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Borges G, Benslimane Y, Harrington L. A CRISPR base editing approach for the functional assessment of telomere biology disorder-related genes in human health and aging. Biogerontology 2024; 25:361-378. [PMID: 38310618 PMCID: PMC10998809 DOI: 10.1007/s10522-024-10094-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/06/2024] [Indexed: 02/06/2024]
Abstract
Telomere Biology Disorders (TBDs) are a group of rare diseases characterized by the presence of short and/or dysfunctional telomeres. They comprise a group of bone marrow failure syndromes, idiopathic pulmonary fibrosis, and liver disease, among other diseases. Genetic alterations (variants) in the genes responsible for telomere homeostasis have been linked to TBDs. Despite the number of variants already identified as pathogenic, an even more significant number must be better understood. The study of TBDs is challenging since identifying these variants is difficult due to their rareness, it is hard to predict their impact on the disease onset, and there are not enough samples to study. Most of our knowledge about pathogenic variants comes from assessing telomerase activity from patients and their relatives affected by a TBD. However, we still lack a cell-based model to identify new variants and to study the long-term impact of such variants on the genes involved in TBDs. Herein, we present a cell-based model using CRISPR base editing to mutagenize the endogenous alleles of 21 genes involved in telomere biology. We identified key residues in the genes encoding 17 different proteins impacting cell growth. We provide functional evidence for variants of uncertain significance in patients with TBDs. We also identified variants resistant to telomerase inhibition that, similar to cells expressing wild-type telomerase, exhibited increased tumorigenic potential using an in vitro tumour growth assay. We believe that such cell-based approaches will significantly advance our understanding of the biology of TBDs and may contribute to the development of new therapies for this group of diseases.
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Affiliation(s)
- Gustavo Borges
- Departments of Medicine and Biochemistry and Molecular Medicine, Molecular Biology Programme, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, H3T 1J4, Canada
| | - Yahya Benslimane
- Departments of Medicine and Biochemistry and Molecular Medicine, Molecular Biology Programme, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, H3T 1J4, Canada
| | - Lea Harrington
- Departments of Medicine and Biochemistry and Molecular Medicine, Molecular Biology Programme, Institute for Research in Immunology and Cancer, University of Montreal, Montreal, QC, H3T 1J4, Canada.
- Department of Biochemistry, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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2
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Alipanahi R, Safari L, Khanteymoori A. CRISPR genome editing using computational approaches: A survey. FRONTIERS IN BIOINFORMATICS 2023; 2:1001131. [PMID: 36710911 PMCID: PMC9875887 DOI: 10.3389/fbinf.2022.1001131] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based gene editing has been widely used in various cell types and organisms. To make genome editing with Clustered regularly interspaced short palindromic repeats far more precise and practical, we must concentrate on the design of optimal gRNA and the selection of appropriate Cas enzymes. Numerous computational tools have been created in recent years to help researchers design the best gRNA for Clustered regularly interspaced short palindromic repeats researches. There are two approaches for designing an appropriate gRNA sequence (which targets our desired sites with high precision): experimental and predicting-based approaches. It is essential to reduce off-target sites when designing an optimal gRNA. Here we review both traditional and machine learning-based approaches for designing an appropriate gRNA sequence and predicting off-target sites. In this review, we summarize the key characteristics of all available tools (as far as possible) and compare them together. Machine learning-based tools and web servers are believed to become the most effective and reliable methods for predicting on-target and off-target activities of Clustered regularly interspaced short palindromic repeats in the future. However, these predictions are not so precise now and the performance of these algorithms -especially deep learning one's-depends on the amount of data used during training phase. So, as more features are discovered and incorporated into these models, predictions become more in line with experimental observations. We must concentrate on the creation of ideal gRNA and the choice of suitable Cas enzymes in order to make genome editing with Clustered regularly interspaced short palindromic repeats far more accurate and feasible.
