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Danaeifar M, Najafi A. Artificial Intelligence and Computational Biology in Gene Therapy: A Review. Biochem Genet 2024:10.1007/s10528-024-10799-1. [PMID: 38635012 DOI: 10.1007/s10528-024-10799-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
One of the trending fields in almost all areas of science and technology is artificial intelligence. Computational biology and artificial intelligence can help gene therapy in many steps including: gene identification, gene editing, vector design, development of new macromolecules and modeling of gene delivery. There are various tools used by computational biology and artificial intelligence in this field, such as genomics, transcriptomic and proteomics data analysis, machine learning algorithms and molecular interaction studies. These tools can introduce new gene targets, novel vectors, optimized experiment conditions, predict the outcomes and suggest the best solutions to avoid undesired immune responses following gene therapy treatment.
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Affiliation(s)
- Mohsen Danaeifar
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Science, P.O. Box 19395-5487, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Science, P.O. Box 19395-5487, Tehran, Iran.
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2
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Kajihara R, Ezaki R, Watanabe T, Ichikawa K, Matsuzaki M, Horiuchi H. Evaluation of expression systems for recombinant protein production in chicken egg bioreactors. Biotechnol J 2024; 19:e2300316. [PMID: 37859508 DOI: 10.1002/biot.202300316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/30/2023] [Accepted: 09/30/2023] [Indexed: 10/21/2023]
Abstract
Chicken eggs have gained attention as excellent bioreactors because of their genetic modifications. However, the development of chicken egg bioreactors requires a long time from the construction of the production system to the evaluation of the products. Therefore, in this study, a chicken cell line producing ovalbumin (OVA) was established and constructed a system for the rapid evaluation of the production system. First, the EF1α promoter was knocked in upstream of the OVA locus in chicken DF-1 cells for continuous OVA expression. Furthermore, an ideal position at the OVA locus for the insertion of useful protein genes to maximize recombinant protein yield was analyzed and identified. The knocking in the EF1α promoter upstream of exon1 yielded the maximum production of OVA protein was achieved. In addition, Linking a recombinant hFGF2 cDNA to the 5' side of the OVA was found to increase production efficiency. Therefore, an OVA-expressing cell line and an evaluation system for proteins in chicken egg bioreactors was established. The findings may improve the efficiency of chicken expression systems and expand their applications in protein production.
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Affiliation(s)
- Ryota Kajihara
- Laboratory of Immunobiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Ryo Ezaki
- Laboratory of Immunobiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Tenkai Watanabe
- Laboratory of Immunobiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Kennosuke Ichikawa
- Laboratory of Immunobiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Mei Matsuzaki
- Laboratory of Immunobiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Hiroyuki Horiuchi
- Laboratory of Immunobiology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
- Genome Editing Innovation Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
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3
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Kumar R, Sinha NR, Mohan RR. Corneal gene therapy: Structural and mechanistic understanding. Ocul Surf 2023; 29:279-297. [PMID: 37244594 DOI: 10.1016/j.jtos.2023.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
Cornea, a dome-shaped and transparent front part of the eye, affords 2/3rd refraction and barrier functions. Globally, corneal diseases are the leading cause of vision impairment. Loss of corneal function including opacification involve the complex crosstalk and perturbation between a variety of cytokines, chemokines and growth factors generated by corneal keratocytes, epithelial cells, lacrimal tissues, nerves, and immune cells. Conventional small-molecule drugs can treat mild-to-moderate traumatic corneal pathology but requires frequent application and often fails to treat severe pathologies. The corneal transplant surgery is a standard of care to restore vision in patients. However, declining availability and rising demand of donor corneas are major concerns to maintain ophthalmic care. Thus, the development of efficient and safe nonsurgical methods to cure corneal disorders and restore vision in vivo is highly desired. Gene-based therapy has huge potential to cure corneal blindness. To achieve a nonimmunogenic, safe and sustained therapeutic response, the selection of a relevant genes, gene editing methods and suitable delivery vectors are vital. This article describes corneal structural and functional features, mechanistic understanding of gene therapy vectors, gene editing methods, gene delivery tools, and status of gene therapy for treating corneal disorders, diseases, and genetic dystrophies.
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Affiliation(s)
- Rajnish Kumar
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; One-health One-medicine Vision Research Program, Departments of Veterinary Medicine and Surgery & Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA; Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow campus, UP, 226028, India
| | - Nishant R Sinha
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; One-health One-medicine Vision Research Program, Departments of Veterinary Medicine and Surgery & Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Rajiv R Mohan
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, 65201, USA; One-health One-medicine Vision Research Program, Departments of Veterinary Medicine and Surgery & Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA; Mason Eye Institute, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.
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4
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Gnanapragasam MN, Planutis A, Glassberg JA, Bieker JJ. Identification of a genomic DNA sequence that quantitatively modulates KLF1 transcription factor expression in differentiating human hematopoietic cells. Sci Rep 2023; 13:7589. [PMID: 37165057 PMCID: PMC10172341 DOI: 10.1038/s41598-023-34805-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 05/08/2023] [Indexed: 05/12/2023] Open
Abstract
The onset of erythropoiesis is under strict developmental control, with direct and indirect inputs influencing its derivation from the hematopoietic stem cell. A major regulator of this transition is KLF1/EKLF, a zinc finger transcription factor that plays a global role in all aspects of erythropoiesis. Here, we have identified a short, conserved enhancer element in KLF1 intron 1 that is important for establishing optimal levels of KLF1 in mouse and human cells. Chromatin accessibility of this site exhibits cell-type specificity and is under developmental control during the differentiation of human CD34+ cells towards the erythroid lineage. This site binds GATA1, SMAD1, TAL1, and ETV6. In vivo editing of this region in cell lines and primary cells reduces KLF1 expression quantitatively. However, we find that, similar to observations seen in pedigrees of families with KLF1 mutations, downstream effects are variable, suggesting that the global architecture of the site is buffered towards keeping the KLF1 genetic region in an active state. We propose that modification of intron 1 in both alleles is not equivalent to complete loss of function of one allele.
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Affiliation(s)
- M N Gnanapragasam
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH, USA
| | - A Planutis
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA
| | - J A Glassberg
- Department of Emergency Medicine, Hematology and Medical Oncology, Mount Sinai School of Medicine, New York, NY, USA
| | - J J Bieker
- Department of Cell, Developmental, and Regenerative Biology, Mount Sinai School of Medicine, One Gustave L. Levy Place, Box 1020, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, USA.
- Tisch Cancer Institute, Mount Sinai School of Medicine, New York, USA.
- Mindich Child Health and Development Institute, Mount Sinai School of Medicine, New York, NY, USA.
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Kar B, Castillo SR, Sabharwal A, Clark KJ, Ekker SC. Mitochondrial Base Editing: Recent Advances towards Therapeutic Opportunities. Int J Mol Sci 2023; 24:5798. [PMID: 36982871 PMCID: PMC10056815 DOI: 10.3390/ijms24065798] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Mitochondria are critical organelles that form networks within our cells, generate energy dynamically, contribute to diverse cell and organ function, and produce a variety of critical signaling molecules, such as cortisol. This intracellular microbiome can differ between cells, tissues, and organs. Mitochondria can change with disease, age, and in response to the environment. Single nucleotide variants in the circular genomes of human mitochondrial DNA are associated with many different life-threatening diseases. Mitochondrial DNA base editing tools have established novel disease models and represent a new possibility toward personalized gene therapies for the treatment of mtDNA-based disorders.
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Affiliation(s)
- Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Santiago R. Castillo
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Mayo Clinic, Rochester, MN 55905, USA
| | - Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Karl J. Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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Rhiel M, Geiger K, Andrieux G, Rositzka J, Boerries M, Cathomen T, Cornu TI. T-CAST: An optimized CAST-Seq pipeline for TALEN confirms superior safety and efficacy of obligate-heterodimeric scaffolds. Front Genome Ed 2023; 5:1130736. [PMID: 36890979 PMCID: PMC9986454 DOI: 10.3389/fgeed.2023.1130736] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Transcription activator-like effector nucleases (TALENs) are programmable nucleases that have entered the clinical stage. Each subunit of the dimer consists of a DNA-binding domain composed of an array of TALE repeats fused to the catalytically active portion of the FokI endonuclease. Upon DNA-binding of both TALEN arms in close proximity, the FokI domains dimerize and induce a staggered-end DNA double strand break. In this present study, we describe the implementation and validation of TALEN-specific CAST-Seq (T-CAST), a pipeline based on CAST-Seq that identifies TALEN-mediated off-target effects, nominates off-target sites with high fidelity, and predicts the TALEN pairing conformation leading to off-target cleavage. We validated T-CAST by assessing off-target effects of two promiscuous TALENs designed to target the CCR5 and TRAC loci. Expression of these TALENs caused high levels of translocations between the target sites and various off-target sites in primary T cells. Introduction of amino acid substitutions to the FokI domains, which render TALENs obligate-heterodimeric (OH-TALEN), mitigated the aforementioned off-target effects without loss of on-target activity. Our findings highlight the significance of T-CAST to assess off-target effects of TALEN designer nucleases and to evaluate mitigation strategies, and advocate the use of obligate-heterodimeric TALEN scaffolds for therapeutic genome editing.
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Affiliation(s)
- Manuel Rhiel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany
| | - Kerstin Geiger
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany
- Ph.D. Program, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julia Rositzka
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Comprehensive Cancer Center Freiburg (CCCF), Medical Center—University of Freiburg, Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tatjana I. Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
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7
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Houghton BC, Panchal N, Haas SA, Chmielewski KO, Hildenbeutel M, Whittaker T, Mussolino C, Cathomen T, Thrasher AJ, Booth C. Genome Editing With TALEN, CRISPR-Cas9 and CRISPR-Cas12a in Combination With AAV6 Homology Donor Restores T Cell Function for XLP. Front Genome Ed 2022; 4:828489. [PMID: 35677600 PMCID: PMC9168036 DOI: 10.3389/fgeed.2022.828489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/06/2022] [Indexed: 12/27/2022] Open
Abstract
X-linked lymphoproliferative disease is a rare inherited immune disorder, caused by mutations or deletions in the SH2D1A gene that encodes an intracellular adapter protein SAP (Slam-associated protein). SAP is essential for mediating several key immune processes and the immune system - T cells in particular - are dysregulated in its absence. Patients present with a spectrum of clinical manifestations, including haemophagocytic lymphohistiocytosis (HLH), dysgammaglobulinemia, lymphoma and autoimmunity. Treatment options are limited, and patients rarely survive to adulthood without an allogeneic haematopoietic stem cell transplant (HSCT). However, this procedure can have poor outcomes in the mismatched donor setting or in the presence of active HLH, leaving an unmet clinical need. Autologous haematopoeitic stem cell or T cell therapy may offer alternative treatment options, removing the need to find a suitable donor for HSCT and any risk of alloreactivity. SAP has a tightly controlled expression profile that a conventional lentiviral gene delivery platform may not be able to fully replicate. A gene editing approach could preserve more of the endogenous regulatory elements that govern SAP expression, potentially providing a more optimum therapy. Here, we assessed the ability of TALEN, CRISPR-Cas9 and CRISPR-Cas12a nucleases to drive targeted insertion of SAP cDNA at the first exon of the SH2D1A locus using an adeno-associated virus serotype 6 (AAV6)-based vector containing the donor template. All nuclease platforms were capable of high efficiency gene editing, which was optimised using a serum-free AAV6 transduction protocol. We show that T cells from XLP patients corrected by gene editing tools have restored physiological levels of SAP gene expression and restore SAP-dependent immune functions, indicating a new therapeutic opportunity for XLP patients.
