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Pe KBA, Yatsuzuka K, Hakariya H, Kida T, Katsuda Y, Fukuda M, Sato SI. RNA-based cooperative protein labeling that permits direct monitoring of the intracellular concentration change of an endogenous protein. Nucleic Acids Res 2021; 49:e132. [PMID: 34581825 PMCID: PMC8682759 DOI: 10.1093/nar/gkab839] [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: 02/01/2021] [Revised: 08/24/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Imaging the dynamics of proteins in living cells is a powerful means for understanding cellular functions at a deeper level. Here, we report a versatile method for spatiotemporal imaging of specific endogenous proteins in living mammalian cells. The method employs a bifunctional aptamer capable of selective protein recognition and fluorescent probe-binding, which is induced only when the aptamer specifically binds to its target protein. An aptamer for β-actin protein preferentially recognizes its monomer forms over filamentous forms, resulting in selective G-actin staining in both fixed and living cells. Through actin-drug treatment, the method permitted direct monitoring of the intracellular concentration change of endogenous G-actin. This protein-labeling method, which is highly selective and non-covalent, provides rich insights into the study of spatiotemporal protein dynamics in living cells.
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Affiliation(s)
| | - Kenji Yatsuzuka
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hayase Hakariya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomoki Kida
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Yousuke Katsuda
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan.,Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Masatora Fukuda
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Shin-Ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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Yamagata M, Sanes JR. CRISPR-mediated Labeling of Cells in Chick Embryos Based on Selectively Expressed Genes. Bio Protoc 2021; 11:e4105. [PMID: 34458399 PMCID: PMC8376491 DOI: 10.21769/bioprotoc.4105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 12/26/2022] Open
Abstract
The abilities to mark and manipulate specific cell types are essential for an increasing number of functional, structural, molecular, and developmental analyses in model organisms. In a few species, this can be accomplished by germline transgenesis; in other species, other methods are needed to selectively label somatic cells based on the genes that they express. Here, we describe a method for CRISPR-based somatic integration of reporters or Cre recombinase into specific genes in the chick genome, followed by visualization of cells in the retina and midbrain. Loci are chosen based on an RNA-seq-based cell atlas. Reporters can be soluble to visualize the morphology of individual cells or appended to the encoded protein to assess subcellular localization. We call the method eCHIKIN for electroporation- and CRISPR-mediated Homology-instructed Knock-IN.
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Affiliation(s)
- Masahito Yamagata
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, 02138, USA
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, 02138, USA
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Holmgaard AB, Askou AL, Jensen EG, Alsing S, Bak RO, Mikkelsen JG, Corydon TJ. Targeted Knockout of the Vegfa Gene in the Retina by Subretinal Injection of RNP Complexes Containing Cas9 Protein and Modified sgRNAs. Mol Ther 2021; 29:191-207. [PMID: 33022212 PMCID: PMC7791085 DOI: 10.1016/j.ymthe.2020.09.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/20/2020] [Accepted: 09/20/2020] [Indexed: 12/21/2022] Open
Abstract
The therapeutic effect of retinal gene therapy using CRISPR/Cas9-mediated genome editing and knockout applications is dependent on efficient and safe delivery of gene-modifying tool kits. Recently, transient administration of single guide RNAs (sgRNAs) and SpCas9 proteins delivered as ribonucleoproteins (RNPs) has provided potent gene knockout in vitro. To improve efficacy of CRISPR-based gene therapy, we delivered RNPs containing SpCas9 protein complexed to chemically modified sgRNAs (msgRNAs). In K562 cells, msgRNAs significantly increased the insertion/deletion (indel) frequency (25%) compared with unmodified counterparts leading to robust knockout of the VEGFA gene encoding vascular endothelial growth factor A (96% indels). Likewise, in HEK293 cells, lipoplexes containing varying amounts of RNP and EGFP mRNA showed efficient VEGFA knockout (43% indels) and strong EGFP expression, indicative of efficacious functional knockout using small amounts of RNP. In mice, subretinal injections of equivalent lipoplexes yielded 6% indels in Vegfa of isolated EGFP-positive RPE cells. However, signs of toxicity following delivery of lipoplexes containing high amounts of RNP were observed. Although the mechanism resulting in the varying efficacy remains to be elucidated, our data suggest that a single subretinal injection of RNPs carrying msgRNAs and SpCas9 induces targeted retinal indel formation, thus providing a clinically relevant strategy relying on nonviral delivery of short-lived nuclease activity.
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Affiliation(s)
| | - Anne Louise Askou
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Sidsel Alsing
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark; Aarhus Institute of Advanced Studies (AIAS), Aarhus University, 8000 Aarhus C, Denmark
| | | | - Thomas J Corydon
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark; Department of Ophthalmology, Aarhus University Hospital, 8200 Aarhus N, Denmark.
