1
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Castillo SR, Simone BW, Clark KJ, Devaux P, Ekker SC. Unconstrained Precision Mitochondrial Genome Editing with αDdCBEs. Hum Gene Ther 2024. [PMID: 39212664 DOI: 10.1089/hum.2024.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
DddA-derived cytosine base editors (DdCBEs) enable the targeted introduction of C•G-to-T•A conversions in mitochondrial DNA (mtDNA). DdCBEs work in pairs, with each arm composed of a transcription activator-like effector (TALE), a split double-stranded DNA deaminase half, and a uracil glycosylase inhibitor. This pioneering technology has helped improve our understanding of cellular processes involving mtDNA and has paved the way for the development of models and therapies for genetic disorders caused by pathogenic mtDNA variants. Nonetheless, given the intrinsic properties of TALE proteins, several target sites in human mtDNA are predicted to remain out of reach to DdCBEs and other TALE-based technologies. Specifically, due to the conventional requirement for a thymine immediately upstream of the TALE target sequences (i.e., the 5'-T constraint), over 150 loci in the human mitochondrial genome are presumed to be inaccessible to DdCBEs. Previous attempts at circumventing this requirement, either by developing monomeric DdCBEs or utilizing DNA-binding domains alternative to TALEs, have resulted in suboptimal specificity profiles with reduced therapeutic potential. Here, aiming to challenge and elucidate the relevance of the 5'-T constraint in the context of DdCBE-mediated mtDNA editing, and to expand the range of motifs that are editable by this technology, we generated DdCBEs containing TALE proteins engineered to recognize all 5' bases. These modified DdCBEs are herein referred to as αDdCBEs. Notably, 5'-T-noncompliant canonical DdCBEs efficiently edited mtDNA at diverse loci. However, they were frequently outperformed by αDdCBEs, which exhibited significant improvements in activity and specificity, regardless of the most 5' bases of their TALE binding sites. Furthermore, we showed that αDdCBEs are compatible with the enhanced DddAtox variants DddA6 and DddA11, and we validated TALE shifting with αDdCBEs as an effective approach to optimize base editing outcomes. Overall, αDdCBEs enable efficient, specific, and unconstrained mitochondrial base editing.
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Affiliation(s)
- Santiago R Castillo
- Virology and Gene Therapy Graduate Program, Mayo Clinic, Rochester, Minnesota, USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Brandon W Simone
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
| | - Patricia Devaux
- Virology and Gene Therapy Graduate Program, Mayo Clinic, Rochester, Minnesota, USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA
- Department of Pediatrics and Department of Molecular Biosciences, Dell Medical School, The University of Texas at Austin, Austin, Texas, USA
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2
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Castillo SR, Simone BW, Clark KJ, Devaux P, Ekker SC. Unconstrained Precision Mitochondrial Genome Editing with αDdCBEs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593977. [PMID: 38798498 PMCID: PMC11118498 DOI: 10.1101/2024.05.13.593977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
DddA-derived cytosine base editors (DdCBEs) enable the targeted introduction of C•G-to-T•A conversions in mitochondrial DNA (mtDNA). DdCBEs are often deployed as pairs, with each arm comprised of a transcription activator-like effector (TALE), a split double-stranded DNA deaminase half, and a uracil glycosylase inhibitor. This pioneering technology has helped improve our understanding of cellular processes involving mtDNA and has paved the way for the development of models and therapies for genetic disorders caused by pathogenic mtDNA variants. Nonetheless, given the intrinsic properties of TALE proteins, several target sites in human mtDNA remain out of reach to DdCBEs and other TALE-based technologies. Specifically, due to the conventional requirement for a thymine immediately upstream of the TALE target sequences (i.e., the 5'-T constraint), over 150 loci in the human mitochondrial genome are presumed to be inaccessible to DdCBEs. Previous attempts at circumventing this constraint, either by developing monomeric DdCBEs or utilizing DNA-binding domains alternative to TALEs, have resulted in suboptimal specificity profiles with reduced therapeutic potential. Here, aiming to challenge and elucidate the relevance of the 5'-T constraint in the context of DdCBE-mediated mtDNA editing, and to expand the range of motifs that are editable by this technology, we generated αDdCBEs that contain modified TALE proteins engineered to recognize all 5' bases. Notably, 5'-T-noncompliant, canonical DdCBEs efficiently edited mtDNA at diverse loci. However, DdCBEs were frequently outperformed by αDdCBEs, which consistently displayed significant improvements in activity and specificity, regardless of the 5'-most bases of their TALE binding sites. Furthermore, we showed that αDdCBEs are compatible with DddA tox and its derivatives DddA6, and DddA11, and we validated TALE shifting with αDdCBEs as an effective approach to optimize base editing outcomes at a single target site. Overall, αDdCBEs enable efficient, specific, and unconstrained mitochondrial base editing.
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3
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Motorina DM, Galimova YA, Battulina NV, Omelina ES. Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals. Int J Mol Sci 2024; 25:5231. [PMID: 38791270 PMCID: PMC11121118 DOI: 10.3390/ijms25105231] [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: 04/15/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.
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Affiliation(s)
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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4
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Hamilton PJ, Lim CJ, Nestler EJ, Heller EA. Neuroepigenetic Editing. Methods Mol Biol 2024; 2842:129-152. [PMID: 39012593 DOI: 10.1007/978-1-0716-4051-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Epigenetic regulation is intrinsic to basic neurobiological function as well as neurological disease. Regulation of chromatin-modifying enzymes in the brain is critical during both development and adulthood and in response to external stimuli. Biochemical studies are complemented by numerous next-generation sequencing (NGS) studies that quantify global changes in gene expression, chromatin accessibility, histone and DNA modifications in neurons and glial cells. Neuroepigenetic editing tools are essential to distinguish between the mere presence and functional relevance of histone and DNA modifications to gene transcription in the brain and animal behavior. This review discusses current advances in neuroepigenetic editing, highlighting methodological considerations pertinent to neuroscience, such as delivery methods and the spatiotemporal specificity of editing and it demonstrates the enormous potential of epigenetic editing for basic neurobiological research and therapeutic application.
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Affiliation(s)
- Peter J Hamilton
- Department of Anatomy & Neurobiology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Carissa J Lim
- Department of Systems Pharmacology and Translational Therapeutics, The University of Pennsylvania, Philadelphia, PA, USA
| | - Eric J Nestler
- The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elizabeth A Heller
- Department of Systems Pharmacology and Translational Therapeutics, The University of Pennsylvania, Philadelphia, PA, USA.
- Department of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics, Philadelphia, PA, USA.
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5
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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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6
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Yano N, Fedulov AV. Targeted DNA Demethylation: Vectors, Effectors and Perspectives. Biomedicines 2023; 11:biomedicines11051334. [PMID: 37239005 DOI: 10.3390/biomedicines11051334] [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: 03/28/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Aberrant DNA hypermethylation at regulatory cis-elements of particular genes is seen in a plethora of pathological conditions including cardiovascular, neurological, immunological, gastrointestinal and renal diseases, as well as in cancer, diabetes and others. Thus, approaches for experimental and therapeutic DNA demethylation have a great potential to demonstrate mechanistic importance, and even causality of epigenetic alterations, and may open novel avenues to epigenetic cures. However, existing methods based on DNA methyltransferase inhibitors that elicit genome-wide demethylation are not suitable for treatment of diseases with specific epimutations and provide a limited experimental value. Therefore, gene-specific epigenetic editing is a critical approach for epigenetic re-activation of silenced genes. Site-specific demethylation can be achieved by utilizing sequence-dependent DNA-binding molecules such as zinc finger protein array (ZFA), transcription activator-like effector (TALE) and clustered regularly interspaced short palindromic repeat-associated dead Cas9 (CRISPR/dCas9). Synthetic proteins, where these DNA-binding domains are fused with the DNA demethylases such as ten-eleven translocation (Tet) and thymine DNA glycosylase (TDG) enzymes, successfully induced or enhanced transcriptional responsiveness at targeted loci. However, a number of challenges, including the dependence on transgenesis for delivery of the fusion constructs, remain issues to be solved. In this review, we detail current and potential approaches to gene-specific DNA demethylation as a novel epigenetic editing-based therapeutic strategy.
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Affiliation(s)
- Naohiro Yano
- Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
| | - Alexey V Fedulov
- Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
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7
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O'Connell RW, Rai K, Piepergerdes TC, Samra KD, Wilson JA, Lin S, Zhang TH, Ramos EM, Sun A, Kille B, Curry KD, Rocks JW, Treangen TJ, Mehta P, Bashor CJ. Ultra-high throughput mapping of genetic design space. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532704. [PMID: 36993481 PMCID: PMC10055055 DOI: 10.1101/2023.03.16.532704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Massively parallel genetic screens have been used to map sequence-to-function relationships for a variety of genetic elements. However, because these approaches only interrogate short sequences, it remains challenging to perform high throughput (HT) assays on constructs containing combinations of sequence elements arranged across multi-kb length scales. Overcoming this barrier could accelerate synthetic biology; by screening diverse gene circuit designs, "composition-to-function" mappings could be created that reveal genetic part composability rules and enable rapid identification of behavior-optimized variants. Here, we introduce CLASSIC, a generalizable genetic screening platform that combines long- and short-read next-generation sequencing (NGS) modalities to quantitatively assess pooled libraries of DNA constructs of arbitrary length. We show that CLASSIC can measure expression profiles of >10 5 drug-inducible gene circuit designs (ranging from 6-9 kb) in a single experiment in human cells. Using statistical inference and machine learning (ML) approaches, we demonstrate that data obtained with CLASSIC enables predictive modeling of an entire circuit design landscape, offering critical insight into underlying design principles. Our work shows that by expanding the throughput and understanding gained with each design-build-test-learn (DBTL) cycle, CLASSIC dramatically augments the pace and scale of synthetic biology and establishes an experimental basis for data-driven design of complex genetic systems.