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Affiliation(s)
- Benjamin C. Houghton
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Neelam Panchal
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Simone A. Haas
- Institute for Transfusion Medicine and Gene Therapy, Medical Center – University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Kay O. Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center – University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Markus Hildenbeutel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center – University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Whittaker
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center – University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center – University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Adrian J Thrasher
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Claire Booth
- Molecular and Cellular Immunology, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA. Nat Biotechnol 2022; 40:1378-1387. [PMID: 35379961 PMCID: PMC9463067 DOI: 10.1038/s41587-022-01256-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 02/08/2022] [Indexed: 12/21/2022]
Abstract
The all-protein cytosine base editor DdCBE uses TALE proteins and a double-stranded DNA-specific cytidine deaminase (DddA) to mediate targeted C•G-to-T•A editing. To improve editing efficiency and overcome the strict TC sequence-context constraint of DddA, we used phage-assisted non-continuous and continuous evolution to evolve DddA variants with improved activity and expanded targeting scope. Compared to canonical DdCBEs, base editors with evolved DddA6 improved mitochondrial DNA (mtDNA) editing efficiencies at TC by 3.3-fold on average. DdCBEs containing evolved DddA11 offered a broadened HC (H = A, C or T) sequence compatibility for both mitochondrial and nuclear base editing, increasing average editing efficiencies at AC and CC targets from less than 10% for canonical DdCBE to 15-30% and up to 50% in cell populations sorted to express both halves of DdCBE. We used these evolved DdCBEs to efficiently install disease-associated mtDNA mutations in human cells at non-TC target sites. DddA6 and DddA11 substantially increase the effectiveness and applicability of all-protein base editing.
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Cui Z, Liu H, Zhang H, Huang Z, Tian R, Li L, Fan W, Chen Y, Chen L, Zhang S, Das BC, Severinov K, Hitzeroth II, Debata PR, Jin Z, Liu J, Huang Z, Xie W, Xie H, Lang B, Ma J, Weng H, Tian X, Hu Z. The comparison of ZFNs, TALENs, and SpCas9 by GUIDE-seq in HPV-targeted gene therapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:1466-1478. [PMID: 34938601 PMCID: PMC8655392 DOI: 10.1016/j.omtn.2021.08.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/10/2021] [Indexed: 12/26/2022]
Abstract
Zinc-finger nucleases (ZFNs), transcription activator-like endonucleases (TALENs), and CRISPR-associated Cas9 endonucleases are three major generations of genome editing tools. However, no parallel comparison about the efficiencies and off-target activity of the three nucleases has been reported, which is critical for the final clinical decision. We for the first time developed the genome-wide unbiased identification of double-stranded breaks enabled by sequencing (GUIDE-seq) method in ZFNs and TALENs with novel bioinformatics algorithms to evaluate the off-targets. By targeting human papillomavirus 16 (HPV16), we compared the performance of ZFNs, TALENs, and SpCas9 in vivo. Our data showed that ZFNs with similar targets could generate distinct massive off-targets (287–1,856), and the specificity could be reversely correlated with the counts of middle “G” in zinc finger proteins (ZFPs). We also compared the TALENs with different N-terminal domains (wild-type [WT]/αN/βN) and G recognition modules (NN/NH) and found the design (αN or NN) to improve the efficiency of TALEN inevitably increased off-targets. Finally, our results showed that SpCas9 was more efficient and specific than ZFNs and TALENs. Specifically, SpCas9 had fewer off-target counts in URR (SpCas9, n = 0; TALEN, n = 1; ZFN, n = 287), E6 (SpCas9, n = 0; TALEN, n = 7), and E7 (SpCas9, n = 4; TALEN, n = 36). Taken together, we suggest that for HPV gene therapies, SpCas9 is a more efficient and safer genome editing tool. Our off-target data could be used to improve the design of ZFNs and TALENs, and the universal in vivo off-target detection pipeline for three generations of artificial nucleases provided useful tools for genome engineering-based gene therapy.
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Affiliation(s)
- Zifeng Cui
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Hui Liu
- Department of Pathology, Xi’an People’s Hospital (Xi’an Fourth Hospital), Shaanxi, China
| | - Hongfeng Zhang
- Department of Pathology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zhaoyue Huang
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Rui Tian
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Lifang Li
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Weiwen Fan
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Yili Chen
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Lijie Chen
- Graduate School, Bengbu Medical College, Bengbu, Anhui 233000, China
| | - Sen Zhang
- Graduate School, Bengbu Medical College, Bengbu, Anhui 233000, China
| | - Bhudev C. Das
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University Uttar Pradesh, Sector 125, Noida 201313, India
| | - Konstantin Severinov
- Skolkovo Institute of Science and Technology 100 Novaya Street, Skolkovo, Moscow Region 143025, Russia
| | - Inga Isabel Hitzeroth
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town 7701, South Africa
| | - Priya Ranjan Debata
- Department of Zoology, North Orissa University, Takatpur, Baripada, Odisha 757003, India
| | - Zhuang Jin
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Jiashuo Liu
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Zheying Huang
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Weiling Xie
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
| | - Hongxian Xie
- Generulor Company Bio-X Lab, Guangzhou 510006, Guangdong, China
| | - Bin Lang
- School of Health Sciences and Sports, Macao Polytechnic Institute, Macao 999078, China
| | - Ji Ma
- Department of Pathology, The Central Hospital of Sui Zhou, Hubei, China
| | - Haiyan Weng
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China
- Corresponding author: Haiyan Weng, Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230036, China.
| | - Xun Tian
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, Hubei, China
- Corresponding author: Xun Tian, Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, Hubei, China.
| | - Zheng Hu
- Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
- Corresponding author: Zheng Hu, Department of Gynecological Oncology, The First Affiliated Hospital, Sun Yat-sen University, Zhongshan 2nd Road, Yuexiu, Guangzhou 510080, Guangdong, China.
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10
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Smith T, Singh P, Chmielewski KO, Bloom K, Cathomen T, Arbuthnot P, Ely A. Improved Specificity and Safety of Anti-Hepatitis B Virus TALENs Using Obligate Heterodimeric FokI Nuclease Domains. Viruses 2021; 13:v13071344. [PMID: 34372550 PMCID: PMC8310341 DOI: 10.3390/v13071344] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/02/2021] [Indexed: 01/04/2023] Open
Abstract
Persistent hepatitis B virus (HBV) infection remains a serious medical problem worldwide, with an estimated global burden of 257 million carriers. Prophylactic and therapeutic interventions, in the form of a vaccine, immunomodulators, and nucleotide and nucleoside analogs, are available. Vaccination, however, offers no therapeutic benefit to chronic sufferers and has had a limited impact on infection rates. Although immunomodulators and nucleotide and nucleoside analogs have been licensed for treatment of chronic HBV, cure rates remain low. Transcription activator-like effector nucleases (TALENs) designed to bind and cleave viral DNA offer a novel therapeutic approach. Importantly, TALENs can target covalently closed circular DNA (cccDNA) directly with the potential of permanently disabling this important viral replicative intermediate. Potential off-target cleavage by engineered nucleases leading to toxicity presents a limitation of this technology. To address this, in the context of HBV gene therapy, existing TALENs targeting the viral core and surface open reading frames were modified with second- and third-generation FokI nuclease domains. As obligate heterodimers these TALENs prevent target cleavage as a result of FokI homodimerization. Second-generation obligate heterodimeric TALENs were as effective at silencing viral gene expression as first-generation counterparts and demonstrated an improved specificity in a mouse model of HBV replication.
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Affiliation(s)
- Tiffany Smith
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa; (T.S.); (P.S.); (K.B.); (P.A.)
| | - Prashika Singh
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa; (T.S.); (P.S.); (K.B.); (P.A.)
| | - Kay Ole Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg & Medical Faculty, University of Freiburg, 79106 Freiburg, Germany; (K.O.C.); (T.C.)
| | - Kristie Bloom
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa; (T.S.); (P.S.); (K.B.); (P.A.)
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg & Medical Faculty, University of Freiburg, 79106 Freiburg, Germany; (K.O.C.); (T.C.)
| | - Patrick Arbuthnot
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa; (T.S.); (P.S.); (K.B.); (P.A.)
| | - Abdullah Ely
- Wits/SAMRC Antiviral Gene Therapy Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, South Africa; (T.S.); (P.S.); (K.B.); (P.A.)
- Correspondence: ; Tel.: +27-(0)11-717-2561
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11
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Sehgal P, Mathew S, Sivadas A, Ray A, Tanwar J, Vishwakarma S, Ranjan G, Shamsudheen KV, Bhoyar RC, Pateria A, Leonard E, Lalwani M, Vats A, Pappuru RR, Tyagi M, Jakati S, Sengupta S, B K B, Chakrabarti S, Kaur I, Motiani RK, Scaria V, Sivasubbu S. LncRNA VEAL2 regulates PRKCB2 to modulate endothelial permeability in diabetic retinopathy. EMBO J 2021; 40:e107134. [PMID: 34180064 PMCID: PMC8327952 DOI: 10.15252/embj.2020107134] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 05/16/2021] [Accepted: 05/21/2021] [Indexed: 12/29/2022] Open
Abstract
Long non‐coding RNAs (lncRNAs) are emerging as key regulators of endothelial cell function. Here, we investigated the role of a novel vascular endothelial‐associated lncRNA (VEAL2) in regulating endothelial permeability. Precise editing of veal2 loci in zebrafish (veal2gib005Δ8/+) induced cranial hemorrhage. In vitro and in vivo studies revealed that veal2 competes with diacylglycerol for interaction with protein kinase C beta‐b (Prkcbb) and regulates its kinase activity. Using PRKCB2 as bait, we identified functional ortholog of veal2 in humans from HUVECs and named it as VEAL2. Overexpression and knockdown of VEAL2 affected tubulogenesis and permeability in HUVECs. VEAL2 was differentially expressed in choroid tissue in eye and blood from patients with diabetic retinopathy, a disease where PRKCB2 is known to be hyperactivated. Further, VEAL2 could rescue the effects of PRKCB2‐mediated turnover of endothelial junctional proteins thus reducing hyperpermeability in hyperglycemic HUVEC model of diabetic retinopathy. Based on evidence from zebrafish and hyperglycemic HUVEC models and diabetic retinopathy patients, we report a hitherto unknown VEAL2 lncRNA‐mediated regulation of PRKCB2, for modulating junctional dynamics and maintenance of endothelial permeability.
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Affiliation(s)
- Paras Sehgal
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Samatha Mathew
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Ambily Sivadas
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Arjun Ray
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Jyoti Tanwar
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India.,Laboratory of Calciomics and Systemic Pathophysiology, Regional Center for Biotechnology, Faridabad, India
| | - Sushma Vishwakarma
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Gyan Ranjan
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - K V Shamsudheen
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Rahul C Bhoyar
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Abhishek Pateria
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Elvin Leonard
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Mukesh Lalwani
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Archana Vats
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Rajeev R Pappuru
- Kannuri Santhamma Centre for Retina and Vitreous, L V Prasad Eye Institute, Hyderabad, India
| | - Mudit Tyagi
- Kannuri Santhamma Centre for Retina and Vitreous, L V Prasad Eye Institute, Hyderabad, India
| | - Saumya Jakati
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Binukumar B K
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | | | - Inderjeet Kaur
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Rajender K Motiani
- Laboratory of Calciomics and Systemic Pathophysiology, Regional Center for Biotechnology, Faridabad, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology, Delhi, India.,Academy of Scientific and Innovative Research, Ghaziabad, India
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12
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Sgro A, Blancafort P. Epigenome engineering: new technologies for precision medicine. Nucleic Acids Res 2021; 48:12453-12482. [PMID: 33196851 PMCID: PMC7736826 DOI: 10.1093/nar/gkaa1000] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/10/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Chromatin adopts different configurations that are regulated by reversible covalent modifications, referred to as epigenetic marks. Epigenetic inhibitors have been approved for clinical use to restore epigenetic aberrations that result in silencing of tumor-suppressor genes, oncogene addictions, and enhancement of immune responses. However, these drugs suffer from major limitations, such as a lack of locus selectivity and potential toxicities. Technological advances have opened a new era of precision molecular medicine to reprogram cellular physiology. The locus-specificity of CRISPR/dCas9/12a to manipulate the epigenome is rapidly becoming a highly promising strategy for personalized medicine. This review focuses on new state-of-the-art epigenome editing approaches to modify the epigenome of neoplasms and other disease models towards a more 'normal-like state', having characteristics of normal tissue counterparts. We highlight biomolecular engineering methodologies to assemble, regulate, and deliver multiple epigenetic effectors that maximize the longevity of the therapeutic effect, and we discuss limitations of the platforms such as targeting efficiency and intracellular delivery for future clinical applications.
