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Lin D, Najam SS, Liu Y, Murgia N, Vinnikov IA. Noodles, the all-in-one system for on-target efficiency analysis of CRISPR guide RNAs. MethodsX 2024; 12:102481. [PMID: 38162150 PMCID: PMC10757036 DOI: 10.1016/j.mex.2023.102481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/09/2023] [Indexed: 01/03/2024] Open
Abstract
The efficiency of clustered regularly interspaced short palindromic repeats (CRISPR) guide RNA (gRNA) targeting is critical for CRISPR associated protein 9 (Cas9)-dependent genomic modifications. Here, we developed Noodles, an all-in-one system to test the on-target activity of gRNAs easily and efficiently. Single-strand annealing repair mechanism of the split luciferase gene allows a positive selection of gRNAs efficiently driving nuclease activity of Cas9 from Streptococcus pyogenes (SpCas9). Our system can reliably validate in silico-predicted gRNAs before implementing them for in vitro and in vivo applications. Altogether, Noodles might be an asset for researchers and bioengineers, saving their time and efforts, while keeping the screening efficient and sensitive. •All-in-one dual-luciferase system to easily probe on-target activity of gRNAs based on homology-directed repair mechanism.•Easy-to-subclone spCas9-based 2-plasmid system comprising Renilla luciferase for transfection efficiency control.
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Affiliation(s)
- Dongfa Lin
- Key Laboratory for Molecular Enzymology and Engineering, School of Life Sciences, Jilin University, Changchun, China
- Laboratory of Molecular Neurobiology, Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Syeda Sadia Najam
- Laboratory of Molecular Neurobiology, Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Liu
- Laboratory of Molecular Neurobiology, Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Nicola Murgia
- Laboratory of Molecular Neurobiology, Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ilya A. Vinnikov
- Laboratory of Molecular Neurobiology, Sheng Yushou Center of Cell Biology and Immunology, Department of Genetics and Developmental Biology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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2
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Godbole N, Quinn A, Carrion F, Pelosi E, Salomon C. Extracellular vesicles as a potential delivery platform for CRISPR-Cas based therapy in epithelial ovarian cancer. Semin Cancer Biol 2023; 96:64-81. [PMID: 37820858 DOI: 10.1016/j.semcancer.2023.10.002] [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] [Received: 05/15/2023] [Revised: 08/27/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
Ovarian Cancer (OC) is the most common gynecological malignancy and the eighth most diagnosed cancer in females worldwide. Presently, it ranks as the fifth leading cause of cancer-related mortality among patients globally. Major factors contributing to the lethality of OC worldwide include delayed diagnosis, chemotherapy resistance, high metastatic rates, and the heterogeneity of subtypes. Despite continuous efforts to develop novel targeted therapies and chemotherapeutic agents, challenges persist in the form of OC resistance and recurrence. In the last decade, CRISPR-Cas-based genome editing has emerged as a powerful tool for modifying genetic and epigenetic mechanisms, holding potential for treating numerous diseases. However, a significant challenge for therapeutic applications of CRISPR-Cas technology is the absence of an optimal vehicle for delivering CRISPR molecular machinery into targeted cells or tissues. Recently, extracellular vesicles (EVs) have gained traction as potential delivery vehicles for various therapeutic agents. These heterogeneous, membrane-derived vesicles are released by nearly all cells into extracellular spaces. They carry a molecular cargo of proteins and nucleic acids within their intraluminal space, encased by a cholesterol-rich phospholipid bilayer membrane. EVs actively engage in cell-to-cell communication by delivering cargo to both neighboring and distant cells. Their inherent ability to shield molecular cargo from degradation and cross biological barriers positions them ideally for delivering CRISPR-Cas ribonucleoproteins (RNP) to target cells. Furthermore, they exhibit higher biocompatibility, lower immunogenicity, and reduced toxicity compared to classical delivery platforms such as adeno-associated virus, lentiviruses, and synthetic nanoparticles. This review explores the potential of employing different CRISPR-Cas systems to target specific genes in OC, while also discussing various methods for engineering EVs to load CRISPR components and enhance their targeting capabilities.
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Affiliation(s)
- Nihar Godbole
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, UQ Centre for Clinical Research, Royal Brisbane and Women's Hospital, Faculty of Medicine, The University of Queensland, Australia
| | - Alexander Quinn
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia; CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, QLD, Australia
| | - Flavio Carrion
- Departamento de Investigación, Postgrado y Educación Continua (DIPEC), Facultad de Ciencias de la Salud, Universidad del Alba, Santiago, Chile
| | - Emanuele Pelosi
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Carlos Salomon
- Translational Extracellular Vesicles in Obstetrics and Gynae-Oncology Group, UQ Centre for Clinical Research, Royal Brisbane and Women's Hospital, Faculty of Medicine, The University of Queensland, Australia; Departamento de Investigación, Postgrado y Educación Continua (DIPEC), Facultad de Ciencias de la Salud, Universidad del Alba, Santiago, Chile.
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3
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Li W, Huang C, Chen J. The application of CRISPR /Cas mediated gene editing in synthetic biology: Challenges and optimizations. Front Bioeng Biotechnol 2022; 10:890155. [PMID: 36091445 PMCID: PMC9452635 DOI: 10.3389/fbioe.2022.890155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated enzymes (Cas) is a simple and convenient genome editing tool that has been used in various cell factories and emerging synthetic biology in the recent past. However, several problems, including off-target effects, cytotoxicity, and low efficiency of multi-gene editing, are associated with the CRISPR/Cas system, which have limited its application in new species. In this review, we briefly describe the mechanisms of CRISPR/Cas engineering and propose strategies to optimize the system based on its defects, including, but not limited to, enhancing targeted specificity, reducing toxicity related to Cas protein, and improving multi-point editing efficiency. In addition, some examples of improvements in synthetic biology are also highlighted. Finally, future perspectives of system optimization are discussed, providing a reference for developing safe genome-editing tools for new species.
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Affiliation(s)
- Wenqian Li
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
| | - Can Huang
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
| | - Jingyu Chen
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
- *Correspondence: Jingyu Chen,
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4
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Ghosh S, Lahiri D, Nag M, Sarkar T, Pati S, Edinur HA, Kumar M, Mohd Zain MRA, Ray RR. Precision targeting of food biofilm-forming genes by microbial scissors: CRISPR-Cas as an effective modulator. Front Microbiol 2022; 13:964848. [PMID: 36016778 PMCID: PMC9396135 DOI: 10.3389/fmicb.2022.964848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
The abrupt emergence of antimicrobial resistant (AMR) bacterial strains has been recognized as one of the biggest public health threats affecting the human race and food processing industries. One of the causes for the emergence of AMR is the ability of the microorganisms to form biofilm as a defense strategy that restricts the penetration of antimicrobial agents into bacterial cells. About 80% of human diseases are caused by biofilm-associated sessile microbes. Bacterial biofilm formation involves a cascade of genes that are regulated via the mechanism of quorum sensing (QS) and signaling pathways that control the production of the extracellular polymeric matrix (EPS), responsible for the three-dimensional architecture of the biofilm. Another defense strategy utilized commonly by various bacteria includes clustered regularly interspaced short palindromic repeats interference (CRISPRi) system that prevents the bacterial cell from viral invasion. Since multigenic signaling pathways and controlling systems are involved in each and every step of biofilm formation, the CRISPRi system can be adopted as an effective strategy to target the genomic system involved in biofilm formation. Overall, this technology enables site-specific integration of genes into the host enabling the development of paratransgenic control strategies to interfere with pathogenic bacterial strains. CRISPR-RNA-guided Cas9 endonuclease, being a promising genome editing tool, can be effectively programmed to re-sensitize the bacteria by targeting AMR-encoding plasmid genes involved in biofilm formation and virulence to revert bacterial resistance to antibiotics. CRISPRi-facilitated silencing of genes encoding regulatory proteins associated with biofilm production is considered by researchers as a dependable approach for editing gene networks in various biofilm-forming bacteria either by inactivating biofilm-forming genes or by integrating genes corresponding to antibiotic resistance or fluorescent markers into the host genome for better analysis of its functions both in vitro and in vivo or by editing genes to stop the secretion of toxins as harmful metabolites in food industries, thereby upgrading the human health status.
