disorders. Ann Rheum Dis 2018; 78:6-15. [PMID: 30077989 DOI: 10.1136/annrheumdis-2018-213454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/02/2018] [Accepted: 07/03/2018] [Indexed: 12/24/2022]
Abstract
Technology for precise and efficient genetic editing is constantly evolving and is now capable of human clinical applications. Autoimmune and inflammatory diseases are chronic, disabling, sometimes life-threatening, conditions that feature heritable components. Both primary genetic lesions and the inflammatory pathobiology underlying these diseases represent fertile soil for new therapies based on the capabilities of gene editing. The ability to orchestrate precise targeted modifications to the genome will likely enable cell-based therapies for inflammatory diseases such as monogenic autoinflammatory disease, acquired autoimmune disease and for regenerative medicine in the setting of an inflammatory environment. Here, we discuss recent advances in genome editing and their evolving applications in immunoinflammatory diseases. Strengths and limitations of older genetic modification tools are compared with CRISPR/Cas9, base editing, RNA editing, targeted activators and repressors of transcription and targeted epigenetic modifiers. Commonly employed delivery vehicles to target cells or tissues of interest with genetic modification machinery, including viral, non-viral and cellular vectors, are described. Finally, applications in animal and human models of inflammatory diseases are discussed. Use of chimeric autoantigen receptor T cells, correction of monogenic diseases with genetically edited haematopoietic stem and progenitor cells, engineering of induced pluripotent stem cells and ex vivo expansion and modification of regulatory T cells for a range of chronic inflammatory diseases are reviewed.
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Affiliation(s)
- David T Ewart
- Division of Rheumatic and Autoimmune Diseases, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Erik J Peterson
- Division of Rheumatic and Autoimmune Diseases, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Clifford J Steer
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minnesota, USA.,Department of Genetics, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, Minnesota, USA
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181
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Xu X, Gao D, Wang P, Chen J, Ruan J, Xu J, Xia X. Efficient homology-directed gene editing by CRISPR/Cas9 in human stem and primary cells using tube electroporation. Sci Rep 2018; 8:11649. [PMID: 30076383 PMCID: PMC6076306 DOI: 10.1038/s41598-018-30227-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 07/20/2018] [Indexed: 12/30/2022] Open
Abstract
CRISPR/Cas9 efficiently generates gene knock-out via nonhomologous end joining (NHEJ), but the efficiency of precise homology-directed repair (HDR) is substantially lower, especially in the hard-to-transfect human stem cells and primary cells. Herein we report a tube electroporation method that can effectively transfect human stem cells and primary cells with minimal cytotoxicity. When applied to genome editing using CRISPR/Cas9 along with single stranded DNA oligonucleotide (ssODN) template in human induced pluripotent stem cells (iPSCs), up to 42.1% HDR rate was achieved, drastically higher than many reported before. We demonstrated that the high HDR efficiency can be utilized to increase the gene ablation rate in cells relevant to clinical applications, by knocking-out β2-microglobulin (B2M) in primary human mesenchymal stem cells (MSCs, 37.3% to 80.2%), and programmed death-1 (PD-1) in primary human T cells (42.6% to 58.6%). Given the generality and efficiency, we expect that the method will have immediate impacts in cell research as well as immuno- and transplantation therapies.
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Affiliation(s)
- Xiaoyun Xu
- Chao Center for BRAIN, Department of Systems Medicine and Bioengineering, Houston Methodist Research Institute, Houston, Texas, USA
| | - Dongbing Gao
- Chao Center for BRAIN, Department of Systems Medicine and Bioengineering, Houston Methodist Research Institute, Houston, Texas, USA
| | - Ping Wang
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jian Chen
- Celetrix Biotechnologies, Manassas, Virginia, USA
| | - Jinxue Ruan
- Center for Advanced Models and Translational Sciences and Therapeutics, University of Michigan Medical School, Ann Arbor, MI, 48109-2800, USA
| | - Jie Xu
- Center for Advanced Models and Translational Sciences and Therapeutics, University of Michigan Medical School, Ann Arbor, MI, 48109-2800, USA.
| | - Xiaofeng Xia
- Chao Center for BRAIN, Department of Systems Medicine and Bioengineering, Houston Methodist Research Institute, Houston, Texas, USA.
- Weill Cornell Medical College, Cornell University, New York, New York, USA.