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Affiliation(s)
- Agustin Sgro
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Laboratory, The Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Human Sciences, The University of Western Australia, Crawley, Perth, Western Australia 6009, Australia.,The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center, San Antonio, TX 78229, USA
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13
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Bao XR, Pan Y, Lee CM, Davis TH, Bao G. Tools for experimental and computational analyses of off-target editing by programmable nucleases. Nat Protoc 2021; 16:10-26. [PMID: 33288953 PMCID: PMC8049448 DOI: 10.1038/s41596-020-00431-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022]
Abstract
Genome editing using programmable nucleases is revolutionizing life science and medicine. Off-target editing by these nucleases remains a considerable concern, especially in therapeutic applications. Here we review tools developed for identifying potential off-target editing sites and compare the ability of these tools to properly analyze off-target effects. Recent advances in both in silico and experimental tools for off-target analysis have generated remarkably concordant results for sites with high off-target editing activity. However, no single tool is able to accurately predict low-frequency off-target editing, presenting a bottleneck in therapeutic genome editing, because even a small number of cells with off-target editing can be detrimental. Therefore, we recommend that at least one in silico tool and one experimental tool should be used together to identify potential off-target sites, and amplicon-based next-generation sequencing (NGS) should be used as the gold standard assay for assessing the true off-target effects at these candidate sites. Future work to improve off-target analysis includes expanding the true off-target editing dataset to evaluate new experimental techniques and to train machine learning algorithms; performing analysis using the particular genome of the cells in question rather than the reference genome; and applying novel NGS techniques to improve the sensitivity of amplicon-based off-target editing quantification.
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Affiliation(s)
- X Robert Bao
- ILISATech, Houston, TX, USA
- Arsenal Biosciences, South San Francisco, CA, USA
| | - Yidan Pan
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Ciaran M Lee
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Timothy H Davis
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA.
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14
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Schwarze LI, Sonntag T, Wild S, Schmitz S, Uhde A, Fehse B. Automated production of CCR5-negative CD4 +-T cells in a GMP-compatible, clinical scale for treatment of HIV-positive patients. Gene Ther 2021; 28:572-587. [PMID: 33867524 PMCID: PMC8455337 DOI: 10.1038/s41434-021-00259-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 03/22/2021] [Accepted: 04/01/2021] [Indexed: 02/02/2023]
Abstract
Ex-vivo gene editing in T lymphocytes paves the way for novel concepts of immunotherapy. One of those strategies is directed at the protection of CD4+-T helper cells from HIV infection in HIV-positive individuals. To this end, we have developed and optimised a CCR5-targeting TALE nuclease, CCR5-Uco-hetTALEN, mediating high-efficiency knockout of C-C motif chemokine receptor 5 (CCR5), the HIV co-receptor essential during initial infection. Clinical translation of the knockout approach requires up-scaling of the manufacturing process to clinically relevant cell numbers in accordance with good manufacturing practice (GMP). Here we present a GMP-compatible mRNA electroporation protocol for the automated production of CCR5-edited CD4+-T cells in the closed CliniMACS Prodigy system. The automated process reliably produced high amounts of CCR5-edited CD4+-T cells (>1.5 × 109 cells with >60% CCR5 editing) within 12 days. Of note, about 40% of total large-scale produced cells showed a biallelic CCR5 editing, and between 25 and 42% of produced cells had a central memory T-cell phenotype. In conclusion, transfection of primary T cells with CCR5-Uco-hetTALEN mRNA is readily scalable for GMP-compatible production and hence suitable for application in HIV gene therapy.
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Affiliation(s)
- Lea Isabell Schwarze
- grid.13648.380000 0001 2180 3484Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany ,grid.452463.2German Centre for Infection Research (DZIF), partner site, Hamburg, Germany
| | - Tanja Sonntag
- grid.13648.380000 0001 2180 3484Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Wild
- grid.59409.310000 0004 0552 5033Miltenyi Biotec, Bergisch Gladbach, Germany
| | - Sabrina Schmitz
- grid.59409.310000 0004 0552 5033Miltenyi Biotec, Bergisch Gladbach, Germany
| | - Almut Uhde
- grid.13648.380000 0001 2180 3484Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Boris Fehse
- grid.13648.380000 0001 2180 3484Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany ,grid.452463.2German Centre for Infection Research (DZIF), partner site, Hamburg, Germany
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15
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Schwarze LI, Głów D, Sonntag T, Uhde A, Fehse B. Optimisation of a TALE nuclease targeting the HIV co-receptor CCR5 for clinical application. Gene Ther 2021; 28:588-601. [PMID: 34112993 PMCID: PMC8455333 DOI: 10.1038/s41434-021-00271-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 02/05/2023]
Abstract
Disruption of the C-C-Chemokine-receptor-5 (CCR5) gene induces resistance towards CCR5-tropic HIV. Here we optimised our previously described CCR5-Uco-TALEN and its delivery by mRNA electroporation. The novel variant, CCR5-Uco-hetTALEN features an obligatory heterodimeric Fok1-cleavage domain, which resulted in complete abrogation of off-target activity at previously found homodimeric as well as 7/8 in silico predicted, potential heterodimeric off-target sites, the only exception being highly homologous CCR2. Prevailing 18- and 10-bp deletions at the on-target site revealed microhomology-mediated end-joining as a major repair pathway. Notably, the CCR5Δ55-60 protein resulting from the 18-bp deletion was almost completely retained in the cytosol. Simultaneous cutting at CCR5 and CCR2 induced rearrangements, mainly 15-kb deletions between the cut sites, in up to 2% of T cells underlining the necessity to restrict TALEN expression. We optimised in vitro mRNA production and showed that CCR5-on- and CCR2 off-target activities of CCR5-Uco-hetTALEN were limited to the first 72 and 24-48 h post-mRNA electroporation, respectively. Using single-cell HRMCA, we discovered high rates of TALEN-induced biallelic gene editing of CCR5, which translated in large numbers of CCR5-negative cells resistant to HIVenv-pseudotyped lentiviral vectors. We conclude that CCR5-Uco-hetTALEN transfected by mRNA electroporation facilitates specific, high-efficiency CCR5 gene-editing (30%-56%) and it is highly suited for clinical translation subject to further characterisation of off-target effects.
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Affiliation(s)
- Lea Isabell Schwarze
- grid.13648.380000 0001 2180 3484Department of Stem Cell Transplantation, Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany ,grid.452463.2German Centre for Infection Research (DZIF), partner site Hamburg, Hamburg, Germany
| | - Dawid Głów
- grid.13648.380000 0001 2180 3484Department of Stem Cell Transplantation, Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Tanja Sonntag
- grid.13648.380000 0001 2180 3484Department of Stem Cell Transplantation, Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Almut Uhde
- grid.13648.380000 0001 2180 3484Department of Stem Cell Transplantation, Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Boris Fehse
- grid.13648.380000 0001 2180 3484Department of Stem Cell Transplantation, Research Department Cell and Gene Therapy, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany ,grid.452463.2German Centre for Infection Research (DZIF), partner site Hamburg, Hamburg, Germany
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16
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Automated generation of gene-edited CAR T cells at clinical scale. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 20:379-388. [PMID: 33575430 PMCID: PMC7848723 DOI: 10.1016/j.omtm.2020.12.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/21/2020] [Indexed: 02/07/2023]
Abstract
The potential of adoptive cell therapy can be extended when combined with genome editing. However, variation in the quality of the starting material and the different manufacturing steps are associated with production failure and product contamination. Here, we present an automated T cell engineering process to produce off-the-shelf chimeric antigen receptor (CAR) T cells on an extended CliniMACS Prodigy platform containing an in-line electroporation unit. This setup was used to combine lentiviral delivery of a CD19-targeting CAR with transfer of mRNA encoding a TRAC locus-targeting transcription activator-like effector nuclease (TALEN). In three runs at clinical scale, the T cell receptor (TCR) alpha chain encoding TRAC locus was disrupted in >35% of cells with high cell viability (>90%) and no detectable off-target activity. A final negative selection step allowed the generation of TCRα/β-free CAR T cells with >99.5% purity. These CAR T cells proliferated well, maintained a T cell memory phenotype, eliminated CD19-positive tumor cells, and released the expected cytokines when exposed to B cell leukemia cells. In conclusion, we established an automated, good manufacturing practice (GMP)-compliant process that integrates lentiviral transduction with electroporation of TALEN mRNA to produce functional TCRα/β-free CAR19 T cells at clinical scale.
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17
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Romito M, Juillerat A, Kok YL, Hildenbeutel M, Rhiel M, Andrieux G, Geiger J, Rudolph C, Mussolino C, Duclert A, Metzner KJ, Duchateau P, Cathomen T, Cornu TI. Preclinical Evaluation of a Novel TALEN Targeting CCR5 Confirms Efficacy and Safety in Conferring Resistance to HIV-1 Infection. Biotechnol J 2020; 16:e2000023. [PMID: 33103367 DOI: 10.1002/biot.202000023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/18/2020] [Indexed: 01/10/2023]
Abstract
Therapies to treat patients infected with human immunodeficiency virus (HIV) aim at preventing viral replication but fail to eliminate the virus. Although transplantation of allogeneic CCR5Δ32 homozygous stem cell grafts provided a cure for a few patients, this approach is not considered a general therapeutic strategy because of potential side effects. Conversely, gene editing to disrupt the C-C chemokine receptor type 5 (CCR5) locus, which encodes the major HIV coreceptor, has shown to confer resistance to CCR5-tropic HIV strains. Here, an engineered transcription activator-like effector nuclease (TALEN) that enables efficient CCR5 editing in hematopoietic cells is presented. After transferring TALEN-encoding mRNA into primary CD4+ T cells, up to 89% of CCR5 alleles are disrupted. Genotyping confirms the genetic stability of the CCR5-edited cells, and genome-wide off-target analyses established the absence of relevant mutagenic events. When challenging the edited T cells with CCR5-tropic HIV, protection in a dose-dependent manner is observed. Functional assessments reveal no significant differences between edited and control cells in terms of proliferation and their ability to secrete cytokines upon exogenous stimuli. In conclusion, a highly active and specific TALEN to disrupt CCR5 is successfully engineered, paving the way for its clinical application in hematopoietic stem cell grafts.
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Affiliation(s)
- Marianna Romito
- Institute for Transfusion Medicine and Gene Therapy, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Freiburg, 79106, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, 79110, Germany
| | | | - Yik Lim Kok
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, 8091, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, 8057, Switzerland
| | - Markus Hildenbeutel
- Institute for Transfusion Medicine and Gene Therapy, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Freiburg, 79106, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, 79110, Germany
| | - Manuel Rhiel
- Institute for Transfusion Medicine and Gene Therapy, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Freiburg, 79106, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, 79110, Germany
| | - Geoffroy Andrieux
- Faculty of Medicine, University of Freiburg, Freiburg, 79110, Germany.,Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, 79110, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany and German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | | | | | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Freiburg, 79106, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, 79110, Germany
| | | | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, 8091, Switzerland.,Institute of Medical Virology, University of Zurich, Zurich, 8057, Switzerland
| | | | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Freiburg, 79106, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, 79110, Germany
| | - Tatjana I Cornu
- Institute for Transfusion Medicine and Gene Therapy, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Freiburg, 79106, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, 79110, Germany
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18
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Graham N, Patil GB, Bubeck DM, Dobert RC, Glenn KC, Gutsche AT, Kumar S, Lindbo JA, Maas L, May GD, Vega-Sanchez ME, Stupar RM, Morrell PL. Plant Genome Editing and the Relevance of Off-Target Changes. PLANT PHYSIOLOGY 2020; 183:1453-1471. [PMID: 32457089 PMCID: PMC7401131 DOI: 10.1104/pp.19.01194] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 05/07/2020] [Indexed: 05/12/2023]
Abstract
Site-directed nucleases (SDNs) used for targeted genome editing are powerful new tools to introduce precise genetic changes into plants. Like traditional approaches, such as conventional crossing and induced mutagenesis, genome editing aims to improve crop yield and nutrition. Next-generation sequencing studies demonstrate that across their genomes, populations of crop species typically carry millions of single nucleotide polymorphisms and many copy number and structural variants. Spontaneous mutations occur at rates of ∼10-8 to 10-9 per site per generation, while variation induced by chemical treatment or ionizing radiation results in higher mutation rates. In the context of SDNs, an off-target change or edit is an unintended, nonspecific mutation occurring at a site with sequence similarity to the targeted edit region. SDN-mediated off-target changes can contribute to a small number of additional genetic variants compared to those that occur naturally in breeding populations or are introduced by induced-mutagenesis methods. Recent studies show that using computational algorithms to design genome editing reagents can mitigate off-target edits in plants. Finally, crops are subject to strong selection to eliminate off-type plants through well-established multigenerational breeding, selection, and commercial variety development practices. Within this context, off-target edits in crops present no new safety concerns compared to other breeding practices. The current generation of genome editing technologies is already proving useful to develop new plant varieties with consumer and farmer benefits. Genome editing will likely undergo improved editing specificity along with new developments in SDN delivery and increasing genomic characterization, further improving reagent design and application.