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Affiliation(s)
- Sreejita Ghosh
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Kolkata, India
| | - Dibyajit Lahiri
- Department of Biotechnology, University of Engineering and Management, Kolkata, India
| | - Moupriya Nag
- Department of Biotechnology, University of Engineering and Management, Kolkata, India
| | - Tanmay Sarkar
- Department of Food Processing Technology, Malda Polytechnic, West Bengal State Council of Technical Education, Govt. of West Bengal, Malda, India
| | - Siddhartha Pati
- Skills Innovation and Academic Network (SIAN) Institute, Association for Biodiversity Conservation and Research (ABC), Balasore, India
- NatNov Bioscience Private Limited, Balasore, India
| | - Hisham Atan Edinur
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai, Maharashtra, India
| | - Muhammad R. A. Mohd Zain
- Department of Orthopaedics, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
- *Correspondence: Muhammad R. A. Mohd Zain
| | - Rina Rani Ray
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Kolkata, India
- Rina Rani Ray
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5
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Barkova OY, Larkina TA, Krutikova AA, Polteva EA, Shcherbakov YS, Peglivanyan GK, Pozovnikova MV. Innovative Approaches to Genome Editing in Chickens. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722020037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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7
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Fajardo-Ortiz D, Shattuck A, Hornbostel S. Mapping the coevolution, leadership and financing of research on viral vectors, RNAi, CRISPR/Cas9 and other genomic editing technologies. PLoS One 2020; 15:e0227593. [PMID: 32294089 PMCID: PMC7159216 DOI: 10.1371/journal.pone.0227593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/24/2020] [Indexed: 11/26/2022] Open
Abstract
Genomic editing technologies are developing rapidly, promising significant developments for biomedicine, agriculture and other fields. In the present investigation, we analyzed and compared the process of innovation for six genomic technologies: viral vectors, RNAi, TALENs, meganucleases, ZFNs and CRISPR/Cas including the profile of the main research institutions and their funders, to understand how innovation evolved and what institutions influenced research trajectories. A Web of Science search of papers on viral vectors RNAi, CRISPR/Cas, TALENs, ZFNs and meganucleases was used to build a citation network of 16,746 papers. An analysis of network clustering combined with text mining was performed. For viral vectors, a long-term process of incremental innovation was identified, which was largely publicly funded in the United States and the European Union. The trajectory of RNAi research included clusters related to the study of RNAi as a biological phenomenon and its use in functional genomics, biomedicine and pest control. A British philanthropic organization and a US pharmaceutical company played a key role in the development of basic RNAi research and clinical application respectively, in addition to government and academic institutions. In the case of CRISPR/Cas research, basic science discoveries led to the technical improvements, and these two in turn provided the information required for the development of biomedical, agricultural, livestock and industrial applications. The trajectory of CRISPR/Cas research exhibits a geopolitical division of the investigation efforts between the US, as the main producer and funder of basic research and technical improvements, and Chinese research institutions increasingly leading applied research. Our results reflect a change in the model for financing science, with reduced public financing for basic science and applied research on publicly funded technological developments in the US, and the emergence of China as a scientific superpower, with implications for the development of applications of genomic technologies.
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Affiliation(s)
- David Fajardo-Ortiz
- Research System and Science Dynamics research area, Deutsche Zentrum für Hochschul- und Wissenschaftsforschung (DZHW), Berlin, Germany
| | - Annie Shattuck
- Department of Geography, Indiana University, Bloomington, Indiana, United States of America
| | - Stefan Hornbostel
- Research System and Science Dynamics research area, Deutsche Zentrum für Hochschul- und Wissenschaftsforschung (DZHW), Berlin, Germany
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8
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Shao YT, Ma L, Zhang TH, Xu TR, Ye YC, Liu Y. The Application of the RNA Interference Technologies for KRAS: Current Status, Future Perspective and Associated Challenges. Curr Top Med Chem 2019; 19:2143-2157. [PMID: 31456522 DOI: 10.2174/1568026619666190828162217] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/26/2019] [Accepted: 07/07/2019] [Indexed: 02/07/2023]
Abstract
KRAS is a member of the murine sarcoma virus oncogene-RAS gene family. It plays an important role in the prevention, diagnosis and treatment of tumors during tumor cell growth and angiogenesis. KRAS is the most commonly mutated oncogene in human cancers, such as pancreatic cancers, colon cancers, and lung cancers. Detection of KRAS gene mutation is an important indicator for tracking the status of oncogenes, highlighting the developmental prognosis of various cancers, and the efficacy of radiotherapy and chemotherapy. However, the efficacy of different patients in clinical treatment is not the same. Since RNA interference (RNAi) technologies can specifically eliminate the expression of specific genes, these technologies have been widely used in the field of gene therapy for exploring gene function, infectious diseases and malignant tumors. RNAi refers to the phenomenon of highly specific degradation of homologous mRNA induced by double-stranded RNA (dsRNA), which is highly conserved during evolution. There are three classical RNAi technologies, including siRNA, shRNA and CRISPR-Cas9 system, and a novel synthetic lethal interaction that selectively targets KRAS mutant cancers. Therefore, the implementation of individualized targeted drug therapy has become the best choice for doctors and patients. Thus, this review focuses on the current status, future perspective and associated challenges in silencing of KRAS with RNAi technology.
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Affiliation(s)
- Yu-Ting Shao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Li Ma
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Tie-Hui Zhang
- The First People's Hospital of Heishan County, Jinzhou city, Liaoning, Jinzhou 121400, China
| | - Tian-Rui Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Yuan-Chao Ye
- Department of Internal Medicine, Gastroenterology and Hepatology, University of Iowa, Iowa City, IA 52242, United States.,Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242, United States
| | - Ying Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
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9
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Deyell M, Ameta S, Nghe P. Large scale control and programming of gene expression using CRISPR. Semin Cell Dev Biol 2019; 96:124-132. [PMID: 31181342 DOI: 10.1016/j.semcdb.2019.05.013] [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: 12/21/2018] [Accepted: 05/14/2019] [Indexed: 12/22/2022]
Abstract
The control of gene expression in cells and organisms allows to unveil gene to function relationships and to reprogram biological responses. Several systems, such as Zinc fingers, TALE (Transcription activator-like effectors), and siRNAs (small-interfering RNAs), have been exploited to achieve this. However, recent advances in Clustered Regularly Interspaced Short Palindromic Repeats and Cas9 (CRISPR-Cas9) have overshadowed them due to high specificity, compatibility with many different organisms, and design flexibility. In this review we summarize state-of-the art for CRISPR-Cas9 technology for large scale gene perturbation studies, including single gene and multiple genes knock-out, knock-down, knock-up libraries, and their associated screening assays. We feature in particular the combination of these methods with single-cell transcriptomics approaches. Finally, we highlight the application of CRISPR-Cas9 systems in building synthetic circuits that can be interfaced with gene networks to control cellular states.
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Affiliation(s)
- Matthew Deyell
- Laboratoire de Biochimie, CNRS UMR8231, Chimie Biologie Innovation, PSL Research University, ESPCI Paris, 10 Rue Vauquelin, 75005, Paris, France
| | - Sandeep Ameta
- Laboratoire de Biochimie, CNRS UMR8231, Chimie Biologie Innovation, PSL Research University, ESPCI Paris, 10 Rue Vauquelin, 75005, Paris, France
| | - Philippe Nghe
- Laboratoire de Biochimie, CNRS UMR8231, Chimie Biologie Innovation, PSL Research University, ESPCI Paris, 10 Rue Vauquelin, 75005, Paris, France.
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10
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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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11
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Walter JM, Schubert MG, Kung SH, Hawkins K, Platt DM, Hernday AD, Mahatdejkul-Meadows T, Szeto W, Chandran SS, Newman JD, Horwitz AA. Method for Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas9. Methods Mol Biol 2019; 2049:39-72. [PMID: 31602604 DOI: 10.1007/978-1-4939-9736-7_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
CRISPR-Cas has proven to be a powerful tool for precision genetic engineering in a variety of difficult genetic systems. In the highly tractable yeast S. cerevisiae, CRISPR-Cas can be used to conduct multiple engineering steps in parallel, allowing for engineering of complex metabolic pathways at multiple genomic loci in as little as 1 week. In addition, CRISPR-Cas can be used to consolidate multiple causal alleles into a single strain, bypassing the laborious traditional methods using marked constructs, or mating. These tools compress the engineering timeline sixfold or more, greatly increasing the productivity of the strain engineer.