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182
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Lampreht Tratar U, Horvat S, Cemazar M. Transgenic Mouse Models in Cancer Research. Front Oncol 2018; 8:268. [PMID: 30079312 PMCID: PMC6062593 DOI: 10.3389/fonc.2018.00268] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/29/2018] [Indexed: 12/26/2022] Open
Abstract
The use of existing mouse models in cancer research is of utmost importance as they aim to explore the casual link between candidate cancer genes and carcinogenesis as well as to provide models to develop and test new therapies. However, faster progress in translating mouse cancer model research into the clinic has been hampered due to the limitations of these models to better reflect the complexities of human tumors. Traditionally, immunocompetent and immunodeficient mice with syngeneic and xenografted tumors transplanted subcutaneously or orthotopically have been used. These models are still being widely employed for many different types of studies, in part due to their widespread availability and low cost. Other types of mouse models used in cancer research comprise transgenic mice in which oncogenes can be constitutively or conditionally expressed and tumor-suppressor genes silenced using conventional methods, such as retroviral infection, microinjection of DNA constructs, and the so-called "gene-targeted transgene" approach. These traditional transgenic models have been very important in studies of carcinogenesis and tumor pathogenesis, as well as in studies evaluating the development of resistance to therapy. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing approach has revolutionized the field of mouse cancer models and has had a profound and rapid impact on the development of more effective systems to study human cancers. The CRISPR/Cas9-based transgenic models have the capacity to engineer a wide spectrum of mutations found in human cancers and provide solutions to problems that were previously unsolvable. Recently, humanized mouse xenograft models that accept patient-derived xenografts and CD34+ cells were developed to better mimic tumor heterogeneity, the tumor microenvironment, and cross-talk between the tumor and stromal/immune cells. These features make them extremely valuable models for the evaluation of investigational cancer therapies, specifically new immunotherapies. Taken together, improvements in both the CRISPR/Cas9 system producing more valid mouse models and in the humanized mouse xenograft models resembling complex interactions between the tumor and its environment might represent one of the successful pathways to precise individualized cancer therapy, leading to improved cancer patient survival and quality of life.
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Affiliation(s)
- Ursa Lampreht Tratar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Simon Horvat
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Cemazar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia.,Faculty of Health Sciences, University of Primorska, Isola, Slovenia
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183
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Razzouk S. CRISPR-Cas9: A cornerstone for the evolution of precision medicine. Ann Hum Genet 2018; 82:331-357. [PMID: 30014471 DOI: 10.1111/ahg.12271] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/04/2018] [Accepted: 06/13/2018] [Indexed: 12/20/2022]
Abstract
Modern genetic therapy incorporates genomic testing and genome editing. It is the finest approach for precision medicine. Genome editing is a state-of-the-art technology to manipulate gene expression thus generating a particular genotype. It encompasses multiple programmable nuclease-based approaches leading to genetic changes. Not surprisingly, this method triggered internationally a wide array of controversies in the scientific community and in the public since it transforms the human genome. Given its importance, the pace of this technology is exceptionally fast. In this report, we introduce one aspect of genome editing, the CRISPR/Cas9 system, highlight its potential to correct genetic mutations and explore its utility in clinical setting. Our goal is to enlighten health care providers about genome editing and incite them to take part of this vital debate.
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Affiliation(s)
- Sleiman Razzouk
- Adjunct Faculty, Department of Periodontology and Implant Dentistry, New York University College of Dentistry, New York.,Private Practice, Beirut, Lebanon
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184
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CCR5 Revisited: How Mechanisms of HIV Entry Govern AIDS Pathogenesis. J Mol Biol 2018; 430:2557-2589. [PMID: 29932942 DOI: 10.1016/j.jmb.2018.06.027] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/10/2018] [Accepted: 06/13/2018] [Indexed: 01/01/2023]
Abstract
The chemokine receptor CCR5 has been the focus of intensive studies since its role as a coreceptor for HIV entry was discovered in 1996. These studies lead to the development of small molecular drugs targeting CCR5, with maraviroc becoming in 2007 the first clinically approved chemokine receptor inhibitor. More recently, the apparent HIV cure in a patient transplanted with hematopoietic stem cells devoid of functional CCR5 rekindled the interest for inactivating CCR5 through gene therapy and pharmacological approaches. Fundamental research on CCR5 has also been boosted by key advances in the field of G-protein coupled receptor research, with the realization that CCR5 adopts a variety of conformations, and that only a subset of these conformations may be targeted by chemokine ligands. In addition, recent genetic and pathogenesis studies have emphasized the central role of CCR5 expression levels in determining the risk of HIV and SIV acquisition and disease progression. In this article, we propose to review the key properties of CCR5 that account for its central role in HIV pathogenesis, with a focus on mechanisms that regulate CCR5 expression, conformation, and interaction with HIV envelope glycoproteins.