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Affiliation(s)
- Nathaniel Graham
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, Minnesota 55108
- Pairwise, Durham, North Carolina 27709
| | - Gunvant B Patil
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | | | | | | | | | | | | | - Luis Maas
- Enza Zaden Research USA, San Juan Bautista, California 95045
| | | | | | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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19
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Generation of HIV-1-infected patients' gene-edited induced pluripotent stem cells using feeder-free culture conditions. AIDS 2020; 34:1127-1139. [PMID: 32501846 DOI: 10.1097/qad.0000000000002535] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVES The discovery of induced pluripotent stem cells (iPSC) has brought promise to regenerative medicine as it breaks the ethical barrier of using embryonic stem cells. Such cell culture-derived patient-specific autologous stem cells are needed for transplantation. Here we report deriving HIV-1-infected patients' iPSC lines under transgene-free methods and under feeder-free and xeno-free culture conditions to meet the requirement for clinical application. METHODS AND RESULTS We have reprogrammed patients' peripheral blood mononuclear cells with EBNA1/OriP episomal vectors, or a defective and persistent Sendai virus vector (SeVdp) to ensure a nonintegrating iPSC generation. Both single picked and pooled iPSC lines demonstrated high pluripotency and were able to differentiate into various lineage cells in vivo. The established cell lines could be modified by genetic editing using the TALENs or CRISPR/Cas 9 technology to have a bi-allelic CCR5Δ32 mutations seamlessly. All generated iPSC lines and modified cell lines had no evidence of HIV integration and maintained normal karyotype after expansion. CONCLUSIONS This study provides a reproducible simple procedure for generating therapeutic grade iPSCs from HIV-infected patients and for engineering these cells to possess a naturally occurring genotype for resistance to HIV-1 infection when differentiated into immune cells.
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20
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Genome Editing of the SNAI1 Gene in Rhabdomyosarcoma: A Novel Model for Studies of Its Role. Cells 2020; 9:cells9051095. [PMID: 32354171 PMCID: PMC7290443 DOI: 10.3390/cells9051095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/17/2020] [Accepted: 04/22/2020] [Indexed: 12/16/2022] Open
Abstract
Genome editing (GE) tools and RNA interference technology enable the modulation of gene expression in cancer research. While GE mediated by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 or transcription activator-like effector nucleases (TALEN) activity can be used to induce gene knockouts, shRNA interacts with the targeted transcript, resulting in gene knockdown. Here, we compare three different methods for SNAI1 knockout or knockdown in rhabdomyosarcoma (RMS) cells. RMS is the most common sarcoma in children and its development has been previously associated with SNAI1 transcription factor activity. To investigate the role of SNAI1 in RMS development, we compared CRISPR/Cas9, TALEN, and shRNA tools to identify the most efficient tool for the modulation of SNAI1 expression with biological effects. Subsequently, the genome sequence, transcript levels, and protein expression of SNAI1 were evaluated. The modulation of SNAI1 using three different approaches affected the morphology of the cells and modulated the expression of myogenic factors and HDAC1. Our study revealed a similar effectiveness of the tested methods. Nevertheless, the low efficiency of the GE tools was a limiting factor in obtaining biallelic gene knockouts. To conclude, we established and characterized three different models of SNAI1 knockout and knockdown that might be used in further studies investigating the role of SNAI1 in RMS.
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21
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Pino-Barrio MJ, Giménez Y, Villanueva M, Hildenbeutel M, Sánchez-Dominguez R, Rodríguez-Perales S, Pujol R, Surrallés J, Río P, Cathomen T, Mussolino C, Bueren JA, Navarro S. TALEN mediated gene editing in a mouse model of Fanconi anemia. Sci Rep 2020; 10:6997. [PMID: 32332829 PMCID: PMC7181878 DOI: 10.1038/s41598-020-63971-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 02/28/2020] [Indexed: 01/05/2023] Open
Abstract
The promising ability to genetically modify hematopoietic stem and progenitor cells by precise gene editing remains challenging due to their sensitivity to in vitro manipulations and poor efficiencies of homologous recombination. This study represents the first evidence of implementing a gene editing strategy in a murine safe harbor locus site that phenotypically corrects primary cells from a mouse model of Fanconi anemia A. By means of the co-delivery of transcription activator-like effector nucleases and a donor therapeutic FANCA template to the Mbs85 locus, we achieved efficient gene targeting (23%) in mFA-A fibroblasts. This resulted in the phenotypic correction of these cells, as revealed by the reduced sensitivity of these cells to mitomycin C. Moreover, robust evidence of targeted integration was observed in murine wild type and FA-A hematopoietic progenitor cells, reaching mean targeted integration values of 21% and 16% respectively, that were associated with the phenotypic correction of these cells. Overall, our results demonstrate the feasibility of implementing a therapeutic targeted integration strategy into the mMbs85 locus, ortholog to the well-validated hAAVS1, constituting the first study of gene editing in mHSC with TALEN, that sets the basis for the use of a new safe harbor locus in mice.
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Affiliation(s)
- Maria José Pino-Barrio
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Yari Giménez
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Mariela Villanueva
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Marcus Hildenbeutel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Rebeca Sánchez-Dominguez
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Sandra Rodríguez-Perales
- Molecular Cytogenetics Group, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernandez Almagro, 3, 28029, Madrid, Spain
| | - Roser Pujol
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
- Genome Instability and DNA Repair Group, Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - Jordi Surrallés
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
- Genome Instability and DNA Repair Group, Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
| | - Paula Río
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, 79106, Freiburg, Germany
| | - Juan Antonio Bueren
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain.
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain.
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain.
| | - Susana Navarro
- Division of Hematopoietic Innovative Therapies, CIEMAT/CIBERER, 28040, Madrid, Spain.
- Advanced Therapies Unit, IIS-Fundación Jimenez Diaz (IIS-FJD, UAM), 28040, Madrid, Spain.
- Center for Biomedical Network Research on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain.
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22
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Fleischer A, Vallejo-Díez S, Martín-Fernández JM, Sánchez-Gilabert A, Castresana M, Del Pozo A, Esquisabel A, Ávila S, Castrillo JL, Gaínza E, Pedraz JL, Viñas M, Bachiller D. iPSC-Derived Intestinal Organoids from Cystic Fibrosis Patients Acquire CFTR Activity upon TALEN-Mediated Repair of the p.F508del Mutation. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:858-870. [PMID: 32373648 PMCID: PMC7195499 DOI: 10.1016/j.omtm.2020.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/13/2020] [Indexed: 12/19/2022]
Abstract
Cystic fibrosis (CF) is the main genetic cause of death among the Caucasian population. The disease is characterized by abnormal fluid and electrolyte mobility across secretory epithelia. The first manifestations occur within hours of birth (meconium ileus), later extending to other organs, generally affecting the respiratory tract. It is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. CFTR encodes a cyclic adenosine monophosphate (cAMP)-dependent, phosphorylation-regulated chloride channel required for transport of chloride and other ions through cell membranes. There are more than 2,000 mutations described in the CFTR gene, but one of them, phenylalanine residue at amino acid position 508 (p.F508del), a recessive allele, is responsible for the vast majority of CF cases worldwide. Here, we present the results of the application of genome-editing techniques to the restoration of CFTR activity in p.F508del patient-derived induced pluripotent stem cells (iPSCs). Gene-edited iPSCs were subsequently used to produce intestinal organoids on which the physiological activity of the restored gene was tested in forskolin-induced swelling tests. The seamless restoration of the p.F508del mutation resulted in normal expression of the mature CFTR glycoprotein, full recovery of CFTR activity, and a normal response of the repaired organoids to treatment with two approved CF therapies: VX-770 and VX-809.
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Affiliation(s)
- Aarne Fleischer
- Karuna Good Cells Technologies S.L., C/Cercas Bajas 13 Bajo, 01001 Vitoria-Gasteiz, Spain
| | - Sara Vallejo-Díez
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Miguel Marqués 21, 07190 Esporles, Spain
| | | | | | - Mónica Castresana
- Karuna Good Cells Technologies S.L., C/Cercas Bajas 13 Bajo, 01001 Vitoria-Gasteiz, Spain
| | | | - Amaia Esquisabel
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.,Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain
| | - Silvia Ávila
- Genetadi Biotech S.L., Parque Tecnológico de Bizkaia, 48160 Derio, Spain
| | | | | | - José Luis Pedraz
- NanoBioCel Group, Laboratory of Pharmaceutics, School of Pharmacy, University of the Basque Country (UPV/EHU), Paseo de la Universidad 7, 01006 Vitoria-Gasteiz, Spain.,Networking Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Vitoria-Gasteiz, Spain
| | - Miguel Viñas
- Laboratory of Molecular Microbiology and Antimicrobials, Department of Pathology and Experimental Therapeutics, University of Barcelona, 08097 Barcelona, Spain
| | - Daniel Bachiller
- Consejo Superior de Investigaciones Científicas (CSIC/IMEDEA), Miguel Marqués 21, 07190 Esporles, Spain
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23
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Zhang ZY, Thrasher AJ, Zhang F. Gene therapy and genome editing for primary immunodeficiency diseases. Genes Dis 2020; 7:38-51. [PMID: 32181274 PMCID: PMC7063425 DOI: 10.1016/j.gendis.2019.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/20/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
In past two decades the gene therapy using genetic modified autologous hematopoietic stem cells (HSCs) transduced with the viral vector has become a promising alternative option for treating primary immunodeficiency diseases (PIDs). Despite of some pitfalls at early stage clinical trials, the field of gene therapy has advanced significantly in the last decade with improvements in viral vector safety, preparatory regime for manufacturing high quality virus, automated CD34 cell purification. Hence, the overall outcome from the clinical trials for the different PIDs has been very encouraging. In addition to the viral vector based gene therapy, the recent fast moving forward developments in genome editing using engineered nucleases in HSCs has provided a new promising platform for the treatment of PIDs. This review provides an overall outcome and progress in gene therapy clinical trials for SCID-X, ADA-SCID, WAS, X- CGD, and the recent developments in genome editing technology applied in HSCs for developing potential therapy, particular in the key studies for PIDs.
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Affiliation(s)
- Zhi-Yong Zhang
- Department of Immunology and Rheumatology, Children's Hospital of Chongqing Medical University, China
| | - Adrian J. Thrasher
- Molecular and Cellular Immunology, Great Ormond Street Institute of Child Health, University Colleage London, UK
| | - Fang Zhang
- Molecular and Cellular Immunology, Great Ormond Street Institute of Child Health, University Colleage London, UK
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24
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Ashmore-Harris C, Fruhwirth GO. The clinical potential of gene editing as a tool to engineer cell-based therapeutics. Clin Transl Med 2020; 9:15. [PMID: 32034584 PMCID: PMC7007464 DOI: 10.1186/s40169-020-0268-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/29/2020] [Indexed: 12/13/2022] Open
Abstract
The clinical application of ex vivo gene edited cell therapies first began a decade ago with zinc finger nuclease editing of autologous CD4+ T-cells. Editing aimed to disrupt expression of the human immunodeficiency virus co-receptor gene CCR5, with the goal of yielding cells resistant to viral entry, prior to re-infusion into the patient. Since then the field has substantially evolved with the arrival of the new editing technologies transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR), and the potential benefits of gene editing in the arenas of immuno-oncology and blood disorders were quickly recognised. As the breadth of cell therapies available clinically continues to rise there is growing interest in allogeneic and off-the-shelf approaches and multiplex editing strategies are increasingly employed. We review here the latest clinical trials utilising these editing technologies and consider the applications on the horizon.