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12
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Yumlu S, Bashir S, Stumm J, Kühn R. Efficient Gene Editing of Human Induced Pluripotent Stem Cells Using CRISPR/Cas9. Methods Mol Biol 2019; 1961:137-151. [PMID: 30912045 DOI: 10.1007/978-1-4939-9170-9_10] [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] [Indexed: 12/20/2022]
Abstract
The generation of targeted mutants is a crucial step toward studying the biomedical effect of genes of interest. The generation of such mutants in human induced pluripotent stem cells (iPSCs) is of an utmost importance as these cells carry the potential to be differentiated into any cell lineage. Using the CRISPR/Cas9 nuclease system for induction of targeted double-strand breaks, gene editing of target loci in iPSCs can be achieved with high efficiency. This chapter covers protocols for the preparation of reagents to target loci of interest, the transfection, and for the genotyping of single cell-derived iPSC clones. Furthermore, we provide a protocol for the convenient generation of plasmids enabling multiplex gene targeting.
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Affiliation(s)
- Saniye Yumlu
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Sanum Bashir
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Jürgen Stumm
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| | - Ralf Kühn
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany. .,Berlin Institute of Health, Berlin, Germany.
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Alkan F, Wenzel A, Anthon C, Havgaard JH, Gorodkin J. CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters. Genome Biol 2018; 19:177. [PMID: 30367669 PMCID: PMC6203265 DOI: 10.1186/s13059-018-1534-x] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 09/11/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Recent experimental efforts of CRISPR-Cas9 systems have shown that off-target binding and cleavage are a concern for the system and that this is highly dependent on the selected guide RNA (gRNA) design. Computational predictions of off-targets have been proposed as an attractive and more feasible alternative to tedious experimental efforts. However, accurate scoring of the high number of putative off-targets plays a key role for the success of computational off-targeting assessment. RESULTS We present an approximate binding energy model for the Cas9-gRNA-DNA complex, which systematically combines the energy parameters obtained for RNA-RNA, DNA-DNA, and RNA-DNA duplexes. Based on this model, two novel off-target assessment methods for gRNA selection in CRISPR-Cas9 applications are introduced: CRISPRoff to assign confidence scores to predicted off-targets and CRISPRspec to measure the specificity of the gRNA. We benchmark the methods against current state-of-the-art methods and show that both are in better agreement with experimental results. Furthermore, we show significant evidence supporting the inverse relationship between the on-target cleavage efficiency and specificity of the system, in which introduced binding energies are key components. CONCLUSIONS The impact of the binding energies provides a direction for further studies of off-targeting mechanisms. The performance of CRISPRoff and CRISPRspec enables more accurate off-target evaluation for gRNA selections, prior to any CRISPR-Cas9 genome-editing application. For given gRNA sequences or all potential gRNAs in a given target region, CRISPRoff-based off-target predictions and CRISPRspec-based specificity evaluations can be carried out through our webserver at https://rth.dk/resources/crispr/ .
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Affiliation(s)
- Ferhat Alkan
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg, Denmark
| | - Anne Wenzel
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg, Denmark
| | - Christian Anthon
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg, Denmark
| | - Jakob Hull Havgaard
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg, Denmark
| | - Jan Gorodkin
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg, Denmark.
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14
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A CRISPR-Cas13a system for efficient and specific therapeutic targeting of mutant KRAS for pancreatic cancer treatment. Cancer Lett 2018; 431:171-181. [DOI: 10.1016/j.canlet.2018.05.042] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/02/2018] [Accepted: 05/26/2018] [Indexed: 02/07/2023]
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15
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Rein LA, Yang H, Chao NJ. Applications of Gene Editing Technologies to Cellular Therapies. Biol Blood Marrow Transplant 2018; 24:1537-1545. [DOI: 10.1016/j.bbmt.2018.03.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/23/2018] [Indexed: 12/26/2022]
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16
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Hijacking CRISPR-Cas for high-throughput bacterial metabolic engineering: advances and prospects. Curr Opin Biotechnol 2018; 50:146-157. [DOI: 10.1016/j.copbio.2018.01.002] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 12/18/2017] [Accepted: 01/02/2018] [Indexed: 12/18/2022]
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17
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Ringer KP, Roth MG, Garey MS, Piorczynski TB, Suli A, Hansen JM, Alder JK. Comparative analysis of lipid-mediated CRISPR-Cas9 genome editing techniques. Cell Biol Int 2018; 42:849-858. [PMID: 29457665 DOI: 10.1002/cbin.10952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/12/2018] [Indexed: 12/11/2022]
Abstract
CRISPR-Cas technology has revolutionized genome engineering. While Cas9 was not the first programmable endonuclease identified, its simplicity of use has driven widespread adoption in a short period of time. While CRISPR-Cas genome editing holds enormous potential for clinical applications, its use in laboratory settings for genotype-phenotype studies and genome-wide screens has led to breakthroughs in the understanding of many molecular pathways. Numerous protocols have been described for introducing CRISPR-Cas components into cells, and here we sought to simplify and optimize a protocol for genome editing using readily available and inexpensive tools. We compared plasmid, ribonucleoprotein (RNP), and RNA transfection to determine which was method was most optimal for editing cells in a laboratory setting. We limited our comparison to lipofection-mediated introduction because the reagents are widely available. To facilitate optimization, we developed a novel reporter assay to measure gene disruption and the introduction of a variety of exogenous DNA tags. Each method efficiently disrupted endogenous genes and was able to stimulate the introduction of foreign DNA at specific sites, albeit to varying efficiencies. RNP transfection produced the highest level of gene disruption and was the most rapid and efficient method overall. Finally, we show that very short homology arms of 30 base pairs can mediate site-specific editing. The methods described here should broaden the accessibility of RNP-mediated lipofection for laboratory genome-editing experiments.
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Affiliation(s)
- Kelsey P Ringer
- Physiology & Developmental Biology, Brigham Young University, Provo, Utah, 84602, USA
| | - Mark G Roth
- Physiology & Developmental Biology, Brigham Young University, Provo, Utah, 84602, USA
| | - Mitchell S Garey
- Physiology & Developmental Biology, Brigham Young University, Provo, Utah, 84602, USA
| | - Ted B Piorczynski
- Physiology & Developmental Biology, Brigham Young University, Provo, Utah, 84602, USA
| | - Arminda Suli
- Physiology & Developmental Biology, Brigham Young University, Provo, Utah, 84602, USA
| | - Jason M Hansen
- Physiology & Developmental Biology, Brigham Young University, Provo, Utah, 84602, USA
| | - Jonathan K Alder
- Physiology & Developmental Biology, Brigham Young University, Provo, Utah, 84602, USA
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18
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Rauscher B, Heigwer F, Henkel L, Hielscher T, Voloshanenko O, Boutros M. Toward an integrated map of genetic interactions in cancer cells. Mol Syst Biol 2018; 14:e7656. [PMID: 29467179 PMCID: PMC5820685 DOI: 10.15252/msb.20177656] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 01/20/2018] [Accepted: 01/23/2018] [Indexed: 12/13/2022] Open
Abstract
Cancer genomes often harbor hundreds of molecular aberrations. Such genetic variants can be drivers or passengers of tumorigenesis and create vulnerabilities for potential therapeutic exploitation. To identify genotype-dependent vulnerabilities, forward genetic screens in different genetic backgrounds have been conducted. We devised MINGLE, a computational framework to integrate CRISPR/Cas9 screens originating from different libraries building on approaches pioneered for genetic network discovery in model organisms. We applied this method to integrate and analyze data from 85 CRISPR/Cas9 screens in human cancer cells combining functional data with information on genetic variants to explore more than 2.1 million gene-background relationships. In addition to known dependencies, we identified new genotype-specific vulnerabilities of cancer cells. Experimental validation of predicted vulnerabilities identified GANAB and PRKCSH as new positive regulators of Wnt/β-catenin signaling. By clustering genes with similar genetic interaction profiles, we drew the largest genetic network in cancer cells to date. Our scalable approach highlights how diverse genetic screens can be integrated to systematically build informative maps of genetic interactions in cancer, which can grow dynamically as more data are included.