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8
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Nash PA, Minczuk M. Manipulation of Murine Mitochondrial DNA Heteroplasmy with mtZFNs. Methods Mol Biol 2023; 2615:329-344. [PMID: 36807802 DOI: 10.1007/978-1-0716-2922-2_23] [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] [Indexed: 02/23/2023]
Abstract
Mouse models of mitochondrial DNA mutations hold promise in the development and optimization of mitochondrial gene therapy technology and for gathering pre-clinical data prior to human trials. Their suitability for this purpose stems from the high similarity of human and murine mitochondrial genomes and the increasing availability of rationally designed AAV vectors capable of selectively transducing murine tissues. Our laboratory routinely optimizes mitochondrially targeted zinc finger nucleases (mtZFNs), the compactness of which makes them highly suitable for downstream AAV-based in vivo mitochondrial gene therapy. This chapter discusses the necessary precautions for the robust and precise genotyping of the murine mitochondrial genome as well as the optimization of mtZFNs intended for subsequent use in vivo.
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Affiliation(s)
- Pavel A Nash
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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9
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Aslan A, Yuka SA. Stem Cell-Based Therapeutic Approaches in Genetic Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1436:19-53. [PMID: 36735185 DOI: 10.1007/5584_2023_761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Stem cells, which can self-renew and differentiate into different cell types, have become the keystone of regenerative medicine due to these properties. With the achievement of superior clinical results in the therapeutic approaches of different diseases, the applications of these cells in the treatment of genetic diseases have also come to the fore. Foremost, conventional approaches of stem cells to genetic diseases are the first approaches in this manner, and they have brought safety issues due to immune reactions caused by allogeneic transplantation. To eliminate these safety issues and phenotypic abnormalities caused by genetic defects, firstly, basic genetic engineering practices such as vectors or RNA modulators were combined with stem cell-based therapeutic approaches. However, due to challenges such as immune reactions and inability to target cells effectively in these applications, advanced molecular methods have been adopted in ZFN, TALEN, and CRISPR/Cas genome editing nucleases, which allow modular designs in stem cell-based genetic diseases' therapeutic approaches. Current studies in genetic diseases are in the direction of creating permanent treatment regimens by genomic manipulation of stem cells with differentiation potential through genome editing tools. In this chapter, the stem cell-based therapeutic approaches of various vital genetic diseases were addressed wide range from conventional applications to genome editing tools.
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Affiliation(s)
- Ayça Aslan
- Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey
| | - Selcen Arı Yuka
- Department of Bioengineering, Yildiz Technical University, Istanbul, Turkey.
- Health Biotechnology Joint Research and Application Center of Excellence, Istanbul, Turkey.
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10
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Li HS, Israni DV, Gagnon KA, Gan KA, Raymond MH, Sander JD, Roybal KT, Joung JK, Wong WW, Khalil AS. Multidimensional control of therapeutic human cell function with synthetic gene circuits. Science 2022; 378:1227-1234. [PMID: 36520914 PMCID: PMC10054295 DOI: 10.1126/science.ade0156] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Synthetic gene circuits that precisely control human cell function could expand the capabilities of gene- and cell-based therapies. However, platforms for developing circuits in primary human cells that drive robust functional changes in vivo and have compositions suitable for clinical use are lacking. Here, we developed synthetic zinc finger transcription regulators (synZiFTRs), which are compact and based largely on human-derived proteins. As a proof of principle, we engineered gene switches and circuits that allow precise, user-defined control over therapeutically relevant genes in primary T cells using orthogonal, US Food and Drug Administration-approved small-molecule inducers. Our circuits can instruct T cells to sequentially activate multiple cellular programs such as proliferation and antitumor activity to drive synergistic therapeutic responses. This platform should accelerate the development and clinical translation of synthetic gene circuits in diverse human cell types and contexts.
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Affiliation(s)
- Hui-Shan Li
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Divya V Israni
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Keith A Gagnon
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Kok Ann Gan
- Biological Design Center, Boston University, Boston, MA, USA.,Program in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, MA, USA
| | - Michael H Raymond
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Jeffry D Sander
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA.,Department of Genomics Technologies, Corteva Agriscience, Johnston, IA, USA
| | - Kole T Roybal
- Cell Design Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.,Parker Institute for Cancer Immunotherapy, University of California, San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Wilson W Wong
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Ahmad S Khalil
- Biological Design Center, Boston University, Boston, MA, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA.,Program in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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11
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Willis JCW, Silva-Pinheiro P, Widdup L, Minczuk M, Liu DR. Compact zinc finger base editors that edit mitochondrial or nuclear DNA in vitro and in vivo. Nat Commun 2022; 13:7204. [PMID: 36418298 PMCID: PMC9684478 DOI: 10.1038/s41467-022-34784-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
DddA-derived cytosine base editors (DdCBEs) use programmable DNA-binding TALE repeat arrays, rather than CRISPR proteins, a split double-stranded DNA cytidine deaminase (DddA), and a uracil glycosylase inhibitor to mediate C•G-to-T•A editing in nuclear and organelle DNA. Here we report the development of zinc finger DdCBEs (ZF-DdCBEs) and the improvement of their editing performance through engineering their architectures, defining improved ZF scaffolds, and installing DddA activity-enhancing mutations. We engineer variants with improved DNA specificity by integrating four strategies to reduce off-target editing. We use optimized ZF-DdCBEs to install or correct disease-associated mutations in mitochondria and in the nucleus. Leveraging their small size, we use a single AAV9 to deliver into heart, liver, and skeletal muscle in post-natal mice ZF-DdCBEs that efficiently install disease-associated mutations. While off-target editing of ZF-DdCBEs is likely too high for therapeutic applications, these findings demonstrate a compact, all-protein base editing research tool for precise editing of organelle or nuclear DNA without double-strand DNA breaks.
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Affiliation(s)
- Julian C W Willis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | | | - Lily Widdup
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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12
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Tak YE, Boulay G, Lee L, Iyer S, Perry NT, Schultz HT, Garcia SP, Broye L, Horng JE, Rengarajan S, Naigles B, Volorio A, Sander JD, Gong J, Riggi N, Joung JK, Rivera MN. Genome-wide functional perturbation of human microsatellite repeats using engineered zinc finger transcription factors. CELL GENOMICS 2022; 2. [PMID: 35967079 PMCID: PMC9374162 DOI: 10.1016/j.xgen.2022.100119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Y. Esther Tak
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Gaylor Boulay
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lukuo Lee
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sowmya Iyer
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Nicholas T. Perry
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Hayley T. Schultz
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sara P. Garcia
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Liliane Broye
- Institute of Pathology, Department of Experimental Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Joy E. Horng
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Shruthi Rengarajan
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Beverly Naigles
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Angela Volorio
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Institute of Pathology, Department of Experimental Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
| | - Jeffry D. Sander
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Jingyi Gong
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Nicolò Riggi
- Institute of Pathology, Department of Experimental Pathology, Centre Hospitalier Universitaire Vaudois, University of Lausanne, 1011 Lausanne, Switzerland
- Corresponding author
| | - J. Keith Joung
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Corresponding author
| | - Miguel N. Rivera
- Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Corresponding author
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13
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Wang J, Thomas HR, Li Z, Yeo NC(F, Scott HE, Dang N, Hossain MI, Andrabi SA, Parant JM. Puma, noxa, p53, and p63 differentially mediate stress pathway induced apoptosis. Cell Death Dis 2021; 12:659. [PMID: 34193827 PMCID: PMC8245518 DOI: 10.1038/s41419-021-03902-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 02/06/2023]
Abstract
Cellular stress can lead to several human disease pathologies due to aberrant cell death. The p53 family (tp53, tp63, and tp73) and downstream transcriptional apoptotic target genes (PUMA/BBC3 and NOXA/PMAIP1) have been implicated as mediators of stress signals. To evaluate the importance of key stress response components in vivo, we have generated zebrafish null alleles in puma, noxa, p53, p63, and p73. Utilizing these genetic mutants, we have deciphered that the apoptotic response to genotoxic stress requires p53 and puma, but not p63, p73, or noxa. We also identified a delayed secondary wave of genotoxic stress-induced apoptosis that is p53/puma independent. Contrary to genotoxic stress, ER stress-induced apoptosis requires p63 and puma, but not p53, p73, or noxa. Lastly, the oxidative stress-induced apoptotic response requires p63, and both noxa and puma. Our data also indicate that while the neural tube is poised for apoptosis due to genotoxic stress, the epidermis is poised for apoptosis due to ER and oxidative stress. These data indicate there are convergent as well as unique molecular pathways involved in the different stress responses. The commonality of puma in these stress pathways, and the lack of gross or tumorigenic phenotypes with puma loss suggest that a inhibitor of Puma may have therapeutic application. In addition, we have also generated a knockout of the negative regulator of p53, mdm2 to further evaluate the p53-induced apoptosis. Our data indicate that the p53 null allele completely rescues the mdm2 null lethality, while the puma null completely rescues the mdm2 null apoptosis but only partially rescues the phenotype. Indicating Puma is the key mediator of p53-dependent apoptosis. Interestingly the p53 homozygous null zebrafish develop tumors faster than the previously described p53 homozygous missense mutant zebrafish, suggesting the missense allele may be hypomorphic allele.
