851
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Zhu X, Clarke R, Puppala AK, Chittori S, Merk A, Merrill BJ, Simonović M, Subramaniam S. Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9. Nat Struct Mol Biol 2019; 26:679-685. [PMID: 31285607 PMCID: PMC6842131 DOI: 10.1038/s41594-019-0258-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/24/2019] [Indexed: 12/27/2022]
Abstract
The RNA-guided Cas9 endonuclease from Streptococcus pyogenes is a single-turnover enzyme that displays a stable product state after double-stranded-DNA cleavage. Here, we present cryo-EM structures of precatalytic, postcatalytic and product states of the active Cas9-sgRNA-DNA complex in the presence of Mg2+. In the precatalytic state, Cas9 adopts the 'checkpoint' conformation with the HNH nuclease domain positioned far away from the DNA. Transition to the postcatalytic state involves a dramatic ~34-Å swing of the HNH domain and disorder of the REC2 recognition domain. The postcatalytic state captures the cleaved substrate bound to the catalytically competent HNH active site. In the product state, the HNH domain is disordered, REC2 returns to the precatalytic conformation, and additional interactions of REC3 and RuvC with nucleic acids are formed. The coupled domain motions and interactions between the enzyme and the RNA-DNA hybrid provide new insights into the mechanism of genome editing by Cas9.
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Affiliation(s)
- Xing Zhu
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan Clarke
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Anupama K Puppala
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Sagar Chittori
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Alan Merk
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bradley J Merrill
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.
- Genome Editing Core, University of Illinois at Chicago, Chicago, IL, USA.
| | - Miljan Simonović
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA.
| | - Sriram Subramaniam
- University of British Columbia, Vancouver, British Columbia, Canada.
- Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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852
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Moon SB, Kim DY, Ko JH, Kim JS, Kim YS. Improving CRISPR Genome Editing by Engineering Guide RNAs. Trends Biotechnol 2019; 37:870-881. [PMID: 30846198 DOI: 10.1016/j.tibtech.2019.01.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 12/26/2022]
Abstract
CRISPR technology is a two-component gene editing system in which the effector protein induces genetic alterations with the aid of a gene targeting guide RNA. Guide RNA can be produced through chemical synthesis, in vitro transcription, or intracellular transcription. Guide RNAs can be engineered to have chemical modifications, alterations in the spacer length, sequence modifications, fusion of RNA or DNA components, and incorporation of deoxynucleotides. Engineered guide RNA can improve genome editing efficiency and target specificity, regulation of biological toxicity, sensitive and specific molecular imaging, multiplexing, and editing flexibility. Therefore, engineered guide RNA will enable more specific, efficient, and safe gene editing, ultimately improving the clinical benefits of gene therapy.
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Affiliation(s)
- Su Bin Moon
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea; KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea; These authors contributed equally to this work
| | - Do Yon Kim
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea; KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea; These authors contributed equally to this work
| | - Jeong-Heon Ko
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea; KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, Republic of Korea; IBS School, Korea University of Science and Technology (UST), Daejeon, Republic of Korea; Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Yong-Sam Kim
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea; KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea.
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853
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Lewis MW, Li S, Franco HL. Transcriptional control by enhancers and enhancer RNAs. Transcription 2019; 10:171-186. [PMID: 31791217 PMCID: PMC6948965 DOI: 10.1080/21541264.2019.1695492] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 11/02/2022] Open
Abstract
The regulation of gene expression is a fundamental cellular process and its misregulation is a key component of disease. Enhancers are one of the most salient regulatory elements in the genome and help orchestrate proper spatiotemporal gene expression during development, in homeostasis, and in response to signaling. Notably, molecular aberrations at enhancers, such as translocations and single nucleotide polymorphisms, are emerging as an important source of human variation and susceptibility to disease. Herein we discuss emerging paradigms addressing how genes are regulated by enhancers, common features of active enhancers, and how non-coding enhancer RNAs (eRNAs) can direct gene expression programs that underlie cellular phenotypes. We survey the current evidence, which suggests that eRNAs can bind to transcription factors, mediate enhancer-promoter interactions, influence RNA Pol II elongation, and act as decoys for repressive cofactors. Furthermore, we discuss current methodologies for the identification of eRNAs and novel approaches to elucidate their functions.
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Affiliation(s)
- Michael W. Lewis
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Shen Li
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Hector L. Franco
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
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854
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Abstract
The past decade has seen an explosion in the field of in vitro disease modelling, in particular the development of organoids. These self-organizing tissues derived from stem cells provide a unique system to examine mechanisms ranging from organ development to homeostasis and disease. Because organoids develop according to intrinsic developmental programmes, the resultant tissue morphology recapitulates organ architecture with remarkable fidelity. Furthermore, the fact that these tissues can be derived from human progenitors allows for the study of uniquely human processes and disorders. This article and accompanying poster highlight the currently available methods, particularly those aimed at modelling human biology, and provide an overview of their capabilities and limitations. We also speculate on possible future technological advances that have the potential for great strides in both disease modelling and future regenerative strategies. Summary: Human organoids are important tools for modelling disease. This At a Glance article summarises the current organoid models of several human diseases, and discusses future prospects for these technologies.
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Affiliation(s)
- Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Meritxell Huch
- The Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK .,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK.,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany
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855
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Leung K, Krishnan Y. Dynamic RNA Nanotechnology Enters the CRISPR Toolbox. ACS CENTRAL SCIENCE 2019; 5:1111-1113. [PMID: 31404241 PMCID: PMC6662155 DOI: 10.1021/acscentsci.9b00550] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
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856
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Kotwica-Rolinska J, Chodakova L, Chvalova D, Kristofova L, Fenclova I, Provaznik J, Bertolutti M, Wu BCH, Dolezel D. CRISPR/Cas9 Genome Editing Introduction and Optimization in the Non-model Insect Pyrrhocoris apterus. Front Physiol 2019; 10:891. [PMID: 31379599 PMCID: PMC6644776 DOI: 10.3389/fphys.2019.00891] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 06/27/2019] [Indexed: 12/20/2022] Open
Abstract
The CRISPR/Cas9 technique is widely used in experimentation with human cell lines as well as with other model systems, such as mice Mus musculus, zebrafish Danio reiro, and the fruit fly Drosophila melanogaster. However, publications describing the use of CRISPR/Cas9 for genome editing in non-model organisms, including non-model insects, are scarce. The introduction of this relatively new method presents many problems even for experienced researchers, especially with the lack of procedures to tackle issues concerning the efficiency of mutant generation. Here we present a protocol for efficient genome editing in the non-model insect species Pyrrhocoris apterus. We collected data from several independent trials that targeted several genes using the CRISPR/Cas9 system and determined that several crucial optimization steps led to a remarkably increased efficiency of mutant production. The main steps are as follows: the timing of embryo injection, the use of the heteroduplex mobility assay as a screening method, in vivo testing of sgRNA efficiency, and G0 germline mosaicism screening. The timing and the method of egg injections used here need to be optimized for other species, but other here-described optimization solutions can be applied immediately for genome editing in other insect species.
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Affiliation(s)
- Joanna Kotwica-Rolinska
- Laboratory of Molecular Chronobiology, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre Czech Academy of Sciences, České Budějovice, Czechia
| | - Lenka Chodakova
- Laboratory of Molecular Chronobiology, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre Czech Academy of Sciences, České Budějovice, Czechia
- Department of Molecular Biology, Faculty of Sciences, University of South Bohemia, České Budějovice, Czechia
| | - Daniela Chvalova
- Laboratory of Molecular Chronobiology, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre Czech Academy of Sciences, České Budějovice, Czechia
| | - Lucie Kristofova
- Laboratory of Molecular Chronobiology, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre Czech Academy of Sciences, České Budějovice, Czechia
| | - Iva Fenclova
- Laboratory of Molecular Chronobiology, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre Czech Academy of Sciences, České Budějovice, Czechia
| | - Jan Provaznik
- Laboratory of Molecular Chronobiology, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre Czech Academy of Sciences, České Budějovice, Czechia
| | - Maly Bertolutti
- Laboratory of Molecular Chronobiology, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre Czech Academy of Sciences, České Budějovice, Czechia
| | - Bulah Chia-Hsiang Wu
- Laboratory of Molecular Chronobiology, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre Czech Academy of Sciences, České Budějovice, Czechia
- Department of Molecular Biology, Faculty of Sciences, University of South Bohemia, České Budějovice, Czechia
| | - David Dolezel
- Laboratory of Molecular Chronobiology, Department of Molecular Biology and Genetics, Institute of Entomology, Biology Centre Czech Academy of Sciences, České Budějovice, Czechia
- Department of Molecular Biology, Faculty of Sciences, University of South Bohemia, České Budějovice, Czechia
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857
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Rabinowitch I. What would a synthetic connectome look like? Phys Life Rev 2019; 33:1-15. [PMID: 31296448 DOI: 10.1016/j.plrev.2019.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/25/2019] [Indexed: 02/07/2023]
Abstract
A major challenge of contemporary neuroscience is to unravel the structure of the connectome, the ensemble of neural connections that link between different functional units of the brain, and to reveal how this structure relates to brain function. This thriving area of research largely follows the general tradition in biology of reverse-engineering, which consists of first observing and characterizing a biological system or process, and then deconstructing it into its fundamental building blocks in order to infer its modes of operation. However, a complementary form of biology has emerged, synthetic biology, which emphasizes construction-based forward-engineering. The synthetic biology approach comprises the assembly of new biological systems out of elementary biological parts. The rationale is that the act of building a system can be a powerful method for gaining deep understanding of how that system works. As the fields of connectomics and synthetic biology are independently growing, I propose to consider the benefits of combining the two, to create synthetic connectomics, a new form of neuroscience and a new form of synthetic biology. The goal of synthetic connectomics would be to artificially design and construct the connectomes of live behaving organisms. Synthetic connectomics could serve as a unifying platform for unraveling the complexities of brain operation and perhaps also for generating new forms of artificial life, and, in general, could provide a valuable opportunity for empirically exploring theoretical predictions about network function. What would a synthetic connectome look like? What purposes would it serve? How could it be constructed? This review delineates the novel notion of a synthetic connectome and aims to lay out the initial steps towards its implementation, contemplating its impact on science and society.