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Affiliation(s)
- Benedikt Rauscher
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Florian Heigwer
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Luisa Henkel
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Thomas Hielscher
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Oksana Voloshanenko
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
| | - Michael Boutros
- Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
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19
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Cook N, Boulton RA, Green J, Trivedi U, Tauber E, Pannebakker BA, Ritchie MG, Shuker DM. Differential gene expression is not required for facultative sex allocation: a transcriptome analysis of brain tissue in the parasitoid wasp Nasonia vitripennis. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171718. [PMID: 29515880 PMCID: PMC5830769 DOI: 10.1098/rsos.171718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/15/2018] [Indexed: 03/14/2024]
Abstract
Whole-transcriptome technologies have been widely used in behavioural genetics to identify genes associated with the performance of a behaviour and provide clues to its mechanistic basis. Here, we consider the genetic basis of sex allocation behaviour in the parasitoid wasp Nasonia vitripennis. Female Nasonia facultatively vary their offspring sex ratio in line with Hamilton's theory of local mate competition (LMC). A single female or 'foundress' laying eggs on a patch will lay just enough sons to fertilize her daughters. As the number of 'foundresses' laying eggs on a patch increases (and LMC declines), females produce increasingly male-biased sex ratios. Phenotypic studies have revealed the cues females use to estimate the level of LMC their sons will experience, but our understanding of the genetics underlying sex allocation is limited. Here, we exposed females to three foundress number conditions, i.e. three LMC conditions, and allowed them to oviposit. mRNA was extracted from only the heads of these females to target the brain tissue. The subsequent RNA-seq experiment confirmed that differential gene expression is not associated with the response to sex allocation cues and that we must instead turn to the underlying neuroscience to reveal the underpinnings of this impressive behavioural plasticity.
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Affiliation(s)
- Nicola Cook
- School of Biology, University of St Andrews, Greenside Place, St Andrews KY16 9TH, UK
| | - Rebecca A. Boulton
- School of Biology, University of St Andrews, Greenside Place, St Andrews KY16 9TH, UK
- Department of Entomology, University of Minnesota, St Paul, MN 55108, USA
| | - Jade Green
- School of Biology, University of St Andrews, Greenside Place, St Andrews KY16 9TH, UK
| | - Urmi Trivedi
- Edinburgh Genomics, University of Edinburgh, Ashworth Laboratories, The King's Buildings, Edinburgh EH9 3FL, UK
| | - Eran Tauber
- Faculty of Natural Sciences, University of Haifa, 199 Aba Khoushy Avenue, Mount Carmel, Haifa 3498838, Israel
| | - Bart A. Pannebakker
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Michael G. Ritchie
- School of Biology, University of St Andrews, Greenside Place, St Andrews KY16 9TH, UK
| | - David M. Shuker
- School of Biology, University of St Andrews, Greenside Place, St Andrews KY16 9TH, UK
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20
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Ali Z, Eid A, Ali S, Mahfouz MM. Pea early-browning virus-mediated genome editing via the CRISPR/Cas9 system in Nicotiana benthamiana and Arabidopsis. Virus Res 2018; 244:333-337. [PMID: 29051052 DOI: 10.1016/j.virusres.2017.10.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/19/2017] [Accepted: 10/13/2017] [Indexed: 01/17/2023]
Abstract
The clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system has enabled efficient genome engineering in diverse plant species. However, delivery of genome engineering reagents, such as the single guide RNA (sgRNA), into plant cells remains challenging. Here, we report the engineering of Tobacco rattle virus (TRV) and Pea early browning virus (PEBV) to deliver one or multiple sgRNAs into Nicotiana benthamiana and Arabidopsis thaliana (Col-0) plants that overexpress a nuclear localization signal containing Cas9. Our data showed that TRV and PEBV can deliver sgRNAs into inoculated and systemic leaves, and this resulted in mutagenesis of the targeted genomic loci. Moreover, in N. benthamiana, PEBV-based sgRNA delivery resulted in more targeted mutations than TRV-based delivery. Our data indicate that TRV and PEBV can facilitate plant genome engineering and can be used to produce targeted mutations for functional analysis and other biotechnological applications across diverse plant species. Key message: Delivery of genome engineering reagents into plant cells is challenging and inefficient and this limit the applications of this technology in many plant species. RNA viruses such as TRV and PEBV provide an efficient tool to systemically deliver sgRNAs for targeted genome modification.
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Affiliation(s)
- Zahir Ali
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Ayman Eid
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shakila Ali
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Environmental and Biological Sciences and Engineering, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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21
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Cystic fibrosis research topics featured at the 14th ECFS Basic Science Conference: Chairman's summary. J Cyst Fibros 2017; 17:S1-S4. [PMID: 29229473 DOI: 10.1016/j.jcf.2017.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 11/19/2017] [Indexed: 01/15/2023]
Abstract
In recent years, tremendous progress has been made in the development of novel drugs targeting the basic defect in patients with cystic fibrosis (CF). This breakthrough is based on a solid foundation of knowledge on CFTR's function in health and how mutations in CFTR cause CF multi-organ disease. This knowledge has been collected and continuously expanded by an active and persistent CF research community and has paved the way for precision medicine for CF. Since 2004, the European Cystic Fibrosis Society (ECFS) has held an annual Basic Science Conference that has evolved as an international forum for interdisciplinary discussion of hot topics and unsolved questions related to CF research. This Special Issue reviews CF research topics featured at the 14th ECFS Basic Science Conference and provides an up-to-date overview of recent progress in our understanding of CFTR structure and function, disease mechanisms implicated in airway mucus plugging, inflammation and abnormal host-pathogen interactions, and advancements with enhanced cell and animal model systems and breakthrough therapies directed at mutant CFTR or alternative targets. In addition, this Special Issue also identifies a number of fundamental questions and hurdles that still have to be overcome to realize the full potential of precision medicine and develop transformative therapies for all patients with CF.
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22
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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23
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Zhang N, Membreno E, Raj S, Zhang H, Khan LA, Gobel V. The C. elegans Excretory Canal as a Model for Intracellular Lumen Morphogenesis and In Vivo Polarized Membrane Biogenesis in a Single Cell: labeling by GFP-fusions, RNAi Interaction Screen and Imaging. J Vis Exp 2017. [PMID: 28994812 DOI: 10.3791/56101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The four C. elegans excretory canals are narrow tubes extended through the length of the animal from a single cell, with almost equally far extended intracellular endotubes that build and stabilize the lumen with a membrane and submembraneous cytoskeleton of apical character. The excretory cell expands its length approximately 2,000 times to generate these canals, making this model unique for the in vivo assessment of de novo polarized membrane biogenesis, intracellular lumen morphogenesis and unicellular tubulogenesis. The protocol presented here shows how to combine standard labeling, gain- and loss-of-function genetic or RNA interference (RNAi)-, and microscopic approaches to use this model to visually dissect and functionally analyze these processes on a molecular level. As an example of a labeling approach, the protocol outlines the generation of transgenic animals with fluorescent fusion proteins for live analysis of tubulogenesis. As an example of a genetic approach, it highlights key points of a visual RNAi-based interaction screen designed to modify a gain-of-function cystic canal phenotype. The specific methods described are how to: label and visualize the canals by expressing fluorescent proteins; construct a targeted RNAi library and strategize RNAi screening for the molecular analysis of canal morphogenesis; visually assess modifications of canal phenotypes; score them by dissecting fluorescence microscopy; characterize subcellular canal components at higher resolution by confocal microscopy; and quantify visual parameters. The approach is useful for the investigator who is interested in taking advantage of the C. elegans excretory canal for identifying and characterizing genes involved in the phylogenetically conserved processes of intracellular lumen and unicellular tube morphogenesis.
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Affiliation(s)
- Nan Zhang
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital for Children, Harvard Medical School; College of Life Sciences, Jilin University
| | - Edward Membreno
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital for Children, Harvard Medical School
| | - Susan Raj
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital for Children, Harvard Medical School
| | - Hongjie Zhang
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital for Children, Harvard Medical School; Faculty of Health Sciences, University of Macau
| | - Liakot A Khan
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital for Children, Harvard Medical School;
| | - Verena Gobel
- Mucosal Immunology and Biology Research Center, Developmental Biology and Genetics Core, Massachusetts General Hospital for Children, Harvard Medical School;
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24
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Animal and model systems for studying cystic fibrosis. J Cyst Fibros 2017; 17:S28-S34. [PMID: 28939349 DOI: 10.1016/j.jcf.2017.09.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/31/2017] [Accepted: 09/01/2017] [Indexed: 01/07/2023]
Abstract
The cystic fibrosis (CF) field is the beneficiary of five species of animal models that lack functional cystic fibrosis transmembrane conductance regulator (CFTR) channel. These models are rapidly informing mechanisms of disease pathogenesis and CFTR function regardless of how faithfully a given organ reproduces the human CF phenotype. New approaches of genetic engineering with RNA-guided nucleases are rapidly expanding both the potential types of models available and the approaches to correct the CFTR defect. The application of new CRISPR/Cas9 genome editing techniques are similarly increasing capabilities for in vitro modeling of CFTR functions in cell lines and primary cells using air-liquid interface cultures and organoids. Gene editing of CFTR mutations in somatic stem cells and induced pluripotent stem cells is also transforming gene therapy approaches for CF. This short review evaluates several areas that are key to building animal and cell systems capable of modeling CF disease and testing potential treatments.