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Affiliation(s)
- Jun Wang
- grid.265892.20000000106344187Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL USA
| | - Holly R. Thomas
- grid.265892.20000000106344187Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL USA
| | - Zhang Li
- grid.265892.20000000106344187Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Nan Cher (Florence) Yeo
- grid.265892.20000000106344187Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL USA
| | - Hannah E. Scott
- grid.265892.20000000106344187Department of Biology, University of Alabama at Birmingham Collage of Arts and Sciences Department and Genetics Department, University of Alabama at Birmingham School of Medicine, Birmingham, AL USA
| | - Nghi Dang
- grid.265892.20000000106344187Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL USA
| | - Mohammed Iqbal Hossain
- grid.265892.20000000106344187Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL USA
| | - Shaida A. Andrabi
- grid.265892.20000000106344187Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL USA ,grid.265892.20000000106344187Department of Neurology, University of Alabama at Birmingham School of Medicine, Birmingham, AL USA
| | - John M. Parant
- grid.265892.20000000106344187Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL USA
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14
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Abstract
Genetically modified animals, especially rodents, are widely used in biomedical research. However, non-rodent models are required for efficient translational medicine and preclinical studies. Owing to the similarity in the physiological traits of pigs and humans, genetically modified pigs may be a valuable resource for biomedical research. Somatic cell nuclear transfer (SCNT) using genetically modified somatic cells has been the primary method for the generation of genetically modified pigs. However, site-specific gene modification in porcine cells is inefficient and requires laborious and time-consuming processes. Recent improvements in gene-editing systems, such as zinc finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas) system, represent major advances. The efficient introduction of site-specific modifications into cells via gene editors dramatically reduces the effort and time required to generate genetically modified pigs. Furthermore, gene editors enable direct gene modification during embryogenesis, bypassing the SCNT procedure. The application of gene editors has progressively expanded, and a range of strategies is now available for porcine gene engineering. This review provides an overview of approaches for the generation of genetically modified pigs using gene editors, and highlights the current trends, as well as the limitations, of gene editing in pigs.
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Affiliation(s)
- Fuminori Tanihara
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima 770-8513, Japan.,Center for Development of Advanced Medical Technology, Jichi Medical University, Tochigi 329-0498, Japan
| | - Maki Hirata
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima 770-8513, Japan
| | - Takeshige Otoi
- Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima 770-8513, Japan
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15
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Bennett EP, Petersen BL, Johansen IE, Niu Y, Yang Z, Chamberlain CA, Met Ö, Wandall HH, Frödin M. INDEL detection, the 'Achilles heel' of precise genome editing: a survey of methods for accurate profiling of gene editing induced indels. Nucleic Acids Res 2020; 48:11958-11981. [PMID: 33170255 PMCID: PMC7708060 DOI: 10.1093/nar/gkaa975] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 10/05/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Advances in genome editing technologies have enabled manipulation of genomes at the single base level. These technologies are based on programmable nucleases (PNs) that include meganucleases, zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated 9 (Cas9) nucleases and have given researchers the ability to delete, insert or replace genomic DNA in cells, tissues and whole organisms. The great flexibility in re-designing the genomic target specificity of PNs has vastly expanded the scope of gene editing applications in life science, and shows great promise for development of the next generation gene therapies. PN technologies share the principle of inducing a DNA double-strand break (DSB) at a user-specified site in the genome, followed by cellular repair of the induced DSB. PN-elicited DSBs are mainly repaired by the non-homologous end joining (NHEJ) and the microhomology-mediated end joining (MMEJ) pathways, which can elicit a variety of small insertion or deletion (indel) mutations. If indels are elicited in a protein coding sequence and shift the reading frame, targeted gene knock out (KO) can readily be achieved using either of the available PNs. Despite the ease by which gene inactivation in principle can be achieved, in practice, successful KO is not only determined by the efficiency of NHEJ and MMEJ repair; it also depends on the design and properties of the PN utilized, delivery format chosen, the preferred indel repair outcomes at the targeted site, the chromatin state of the target site and the relative activities of the repair pathways in the edited cells. These variables preclude accurate prediction of the nature and frequency of PN induced indels. A key step of any gene KO experiment therefore becomes the detection, characterization and quantification of the indel(s) induced at the targeted genomic site in cells, tissues or whole organisms. In this survey, we briefly review naturally occurring indels and their detection. Next, we review the methods that have been developed for detection of PN-induced indels. We briefly outline the experimental steps and describe the pros and cons of the various methods to help users decide a suitable method for their editing application. We highlight recent advances that enable accurate and sensitive quantification of indel events in cells regardless of their genome complexity, turning a complex pool of different indel events into informative indel profiles. Finally, we review what has been learned about PN-elicited indel formation through the use of the new methods and how this insight is helping to further advance the genome editing field.
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Affiliation(s)
- Eric Paul Bennett
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Ida Elisabeth Johansen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Yiyuan Niu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- College of Animal Science and Technology, Northwest A&F University, Yangling Shaanxi, China
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | | | - Özcan Met
- Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans H Wandall
- Copenhagen Center for Glycomics, Department of Odontology and Molecular and Cellular Medicine, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Morten Frödin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
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16
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Alagoz M, Kherad N. Advance genome editing technologies in the treatment of human diseases: CRISPR therapy (Review). Int J Mol Med 2020; 46:521-534. [PMID: 32467995 PMCID: PMC7307811 DOI: 10.3892/ijmm.2020.4609] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
Genome editing techniques are considered to be one of the most challenging yet efficient tools for assisting therapeutic approaches. Several studies have focused on the development of novel methods to improve the efficiency of gene editing, as well as minimise their off-target effects. Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas9) is a tool that has revolutionised genome editing technologies. New applications of CRISPR/Cas9 in a broad range of diseases have demonstrated its efficiency and have been used in ex vivo models of somatic and pluripotent stem cells, as well as in in vivo animal models, and may eventually be used to correct defective genes. The focus of the present review was the recent applications of CRISPR/Cas9 and its contribution to the treatment of challenging human diseases, such as various types of cancer, neurodegenerative diseases and a broad spectrum of other disorders. CRISPR technology is a novel method for disease treatment, enhancing the effectiveness of drugs and improving the development of personalised medicine.
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Affiliation(s)
- Meryem Alagoz
- Molecular Biology and Genetics, Biruni Universitesi, Istanbul 34010, Turkey
| | - Nasim Kherad
- Molecular Biology and Genetics, Biruni Universitesi, Istanbul 34010, Turkey
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17
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Batista FA, Gyau B, Vilacha JF, Bosch SS, Lunev S, Wrenger C, Groves MR. New directions in antimalarial target validation. Expert Opin Drug Discov 2020; 15:189-202. [PMID: 31959021 DOI: 10.1080/17460441.2020.1691996] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Introduction: Malaria is one of the most prevalent human infections worldwide with over 40% of the world's population living in malaria-endemic areas. In the absence of an effective vaccine, emergence of drug-resistant strains requires urgent drug development. Current methods applied to drug target validation, a crucial step in drug discovery, possess limitations in malaria. These constraints require the development of techniques capable of simplifying the validation of Plasmodial targets.Areas covered: The authors review the current state of the art in techniques used to validate drug targets in malaria, including our contribution - the protein interference assay (PIA) - as an additional tool in rapid in vivo target validation.Expert opinion: Each technique in this review has advantages and disadvantages, implying that future validation efforts should not focus on a single approach, but integrate multiple approaches. PIA is a significant addition to the current toolset of antimalarial validation. Validation of aspartate metabolism as a druggable pathway provided proof of concept of how oligomeric interfaces can be exploited to control specific activity in vivo. PIA has the potential to be applied not only to other enzymes/pathways of the malaria parasite but could, in principle, be extrapolated to other infectious diseases.
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Affiliation(s)
- Fernando A Batista
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands.,Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Benjamin Gyau
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Juliana F Vilacha
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Soraya S Bosch
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands.,Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Sergey Lunev
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Matthew R Groves
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
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18
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Recacha E, Machuca J, Díaz-Díaz S, García-Duque A, Ramos-Guelfo M, Docobo-Pérez F, Blázquez J, Pascual A, Rodríguez-Martínez JM. Suppression of the SOS response modifies spatiotemporal evolution, post-antibiotic effect, bacterial fitness and biofilm formation in quinolone-resistant Escherichia coli. J Antimicrob Chemother 2020; 74:66-73. [PMID: 30329046 DOI: 10.1093/jac/dky407] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/10/2018] [Indexed: 01/24/2023] Open
Abstract
Background Suppression of the SOS response has been proposed as a therapeutic strategy for potentiating quinolones against susceptible, low-level quinolone-resistant (LLQR) and resistant Enterobacteriaceae. Objectives To monitor the functionality of the SOS response in the evolution towards clinical quinolone resistance and study its impact on the evolution of spatiotemporal resistance. Methods An isogenic collection of Escherichia coli (derived from the strain ATCC 25922) carrying combinations of chromosomally and plasmid-mediated quinolone resistance mechanisms (including susceptible, LLQR and resistant phenotypes) and exhibiting a spectrum of SOS activity was used. Relevant clinical parameters such as mutation rate, mutant prevention concentration (MPC), bacterial fitness, biofilm formation and post-antibiotic effect (PAE) were evaluated. Results Inactivating the SOS response (recA deletion) led to a decrease in mutation rate (∼103 fold) in LLQR compared with WT strains at ciprofloxacin concentrations of 1 mg/L (the EUCAST breakpoint for resistance) and 2.5 mg/L (Cmax), as well as a remarkable delay in the spatiotemporal evolution of quinolone resistance. For all strains, there was an 8-fold decrease in MPC in RecA-deficient strains, with values for LLQR strains decreasing below the Cmax of ciprofloxacin. Inactivation of the SOS response reduced competitive fitness by 33%-50%, biofilm production by 22%-80% and increased the PAE by ∼3-4 h at sub-MIC concentrations of ciprofloxacin. Conclusions Our data indicate that suppression of the SOS response affects key bacterial traits and is a promising strategy for reversing and tackling the evolution of antibiotic resistance in E. coli, including low-level and resistant phenotypes at therapeutic quinolone concentrations.