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Affiliation(s)
| | - Leila Safari
- Department of Computer Engineering, University of Zanjan, Zanjan, Iran,*Correspondence: Leila Safari,
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3
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Kuluev BR, Mikhailova EV, Kuluev AR, Galimova AA, Zaikina EA, Khlestkina EK. Genome Editing in Species of the Tribe Triticeae with the CRISPR/Cas System. Mol Biol 2022. [DOI: 10.1134/s0026893322060127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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4
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Huang Y, Shang M, Liu T, Wang K. High-throughput methods for genome editing: the more the better. PLANT PHYSIOLOGY 2022; 188:1731-1745. [PMID: 35134245 PMCID: PMC8968257 DOI: 10.1093/plphys/kiac017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/29/2021] [Indexed: 05/04/2023]
Abstract
During the last decade, targeted genome-editing technologies, especially clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) technologies, have permitted efficient targeting of genomes, thereby modifying these genomes to offer tremendous opportunities for deciphering gene function and engineering beneficial traits in many biological systems. As a powerful genome-editing tool, the CRISPR/Cas systems, combined with the development of next-generation sequencing and many other high-throughput techniques, have thus been quickly developed into a high-throughput engineering strategy in animals and plants. Therefore, here, we review recent advances in using high-throughput genome-editing technologies in animals and plants, such as the high-throughput design of targeted guide RNA (gRNA), construction of large-scale pooled gRNA, and high-throughput genome-editing libraries, high-throughput detection of editing events, and high-throughput supervision of genome-editing products. Moreover, we outline perspectives for future applications, ranging from medication using gene therapy to crop improvement using high-throughput genome-editing technologies.
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Affiliation(s)
- Yong Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Meiqi Shang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Tingting Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Kejian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
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5
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Cárdenas P, Esherick LY, Chambonnier G, Dey S, Turlo CV, Nasamu AS, Niles JC. GeneTargeter: Automated In Silico Design for Genome Editing in the Malaria Parasite, Plasmodium falciparum. CRISPR J 2022; 5:155-164. [PMID: 35191751 PMCID: PMC8892962 DOI: 10.1089/crispr.2021.0069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Functional characterization of the multitude of poorly described proteins in the human malarial pathogen, Plasmodium falciparum, requires tools to enable genome-scale perturbation studies. Here, we present GeneTargeter (genetargeter.mit.edu), a software tool for automating the design of homology-directed repair donor vectors to achieve gene knockouts, conditional knockdowns, and epitope tagging of P. falciparum genes. We demonstrate GeneTargeter-facilitated genome-scale design of six different types of knockout and conditional knockdown constructs for the P. falciparum genome and validate the computational design process experimentally with successful donor vector assembly and transfection. The software's modular nature accommodates arbitrary destination vectors and allows customizable designs that extend the genome manipulation outcomes attainable in Plasmodium and other organisms.
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Affiliation(s)
- Pablo Cárdenas
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Lisl Y. Esherick
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gaël Chambonnier
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Christopher V. Turlo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Armiyaw Sebastian Nasamu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Address correspondence to: Jacquin C. Niles, MD, PhD, Department of Biological Engineering, Massachusetts Institute of Technology, Room 56-341, 77 Massachusetts Avenue, Cambridge, MA 02139-4307, USA,
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6
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Kirillov B, Savitskaya E, Panov M, Ogurtsov AY, Shabalina S, Koonin E, Severinov KV. Uncertainty-aware and interpretable evaluation of Cas9-gRNA and Cas12a-gRNA specificity for fully matched and partially mismatched targets with Deep Kernel Learning. Nucleic Acids Res 2022; 50:e11. [PMID: 34791389 PMCID: PMC8789050 DOI: 10.1093/nar/gkab1065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/25/2021] [Accepted: 11/12/2021] [Indexed: 12/26/2022] Open
Abstract
The choice of guide RNA (gRNA) for CRISPR-based gene targeting is an essential step in gene editing applications, but the prediction of gRNA specificity remains challenging. Lack of transparency and focus on point estimates of efficiency disregarding the information on possible error sources in the model limit the power of existing Deep Learning-based methods. To overcome these problems, we present a new approach, a hybrid of Capsule Networks and Gaussian Processes. Our method predicts the cleavage efficiency of a gRNA with a corresponding confidence interval, which allows the user to incorporate information regarding possible model errors into the experimental design. We provide the first utilization of uncertainty estimation in computational gRNA design, which is a critical step toward accurate decision-making for future CRISPR applications. The proposed solution demonstrates acceptable confidence intervals for most test sets and shows regression quality similar to existing models. We introduce a set of criteria for gRNA selection based on off-target cleavage efficiency and its variance and present a collection of pre-computed gRNAs for human chromosome 22. Using Neural Network Interpretation methods, we show that our model rediscovers an established biological factor underlying cleavage efficiency, the importance of the seed region in gRNA.