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Affiliation(s)
- Candice Ashmore-Harris
- Imaging Therapy and Cancer Group, Dept of Imaging Chemistry & Biology, School of Biomedical Engineering & Imaging Sciences, St Thomas' Hospital, King's College London (KCL), London, SE1 7EH, UK
- Centre for Stem Cells & Regenerative Medicine, School of Basic and Medical Biosciences, Guy's Hospital, KCL, London, SE1 9RT, UK
| | - Gilbert O Fruhwirth
- Imaging Therapy and Cancer Group, Dept of Imaging Chemistry & Biology, School of Biomedical Engineering & Imaging Sciences, St Thomas' Hospital, King's College London (KCL), London, SE1 7EH, UK.
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25
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Wan H, Li JM, Ding H, Lin SX, Tu SQ, Tian XH, Hu JP, Chang S. An Overview of Computational Tools of Nucleic Acid Binding Site Prediction for Site-specific Proteins and Nucleases. Protein Pept Lett 2019; 27:370-384. [PMID: 31746287 DOI: 10.2174/0929866526666191028162302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/24/2019] [Accepted: 09/24/2019] [Indexed: 12/26/2022]
Abstract
Understanding the interaction mechanism of proteins and nucleic acids is one of the most fundamental problems for genome editing with engineered nucleases. Due to some limitations of experimental investigations, computational methods have played an important role in obtaining the knowledge of protein-nucleic acid interaction. Over the past few years, dozens of computational tools have been used for identification of nucleic acid binding site for site-specific proteins and design of site-specific nucleases because of their significant advantages in genome editing. Here, we review existing widely-used computational tools for target prediction of site-specific proteins as well as off-target prediction of site-specific nucleases. This article provides a list of on-line prediction tools according to their features followed by the description of computational methods used by these tools, which range from various sequence mapping algorithms (like Bowtie, FetchGWI and BLAST) to different machine learning methods (such as Support Vector Machine, hidden Markov models, Random Forest, elastic network and deep neural networks). We also make suggestions on the further development in improving the accuracy of prediction methods. This survey will provide a reference guide for computational biologists working in the field of genome editing.
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Affiliation(s)
- Hua Wan
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Ming Li
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Huang Ding
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Shuo-Xin Lin
- Department of Electrical and Computer Engineering, James Clark School of Engineering, University of Maryland, College Park, MD 20742, United States
| | - Shu-Qin Tu
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Xu-Hong Tian
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Ping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu 610106, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
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26
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Kuo CY, Long JD, Campo-Fernandez B, de Oliveira S, Cooper AR, Romero Z, Hoban MD, Joglekar AV, Lill GR, Kaufman ML, Fitz-Gibbon S, Wang X, Hollis RP, Kohn DB. Site-Specific Gene Editing of Human Hematopoietic Stem Cells for X-Linked Hyper-IgM Syndrome. Cell Rep 2019; 23:2606-2616. [PMID: 29847792 DOI: 10.1016/j.celrep.2018.04.103] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/29/2018] [Accepted: 04/24/2018] [Indexed: 10/16/2022] Open
Abstract
X-linked hyper-immunoglobulin M (hyper-IgM) syndrome (XHIM) is a primary immunodeficiency due to mutations in CD40 ligand that affect immunoglobulin class-switch recombination and somatic hypermutation. The disease is amenable to gene therapy using retroviral vectors, but dysregulated gene expression results in abnormal lymphoproliferation in mouse models, highlighting the need for alternative strategies. Here, we demonstrate the ability of both the transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) platforms to efficiently drive integration of a normal copy of the CD40L cDNA delivered by Adeno-Associated Virus. Site-specific insertion of the donor sequence downstream of the endogenous CD40L promoter maintained physiologic expression of CD40L while overriding all reported downstream mutations. High levels of gene modification were achieved in primary human hematopoietic stem cells (HSCs), as well as in cell lines and XHIM-patient-derived T cells. Notably, gene-corrected HSCs engrafted in immunodeficient mice at clinically relevant frequencies. These studies provide the foundation for a permanent curative therapy in XHIM.
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Affiliation(s)
- Caroline Y Kuo
- Division of Allergy & Immunology, Department of Pediatrics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Joseph D Long
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Beatriz Campo-Fernandez
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Satiro de Oliveira
- Division of Hematology & Oncology, Department of Pediatrics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aaron R Cooper
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zulema Romero
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Megan D Hoban
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alok V Joglekar
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Georgia R Lill
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael L Kaufman
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sorel Fitz-Gibbon
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xiaoyan Wang
- Department of General Internal Medicine and Health Services Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Roger P Hollis
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Donald B Kohn
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Division of Hematology & Oncology, Department of Pediatrics, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA 90095, USA
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27
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Shigemura T, Matsuda K, Kurata T, Sakashita K, Okuno Y, Muramatsu H, Yue F, Ebihara Y, Tsuji K, Sasaki K, Nakahata T, Nakazawa Y, Koike K. Essential role of PTPN11 mutation in enhanced haematopoietic differentiation potential of induced pluripotent stem cells of juvenile myelomonocytic leukaemia. Br J Haematol 2019; 187:163-173. [PMID: 31222725 DOI: 10.1111/bjh.16060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/03/2019] [Indexed: 12/13/2022]
Abstract
We established mutated and non-mutated induced pluripotent stem cell (iPSC) clones from a patient with PTPN11 (c.226G>A)-mutated juvenile myelomonocytic leukaemia (JMML). Both types of iPSCs fulfilled the quality criteria. Mutated iPSC colonies generated significantly more CD34+ and CD34+ CD45+ cells compared to non-mutated iPSC colonies in a culture coated with irradiated AGM-S3 cells to which four growth factors were added sequentially or simultaneously. The haematopoietic differentiation potential of non-mutated JMML iPSC colonies was similar to or lower than that of iPSC colonies from a healthy individual. The PTPN11 mutation coexisted with the OSBP2 c.389C>T mutation. Zinc-finger nuclease-mediated homologous recombination revealed that correction of PTPN11 mutation in iPSCs with PTPN11 and OSBP2 mutations resulted in reduced CD34+ cell generation to a level similar to that obtained with JMML iPSC colonies with the wild-type of both genes, and interestingly, to that obtained with normal iPSC colonies. Transduction of the PTPN11 mutation into JMML iPSCs with the wild-type of both genes increased CD34+ cell production to a level comparable to that obtained with JMML iPSC colonies harbouring the two genetic mutations. Thus, PTPN11 mutation may be the most essential abnormality to confer an aberrant haematopoietic differentiation potential in this disorder.
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Affiliation(s)
- Tomonari Shigemura
- Department of Paediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kazuyuki Matsuda
- Department of Health and Medical Sciences, Graduate School of Medicine, Shinshu University, Matsumoto, Japan
| | - Takashi Kurata
- Department of Paediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kazuo Sakashita
- Department of Haematology/Oncology, Nagano Children's Hospital, Azumino, Japan
| | - Yusuke Okuno
- Department of Paediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Paediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Fengming Yue
- Department of Anatomy and Organ Technology, Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, Shinshu University Graduate School of Medicine, Matsumoto, Japan
| | - Yasuhiro Ebihara
- Department of Laboratory Medicine, International Medical Centre, Saitama Medical University, Hidaka, Japan
| | - Kohichiro Tsuji
- Department of Paediatrics, Komoro Kogen Hospital, Komoro, Japan
| | - Katsunori Sasaki
- Department of Anatomy and Organ Technology, Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, Shinshu University Graduate School of Medicine, Matsumoto, Japan
| | - Tatsutoshi Nakahata
- Department of Clinical Application, Centre for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Yozo Nakazawa
- Department of Paediatrics, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kenichi Koike
- Department of Paediatrics, Shinshu University School of Medicine, Matsumoto, Japan.,Minami Nagano Medical Centre, Shinonoi General Hospital, Nagano, Japan
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28
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Uniyal AP, Mansotra K, Yadav SK, Kumar V. An overview of designing and selection of sgRNAs for precise genome editing by the CRISPR-Cas9 system in plants. 3 Biotech 2019; 9:223. [PMID: 31139538 PMCID: PMC6529479 DOI: 10.1007/s13205-019-1760-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 05/13/2019] [Indexed: 12/26/2022] Open
Abstract
A large number of computational tools have been documented in recent years for identification of target-specific valid single-guide (sg) RNAs (18-20 nucleotide long sequence) that is an important component for the efficient utilization of the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated Protein) system. Despite optimization of Cas9, other major concerns are on-target efficiency and off-target activity that depend upon the sequence(s) of target-specific sgRNA(s). However, a very little attention has been paid for identification of the best-hit sgRNA for precise targeting as well as minimizing the off-target effects. The aim of this present work is to offer comparative insight into existing CRISPR software tools with their unique features (including targeted genome) and utilities. These available web tools were found to be designed based upon only a few limited mathematical models. Among all these available web tools, three (Benchling, Desktop and CRISPR-P) have been curated as exclusively available for plant genome-editing purpose. These three software tools have been comprehensively described and analyzed with single same target enquiry from two randomly selected genes (IDM2 and IDM3 from Arabidopsis thaliana). Interestingly, all these selected tools generated different results (sgRNAs) even for the same query. In fact, the sequence of sgRNA is considered an important parameter to determine the efficiency and specificity of sgRNAs for precise genome editing. Thus, there is an urgent requirement to pay attention for a validated sgRNA-designing tool for precise DNA editing in plants. In conclusion, this work will encourage building up a consensus for developing a universal valid sgRNA designing for different organisms including plants.
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Affiliation(s)
- Ajay Prakash Uniyal
- Department of Plant Sciences, School for Basic and Applied Sciences, Central University of Punjab, Bathinda, 161001 India
| | - Komal Mansotra
- Department of Plant Sciences, School for Basic and Applied Sciences, Central University of Punjab, Bathinda, 161001 India
| | | | - Vinay Kumar
- Department of Plant Sciences, School for Basic and Applied Sciences, Central University of Punjab, Bathinda, 161001 India
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29
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Anephrogenic phenotype induced by SALL1 gene knockout in pigs. Sci Rep 2019; 9:8016. [PMID: 31142767 PMCID: PMC6541644 DOI: 10.1038/s41598-019-44387-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 05/13/2019] [Indexed: 11/08/2022] Open
Abstract
To combat organ shortage in transplantation medicine, a novel strategy has been proposed to generate human organs from exogenous pluripotent stem cells utilizing the developmental mechanisms of pig embryos/foetuses. Genetically modified pigs missing specific organs are key elements in this strategy. In this study, we demonstrate the feasibility of using a genome-editing approach to generate anephrogenic foetuses in a genetically engineered pig model. SALL1 knockout (KO) was successfully induced by injecting genome-editing molecules into the cytoplasm of pig zygotes, which generated the anephrogenic phenotype. Extinguished SALL1 expression and marked dysgenesis of nephron structures were observed in the rudimentary kidney tissue of SALL1-KO foetuses. Biallelic KO mutations of the target gene induced nephrogenic defects; however, biallelic mutations involving small in-frame deletions did not induce the anephrogenic phenotype. Through production of F1 progeny from mutant founder pigs, we identified mutations that could reliably induce the anephrogenic phenotype and hence established a line of fertile SALL1-mutant pigs. Our study lays important technical groundwork for the realization of human kidney regeneration through the use of an empty developmental niche in pig foetuses.
