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Ju DU, Park D, Kim IH, Kim S, Yoo HM. Development of Human Rhinovirus RNA Reference Material Using Digital PCR. Genes (Basel) 2023; 14:2210. [PMID: 38137032 PMCID: PMC10742479 DOI: 10.3390/genes14122210] [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: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The human rhinovirus (RV) is a positive-stranded RNA virus that causes respiratory tract diseases affecting both the upper and lower halves of the respiratory system. RV enhances its replication by concentrating RNA synthesis within a modified host membrane in an intracellular compartment. RV infections often occur alongside infections caused by other respiratory viruses, and the RV virus may remain asymptomatic for extended periods. Alongside qualitative detection, it is essential to accurately quantify RV RNA from clinical samples to explore the relationships between RV viral load, infections caused by the virus, and the resulting symptoms observed in patients. A reference material (RM) is required for quality evaluation, the performance evaluation of molecular diagnostic products, and evaluation of antiviral agents in the laboratory. The preparation process for the RM involves creating an RV RNA mixture by combining RV viral RNA with RNA storage solution and matrix. The resulting RV RNA mixture is scaled up to a volume of 25 mL, then dispensed at 100 µL per vial and stored at -80 °C. The process of measuring the stability and homogeneity of RV RMs was conducted by employing reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Digital PCR is useful for the analysis of standards and can help to improve measurement compatibility: it represents the equivalence of a series of outcomes for reference materials and samples being analyzed when a few measurement procedures are employed, enabling objective comparisons between quantitative findings obtained through various experiments. The number of copies value represents a measured result of approximately 1.6 × 105 copies/μL. The RM has about an 11% bottle-to-bottle homogeneity and shows stable results for 1 week at temperatures of 4 °C and -20 °C and for 12 months at a temperature of -80 °C. The developed RM can enhance the dependability of RV molecular tests by providing a precise reference value for the absolute copy number of a viral target gene. Additionally, it can serve as a reference for diverse studies.
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Affiliation(s)
- Dong U Ju
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Dongju Park
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Il-Hwan Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Seil Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
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Qu S, Huang C, Zhu T, Wang K, Zhang H, Wang L, Xu R, Zheng H, Yuan X, Liu G, Zhu R, Qu J, Yi G, Qi S. OLFML3, as a potential predictor of prognosis and therapeutic target for glioma, is closely related to immune cell infiltration. VIEW 2023. [DOI: 10.1002/viw.20220052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Affiliation(s)
- Shanqiang Qu
- Department of Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
- The Laboratory for Precision Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Chengying Huang
- Department of Obstetrics and Gynecology Baiyun Branch, Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Taichen Zhu
- The First Clinical Medical College of Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Kaicheng Wang
- The First Clinical Medical College of Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Huayang Zhang
- Department of Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
- The Laboratory for Precision Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Luyao Wang
- The First Clinical Medical College of Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Rongyang Xu
- The First Clinical Medical College of Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Haojie Zheng
- Department of Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
- The Laboratory for Precision Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Xi Yuan
- Department of Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
- The Laboratory for Precision Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Guangjie Liu
- Department of Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
- The Laboratory for Precision Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Rongzhang Zhu
- The First Clinical Medical College of Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Jiayi Qu
- Department of Plant Sciences University of California Davis Davis California USA
| | - Guozhong Yi
- Department of Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
- Nanfang Glioma Center Guangzhou Guangdong People's Republic of China
- Institute of Brain disease Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Songtao Qi
- Department of Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
- Nanfang Glioma Center Guangzhou Guangdong People's Republic of China
- Institute of Brain disease Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
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Zimmerman O, Holmes AC, Kafai NM, Adams LJ, Diamond MS. Entry receptors - the gateway to alphavirus infection. J Clin Invest 2023; 133:e165307. [PMID: 36647825 PMCID: PMC9843064 DOI: 10.1172/jci165307] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Alphaviruses are enveloped, insect-transmitted, positive-sense RNA viruses that infect humans and other animals and cause a range of clinical manifestations, including arthritis, musculoskeletal disease, meningitis, encephalitis, and death. Over the past four years, aided by CRISPR/Cas9-based genetic screening approaches, intensive research efforts have focused on identifying entry receptors for alphaviruses to better understand the basis for cellular and species tropism. Herein, we review approaches to alphavirus receptor identification and how these were used for discovery. The identification of new receptors advances our understanding of viral pathogenesis, tropism, and evolution and is expected to contribute to the development of novel strategies for prevention and treatment of alphavirus infection.
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Affiliation(s)
| | | | | | | | - Michael S. Diamond
- Department of Medicine
- Department of Pathology and Immunology
- Department of Molecular Microbiology, and
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, Missouri, USA
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Mei H, Gu Q, Wang W, Meng Y, Jiang L, Liu J. CRISPR-surfaceome: An online tool for designing highly efficient sgRNAs targeting cell surface proteins. Comput Struct Biotechnol J 2022; 20:3833-3838. [PMID: 35891797 PMCID: PMC9307495 DOI: 10.1016/j.csbj.2022.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/17/2022] Open
Abstract
CRISPR-based genome-editing tools have emerged as an efficient tool for functional genomics studies. Online tools and databases have been developed to facilitate the design and selection of CRISPR single guide RNA (sgRNA) for gene modifications. However, to the best of our knowledge, none of these tools or database are designated to cell surface proteins. In a previous study, we described the development and application of surfaceome CRISPR libraries targeting to cell surface proteins on human cells. Here, we present the design and construction of an online tool and database (https://crispr-surfaceome.siais.shanghaitech.edu.cn/home), named CRISPR-Surfaceome, for the design of highly efficient sgRNA targeting to the surface proteins on human cells. To show case and validate the efficiencies of sgRNAs designed by this online tool, we chose ICAM-1 gene for knockout studies and found that all the 10 designed ICAM-1 sgRNAs could efficiently generate knockout cells, with more than 80% gene disruption rates. These ICAM-1 knockout cells were found to be resistant to the infection of rhinovirus (RV), which utilizes ICAM-1 as the receptor. Therefore, CRISPR-Surfaceome can serve the research community for the functional genomics studies on cell surface proteins, such as identification of pathogen receptors and discovery of drug targets.