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25
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Ye ZF, Liu XL, Han Q, Liao H, Dong XT, Zhu GH, Dong SL. Functional characterization of PBP1 gene in Helicoverpa armigera (Lepidoptera: Noctuidae) by using the CRISPR/Cas9 system. Sci Rep 2017; 7:8470. [PMID: 28814748 PMCID: PMC5559583 DOI: 10.1038/s41598-017-08769-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/12/2017] [Indexed: 01/10/2023] Open
Abstract
Pheromone binding proteins (PBPs) are thought to play crucial roles in perception of the sex pheromones particularly in noctuid moths, but this is rarely in vivo evidenced due to lacking an effective technique. Here, we reported an in vivo functional study of PBP1 in the important lepidopteran pest Helicoverpa armigera (HarmPBP1), by using the CRISPR/Cas9 system. Efficient and heritable mutagenesis was achieved by egg injection of mixture of Cas9-mRNA and HarmPBP1-sgRNA. The TA cloning and sequencing revealed various insertion and/or deletion (indel) mutations at the target site. Among those, one mutation resulted in a premature stop codon at the target site, which led to a highly truncated protein with only 10 amino acids. The HarmPBP1 with this mutation would completely loss its function, and thus was used to select the homozygous mutant insects for functional analysis. The electroantennogram recording showed that the mutant male adults displayed severely impaired responses to all three sex pheromone components (Z11-16:Ald, Z9-16:Ald and Z9-14:Ald). Our study provides the first in vivo evidence that HarmPBP1 plays important role in perception of female sex pheromones, and also an effective methodology for using CRISPR/Cas9 system in functional genetic study in H. armigera as well as other insects.
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Affiliation(s)
- Zhan-Feng Ye
- Key Laboratory of Integrated Pest Management in Crops in Eastern China (Ministry of Agriculture of China), College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiao-Long Liu
- Key Laboratory of Integrated Pest Management in Crops in Eastern China (Ministry of Agriculture of China), College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qi Han
- Key Laboratory of Integrated Pest Management in Crops in Eastern China (Ministry of Agriculture of China), College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hui Liao
- Key Laboratory of Integrated Pest Management in Crops in Eastern China (Ministry of Agriculture of China), College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiao-Tong Dong
- Key Laboratory of Integrated Pest Management in Crops in Eastern China (Ministry of Agriculture of China), College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guan-Heng Zhu
- Key Laboratory of Integrated Pest Management in Crops in Eastern China (Ministry of Agriculture of China), College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuang-Lin Dong
- Key Laboratory of Integrated Pest Management in Crops in Eastern China (Ministry of Agriculture of China), College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
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26
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Gulbransen BD. Emerging tools to study enteric neuromuscular function. Am J Physiol Gastrointest Liver Physiol 2017; 312:G420-G426. [PMID: 28280142 PMCID: PMC5451564 DOI: 10.1152/ajpgi.00049.2017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/07/2017] [Accepted: 03/07/2017] [Indexed: 01/31/2023]
Abstract
Investigating enteric neuromuscular function poses specific challenges that are not encountered in other systems. The gut has a complex cellular composition, and methods to study diverse multicellular interactions during physiological gut functions have been limited. However, new technologies are emerging in optics, genetics, and bioengineering that greatly expand the capabilities to study integrative functions in the gut. In this mini-review, I discuss several areas where the application of these technologies could benefit ongoing efforts to understand enteric neuromuscular function. I specifically focus on technologies that can be applied to study specific cellular networks and the mechanisms that link activity to function.
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Affiliation(s)
- Brian D. Gulbransen
- Neuroscience Program, Department of Physiology, Michigan State University, East Lansing, Michigan
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27
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Abstract
Identifying genes and pathways that contribute to differences in neurobehavioural traits is a key goal in psychiatric research. Despite considerable success in identifying quantitative trait loci (QTLs) associated with behaviour in laboratory rodents, pinpointing the causal variants and genes is more challenging. For a long time, the main obstacle was the size of QTLs, which could encompass tens if not hundreds of genes. However, recent studies have exploited mouse and rat resources that allow mapping of phenotypes to narrow intervals, encompassing only a few genes. Here, we review these studies, showcase the rodent resources they have used and highlight the insights into neurobehavioural traits provided to date. We discuss what we see as the biggest challenge in the field - translating QTLs into biological knowledge by experimentally validating and functionally characterizing candidate genes - and propose that the CRISPR/Cas genome-editing system holds the key to overcoming this obstacle. Finally, we challenge traditional views on inbred versus outbred resources in the light of recent resource and technology developments.
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Affiliation(s)
- Amelie Baud
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jonathan Flint
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095-1761, USA
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28
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Abstract
The CRISPR system for gene editing can break, repair, and replace targeted sections of DNA. Although CRISPR gene editing has important therapeutic potential, it raises several ethical concerns. Some bioethicists worry CRISPR is a prelude to a dystopian future, while others maintain it should not be feared because it is analogous to past biotechnologies. In the scientific literature, CRISPR is often discussed as a revolutionary technology. In this paper we unpack the framing of CRISPR as a revolutionary technology and contrast it with framing it as a value-threatening biotechnology or business-as-usual. By drawing on a comparison between CRISPR and the Ford Model T, we argue CRISPR is revolutionary as a product, process, and as a force for social change. This characterization of CRISPR offers important conceptual clarity to the existing debates surrounding CRISPR. In particular, conceptualizing CRISPR as a revolutionary technology structures regulatory goals with respect to this new technology. Revolutionary technologies have characteristic patterns of implementation, entrenchment, and social impact. As such, early identification of technologies as revolutionary may help construct more nuanced and effective ethical frameworks for public policy.
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29
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Stout E, Klaenhammer T, Barrangou R. CRISPR-Cas Technologies and Applications in Food Bacteria. Annu Rev Food Sci Technol 2017; 8:413-437. [DOI: 10.1146/annurev-food-072816-024723] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins form adaptive immune systems that occur in many bacteria and most archaea. In addition to protecting bacteria from phages and other invasive mobile genetic elements, CRISPR-Cas molecular machines can be repurposed as tool kits for applications relevant to the food industry. A primary concern of the food industry has long been the proper management of food-related bacteria, with a focus on both enhancing the outcomes of beneficial microorganisms such as starter cultures and probiotics and limiting the presence of detrimental organisms such as pathogens and spoilage microorganisms. This review introduces CRISPR-Cas as a novel set of technologies to manage food bacteria and offers insights into CRISPR-Cas biology. It primarily focuses on the applications of CRISPR-Cas systems and tools in starter cultures and probiotics, encompassing strain-typing, phage resistance, plasmid vaccination, genome editing, and antimicrobial activity.
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Affiliation(s)
- Emily Stout
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Todd Klaenhammer
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing, and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695
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30
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Abstract
Genome editing is driving a revolution in the biomedical sciences that carries the promise for future treatments of genetic diseases. The CRISPR/Cas9 system of RNA-guided genome editing has been successfully applied to modify the genome of a wide spectrum of organisms. We recently showed that this technique can be combined with in vivo electroporation to inhibit the function of genes of interest in somatic cells of the developing chicken embryo. We present here a simplified version of the previously described technique that leads to effective gene loss-of-function.