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Affiliation(s)
- Ithai Rabinowitch
- Department of Medical Neurobiology, IMRIC - Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem Campus, Jerusalem, 9112002, Israel.
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858
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Berckman EA, Chen W. Exploiting dCas9 fusion proteins for dynamic assembly of synthetic metabolons. Chem Commun (Camb) 2019; 55:8219-8222. [PMID: 31210215 PMCID: PMC7725109 DOI: 10.1039/c9cc04002a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Here we reported a new strategy to construct synthetic metabolons using dCas9-guided assembly. Three orthogonal dCas9 proteins were exploited to guide the independent and site-specific assembly of their fusion partners onto a single DNA scaffold. This new platform was applied towards the construction of a two-component cellulosome. Because of the superior binding affinity, the resulting structures exhibited both improved assembly and reducing sugar production. Conditional enzyme assembly was made possible by utilizing toehold-gated sgRNA (thgRNA), which blocks cellulosome formation until the spacer region is unblocked by a RNA trigger. This platform is highly modular owing to the ease of target synthesis, combinations of possible Cas9-fusion arrangements, and expansion to other metabolic pathways.
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Affiliation(s)
- Emily A Berckman
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA. and Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
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859
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Ahmad N, Rahman M, Mukhtar Z, Zafar Y, Zhang B. A critical look on CRISPR‐based genome editing in plants. J Cell Physiol 2019; 235:666-682. [DOI: 10.1002/jcp.29052] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 02/12/2019] [Accepted: 06/06/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Niaz Ahmad
- Agricultural Biotechnology Division National Institute for Biotechnology & Genetic Engineering (NIBGE) Faisalabad Pakistan
| | - Mehboob‐ur Rahman
- Agricultural Biotechnology Division National Institute for Biotechnology & Genetic Engineering (NIBGE) Faisalabad Pakistan
| | - Zahid Mukhtar
- Agricultural Biotechnology Division National Institute for Biotechnology & Genetic Engineering (NIBGE) Faisalabad Pakistan
| | - Yusuf Zafar
- Pakistan Agriculture Research Council Islamabad Pakistan
| | - Baohong Zhang
- Department of Biology East Carolina University Greenville North Caroline
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860
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Çiçek YA, Luther DC, Kretzmann JA, Rotello VM. Advances in CRISPR/Cas9 Technology for in Vivo Translation. Biol Pharm Bull 2019; 42:304-311. [PMID: 30828060 DOI: 10.1248/bpb.b18-00811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) technology has revolutionized therapeutic gene editing by providing researchers with a new method to study and cure diseases previously considered untreatable. While the full range and power of CRISPR technology for therapeutics is being elucidated through in vitro studies, translation to in vivo studies is slow. To date there is no totally effective delivery strategy to carry CRISPR components to the target site in vivo. The complexity of in vivo delivery is furthered by the number of potential delivery methods, the different forms in which CRISPR can be delivered as a therapeutic, and the disease target and tissue type in question. There are major challenges and limitations to delivery strategies, and it is imperative that future directions are guided by well-conducted studies that consider the full effect these variables have on the eventual outcome. In this review we will discuss the advances of the latest in vivo CRISPR/Cas9 delivery strategies and highlight the challenges yet to be overcome.
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Affiliation(s)
- Yağız Anıl Çiçek
- Department of Chemistry, Middle East Technical University (METU)
| | | | - Jessica A Kretzmann
- Department of Chemistry, University of Massachusetts.,School of Molecular Sciences, The University of Western Australia
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861
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Adaptation processes that build CRISPR immunity: creative destruction, updated. Essays Biochem 2019; 63:227-235. [PMID: 31186288 DOI: 10.1042/ebc20180073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 01/01/2023]
Abstract
Prokaryotes can defend themselves against invading mobile genetic elements (MGEs) by acquiring immune memory against them. The memory is a DNA database located at specific chromosomal sites called CRISPRs (clustered regularly interspaced short palindromic repeats) that store fragments of MGE DNA. These are utilised to target and destroy returning MGEs, preventing re-infection. The effectiveness of CRISPR-based immune defence depends on 'adaptation' reactions that capture and integrate MGE DNA fragments into CRISPRs. This provides the means for immunity to be delivered against MGEs in 'interference' reactions. Adaptation and interference are catalysed by Cas (CRISPR-associated) proteins, aided by enzymes well known for other roles in cells. We survey the molecular biology of CRISPR adaptation, highlighting entirely new developments that may help us to understand how MGE DNA is captured. We focus on processes in Escherichia coli, punctuated with reference to other prokaryotes that illustrate how common requirements for adaptation, DNA capture and integration, can be achieved in different ways. We also comment on how CRISPR adaptation enzymes, and their antecedents, can be utilised for biotechnology.
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862
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Barnby E, Reynolds M, O'Neal P. Genomic Science-From 2001 to Present Day: What School Nurses Need to Know. NASN Sch Nurse 2019; 34:235-239. [PMID: 30382772 DOI: 10.1177/1942602x18810790] [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: 06/08/2023]
Abstract
Genetic science has made remarkable advances in the 21st century. As genetic and genomic sciences continue to expand, school nurses will become thoroughly immersed in data, information, and technology. As new diseases, treatments, and therapies are discovered, school nurses will need to implement and assess best practices for the complex and medically fragile student population. This article will discuss the top 10 recent discoveries in genomic science and how school nurses can use this information in clinical practice.
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Affiliation(s)
- Elizabeth Barnby
- Clinical Associate Professor, University of Alabama in Huntsville, Huntsville, AL
| | - Mark Reynolds
- Clinical Assistant Professor; RN-BSN/MSN, Program Coordinator, University of Alabama in Huntsville, Huntsville, AL
| | - Pamela O'Neal
- Associate Professor, University of Alabama in Huntsville, Huntsville, AL
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863
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van Krieken PP, Voznesenskaya A, Dicker A, Xiong Y, Park JH, Lee JI, Ilegems E, Berggren PO. Translational assessment of a genetic engineering methodology to improve islet function for transplantation. EBioMedicine 2019; 45:529-541. [PMID: 31262716 PMCID: PMC6642289 DOI: 10.1016/j.ebiom.2019.06.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 06/17/2019] [Accepted: 06/21/2019] [Indexed: 11/05/2022] Open
Abstract
Background The functional quality of insulin-secreting islet beta cells is a major factor determining the outcome of clinical transplantations for diabetes. It is therefore of importance to develop methodological strategies aiming at optimizing islet cell function prior to transplantation. In this study we propose a synthetic biology approach to genetically engineer cellular signalling pathways in islet cells. Methods We established a novel procedure to modify islet beta cell function by combining adenovirus-mediated transduction with reaggregation of islet cells into pseudoislets. As a proof-of-concept for the genetic engineering of islets prior to transplantation, this methodology was applied to increase the expression of the V1b receptor specifically in insulin-secreting beta cells. The functional outcomes were assessed in vitro and in vivo following transplantation into the anterior chamber of the eye. Findings Pseudoislets produced from mouse dissociated islet cells displayed basic functions similar to intact native islets in terms of glucose induced intracellular signalling and insulin release, and after transplantation were properly vascularized and contributed to blood glucose homeostasis. The synthetic amplification of the V1b receptor signalling in beta cells successfully modulated pseudoislet function in vitro. Finally, in vivo responses of these pseudoislet grafts to vasopressin allowed evaluation of the potential benefits of this approach in regenerative medicine. Interpretation These results are promising first steps towards the generation of high-quality islets and suggest synthetic biology as an important tool in future clinical islet transplantations. Moreover, the presented methodology might serve as a useful research strategy to dissect cellular signalling mechanisms of relevance for optimal islet function.