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Affiliation(s)
- Bogdan Kirillov
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Ekaterina Savitskaya
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Maxim Panov
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Aleksey Y Ogurtsov
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Konstantin V Severinov
- Center for Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
- Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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7
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Cai H, Chew SK, Li C, Tsai MK, Andrejka L, Murray CW, Hughes NW, Shuldiner EG, Ashkin EL, Tang R, Hung KL, Chen LC, Lee SYC, Yousefi M, Lin WY, Kunder CA, Cong L, McFarland CD, Petrov DA, Swanton C, Winslow MM. A Functional Taxonomy of Tumor Suppression in Oncogenic KRAS-Driven Lung Cancer. Cancer Discov 2021; 11:1754-1773. [PMID: 33608386 PMCID: PMC8292166 DOI: 10.1158/2159-8290.cd-20-1325] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/25/2020] [Accepted: 02/12/2021] [Indexed: 12/13/2022]
Abstract
Cancer genotyping has identified a large number of putative tumor suppressor genes. Carcinogenesis is a multistep process, but the importance and specific roles of many of these genes during tumor initiation, growth, and progression remain unknown. Here we use a multiplexed mouse model of oncogenic KRAS-driven lung cancer to quantify the impact of 48 known and putative tumor suppressor genes on diverse aspects of carcinogenesis at an unprecedented scale and resolution. We uncover many previously understudied functional tumor suppressors that constrain cancer in vivo. Inactivation of some genes substantially increased growth, whereas the inactivation of others increases tumor initiation and/or the emergence of exceptionally large tumors. These functional in vivo analyses revealed an unexpectedly complex landscape of tumor suppression that has implications for understanding cancer evolution, interpreting clinical cancer genome sequencing data, and directing approaches to limit tumor initiation and progression. SIGNIFICANCE: Our high-throughput and high-resolution analysis of tumor suppression uncovered novel genetic determinants of oncogenic KRAS-driven lung cancer initiation, overall growth, and exceptional growth. This taxonomy is consistent with changing constraints during the life history of cancer and highlights the value of quantitative in vivo genetic analyses in autochthonous cancer models.This article is highlighted in the In This Issue feature, p. 1601.
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Affiliation(s)
- Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Su Kit Chew
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Chuan Li
- Department of Biology, Stanford University, Stanford, California
| | - Min K Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Christopher W Murray
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Nicholas W Hughes
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | | | - Emily L Ashkin
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Rui Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - King L Hung
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Leo C Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Shi Ya C Lee
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Maryam Yousefi
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Wen-Yang Lin
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Le Cong
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, California.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, United Kingdom.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, California.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
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8
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Mukhopadhyay S, Bhutia SK. Trends in CRISPR-Cas9 technology application in cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 178:175-192. [PMID: 33685596 DOI: 10.1016/bs.pmbts.2020.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The evolution of the CRISPR-Cas9 technology in cancer research has tremendous potential to shape the future of oncology. Although this gene-editing tool's pre-clinical progress is into its nascent stage, there are many unanswered questions regarding health benefits and therapy precision using CRISPR. The application of CRISPR is highly specific, economically sustainable, and is a high throughput technique, but on the other hand, its application involves measured risk of countering the toxic immune response of Cas protein, off-target effects, limitation of delivering the edited cells back into cancer patients. The current chapter highlights the possibilities and perils of the present-day CRISPR engineering in cancer that should highlight CRISPR translation to therapy.
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Affiliation(s)
- Subhadip Mukhopadhyay
- Department of Radiation Oncology, Laura and Isaac Perlmutter Cancer Center, NYU Medical School, New York, NY, United States.
| | - Sujit Kumar Bhutia
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, India.