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Yamagata M, Yan W, Sanes JR. A cell atlas of the chick retina based on single-cell transcriptomics. eLife 2021; 10:e63907. [PMID: 33393903 PMCID: PMC7837701 DOI: 10.7554/elife.63907] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/01/2021] [Indexed: 12/14/2022] Open
Abstract
Retinal structure and function have been studied in many vertebrate orders, but molecular characterization has been largely confined to mammals. We used single-cell RNA sequencing (scRNA-seq) to generate a cell atlas of the chick retina. We identified 136 cell types plus 14 positional or developmental intermediates distributed among the six classes conserved across vertebrates - photoreceptor, horizontal, bipolar, amacrine, retinal ganglion, and glial cells. To assess morphology of molecularly defined types, we adapted a method for CRISPR-based integration of reporters into selectively expressed genes. For Müller glia, we found that transcriptionally distinct cells were regionally localized along the anterior-posterior, dorsal-ventral, and central-peripheral retinal axes. We also identified immature photoreceptor, horizontal cell, and oligodendrocyte types that persist into late embryonic stages. Finally, we analyzed relationships among chick, mouse, and primate retinal cell classes and types. Our results provide a foundation for anatomical, physiological, evolutionary, and developmental studies of the avian visual system.
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Affiliation(s)
- Masahito Yamagata
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Wenjun Yan
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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Song X, Liu C, Wang N, Huang H, He S, Gong C, Wei Y. Delivery of CRISPR/Cas systems for cancer gene therapy and immunotherapy. Adv Drug Deliv Rev 2021; 168:158-180. [PMID: 32360576 DOI: 10.1016/j.addr.2020.04.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/19/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
The clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) systems are efficient and versatile gene editing tools, which offer enormous potential to treat cancer by editing genome, transcriptome or epigenome of tumor cells and/or immune cells. A large body of works have been done with CRISPR/Cas systems for genetic modification, and 16 clinical trials were conducted to treat cancer by ex vivo or in vivo gene editing approaches. Now, promising preclinical works have begun using CRISPR/Cas systems in vivo. However, efficient and safe delivery of CRISPR/Cas systems in vivo is still a critical challenge for their clinical applications. This article summarizes delivery of CRISPR/Cas systems by physical methods, viral vectors and non-viral vectors for cancer gene therapy and immunotherapy. The prospects for the development of physical methods, viral vectors and non-viral vectors for delivery of CRISPR/Cas systems are reviewed, and promising advances in cancer treatment using CRISPR/Cas systems are discussed.
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Affiliation(s)
- Xiangrong Song
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Chao Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Ning Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Hai Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Siyan He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Changyang Gong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China.
| | - Yuquan Wei
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China.
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Mashel TV, Tarakanchikova YV, Muslimov AR, Zyuzin MV, Timin AS, Lepik KV, Fehse B. Overcoming the delivery problem for therapeutic genome editing: Current status and perspective of non-viral methods. Biomaterials 2020; 258:120282. [DOI: 10.1016/j.biomaterials.2020.120282] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/22/2020] [Accepted: 08/01/2020] [Indexed: 12/11/2022]
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Mori Y, Yoshida Y, Satoh A, Moriya H. Development of an experimental method of systematically estimating protein expression limits in HEK293 cells. Sci Rep 2020; 10:4798. [PMID: 32179769 PMCID: PMC7075890 DOI: 10.1038/s41598-020-61646-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/28/2020] [Indexed: 11/25/2022] Open
Abstract
Protein overexpression sometimes causes cellular defects, although the underlying mechanism is still unknown. A protein's expression limit, which triggers cellular defects, is a useful indication of the underlying mechanism. In this study, we developed an experimental method of estimating the expression limits of target proteins in the human embryonic kidney cell line HEK293 by measuring the proteins' expression levels in cells that survived after the high-copy introduction of plasmid DNA by which the proteins were expressed under a strong cytomegalovirus promoter. The expression limits of nonfluorescent target proteins were indirectly estimated by measuring the levels of green fluorescent protein (GFP) connected to the target proteins with the self-cleaving sequence P2A. The expression limit of a model GFP was ~5.0% of the total protein, and sustained GFP overexpression caused cell death. The expression limits of GFPs with mitochondria-targeting signals and endoplasmic reticulum localization signals were 1.6% and 0.38%, respectively. The expression limits of four proteins involved in vesicular trafficking were far lower compared to a red fluorescent protein. The protein expression limit estimation method developed will be valuable for defining toxic proteins and consequences of protein overexpression.
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Affiliation(s)
- Yoshihiro Mori
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Yuki Yoshida
- Sony Computer Science Laboratories, Tokyo, Japan
| | - Ayano Satoh
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
| | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan.
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
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