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Affiliation(s)
- E Recacha
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain
| | - J Machuca
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain
| | - S Díaz-Díaz
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
| | - A García-Duque
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain
| | - M Ramos-Guelfo
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain
| | - F Docobo-Pérez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
| | - J Blázquez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - A Pascual
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Seville, Spain.,Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
| | - J M Rodríguez-Martínez
- Departamento de Microbiología, Facultad de Medicina, Universidad de Sevilla, Seville, Spain.,Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos III, Madrid, Spain.,Instituto de Biomedicina de Sevilla IBIS, Hospital Universitario Virgen Macarena/CSIC/Departamento de Microbiología, Universidad de Sevilla, Seville, Spain
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19
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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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20
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Hussey BJ, McMillen DR. Programmable T7-based synthetic transcription factors. Nucleic Acids Res 2019; 46:9842-9854. [PMID: 30169636 PMCID: PMC6182181 DOI: 10.1093/nar/gky785] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/21/2018] [Indexed: 12/31/2022] Open
Abstract
Despite recent progress on synthetic transcription factor generation in eukaryotes, there remains a need for high-activity bacterial versions of these systems. In synthetic biology applications, it is useful for transcription factors to have two key features: they should be orthogonal (influencing only their own targets, with minimal off-target effects), and programmable (able to be directed to a wide range of user-specified transcriptional start sites). The RNA polymerase of the bacteriophage T7 has a number of appealing properties for synthetic biological designs: it can produce high transcription rates; it is a compact, single-subunit polymerase that has been functionally expressed in a variety of organisms; and its viral origin reduces the connection between its activity and that of its host's transcriptional machinery. We have created a system where a T7 RNA polymerase is recruited to transcriptional start sites by DNA binding proteins, either directly or bridged through protein–protein interactions, yielding a modular and programmable system for strong transcriptional activation of multiple orthogonal synthetic transcription factor variants in Escherichia coli. To our knowledge this is the first exogenous, programmable activator system in bacteria.
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Affiliation(s)
- Brendan J Hussey
- Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Cell and Systems Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Impact Centre, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - David R McMillen
- Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Cell and Systems Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Impact Centre, University of Toronto, Toronto, Ontario M5S 1A7, Canada
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21
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Gene expression engineering in fungi. Curr Opin Biotechnol 2019; 59:141-149. [PMID: 31154079 DOI: 10.1016/j.copbio.2019.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/27/2019] [Accepted: 04/24/2019] [Indexed: 02/03/2023]
Abstract
Fungi are a highly diverse group of microbial species that possess a plethora of biotechnologically useful metabolic and physiological properties. Important enablers for fungal biology studies and their biotechnological use are well-performing gene expression tools. Different types of gene expression tools exist; however, typically they are at best only functional in one or a few closely related species. This has hampered research and development of industrially relevant production systems. Here, we review operational principles and concepts of fungal gene expression tools. We present an overview on tools that utilize endogenous fungal promoters and modified hybrid expression systems composed of engineered promoters and transcription factors. Finally, we review synthetic expression tools that are functional across a broad range of fungal species.
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22
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Bonjoch L, Mur P, Arnau-Collell C, Vargas-Parra G, Shamloo B, Franch-Expósito S, Pineda M, Capellà G, Erman B, Castellví-Bel S. Approaches to functionally validate candidate genetic variants involved in colorectal cancer predisposition. Mol Aspects Med 2019; 69:27-40. [PMID: 30935834 DOI: 10.1016/j.mam.2019.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 02/07/2023]
Abstract
Most next generation sequencing (NGS) studies identified candidate genetic variants predisposing to colorectal cancer (CRC) but do not tackle its functional interpretation to unequivocally recognize a new hereditary CRC gene. Besides, germline variants in already established hereditary CRC-predisposing genes or somatic variants share the same need when trying to categorize those with relevant significance. Functional genomics approaches have an important role in identifying the causal links between genetic architecture and phenotypes, in order to decipher cellular function in health and disease. Therefore, functional interpretation of identified genetic variants by NGS platforms is now essential. Available approaches nowadays include bioinformatics, cell and molecular biology and animal models. Recent advances, such as the CRISPR-Cas9, ZFN and TALEN systems, have been already used as a powerful tool with this objective. However, the use of cell lines is of limited value due to the CRC heterogeneity and its close interaction with microenvironment. Access to tridimensional cultures or organoids and xenograft models that mimic the in vivo tissue architecture could revolutionize functional analysis. This review will focus on the application of state-of-the-art functional studies to better tackle new genes involved in germline predisposition to this neoplasm.
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Affiliation(s)
- Laia Bonjoch
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Coral Arnau-Collell
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Gardenia Vargas-Parra
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Bahar Shamloo
- Molecular Biology, Genetics, and Bioengineering Department, Legacy Research Institute, Portland, OR, USA
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Gabriel Capellà
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain
| | - Batu Erman
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain.
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23
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Shankar S, Sreekumar A, Prasad D, Das AV, Pillai MR. Genome editing of oncogenes with ZFNs and TALENs: caveats in nuclease design. Cancer Cell Int 2018; 18:169. [PMID: 30386178 PMCID: PMC6198504 DOI: 10.1186/s12935-018-0666-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 10/17/2018] [Indexed: 01/18/2023] Open
Abstract
Background Gene knockout technologies involving programmable nucleases have been used to create knockouts in several applications. Gene editing using Zinc-finger nucleases (ZFNs), Transcription activator like effectors (TALEs) and CRISPR/Cas systems has been used to create changes in the genome in order to make it non-functional. In the present study, we have looked into the possibility of using six fingered CompoZr ZFN pair to target the E6 gene of HPV 16 genome. Methods HPV 16+ve cell lines; SiHa and CaSki were used for experiments. CompoZr ZFNs targeting E6 gene were designed and constructed by Sigma-Aldrich. TALENs targeting E6 and E7 genes were made using TALEN assembly kit. Gene editing was monitored by T7E1 mismatch nuclease and Nuclease resistance assays. Levels of E6 and E7 were further analyzed by RT-PCR, western blot as well as immunoflourescence analyses. To check if there is any interference due to methylation, cell lines were treated with sodium butyrate, and Nocodazole. Results Although ZFN editing activity in yeast based MEL-I assay was high, it yielded very low activity in tumor cell lines; only 6% editing in CaSki and negligible activity in SiHa cell lines. Though editing efficiency was better in CaSki, no significant reduction in E6 protein levels was observed in immunocytochemical analysis. Further, in silico analysis of DNA binding prediction revealed that some of the ZFN modules bound to sequence that did not match the target sequence. Hence, alternate ZFN pairs for E6 and E7 were not synthesized since no further active sites could be identified by in silico analyses. Then we designed TALENs to target E6 and E7 gene. TALENs designed to target E7 gene led to reduction of E7 levels in CaSki and SiHa cervical cancer cell lines. However, TALEN designed to target E6 gene did not yield any editing activity. Conclusions Our study highlights that designed nucleases intended to obtain bulk effect should have a reasonable editing activity which reflects phenotypically as well. Nucleases with low editing efficiency, intended for generation of knockout cell lines nucleases could be obtained by single cell cloning. This could serve as a criterion for designing ZFNs and TALENs. Electronic supplementary material The online version of this article (10.1186/s12935-018-0666-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sumitra Shankar
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Ahalya Sreekumar
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Deepti Prasad
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Ani V Das
- Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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24
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Engineered Zinc Finger DNA-Binding Domains: Synthesis, Assessment of DNA-Binding Affinity, and Direct Protein Delivery to Mammalian Cells. Methods Mol Biol 2018; 1654:361-375. [PMID: 28986805 DOI: 10.1007/978-1-4939-7231-9_27] [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] [Indexed: 03/06/2023]
Abstract
Zinc finger proteins are the most common among families of DNA-binding transcription factors. Designer transcription factors generated by the fusion of engineered zinc finger DNA-binding domains (ZF-DBDs) to effector domains have been valuable tools for the modulation of gene expression and for targeted genome editing. However, ZF-DBDs without effector domains have also been shown to effectively modulate gene expression by competing with sequence-specific DNA-binding transcription factors. Here, we describe the methodology and provide a detailed workflow for the cloning, expression, purification, and direct cell delivery of engineered ZF-DBDs. Using this protocol, ZF-DBDs can be generated with high efficiency in less than 2 weeks. We also describe a nonradioactive method for measuring DNA binding affinity of the purified ZF-DBD proteins as well as a method for direct delivery of the purified ZF-DBDs to mammalian cells.
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25
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Liang P, Zhang X, Chen Y, Huang J. Developmental history and application of CRISPR in human disease. J Gene Med 2018. [PMID: 28623876 DOI: 10.1002/jgm.2963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genome-editing tools are programmable artificial nucleases, mainly including zinc-finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short palindromic repeat (CRISPR). By recognizing and cleaving specific DNA sequences, genome-editing tools make it possible to generate site-specific DNA double-strand breaks (DSBs) in the genome. DSBs will then be repaired by either error-prone nonhomologous end joining or high-fidelity homologous recombination mechanisms. Through these two different mechanisms, endogenous genes can be knocked out or precisely repaired/modified. Rapid developments in genome-editing tools, especially CRISPR, have revolutionized human disease models generation, for example, various zebrafish, mouse, rat, pig, monkey and human cell lines have been constructed. Here, we review the developmental history of CRISPR and its application in studies of human diseases. In addition, we also briefly discussed the therapeutic application of CRISPR in the near future.