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9
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Gerashchenkov GA, Rozhnova NA, Kuluev BR, Kiryanova OY, Gumerova GR, Knyazev AV, Vershinina ZR, Mikhailova EV, Chemeris DA, Matniyazov RT, Baimiev AK, Gubaidullin IM, Baimiev AK, Chemeris AV. Design of Guide RNA for CRISPR/Cas Plant Genome Editing. Mol Biol 2020. [DOI: 10.1134/s0026893320010069] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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Kelkar A, Zhu Y, Groth T, Stolfa G, Stablewski AB, Singhi N, Nemeth M, Neelamegham S. Doxycycline-Dependent Self-Inactivation of CRISPR-Cas9 to Temporally Regulate On- and Off-Target Editing. Mol Ther 2020; 28:29-41. [PMID: 31601489 PMCID: PMC6952177 DOI: 10.1016/j.ymthe.2019.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 12/23/2022] Open
Abstract
Exome and deep sequencing of cells treated with a panel of lentiviral guide RNA demonstrate that both on- and off-target editing proceed in a time-dependent manner. Thus, methods to temporally control Cas9 activity would be beneficial. To address this need, we describe a "self-inactivating CRISPR (SiC)" system consisting of a single guide RNA that deactivates the Streptococcus pyogenes Cas9 nuclease in a doxycycline-dependent manner. This enables defined, temporal control of Cas9 activity in any cell type and also in vivo. Results show that SiC may enable a reduction in off-target editing, with less effect on on-target editing rates. This tool facilitates diverse applications including (1) the timed regulation of genetic knockouts in hard-to-transfect cells using lentivirus, including human leukocytes for the identification of glycogenes regulating leukocyte-endothelial cell adhesion; (2) genome-wide lentiviral sgRNA (single guide RNA) library applications where Cas9 activity is ablated after allowing pre-determined editing times. Thus, stable knockout cell pools are created for functional screens; and (3) temporal control of Cas9-mediated editing of myeloid and lymphoid cells in vivo, both in mouse peripheral blood and bone marrow. Overall, SiC enables temporal control of gene editing and may be applied in diverse application including studies that aim to reduce off-target genome editing.
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Affiliation(s)
- Anju Kelkar
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA; Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Yuqi Zhu
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA; Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Theodore Groth
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Gino Stolfa
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Aimee B Stablewski
- Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Naina Singhi
- Immunology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Michael Nemeth
- Immunology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Sriram Neelamegham
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, NY, USA; Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, NY, USA; Department of Medicine, University at Buffalo, State University of New York, Buffalo, NY, USA.
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11
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Haldeman JM, Conway AE, Arlotto ME, Slentz DH, Muoio DM, Becker TC, Newgard CB. Creation of versatile cloning platforms for transgene expression and dCas9-based epigenome editing. Nucleic Acids Res 2019; 47:e23. [PMID: 30590691 PMCID: PMC6393299 DOI: 10.1093/nar/gky1286] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 12/11/2018] [Accepted: 12/16/2018] [Indexed: 01/09/2023] Open
Abstract
Genetic manipulation via transgene overexpression, RNAi, or Cas9-based methods is central to biomedical research. Unfortunately, use of these tools is often limited by vector options. We have created a modular platform (pMVP) that allows a gene of interest to be studied in the context of an array of promoters, epitope tags, conditional expression modalities, and fluorescent reporters, packaged in 35 custom destination vectors, including adenovirus, lentivirus, PiggyBac transposon, and Sleeping Beauty transposon, in aggregate >108,000 vector permutations. We also used pMVP to build an epigenetic engineering platform, pMAGIC, that packages multiple gRNAs and either Sa-dCas9 or x-dCas9(3.7) fused to one of five epigenetic modifiers. Importantly, via its compatibility with adenoviral vectors, pMAGIC uniquely enables use of dCas9/LSD1 fusions to interrogate enhancers within primary cells. To demonstrate this, we used pMAGIC to target Sa-dCas9/LSD1 and modify the epigenetic status of a conserved enhancer, resulting in altered expression of the homeobox transcription factor PDX1 and its target genes in pancreatic islets and insulinoma cells. In sum, the pMVP and pMAGIC systems empower researchers to rapidly generate purpose-built, customized vectors for manipulation of gene expression, including via targeted epigenetic modification of regulatory elements in a broad range of disease-relevant cell types.