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185
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Huang CH, Lee KC, Doudna JA. Applications of CRISPR-Cas Enzymes in Cancer Therapeutics and Detection. Trends Cancer 2018; 4:499-512. [PMID: 29937048 PMCID: PMC6299457 DOI: 10.1016/j.trecan.2018.05.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 12/22/2022]
Abstract
Cancer is a complex disease caused by combinations of cellular genetic alterations and heterogeneous microenvironments. The use of the robust and programmable CRISPR-Cas systems has greatly improved genome editing for precision cancer modeling and enabled multiplexed genetic manipulation for cancer treatment and mutation detection. In this review, we outline the current CRISPR-Cas toolkit, and discuss the promises and hurdles in translating this revolutionary technology into effective and safe clinical applications for cancer treatment and diagnosis.
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Affiliation(s)
- Chun-Hao Huang
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Ko-Chuan Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
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186
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Chandrasekaran AP, Song M, Kim KS, Ramakrishna S. Different Methods of Delivering CRISPR/Cas9 Into Cells. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 159:157-176. [PMID: 30340786 DOI: 10.1016/bs.pmbts.2018.05.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas) is comprised of repetitive bases followed by short fragments of DNA from a previously invading organism that provide immunity to the most prokaryotic organisms. An RNA-dependent spacer is required for CRISPR/Cas9 to recognize the target DNA. Delivery of the CRISPR/Cas9-guide RNA (gRNA) complex to any cell results in modification of the target sequence. The CRISPR/Cas9-mediated genome editing technique is currently in the spotlight and has several research interests, including molecular medicine and agriculture. There are several factors that hinder the delivery of this complex, such as the large size of the plasmid or high dosage of the chemical agent. There are several methods available to deliver CRISPR/Cas9 and its components to the target cells. It includes viral, non-viral and physical methods to deliver plasmid or ribonucleoprotein (RNP) of CRISPR components. But in vivo CRISPR/Cas9 delivery remains challenging to the researchers due to insertional mutagenesis, targeted delivery, immunogenicity, and off-targets. However, studies suggesting that the CRISPR/Cas9-RNP delivery can overcome these hurdles. Here, we review the various methods for delivery of CRISPR/Cas9 and gRNA to several cell lines, highlighting the limitations of each approach, and suggest possible alternative methods.
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Affiliation(s)
| | - Minjung Song
- Department of Food Biotechnology, College of Medical and Life Science, Silla University, Seoul, South Korea
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul, South Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul, South Korea.
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187
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Tothova Z, Krill-Burger JM, Popova KD, Landers CC, Sievers QL, Yudovich D, Belizaire R, Aster JC, Morgan EA, Tsherniak A, Ebert BL. Multiplex CRISPR/Cas9-Based Genome Editing in Human Hematopoietic Stem Cells Models Clonal Hematopoiesis and Myeloid Neoplasia. Cell Stem Cell 2018; 21:547-555.e8. [PMID: 28985529 DOI: 10.1016/j.stem.2017.07.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/18/2017] [Accepted: 07/30/2017] [Indexed: 12/01/2022]
Abstract
Hematologic malignancies are driven by combinations of genetic lesions that have been difficult to model in human cells. We used CRISPR/Cas9 genome engineering of primary adult and umbilical cord blood CD34+ human hematopoietic stem and progenitor cells (HSPCs), the cells of origin for myeloid pre-malignant and malignant diseases, followed by transplantation into immunodeficient mice to generate genetic models of clonal hematopoiesis and neoplasia. Human hematopoietic cells bearing mutations in combinations of genes, including cohesin complex genes, observed in myeloid malignancies generated immunophenotypically defined neoplastic clones capable of long-term, multi-lineage reconstitution and serial transplantation. Employing these models to investigate therapeutic efficacy, we found that TET2 and cohesin-mutated hematopoietic cells were sensitive to azacitidine treatment. These findings demonstrate the potential for generating genetically defined models of human myeloid diseases, and they are suitable for examining the biological consequences of somatic mutations and the testing of therapeutic agents.