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Affiliation(s)
- Puping Liang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of G uangdong Province, The Third Affiliated Hospital, Guangzhou Medical University and School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiya Zhang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuxi Chen
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Junjiu Huang
- Key Laboratory of Gene Engineering of the Ministry of Education and State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Key Laboratory of Reproductive Medicine of G uangdong Province, The Third Affiliated Hospital, Guangzhou Medical University and School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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26
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Cooper CA, Doran TJ, Challagulla A, Tizard MLV, Jenkins KA. Innovative approaches to genome editing in avian species. J Anim Sci Biotechnol 2018; 9:15. [PMID: 29449939 PMCID: PMC5806378 DOI: 10.1186/s40104-018-0231-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 01/08/2018] [Indexed: 11/22/2022] Open
Abstract
The tools available for genome engineering have significantly improved over the last 5 years, allowing scientist to make precise edits to the genome. Along with the development of these new genome editing tools has come advancements in technologies used to deliver them. In mammals genome engineering tools are typically delivered into in vitro fertilized single cell embryos which are subsequently cultured and then implanted into a recipient animal. In avian species this is not possible, so other methods have been developed for genome engineering in birds. The most common involves in vitro culturing of primordial germ cells (PGCs), which are cells that migrate through the embryonic circulatory system to the developing gonad and colonize the gonad, eventually differentiating into the gonadocytes which produce either sperm or ova. While in culture the PGCs can be modified to carry novel transgenes or gene edits, the population can be screened and enriched, and then transferred into a recipient embryo. The largest drawback of PGC culture is that culture methods do not transfer well across avian species, thus there are reliable culture methods for only a few species including the chicken. Two newer technologies that appear to be more easily adapted in a wider range of avian species are direct injection and sperm transfection assisted gene editing (STAGE). The direct injection method involves injecting genome engineering tools into the circulatory system of the developing embryo just prior to the developmental time point when the PGCs are migrating to the gonads. The genome engineering tools are complexed with transfection reagents, allowing for in vivo transfection of the PGCs. STAGE utilizes sperm transfection to deliver genome engineering tools directly to the newly fertilized embryo. Preliminary evidence indicates that both methodologies have the potential to be adapted for use in birds species other than the chicken, however further work is needed in this area.
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Affiliation(s)
- Caitlin A Cooper
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Private Bag 24, Geelong, VIC 3220 Australia
| | - Timothy J Doran
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Private Bag 24, Geelong, VIC 3220 Australia
| | - Arjun Challagulla
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Private Bag 24, Geelong, VIC 3220 Australia
| | - Mark L V Tizard
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Private Bag 24, Geelong, VIC 3220 Australia
| | - Kristie A Jenkins
- CSIRO Health and Biosecurity, Australian Animal Health Laboratory, Private Bag 24, Geelong, VIC 3220 Australia
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27
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Waryah CB, Moses C, Arooj M, Blancafort P. Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing. Methods Mol Biol 2018. [PMID: 29524128 DOI: 10.1007/978-1-4939-7774-1_2] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The completion of genome, epigenome, and transcriptome mapping in multiple cell types has created a demand for precision biomolecular tools that allow researchers to functionally manipulate DNA, reconfigure chromatin structure, and ultimately reshape gene expression patterns. Epigenetic editing tools provide the ability to interrogate the relationship between epigenetic modifications and gene expression. Importantly, this information can be exploited to reprogram cell fate for both basic research and therapeutic applications. Three different molecular platforms for epigenetic editing have been developed: zinc finger proteins (ZFs), transcription activator-like effectors (TALEs), and the system of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins. These platforms serve as custom DNA-binding domains (DBDs), which are fused to epigenetic modifying domains to manipulate epigenetic marks at specific sites in the genome. The addition and/or removal of epigenetic modifications reconfigures local chromatin structure, with the potential to provoke long-lasting changes in gene transcription. Here we summarize the molecular structure and mechanism of action of ZF, TALE, and CRISPR platforms and describe their applications for the locus-specific manipulation of the epigenome. The advantages and disadvantages of each platform will be discussed with regard to genomic specificity, potency in regulating gene expression, and reprogramming cell phenotypes, as well as ease of design, construction, and delivery. Finally, we outline potential applications for these tools in molecular biology and biomedicine and identify possible barriers to their future clinical implementation.
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Affiliation(s)
- Charlene Babra Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
| | - Colette Moses
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Mahira Arooj
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia.
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia.
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28
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Abstract
Studies of the mammalian nervous system have revealed widespread epigenetic regulation underlying gene expression intrinsic to basic neurobiological function as well as neurological disease. Over the past decade, a critical role has emerged for the neural regulation of chromatin-modifying enzymes during both development and adulthood, and in response to external stimuli. These biochemical data are complemented by numerous next generation sequencing (NGS) studies that quantify the extent of chromatin and DNA modifications in neurons. Neuroepigenetic editing tools can be applied to distinguish between the mere presence and functional relevance of such modifications to neural transcription and animal behavior. This review discusses current advances in neuroepigenetic editing, highlighting methodological considerations pertinent to neuroscience, such as delivery methods and the spatiotemporal specificity of editing. Although neuroepigenetic editing is a nascent field, the studies presented in this review demonstrate the enormous potential of this approach for basic neurobiological research and therapeutic application.
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Affiliation(s)
- Peter J Hamilton
- The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NY, New York, USA
| | - Carissa J Lim
- Department of Pharmacology, The University of Pennsylvania, Philadelphia, PA, USA
| | - Eric J Nestler
- The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, NY, New York, USA
| | - Elizabeth A Heller
- Department of Pharmacology, The University of Pennsylvania, Philadelphia, PA, USA. .,Penn Epigenetics Institute, The University of Pennsylvania, Philadelphia, PA, USA.
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29
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Alotaibi SMI, Ayibiekea A, Pedersen AF, Jakobsen L, Pinholt M, Gumpert H, Hammerum AM, Westh H, Ingmer H. Susceptibility of vancomycin-resistant and -sensitive Enterococcus faecium obtained from Danish hospitals to benzalkonium chloride, chlorhexidine and hydrogen peroxide biocides. J Med Microbiol 2017; 66:1744-1751. [PMID: 29134935 DOI: 10.1099/jmm.0.000642] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
PURPOSE In Danish hospitals, the number of infections caused by vancomycin-resistant Enterococcus faecium (VRE faecium) has dramatically increased in recent years. Hospital disinfectants are essential in eliminating pathogenic microorganisms, and reduced susceptibility may contribute to hospital-associated infections. We have addressed whether clinical VRE faecium display decreased biocide susceptibility when compared to vancomycin-sensitive Enterococcus faecium (VSE faecium) isolates. METHODOLOGY In total 12 VSE faecium and 37 VRE faecium isolates obtained from Danish hospitals over an extended time period were tested for susceptibility towards three commonly applied biocides, namely benzalkonium chloride, chlorhexidine and hydrogen peroxide. RESULTS For benzalkonium chloride, 89 % of VRE faecium strains had a minimal inhibitory concentration (MIC) of 8 mg l-1, whereas for VSE faecium, only 25 % of the strains had an MIC of 8 mg l-1. For chlorhexidine, the MIC of 95 % of VRE faecium strains was 4 mg l-1 or higher, while only 33 % of VSE faecium strains displayed MIC values at the same level. In contrast, both VRE and VSE faecium displayed equal susceptibility to hydrogen peroxide, but a higher minimal bactericidal concentration (MBC) was found for the former. The efflux activity was also assessed, and this was generally higher for the VRE faecium strains compared to VSE faecium. CONCLUSION VRE faecium from Danish hospitals demonstrated decreased susceptibility towards benzalkonium chloride and chlorhexidine compared to VSE faecium, where the use of chlorhexidine is particularly heavy in the hospital environment. These findings suggest that biocide tolerance may characterize VRE faecium isolated in Danish hospitals.
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Affiliation(s)
- Sulaiman M I Alotaibi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark.,Foodborne Diseases Surveillance Center, Executive Department of Surveillance Centers & Crisis Management, Saudi Food & Drug Authority, Riyadh, Saudi Arabia
| | - Alafate Ayibiekea
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Annemette Frøling Pedersen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Lotte Jakobsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Mette Pinholt
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Heidi Gumpert
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Anette M Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik Westh
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.,Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
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30
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Machens F, Balazadeh S, Mueller-Roeber B, Messerschmidt K. Synthetic Promoters and Transcription Factors for Heterologous Protein Expression in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2017; 5:63. [PMID: 29098147 PMCID: PMC5653697 DOI: 10.3389/fbioe.2017.00063] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/29/2017] [Indexed: 12/19/2022] Open
Abstract
Orthogonal systems for heterologous protein expression as well as for the engineering of synthetic gene regulatory circuits in hosts like Saccharomyces cerevisiae depend on synthetic transcription factors (synTFs) and corresponding cis-regulatory binding sites. We have constructed and characterized a set of synTFs based on either transcription activator-like effectors or CRISPR/Cas9, and corresponding small synthetic promoters (synPs) with minimal sequence identity to the host’s endogenous promoters. The resulting collection of functional synTF/synP pairs confers very low background expression under uninduced conditions, while expression output upon induction of the various synTFs covers a wide range and reaches induction factors of up to 400. The broad spectrum of expression strengths that is achieved will be useful for various experimental setups, e.g., the transcriptional balancing of expression levels within heterologous pathways or the construction of artificial regulatory networks. Furthermore, our analyses reveal simple rules that enable the tuning of synTF expression output, thereby allowing easy modification of a given synTF/synP pair. This will make it easier for researchers to construct tailored transcriptional control systems.