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Affiliation(s)
- Pim P van Krieken
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Stockholm, Sweden
| | - Anna Voznesenskaya
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Stockholm, Sweden
| | - Andrea Dicker
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Stockholm, Sweden
| | - Yan Xiong
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Stockholm, Sweden
| | - Jae Hong Park
- Department of Otolaryngology-Head and Neck Surgery, Soonchunhyang University College of Medicine, Cheonan, Republic of Korea
| | - Jeong Ik Lee
- Department of Veterinary Obstetrics and Theriogenology, College of Veterinary Medicine, Konkuk University, Seoul, Republic of Korea; Department of Biomedical Science and Technology, Institute of Biomedical Science & Technology (IBST), Konkuk University, Seoul, Republic of Korea
| | - Erwin Ilegems
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Stockholm, Sweden.
| | - Per-Olof Berggren
- The Rolf Luft Research Center for Diabetes and Endocrinology, Karolinska Institutet, Stockholm, Sweden; Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, USA; Lee Kong Chian School of Medicine, Nanyang Technological University, Imperial College London, Novena Campus, Singapore, Singapore
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864
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Ruppel NJ, Estell LE, Jackson RI, Wolyniak MJ. An Undergraduate Research Project Utilizing CRISPR-Cas9 Gene Editing Technology to Study Gene Function in Arabidopsis thaliana. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2019; 20:20.2.31. [PMID: 31316687 PMCID: PMC6608611 DOI: 10.1128/jmbe.v20i2.1666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 02/26/2019] [Indexed: 05/25/2023]
Abstract
The CRISPR-Cas9 system functions in microbial viral pathogen recognition pathways by identifying and targeting foreign DNA for degradation. Recently, biotechnological advances have allowed scientists to use CRISPR-Cas9-based elements as a molecular tool to selectively modify DNA in a wide variety of other living systems. Given the emerging need to bring engaging CRISPR-Cas9 laboratory experiences to an undergraduate audience, we incorporated a CRISPR-based research project into our Genetics class laboratories, emphasizing its use in plants. Our genetic manipulations were designed for Arabidopsis thaliana, which despite serving as a plant research model, has traditionally been difficult to use in a classroom setting. For this project, students transformed plasmid DNA containing the essential CRISPR-Cas9 gene editing elements into A. thaliana. Expression of these elements in the plant genome was expected to create a deletion at one of six targeted genes. The genes we chose had a known seedling and/or juvenile loss-of-function phenotype, which made genetic analysis by students with a limited background possible. It also allowed the project to reach completion in a typical undergraduate semester timeframe. Assessment efforts demonstrated several learning gains, including students' understanding of CRISPR-Cas9 content, their ability to apply CRISPR-Cas9 gene editing tools using bioinformatics and genetics, their ability to employ elements of experimental design, and improved science communication skills. They also felt a stronger connection to their scientific education and were more likely to continue on a STEM career path. Overall, this project can be used to introduce CRISPR-Cas9 technology to undergraduates using plants in a single-semester laboratory course.
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Affiliation(s)
| | - Lauren E Estell
- Department of Biology, Randolph-Macon College, Ashland, VA 23005
| | - Robert I Jackson
- Department of Biology, Hampden-Sydney College, Hampden-Sydney, VA 23943
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865
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Abstract
DNA outperforms most conventional storage media in terms of information retention time, physical density, and volumetric coding capacity. Advances in synthesis and sequencing technologies have enabled implementations of large synthetic DNA databases with impressive storage capacity and reliable data recovery. Several robust DNA storage architectures featuring random access, error correction, and content rewritability have been constructed with the potential for scalability and cost reduction. We survey these recent achievements and discuss alternative routes for overcoming the hurdles of engineering practical DNA storage systems. We also review recent exciting work on in vivo DNA memory including intracellular recorders constructed by programmable genome editing tools. Besides information storage, DNA could serve as a versatile molecular computing substrate. We highlight several state-of-the-art DNA computing techniques such as strand displacement, localized hybridization chain reactions, and enzymatic reaction networks. We summarize how these simple primitives have facilitated rational designs and implementations of in vitro DNA reaction networks that emulate digital/analog circuits, artificial neural networks, or nonlinear dynamic systems. We envision these modular primitives could be strategically adapted for sophisticated database operations and massively parallel computations on DNA databases. We also highlight in vivo DNA computing modules such as CRISPR logic gates for building scalable genetic circuits in living cells. To conclude, we discuss various implications and challenges of DNA-based storage and computing, and we particularly encourage innovative work on bridging these two areas of research to further explore molecular parallelism and near-data processing. Such integrated molecular systems could lead to far-reaching applications in biocomputing, security, and medicine.
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866
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CRISPR/Cas9 guided genome and epigenome engineering and its therapeutic applications in immune mediated diseases. Semin Cell Dev Biol 2019; 96:32-43. [PMID: 31112800 DOI: 10.1016/j.semcdb.2019.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 12/21/2022]
Abstract
Recent developments in the nucleic acid editing technologies have provided a powerful tool to precisely engineer the genome and epigenome for studying many aspects of immune cell differentiation and development as well as several immune mediated diseases (IMDs) including autoimmunity and cancer. Here, we discuss the recent technological achievements of the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based RNA-guided genome and epigenome editing toolkit and provide an insight into how CRISPR/Cas9 (CRISPR Associated Protein 9) toolbox could be used to examine genetic and epigenetic mechanisms underlying IMDs. In addition, we will review the progress in CRISPR/Cas9-based genome-wide genome and epigenome screens in various cell types including immune cells. Finally, we will discuss the potential of CRISPR/Cas9 in defining the molecular function of disease associated SNPs overlapping gene regulatory elements.
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867
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Tang XD, Gao F, Liu MJ, Fan QL, Chen DK, Ma WT. Methods for Enhancing Clustered Regularly Interspaced Short Palindromic Repeats/Cas9-Mediated Homology-Directed Repair Efficiency. Front Genet 2019; 10:551. [PMID: 31263478 PMCID: PMC6590329 DOI: 10.3389/fgene.2019.00551] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 05/24/2019] [Indexed: 12/26/2022] Open
Abstract
The evolution of organisms has provided a variety of mechanisms to maintain the integrity of its genome, but as damage occurs, DNA damage repair pathways are necessary to resolve errors. Among them, the DNA double-strand break repair pathway is highly conserved in eukaryotes, including mammals. Nonhomologous DNA end joining and homologous directed repair are two major DNA repair pathways that are synergistic or antagonistic. Clustered regularly interspaced short palindromic repeats genome editing techniques based on the nonhomologous DNA end joining repair pathway have been used to generate highly efficient insertions or deletions of variable-sized genes but are error-prone and inaccurate. By combining the homology-directed repair pathway with clustered regularly interspaced short palindromic repeats cleavage, more precise genome editing via insertion or deletion of the desired fragment can be performed. However, homologous directed repair is not efficient and needs further improvement. Here, we describe several ways to improve the efficiency of homologous directed repair by regulating the cell cycle, expressing key proteins involved in homologous recombination and selecting appropriate donor DNA.
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Affiliation(s)
- Xi-Dian Tang
- Veterinary Immunology Laboratory, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, China
| | - Fei Gao
- Veterinary Immunology Laboratory, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, China
| | - Ming-Jie Liu
- Veterinary Immunology Laboratory, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, China
| | - Qin-Lei Fan
- China Animal Health and Epidemiology Center, Qingdao, China
| | - De-Kun Chen
- Veterinary Immunology Laboratory, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, China
| | - Wen-Tao Ma
- Veterinary Immunology Laboratory, Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, China
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868
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Ishiguro S, Mori H, Yachie N. DNA event recorders send past information of cells to the time of observation. Curr Opin Chem Biol 2019; 52:54-62. [PMID: 31200335 DOI: 10.1016/j.cbpa.2019.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/26/2019] [Accepted: 05/10/2019] [Indexed: 11/17/2022]
Abstract
While current omics and single cell technologies have enabled measurements of high-resolution molecular snapshots of cells at a large scale, these technologies all require destruction of samples and prevent us from analyzing dynamic changes in molecular profiles, phenotypes, and behaviors of individual cells in a complex system. One possible direction to overcome this issue is the development of a cell-embedded 'event recorder' system, whereby molecular and phenotypic information of a cell(s) can be obtained at the time of observation with their past event information stored in 'heritable polymers' of the same cell. This concept has been demonstrated by many synthetic cellular circuits that monitor and transmit a certain set of environmental and intracellular signals into DNA, and have now been further accelerated by recent CRISPR-related technologies. Notably, the discovery of the RT-Cas1-Cas2 system, which acquires sequences of cellular transcripts into a specific host genomic region, has enabled recording of a broader range of molecular profile histories in the DNA tapes of cells, to understand the dynamics of complex biological processes that cannot be addressed by current technologies.
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Affiliation(s)
- Soh Ishiguro
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan; Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Hideto Mori
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan; Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Nozomu Yachie
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan; Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0035, Japan; Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan; Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo 113-0033, Japan; PRESTO, Japan Science and Technology Agency (JST), Tokyo 153-8904, Japan.