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Affiliation(s)
- Zuzana Tothova
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA; Division of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Katerina D Popova
- Division of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Catherine C Landers
- Division of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Quinlan L Sievers
- Division of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | - David Yudovich
- Division of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Roger Belizaire
- Division of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Elizabeth A Morgan
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Aviad Tsherniak
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA; Division of Hematology, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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188
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Cornel AM, van Til NP, Boelens JJ, Nierkens S. Strategies to Genetically Modulate Dendritic Cells to Potentiate Anti-Tumor Responses in Hematologic Malignancies. Front Immunol 2018; 9:982. [PMID: 29867960 PMCID: PMC5968097 DOI: 10.3389/fimmu.2018.00982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/20/2018] [Indexed: 12/12/2022] Open
Abstract
Dendritic cell (DC) vaccination has been investigated as a potential strategy to target hematologic malignancies, while generating sustained immunological responses to control potential future relapse. Nonetheless, few clinical trials have shown robust long-term efficacy. It has been suggested that a combination of surmountable shortcomings, such as selection of utilized DC subsets, DC loading and maturation strategies, as well as tumor-induced immunosuppression may be targeted to maximize anti-tumor responses of DC vaccines. Generation of DC from CD34+ hematopoietic stem and progenitor cells (HSPCs) may provide potential in patients undergoing allogeneic HSPC transplantations for hematologic malignancies. CD34+ HSPC from the graft can be genetically modified to optimize antigen presentation and to provide sufficient T cell stimulatory signals. We here describe beneficial (gene)-modifications that can be implemented in various processes in T cell activation by DC, among which major histocompatibility complex (MHC) class I and MHC class II presentation, DC maturation and migration, cross-presentation, co-stimulation, and immunosuppression to improve anti-tumor responses.
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Affiliation(s)
- Annelisa M Cornel
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Niek P van Til
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Jaap Jan Boelens
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands.,Pediatric Blood and Marrow Transplantation Program, University Medical Center Utrecht, Utrecht, Netherlands.,Blood and Marrow Transplantation Program, Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Stefan Nierkens
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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189
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Clonal expansion and myeloid leukemia progression modeled by multiplex gene editing of murine hematopoietic progenitor cells. Exp Hematol 2018; 64:33-44.e5. [PMID: 29751067 DOI: 10.1016/j.exphem.2018.04.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 01/22/2023]
Abstract
Recent advances in next-generation sequencing have identified novel mutations and revealed complex genetic architectures in human hematological malignancies. Moving forward, new methods to quickly generate animal models that recapitulate the complex genetics of human hematological disorders are needed to transform the genetic information to new therapies. Here, we used a ribonucleoprotein-based CRISPR/Cas9 system to model human clonal hematopoiesis of indeterminate potential and acute myeloid leukemia (AML). We edited multiple genes recurrently mutated in hematological disorders, including those encoding epigenetic regulators, transcriptional regulators, and signaling components in murine hematopoietic stem/progenitor cells. Tracking the clonal dynamics by sequencing the indels induced by CRISPR/Cas9 revealed clonal expansion in some recipient mice that progressed to AML initiated by leukemia-initiating cells. Our results establish that the CRISPR/Cas9-mediated multiplex mutagenesis can be used to engineer a variety of murine models of hematological malignancies with complex genetic architectures seen in human disease.
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190
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Singh K, Evens H, Nair N, Rincón MY, Sarcar S, Samara-Kuko E, Chuah MK, VandenDriessche T. Efficient In Vivo Liver-Directed Gene Editing Using CRISPR/Cas9. Mol Ther 2018; 26:1241-1254. [PMID: 29599079 PMCID: PMC5993986 DOI: 10.1016/j.ymthe.2018.02.023] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/21/2018] [Accepted: 02/21/2018] [Indexed: 12/14/2022] Open
Abstract
In vivo tissue-specific genome editing at the desired loci is still a challenge. Here, we report that AAV9-delivery of truncated guide RNAs (gRNAs) and Cas9 under the control of a computationally designed hepatocyte-specific promoter lead to liver-specific and sequence-specific targeting in the mouse factor IX (F9) gene. The efficiency of in vivo targeting was assessed by T7E1 assays, site-specific Sanger sequencing, and deep sequencing of on-target and putative off-target sites. Though AAV9 transduction was apparent in multiple tissues and organs, Cas9 expression was restricted mainly to the liver, with only minimal or no expression in other non-hepatic tissues. Consequently, the insertions and deletion (indel) frequency was robust in the liver (up to 50%) in the desired target loci of the F9 gene, with no evidence of targeting in other organs or other putative off-target sites. This resulted in a substantial loss of FIX activity and the emergence of a bleeding phenotype, consistent with hemophilia B. The in vivo efficacy of the truncated gRNA was as high as that of full-length gRNA. Cas9 expression was transient in neonates, representing an attractive "hit-and-run" paradigm. Our findings have potentially broad implications for somatic gene targeting in the liver using the CRISPR/Cas9 platform.