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Affiliation(s)
- Fabian Machens
- University of Potsdam, Cell2Fab Research Unit, Potsdam, Germany
| | - Salma Balazadeh
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Department Molecular Biology, University of Potsdam, Potsdam, Germany
| | - Bernd Mueller-Roeber
- Max-Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Department Molecular Biology, University of Potsdam, Potsdam, Germany
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31
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Chandrasekaran AP, Song M, Ramakrishna S. Genome editing: a robust technology for human stem cells. Cell Mol Life Sci 2017; 74:3335-3346. [PMID: 28405721 PMCID: PMC11107609 DOI: 10.1007/s00018-017-2522-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 12/20/2022]
Abstract
Human pluripotent stem cells comprise induced pluripotent and embryonic stem cells, which have tremendous potential for biological and therapeutic applications. The development of efficient technologies for the targeted genome alteration of stem cells in disease models is a prerequisite for utilizing stem cells to their full potential. Genome editing of stem cells is possible with the help of synthetic nucleases that facilitate site-specific modification of a gene of interest. Recent advances in genome editing techniques have improved the efficiency and speed of the development of stem cells for human disease models. Zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system are powerful tools for editing DNA at specific loci. Here, we discuss recent technological advances in genome editing with site-specific nucleases in human stem cells.
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Affiliation(s)
| | - Minjung Song
- Division of Bioindustry, Department of Food Biotechnology, College of Medical and Life Science, Silla University, Seoul, Republic of Korea.
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, Republic of Korea.
- College of Medicine, Hanyang University, Seoul, Republic of Korea.
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32
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Kim MS, Kini AG. Engineering and Application of Zinc Finger Proteins and TALEs for Biomedical Research. Mol Cells 2017; 40:533-541. [PMID: 28835021 PMCID: PMC5582299 DOI: 10.14348/molcells.2017.0139] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/13/2022] Open
Abstract
Engineered DNA-binding domains provide a powerful technology for numerous biomedical studies due to their ability to recognize specific DNA sequences. Zinc fingers (ZF) are one of the most common DNA-binding domains and have been extensively studied for a variety of applications, such as gene regulation, genome engineering and diagnostics. Another novel DNA-binding domain known as a transcriptional activator-like effector (TALE) has been more recently discovered, which has a previously undescribed DNA-binding mode. Due to their modular architecture and flexibility, TALEs have been rapidly developed into artificial gene targeting reagents. Here, we describe the methods used to design these DNA-binding proteins and their key applications in biomedical research.
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Affiliation(s)
- Moon-Soo Kim
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, KY 42101,
USA
| | - Anu Ganesh Kini
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, KY 42101,
USA
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33
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Czapiński J, Kiełbus M, Kałafut J, Kos M, Stepulak A, Rivero-Müller A. How to Train a Cell-Cutting-Edge Molecular Tools. Front Chem 2017; 5:12. [PMID: 28344971 PMCID: PMC5344921 DOI: 10.3389/fchem.2017.00012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/20/2017] [Indexed: 12/28/2022] Open
Abstract
In biological systems, the formation of molecular complexes is the currency for all cellular processes. Traditionally, functional experimentation was targeted to single molecular players in order to understand its effects in a cell or animal phenotype. In the last few years, we have been experiencing rapid progress in the development of ground-breaking molecular biology tools that affect the metabolic, structural, morphological, and (epi)genetic instructions of cells by chemical, optical (optogenetic) and mechanical inputs. Such precise dissection of cellular processes is not only essential for a better understanding of biological systems, but will also allow us to better diagnose and fix common dysfunctions. Here, we present several of these emerging and innovative techniques by providing the reader with elegant examples on how these tools have been implemented in cells, and, in some cases, organisms, to unravel molecular processes in minute detail. We also discuss their advantages and disadvantages with particular focus on their translation to multicellular organisms for in vivo spatiotemporal regulation. We envision that further developments of these tools will not only help solve the processes of life, but will give rise to novel clinical and industrial applications.
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Affiliation(s)
- Jakub Czapiński
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
- Postgraduate School of Molecular Medicine, Medical University of WarsawWarsaw, Poland
| | - Michał Kiełbus
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Joanna Kałafut
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Michał Kos
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Andrzej Stepulak
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
| | - Adolfo Rivero-Müller
- Department of Biochemistry and Molecular Biology, Medical University of LublinLublin, Poland
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi UniversityTurku, Finland
- Department of Biosciences, Åbo Akademi UniversityTurku, Finland
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34
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Genome editing using FACS enrichment of nuclease-expressing cells and indel detection by amplicon analysis. Nat Protoc 2017; 12:581-603. [PMID: 28207001 DOI: 10.1038/nprot.2016.165] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This protocol describes methods for increasing and evaluating the efficiency of genome editing based on the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated 9) system, transcription activator-like effector nucleases (TALENs) or zinc-finger nucleases (ZFNs). First, Indel Detection by Amplicon Analysis (IDAA) determines the size and frequency of insertions and deletions elicited by nucleases in cells, tissues or embryos through analysis of fluorophore-labeled PCR amplicons covering the nuclease target site by capillary electrophoresis in a sequenator. Second, FACS enrichment of cells expressing nucleases linked to fluorescent proteins can be used to maximize knockout or knock-in editing efficiencies or to balance editing efficiency and toxic/off-target effects. The two methods can be combined to form a pipeline for cell-line editing that facilitates the testing of new nuclease reagents and the generation of edited cell pools or clonal cell lines, reducing the number of clones that need to be generated and increasing the ease with which they are screened. The pipeline shortens the time line, but it most prominently reduces the workload of cell-line editing, which may be completed within 4 weeks.
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35
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Dutta S, Madan S, Parikh H, Sundar D. An ensemble micro neural network approach for elucidating interactions between zinc finger proteins and their target DNA. BMC Genomics 2016; 17:1033. [PMID: 28155662 PMCID: PMC5260015 DOI: 10.1186/s12864-016-3323-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The ability to engineer zinc finger proteins binding to a DNA sequence of choice is essential for targeted genome editing to be possible. Experimental techniques and molecular docking have been successful in predicting protein-DNA interactions, however, they are highly time and resource intensive. Here, we present a novel algorithm designed for high throughput prediction of optimal zinc finger protein for 9 bp DNA sequences of choice. In accordance with the principles of information theory, a subset identified by using K-means clustering was used as a representative for the space of all possible 9 bp DNA sequences. The modeling and simulation results assuming synergistic mode of binding obtained from this subset were used to train an ensemble micro neural network. Synergistic mode of binding is the closest to the DNA-protein binding seen in nature, and gives much higher quality predictions, while the time and resources increase exponentially in the trade off. Our algorithm is inspired from an ensemble machine learning approach, and incorporates the predictions made by 100 parallel neural networks, each with a different hidden layer architecture designed to pick up different features from the training dataset to predict optimal zinc finger proteins for any 9 bp target DNA. RESULTS The model gave an accuracy of an average 83% sequence identity for the testing dataset. The BLAST e-value are well within the statistical confidence interval of E-05 for 100% of the testing samples. The geometric mean and median value for the BLAST e-values were found to be 1.70E-12 and 7.00E-12 respectively. For final validation of approach, we compared our predictions against optimal ZFPs reported in literature for a set of experimentally studied DNA sequences. The accuracy, as measured by the average string identity between our predictions and the optimal zinc finger protein reported in literature for a 9 bp DNA target was found to be as high as 81% for DNA targets with a consensus sequence GCNGNNGCN reported in literature. Moreover, the average string identity of our predictions for a catalogue of over 100 9 bp DNA for which the optimal zinc finger protein has been reported in literature was found to be 71%. CONCLUSIONS Validation with experimental data shows that our tool is capable of domain adaptation and thus scales well to datasets other than the training set with high accuracy. As synergistic binding comes the closest to the ideal mode of binding, our algorithm predicts biologically relevant results in sync with the experimental data present in the literature. While there have been disjointed attempts to approach this problem synergistically reported in literature, there is no work covering the whole sample space. Our algorithm allows designing zinc finger proteins for DNA targets of the user's choice, opening up new frontiers in the field of targeted genome editing. This algorithm is also available as an easy to use web server, ZifNN, at http://web.iitd.ac.in/~sundar/ZifNN/ .