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30
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Pathak BP, Pruett E, Guan H, Srivastava V. Utility of I-SceI and CCR5-ZFN nucleases in excising selectable marker genes from transgenic plants. BMC Res Notes 2019; 12:272. [PMID: 31088537 PMCID: PMC6518718 DOI: 10.1186/s13104-019-4304-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/04/2019] [Indexed: 11/21/2022] Open
Abstract
Objectives Removal of selection marker genes from transgenic plants is highly desirable for their regulatory approval and public acceptance. This study evaluated the use of two nucleases, the yeast homing endonuclease, I-SceI, and the designed zinc finger nuclease, CCR5-ZFN, in excising marker genes from plants using rice and Arabidopsis as the models. Results In an in vitro culture assay, both nucleases were effective in precisely excising the DNA fragments marked by the nuclease target sites. However, rice cultures were found to be refractory to transformation with the I-SceI and CCR5-ZFN overexpressing constructs. The inducible I-SceI expression was also problematic in rice as the progeny of the transgenic lines expressing the heat-inducible I-SceI did not inherit the functional gene. On the other hand, heat-inducible I-SceI expression in Arabidopsis was effective in creating somatic excisions in transgenic plants but ineffective in generating heritable excisions. The inducible expression of CCR5-ZFN in rice, although transmitted stably to the progeny, appeared ineffective in creating detectable excisions. Therefore, toxicity of these nucleases in plant cells poses major bottleneck in their application in plant biotechnology, which could be avoided by expressing them transiently in cultures in vitro. Electronic supplementary material The online version of this article (10.1186/s13104-019-4304-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bhuvan P Pathak
- Dept. of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA.,Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
| | - Eliott Pruett
- Dept. of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA.,Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
| | - Huazhong Guan
- Dept. of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA.,Fujian Provincial Key Laboratory of Crop Breeding, Fujian Agricultural & Forestry University, Fuzhou, China
| | - Vibha Srivastava
- Dept. of Crop, Soil & Environmental Sciences, University of Arkansas, Fayetteville, AR, USA. .,Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA. .,Dept. of Horticulture, University of Arkansas, Fayetteville, AR, USA.
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31
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Patsali P, Turchiano G, Papasavva P, Romito M, Loucari CC, Stephanou C, Christou S, Sitarou M, Mussolino C, Cornu TI, Antoniou MN, Lederer CW, Cathomen T, Kleanthous M. Correction of IVS I-110(G>A) β-thalassemia by CRISPR/Cas-and TALEN-mediated disruption of aberrant regulatory elements in human hematopoietic stem and progenitor cells. Haematologica 2019; 104:e497-e501. [PMID: 31004018 DOI: 10.3324/haematol.2018.215178] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Giandomenico Turchiano
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany
| | - Panayiota Papasavva
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Marianna Romito
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany
| | - Constantinos C Loucari
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Coralea Stephanou
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,Department of Medical and Molecular Genetics, King's College London, London, UK
| | | | - Maria Sitarou
- Thalassemia Center, Cyprus Ministry of Health, Cyprus
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany
| | - Tatjana I Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany
| | - Michael N Antoniou
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Carsten W Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus .,Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center, University of Freiburg, Freiburg, Germany .,Center for Chronic Immunodeficiency, Medical Center, University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus .,Cyprus School of Molecular Medicine, Nicosia, Cyprus
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32
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Passricha N, Saifi SK, Kharb P, Tuteja N. Marker-free transgenic rice plant overexpressing pea LecRLK imparts salinity tolerance by inhibiting sodium accumulation. PLANT MOLECULAR BIOLOGY 2019; 99:265-281. [PMID: 30604324 DOI: 10.1007/s11103-018-0816-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 12/18/2018] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE PsLecRLK overexpression in rice provides tolerance against salinity stress and cause upregulation of SOS1 pathway genes, which are responsible for extrusion of excess Na+ ion under stress condition. Soil salinity is one of the most devastating factors threatening cultivable land. Rice is a major staple crop and immensely affected by soil salinity. The small genome size of rice relative to wheat and barley, together with its salt sensitivity, makes it an ideal candidate for studies on salt stress response caused by a particular gene. Under stress conditions crosstalk between organelles and cell to cell response is imperative. LecRLK is an important family, which plays a key role under stress conditions and regulates the physiology of the plant. Here we have functionally validated the PsLecRLK gene in rice for salinity stress tolerance and hypothesized the model for its working. Salt stress sensitive rice variety IR64 was used for developing marker-free transgenic with modified binary vector pCAMBIA1300 overexpressing PsLecRLK gene. Comparison of transgenic and wild-type (WT) plants showed better physiological and biochemical results in transgenic lines with a low level of ROS, MDA and ion accumulation and a higher level of proline, relative water content, root/shoot ration, enzymatic activities of ROS scavengers and upregulation of stress-responsive genes. Based on the relative expression of stress-responsive genes and ionic content, the working model highlights the role of PsLecRLK in the extrusion of Na+ ion from the cell. This extrusion of Na+ ion is facilitated by higher expression of SOS1 (Na+/K+ channel) in transgenic plants as compared to WT plants. Altered expression of stress-responsive genes and change in biochemical and physiological properties of the cell suggests an extensive reprogramming of the stress-responsive metabolic pathways by PsLecRLK under stress condition, which could be responsible for the salt tolerance capability.
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MESH Headings
- Adaptation, Physiological/drug effects
- Adaptation, Physiological/genetics
- Calcium/metabolism
- Cell Death
- Cell Membrane/drug effects
- Cloning, Molecular
- Gene Expression Regulation, Plant/drug effects
- Gene Expression Regulation, Plant/genetics
- Genes, Plant
- Germination
- Homozygote
- Ions
- Oryza/genetics
- Oryza/metabolism
- Pisum sativum/genetics
- Pisum sativum/metabolism
- Plant Proteins/genetics
- Plant Proteins/metabolism
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Protein Transport/drug effects
- Reactive Oxygen Species/metabolism
- Receptors, Mitogen/genetics
- Receptors, Mitogen/metabolism
- SOS1 Protein/genetics
- SOS1 Protein/metabolism
- Salinity
- Salt Tolerance/genetics
- Salt Tolerance/physiology
- Sodium/metabolism
- Sodium Chloride/metabolism
- Sodium Chloride/pharmacology
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Up-Regulation
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Affiliation(s)
- Nishat Passricha
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shabnam K Saifi
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Pushpa Kharb
- Department of Molecular Biology, Biotechnology and Bioinformatics, COBS&H, CCS Haryana Agricultural University, Hisar, Haryana, 125004, India
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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33
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TALEN-Mediated Gene Editing of HBG in Human Hematopoietic Stem Cells Leads to Therapeutic Fetal Hemoglobin Induction. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 12:175-183. [PMID: 30705922 PMCID: PMC6348980 DOI: 10.1016/j.omtm.2018.12.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/22/2018] [Indexed: 01/03/2023]
Abstract
Elements within the γ-hemoglobin promoters (HBG1 and HBG2) function to bind transcription complexes that mediate repression of fetal hemoglobin expression. Sickle cell disease (SCD) subjects with a 13-bp deletion in the HBG1 promoter exhibit a clinically favorable hereditary persistence of fetal hemoglobin (HPFH) phenotype. We developed TALENs targeting the homologous HBG promoters to de-repress fetal hemoglobin. Transfection of human CD34+ cells with TALEN mRNA resulted in indel generation in HBG1 (43%) and HBG2 (74%) including the 13-bp HPFH deletion (∼6%). Erythroid differentiation of edited cells revealed a 4.6-fold increase in γ-hemoglobin expression as detected by HPLC. Assessment of TALEN-edited CD34+ cells in vivo in a humanized mouse model demonstrated sustained presence of indels in hematopoietic cells up to 24 weeks. Indel rates remained unchanged following secondary transplantation consistent with editing of long-term repopulating stem cells (LT-HSCs). Human γ-hemoglobin expressing F cells were detected by flow cytometry approximately 50% more frequently in edited animals compared to mock. Together, these findings demonstrate that TALEN-mediated indel generation in the γ-hemoglobin promoter leads to high levels of fetal hemoglobin expression in vitro and in vivo, suggesting that this approach can provide therapeutic benefit in patients with SCD or β-thalassemia.
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34
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Kadam US, Shelake RM, Chavhan RL, Suprasanna P. Concerns regarding 'off-target' activity of genome editing endonucleases. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 131:22-30. [PMID: 29653762 DOI: 10.1016/j.plaphy.2018.03.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 03/21/2018] [Accepted: 03/23/2018] [Indexed: 05/15/2023]
Abstract
Genome editing (GE) tools ensure targeted mutagenesis and sequence-specific modification in plants using a wide resource of customized endonucleases; namely, zinc-finger nucleases (ZFNs), and transcription activator-like effector nucleases (TALENs), and the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated protein) system. Among these, in recent times CRISPR/Cas9 has been widely used in functional genomics and plant genetic modification. A significant concern in the application of GE tools is the occurrence of 'off-target' activity and induced mutations, which may impede functional analysis and gene activity studies. Moreover, the 'off-target' activity results in either not reported or unknown, difficult to detect, produce non-quantifiable cellular signaling and physiological effects. In the past few years, several experimental methods have been developed to identify undesired mutations and to curtail 'off-target' cleavage. Improvement in target specificity and minimizing 'off-target' activity will offer better applications of GE technology in plant biology and crop improvement.
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Affiliation(s)
- Ulhas Sopanrao Kadam
- VD College of Agricultural Biotechnology, Latur, Maharashtra, India; Max-Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Rahul Mahadev Shelake
- Plant Molecular Biology & Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Rahul L Chavhan
- VD College of Agricultural Biotechnology, Latur, Maharashtra, India
| | - Penna Suprasanna
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
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35
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Targeted Genome Engineering in Xenopus Using the Transcription Activator-Like Effector Nuclease (TALEN) Technology. Methods Mol Biol 2018; 1865:55-65. [PMID: 30151758 DOI: 10.1007/978-1-4939-8784-9_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Targeted genome engineering technologies are revolutionizing the field of functional genomics and have been extensively used in a variety of model organisms, including X. tropicalis and X. laevis. The original methods based on Zn-finger proteins coupled to endonuclease domains were initially replaced by the more efficient and straightforward transcription activator-like effector nucleases (TALENs), adapted from plant pathogenic Xanthomonas species. Although functional genomics are more recently dominated by the even faster and more convenient CRISPR/Cas9 technology, the use of TALENs may still be preferred in a number of cases. We have successfully implemented this technology in Xenopus and in this chapter we describe our working protocol for targeted genome editing in X. tropicalis using TALENs.
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36
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Horvat F, Fulka H, Jankele R, Malik R, Jun M, Solcova K, Sedlacek R, Vlahovicek K, Schultz RM, Svoboda P. Role of Cnot6l in maternal mRNA turnover. Life Sci Alliance 2018; 1:e201800084. [PMID: 30456367 PMCID: PMC6238536 DOI: 10.26508/lsa.201800084] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/04/2018] [Accepted: 07/05/2018] [Indexed: 01/09/2023] Open
Abstract
Removal of poly(A) tail is an important mechanism controlling eukaryotic mRNA turnover. The major eukaryotic deadenylase complex CCR4-NOT contains two deadenylase components, CCR4 and CAF1, for which mammalian CCR4 is encoded by Cnot6 or Cnot6l paralogs. We show that Cnot6l apparently supplies the majority of CCR4 in the maternal CCR4-NOT in mouse, hamster, and bovine oocytes. Deletion of Cnot6l yielded viable mice, but Cnot6l -/- females exhibited ∼40% smaller litter size. The main onset of the phenotype was post-zygotic: fertilized Cnot6l -/- eggs developed slower and arrested more frequently than Cnot6l +/- eggs, suggesting that maternal CNOT6L is necessary for accurate oocyte-to-embryo transition. Transcriptome analysis revealed major transcriptome changes in Cnot6l -/- ovulated eggs and one-cell zygotes. In contrast, minimal transcriptome changes in preovulatory Cnot6l -/- oocytes were consistent with reported Cnot6l mRNA dormancy. A minimal overlap between transcripts sensitive to decapping inhibition and Cnot6l loss suggests that decapping and CNOT6L-mediated deadenylation selectively target distinct subsets of mRNAs during oocyte-to-embryo transition in mouse.