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869
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Zhang F, Song G, Tian Y. Anti-CRISPRs: The natural inhibitors for CRISPR-Cas systems. Animal Model Exp Med 2019; 2:69-75. [PMID: 31392299 PMCID: PMC6600654 DOI: 10.1002/ame2.12069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 04/29/2019] [Accepted: 05/06/2019] [Indexed: 12/22/2022] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR associated protein) systems serve as the adaptive immune system by which prokaryotes defend themselves against phages. It has also been developed into a series of powerful gene-editing tools. As the natural inhibitors of CRISPR-Cas systems, anti-CRISPRs (Acrs) can be used as the "off-switch" for CRISPR-Cas systems to limit the off-target effects caused by Cas9. Since the discovery of CRISPR-Cas systems, much research has focused on the identification, mechanisms and applications of Acrs. In light of the rapid development and scientific significance of this field, this review summarizes the history and research status of Acrs, and considers future applications.
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Affiliation(s)
- Fei Zhang
- CAS Key Laboratory of RNA BiologyInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guoxu Song
- CAS Key Laboratory of RNA BiologyInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Yong Tian
- CAS Key Laboratory of RNA BiologyInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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870
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Hajian R, Balderston S, Tran T, deBoer T, Etienne J, Sandhu M, Wauford NA, Chung JY, Nokes J, Athaiya M, Paredes J, Peytavi R, Goldsmith B, Murthy N, Conboy IM, Aran K. Detection of unamplified target genes via CRISPR-Cas9 immobilized on a graphene field-effect transistor. Nat Biomed Eng 2019; 3:427-437. [PMID: 31097816 PMCID: PMC6556128 DOI: 10.1038/s41551-019-0371-x] [Citation(s) in RCA: 351] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 02/19/2019] [Indexed: 12/25/2022]
Abstract
Most methods for the detection of nucleic acids require many reagents and expensive and bulky instrumentation. Here, we report the development and testing of a graphene-based field-effect transistor that uses clustered regularly interspaced short palindromic repeats (CRISPR) technology to enable the digital detection of a target sequence within intact genomic material. Termed CRISPR-Chip, the biosensor uses the gene-targeting capacity of catalytically deactivated CRISPR-associated protein 9 (Cas9) complexed with a specific single-guide RNA and immobilized on the transistor to yield a label-free nucleic-acid-testing device whose output signal can be measured with a simple handheld reader. We used CRISPR-Chip to analyse DNA samples collected from HEK293T cell lines expressing blue fluorescent protein, and clinical samples of DNA with two distinct mutations at exons commonly deleted in individuals with Duchenne muscular dystrophy. In the presence of genomic DNA containing the target gene, CRISPR-Chip generates, within 15 min, with a sensitivity of 1.7 fM and without the need for amplification, a significant enhancement in output signal relative to samples lacking the target sequence. CRISPR-Chip expands the applications of CRISPR-Cas9 technology to the on-chip electrical detection of nucleic acids.
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Affiliation(s)
- Reza Hajian
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Sarah Balderston
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Thanhtra Tran
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Tara deBoer
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jessy Etienne
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Mandeep Sandhu
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Noreen A Wauford
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Jing-Yi Chung
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Mitre Athaiya
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Jacobo Paredes
- Tecnun, School of Engineering, University of Navarra, San Sebastián, Spain
| | | | | | - Niren Murthy
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Irina M Conboy
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Nanosens Innovations, San Diego, CA, USA.
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871
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Li Z, Wang F, Li JF. Targeted Transcriptional Activation in Plants Using a Potent Dead Cas9-Derived Synthetic Gene Activator. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2019; 127:e89. [PMID: 31237422 DOI: 10.1002/cpmb.89] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genetic tools for specific perturbation of endogenous gene expression are highly desirable for interrogation of plant gene functions and improvement of crop traits. Synthetic transcriptional activators derived from the CRISPR/Cas9 system are emerging as powerful new tools for activating the endogenous expression of genes of interest in plants. These synthetic constructs, generated by tethering transcriptional activation domains to a nuclease-dead Cas9 (dCas9), can be directed to the promoters of endogenous target genes by single guide RNAs (sgRNAs) to activate transcription. Here, we provide a detailed protocol for targeted transcriptional activation in plants using a recently developed, highly potent dCas9 gene activator construct referred to as dCas9-TV. This protocol covers selection of sgRNA targets, construction of sgRNA expression cassettes, and screening for an optimal sgRNA using a protoplast-based promoter-luciferase assay. Finally, the dCas9-TV gene activator coupled with the optimal sgRNA is delivered into plants via Agrobacterium-mediated transformation, thereby enabling robust upregulation of target gene expression in transgenic Arabidopsis and rice plants. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Zhenxiang Li
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Fengzhu Wang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jian-Feng Li
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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872
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Campenhout CV, Cabochette P, Veillard AC, Laczik M, Zelisko-Schmidt A, Sabatel C, Dhainaut M, Vanhollebeke B, Gueydan C, Kruys V. Guidelines for optimized gene knockout using CRISPR/Cas9. Biotechniques 2019; 66:295-302. [PMID: 31039627 DOI: 10.2144/btn-2018-0187] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
CRISPR/Cas9 technology has evolved as the most powerful approach to generate genetic models both for fundamental and preclinical research. Despite its apparent simplicity, the outcome of a genome-editing experiment can be substantially impacted by technical parameters and biological considerations. Here, we present guidelines and tools to optimize CRISPR/Cas9 genome-targeting efficiency and specificity. The nature of the target locus, the design of the single guide RNA and the choice of the delivery method should all be carefully considered prior to a genome-editing experiment. Different methods can also be used to detect off-target cleavages and decrease the risk of unwanted mutations. Together, these optimized tools and proper controls are essential to the assessment of CRISPR/Cas9 genome-editing experiments.
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Affiliation(s)
| | - Pauline Cabochette
- Laboratoire de Signalisation Neurovasculaire, Faculté des Sciences, Université libre de Bruxelles (ULB), 12 rue des Profs. Jeener et Brachet, 6041 Gosselies, Belgium
| | | | - Miklos Laczik
- Diagenode, SA, Liège Science Park, 4102 Seraing, Belgium
| | | | - Céline Sabatel
- Diagenode, SA, Liège Science Park, 4102 Seraing, Belgium
| | - Maxime Dhainaut
- Precision Immunology Institute, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benoit Vanhollebeke
- Laboratoire de Signalisation Neurovasculaire, Faculté des Sciences, Université libre de Bruxelles (ULB), 12 rue des Profs. Jeener et Brachet, 6041 Gosselies, Belgium
- Walloon Excellence in Life Sciences & Biotechnology (WELBIO), Belgium
| | - Cyril Gueydan
- Laboratoire de Biologie Moléculaire du Gène, Faculté des Sciences, Université libre de Bruxelles (ULB), 12 rue des Profs. Jeener et Brachet, 6041 Gosselies, Belgium
| | - Véronique Kruys
- Laboratoire de Biologie Moléculaire du Gène, Faculté des Sciences, Université libre de Bruxelles (ULB), 12 rue des Profs. Jeener et Brachet, 6041 Gosselies, Belgium
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873
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Brunner E, Yagi R, Debrunner M, Beck-Schneider D, Burger A, Escher E, Mosimann C, Hausmann G, Basler K. CRISPR-induced double-strand breaks trigger recombination between homologous chromosome arms. Life Sci Alliance 2019; 2:e201800267. [PMID: 31196871 PMCID: PMC6587125 DOI: 10.26508/lsa.201800267] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/27/2022] Open
Abstract
CRISPR-Cas9-based genome editing has transformed the life sciences, enabling virtually unlimited genetic manipulation of genomes: The RNA-guided Cas9 endonuclease cuts DNA at a specific target sequence and the resulting double-strand breaks are mended by one of the intrinsic cellular repair pathways. Imprecise double-strand repair will introduce random mutations such as indels or point mutations, whereas precise editing will restore or specifically edit the locus as mandated by an endogenous or exogenously provided template. Recent studies indicate that CRISPR-induced DNA cuts may also result in the exchange of genetic information between homologous chromosome arms. However, conclusive data of such recombination events in higher eukaryotes are lacking. Here, we show that in Drosophila, the detected Cas9-mediated editing events frequently resulted in germline-transmitted exchange of chromosome arms-often without indels. These findings demonstrate the feasibility of using the system for generating recombinants and also highlight an unforeseen risk of using CRISPR-Cas9 for therapeutic intervention.
