1
|
Guo M, Xiong M, Peng J, Guan T, Su H, Huang Y, Yang CG, Li Y, Boraschi D, Pillaiyar T, Wang G, Yi C, Xu Y, Chen C. Multi-omics for COVID-19: driving development of therapeutics and vaccines. Natl Sci Rev 2023; 10:nwad161. [PMID: 37936830 PMCID: PMC10627145 DOI: 10.1093/nsr/nwad161] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 11/09/2023] Open
Abstract
The ongoing COVID-19 pandemic caused by SARS-CoV-2 has raised global concern for public health and economy. The development of therapeutics and vaccines to combat this virus is continuously progressing. Multi-omics approaches, including genomics, transcriptomics, proteomics, metabolomics, epigenomics and metallomics, have helped understand the structural and molecular features of the virus, thereby assisting in the design of potential therapeutics and accelerating vaccine development for COVID-19. Here, we provide an up-to-date overview of the latest applications of multi-omics technologies in strategies addressing COVID-19, in order to provide suggestions towards the development of highly effective knowledge-based therapeutics and vaccines.
Collapse
Affiliation(s)
- Mengyu Guo
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Muya Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinying Peng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Tong Guan
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixia Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyi Huang
- Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 528107, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
| | - Cai-Guang Yang
- State Key Laboratory of Drug Research, Centre for Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Li
- Laboratory of Immunology and Nanomedicine, and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Diana Boraschi
- Laboratory of Immunology and Nanomedicine, and China-Italy Joint Laboratory of Pharmacobiotechnology for Medical Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Institute of Biochemistry and Cell Biology, National Research Council, Napoli 80131, Italy
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Tübingen 72076, Germany
| | - Guanbo Wang
- Biomedical Pioneering Innovation Centre, Peking University, Beijing 100871, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 528107, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yechun Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunying Chen
- CAS Key Laboratory of Biomedical Effects of Nanomaterials and Nanosafety, and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- GBA National Institute for Nanotechnology Innovation, Guangzhou 510700, China
| |
Collapse
|
3
|
The Correlation between Subolesin-Reactive Epitopes and Vaccine Efficacy. Vaccines (Basel) 2022; 10:vaccines10081327. [PMID: 36016215 PMCID: PMC9414912 DOI: 10.3390/vaccines10081327] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/10/2022] [Accepted: 08/14/2022] [Indexed: 11/16/2022] Open
Abstract
Vaccination is an environmentally-friendly alternative for tick control. The tick antigen Subolesin (SUB) has shown protection in vaccines for the control of multiple tick species in cattle. Additionally, recent approaches in quantum vaccinomics have predicted SUB-protective epitopes and the peptide sequences involved in protein−protein interactions in this tick antigen. Therefore, the identification of B-cell−reactive epitopes by epitope mapping using a SUB peptide array could be essential as a novel strategy for vaccine development. Subolesin can be used as a model to evaluate the effectiveness of these approaches for the identification of protective epitopes related to vaccine protection and efficacy. In this study, the mapping of B-cell linear epitopes of SUB from three different tick species common in Uganda (Rhipicephalus appendiculatus, R. decoloratus, and Amblyomma variegatum) was conducted using serum samples from two cattle breeds immunized with SUB-based vaccines. The results showed that in cattle immunized with SUB from R. appendiculatus (SUBra) all the reactive peptides (Z-score > 2) recognized by IgG were also significant (Z-ratio > 1.96) when compared to the control group. Additionally, some of the reactive peptides recognized by IgG from the control group were also recognized in SUB cocktail−immunized groups. As a significant result, cattle groups that showed the highest vaccine efficacy were Bos indicus immunized with a SUB cocktail (92%), and crossbred cattle were immunized with SUBra (90%) against R. appendiculatus ticks; the IgG from these groups recognized overlapping epitopes from the peptide SPTGLSPGLSPVRDQPLFTFRQVGLICERMMKERESQIRDEYDHVLSAKLAEQYDTFVKFTYDQKRFEGATPSYLS (Z-ratio > 1.96), which partially corresponded to a Q38 peptide and the SUB protein interaction domain. These identified epitopes could be related to the protection and efficacy of the SUB-based vaccines, and new chimeras containing these protective epitopes could be designed using this new approach.
Collapse
|
4
|
Li Z, Wang Y, Liu J, Rawding P, Bu J, Hong S, Hu Q. Chemically and Biologically Engineered Bacteria-Based Delivery Systems for Emerging Diagnosis and Advanced Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2102580. [PMID: 34347325 DOI: 10.1002/adma.202102580] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/10/2021] [Indexed: 06/13/2023]
Abstract
Bacteria are one of the main groups of organisms, which dynamically and closely participate in human health and disease development. With the integration of chemical biotechnology, bacteria have been utilized as an emerging delivery system for various biomedical applications. Given the unique features of bacteria such as their intrinsic biocompatibility and motility, bacteria-based delivery systems have drawn wide interest in the diagnosis and treatment of various diseases, including cancer, infectious diseases, kidney failure, and hyperammonemia. Notably, at the interface of chemical biotechnology and bacteria, many research opportunities have been initiated, opening a promising frontier in biomedical application. Herein, the current synergy of chemical biotechnology and bacteria, the design principles for bacteria-based delivery systems, the microbial modulation, and the clinical translation are reviewed, with a special focus on the emerging advances in diagnosis and therapy.
Collapse
Affiliation(s)
- Zhaoting Li
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Yixin Wang
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Jun Liu
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Piper Rawding
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Jiyoon Bu
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Seungpyo Hong
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| | - Quanyin Hu
- Pharmaceutical Sciences Division, School of Pharmacy, Wisconsin Center for NanoBioSystems, Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison (UW-Madison), Madison, Wisconsin, 53705, USA
| |
Collapse
|