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Affiliation(s)
- Kshitiz Singh
- Department of Gene Therapy and Regenerative Medicine, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Hanneke Evens
- Department of Gene Therapy and Regenerative Medicine, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Nisha Nair
- Department of Gene Therapy and Regenerative Medicine, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Melvin Y Rincón
- Department of Gene Therapy and Regenerative Medicine, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium; Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, 3000 Leuven, Belgium; Centro de Investigaciones, Fundacion Cardiovascular de Colombia, 681004 Floridablanca, Colombia
| | - Shilpita Sarcar
- Department of Gene Therapy and Regenerative Medicine, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Ermira Samara-Kuko
- Department of Gene Therapy and Regenerative Medicine, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium
| | - Marinee K Chuah
- Department of Gene Therapy and Regenerative Medicine, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium; Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, 3000 Leuven, Belgium.
| | - Thierry VandenDriessche
- Department of Gene Therapy and Regenerative Medicine, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), 1090 Brussels, Belgium; Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, 3000 Leuven, Belgium.
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191
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Brunetti L, Gundry MC, Kitano A, Nakada D, Goodell MA. Highly Efficient Gene Disruption of Murine and Human Hematopoietic Progenitor Cells by CRISPR/Cas9. J Vis Exp 2018. [PMID: 29708546 PMCID: PMC5933422 DOI: 10.3791/57278] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Advances in the hematopoietic stem cell (HSCs) field have been aided by methods to genetically engineer primary progenitor cells as well as animal models. Complete gene ablation in HSCs required the generation of knockout mice from which HSCs could be isolated, and gene ablation in primary human HSCs was not possible. Viral transduction could be used for knock-down approaches, but these suffered from variable efficacy. In general, genetic manipulation of human and mouse hematopoietic cells was hampered by low efficiencies and extensive time and cost commitments. Recently, CRISPR/Cas9 has dramatically expanded the ability to engineer the DNA of mammalian cells. However, the application of CRISPR/Cas9 to hematopoietic cells has been challenging, mainly due to their low transfection efficiencies, the toxicity of plasmid-based approaches and the slow turnaround time of virus-based protocols. A rapid method to perform CRISPR/Cas9-mediated gene editing in murine and human hematopoietic stem and progenitor cells with knockout efficiencies of up to 90% is provided in this article. This approach utilizes a ribonucleoprotein (RNP) delivery strategy with a streamlined three-day workflow. The use of Cas9-sgRNA RNP allows for a hit-and-run approach, introducing no exogenous DNA sequences in the genome of edited cells and reducing off-target effects. The RNP-based method is fast and straightforward: it does not require cloning of sgRNAs, virus preparation or specific sgRNA chemical modification. With this protocol, scientists should be able to successfully generate knockouts of a gene of interest in primary hematopoietic cells within a week, including downtimes for oligonucleotide synthesis. This approach will allow a much broader group of users to adapt this protocol for their needs.
