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Kim C, Jeong YK, Yu J, Shin HJ, Ku KB, Cha HJ, Han JH, Hong SA, Kim BT, Kim SJ, Woo JS, Bae S. Efficient Human Cell Coexpression System and Its Application to the Production of Multiple Coronavirus Antigens. Adv Biol (Weinh) 2021; 5:e2000154. [PMID: 33852178 DOI: 10.1002/adbi.202000154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 01/08/2021] [Indexed: 01/14/2023]
Abstract
Coproduction of multiple proteins at high levels in a single human cell line would be extremely useful for basic research and medical applications. Here, a novel strategy for the stable expression of multiple proteins by integrating the genes into defined transcriptional hotspots in the human genome is presented. As a proof-of-concept, it is shown that EYFP is expressed at similar levels from hotspots and that the EYFP expression increases proportionally with the copy number. It is confirmed that three different fluorescent proteins, encoded by genes integrated at different loci, can be coexpressed at high levels. Further, a stable cell line is generated, producing antigens from different human coronaviruses: MERS-CoV and HCoV-OC43. Antibodies raised against these antigens, which contain human N-glycosylation, show neutralizing activities against both viruses, suggesting that the coexpression system provides a quick and predictable way to produce multiple coronavirus antigens, such as the recent 2019 novel human coronavirus.
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Affiliation(s)
- Chonsaeng Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, South Korea
| | - You Kyeong Jeong
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea.,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Jihyeon Yu
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea.,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Hye Jin Shin
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, South Korea
| | - Keun Bon Ku
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, South Korea
| | - Hyung Jin Cha
- Department of Life Sciences, Korea University, Seoul, 02841, South Korea
| | - Jun Hee Han
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea.,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Sung-Ah Hong
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea.,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Bum-Tae Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, South Korea
| | - Seong-Jun Kim
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, South Korea
| | - Jae-Sung Woo
- Department of Life Sciences, Korea University, Seoul, 02841, South Korea
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea.,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea
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2
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Jeong YK, Yu J, Bae S. Construction of non-canonical PAM-targeting adenosine base editors by restriction enzyme-free DNA cloning using CRISPR-Cas9. Sci Rep 2019; 9:4939. [PMID: 30894632 PMCID: PMC6426851 DOI: 10.1038/s41598-019-41356-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 03/06/2019] [Indexed: 02/06/2023] Open
Abstract
Molecular cloning is an essential technique in molecular biology and biochemistry, but it is frequently laborious when adequate restriction enzyme recognition sites are absent. Cas9 endonucleases can induce site-specific DNA double-strand breaks at sites homologous to their guide RNAs, rendering an alternative to restriction enzymes. Here, by combining DNA cleavage via a Cas9 endonuclease and DNA ligation via Gibson assembly, we demonstrate a precise and practical DNA cloning method for replacing part of a backbone plasmid. We first replaced a resistance marker gene as a proof of concept and next generated DNA plasmids that encode engineered Cas9 variants (VQR, VRER and SpCas9-NG), which target non-canonical NGA, NGCG and NG protospacer-adjacent motif (PAM) sequences, fused with adenosine deaminases for adenine base editing (named VQR-ABE, VRER-ABE and NG-ABE, respectively). Ultimately, we confirmed that the re-constructed plasmids can successfully convert adenosine to guanine at endogenous target sites containing the non-canonical NGA, NGCG and NG PAMs, expanding the targetable range of the adenine base editing.
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Affiliation(s)
- You Kyeong Jeong
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea
| | - Jihyeon Yu
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul, 04763, South Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, 04763, South Korea.
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3
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Lee SH, Yu J, Hwang GH, Kim S, Kim HS, Ye S, Kim K, Park J, Park DY, Cho YK, Kim JS, Bae S. CUT-PCR: CRISPR-mediated, ultrasensitive detection of target DNA using PCR. Oncogene 2017; 36:6823-6829. [PMID: 28846115 PMCID: PMC5736524 DOI: 10.1038/onc.2017.281] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/29/2017] [Indexed: 12/19/2022]
Abstract
Circulating tumor DNA (ctDNA) has emerged as a tumor-specific biomarker for the early detection of various cancers. To date, several techniques have been devised to enrich the extremely small amounts of ctDNA present in plasma, but they are still insufficient for cancer diagnosis, especially at the early stage. Here, we developed a novel method, CUT (CRISPR-mediated, Ultrasensitive detection of Target DNA)-PCR, which uses CRISPR endonucleases to enrich and detect the extremely small amounts of tumor DNA fragments among the much more abundant wild-type DNA fragments by specifically eliminating the wild-type sequences. We computed that by using various orthologonal CRISPR endonucleases such as SpCas9 and FnCpf1, the CUT-PCR method would be applicable to 80% of known cancer-linked substitution mutations registered in the COSMIC database. We further verified that CUT-PCR together with targeted deep sequencing enables detection of a broad range of oncogenes with high sensitivity (<0.01%) and accuracy, which is superior to conventional targeted deep sequencing. In the end, we successfully applied CUT-PCR to detect sequences with oncogenic mutations in the ctDNA of colorectal cancer patients’ blood, suggesting that our technique could be adopted for diagnosing various types of cancer at early stages.
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Affiliation(s)
- S H Lee
- Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea
| | - J Yu
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - G-H Hwang
- Department of Chemistry, Hanyang University, Seoul, South Korea
| | - S Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea
| | - H S Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea.,Department of Chemistry, Seoul National University, Seoul, South Korea
| | - S Ye
- Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea
| | - K Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea
| | - J Park
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, South Korea
| | - D Y Park
- Department of Pathology, Pusan National University School of Medicine and Biomedical Research Institute, Pusan National University Hospital, Busan, South Korea
| | - Y-K Cho
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan, South Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - J-S Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul, South Korea.,Department of Chemistry, Seoul National University, Seoul, South Korea
| | - S Bae
- Department of Chemistry, Hanyang University, Seoul, South Korea.,Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea
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4
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Shen S, Loh TJ, Shen H, Zheng X, Shen H. CRISPR as a strong gene editing tool. BMB Rep 2017; 50:20-24. [PMID: 27616359 PMCID: PMC5319660 DOI: 10.5483/bmbrep.2017.50.1.128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/16/2016] [Accepted: 09/07/2016] [Indexed: 11/20/2022] Open
Abstract
Clustered regularly-interspaced short palindromic repeats (CRISPR) is a new and effective genetic editing tool. CRISPR was initially found in bacteria to protect it from virus invasions. In the first step, specific DNA strands of virus are identified by guide RNA that is composed of crRNA and tracrRNA. Then RNAse III is required for producing crRNA from pre-crRNA. In The second step, a crRNA:tracrRNA:Cas9 complex guides RNase III to cleave target DNA. After cleavage of DNA by CRISPR-Cas9, DNA can be fixed by Non- Homologous End Joining (NHEJ) and Homology Directed Repair (HDR). Whereas NHEJ is simple and random, HDR is much more complex and accurate. Gene editing by CRISPR is able to be applied to various biological field such as agriculture and treating genetic diseases in human. [BMB Reports 2017; 50(1): 20-24].
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Affiliation(s)
- Shengfu Shen
- Willston Northampton School, Easthampton, MA 01027,
USA
| | - Tiing Jen Loh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Hongling Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005,
Korea
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