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Affiliation(s)
- Filip Horvat
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Helena Fulka
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Institute of Animal Science, Prague, Czech Republic
| | - Radek Jankele
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radek Malik
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ma Jun
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Katerina Solcova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics and Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v. v. i., Vestec, Czech Republic
| | - Kristian Vlahovicek
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.,Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Petr Svoboda
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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37
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Hu Z, Wu Y, Zhou M, Wang X, Pang J, Li Z, Feng M, Wang Y, Hu Q, Zhao J, Liu X, Wu L, Liang D. Generation of reporter hESCs by targeting EGFP at the CD144 locus to facilitate the endothelial differentiation. Dev Growth Differ 2018; 60:205-215. [PMID: 29696633 DOI: 10.1111/dgd.12433] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/14/2018] [Accepted: 03/19/2018] [Indexed: 12/31/2022]
Abstract
Reporter embryonic stem cell (ESC) lines with tissue-specific reporter genes may contribute to optimizing the differentiation conditions in vitro as well as trafficking transplanted cells in vivo. To optimize and monitor endothelial cell (EC) differentiation specifically, here we targeted the enhanced green fluorescent protein (EGFP) reporter gene at the junction of 5'UTR and exon2 of the endothelial specific marker gene CD144 using TALENs in human ESCs (H9) to generate a EGFP-CD144-reporter ESC line. The reporter cells expressed EGFP and CD144 increasingly and specifically without unexpected effects during the EC differentiation. The EC differentiation protocol was optimized and applied to EC differentiation from hiPSCs, resulting in an efficient and simplified endothelial differentiation approach. Here we created our own optimized and robust protocol for EC differentiation of hESCs and hiPSCs by generating the lineage-specific site-specific integration reporter cell lines, showing great potential to be applied in the fields such as trafficking gene and cell fate in vivo in preclinical animal models.
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Affiliation(s)
- Zhiqing Hu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yong Wu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Miaojin Zhou
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xiaolin Wang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jialun Pang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhuo Li
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Mai Feng
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yanchi Wang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qian Hu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Junya Zhao
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xionghao Liu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lingqian Wu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Desheng Liang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
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38
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Tanaka Y, Sone T, Higurashi N, Sakuma T, Suzuki S, Ishikawa M, Yamamoto T, Mitsui J, Tsuji H, Okano H, Hirose S. Generation of D1-1 TALEN isogenic control cell line from Dravet syndrome patient iPSCs using TALEN-mediated editing of the SCN1A gene. Stem Cell Res 2018; 28:100-104. [DOI: 10.1016/j.scr.2018.01.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 01/19/2018] [Accepted: 01/24/2018] [Indexed: 10/18/2022] Open
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39
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Mencía Á, Chamorro C, Bonafont J, Duarte B, Holguin A, Illera N, Llames SG, Escámez MJ, Hausser I, Del Río M, Larcher F, Murillas R. Deletion of a Pathogenic Mutation-Containing Exon of COL7A1 Allows Clonal Gene Editing Correction of RDEB Patient Epidermal Stem Cells. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 11:68-78. [PMID: 29858091 PMCID: PMC5852297 DOI: 10.1016/j.omtn.2018.01.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/23/2018] [Accepted: 01/23/2018] [Indexed: 11/18/2022]
Abstract
Recessive dystrophic epidermolysis bullosa is a severe skin fragility disease caused by loss of functional type VII collagen at the dermal-epidermal junction. A frameshift mutation in exon 80 of COL7A1 gene, c.6527insC, is highly prevalent in the Spanish patient population. We have implemented gene-editing strategies for COL7A1 frame restoration by NHEJ-induced indels in epidermal stem cells from patients carrying this mutation. TALEN nucleases designed to cut within the COL7A1 exon 80 sequence were delivered to primary patient keratinocyte cultures by non-integrating viral vectors. After genotyping a large collection of vector-transduced patient keratinocyte clones with high proliferative potential, we identified a significant percentage of clones with COL7A1 reading frame recovery and Collagen VII protein expression. Skin equivalents generated with cells from a clone lacking exon 80 entirely were able to regenerate phenotypically normal human skin upon their grafting onto immunodeficient mice. These patient-derived human skin grafts showed Collagen VII deposition at the basement membrane zone, formation of anchoring fibrils, and structural integrity when analyzed 12 weeks after grafting. Our data provide a proof-of-principle for recessive dystrophic epidermolysis bullosa treatment through ex vivo gene editing based on removal of pathogenic mutation-containing, functionally expendable COL7A1 exons in patient epidermal stem cells.
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Affiliation(s)
- Ángeles Mencía
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain
| | - Cristina Chamorro
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain
| | - Jose Bonafont
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain
| | - Blanca Duarte
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain
| | - Almudena Holguin
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain
| | - Nuria Illera
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain
| | - Sara G Llames
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain
| | - Maria José Escámez
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain
| | - Ingrid Hausser
- Institute of Pathology, Universitätsklinikum Heidelberg, Heidelberg, Germany
| | - Marcela Del Río
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain
| | - Fernando Larcher
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain.
| | - Rodolfo Murillas
- Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain; Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER) U714, Madrid, Spain.
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40
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Rinaldi FC, Doyle LA, Stoddard BL, Bogdanove AJ. The effect of increasing numbers of repeats on TAL effector DNA binding specificity. Nucleic Acids Res 2017; 45:6960-6970. [PMID: 28460076 PMCID: PMC5499867 DOI: 10.1093/nar/gkx342] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/21/2017] [Indexed: 01/27/2023] Open
Abstract
Transcription activator-like effectors (TALEs) recognize their DNA targets via tandem repeats, each specifying a single nucleotide base in a one-to-one sequential arrangement. Due to this modularity and their ability to bind long DNA sequences with high specificity, TALEs have been used in many applications. Contributions of individual repeat-nucleotide associations to affinity and specificity have been characterized. Here, using in vitro binding assays, we examined the relationship between the number of repeats in a TALE and its affinity, for both target and non-target DNA. Each additional repeat provides extra binding energy for the target DNA, with the gain decaying exponentially such that binding energy saturates. Affinity for non-target DNA also increases non-linearly with the number of repeats, but with a slower decay of gain. The difference between the effect of length on affinity for target versus non-target DNA manifests in specificity increasing then diminishing with increasing TALE length, peaking between 15 and 19 repeats. Modeling across different hypothetical saturation levels and rates of gain decay, reflecting different repeat compositions, yielded a similar range of specificity optima. This range encompasses the mean and median length of native TALEs, suggesting that these proteins as a group have evolved for maximum specificity.
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Affiliation(s)
- Fabio C Rinaldi
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Lindsey A Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research, Seattle, WA 98019, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research, Seattle, WA 98019, USA
| | - Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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41
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Leonard JL, Leonard DM, Wolfe SA, Liu J, Rivera J, Yang M, Leonard RT, Johnson JPS, Kumar P, Liebmann KL, Tutto AA, Mou Z, Simin KJ. The Dkk3 gene encodes a vital intracellular regulator of cell proliferation. PLoS One 2017; 12:e0181724. [PMID: 28738084 PMCID: PMC5524345 DOI: 10.1371/journal.pone.0181724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/06/2017] [Indexed: 11/18/2022] Open
Abstract
Members of the Dickkopf (Dkk) family of Wnt antagonists interrupt Wnt-induced receptor assembly and participate in axial patterning and cell fate determination. One family member, DKK3, does not block Wnt receptor activation. Loss of Dkk3 expression in cancer is associated with hyperproliferation and dysregulated ß-catenin signaling, and ectopic expression of Dkk3 halts cancer growth. The molecular events mediating the DKK3-dependent arrest of ß-catenin-driven cell proliferation in cancer cells are unknown. Here we report the identification of a new intracellular gene product originating from the Dkk3 locus. This Dkk3b transcript originates from a second transcriptional start site located in intron 2 of the Dkk3 gene. It is essential for early mouse development and is a newly recognized regulator of ß-catenin signaling and cell proliferation. Dkk3b interrupts nuclear translocation ß-catenin by capturing cytoplasmic, unphosphorylated ß-catenin in an extra-nuclear complex with ß-TrCP. These data reveal a new regulator of one of the most studied signal transduction pathways in metazoans and provides a novel, completely untapped therapeutic target for silencing the aberrant ß-catenin signaling that drives hyperproliferation in many cancers.
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Affiliation(s)
- Jack L. Leonard
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
| | - Deborah M. Leonard
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Scot A. Wolfe
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jilin Liu
- Department of Cell and Molecular Physiology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jaime Rivera
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Michelle Yang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Ryan T. Leonard
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Jacob P. S. Johnson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Prashant Kumar
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Kate L. Liebmann
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Amanda A. Tutto
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Zhongming Mou
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Karl J. Simin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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42
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Niyonzima N, Lambert AR, Werther R, De Silva Feelixge H, Roychoudhury P, Greninger AL, Stone D, Stoddard BL, Jerome KR. Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses. Protein Eng Des Sel 2017; 30:503-522. [PMID: 28873986 PMCID: PMC5914421 DOI: 10.1093/protein/gzx037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/19/2017] [Accepted: 07/06/2017] [Indexed: 11/14/2022] Open
Abstract
The combination of yeast surface display and flow cytometric analyses and selections is being used with increasing frequency to alter specificity of macromolecular recognition, including both protein-protein and protein-nucleic acid interactions. Here we describe the use of yeast surface display and cleavage-dependent flow cytometric assays to increase the specificity of an engineered meganuclease. The re-engineered meganuclease displays a significantly tightened specificity profile, while binding its cognate target site with a slightly lower, but still sub-nanomolar affinity. When incorporated into otherwise identical megaTAL protein scaffolds, these two nucleases display significantly different activity and toxicity profiles in cellulo. The structural basis for reprogrammed DNA cleavage specificity was further examined via high-resolution X-ray crystal structures of both enzymes. This analysis illustrated the altered protein-DNA contacts produced by mutagenesis and selection, that resulted both in altered readout of those based and a necessary reduction in DNA binding affinity that were necessary to improve specificity across the target site. The results of this study provide an illustrative example of the potential (and the challenges) associated with the use of surface display and flow cytometry for the retargeting and optimization of enzymes that act on nucleic acid substrates in a sequence-specific manner.
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Affiliation(s)
- Nixon Niyonzima
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Abigail R. Lambert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Rachel Werther
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Harshana De Silva Feelixge
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Pavitra Roychoudhury
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Alexander L. Greninger
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
- Virology Division, Department of Laboratory Medicine, University of Washington, 1616 Eastlake Ave. E, Seattle WA 98102, USA
| | - Daniel Stone
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Barry L. Stoddard
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Keith R. Jerome
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
- Virology Division, Department of Laboratory Medicine, University of Washington, 1616 Eastlake Ave. E, Seattle WA 98102, USA
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Abstract
Therapeutic gene editing is significant for medical advancement. Safety is intricately linked to the specificity of the editing tools used to cut at precise genomic targets. Improvements can be achieved by thoughtful design of nucleases and repair templates, analysis of off-target editing, and careful utilization of viral vectors. Advancements in DNA repair mechanisms and development of new generations of tools improve targeting of specific sequences while minimizing risks. It is important to plot a safe course for future clinical trials. This article reviews safety and specificity for therapeutic gene editing to spur dialogue and advancement.
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Affiliation(s)
- Christopher T Lux
- Department of Pediatrics, Cancer and Blood Disorders Center, Seattle Children's Hospital, 4800 Sand Point Way NE, Seattle, WA 98105, USA
| | - Andrew M Scharenberg
- Department of Pediatrics, Seattle Children's Hospital, 4800 Sand Point Way NE, Seattle, WA 98105, USA; Department of Immunology, Seattle Children's Hospital, 4800 Sand Point Way NE, Seattle, WA 98105, USA.