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Affiliation(s)
- Valérie Morin
- Institut NeuroMyoGène, INMG, Faculty of Medicine Laënnec, University Lyon1, Bâtiment B, 7 rue Guillaume Paradin, 69008, Lyon, France
| | - Nadège Véron
- EMBL Australia, Australian Regenerative Medicine Institute, Monash University, 15 Innovation Walk, Clayton, VIC, 3800, Australia
| | - Christophe Marcelle
- Institut NeuroMyoGène, INMG, Faculty of Medicine Laënnec, University Lyon1, Bâtiment B, 7 rue Guillaume Paradin, 69008, Lyon, France. .,EMBL Australia, Australian Regenerative Medicine Institute, Monash University, 15 Innovation Walk, Clayton, VIC, 3800, Australia.
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31
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HAMDOUN Z, EHSAN H. Aftermath of the Human Genome Project: an era of struggle and discovery. Turk J Biol 2017. [DOI: 10.3906/biy-1609-77] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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32
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Abstract
Prokaryotes use diverse strategies to improve fitness in the face of different environmental threats and stresses, including those posed by mobile genetic elements (e.g., bacteriophages and plasmids). To defend against these elements, many bacteria and archaea use elegant, RNA-directed, nucleic acid-targeting adaptive restriction machineries called CRISPR -: Cas (CRISPR-associated) systems. While providing an effective defense against foreign genetic elements, these systems have also been observed to play critical roles in regulating bacterial physiology during environmental stress. Increasingly, CRISPR-Cas systems, in particular the Type II systems containing the Cas9 endonuclease, have been exploited for their ability to bind desired nucleic acid sequences, as well as direct sequence-specific cleavage of their targets. Cas9-mediated genome engineering is transcending biological research as a versatile and portable platform for manipulating genetic content in myriad systems. Here, we present a systematic overview of CRISPR-Cas history and biology, highlighting the revolutionary tools derived from these systems, which greatly expand the molecular biologists' toolkit.
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Affiliation(s)
- Hannah K Ratner
- Department of Microbiology and Immunology, Microbiology and Molecular Genetics Program, Emory University, Atlanta, Georgia 30329
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
| | - Timothy R Sampson
- Department of Microbiology and Immunology, Microbiology and Molecular Genetics Program, Emory University, Atlanta, Georgia 30329
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
| | - David S Weiss
- Emory Vaccine Center, Emory University, Atlanta, Georgia 30329
- Yerkes National Primate Research Center, Emory University, Atlanta, Georgia 30329
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia 30329
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33
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Barrangou R, Doudna JA. Applications of CRISPR technologies in research and beyond. Nat Biotechnol 2016; 34:933-941. [DOI: 10.1038/nbt.3659] [Citation(s) in RCA: 577] [Impact Index Per Article: 72.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 07/31/2016] [Indexed: 02/06/2023]
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34
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Zhu GH, Xu J, Cui Z, Dong XT, Ye ZF, Niu DJ, Huang YP, Dong SL. Functional characterization of SlitPBP3 in Spodoptera litura by CRISPR/Cas9 mediated genome editing. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 75:1-9. [PMID: 27192033 DOI: 10.1016/j.ibmb.2016.05.006] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/09/2016] [Accepted: 05/12/2016] [Indexed: 05/12/2023]
Abstract
Functional gene analysis by using genome editing techniques is limited only in few model insects. Here, we reported an efficient and heritable gene mutagenesis analysis in an important lepidopteran pest, Spodoptera litura, using the CRISPR/Cas9 system. By using this system, we successfully obtained the homozygous S. litura strain by targeting the pheromone binding protein 3 gene (SlitPBP3), which allowed us to elucidate the role of this gene in the olfaction of the female sex pheromones. By co-injection of Cas9 mRNA and sgRNA into S. litura eggs, highly efficient chimera mutation in SlitPBP3 loci was detected both in injected eggs (39.1%) and in the resulting individual moths (87.5%). We used the mutant moths as parents to obtain the G1 offspring and the homozygous mutant strain in G2. The function of SlitPBP3 was explored by Electroantennogram (EAG) recordings with a homozygous mutant strain. The result showed that the EAG responses were significantly decreased in mutant males than in control males when treated with the major sex pheromone component (Z9,E11-14:Ac) and a minor component (Z9-14:Ac) at higher dosages. The results demonstrate that s SlitPBP3 gene plays a minor role in the perception of the female sex pheromones. Furthermore, our study provides a useful methodology with the CRISPR/Cas9 system for gene in vivo functional study, particular for lepidopteran species in which the RNAi approach is not efficient.
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Affiliation(s)
- Guan-Heng Zhu
- Education Ministry Key Laboratory of Integrated Management of Crop Disease and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Xu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai Institutes for Biological Sciences, Shanghai 200032, China
| | - Zhen Cui
- Education Ministry Key Laboratory of Integrated Management of Crop Disease and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao-Tong Dong
- Education Ministry Key Laboratory of Integrated Management of Crop Disease and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhan-Feng Ye
- Education Ministry Key Laboratory of Integrated Management of Crop Disease and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong-Juan Niu
- Education Ministry Key Laboratory of Integrated Management of Crop Disease and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Yong-Ping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai Institutes for Biological Sciences, Shanghai 200032, China
| | - Shuang-Lin Dong
- Education Ministry Key Laboratory of Integrated Management of Crop Disease and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
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Haeussler M, Schönig K, Eckert H, Eschstruth A, Mianné J, Renaud JB, Schneider-Maunoury S, Shkumatava A, Teboul L, Kent J, Joly JS, Concordet JP. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol 2016; 17:148. [PMID: 27380939 PMCID: PMC4934014 DOI: 10.1186/s13059-016-1012-2] [Citation(s) in RCA: 1054] [Impact Index Per Article: 131.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The success of the CRISPR/Cas9 genome editing technique depends on the choice of the guide RNA sequence, which is facilitated by various websites. Despite the importance and popularity of these algorithms, it is unclear to which extent their predictions are in agreement with actual measurements. RESULTS We conduct the first independent evaluation of CRISPR/Cas9 predictions. To this end, we collect data from eight SpCas9 off-target studies and compare them with the sites predicted by popular algorithms. We identify problems in one implementation but found that sequence-based off-target predictions are very reliable, identifying most off-targets with mutation rates superior to 0.1 %, while the number of false positives can be largely reduced with a cutoff on the off-target score. We also evaluate on-target efficiency prediction algorithms against available datasets. The correlation between the predictions and the guide activity varied considerably, especially for zebrafish. Together with novel data from our labs, we find that the optimal on-target efficiency prediction model strongly depends on whether the guide RNA is expressed from a U6 promoter or transcribed in vitro. We further demonstrate that the best predictions can significantly reduce the time spent on guide screening. CONCLUSIONS To make these guidelines easily accessible to anyone planning a CRISPR genome editing experiment, we built a new website ( http://crispor.org ) that predicts off-targets and helps select and clone efficient guide sequences for more than 120 genomes using different Cas9 proteins and the eight efficiency scoring systems evaluated here.
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Affiliation(s)
- Maximilian Haeussler
- Santa Cruz Genomics Institute, MS CBSE, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA.
| | - Kai Schönig
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, Mannheim, 68159, Germany
| | - Hélène Eckert
- Institut Curie, CNRS UMR3215, INSERM U934, Paris, Cedex, 05 75248, France
| | - Alexis Eschstruth
- CNRS UMR 7622, INSERM U1156, Sorbonne Université Paris 06, Paris, France
| | | | | | | | - Alena Shkumatava
- Institut Curie, CNRS UMR3215, INSERM U934, Paris, Cedex, 05 75248, France
| | | | - Jim Kent
- Santa Cruz Genomics Institute, MS CBSE, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | | | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR 7196, Muséum National d'Histoire Naturelle, Paris, France.