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Affiliation(s)
- Lorenzo Brunetti
- Stem Cells & Regenerative Medicine Center, Baylor College of Medicine; Center for Cell and Gene Therapy, Baylor College of Medicine; Centro di Ricerca Emato-Oncologica (CREO), University of Perugia
| | - Michael C Gundry
- Stem Cells & Regenerative Medicine Center, Baylor College of Medicine; Center for Cell and Gene Therapy, Baylor College of Medicine; Department of Molecular & Human Genetics, Baylor College of Medicine
| | - Ayumi Kitano
- Department of Molecular & Human Genetics, Baylor College of Medicine
| | - Daisuke Nakada
- Stem Cells & Regenerative Medicine Center, Baylor College of Medicine; Center for Cell and Gene Therapy, Baylor College of Medicine; Department of Molecular & Human Genetics, Baylor College of Medicine
| | - Margaret A Goodell
- Stem Cells & Regenerative Medicine Center, Baylor College of Medicine; Center for Cell and Gene Therapy, Baylor College of Medicine; Department of Molecular & Human Genetics, Baylor College of Medicine; Texas Children's Hospital & Houston Methodist Hospital;
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192
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Liang P, Zhang X, Chen Y, Huang J. Developmental history and application of CRISPR in human disease. J Gene Med 2018. [PMID: 28623876 DOI: 10.1002/jgm.2963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genome-editing tools are programmable artificial nucleases, mainly including zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeat (CRISPR). By recognizing and cleaving specific DNA sequences, genome-editing tools make it possible to generate site-specific DNA double-strand breaks (DSBs) in the genome. DSBs will then be repaired by either error-prone nonhomologous end joining or high-fidelity homologous recombination mechanisms. Through these two different mechanisms, endogenous genes can be knocked out or precisely repaired/modified. Rapid developments in genome-editing tools, especially CRISPR, have revolutionized human disease models generation, for example, various zebrafish, mouse, rat, pig, monkey and human cell lines have been constructed. Here, we review the developmental history of CRISPR and its application in studies of human diseases. In addition, we also briefly discussed the therapeutic application of CRISPR in the near future.
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Affiliation(s)
- Puping Liang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of G uangdong Province, The Third Affiliated Hospital, Guangzhou Medical University and School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiya Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuxi Chen
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Junjiu Huang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of G uangdong Province, The Third Affiliated Hospital, Guangzhou Medical University and School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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193
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Hochheiser K, Kueh AJ, Gebhardt T, Herold MJ. CRISPR/Cas9: A tool for immunological research. Eur J Immunol 2018; 48:576-583. [PMID: 29415333 DOI: 10.1002/eji.201747131] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 12/01/2017] [Accepted: 02/02/2018] [Indexed: 12/27/2022]
Abstract
The CRISPR/Cas9-system was originally identified as part of the adaptive immune system in bacteria and has since been adapted for the genetic manipulation of eukaryotic cells. The technique is of particular value for biomedical sciences, as it enables the genetic manipulation of cell lines and primary cells as well as whole organisms with unprecedented ease and efficiency. Furthermore, the CRISPR/Cas9-technology has the potential for future therapeutic applications in the clinic. Here, we discuss the use of CRISPR/Cas9 for the genetic modification of haematopoietic cells and the generation of mouse models for immunological research. Additionally, we explain how the technique can be applied as a screening-tool to identify genes involved in different immunological processes. Moreover, we will talk about recent extensions of using the CRISPR/Cas9 technology, such as a transcriptional activator or repressor. Finally, we discuss the first clinical trials that use CRISPR/Cas9 and discuss potential future applications.
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Affiliation(s)
- Katharina Hochheiser
- Department of Microbiology & Immunology, The University of Melbourne, the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Andrew J Kueh
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Thomas Gebhardt
- Department of Microbiology & Immunology, The University of Melbourne, the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Marco J Herold
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
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194
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McCreedy BJ, Senyukov VV, Nguyen KT. Off the shelf T cell therapies for hematologic malignancies. Best Pract Res Clin Haematol 2018; 31:166-175. [PMID: 29909917 DOI: 10.1016/j.beha.2018.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/02/2018] [Accepted: 03/08/2018] [Indexed: 10/17/2022]
Abstract
Adoptive transfer of autologous CAR-T cells can induce durable remissions in patients with relapsed/refractory hematologic malignancies. However, multiple challenges exist for manufacturing CAR-T cells from patients with advanced disease including inability to manufacture a product, disease progression or death while waiting for the CAR-T product to be available, and heterogeneity among autologous CAR-T products that contributes to unpredictable and variable clinical activity. Healthy donor T cells can provide a source for production of universal CAR-T cells when combined with gene editing to prevent expression of endogenous TCRs and avoid generation of GvHD in HLA mismatched recipients. Additional gene edits can be included to impart resistance to immunosuppression or improve trafficking to tumor sites. Recent advances in cell manufacturing and analytics technology can provide for consistent batch to batch manufacturing of gene edited allogeneic CAR-T cells in sufficient quantity to treat thousands of patients when needed as off the shelf products.