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TALEN-Mediated Knockout of CCR5 Confers Protection Against Infection of Human Immunodeficiency Virus. J Acquir Immune Defic Syndr 2017; 74:229-241. [PMID: 27749600 DOI: 10.1097/qai.0000000000001190] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Transcription activator-like effector nuclease (TALEN) represents a valuable tool for genomic engineering due to its single-nucleotide precision, high nuclease activity, and low cytotoxicity. We report here systematic design and characterization of 28 novel TALENs targeting multiple regions of CCR5 gene (CCR5-TALEN) which encodes the co-receptor critical for entry of human immunodeficiency virus type I (HIV-1). By systemic characterization of these CCR5-TALENs, we have identified one (CCR5-TALEN-515) with higher nuclease activity, specificity, and lower cytotoxicity compared with zinc-finger nuclease (CCR5-ZFN) currently undergoing clinical trials. Sequence analysis of target cell line GHOST-CCR5-CXCR4 and human primary CD4 T cells showed that the double-strand breaks at the TALEN targeted sites resulted in truncated or nonfunctional CCR5 proteins thereby conferring protection against HIV-1 infection in vitro. None of the CCR5-TALENs had detectable levels of off-target nuclease activity against the homologous region in CCR2 although substantial level was identified for CCR5-ZFN in the primary CD4 T cells. Our results suggest that the CCR5-TALENs identified here are highly functional nucleases that produce protective genetic alterations to human CCR5. Application of these TALENs directly to the primary CD4 T cells and CD34 hematopoietic stem cells (HSCs) of infected individuals could help to create an immune system resistant to HIV-1 infection, recapitulating the success of "Berlin patient" and serving as an essential first step towards a "functional" cure of AIDS.
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45
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Naert T, Van Nieuwenhuysen T, Vleminckx K. TALENs and CRISPR/Cas9 fuel genetically engineered clinically relevant Xenopus tropicalis tumor models. Genesis 2017; 55. [PMID: 28095622 DOI: 10.1002/dvg.23005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 11/18/2016] [Accepted: 11/19/2016] [Indexed: 12/12/2022]
Abstract
The targeted nuclease revolution (TALENs, CRISPR/Cas9) now allows Xenopus researchers to rapidly generate custom on-demand genetic knockout models. These novel methods to perform reverse genetics are unprecedented and are fueling a wide array of human disease models within the aquatic diploid model organism Xenopus tropicalis (X. tropicalis). This emerging technology review focuses on the tools to rapidly generate genetically engineered X. tropicalis models (GEXM), with a focus on establishment of genuine genetic and clinically relevant cancer models. We believe that due to particular advantageous characteristics, outlined within this review, GEXM will become a valuable alternative animal model for modeling human cancer. Furthermore, we provide perspectives of how GEXM will be used as a platform for elucidation of novel therapeutic targets and for preclinical drug validation. Finally, we also discuss some future prospects on how the recent expansions and adaptations of the CRISPR/Cas9 toolbox might influence and push forward X. tropicalis cancer research.
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Affiliation(s)
- Thomas Naert
- Developmental Biology Unit, Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Tom Van Nieuwenhuysen
- Developmental Biology Unit, Department of Biomedical Molecular Biology, Ghent University, Belgium
| | - Kris Vleminckx
- Developmental Biology Unit, Department of Biomedical Molecular Biology, Ghent University, Belgium.,Center for Medical Genetics, Ghent University and Ghent University Hospital, Belgium
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46
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Mehrotra R, Renganaath K, Kanodia H, Loake GJ, Mehrotra S. Towards combinatorial transcriptional engineering. Biotechnol Adv 2017; 35:390-405. [PMID: 28300614 DOI: 10.1016/j.biotechadv.2017.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/22/2017] [Accepted: 03/09/2017] [Indexed: 01/31/2023]
Abstract
The modular nature of the transcriptional unit makes it possible to design robust modules with predictable input-output characteristics using a ‘parts- off a shelf’ approach. Customized regulatory circuits composed of multiple such transcriptional units have immense scope for application in diverse fields of basic and applied research. Synthetic transcriptional engineering seeks to construct such genetic cascades. Here, we discuss the three principle strands of transcriptional engineering: promoter and transcriptional factor engineering, and programming inducibilty into synthetic modules. In this context, we review the scope and limitations of some recent technologies that seek to achieve these ends. Our discussion emphasizes a requirement for rational combinatorial engineering principles and the promise this approach holds for the future development of this field.
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Affiliation(s)
- Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani 333031, Rajasthan, India.
| | - Kaushik Renganaath
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani 333031, Rajasthan, India
| | - Harsh Kanodia
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani 333031, Rajasthan, India
| | - Gary J Loake
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh EH9 3BF, United Kingdom
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS) Pilani, Pilani 333031, Rajasthan, India
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47
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Karakikes I, Termglinchan V, Cepeda DA, Lee J, Diecke S, Hendel A, Itzhaki I, Ameen M, Shrestha R, Wu H, Ma N, Shao NY, Seeger T, Woo N, Wilson KD, Matsa E, Porteus MH, Sebastiano V, Wu JC. A Comprehensive TALEN-Based Knockout Library for Generating Human-Induced Pluripotent Stem Cell-Based Models for Cardiovascular Diseases. Circ Res 2017; 120:1561-1571. [PMID: 28246128 DOI: 10.1161/circresaha.116.309948] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 02/23/2017] [Accepted: 02/28/2017] [Indexed: 12/21/2022]
Abstract
RATIONALE Targeted genetic engineering using programmable nucleases such as transcription activator-like effector nucleases (TALENs) is a valuable tool for precise, site-specific genetic modification in the human genome. OBJECTIVE The emergence of novel technologies such as human induced pluripotent stem cells (iPSCs) and nuclease-mediated genome editing represent a unique opportunity for studying cardiovascular diseases in vitro. METHODS AND RESULTS By incorporating extensive literature and database searches, we designed a collection of TALEN constructs to knockout 88 human genes that are associated with cardiomyopathies and congenital heart diseases. The TALEN pairs were designed to induce double-strand DNA break near the starting codon of each gene that either disrupted the start codon or introduced a frameshift mutation in the early coding region, ensuring faithful gene knockout. We observed that all the constructs were active and disrupted the target locus at high frequencies. To illustrate the utility of the TALEN-mediated knockout technique, 6 individual genes (TNNT2, LMNA/C, TBX5, MYH7, ANKRD1, and NKX2.5) were knocked out with high efficiency and specificity in human iPSCs. By selectively targeting a pathogenic mutation (TNNT2 p.R173W) in patient-specific iPSC-derived cardiac myocytes, we demonstrated that the knockout strategy ameliorates the dilated cardiomyopathy phenotype in vitro. In addition, we modeled the Holt-Oram syndrome in iPSC-cardiac myocytes in vitro and uncovered novel pathways regulated by TBX5 in human cardiac myocyte development. CONCLUSIONS Collectively, our study illustrates the powerful combination of iPSCs and genome editing technologies for understanding the biological function of genes, and the pathological significance of genetic variants in human cardiovascular diseases. The methods, strategies, constructs, and iPSC lines developed in this study provide a validated, readily available resource for cardiovascular research.
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Affiliation(s)
- Ioannis Karakikes
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Vittavat Termglinchan
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Diana A Cepeda
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Jaecheol Lee
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Sebastian Diecke
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Ayal Hendel
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Ilanit Itzhaki
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Mohamed Ameen
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Rajani Shrestha
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Haodi Wu
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Ning Ma
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Ning-Yi Shao
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Timon Seeger
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Nicole Woo
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Kitchener D Wilson
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Elena Matsa
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Matthew H Porteus
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.)
| | - Vittorio Sebastiano
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.).
| | - Joseph C Wu
- From the Stanford Cardiovascular Institute (I.K., V.T., J.L., S.D., I.I., M.A., R.S., H.W., N.M., N.-Y.S., T.S., N.W., K.D.W., E.M., J.C.W.), Department of Cardiothoracic Surgery (I.K.), Division of Cardiovascular Medicine, Department of Medicine (V.T., J.C.W.), CA; Institute of Stem Cell Biology and Regenerative Medicine (D.A.C., V.S., J.C.W.), Departments of Pediatrics (A.H., M.H.P.), Pathology (K.D.W.), and Obstetrics and Gynecology (V.S.), Stanford University School of Medicine, CA; Berlin Institute of Health, Germany (S.D.); and Max Delbrueck Center, Berlin, Germany (S.D.).
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48
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Knipping F, Osborn MJ, Petri K, Tolar J, Glimm H, von Kalle C, Schmidt M, Gabriel R. Genome-wide Specificity of Highly Efficient TALENs and CRISPR/Cas9 for T Cell Receptor Modification. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 4:213-224. [PMID: 28345006 PMCID: PMC5363317 DOI: 10.1016/j.omtm.2017.01.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 01/25/2017] [Indexed: 12/11/2022]
Abstract
In T cells with transgenic high-avidity T cell receptors (TCRs), endogenous and transferred TCR chains compete for surface expression and may pair inappropriately, potentially causing autoimmunity. To knock out endogenous TCR expression, we assembled 12 transcription activator-like effector nucleases (TALENs) and five guide RNAs (gRNAs) from the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system. Using TALEN mRNA, TCR knockout was successful in up to 81% of T cells. Additionally, we were able to verify targeted gene addition of a GFP gene by homology-directed repair at the TALEN target site, using a donor suitable for replacement of the reporter transgene with therapeutic TCR chains. Remarkably, analysis of TALEN and CRISPR/Cas9 specificity using integrase-defective lentiviral vector capture revealed only one off-target site for one of the gRNAs and three off-target sites for both of the TALENs, indicating a high level of specificity. Collectively, our work shows highly efficient and specific nucleases for T cell engineering.
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Affiliation(s)
- Friederike Knipping
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, 69120 Heidelberg, Germany
| | - Mark J Osborn
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Asan-Minnesota Institute for Innovating Transplantation, Seoul 05505, Republic of Korea
| | - Karl Petri
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, 69120 Heidelberg, Germany
| | - Jakub Tolar
- Division of Blood and Marrow Transplantation, Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA; Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA; Asan-Minnesota Institute for Innovating Transplantation, Seoul 05505, Republic of Korea
| | - Hanno Glimm
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, 69120 Heidelberg, Germany
| | - Christof von Kalle
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, 69120 Heidelberg, Germany
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, 69120 Heidelberg, Germany
| | - Richard Gabriel
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, 69120 Heidelberg, Germany
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49
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Hendriks WT, Warren CR, Cowan CA. Genome Editing in Human Pluripotent Stem Cells: Approaches, Pitfalls, and Solutions. Cell Stem Cell 2016; 18:53-65. [PMID: 26748756 DOI: 10.1016/j.stem.2015.12.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human pluripotent stem cells (hPSCs) with knockout or mutant alleles can be generated using custom-engineered nucleases. Transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 nucleases are the most commonly employed technologies for editing hPSC genomes. In this Protocol Review, we provide a brief overview of custom-engineered nucleases in the context of gene editing in hPSCs with a focus on the application of TALENs and CRISPR/Cas9. We will highlight the advantages and disadvantages of each method and discuss theoretical and technical considerations for experimental design.
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Affiliation(s)
- William T Hendriks
- The Collaborative Center for X-Linked Dystonia Parkinsonism, Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Brain Science Initiative, Harvard Medical School, Boston, MA 02114, USA
| | - Curtis R Warren
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Chad A Cowan
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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50
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Abstract
The recent advent of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated protein 9 (Cas9) system for precise genome editing has revolutionized methodologies in haematology and oncology studies. CRISPR-Cas9 technology can be used to remove and correct genes or mutations, and to introduce site-specific therapeutic genes in human cells. Inherited haematological disorders represent ideal targets for CRISPR-Cas9-mediated gene therapy. Correcting disease-causing mutations could alleviate disease-related symptoms in the near future. The CRISPR-Cas9 system is also a useful tool for delineating molecular mechanisms involving haematological malignancies. Prior to the use of CRISPR-Cas9-mediated gene correction in humans, appropriate delivery systems with higher efficiency and specificity must be identified, and ethical guidelines for applying the technology with controllable safety must be established. Here, the latest applications of CRISPR-Cas9 technology in haematological disorders, current challenges and future directions are reviewed and discussed.
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Affiliation(s)
- Han Zhang
- The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas-Health Science Centre at Houston, Houston, TX, USA
| | - Nami McCarty
- The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), University of Texas-Health Science Centre at Houston, Houston, TX, USA.
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