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Affiliation(s)
- Shayoni Dutta
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, New Delhi, 110016 India
| | - Spandan Madan
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, New Delhi, 110016 India
| | - Harsh Parikh
- Department of Computer Science and Engineering, Indian Institute of Technology Delhi, New Delhi, 110016 India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, New Delhi, 110016 India
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Dutta S, Madan S, Sundar D. Exploiting the recognition code for elucidating the mechanism of zinc finger protein-DNA interactions. BMC Genomics 2016; 17:1037. [PMID: 28155654 PMCID: PMC5260074 DOI: 10.1186/s12864-016-3324-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background Engineering zinc finger protein motifs for specific binding to double-stranded DNA is critical for targeted genome editing. Most existing tools for predicting DNA-binding specificity in zinc fingers are trained on data obtained from naturally occurring proteins, thereby skewing the predictions. Moreover, these mostly neglect the cooperativity exhibited by zinc fingers. Methods Here, we present an ab-initio method that is based on mutation of the key α-helical residues of individual fingers of the parent template for Zif-268 and its consensus sequence (PDB ID: 1AAY). In an attempt to elucidate the mechanism of zinc finger protein-DNA interactions, we evaluated and compared three approaches, differing in the amino acid mutations introduced in the Zif-268 parent template, and the mode of binding they try to mimic, i.e., modular and synergistic mode of binding. Results Comparative evaluation of the three strategies reveals that the synergistic mode of binding appears to mimic the ideal mechanism of DNA-zinc finger protein binding. Analysis of the predictions made by all three strategies indicate strong dependence of zinc finger binding specificity on the amino acid propensity and the position of a 3-bp DNA sub-site in the target DNA sequence. Moreover, the binding affinity of the individual zinc fingers was found to increase in the order Finger 1 < Finger 2 < Finger 3, thus confirming the cooperative effect. Conclusions Our analysis offers novel insights into the prediction of ZFPs for target DNA sequences and the approaches have been made available as an easy to use web server at http://web.iitd.ac.in/~sundar/zifpredict_ihbe Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3324-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shayoni Dutta
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Spandan Madan
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Durai Sundar
- Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB), Indian Institute of Technology Delhi, New Delhi, 110016, India.
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Osborn MJ, Belanto JJ, Tolar J, Voytas DF. Gene editing and its application for hematological diseases. Int J Hematol 2016; 104:18-28. [PMID: 27233509 PMCID: PMC5595242 DOI: 10.1007/s12185-016-2017-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/08/2016] [Accepted: 03/02/2016] [Indexed: 11/27/2022]
Abstract
The use of precise, rationally designed gene-editing nucleases allows for targeted genome and transcriptome modification, and at present, four major classes of nucleases are being employed: zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), meganucleases (MNs), and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9. Each reagent shares the ability to recognize and bind a target sequence of DNA. Depending on the properties of the reagent, the DNA can be cleaved on one or both strands, or epigenetic changes can be mediated. These novel properties can impact hematological disease by allowing for: (1) direct modification of hematopoietic stem/progenitor cells (HSPCs), (2) gene alteration of hematopoietic lineage committed terminal effectors, (3) genome engineering in non-hematopoietic cells with reprogramming to a hematopoietic phenotype, and (4) transcriptome modulation for gene regulation, modeling, and discovery.
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Affiliation(s)
- Mark J Osborn
- University of Minnesota Twin Cities, Minneapolis, MN, USA
| | | | - Jakub Tolar
- University of Minnesota Twin Cities, Minneapolis, MN, USA.
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38
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Lin J, Musunuru K. Genome engineering tools for building cellular models of disease. FEBS J 2016; 283:3222-31. [PMID: 27218233 DOI: 10.1111/febs.13763] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/16/2016] [Accepted: 05/21/2016] [Indexed: 12/18/2022]
Abstract
With the recent development of methods for genome editing of human pluripotent stem cells, study of the genetic basis of human diseases has been rapidly advancing. Genome-edited differentiated stem cells have provided new and more accurate insights into genomic underpinnings of diseases for which there have not been adequate treatments, and moving toward clinical application of genome editing holds great promise for acceleration of therapeutic translation. Here, we review recent advances in genome-editing technologies and their application to human biology in disease modeling and beyond.
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Affiliation(s)
- Jennie Lin
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Kiran Musunuru
- Cardiovascular Institute, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
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39
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Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nat Methods 2016; 13:127-37. [PMID: 26820547 DOI: 10.1038/nmeth.3733] [Citation(s) in RCA: 296] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/16/2015] [Indexed: 02/08/2023]
Abstract
Gene regulation is a complex and tightly controlled process that defines cell identity, health and disease, and response to pharmacologic and environmental signals. Recently developed DNA-targeting platforms, including zinc finger proteins, transcription activator-like effectors (TALEs) and the clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 system, have enabled the recruitment of transcriptional modulators and epigenome-modifying factors to any genomic site, leading to new insights into the function of epigenetic marks in gene expression. Additionally, custom transcriptional and epigenetic regulation is facilitating refined control over cell function and decision making. The unique properties of the CRISPR-Cas9 system have created new opportunities for high-throughput genetic screens and multiplexing targets to manipulate complex gene expression patterns. This Review summarizes recent technological developments in this area and their application to biomedical challenges. We also discuss remaining limitations and necessary future directions for this field.
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Lee J, Chung JH, Kim HM, Kim DW, Kim H. Designed nucleases for targeted genome editing. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:448-62. [PMID: 26369767 DOI: 10.1111/pbi.12465] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 05/20/2023]
Abstract
Targeted genome-editing technology using designed nucleases has been evolving rapidly, and its applications are widely expanding in research, medicine and biotechnology. Using this genome-modifying technology, researchers can precisely and efficiently insert, remove or change specific sequences in various cultured cells, micro-organisms, animals and plants. This genome editing is based on the generation of double-strand breaks (DSBs), repair of which modifies the genome through nonhomologous end-joining (NHEJ) or homology-directed repair (HDR). In addition, designed nickase-induced generation of single-strand breaks can also lead to precise genome editing through HDR, albeit at relatively lower efficiencies than that induced by nucleases. Three kinds of designed nucleases have been used for targeted DSB formation: zinc-finger nucleases, transcription activator-like effector nucleases, and RNA-guided engineered nucleases derived from the bacterial clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) system. A growing number of researchers are using genome-editing technologies, which have become more accessible and affordable since the discovery and adaptation of CRISPR-Cas9. Here, the repair mechanism and outcomes of DSBs are reviewed and the three types of designed nucleases are discussed with the hope that such understanding will facilitate applications to genome editing.
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Affiliation(s)
- Junwon Lee
- Department of Physiology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Jae-Hee Chung
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Ho Min Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Dong-Wook Kim
- Department of Physiology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Hyongbum Kim
- Department of Pharmacology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
- Graduate Program of Nano Science and Technology, Yonsei University, Seoul, Korea
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41
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Cloning and evaluation of different constitutive promoters in the oleaginous yeastRhodosporidium toruloides. Yeast 2016; 33:99-106. [DOI: 10.1002/yea.3145] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Revised: 11/04/2015] [Accepted: 11/27/2015] [Indexed: 12/17/2022] Open
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Shahbazi Dastjerdeh M, Kouhpayeh S, Sabzehei F, Khanahmad H, Salehi M, Mohammadi Z, Shariati L, Hejazi Z, Rabiei P, Manian M. Zinc Finger Nuclease: A New Approach to Overcome Beta-Lactam Antibiotic Resistance. Jundishapur J Microbiol 2016; 9:e29384. [PMID: 27099691 PMCID: PMC4833962 DOI: 10.5812/jjm.29384] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 09/05/2015] [Accepted: 10/07/2015] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The evolution of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) has been accelerated recently by the indiscriminate application of antibiotics. Antibiotic resistance has challenged the success of medical interventions and therefore is considered a hazardous threat to human health. OBJECTIVES The present study aimed to describe the use of zinc finger nuclease (ZFN) technology to target and disrupt a plasmid-encoded β-lactamase, which prevents horizontal gene transfer-mediated evolution of ARBs. MATERIALS AND METHODS An engineered ZFN was designed to target a specific sequence in the ampicillin resistance gene (amp(R)) of the pTZ57R plasmid. The Escherichia coli bacteria already contained the pZFN kanamycin-resistant (kana(R)) plasmid as the case or the pP15A, kana(R) empty vector as the control, were transformed with the pTZ57R; the ability of the designed ZFN to disrupt the β-lactamase gene was evaluated with the subsequent disturbed ability of the bacteria to grow on ampicillin (amp) and ampicillin-kanamycin (amp-kana)-containing media. The effect of mild hypothermia on the ZFN gene targeting efficiency was also evaluated. RESULTS The growth of bacteria in the case group on the amp and amp-kana-containing media was significantly lower compared with the control group at 37°C (P < 0.001). Despite being more efficient in hypothermic conditions at 30°C (P < 0.001), there were no significant associations between the incubation temperature and the ZFN gene targeting efficiency. CONCLUSIONS Our findings revealed that the ZFN technology could be employed to overcome ampicillin resistance by the targeted disruption of the ampicillin resistance gene, which leads to inactivation of β-lactam synthesis. Therefore, ZFN technology could be engaged to decrease the antibiotic resistance issue with the construction of a ZFN archive against different ARGs. To tackle the resistance issue at the environmental level, recombinant phages expressing ZFNs against different ARGs could be constructed and released into both hospital and urban wastewater systems.
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Affiliation(s)
- Mansoureh Shahbazi Dastjerdeh
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Shirin Kouhpayeh
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Faezeh Sabzehei
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
- Corresponding author: Hossein Khanahmad, Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran. Tel: +98-031337922487, Fax: +98-031-3668859, E-mail:
| | - Mansour Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Zahra Mohammadi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Laleh Shariati
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Zahra Hejazi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Parisa Rabiei
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
| | - Mostafa Manian
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, IR Iran
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43
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Cellular Engineering and Disease Modeling with Gene-Editing Nucleases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [DOI: 10.1007/978-1-4939-3509-3_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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44
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Parant JM, Yeh JRJ. Approaches to Inactivate Genes in Zebrafish. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:61-86. [PMID: 27165349 DOI: 10.1007/978-3-319-30654-4_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Animal models of tumor initiation and tumor progression are essential components toward understanding cancer and designing/validating future therapies. Zebrafish is a powerful model for studying tumorigenesis and has been successfully exploited in drug discovery. According to the zebrafish reference genome, 82 % of disease-associated genes in the Online Mendelian Inheritance in Man (OMIM) database have clear zebrafish orthologues. Using a variety of large-scale random mutagenesis methods developed to date, zebrafish can provide a unique opportunity to identify gene mutations that may be associated with cancer predisposition. On the other hand, newer technologies enabling targeted mutagenesis can facilitate reverse cancer genetic studies and open the door for complex genetic analysis of tumorigenesis. In this chapter, we will describe the various technologies for conducting genome editing in zebrafish with special emphasis on the approaches to inactivate genes.