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Affiliation(s)
- Jonathan M Haldeman
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27701, USA
| | - Amanda E Conway
- Epigenetics & Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Michelle E Arlotto
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - Dorothy H Slentz
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
| | - Deborah M Muoio
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27701, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27701, USA
| | - Thomas C Becker
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27701, USA
| | - Christopher B Newgard
- Sarah W. Stedman Nutrition and Metabolism Center, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27701, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27701, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27701, USA
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12
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Rodríguez-Rodríguez DR, Ramírez-Solís R, Garza-Elizondo MA, Garza-Rodríguez MDL, Barrera-Saldaña HA. Genome editing: A perspective on the application of CRISPR/Cas9 to study human diseases (Review). Int J Mol Med 2019; 43:1559-1574. [PMID: 30816503 PMCID: PMC6414166 DOI: 10.3892/ijmm.2019.4112] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 08/01/2018] [Indexed: 02/06/2023] Open
Abstract
Genome editing reemerged in 2012 with the development of CRISPR/Cas9 technology, which is a genetic manipulation tool derived from the defense system of certain bacteria against viruses and plasmids. This method is easy to apply and has been used in a wide variety of experimental models, including cell lines, laboratory animals, plants, and even in human clinical trials. The CRISPR/Cas9 system consists of directing the Cas9 nuclease to create a site-directed double-strand DNA break using a small RNA molecule as a guide. A process that allows a permanent modification of the genomic target sequence can repair the damage caused to DNA. In the present study, the basic principles of the CRISPR/Cas9 system are reviewed, as well as the strategies and modifications of the enzyme Cas9 to eliminate the off-target cuts, and the different applications of CRISPR/Cas9 as a system for visualization and gene expression activation or suppression. In addition, the review emphasizes on the potential application of this system in the treatment of different diseases, such as pulmonary, gastrointestinal, hematologic, immune system, viral, autoimmune and inflammatory diseases, and cancer.
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Affiliation(s)
- Diana Raquel Rodríguez-Rodríguez
- Universidad Autónoma de Nuevo León, Department of Biochemistry and Molecular Medicine, School of Medicine and University Hospital 'Dr. José E. González', Monterrey, Nuevo León 64460, México
| | - Ramiro Ramírez-Solís
- Institutional Core Laboratories, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Mario Alberto Garza-Elizondo
- Universidad Autónoma de Nuevo León, Service of Rheumatology, School of Medicine and University Hospital 'Dr. José E. González', Monterrey, Nuevo León 64460, México
| | - María De Lourdes Garza-Rodríguez
- Universidad Autónoma de Nuevo León, Department of Biochemistry and Molecular Medicine, School of Medicine and University Hospital 'Dr. José E. González', Monterrey, Nuevo León 64460, México
| | - Hugo Alberto Barrera-Saldaña
- Universidad Autónoma de Nuevo León, Department of Biochemistry and Molecular Medicine, School of Medicine and University Hospital 'Dr. José E. González', Monterrey, Nuevo León 64460, México
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13
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Klimke A, Güttler S, Kuballa P, Janzen S, Ortmann S, Flora A. Use of CRISPR/Cas9 for the Modification of the Mouse Genome. Methods Mol Biol 2019; 1953:213-230. [PMID: 30912024 DOI: 10.1007/978-1-4939-9145-7_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The use of CRISPR/Cas9 to modify the mouse genome has gained immense interest in the past few years since it allows the direct modification of embryos, bypassing the need of labor-intensive procedures for the manipulation of embryonic stem cells. By shortening the overall timelines and reducing the costs for the generation of new genetically modified mouse lines (Li et al., Nat Biotechnol 31: 681-683, 2013), this technology has rapidly become a major tool for in vivo drug discovery applications.
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Affiliation(s)
| | | | | | | | | | - Adriano Flora
- PerkinElmer chemagen Technologie GmbH, Baesweiler, Germany.
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14
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Noiman T, Kahana C. A Simple Combined Use of CRISPR-Cas9 and Cre-LoxP Technologies for Generating Conditional Gene Knockouts in Mammalian Cells. CRISPR J 2018; 1:278-285. [PMID: 31021220 DOI: 10.1089/crispr.2018.0010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Gene knockout technologies have contributed fundamentally to our understanding of the cellular functions of various genes. Two prevalent systems used for the efficient elimination of the expression of specific genes are the Cre-LoxP system and the CRISPR-Cas9 system. Here, we present a simple method that combines the use of CRISPR-Cas9 and Cre-LoxP for the conditional deletion of essential genes in mammalian cells. First, an inducible Cre recombinase is stably expressed in the cells. Next, CRISPR-Cas9 is used to knock out an essential gene, whose function is complemented by stable expression of a FLAG-tagged version of the same protein encoded from a floxed transcription unit containing silent mutations, making it refractory to the CRISPR-Cas9 guide. This FLAG-tagged protein can be deleted by activating the expressed Cre protein, enabling evaluation of the cellular consequences of its deletion. We have further used this system to evaluate the ability of phylogenic homologues and of potential mutants to cover functionally for the deleted gene.
