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Chen YL, Reddy S, Suzuki A. Reversible and effective cell cycle synchronization method for studying stage-specific investigations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.02.610832. [PMID: 39282459 PMCID: PMC11398389 DOI: 10.1101/2024.09.02.610832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
The cell cycle is a crucial process for cell proliferation, differentiation, and development. Numerous genes and proteins play pivotal roles at specific cell cycle stages to regulate these events precisely. Studying the stage-specific functions of the cell cycle requires accumulating cell populations at the desired cell cycle stage. Cell synchronization, achieved through the use of cell cycle kinase and protein inhibitors, is often employed for this purpose. However, suboptimal concentrations of these inhibitors can result in reduced efficiency, irreversibility, and undesirable cell cycle defects. In this study, we have optimized effective and reversible techniques to synchronize the cell cycle at each stage in human RPE1 cells, utilizing both fixed high-precision cell cycle identification methods and high-temporal live-cell imaging. These reproducible synchronization methods are invaluable for investigating the regulatory mechanisms specific to each cell cycle stage.
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Qi G, Zou H, Peng X, He S, Zhang Q, Ye W, Jiang Y, Wang W, Ren G, Qu X. Metabolic Footprinting-Based DNA-AuNP Encoders for Extracellular Metabolic Response Profiling. Anal Chem 2023; 95:8088-8096. [PMID: 37155931 DOI: 10.1021/acs.analchem.3c01109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Metabolic footprinting as a convenient and non-invasive cell metabolomics strategy relies on monitoring the whole extracellular metabolic process. It covers nutrient consumption and metabolite secretion of in vitro cell culture, which is hindered by low universality owing to pre-treatment of the cell medium and special equipment. Here, we report the design and a variety of applicability, for quantifying extracellular metabolism, of fluorescently labeled single-stranded DNA (ssDNA)-AuNP encoders, whose multi-modal signal response is triggered by extracellular metabolites. We constructed metabolic response profiling of cells by detecting extracellular metabolites in different tumor cells and drug-induced extracellular metabolites. We further assessed the extracellular metabolism differences using a machine learning algorithm. This metabolic response profiling based on the DNA-AuNP encoder strategy is a powerful complement to metabolic footprinting, which significantly applies potential non-invasive identification of tumor cell heterogeneity.
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Affiliation(s)
- Guangpei Qi
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Haixia Zou
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | | | - Shiliang He
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen 518118, China
| | - Qiqi Zhang
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Wei Ye
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Yizhou Jiang
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Wentao Wang
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
| | - Guangli Ren
- Department of Pediatrics, General Hospital of Southern Theater Command of PLA, Guangzhou 510010, China
| | - Xiangmeng Qu
- Key Laboratory of Sensing Technology and Biomedical Instruments of Guangdong Province and School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, China
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Common Markers and Small Molecule Inhibitors in Golgi Studies. Methods Mol Biol 2022; 2557:453-493. [PMID: 36512231 PMCID: PMC10178357 DOI: 10.1007/978-1-0716-2639-9_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this chapter, we provide a detailed guide for the application of commonly used small molecules to study Golgi structure and function in vitro. Furthermore, we have curated a concise, validated list of endomembrane markers typically used in downstream assays to examine the consequent effect on the Golgi via microscopy and western blot after drug treatment. This chapter will be useful for researchers beginning their foray into the field of intracellular trafficking and Golgi biology.
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Zhu Q, Su M, Wei S, Shi D, Li L, Wang J, Sun H, Wang M, Li C, Guo D, Sun D. Up-regulated 60S ribosomal protein L18 in PEDV N protein-induced S-phase arrested host cells promotes viral replication. Virus Res 2022; 321:198916. [PMID: 36084747 PMCID: PMC9446558 DOI: 10.1016/j.virusres.2022.198916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 12/24/2022]
Abstract
Coronavirus subverts the host cell cycle to create a favorable cellular environment that enhances viral replication in host cells. Previous studies have revealed that nucleocapsid (N) protein of the coronavirus porcine epidemic diarrhea virus (PEDV) interacts with p53 to induce cell cycle arrest in S-phase and promotes viral replication. However, the mechanism by which viral replication is increased in the PEDV N protein-induced S-phase arrested cells remains unknown. In the current study, the protein expression profiles of PEDV N protein-induced S-phase arrested Vero E6 cells and thymidine-induced S-phase arrested Vero E6 cells were characterized by tandem mass tag-labeled quantitative proteomic technology. The effect of differentially expressed proteins (DEPs) on PEDV replication was investigated. The results indicated that a total of 5709 proteins, including 20,560 peptides, were identified, of which 58 and 26 DEPs were identified in the PEDV N group and thymidine group, respectively (P < 0.05; ratio ≥ 1.2 or ≤ 0.8). The unique DEPs identified in the PEDV N group were mainly involved in DNA replication, transcription, and protein synthesis, of which 60S ribosomal protein L18 (RPL18) exhibited significantly up-regulated expression in the PEDV N protein-induced S-phase arrested Vero E6/IPEC-J2 cells and PEDV-infected IPEC-J2 cells (P < 0.05). Further studies revealed that the RPL18 protein could significantly enhance PEDV replication (P < 0.05). Our findings reveal a mechanism regarding increased viral replication when the PEDV N protein-induced host cells are in S-phase arrest. These data also provide evidence that PEDV maintains its own replication by utilizing protein synthesis-associated ribosomal proteins.