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Affiliation(s)
- Erich Brunner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ryohei Yagi
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
| | - Marc Debrunner
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Alexa Burger
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Eliane Escher
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Christian Mosimann
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - George Hausmann
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Konrad Basler
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
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874
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Yeo WL, Heng E, Tan LL, Lim YW, Lim YH, Hoon S, Zhao H, Zhang MM, Wong FT. Characterization of Cas proteins for CRISPR-Cas editing in streptomycetes. Biotechnol Bioeng 2019; 116:2330-2338. [PMID: 31090220 DOI: 10.1002/bit.27021] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 04/02/2019] [Accepted: 05/09/2019] [Indexed: 12/26/2022]
Abstract
Application of the well-characterized Streptococcus pyogenes CRISPR-Cas9 system in actinomycetes streptomycetes has enabled high-efficiency multiplex genome editing and CRISPRi-mediated transcriptional regulation in these prolific bioactive metabolite producers. Nonetheless, SpCas9 has its limitations and can be ineffective depending on the strains and target sites. Here, we built and tested alternative CRISPR-Cas constructs based on the standalone pCRISPomyces-2 editing plasmid. We showed that Streptococcus thermophilus CRISPR1 Cas9 (sth1Cas9), Staphylococcus aureus Cas9 (saCas9), and Francisella tularensis subsp. novicida U112 Cpf1 (fnCpf1) are functional in multiple streptomycetes, enabling efficient homology-directed repair-mediated knock-in and deletion. In strains where spCas9 was nonfunctional, these alternative Cas systems enabled precise genomic modifications within biosynthetic gene clusters for the discovery, production, and diversification of natural products. These additional Cas proteins provide us with the versatility to overcome the limitations of individual CRISPR-Cas systems for genome editing and transcriptional regulation of these industrially important bacteria.
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Affiliation(s)
- Wan Lin Yeo
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, A*STAR, Singapore, Singapore
| | - Elena Heng
- Molecular Engineering Laboratory, Biomedical Institutes of Sciences, A*STAR, Singapore, Singapore
| | - Lee Ling Tan
- Molecular Engineering Laboratory, Biomedical Institutes of Sciences, A*STAR, Singapore, Singapore
| | - Yi Wee Lim
- Organic Chemistry, Institute of Chemical and Engineering Sciences, A*STAR, Singapore, Singapore
| | - Yee Hwee Lim
- Organic Chemistry, Institute of Chemical and Engineering Sciences, A*STAR, Singapore, Singapore
| | - Shawn Hoon
- Molecular Engineering Laboratory, Biomedical Institutes of Sciences, A*STAR, Singapore, Singapore
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, A*STAR, Singapore, Singapore
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana-Champaign, Illinois, United States
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois, United States
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Illinois, United States
| | - Mingzi M Zhang
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, A*STAR, Singapore, Singapore
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan, R.O.C
| | - Fong Tian Wong
- Molecular Engineering Laboratory, Biomedical Institutes of Sciences, A*STAR, Singapore, Singapore
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875
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Genome Editing as a Treatment for the Most Prevalent Causative Genes of Autosomal Dominant Retinitis Pigmentosa. Int J Mol Sci 2019; 20:ijms20102542. [PMID: 31126147 PMCID: PMC6567127 DOI: 10.3390/ijms20102542] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 02/07/2023] Open
Abstract
: Inherited retinal dystrophies (IRDs) are a clinically and genetically heterogeneous group of diseases with more than 250 causative genes. The most common form is retinitis pigmentosa. IRDs lead to vision impairment for which there is no universal cure. Encouragingly, a first gene supplementation therapy has been approved for an autosomal recessive IRD. However, for autosomal dominant IRDs, gene supplementation therapy is not always pertinent because haploinsufficiency is not the only cause. Disease-causing mechanisms are often gain-of-function or dominant-negative, which usually require alternative therapeutic approaches. In such cases, genome-editing technology has raised hopes for treatment. Genome editing could be used to i) invalidate both alleles, followed by supplementation of the wild type gene, ii) specifically invalidate the mutant allele, with or without gene supplementation, or iii) to correct the mutant allele. We review here the most prevalent genes causing autosomal dominant retinitis pigmentosa and the most appropriate genome-editing strategy that could be used to target their different causative mutations.
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876
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Sokolov A, Ashenden S, Sahin N, Lewis R, Erdem N, Ozaltan E, Bender A, Roth FP, Cokol M. Characterizing ABC-Transporter Substrate-Likeness Using a Clean-Slate Genetic Background. Front Pharmacol 2019; 10:448. [PMID: 31105571 PMCID: PMC6494965 DOI: 10.3389/fphar.2019.00448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/08/2019] [Indexed: 12/02/2022] Open
Abstract
Mutations in ATP Binding Cassette (ABC)-transporter genes can have major effects on the bioavailability and toxicity of the drugs that are ABC-transporter substrates. Consequently, methods to predict if a drug is an ABC-transporter substrate are useful for drug development. Such methods traditionally relied on literature curated collections of ABC-transporter dependent membrane transfer assays. Here, we used a single large-scale dataset of 376 drugs with relative efficacy on an engineered yeast strain with all ABC-transporter genes deleted (ABC-16), to explore the relationship between a drug’s chemical structure and ABC-transporter substrate-likeness. We represented a drug’s chemical structure by an array of substructure keys and explored several machine learning methods to predict the drug’s efficacy in an ABC-16 yeast strain. Gradient-Boosted Random Forest models outperformed all other methods with an AUC of 0.723. We prospectively validated the model using new experimental data and found significant agreement with predictions. Our analysis expands the previously reported chemical substructures associated with ABC-transporter substrates and provides an alternative means to investigate ABC-transporter substrate-likeness.
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Affiliation(s)
- Artem Sokolov
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, United States
| | - Stephanie Ashenden
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.,Discovery Sciences, IMed Biotech Unit, AstraZeneca R&D, Cambridge, United Kingdom
| | - Nil Sahin
- Faculty of Engineering and Natural Sciences, Sabancı University, Istanbul, Turkey.,Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Richard Lewis
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Nurdan Erdem
- Faculty of Engineering and Natural Sciences, Sabancı University, Istanbul, Turkey
| | - Elif Ozaltan
- Faculty of Engineering and Natural Sciences, Sabancı University, Istanbul, Turkey
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON, Canada.,Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - Murat Cokol
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, United States.,Faculty of Engineering and Natural Sciences, Sabancı University, Istanbul, Turkey.,Donnelly Centre, University of Toronto, Toronto, ON, Canada.,Axcella Health, Cambridge, MA, United States
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877
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Zhao J, Lai L, Ji W, Zhou Q. Genome editing in large animals: current status and future prospects. Natl Sci Rev 2019; 6:402-420. [PMID: 34691891 PMCID: PMC8291540 DOI: 10.1093/nsr/nwz013] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 01/09/2019] [Accepted: 01/30/2019] [Indexed: 12/14/2022] Open
Abstract
Large animals (non-human primates, livestock and dogs) are playing important roles in biomedical research, and large livestock animals serve as important sources of meat and milk. The recently developed programmable DNA nucleases have revolutionized the generation of gene-modified large animals that are used for biological and biomedical research. In this review, we briefly introduce the recent advances in nuclease-meditated gene editing tools, and we outline these editing tools' applications in human disease modeling, regenerative medicine and agriculture. Additionally, we provide perspectives regarding the challenges and prospects of the new genome editing technology.
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Affiliation(s)
- Jianguo Zhao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Liangxue Lai
- South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Weizhi Ji
- Yunnan Key Laboratory of Primate Biomedicine Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming 650500, China
- CAS Center for Excellence in Brain Science and Intelligence Technology (CEBSIT), Shanghai 200031, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
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878
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Kuo PC. Invited Commentary: CRISPR and the potential for human genome editing. Surgery 2019; 166:139-140. [PMID: 31030974 DOI: 10.1016/j.surg.2019.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 11/17/2022]
Affiliation(s)
- Paul C Kuo
- Department of Surgery, University of South Florida, Tampa, FL.
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879
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Schuster M, Kahmann R. CRISPR-Cas9 genome editing approaches in filamentous fungi and oomycetes. Fungal Genet Biol 2019; 130:43-53. [PMID: 31048007 DOI: 10.1016/j.fgb.2019.04.016] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/27/2019] [Accepted: 04/28/2019] [Indexed: 12/26/2022]
Abstract
Due to their biotechnological relevance as well as their importance as disease agents, filamentous fungi and oomycetes have been prime candidates for genetic selection and in vitro manipulation for decades. With the advent of new genome editing technologies such manipulations have reached a new level of speed and sophistication. The CRISPR-Cas9 genome editing technology in particular has revolutionized the ways how desired mutations can be introduced. To date, the CRISPR-Cas9 genome editing system has been established in more than 40 different species of filamentous fungi and oomycetes. In this review we describe the various approaches taken to assure expression of the components necessary for editing and describe the varying strategies used to achieve gene disruptions, gene replacements and precise editing. We discuss potential problems faced when establishing the system, propose ways to circumvent them and suggest future approaches not yet realized in filamentous fungi or oomycetes.
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Affiliation(s)
- Mariana Schuster
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, 35043 Marburg, Germany.
| | - Regine Kahmann
- Max Planck Institute for Terrestrial Microbiology, Dept. Organismic Interactions, 35043 Marburg, Germany.