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36
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Haeussler M, Concordet JP. Genome Editing with CRISPR-Cas9: Can It Get Any Better? J Genet Genomics 2016; 43:239-50. [PMID: 27210042 PMCID: PMC5708852 DOI: 10.1016/j.jgg.2016.04.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/13/2016] [Accepted: 04/23/2016] [Indexed: 12/26/2022]
Abstract
The CRISPR-Cas revolution is taking place in virtually all fields of life sciences. Harnessing DNA cleavage with the CRISPR-Cas9 system of Streptococcus pyogenes has proven to be extraordinarily simple and efficient, relying only on the design of a synthetic single guide RNA (sgRNA) and its co-expression with Cas9. Here, we review the progress in the design of sgRNA from the original dual RNA guide for S. pyogenes and Staphylococcus aureus Cas9 (SpCas9 and SaCas9). New assays for genome-wide identification of off-targets have provided important insights into the issue of cleavage specificity in vivo. At the same time, the on-target activity of thousands of guides has been determined. These data have led to numerous online tools that facilitate the selection of guide RNAs in target sequences. It appears that for most basic research applications, cleavage activity can be maximized and off-targets minimized by carefully choosing guide RNAs based on computational predictions. Moreover, recent studies of Cas proteins have further improved the flexibility and precision of the CRISPR-Cas toolkit for genome editing. Inspired by the crystal structure of the complex of sgRNA-SpCas9 bound to target DNA, several variants of SpCas9 have recently been engineered, either with novel protospacer adjacent motifs (PAMs) or with drastically reduced off-targets. Novel Cas9 and Cas9-like proteins called Cpf1 have also been characterized from other bacteria and will benefit from the insights obtained from SpCas9. Genome editing with CRISPR-Cas9 may also progress with better understanding and control of cellular DNA repair pathways activated after Cas9-induced DNA cleavage.
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Affiliation(s)
- Maximilian Haeussler
- Santa Cruz Genomics Institute, MS CBSE, 1156 High Street, University of California, Santa Cruz, CA 95064, USA
| | - Jean-Paul Concordet
- Laboratoire Structure et Instabilité des Génomes, Inserm U1154, CNRS UMR7196, Muséum national d'Histoire naturelle, 43 rue Cuvier, 75005 Paris, France.
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Li Y, Artés JM, Qi J, Morelan IA, Feldstein P, Anantram MP, Hihath J. Comparing Charge Transport in Oligonucleotides: RNA:DNA Hybrids and DNA Duplexes. J Phys Chem Lett 2016; 7:1888-1894. [PMID: 27145167 DOI: 10.1021/acs.jpclett.6b00749] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Understanding the electronic properties of oligonucleotide systems is important for applications in nanotechnology, biology, and sensing systems. Here the charge-transport properties of guanine-rich RNA:DNA hybrids are compared to double-stranded DNA (dsDNA) duplexes with identical sequences. The conductance of the RNA:DNA hybrids is ∼10 times higher than the equivalent dsDNA, and conformational differences are determined to be the primary reason for this difference. The conductance of the RNA:DNA hybrids is also found to decrease more rapidly than dsDNA when the length is increased. Ab initio electronic structure and Green's function-based density of states calculations demonstrate that these differences arise because the energy levels are more spatially distributed in the RNA:DNA hybrid but that the number of accessible hopping sites is smaller. These combination results indicate that a simple hopping model that treats each individual guanine as a hopping site is insufficient to explain both a higher conductance and β value for RNA:DNA hybrids, and larger delocalization lengths must be considered.
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Affiliation(s)
- Yuanhui Li
- Electrical and Computer Engineering Department, University of California Davis , Davis, California 95616, United States
| | - Juan M Artés
- Electrical and Computer Engineering Department, University of California Davis , Davis, California 95616, United States
| | - Jianqing Qi
- Department of Electrical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Ian A Morelan
- Department of Plant Pathology, University of California Davis , Davis, California 95616, United States
| | - Paul Feldstein
- Department of Plant Pathology, University of California Davis , Davis, California 95616, United States
| | - M P Anantram
- Department of Electrical Engineering, University of Washington , Seattle, Washington 98195, United States
| | - Joshua Hihath
- Electrical and Computer Engineering Department, University of California Davis , Davis, California 95616, United States
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38
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Abstract
The CRISPR-Cas system has emerged as a fascinating and important genome editing tool. It is now widely used in biology, biotechnology, and biomedical research in both academic and industrial settings. To improve the specificity and efficiency of Cas nucleases and to extend the applications of these systems for other areas of research, an understanding of their precise working mechanisms is crucial. In this review, we summarize current studies on the molecular structures and dynamic functions of type I and type II Cas nucleases, with a focus on target DNA searching and cleavage processes as revealed by single-molecule observations. [BMB Reports 2016; 49(4): 201-207].
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Affiliation(s)
- Seung Hwan Lee
- Center for Genome Engineering, Institute for Basic Science, Seoul 08826
| | - Sangsu Bae
- Department of Chemistry
- Institute for Materials Design, Hanyang University, Seoul 04763, Korea
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39
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Anders C, Bargsten K, Jinek M. Structural Plasticity of PAM Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9. Mol Cell 2016; 61:895-902. [PMID: 26990992 PMCID: PMC5065715 DOI: 10.1016/j.molcel.2016.02.020] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 01/19/2023]
Abstract
The RNA-guided endonuclease Cas9 from Streptococcus pyogenes (SpCas9) forms the core of a powerful genome editing technology. DNA cleavage by SpCas9 is dependent on the presence of a 5'-NGG-3' protospacer adjacent motif (PAM) in the target DNA, restricting the choice of targetable sequences. To address this limitation, artificial SpCas9 variants with altered PAM specificities have recently been developed. Here we report crystal structures of the VQR, EQR, and VRER SpCas9 variants bound to target DNAs containing their preferred PAM sequences. The structures reveal that the non-canonical PAMs are recognized by an induced fit mechanism. Besides mediating sequence-specific base recognition, the amino acid substitutions introduced in the SpCas9 variants facilitate conformational remodeling of the PAM region of the bound DNA. Guided by the structural data, we engineered a SpCas9 variant that specifically recognizes NAAG PAMs. Taken together, these studies inform further development of Cas9-based genome editing tools.
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Affiliation(s)
- Carolin Anders
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Katja Bargsten
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
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40
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Liu T, Shen JK, Li Z, Choy E, Hornicek FJ, Duan Z. Development and potential applications of CRISPR-Cas9 genome editing technology in sarcoma. Cancer Lett 2016; 373:109-118. [PMID: 26806808 DOI: 10.1016/j.canlet.2016.01.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 02/07/2023]
Abstract
Sarcomas include some of the most aggressive tumors and typically respond poorly to chemotherapy. In recent years, specific gene fusion/mutations and gene over-expression/activation have been shown to drive sarcoma pathogenesis and development. These emerging genomic alterations may provide targets for novel therapeutic strategies and have the potential to transform sarcoma patient care. The RNA-guided nuclease CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated protein-9 nuclease) is a convenient and versatile platform for site-specific genome editing and epigenome targeted modulation. Given that sarcoma is believed to develop as a result of genetic alterations in mesenchymal progenitor/stem cells, CRISPR-Cas9 genome editing technologies hold extensive application potentials in sarcoma models and therapies. We review the development and mechanisms of the CRISPR-Cas9 system in genome editing and introduce its application in sarcoma research and potential therapy in clinic. Additionally, we propose future directions and discuss the challenges faced with these applications, providing concise and enlightening information for readers interested in this area.
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Affiliation(s)
- Tang Liu
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States; Department of Orthopaedic, the 2nd Xiangya Hospital of Central South University, 139 Renmin Road, Changsha, Hunan 410011, China
| | - Jacson K Shen
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States
| | - Zhihong Li
- Department of Orthopaedic, the 2nd Xiangya Hospital of Central South University, 139 Renmin Road, Changsha, Hunan 410011, China
| | - Edwin Choy
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States
| | - Francis J Hornicek
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States
| | - Zhenfeng Duan
- Sarcoma Biology Laboratory, Department of Orthopaedic Surgery, Massachusetts General Hospital and Harvard Medical School, 55 Fruit Street, Jackson 1115, Boston, MA 02114, United States.
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41
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Lin CY, Su YH. Genome editing in sea urchin embryos by using a CRISPR/Cas9 system. Dev Biol 2016; 409:420-8. [PMID: 26632489 DOI: 10.1016/j.ydbio.2015.11.018] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/20/2015] [Accepted: 11/22/2015] [Indexed: 11/23/2022]
Abstract
Sea urchin embryos are a useful model system for investigating early developmental processes and the underlying gene regulatory networks. Most functional studies using sea urchin embryos rely on antisense morpholino oligonucleotides to knockdown gene functions. However, major concerns related to this technique include off-target effects, variations in morpholino efficiency, and potential morpholino toxicity; furthermore, such problems are difficult to discern. Recent advances in genome editing technologies have introduced the prospect of not only generating sequence-specific knockouts, but also providing genome-engineering applications. Two genome editing tools, zinc-finger nuclease (ZFN) and transcription activator-like effector nucleases (TALENs), have been utilized in sea urchin embryos, but the resulting efficiencies are far from satisfactory. The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated nuclease 9) system serves as an easy and efficient method with which to edit the genomes of several established and emerging model organisms in the field of developmental biology. Here, we apply the CRISPR/Cas9 system to the sea urchin embryo. We designed six guide RNAs (gRNAs) against the well-studied nodal gene and discovered that five of the gRNAs induced the expected phenotype in 60-80% of the injected embryos. In addition, we developed a simple method for isolating genomic DNA from individual embryos, enabling phenotype to be precisely linked to genotype, and revealed that the mutation rates were 67-100% among the sequenced clones. Of the two potential off-target sites we examined, no off-target effects were observed. The detailed procedures described herein promise to accelerate the usage of CRISPR/Cas9 system for genome editing in sea urchin embryos.
