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Lee D, Sangket U. VOE: automated analysis of variant epitopes of SARS-CoV-2 for the development of diagnostic tests or vaccines for COVID-19. PeerJ 2024; 12:e17504. [PMID: 38912043 PMCID: PMC11193398 DOI: 10.7717/peerj.17504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/13/2024] [Indexed: 06/25/2024] Open
Abstract
Background The development of serodiagnostic tests and vaccines for COVID-19 depends on the identification of epitopes from the SARS-CoV-2 genome. An epitope is the specific part of an antigen that is recognized by the immune system and can elicit an immune response. However, when the genetic variants contained in epitopes are used to develop rapid antigen tests (Ag-RDTs) and DNA or RNA vaccines, test sensitivity and vaccine efficacy can be low. Methods Here, we developed a "variant on epitope (VOE)" software, a new Python script for identifying variants located on an epitope. Variant analysis and sensitivity calculation for seven recommended epitopes were processed by VOE. Variants in 1,011 Omicron SRA reads from two variant databases (BCFtools and SARS-CoV-2-Freebayes) were processed by VOE. Results A variant with HIGH or MODERATE impact was found on all epitopes from both variant databases except the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK on the S gene and ORF7a gene. All epitope variants from the BCFtools and SARS-CoV-2 Freebayes variant databases showed about 100% sensitivity except epitopes APGQTGK and DSKVGGNYN on the S gene, which showed respective sensitivities of 28.4866% and 6.8249%, and 87.7349% and 71.1177%. Conclusions Therefore, the epitopes KLNDLCFTNV, RVQPTES, LKPFERD, and ITLCFTLKRK may be useful for the development of an epitope-based peptide vaccine and GGDGKMKD on the N gene may be useful for the development of serodiagnostic tests. Moreover, VOE can also be used to analyze other epitopes, and a new variant database for VOE may be further established when a new variant of SARS-CoV-2 emerges.
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Affiliation(s)
- Danusorn Lee
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | - Unitsa Sangket
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
- Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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Li J, Xiao H, Zhang C, Liu G, Liu X. From virus to immune system: Harnessing membrane-derived vesicles to fight COVID-19 by interacting with biological molecules. Eur J Immunol 2024:e2350916. [PMID: 38778737 DOI: 10.1002/eji.202350916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Emerging and re-emerging viral pandemics have emerged as a major public health concern. Highly pathogenic coronaviruses, which cause severe respiratory disease, threaten human health and socioeconomic development. Great efforts are being devoted to the development of safe and efficacious therapeutic agents and preventive vaccines to combat them. Nevertheless, the highly mutated virus poses a challenge to drug development and vaccine efficacy, and the use of common immunomodulatory agents lacks specificity. Benefiting from the burgeoning intersection of biological engineering and biotechnology, membrane-derived vesicles have shown superior potential as therapeutics due to their biocompatibility, design flexibility, remarkable bionics, and inherent interaction with phagocytes. The interactions between membrane-derived vesicles, viruses, and the immune system have emerged as a new and promising topic. This review provides insight into considerations for developing innovative antiviral strategies and vaccines against SARS-CoV-2. First, membrane-derived vesicles may provide potential biomimetic decoys with a high affinity for viruses to block virus-receptor interactions for early interruption of infection. Second, membrane-derived vesicles could help achieve a balanced interplay between the virus and the host's innate immunity. Finally, membrane-derived vesicles have revealed numerous possibilities for their employment as vaccines.
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Affiliation(s)
- Jiayuan Li
- State Key Laboratory of Infectious Disease Vaccine Development, Xiang An Biomedicine Laboratory & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Haiqing Xiao
- State Key Laboratory of Infectious Disease Vaccine Development, Xiang An Biomedicine Laboratory & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Chang Zhang
- Clinical Center for Biotherapy, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
| | - Gang Liu
- State Key Laboratory of Infectious Disease Vaccine Development, Xiang An Biomedicine Laboratory & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen, China
| | - Xuan Liu
- Clinical Center for Biotherapy, Zhongshan Hospital (Xiamen), Fudan University, Xiamen, China
- Shen Zhen Research Institute of Xiamen University, Xiamen University, Shenzhen, China
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Cummings SE, Delaney SP, St-Denis Bissonnette F, Stalker A, Muradia G, Mehic J, Graber TE, Alain T, Lavoie JR. SARS-CoV-2 antigen-carrying extracellular vesicles activate T cell responses in a human immunogenicity model. iScience 2024; 27:108708. [PMID: 38226155 PMCID: PMC10788222 DOI: 10.1016/j.isci.2023.108708] [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: 01/13/2023] [Revised: 10/16/2023] [Accepted: 12/08/2023] [Indexed: 01/17/2024] Open
Abstract
Extracellular vesicles (EVs) are entering the clinical arena as novel biologics for infectious diseases, potentially serving as the immunogenic components of next generation vaccines. However, relevant human assays to evaluate the immunogenicity of EVs carrying viral antigens are lacking, contributing to challenges in translating rodent studies to human clinical trials. Here, we engineered EVs to carry SARS-CoV-2 Spike to evaluate the immunogenicity of antigen-carrying EVs using human peripheral blood mononuclear cells (PBMCs). Delivery of Spike EVs to PBMCs resulted in specific immune cell activation as assessed through T cell activation marker expression. Further, Spike EVs were taken up largely by antigen-presenting cells (monocytes, dendritic cells and B cells). Taken together, this human PBMC-based system models physiologically relevant pathways of antigen delivery, uptake and presentation. In summary, the current study highlights the suitability of using human PBMCs for evaluating the immunogenicity of EVs engineered to carry antigens for infectious disease therapeutics.