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880
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Kim B, Sailor MJ. Synthesis, Functionalization, and Characterization of Fusogenic Porous Silicon Nanoparticles for Oligonucleotide Delivery. J Vis Exp 2019. [PMID: 31058889 DOI: 10.3791/59440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
With the advent of gene therapy, the development of an effective in vivo nucleotide-payload delivery system has become of parallel import. Fusogenic porous silicon nanoparticles (F-pSiNPs) have recently demonstrated high in vivo gene silencing efficacy due to its high oligonucleotide loading capacity and unique cellular uptake pathway that avoids endocytosis. The synthesis of F-pSiNPs is a multi-step process that includes: (1) loading and sealing of oligonucleotide payloads in the silicon pores; (2) simultaneous coating and sizing of fusogenic lipids around the porous silicon cores; and (3) conjugation of targeting peptides and washing to remove excess oligonucleotide, silicon debris, and peptide. The particle's size uniformity is characterized by dynamic light scattering, and its core-shell structure may be verified by transmission electron microscopy. The fusogenic uptake is validated by loading a lipophilic dye, 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI), into the fusogenic lipid bilayer and treating it to cells in vitro to observe for plasma membrane staining versus endocytic localizations. The targeting and in vivo gene silencing efficacies were previously quantified in a mouse model of Staphylococcus aureus pneumonia, in which the targeting peptide is expected to help the F-pSiNPs to home to the site of infection. Beyond its application in S. aureus infection, the F-pSiNP system may be used to deliver any oligonucleotide for gene therapy of a wide range of diseases, including viral infections, cancer, and autoimmune diseases.
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Affiliation(s)
- Byungji Kim
- Materials Science and Engineering Program, University of California, San Diego;
| | - Michael J Sailor
- Materials Science and Engineering Program, University of California, San Diego; Department of Chemistry and Biochemistry, University of California, San Diego
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881
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Prahallad A, Jensen MR, Chapeau EA. Deciphering mechanisms of response and resistance in large-scale mouse cancer screens. Curr Opin Genet Dev 2019; 54:48-54. [PMID: 30954760 DOI: 10.1016/j.gde.2019.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/08/2019] [Accepted: 02/16/2019] [Indexed: 11/27/2022]
Abstract
Acquired resistance is a major limitation for the successful treatment of cancer patients. Although numerous efficacious cancer therapeutics have been developed in the past decades, resistance arises due to a variety of reasons including tumoral genetic alterations, or modulation of factors in the tumor environment. Understanding the mechanistic reasons for tumor relapse supports the identification of novel combination therapies that could lead to more durable responses. Here, we will review large-scale in vivo screens in pre-clinical cancer models that employed genetic and pharmacological agents toward elucidating acquired drug resistance and informing on beneficial combinations to be tested in clinical trials.
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Affiliation(s)
- Anirudh Prahallad
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | | | - Emilie Anne Chapeau
- Oncology Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland.
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882
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Ukai H, Sumiyama K, Ueda HR. Next-generation human genetics for organism-level systems biology. Curr Opin Biotechnol 2019; 58:137-145. [PMID: 30954899 DOI: 10.1016/j.copbio.2019.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 01/10/2023]
Abstract
Systems-biological approaches, such as comprehensive identification and analysis of system components and networks, are necessary to understand design principles of human physiology and pathology. Although reverse genetics using mouse models have been used previously, it is a low throughput method because of the need for repetitive crossing to produce mice having all cells of the body with knock-out or knock-in mutations. Moreover, there are often issues from the interspecific gap between humans and mice. To overcome these problems, high-throughput methods for producing knock-out or knock-in mice are necessary. In this review, we describe 'next-generation' human genetics, which can be defined as high-throughput mammalian genetics without crossing to knock out human-mouse ortholog genes or to knock in genetically humanized mutations.
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Affiliation(s)
- Hideki Ukai
- ES-mouse/Virus Core, International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kenta Sumiyama
- Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroki R Ueda
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan; Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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883
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Salas-Mckee J, Kong W, Gladney WL, Jadlowsky JK, Plesa G, Davis MM, Fraietta JA. CRISPR/Cas9-based genome editing in the era of CAR T cell immunotherapy. Hum Vaccin Immunother 2019; 15:1126-1132. [PMID: 30735463 DOI: 10.1080/21645515.2019.1571893] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The advent of engineered T cells as a form of immunotherapy marks the beginning of a new era in medicine, providing a transformative way to combat complex diseases such as cancer. Following FDA approval of CAR T cells directed against the CD19 protein for the treatment of acute lymphoblastic leukemia and diffuse large B cell lymphoma, CAR T cells are poised to enter mainstream oncology. Despite this success, a number of patients are unable to receive this therapy due to inadequate T cell numbers or rapid disease progression. Furthermore, lack of response to CAR T cell treatment is due in some cases to intrinsic autologous T cell defects and/or the inability of these cells to function optimally in a strongly immunosuppressive tumor microenvironment. We describe recent efforts to overcome these limitations using CRISPR/Cas9 technology, with the goal of enhancing potency and increasing the availability of CAR-based therapies. We further discuss issues related to the efficiency/scalability of CRISPR/Cas9-mediated genome editing in CAR T cells and safety considerations. By combining the tools of synthetic biology such as CARs and CRISPR/Cas9, we have an unprecedented opportunity to optimally program T cells and improve adoptive immunotherapy for most, if not all future patients.
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Affiliation(s)
- January Salas-Mckee
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA
| | - Weimin Kong
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA
| | - Whitney L Gladney
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA
| | - Julie K Jadlowsky
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA
| | - Gabriela Plesa
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA
| | - Megan M Davis
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA.,b Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Joseph A Fraietta
- a Center for Cellular Immunotherapies, Abramson Cancer Center , University of Pennsylvania , Philadelphia , PA , USA.,b Department of Pathology and Laboratory Medicine, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA.,c Parker Institute for Cancer Immunotherapy , University of Pennsylvania , Philadelphia , PA , USA.,d Department of Microbiology, Perelman School of Medicine , University of Pennsylvania , Philadelphia, PA , USA
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884
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Ortega-Pinazo J, Díaz T, Martínez B, Jiménez A, Pinto-Medel MJ, Ferro P. Quality assessment on the long-term cryopreservation and nucleic acids extraction processes implemented in the andalusian public biobank. Cell Tissue Bank 2019; 20:255-265. [PMID: 30903409 DOI: 10.1007/s10561-019-09764-9] [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: 11/28/2018] [Accepted: 03/14/2019] [Indexed: 12/11/2022]
Abstract
Human samples are commonly collected and long-term stored in biobanks for current and future analyses. Even though techniques for freezing human blood are well established, the storage time can compromise the cell viability as well as the yield and quality of nucleic acids (RNA and DNA) extracted from them. In this study, a protocol to obtain peripheral blood mononuclear cells (PBMCs) from 70 subjects, which were stored at - 196 °C from EDTA tubes for a long-term, was assessed. In parallel; a protocol to obtain DNA from the same subjects, which were stored at - 80 °C from citrate tubes, was also studied. Samples stored from 2008 to 2012 were studied and the results obtained showed that there were no statistically significant differences in the RNA or DNA extracted in terms of purity, integrity and functionality The freezing protocol used by the Málaga Biobank shows that viable PBMCs and DNA could be kept for a period of, at least, 10 years, with a high quality and performance. Furthermore, RNA extracted from these PBMCs presents also a good quality and performance. Therefore, the samples frozen according to the conditions of the protocols assessed in this study could be optimal for biomedical research.
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Affiliation(s)
- J Ortega-Pinazo
- Neuroscience UGC, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - T Díaz
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - B Martínez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - A Jiménez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - M J Pinto-Medel
- Neuroscience UGC, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain
| | - P Ferro
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Sanitary Distric of Málaga, University of Málaga, Málaga, Spain.
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885
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Regulation of fibroblast-like synoviocyte transformation by transcription factors in arthritic diseases. Biochem Pharmacol 2019; 165:145-151. [PMID: 30878552 DOI: 10.1016/j.bcp.2019.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/12/2019] [Indexed: 02/07/2023]
Abstract
Inflammation in the synovium is known to mediate joint destruction in several forms of arthritis. Fibroblast-like synoviocytes (FLS) are cells that reside in the synovial lining of joints and are known to be key contributors to inflammation associated with arthritis. FLS are a major source of inflammatory cytokines and catabolic enzymes that promote joint degeneration. We now know that there exists a direct correlation between the signaling pathways that are activated by the pro-inflammatory molecules produced by the FLS, and the severity of joint degeneration in arthritis. Research focused on understanding the signaling pathways that are activated by these pro-inflammatory molecules has led to major advancements in the understanding of the joint pathology in arthritis. Transcription factors (TFs) that act as downstream mediators of the pro-inflammatory signaling cascades in various cell types have been reported to play an important role in inducing the deleterious transformation of the FLS. Interestingly, recent studies have started uncovering that several TFs that were previously reported to play role in embryonic development and cancer, but not known to have pronounced roles in tissue inflammation, can actually play crucial roles in the regulation of the pathological properties of the FLS. In this review, we will discuss reports that have been able to impart novel arthritogenic roles to TFs that are specialized in embryonic development. We also discuss the therapeutic potential of targeting these newly identified regulators of FLS transformation in the treatment of arthritis.