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Affiliation(s)
- Che-Yi Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Hsien Su
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan.
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42
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Poulsen EG, Nielsen SV, Pietras EJ, Johansen JV, Steinhauer C, Hartmann-Petersen R. High-Throughput siRNA Screening Applied to the Ubiquitin-Proteasome System. Methods Mol Biol 2016; 1449:421-439. [PMID: 27613054 DOI: 10.1007/978-1-4939-3756-1_28] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The ubiquitin-proteasome system is the major pathway for intracellular protein degradation in eukaryotic cells. Due to the large number of genes dedicated to the ubiquitin-proteasome system, mapping degradation pathways for short lived proteins is a daunting task, in particular in mammalian cells that are not genetically tractable as, for instance, a yeast model system. Here, we describe a method relying on high-throughput cellular imaging of cells transfected with a targeted siRNA library to screen for components involved in degradation of a protein of interest. This method is a rapid and cost-effective tool which is also highly applicable for other studies on gene function.
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Affiliation(s)
- Esben G Poulsen
- Department of Biology, Section for Biomolecular Sciences, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark
| | - Sofie V Nielsen
- Department of Biology, Section for Biomolecular Sciences, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark
| | - Elin J Pietras
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark
| | - Jens V Johansen
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark
| | - Cornelia Steinhauer
- Biotech Research and Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, Section for Biomolecular Sciences, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark.
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43
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Tak YG, Farnham PJ. Making sense of GWAS: using epigenomics and genome engineering to understand the functional relevance of SNPs in non-coding regions of the human genome. Epigenetics Chromatin 2015; 8:57. [PMID: 26719772 PMCID: PMC4696349 DOI: 10.1186/s13072-015-0050-4] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 12/09/2015] [Indexed: 12/13/2022] Open
Abstract
Considerable progress towards an understanding of complex diseases has been made in recent years due to the development of high-throughput genotyping technologies. Using microarrays that contain millions of single-nucleotide polymorphisms (SNPs), Genome Wide Association Studies (GWASs) have identified SNPs that are associated with many complex diseases or traits. For example, as of February 2015, 2111 association studies have identified 15,396 SNPs for various diseases and traits, with the number of identified SNP-disease/trait associations increasing rapidly in recent years. However, it has been difficult for researchers to understand disease risk from GWAS results. This is because most GWAS-identified SNPs are located in non-coding regions of the genome. It is important to consider that the GWAS-identified SNPs serve only as representatives for all SNPs in the same haplotype block, and it is equally likely that other SNPs in high linkage disequilibrium (LD) with the array-identified SNPs are causal for the disease. Because it was hoped that disease-associated coding variants would be identified if the true casual SNPs were known, investigators have expanded their analyses using LD calculation and fine-mapping. However, such analyses also identified risk-associated SNPs located in non-coding regions. Thus, the GWAS field has been left with the conundrum as to how a single-nucleotide change in a non-coding region could confer increased risk for a specific disease. One possible answer to this puzzle is that the variant SNPs cause changes in gene expression levels rather than causing changes in protein function. This review provides a description of (1) advances in genomic and epigenomic approaches that incorporate functional annotation of regulatory elements to prioritize the disease risk-associated SNPs that are located in non-coding regions of the genome for follow-up studies, (2) various computational tools that aid in identifying gene expression changes caused by the non-coding disease-associated SNPs, and (3) experimental approaches to identify target genes of, and study the biological phenotypes conferred by, non-coding disease-associated SNPs.
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Affiliation(s)
- Yu Gyoung Tak
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Biology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089 USA
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44
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Tobita T, Guzman-Lepe J, Collin de l'Hortet A. From hacking the human genome to editing organs. Organogenesis 2015; 11:173-82. [PMID: 26588350 DOI: 10.1080/15476278.2015.1120047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In the recent decades, human genome engineering has been one of the major interesting research subjects, essentially because it raises new possibilities for personalized medicine and biotechnologies. With the development of engineered nucleases such as the Zinc Finger Nucleases (ZFNs), the Transcription activator-like effector nucleases (TALENs) and more recently the Clustered Regularly Interspaced short Palindromic Repeats (CRISPR), the field of human genome edition has evolved very rapidly. Every new genetic tool is broadening the scope of applications on human tissues, even before we can completely master each of these tools. In this review, we will present the recent advances regarding human genome edition tools, we will discuss the numerous implications they have in research and medicine, and we will mention the limits and concerns about such technologies.
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Affiliation(s)
- Takamasa Tobita
- a Department of Pathology ; University of Pittsburgh ; Pittsburgh ; PA USA
| | - Jorge Guzman-Lepe
- a Department of Pathology ; University of Pittsburgh ; Pittsburgh ; PA USA
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45
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Abstract
Bacterial adaptive immunity hinges on CRISPR-Cas systems that provide DNA-encoded, RNA-mediated targeting of exogenous nucleic acids. A plethora of CRISPR molecular machines occur broadly in prokaryotic genomes, with a diversity of Cas nucleases that can be repurposed for various applications.
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Affiliation(s)
- Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
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46
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Kirchner M, Schneider S. CRISPR-Cas: von einem bakteriellen adaptiven Immunsystem zu einem vielseitigen Werkzeug für die Gentechnik. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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47
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Kirchner M, Schneider S. CRISPR-Cas: From the Bacterial Adaptive Immune System to a Versatile Tool for Genome Engineering. Angew Chem Int Ed Engl 2015; 54:13508-14. [DOI: 10.1002/anie.201504741] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/08/2015] [Indexed: 12/13/2022]
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48
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Véron N, Qu Z, Kipen PAS, Hirst CE, Marcelle C. CRISPR mediated somatic cell genome engineering in the chicken. Dev Biol 2015; 407:68-74. [PMID: 26277216 DOI: 10.1016/j.ydbio.2015.08.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 08/07/2015] [Accepted: 08/11/2015] [Indexed: 01/17/2023]
Abstract
Gene-targeted knockout technologies are invaluable tools for understanding the functions of genes in vivo. CRISPR/Cas9 system of RNA-guided genome editing is revolutionizing genetics research in a wide spectrum of organisms. Here, we combined CRISPR with in vivo electroporation in the chicken embryo to efficiently target the transcription factor PAX7 in tissues of the developing embryo. This approach generated mosaic genetic mutations within a wild-type cellular background. This series of proof-of-principle experiments indicate that in vivo CRISPR-mediated cell genome engineering is an effective method to achieve gene loss-of-function in the tissues of the chicken embryo and it completes the growing genetic toolbox to study the molecular mechanisms regulating development in this important animal model.
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Affiliation(s)
- Nadège Véron
- EMBL Australia, Australian Regenerative Medicine Institute, Monash University, Building 75, Clayton, VIC 3800, Australia
| | - Zhengdong Qu
- EMBL Australia, Australian Regenerative Medicine Institute, Monash University, Building 75, Clayton, VIC 3800, Australia
| | - Phoebe A S Kipen
- EMBL Australia, Australian Regenerative Medicine Institute, Monash University, Building 75, Clayton, VIC 3800, Australia
| | - Claire E Hirst
- EMBL Australia, Australian Regenerative Medicine Institute, Monash University, Building 75, Clayton, VIC 3800, Australia
| | - Christophe Marcelle
- EMBL Australia, Australian Regenerative Medicine Institute, Monash University, Building 75, Clayton, VIC 3800, Australia.
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49
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Larsen CJ. La technologie CRISPR-Cas9 : une des clés des thérapies personnalisées ? Bull Cancer 2015; 102:199-200. [DOI: 10.1016/j.bulcan.2015.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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50
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