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Hasan MN, Hyodo T, Biswas M, Rahman ML, Mihara Y, Karnan S, Ota A, Tsuzuki S, Hosokawa Y, Konishi H. Flow cytometry-based quantification of genome editing efficiency in human cell lines using the L1CAM gene. PLoS One 2023; 18:e0294146. [PMID: 37943774 PMCID: PMC10635454 DOI: 10.1371/journal.pone.0294146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
CRISPR/Cas9 is a powerful genome editing system that has remarkably facilitated gene knockout and targeted knock-in. To accelerate the practical use of CRISPR/Cas9, however, it remains crucial to improve the efficiency, precision, and specificity of genome editing, particularly targeted knock-in, achieved with this system. To improve genome editing efficiency, researchers should first have a molecular assay that allows sensitive monitoring of genome editing events with simple procedures. In the current study, we demonstrate that genome editing events occurring in L1CAM, an X-chromosome gene encoding a cell surface protein, can be readily monitored using flow cytometry (FCM) in multiple human cell lines including neuroblastoma cell lines. The abrogation of L1CAM was efficiently achieved using Cas9 nucleases which disrupt exons encoding the L1CAM extracellular domain, and was easily detected by FCM using anti-L1CAM antibodies. Notably, L1CAM-abrogated cells could be quantified by FCM in four days after transfection with a Cas9 nuclease, which is much faster than an established assay based on the PIGA gene. In addition, the L1CAM-based assay allowed us to measure the efficiency of targeted knock-in (correction of L1CAM mutations) accomplished through different strategies, including a Cas9 nuclease-mediated method, tandem paired nicking, and prime editing. Our L1CAM-based assay using FCM enables rapid and sensitive quantification of genome editing efficiencies and will thereby help researchers improve genome editing technologies.
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Affiliation(s)
- Muhammad Nazmul Hasan
- Department of Biochemistry, School of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
| | - Toshinori Hyodo
- Department of Biochemistry, School of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
| | - Mrityunjoy Biswas
- Department of Biochemistry, School of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
- Department of Microbiology and Immunology, School of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
| | - Md. Lutfur Rahman
- Department of Biochemistry, School of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
| | - Yuko Mihara
- Department of Biochemistry, School of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
| | - Sivasundaram Karnan
- Department of Biochemistry, School of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
| | - Akinobu Ota
- Department of Biochemistry, School of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
| | - Shinobu Tsuzuki
- Department of Biochemistry, School of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
| | - Yoshitaka Hosokawa
- Department of Biochemistry, School of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
| | - Hiroyuki Konishi
- Department of Biochemistry, School of Medicine, Aichi Medical University, Nagakute, Aichi, Japan
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Ageta H, Tsuchida K. Post-translational modification and protein sorting to small extracellular vesicles including exosomes by ubiquitin and UBLs. Cell Mol Life Sci 2019; 76:4829-4848. [PMID: 31363817 PMCID: PMC11105257 DOI: 10.1007/s00018-019-03246-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/06/2019] [Accepted: 07/23/2019] [Indexed: 02/06/2023]
Abstract
Exosomes, a type of small extracellular vesicles (sEVs), are secreted membrane vesicles that are derived from various cell types, including cancer cells, mesenchymal stem cells, and immune cells via multivesicular bodies (MVBs). These sEVs contain RNAs (mRNA, miRNA, lncRNA, and rRNA), lipids, DNA, proteins, and metabolites, all of which mediate cell-to-cell communication. This communication is known to be implicated in a diverse set of diseases such as cancers and their metastases and degenerative diseases. The molecular mechanisms, by which proteins are modified and sorted to sEVs, are not fully understood. Various cellular processes, including degradation, transcription, DNA repair, cell cycle, signal transduction, and autophagy, are known to be associated with ubiquitin and ubiquitin-like proteins (UBLs). Recent studies have revealed that ubiquitin and UBLs also regulate MVBs and protein sorting to sEVs. Ubiquitin-like 3 (UBL3)/membrane-anchored Ub-fold protein (MUB) acts as a post-translational modification (PTM) factor to regulate efficient protein sorting to sEVs. In this review, we focus on the mechanism of PTM by ubiquitin and UBLs and the pathway of protein sorting into sEVs and discuss the potential biological significance of these processes.
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Affiliation(s)
- Hiroshi Ageta
- Division for Therapies Against Intractable Diseases, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Kunihiro Tsuchida
- Division for Therapies Against Intractable Diseases, Institute for Comprehensive Medical Science, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan.
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