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Affiliation(s)
- Qinghe Zhu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Mingjun Su
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China,Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics and Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology and College of Veterinary Medicine of Zhejiang A&F University, 666 Wusu Street, Lin'an District, Hangzhou, Zhejiang 311300, China
| | - Shan Wei
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Da Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Lu Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Jun Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Haibo Sun
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Meijiao Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Chunqiu Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Donghua Guo
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China
| | - Dongbo Sun
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, No. 5 Xinfeng Road, Sartu District, Daqing 163319, China,Corresponding author
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Jiao F, Xu J, Zhao Y, Ye C, Sun Q, Liu C, Huo B. Synergistic effects of fluid shear stress and adhesion morphology on the apoptosis and osteogenesis of mesenchymal stem cells. J Biomed Mater Res A 2022; 110:1636-1644. [DOI: 10.1002/jbm.a.37413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/03/2022] [Accepted: 05/13/2022] [Indexed: 12/25/2022]
Affiliation(s)
- Fei Jiao
- Biomechanics Lab, Department of Mechanics School of Aerospace Engineering, Beijing Institute of Technology Beijing People's Republic of China
| | - Jiayi Xu
- Biomechanics Lab, Department of Mechanics School of Aerospace Engineering, Beijing Institute of Technology Beijing People's Republic of China
| | - Yang Zhao
- Biomechanics Lab, Department of Mechanics School of Aerospace Engineering, Beijing Institute of Technology Beijing People's Republic of China
| | - Chongyang Ye
- Biomechanics Lab, Department of Mechanics School of Aerospace Engineering, Beijing Institute of Technology Beijing People's Republic of China
| | - Qing Sun
- Biomechanics Lab, Department of Mechanics School of Aerospace Engineering, Beijing Institute of Technology Beijing People's Republic of China
| | - Chenglin Liu
- Sports Artificial Intelligence Institute Capital University of Physical Education and Sports Beijing People's Republic of China
| | - Bo Huo
- Biomechanics Lab, Department of Mechanics School of Aerospace Engineering, Beijing Institute of Technology Beijing People's Republic of China
- Sports Artificial Intelligence Institute Capital University of Physical Education and Sports Beijing People's Republic of China
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Hadfield JD, Sokhi S, Chan GK. Cell Synchronization Techniques for Studying Mitosis. Methods Mol Biol 2022; 2579:73-86. [PMID: 36045199 DOI: 10.1007/978-1-0716-2736-5_6] [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] [Indexed: 06/15/2023]
Abstract
Cell synchronization allows the examination of cell cycle progression. Nocodazole and other microtubule poisons have been used extensively to interfere with microtubule function and arrest cells in mitosis. Since microtubules are important for many cellular functions, alternative cell cycle synchronization techniques independent of microtubule inhibition are also used for synchronizing cells in mitosis. Here we describe using nocodazole, STLC, and combining thymidine block with MG132 to synchronize cells in mitosis. These inhibitors are reversible and mitotic cells can be released into the G1 phase synchronously. These techniques can be applied to both Western blot and timelapse imaging to study mitotic progression.
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Affiliation(s)
- Joanne D Hadfield
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
- Experimental Oncology, Cross Cancer Institute, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Sargun Sokhi
- Department of Oncology, University of Alberta, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Gordon K Chan
- Department of Oncology, University of Alberta, Edmonton, AB, Canada.
- Experimental Oncology, Cross Cancer Institute, Edmonton, AB, Canada.
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada.
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