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Affiliation(s)
- Bruce J McCreedy
- Precision BioSciences, Inc., 302 East Pettigrew Street, Durham, NC 27701, USA.
| | - Vladimir V Senyukov
- Precision BioSciences, Inc., 302 East Pettigrew Street, Durham, NC 27701, USA.
| | - Kim T Nguyen
- Precision BioSciences, Inc., 302 East Pettigrew Street, Durham, NC 27701, USA.
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195
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Nerys-Junior A, Braga-Dias LP, Pezzuto P, Cotta-de-Almeida V, Tanuri A. Comparison of the editing patterns and editing efficiencies of TALEN and CRISPR-Cas9 when targeting the human CCR5 gene. Genet Mol Biol 2018; 41:167-179. [PMID: 29583154 PMCID: PMC5901495 DOI: 10.1590/1678-4685-gmb-2017-0065] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 06/07/2017] [Indexed: 01/02/2023] Open
Abstract
The human C-C chemokine receptor type-5 (CCR5) is the major transmembrane
co-receptor that mediates HIV-1 entry into target CD4+ cells. Gene therapy to
knock-out the CCR5 gene has shown encouraging results in providing a functional
cure for HIV-1 infection. In gene therapy strategies, the initial region of the
CCR5 gene is a hotspot for producing functional gene knock-out. Such target gene
editing can be done using programmable endonucleases such as transcription
activator-like effector nucleases (TALEN) or clustered regularly interspaced
short palindromic repeats (CRISPR-Cas9). These two gene editing approaches are
the most modern and effective tools for precise gene modification. However,
little is known of potential differences in the efficiencies of TALEN and
CRISPR-Cas9 for editing the beginning of the CCR5 gene. To examine which of
these two methods is best for gene therapy, we compared the patterns and amount
of editing at the beginning of the CCR5 gene using TALEN and CRISPR-Cas9
followed by DNA sequencing. This comparison revealed that CRISPR-Cas9 mediated
the sorting of cells that contained 4.8 times more gene editing than TALEN+
transfected cells.
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Affiliation(s)
- Arildo Nerys-Junior
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Luciene P Braga-Dias
- Laboratório do Serviço de Biotecnologia e Desenvolvimento Animal, Instituto de Ciência e Tecnologia em Biomodelos, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Paula Pezzuto
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | | | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
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196
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Seki A, Rutz S. Optimized RNP transfection for highly efficient CRISPR/Cas9-mediated gene knockout in primary T cells. J Exp Med 2018; 215:985-997. [PMID: 29436394 PMCID: PMC5839763 DOI: 10.1084/jem.20171626] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/20/2017] [Accepted: 01/18/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR (clustered, regularly interspaced, short palindromic repeats)/Cas9 (CRISPR-associated protein 9) has become the tool of choice for generating gene knockouts across a variety of species. The ability for efficient gene editing in primary T cells not only represents a valuable research tool to study gene function but also holds great promise for T cell-based immunotherapies, such as next-generation chimeric antigen receptor (CAR) T cells. Previous attempts to apply CRIPSR/Cas9 for gene editing in primary T cells have resulted in highly variable knockout efficiency and required T cell receptor (TCR) stimulation, thus largely precluding the study of genes involved in T cell activation or differentiation. Here, we describe an optimized approach for Cas9/RNP transfection of primary mouse and human T cells without TCR stimulation that results in near complete loss of target gene expression at the population level, mitigating the need for selection. We believe that this method will greatly extend the feasibly of target gene discovery and validation in primary T cells and simplify the gene editing process for next-generation immunotherapies.