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Affiliation(s)
- Sarah E. Cummings
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Sean P. Delaney
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Frederic St-Denis Bissonnette
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Andrew Stalker
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
| | - Gauri Muradia
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
| | - Jelica Mehic
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
| | - Tyson E. Graber
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, 401 Smyth Road, Ottawa, ON K1H 8L1 Canada
| | - Tommy Alain
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, 401 Smyth Road, Ottawa, ON K1H 8L1 Canada
| | - Jessie R. Lavoie
- Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
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Wang Y, Shen X, Song S, Chen Y, Wang Y, Liao J, Chen N, Zeng L. Mesenchymal stem cell-derived exosomes and skin photoaging: From basic research to practical application. PHOTODERMATOLOGY, PHOTOIMMUNOLOGY & PHOTOMEDICINE 2023; 39:556-566. [PMID: 37605539 DOI: 10.1111/phpp.12910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/25/2023] [Accepted: 08/01/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Skin photoaging is a condition caused by long-term exposure to ultraviolet irradiation, resulting in a variety of changes in the skin, such as capillary dilation, increased or absent pigmentation, dryness, sagging, and wrinkles. Stem cells possess a remarkable antioxidant capacity and the ability to proliferate, differentiate, and migrate, and their main mode of action is through paracrine secretion, with exosomes being the primary form of secretion. Stem cell-derived exosomes contain a variety of growth factors and cytokines and may have great potential to promote skin repair and delay skin ageing. METHODS This review focuses on the mechanisms of UV-induced skin photoaging, the research progress of stem cell exosomes against skin photoaging, emerging application approaches and limitations in the application of exosome therapy. RESULT Exosomes derived from various stem cells have the potential to prevent skin photoaging. CONCLUSION The combination with novel materials may be a key step for their practical application, which could be an important direction for future basic research and practical applications.
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Affiliation(s)
- Yihao Wang
- Center of Burn & Plastic and Wound Healing Surgery, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Xu Shen
- Center of Burn & Plastic and Wound Healing Surgery, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Shenghua Song
- Center of Burn & Plastic and Wound Healing Surgery, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Yan Chen
- Center of Burn & Plastic and Wound Healing Surgery, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Yiping Wang
- Center of Burn & Plastic and Wound Healing Surgery, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Junlin Liao
- Center of Burn & Plastic and Wound Healing Surgery, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Nian Chen
- Center of Burn & Plastic and Wound Healing Surgery, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Li Zeng
- Center of Burn & Plastic and Wound Healing Surgery, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, China
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Su P, Wu Y, Xie F, Zheng Q, Chen L, Liu Z, Meng X, Zhou F, Zhang L. A Review of Extracellular Vesicles in COVID-19 Diagnosis, Treatment, and Prevention. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023:e2206095. [PMID: 37144543 DOI: 10.1002/advs.202206095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/15/2023] [Indexed: 05/06/2023]
Abstract
The 2019 novel coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is ongoing, and has necessitated scientific efforts in disease diagnosis, treatment, and prevention. Interestingly, extracellular vesicles (EVs) have been crucial in these developments. EVs are a collection of various nanovesicles which are delimited by a lipid bilayer. They are enriched in proteins, nucleic acids, lipids, and metabolites, and naturally released from different cells. Their natural material transport properties, inherent long-term recycling ability, excellent biocompatibility, editable targeting, and inheritance of parental cell properties make EVs one of the most promising next-generation drug delivery nanocarriers and active biologics. During the COVID-19 pandemic, many efforts have been made to exploit the payload of natural EVs for the treatment of COVID-19. Furthermore, strategies that use engineered EVs to manufacture vaccines and neutralization traps have produced excellent efficacy in animal experiments and clinical trials. Here, the recent literature on the application of EVs in COVID-19 diagnosis, treatment, damage repair, and prevention is reviewed. And the therapeutic value, application strategies, safety, and biotoxicity in the production and clinical applications of EV agents for COVID-19 treatment, as well as inspiration for using EVs to block and eliminate novel viruses are discussed.