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886
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Abstract
The discovery and characterization of the prokaryotic CRISPR-Cas immune system has led to a revolution in genome editing and engineering technologies. Despite the fact that most applications emerged after the discovery of the type II-A CRISPR-Cas9 system of Streptococcus pyogenes, its biological importance in this organism has received little attention. Here, we provide a comprehensive overview of the current knowledge about CRISPR-Cas systems from S. pyogenes. We discuss how the interplay between CRISPR-mediated immunity and horizontal gene transfer might have modeled the evolution of this pathogen. We review the current literature about the CRISPR-Cas systems present in S. pyogenes (types I-C and II-A), and describe their distinctive biochemical and functional features. Finally, we summarize the main biotechnological applications that have arisen from the discovery of the CRISPR-Cas9 system in S. pyogenes.
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Affiliation(s)
- Anaïs Le Rhun
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany
| | - Andrés Escalera-Maurer
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Majda Bratovič
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
| | - Emmanuelle Charpentier
- a Max Planck Unit for the Science of Pathogens , Berlin , Germany.,b Institute for Biology , Humboldt University , Berlin , Germany
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887
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Saha SK, Saikot FK, Rahman MS, Jamal MAHM, Rahman SMK, Islam SMR, Kim KH. Programmable Molecular Scissors: Applications of a New Tool for Genome Editing in Biotech. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 14:212-238. [PMID: 30641475 PMCID: PMC6330515 DOI: 10.1016/j.omtn.2018.11.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 11/23/2018] [Accepted: 11/23/2018] [Indexed: 01/04/2023]
Abstract
Targeted genome editing is an advanced technique that enables precise modification of the nucleic acid sequences in a genome. Genome editing is typically performed using tools, such as molecular scissors, to cut a defined location in a specific gene. Genome editing has impacted various fields of biotechnology, such as agriculture; biopharmaceutical production; studies on the structure, regulation, and function of the genome; and the creation of transgenic organisms and cell lines. Although genome editing is used frequently, it has several limitations. Here, we provide an overview of well-studied genome-editing nucleases, including single-stranded oligodeoxynucleotides (ssODNs), transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs), and CRISPR-Cas9 RNA-guided nucleases (CRISPR-Cas9). To this end, we describe the progress toward editable nuclease-based therapies and discuss the minimization of off-target mutagenesis. Future prospects of this challenging scientific field are also discussed.
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Affiliation(s)
- Subbroto Kumar Saha
- Department of Stem Cell and Regenerative Biotechnology, Konkuk University, 120 Neungdong-Ro, Seoul 05029, Republic of Korea.
| | - Forhad Karim Saikot
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | | | - S M Khaledur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - S M Riazul Islam
- Department of Computer Science and Engineering, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul 05006, South Korea
| | - Ki-Hyun Kim
- Department of Civil & Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
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888
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Bucevičius J, Keller-Findeisen J, Gilat T, Hell SW, Lukinavičius G. Rhodamine-Hoechst positional isomers for highly efficient staining of heterochromatin. Chem Sci 2019; 10:1962-1970. [PMID: 30881625 PMCID: PMC6385482 DOI: 10.1039/c8sc05082a] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/11/2018] [Indexed: 12/13/2022] Open
Abstract
Hoechst conjugates to fluorescent dyes are popular DNA stains for live-cell imaging, but the relationship between their structure and performance remains elusive. This study of carboxyrhodamine-Hoechst 33258 conjugates reveals that a minimal change in the attachment point of the dye has dramatic effects on the properties of the final probe. All tested 6'-carboxyl dye-containing probes exhibited dual-mode binding to DNA and formed a dimmer complex at high DNA concentrations. The 5'-carboxyl dye-containing probes exhibited single-mode binding to DNA which translated into increased brightness and lower cytotoxicity. Up to 10-fold brighter nuclear staining by the newly developed probes allowed acquisition of stimulated emission depletion (STED) nanoscopy images of outstanding quality in living and fixed cells. Therefore we were able to estimate a diameter of ∼155 nm of the heterochromatin exclusion zones in the nuclear pore region in living cells and intact chicken erythrocytes and to localize telomeres relative to heterochromatin in living U-2 OS cells. Employing the highly efficient probes for two-color STED allowed visualization of DNA and tubulin structures in intact nucleated erythrocytes - a system where imaging is greatly hampered by high haemoglobin absorbance.
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Affiliation(s)
- Jonas Bucevičius
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Jan Keller-Findeisen
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Tanja Gilat
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Stefan W Hell
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
| | - Gražvydas Lukinavičius
- Department of NanoBiophotonics , Max Planck Institute for Biophysical Chemistry , Am Fassberg 11 , Göttingen , 37077 , Germany .
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889
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Czerwińska P, Mazurek S, Kołodziejczak I, Wiznerowicz M. Gene delivery methods and genome editing of human pluripotent stem cells. Rep Pract Oncol Radiother 2019; 24:180-187. [PMID: 30820192 DOI: 10.1016/j.rpor.2019.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/21/2018] [Accepted: 01/27/2019] [Indexed: 12/24/2022] Open
Abstract
Induced pluripotent stem cells derived from normal somatic cells could be utilized to study tumorigenesis through overexpression of specific oncogenes, downregulation of tumor suppressors and dysregulation of other factors thought to promote tumorigenesis. Therefore, effective approaches that provide direct modifications of induced pluripotent stem cell genome are extremely needed. Emerging strategies are expected to provide the ability to more effectively introduce diverse genetic alterations, from as small as single-nucleotide modifications to whole gene amplification or deletion, all with a high degree of target specificity. To date, several techniques have been applied in stem cell studies to directly edit cell genome (ZFNs, TALENs or CRISPR/Cas9). In this review, we summarize specific gene delivery strategies that were applied to stem cell studies together with genome editing techniques, which enable a direct modification of endogenous DNA sequences in the context of cancer studies.
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Affiliation(s)
- Patrycja Czerwińska
- Laboratory of Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland.,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Sylwia Mazurek
- Laboratory of Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland.,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Iga Kołodziejczak
- Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
| | - Maciej Wiznerowicz
- Laboratory of Gene Therapy, Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, Poznan, Poland.,Department of Cancer Immunology, Chair of Medical Biotechnology, Poznan University of Medical Sciences, Poznan, Poland
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890
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Henriksson J, Chen X, Gomes T, Ullah U, Meyer KB, Miragaia R, Duddy G, Pramanik J, Yusa K, Lahesmaa R, Teichmann SA. Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation. Cell 2019; 176:882-896.e18. [PMID: 30639098 PMCID: PMC6370901 DOI: 10.1016/j.cell.2018.11.044] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 09/19/2018] [Accepted: 11/28/2018] [Indexed: 12/24/2022]
Abstract
T helper type 2 (Th2) cells are important regulators of mammalian adaptive immunity and have relevance for infection, autoimmunity, and tumor immunology. Using a newly developed, genome-wide retroviral CRISPR knockout (KO) library, combined with RNA-seq, ATAC-seq, and ChIP-seq, we have dissected the regulatory circuitry governing activation and differentiation of these cells. Our experiments distinguish cell activation versus differentiation in a quantitative framework. We demonstrate that these two processes are tightly coupled and are jointly controlled by many transcription factors, metabolic genes, and cytokine/receptor pairs. There are only a small number of genes regulating differentiation without any role in activation. By combining biochemical and genetic data, we provide an atlas for Th2 differentiation, validating known regulators and identifying factors, such as Pparg and Bhlhe40, as part of the core regulatory network governing Th2 helper cell fates.
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Affiliation(s)
- Johan Henriksson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 7, Novum, SE-141 83, Huddinge, Sweden
| | - Xi Chen
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tomás Gomes
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ubaid Ullah
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 FI-20520, Turku, Finland
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ricardo Miragaia
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Graham Duddy
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Jhuma Pramanik
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Kosuke Yusa
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6 FI-20520, Turku, Finland
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, UK.
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891
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Galizi R, Jaramillo A. Engineering CRISPR guide RNA riboswitches for in vivo applications. Curr Opin Biotechnol 2019; 55:103-113. [PMID: 30265865 DOI: 10.1016/j.copbio.2018.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 02/07/2023]
Abstract
CRISPR-based genome editing provides a simple and scalable toolbox for a variety of therapeutic and biotechnology applications. Whilst the fundamental properties of CRISPR proved easily transferable from the native prokaryotic hosts to eukaryotic and multicellular organisms, the tight control of the CRISPR-editing activity remains a major challenge. Here we summarise recent developments of CRISPR and riboswitch technologies and recommend novel functionalised synthetic-gRNA (sgRNA) designs to achieve inducible and spatiotemporal regulation of CRISPR-based genetic editors in response to cellular or extracellular stimuli. We believe that future advances of these tools will have major implications for both basic and applied research, spanning from fundamental genetic studies and synthetic biology to genetic editing and gene therapy.
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Affiliation(s)
- Roberto Galizi
- Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, CV4 7AL Coventry, United Kingdom; ISSB, CNRS, Univ Evry, CEA, Université Paris-Saclay, 91025 Evry, France; Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, 46980 Paterna, Spain.