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Affiliation(s)
- Hong Mei
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Qian Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yu Meng
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lichun Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- Corresponding authors at: Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 201210, China
- Corresponding authors at: Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
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Hirano J, Murakami K, Hayashi T. CRISPR-Cas9-Based Technology for Studying Enteric Virus Infection. Front Genome Ed 2022; 4:888878. [PMID: 35755450 PMCID: PMC9213734 DOI: 10.3389/fgeed.2022.888878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Enteric viruses, including numerous viruses that initiate infection in enteric canal, are recognized as important agents that cause wide spectrum of illnesses in humans, depending on the virus type. They are mainly transmitted by fecal-oral route with several vector such as contaminated water or food. Infections by enteric viruses, such as noroviruses and rotaviruses, frequently cause widespread acute gastroenteritis, leading to significant health and economic burdens and therefore remain a public health concern. Like other viruses, enteric viruses ''hijack'' certain host factors (so called pro-viral factors) for replication in infected cells, while escaping the host defense system by antagonizing host anti-viral factors. Identification(s) of these factors is needed to better understand the molecular mechanisms underlying viral replication and pathogenicity, which will aid the development of efficient antiviral strategies. Recently, the advancement of genome-editing technology, especially the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 system, has precipitated numerous breakthroughs across the field of virology, including enteric virus research. For instance, unbiased genome-wide screening employing the CRISPR-Cas9 system has successfully identified a number of previously unrecognized host factors associated with infection by clinically relevant enteric viruses. In this review, we briefly introduce the common techniques of the CRISPR-Cas9 system applied to virological studies and discuss the major findings using this system for studying enteric virus infection.
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Affiliation(s)
- Junki Hirano
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kosuke Murakami
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Hayashi
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
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Mei H, Zha Z, Wang W, Xie Y, Huang Y, Li W, Wei D, Zhang X, Qu J, Liu J. Correction: Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist. Genome Biol 2021; 22:314. [PMID: 34782001 PMCID: PMC8591863 DOI: 10.1186/s13059-021-02534-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Hong Mei
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Zhao Zha
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Yusang Xie
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital and Institutes of Respiratory Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yuege Huang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenping Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong Wei
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Xinxin Zhang
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jieming Qu
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital and Institutes of Respiratory Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China. .,Shanghai Clinical Research and Trial Center, Shanghai, 201210, People's Republic of China. .,State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 510182, Guangdong Province, China. .,Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China. .,Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China.
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Mei H, Zha Z, Wang W, Xie Y, Huang Y, Li W, Wei D, Zhang X, Qu J, Liu J. Surfaceome CRISPR screen identifies OLFML3 as a rhinovirus-inducible IFN antagonist. Genome Biol 2021; 22:297. [PMID: 34686207 PMCID: PMC8532573 DOI: 10.1186/s13059-021-02513-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
Background Rhinoviruses (RVs) cause more than half of common colds and, in some cases, more severe diseases. Functional genomics analyses of RVs using siRNA or genome-wide CRISPR screen uncovered a limited set of host factors, few of which have proven clinical relevance. Results Herein, we systematically compare genome-wide CRISPR screen and surface protein-focused CRISPR screen, referred to as surfaceome CRISPR screen, for their efficiencies in identifying RV host factors. We find that surfaceome screen outperforms the genome-wide screen in the success rate of hit identification. Importantly, using the surfaceome screen, we identify olfactomedin-like 3 (OLFML3) as a novel host factor of RV serotypes A and B, including a clinical isolate. We find that OLFML3 is a RV-inducible suppressor of the innate immune response and that OLFML3 antagonizes type I interferon (IFN) signaling in a SOCS3-dependent manner. Conclusion Our study suggests that RV-induced OLFML3 expression is an important mechanism for RV to hijack the immune system and underscores surfaceome CRISPR screen in identifying viral host factors. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02513-w.
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Affiliation(s)
- Hong Mei
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Zhao Zha
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China
| | - Yusang Xie
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital and Institutes of Respiratory Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yuege Huang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China.,University of Chinese Academy of Science, 100049, Beijing, People's Republic of China
| | - Wenping Li
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China.,University of Chinese Academy of Science, 100049, Beijing, People's Republic of China
| | - Dong Wei
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Xinxin Zhang
- Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jieming Qu
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital and Institutes of Respiratory Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, People's Republic of China. .,Shanghai Clinical Research and Trial Center, 201210, Shanghai, People's Republic of China. .,State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, 510182, Guangdong Province, China. .,Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, People's Republic of China. .,Guangzhou Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou Interntional Bio Island, Guangdong Province, 510005, Guangzhou, China.
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