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Affiliation(s)
- Peng Su
- Department of Breast Surgery, Zhejiang Provincial People's Hospital, Hangzhou, 310014, P. R. China
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, P. R. China
| | - Yuchen Wu
- Department of Clinical Medicine, The First School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, P. R. China
| | - Feng Xie
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, P. R. China
| | - Qinghui Zheng
- Department of Breast Surgery, Zhejiang Provincial People's Hospital, Hangzhou, 310014, P. R. China
| | - Long Chen
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang, Jiangsu, 215600, China
| | - Zhuang Liu
- Institute of Functional Nano and Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Xuli Meng
- Department of Breast Surgery, Zhejiang Provincial People's Hospital, Hangzhou, 310014, P. R. China
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, P. R. China
| | - Long Zhang
- Department of Breast Surgery, Zhejiang Provincial People's Hospital, Hangzhou, 310014, P. R. China
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, P. R. China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, P. R. China
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Chen X, Li H, Song H, Wang J, Zhang X, Han P, Wang X. Meet changes with constancy: Defence, antagonism, recovery, and immunity roles of extracellular vesicles in confronting SARS-CoV-2. J Extracell Vesicles 2022; 11:e12288. [PMID: 36450704 PMCID: PMC9712136 DOI: 10.1002/jev2.12288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has wrought havoc on the world economy and people's daily lives. The inability to comprehensively control COVID-19 is due to the difficulty of early and timely diagnosis, the lack of effective therapeutic drugs, and the limited effectiveness of vaccines. The body contains billions of extracellular vesicles (EVs), which have shown remarkable potential in disease diagnosis, drug development, and vaccine carriers. Recently, increasing evidence has indicated that EVs may participate or assist the body in defence, antagonism, recovery and acquired immunity against SARS-CoV-2. On the one hand, intercepting and decrypting the general intelligence carried in circulating EVs from COVID-19 patients will provide an important hint for diagnosis and treatment; on the other hand, engineered EVs modified by gene editing in the laboratory will amplify the effectiveness of inhibiting infection, replication and destruction of ever-mutating SARS-CoV-2, facilitating tissue repair and making a better vaccine. To comprehensively understand the interaction between EVs and SARS-CoV-2, providing new insights to overcome some difficulties in the diagnosis, prevention and treatment of COVID-19, we conducted a rounded review in this area. We also explain numerous critical challenges that these tactics face before they enter the clinic, and this work will provide previous 'meet change with constancy' lessons for responding to future similar public health disasters. Extracellular vesicles (EVs) provide a 'meet changes with constancy' strategy to combat SARS-CoV-2 that spans defence, antagonism, recovery, and acquired immunity. Targets for COVID-19 diagnosis, therapy, and prevention of progression may be found by capture of the message decoding in circulating EVs. Engineered and biomimetic EVs can boost effects of the natural EVs, especially anti-SARS-CoV-2, targeted repair of damaged tissue, and improvement of vaccine efficacy.
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Affiliation(s)
- Xiaohang Chen
- Shanxi Medical University School and Hospital of StomatologyTaiyuanChina
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New MaterialsTaiyuanChina
- Fujian Key Laboratory of Oral Diseases, School and Hospital of StomatologyFujian Medical UniversityFuzhouChina
| | - Huifei Li
- Shanxi Medical University School and Hospital of StomatologyTaiyuanChina
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New MaterialsTaiyuanChina
| | - Haoyue Song
- Shanxi Medical University School and Hospital of StomatologyTaiyuanChina
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New MaterialsTaiyuanChina
| | - Jie Wang
- Shanxi Medical University School and Hospital of StomatologyTaiyuanChina
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New MaterialsTaiyuanChina
| | - Xiaoxuan Zhang
- Shanxi Medical University School and Hospital of StomatologyTaiyuanChina
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New MaterialsTaiyuanChina
| | - Pengcheng Han
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- School of MedicineZhongda Hospital, Southeast UniversityNanjingChina
| | - Xing Wang
- Shanxi Medical University School and Hospital of StomatologyTaiyuanChina
- Shanxi Province Key Laboratory of Oral Diseases Prevention and New MaterialsTaiyuanChina
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