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Affiliation(s)
- Akiko Seki
- Department of Cancer Immunology, Genentech, South San Francisco, CA
| | - Sascha Rutz
- Department of Cancer Immunology, Genentech, South San Francisco, CA
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197
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Gutierrez-Guerrero A, Sanchez-Hernandez S, Galvani G, Pinedo-Gomez J, Martin-Guerra R, Sanchez-Gilabert A, Aguilar-González A, Cobo M, Gregory P, Holmes M, Benabdellah K, Martin F. Comparison of Zinc Finger Nucleases Versus CRISPR-Specific Nucleases for Genome Editing of the Wiskott-Aldrich Syndrome Locus. Hum Gene Ther 2018; 29:366-380. [DOI: 10.1089/hum.2017.047] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Alejandra Gutierrez-Guerrero
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Sabina Sanchez-Hernandez
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Giuseppe Galvani
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Javier Pinedo-Gomez
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Rocio Martin-Guerra
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Almudena Sanchez-Gilabert
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Araceli Aguilar-González
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
| | - Marién Cobo
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
- LentiStem Biotech, Granada, Spain
| | - Philip Gregory
- Sangamo BioSciences, Point Richmond Tech Center, Richmond, California
| | - Michael Holmes
- Sangamo BioSciences, Point Richmond Tech Center, Richmond, California
| | - Karim Benabdellah
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
- LentiStem Biotech, Granada, Spain
| | - Francisco Martin
- Centre for Genomics and Oncological Research (GENYO), Pfizer/University of Granada/Andalusian Regional Government, Genomic Medicine Department, Granada, Spain
- LentiStem Biotech, Granada, Spain
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198
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Ahmad G, Amiji M. Use of CRISPR/Cas9 gene-editing tools for developing models in drug discovery. Drug Discov Today 2018; 23:519-533. [DOI: 10.1016/j.drudis.2018.01.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 11/09/2017] [Accepted: 01/04/2018] [Indexed: 12/20/2022]
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199
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Bertero A, Yiangou L, Brown S, Ortmann D, Pawlowski M, Vallier L. Conditional Manipulation of Gene Function in Human Cells with Optimized Inducible shRNA. ACTA ACUST UNITED AC 2018; 44:5C.4.1-5C.4.48. [PMID: 29512130 DOI: 10.1002/cpsc.45] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The difficulties involved in conditionally perturbing complex gene expression networks represent major challenges toward defining the mechanisms controlling human development, physiology, and disease. We developed an OPTimized inducible KnockDown (OPTiKD) platform that addresses the limitations of previous approaches by allowing streamlined, tightly-controlled, and potent loss-of-function experiments for both single and multiple genes. The method relies on single-step genetic engineering of the AAVS1 genomic safe harbor with an optimized tetracycline-responsive cassette driving one or more inducible short hairpin RNAs (shRNAs). OPTiKD provides homogeneous, dose-responsive, and reversible gene knockdown. When implemented in human pluripotent stem cells (hPSCs), the approach can be then applied to a broad range of hPSC-derived mature cell lineages that include neurons, cardiomyocytes, and hepatocytes. Generation of OPTiKD hPSCs in commonly used culture conditions is simple (plasmid based), rapid (two weeks), and highly efficient (>95%). Overall, this method facilitates the functional annotation of the human genome in health and disease. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Alessandro Bertero
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- Department of Pathology, University of Washington, Seattle, Washington
| | - Loukia Yiangou
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stephanie Brown
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Ortmann
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Matthias Pawlowski
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Ludovic Vallier
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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200
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The changing landscape of gene editing in hematopoietic stem cells: a step towards Cas9 clinical translation. Curr Opin Hematol 2018; 24:481-488. [PMID: 28806273 DOI: 10.1097/moh.0000000000000385] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW Since the discovery two decades ago that programmable endonucleases can be engineered to modify human cells at single nucleotide resolution, the concept of genome editing was born. Now these technologies are being applied to therapeutically relevant cell types, including hematopoietic stem cells (HSC), which possess the power to repopulate an entire blood and immune system. The purpose of this review is to discuss the changing landscape of genome editing in hematopoietic stem cells (GE-HSC) from the discovery stage to the preclinical stage, with the imminent goal of clinical translation for the treatment of serious genetic diseases of the blood and immune system. RECENT FINDINGS With the discovery that the RNA-programmable (sgRNA) clustered regularly interspace short palindromic repeats (CRISPR)-Cas9 nuclease (Cas9/sgRNA) systems can be easily used to precisely modify the human genome in 2012, a genome-editing revolution of hematopoietic stem cells (HSC) has bloomed. We have observed that over the last 2 years, academic institutions and small biotech companies are developing HSC-based Cas9/sgRNA genome-editing curative strategies to treat monogenic disorders, including β-hemoglobinopathies and primary immunodeficiencies. We will focus on recent publications (within the past 2 years) that employ different genome-editing strategies to 'hijack' the cell's endogenous double-strand repair pathways to confer a disease-specific therapeutic advantage. SUMMARY The number of genome-editing strategies in HSCs that could offer therapeutic potential for diseases of the blood and immune system have dramatically risen over the past 2 years. The HSC-based genome-editing field is primed to enter clinical trials in the subsequent years. We will summarize the major advancements for the development of novel autologous GE-HSC cell and gene therapy strategies for hematopoietic diseases that are candidates for curative allogeneic bone marrow transplantation.
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