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Affiliation(s)
- John M Parant
- Department of Pharmacology and Toxicology, UAB Comprehensive Cancer Center, University of Alabama at Birmingham School of Medicine, Birmingham, AL, 35294, USA.
| | - Jing-Ruey Joanna Yeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, 02129, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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45
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Moehrle BM, Nattamai K, Brown A, Florian MC, Ryan M, Vogel M, Bliederhaeuser C, Soller K, Prows DR, Abdollahi A, Schleimer D, Walter D, Milsom MD, Stambrook P, Porteus M, Geiger H. Stem Cell-Specific Mechanisms Ensure Genomic Fidelity within HSCs and upon Aging of HSCs. Cell Rep 2015; 13:2412-2424. [PMID: 26686632 DOI: 10.1016/j.celrep.2015.11.030] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/13/2015] [Accepted: 11/08/2015] [Indexed: 01/22/2023] Open
Abstract
Whether aged hematopoietic stem and progenitor cells (HSPCs) have impaired DNA damage repair is controversial. Using a combination of DNA mutation indicator assays, we observe a 2- to 3-fold increase in the number of DNA mutations in the hematopoietic system upon aging. Young and aged hematopoietic stem cells (HSCs) and hematopoietic progenitor cells (HPCs) do not show an increase in mutation upon irradiation-induced DNA damage repair, and young and aged HSPCs respond very similarly to DNA damage with respect to cell-cycle checkpoint activation and apoptosis. Both young and aged HSPCs show impaired activation of the DNA-damage-induced G1-S checkpoint. Induction of chronic DNA double-strand breaks by zinc-finger nucleases suggests that HSPCs undergo apoptosis rather than faulty repair. These data reveal a protective mechanism in both the young and aged hematopoietic system against accumulation of mutations in response to DNA damage.
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Affiliation(s)
- Bettina M Moehrle
- Institute of Molecular Medicine, University of Ulm, 89081 Ulm, Germany
| | - Kalpana Nattamai
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH 45229, USA
| | - Andreas Brown
- Institute of Molecular Medicine, University of Ulm, 89081 Ulm, Germany
| | - Maria C Florian
- Institute of Molecular Medicine, University of Ulm, 89081 Ulm, Germany
| | - Marnie Ryan
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH 45229, USA
| | - Mona Vogel
- Institute of Molecular Medicine, University of Ulm, 89081 Ulm, Germany
| | | | - Karin Soller
- Institute of Molecular Medicine, University of Ulm, 89081 Ulm, Germany
| | - Daniel R Prows
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH 45229, USA
| | - Amir Abdollahi
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; Molecular and Translational Radiation Oncology, Heidelberg Ion Therapy Center (HIT), 69120 Heidelberg, Germany
| | - David Schleimer
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH 45229, USA
| | - Dagmar Walter
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH (HI-STEM), 69120 Heidelberg, Germany
| | - Michael D Milsom
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine gGmbH (HI-STEM), 69120 Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), Division of Stem Cells and Cancer, Experimental Hematology Group, 69120 Heidelberg, Germany
| | - Peter Stambrook
- Department of Molecular Genetics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Matthew Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Hartmut Geiger
- Institute of Molecular Medicine, University of Ulm, 89081 Ulm, Germany; Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH 45229, USA.
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Sertori R, Trengove M, Basheer F, Ward AC, Liongue C. Genome editing in zebrafish: a practical overview. Brief Funct Genomics 2015; 15:322-30. [DOI: 10.1093/bfgp/elv051] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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Lu JW, Ho YJ, Yang YJ, Liao HA, Ciou SC, Lin LI, Ou DL. Zebrafish as a disease model for studying human hepatocellular carcinoma. World J Gastroenterol 2015; 21:12042-12058. [PMID: 26576090 PMCID: PMC4641123 DOI: 10.3748/wjg.v21.i42.12042] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 05/28/2015] [Accepted: 08/31/2015] [Indexed: 02/07/2023] Open
Abstract
Liver cancer is one of the world’s most common cancers and the second leading cause of cancer deaths. Hepatocellular carcinoma (HCC), a primary hepatic cancer, accounts for 90%-95% of liver cancer cases. The pathogenesis of HCC consists of a stepwise process of liver damage that extends over decades, due to hepatitis, fatty liver, fibrosis, and cirrhosis before developing fully into HCC. Multiple risk factors are highly correlated with HCC, including infection with the hepatitis B or C viruses, alcohol abuse, aflatoxin exposure, and metabolic diseases. Over the last decade, genetic alterations, which include the regulation of multiple oncogenes or tumor suppressor genes and the activation of tumorigenesis-related pathways, have also been identified as important factors in HCC. Recently, zebrafish have become an important living vertebrate model organism, especially for translational medical research. In studies focusing on the biology of cancer, carcinogen induced tumors in zebrafish were found to have many similarities to human tumors. Several zebrafish models have therefore been developed to provide insight into the pathogenesis of liver cancer and the related drug discovery and toxicology, and to enable the evaluation of novel small-molecule inhibitors. This review will focus on illustrative examples involving the application of zebrafish models to the study of human liver disease and HCC, through transgenesis, genome editing technology, xenografts, drug discovery, and drug-induced toxic liver injury.
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48
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Liu J, Gaj T, Yang Y, Wang N, Shui S, Kim S, Kanchiswamy CN, Kim JS, Barbas CF. Efficient delivery of nuclease proteins for genome editing in human stem cells and primary cells. Nat Protoc 2015; 10:1842-59. [DOI: 10.1038/nprot.2015.117] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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49
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Jo YI, Kim H, Ramakrishna S. Recent developments and clinical studies utilizing engineered zinc finger nuclease technology. Cell Mol Life Sci 2015; 72:3819-30. [PMID: 26089249 PMCID: PMC11113831 DOI: 10.1007/s00018-015-1956-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/08/2015] [Accepted: 06/10/2015] [Indexed: 12/27/2022]
Abstract
Efficient methods for creating targeted genetic modifications have long been sought for the investigation of gene function and the development of therapeutic modalities for various diseases, including genetic disorders. Although such modifications are possible using homologous recombination, the efficiency is extremely low. Zinc finger nucleases (ZFNs) are custom-designed artificial nucleases that make double-strand breaks at specific sequences, enabling efficient targeted genetic modifications such as corrections, additions, gene knockouts and structural variations. ZFNs are composed of two domains: (i) a DNA-binding domain comprised of zinc finger modules and (ii) the FokI nuclease domain that cleaves the DNA strand. Over 17 years after ZFNs were initially developed, a number of improvements have been made. Here, we will review the developments and future perspectives of ZFN technology. For example, ZFN activity and specificity have been significantly enhanced by modifying the DNA-binding domain and FokI cleavage domain. Advances in culture methods, such as the application of a cold shock and the use of small molecules that affect ZFN stability, have also increased ZFN activity. Furthermore, ZFN-induced mutant cells can be enriched using episomal surrogate reporters. Additionally, we discuss several ongoing clinical studies that are based on ZFN-mediated genome editing in humans. These breakthroughs have substantially facilitated the use of ZFNs in research, medicine and biotechnology.
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Affiliation(s)
| | - Hyongbum Kim
- Department of Pharmacology and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
- Graduate Program of Nano Science and Technology, Yonsei University, Seoul, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Sungdong-gu, Seoul, South Korea.
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Pellagatti A, Dolatshad H, Yip BH, Valletta S, Boultwood J. Application of genome editing technologies to the study and treatment of hematological disease. Adv Biol Regul 2015; 60:122-134. [PMID: 26433620 DOI: 10.1016/j.jbior.2015.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 09/07/2015] [Accepted: 09/09/2015] [Indexed: 11/29/2022]
Abstract
Genome editing technologies have advanced significantly over the past few years, providing a fast and effective tool to precisely manipulate the genome at specific locations. The three commonly used genome editing technologies are Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs), and the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated Cas9 (CRISPR/Cas9) system. ZFNs and TALENs consist of endonucleases fused to a DNA-binding domain, while the CRISPR/Cas9 system uses guide RNAs to target the bacterial Cas9 endonuclease to the desired genomic location. The double-strand breaks made by these endonucleases are repaired in the cells either by non-homologous end joining, resulting in the introduction of insertions/deletions, or, if a repair template is provided, by homology directed repair. The ZFNs, TALENs and CRISPR/Cas9 systems take advantage of these repair mechanisms for targeted genome modification and have been successfully used to manipulate the genome in human cells. These genome editing tools can be used to investigate gene function, to discover new therapeutic targets, and to develop disease models. Moreover, these genome editing technologies have great potential in gene therapy. Here, we review the latest advances in the application of genome editing technology to the study and treatment of hematological disorders.
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Affiliation(s)
- Andrea Pellagatti
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and NIHR Biomedical Research Centre, Oxford, UK.
| | - Hamid Dolatshad
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and NIHR Biomedical Research Centre, Oxford, UK
| | - Bon Ham Yip
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and NIHR Biomedical Research Centre, Oxford, UK
| | - Simona Valletta
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and NIHR Biomedical Research Centre, Oxford, UK
| | - Jacqueline Boultwood
- Bloodwise Molecular Haematology Unit, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, and NIHR Biomedical Research Centre, Oxford, UK.
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