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892
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Fujii M, Clevers H, Sato T. Modeling Human Digestive Diseases With CRISPR-Cas9-Modified Organoids. Gastroenterology 2019; 156:562-576. [PMID: 30476497 DOI: 10.1053/j.gastro.2018.11.048] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/10/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
Abstract
Insights into the stem cell niche have allowed researchers to cultivate adult tissue stem cells as organoids that display structural and phenotypic features of healthy and diseased epithelial tissues. Organoids derived from patients' tissues are used as models of disease and to test drugs. CRISPR-Cas9 technology can be used to genetically engineer organoids for studies of monogenic diseases and cancer. We review the derivation of organoids from human gastrointestinal tissues and how CRISPR-Cas9 technology can be used to study these organoids. We discuss burgeoning technologies that are broadening our understanding of diseases of the digestive system.
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Affiliation(s)
- Masayuki Fujii
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan
| | - Hans Clevers
- Hubrecht Institute, University Medical Center Utrecht and Princess Maxima Center, Utrecht, The Netherlands
| | - Toshiro Sato
- Department of Gastroenterology, Keio University School of Medicine, Tokyo, Japan.
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893
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Mair B, Moffat J, Boone C, Andrews BJ. Genetic interaction networks in cancer cells. Curr Opin Genet Dev 2019; 54:64-72. [PMID: 30974317 PMCID: PMC6820710 DOI: 10.1016/j.gde.2019.03.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/02/2019] [Indexed: 01/12/2023]
Abstract
The genotype-to-phenotype relationship in health and disease is complex and influenced by both an individual's environment and their unique genome. Personal genetic variants can modulate gene function to generate a phenotype either through a single gene effect or through genetic interactions involving two or more genes. The relevance of genetic interactions to disease phenotypes has been particularly clear in cancer research, where an extreme genetic interaction, synthetic lethality, has been exploited as a therapeutic strategy. The obvious benefits of unmasking genetic background-specific vulnerabilities, coupled with the power of systematic genome editing, have fueled efforts to translate genetic interaction mapping from model organisms to human cells. Here, we review recent developments in genetic interaction mapping, with a focus on CRISPR-based genome editing technologies and cancer.
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Affiliation(s)
- Barbara Mair
- Donnelly Centre, University of Toronto, ON, Canada
| | - Jason Moffat
- Donnelly Centre, University of Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, ON, Canada
| | - Charles Boone
- Donnelly Centre, University of Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, ON, Canada
| | - Brenda J Andrews
- Donnelly Centre, University of Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, ON, Canada.
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894
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895
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Abstract
Proximity-based labeling has emerged as a powerful complementary approach to classic affinity purification of multiprotein complexes in the mapping of protein-protein interactions. Ongoing optimization of enzyme tags and delivery methods has improved both temporal and spatial resolution, and the technique has been successfully employed in numerous small-scale (single complex mapping) and large-scale (network mapping) initiatives. When paired with quantitative proteomic approaches, the ability of these assays to provide snapshots of stable and transient interactions over time greatly facilitates the mapping of dynamic interactomes. Furthermore, recent innovations have extended biotin-based proximity labeling techniques such as BioID and APEX beyond classic protein-centric assays (tag a protein to label neighboring proteins) to include RNA-centric (tag an RNA species to label RNA-binding proteins) and DNA-centric (tag a gene locus to label associated protein complexes) assays.
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Affiliation(s)
- Laura Trinkle-Mulcahy
- Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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896
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Yrigollen CM, Davidson BL. CRISPR to the Rescue: Advances in Gene Editing for the FMR1 Gene. Brain Sci 2019; 9:E17. [PMID: 30669625 PMCID: PMC6357057 DOI: 10.3390/brainsci9010017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/13/2019] [Accepted: 01/15/2019] [Indexed: 12/17/2022] Open
Abstract
Gene-editing using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is promising as a potential therapeutic strategy for many genetic disorders. CRISPR-based therapies are already being assessed in clinical trials, and evaluation of this technology in Fragile X syndrome has been performed by a number of groups. The findings from these studies and the advancement of CRISPR-based technologies are insightful as the field continues towards treatments and cures of Fragile X-Associated Disorders (FXADs). In this review, we summarize reports using CRISPR-editing strategies to target Fragile X syndrome (FXS) molecular dysregulation, and highlight how differences in FXS and Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) might alter treatment strategies for each syndrome. We discuss the various modifications and evolutions of the CRISPR toolkit that expand its therapeutic potential, and other considerations for moving these strategies from bench to bedside. The rapidly growing field of CRISPR therapeutics is providing a myriad of approaches to target a gene, pathway, or transcript for modification. As cures for FXADs have remained elusive, CRISPR opens new avenues to pursue.
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Affiliation(s)
- Carolyn M Yrigollen
- The Raymond G. Perelman Center of Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Beverly L Davidson
- The Raymond G. Perelman Center of Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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897
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Ghosh D, Venkataramani P, Nandi S, Bhattacharjee S. CRISPR-Cas9 a boon or bane: the bumpy road ahead to cancer therapeutics. Cancer Cell Int 2019; 19:12. [PMID: 30636933 PMCID: PMC6325665 DOI: 10.1186/s12935-019-0726-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/02/2019] [Indexed: 12/13/2022] Open
Abstract
Genome editing allows for the precise manipulation of DNA sequences in a cell making this technology essential for understanding gene function. CRISPR/Cas9 is a targeted genome-editing platform derived from bacterial adaptive immune system and has been repurposed into a genome-editing tool. The RNA-guided DNA endonuclease, Cas9 can be easily programmed to target new sites by altering its guide RNA sequence, making this technology easier, more efficient, scalable and an indispensable tool in biological research. This technology has helped genetically engineer animal models to understand disease mechanisms and elucidate molecular details that can be exploited for improved therapeutic outcomes. In this review, we describe the CRISPR-Cas9 gene-editing mechanism, CRISPR-screening methods, therapeutic targeting of CRISPR in animal models and in cancer immunotherapy. We also discuss the ongoing clinical trials using this tool, limitations of this tool that might impede the clinical applicability of CRISPR-Cas9 and future directions for developing effective CRISPR-Cas9 delivery systems that may improve cancer therapeutics.
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Affiliation(s)
- Debarati Ghosh
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | | | - Saikat Nandi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
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898
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Brokowski C, Adli M. CRISPR Ethics: Moral Considerations for Applications of a Powerful Tool. J Mol Biol 2019; 431:88-101. [PMID: 29885329 PMCID: PMC6286228 DOI: 10.1016/j.jmb.2018.05.044] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 12/26/2022]
Abstract
With the emergence of CRISPR technology, targeted editing of a wide variety of genomes is no longer an abstract hypothetical, but occurs regularly. As application areas of CRISPR are exceeding beyond research and biomedical therapies, new and existing ethical concerns abound throughout the global community about the appropriate scope of the systems' use. Here we review fundamental ethical issues including the following: 1) the extent to which CRISPR use should be permitted; 2) access to CRISPR applications; 3) whether a regulatory framework(s) for clinical research involving human subjects might accommodate all types of human genome editing, including editing of the germline; and 4) whether international regulations governing inappropriate CRISPR utilization should be crafted and publicized. We conclude that moral decision making should evolve as the science of genomic engineering advances and hold that it would be reasonable for national and supranational legislatures to consider evidence-based regulation of certain CRISPR applications for the betterment of human health and progress.
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Affiliation(s)
- Carolyn Brokowski
- Department of Emergency Medicine, Yale School of Medicine, 464 Congress Avenue, New Haven, CT 06519-1362, USA
| | - Mazhar Adli
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA 22908, USA.
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899
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Foss DV, Hochstrasser ML, Wilson RC. Clinical applications of CRISPR-based genome editing and diagnostics. Transfusion 2019; 59:1389-1399. [PMID: 30600536 DOI: 10.1111/trf.15126] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 12/12/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-driven genome editing has rapidly transformed preclinical biomedical research by eliminating the underlying genetic basis of many diseases in model systems and facilitating the study of disease etiology. Translation to the clinic is under way, with announced or impending clinical trials utilizing ex vivo strategies for anticancer immunotherapy or correction of hemoglobinopathies. These exciting applications represent just a fraction of what is theoretically possible for this emerging technology, but many technical hurdles must be overcome before CRISPR-based genome editing technology can reach its full potential. One exciting recent development is the use of CRISPR systems for diagnostic detection of genetic sequences associated with pathogens or cancer. We review the biologic origins and functional mechanism of CRISPR systems and highlight several current and future clinical applications of genome editing.
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Affiliation(s)
- Dana V Foss
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California
| | - Megan L Hochstrasser
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California
| | - Ross C Wilson
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California.,California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California
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900
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Genome Editing in Zebrafish Using CRISPR-Cas9: Applications for Developmental Toxicology. Methods Mol Biol 2019; 1965:235-250. [PMID: 31069679 DOI: 10.1007/978-1-4939-9182-2_16] [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] [Indexed: 12/12/2022]
Abstract
Environment-gene interactions have a powerful impact on embryo development. The ability to precisely edit the genome makes it possible to address questions concerning the specific roles that genes or variants play in modulating the response to environmental challenges. In this chapter, we provide a simplified protocol using CRISPR-Cas9 ribonucleoproteins for genome editing in the zebrafish model organism. The genetic manipulation can then be coupled with chemical screens to identify and understand the mechanism behind toxicants or compounds that modulate development.
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