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Affiliation(s)
- Tzahi Noiman
- Department of Molecular Genetics, The Weizmann Institute of Science , Rehovot, Israel
| | - Chaim Kahana
- Department of Molecular Genetics, The Weizmann Institute of Science , Rehovot, Israel
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15
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Cui Y, Xu J, Cheng M, Liao X, Peng S. Review of CRISPR/Cas9 sgRNA Design Tools. Interdiscip Sci 2018; 10:455-465. [PMID: 29644494 DOI: 10.1007/s12539-018-0298-z] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/02/2018] [Accepted: 04/04/2018] [Indexed: 12/22/2022]
Abstract
The adaptive immunity system in bacteria and archaea, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-associate (CRISPR/Cas), has been adapted as a powerful gene editing tool and got a broad application in genome research field due to its ease of use and cost-effectiveness. The performance of CRISPR/Cas relies on well-designed single-guide RNA (sgRNA), so a lot of bioinformatic tools have been developed to assist the design of highly active and specific sgRNA. These tools vary in design specifications, parameters, genomes and so on. To help researchers to choose their proper tools, we reviewed various sgRNA design tools, mainly focusing on their on-target efficiency prediction model and off-target detection algorithm.
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Affiliation(s)
- Yingbo Cui
- College of Computer, National University of Defense Technology, Changsha, 410073, China
| | - Jiaming Xu
- College of Computer, National University of Defense Technology, Changsha, 410073, China
| | - Minxia Cheng
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Xiangke Liao
- College of Computer, National University of Defense Technology, Changsha, 410073, China
| | - Shaoliang Peng
- College of Computer, National University of Defense Technology, Changsha, 410073, China.
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China.
- National Supercomputing Center in Changsha, Changsha, 410082, China.
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16
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Gertsenstein M, Nutter LMJ. Engineering Point Mutant and Epitope-Tagged Alleles in Mice Using Cas9 RNA-Guided Nuclease. CURRENT PROTOCOLS IN MOUSE BIOLOGY 2018; 8:28-53. [PMID: 30040228 PMCID: PMC9249120 DOI: 10.1002/cpmo.40] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mice carrying patient-associated point mutations are powerful tools to define the causality of single-nucleotide variants to disease states. Epitope tags enable immuno-based studies of genes for which no antibodies are available. These alleles enable detailed and precise developmental, mechanistic, and translational research. The first step in generating these alleles is to identify within the target sequence-the orthologous sequence for point mutations or the N or C terminus for epitope tags-appropriate Cas9 protospacer sequences. Subsequent steps include design and acquisition of a single-stranded oligonucleotide repair template, synthesis of a single guide RNA (sgRNA), collection of zygotes, and microinjection or electroporation of zygotes with Cas9 mRNA or protein, sgRNA, and repair template followed by screening of born mice for the presence of the desired sequence change. Quality control of mouse lines includes screening for random or multicopy insertions of the repair template and, depending on sgRNA sequence, off-target mutations introduced by Cas9. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, Ontario, Canada
- Translational Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
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17
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Abstract
Exciting new technologies are often self-limiting in their rollout, as access to state-of-the-art instrumentation or the need for years of hands-on experience, for better or worse, ensures slow adoption by the community. CRISPR technology, however, presents the opposite dilemma, where the simplicity of the system enabled the parallel development of many applications, improvements and derivatives, and new users are now presented with an almost paralyzing abundance of choices. This Review intends to guide users through the process of applying CRISPR technology to their biological problems of interest, especially in the context of discovering gene function at scale.
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Affiliation(s)
- John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA
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18
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Hough SH, Kancleris K, Brody L, Humphryes-Kirilov N, Wolanski J, Dunaway K, Ajetunmobi A, Dillard V. Erratum to: Guide Picker is a comprehensive design tool for visualizing and selecting guides for CRISPR experiments. BMC Bioinformatics 2017; 18:202. [PMID: 28376719 PMCID: PMC5379749 DOI: 10.1186/s12859-017-1618-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Soren H Hough
- , Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR, UK.
| | - Kris Kancleris
- , Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR, UK
| | - Leigh Brody
- , Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR, UK
| | | | - Joseph Wolanski
- , Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR, UK
| | - Keith Dunaway
- , Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR, UK
| | | | - Victor Dillard
- , Desktop Genetics, Ltd., 28 Hanbury Street, London, E1 6QR, UK
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