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Wang S, Ran W, Sun L, Fan Q, Zhao Y, Wang B, Yang J, He Y, Wu Y, Wang Y, Chen L, Chuchuay A, You Y, Zhu X, Wang X, Chen Y, Wang Y, Chen YQ, Yuan Y, Zhao J, Mao Y. Sequential glycosylations at the multibasic cleavage site of SARS-CoV-2 spike protein regulate viral activity. Nat Commun 2024; 15:4162. [PMID: 38755139 PMCID: PMC11099032 DOI: 10.1038/s41467-024-48503-x] [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: 05/18/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
The multibasic furin cleavage site at the S1/S2 boundary of the spike protein is a hallmark of SARS-CoV-2 and plays a crucial role in viral infection. However, the mechanism underlying furin activation and its regulation remain poorly understood. Here, we show that GalNAc-T3 and T7 jointly initiate clustered O-glycosylations in the furin cleavage site of the SARS-CoV-2 spike protein, which inhibit furin processing, suppress the incorporation of the spike protein into virus-like-particles and affect viral infection. Mechanistic analysis reveals that the assembly of the spike protein into virus-like particles relies on interactions between the furin-cleaved spike protein and the membrane protein of SARS-CoV-2, suggesting a possible mechanism for furin activation. Interestingly, mutations in the spike protein of the alpha and delta variants of the virus confer resistance against glycosylation by GalNAc-T3 and T7. In the omicron variant, additional mutations reverse this resistance, making the spike protein susceptible to glycosylation in vitro and sensitive to GalNAc-T3 and T7 expression in human lung cells. Our findings highlight the role of glycosylation as a defense mechanism employed by host cells against SARS-CoV-2 and shed light on the evolutionary interplay between the host and the virus.
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Affiliation(s)
- Shengjun Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Wei Ran
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lingyu Sun
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qingchi Fan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanqi Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Foshan Institute for Food and Drug Control, Foshan, China
| | - Bowen Wang
- College of Life Science, Northwest University, Xi'an, China
| | - Jinghong Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuqi He
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanyuan Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Luoyi Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Arpaporn Chuchuay
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuyu You
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xinhai Zhu
- Instrumental Analysis & Research Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaojuan Wang
- Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ye Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanqun Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Yanqiu Yuan
- State Key Laboratory of Anti-Infective Drug Discovery and Development, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
- Institute of Infectious Disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, China.
- Guangzhou Laboratory, Bio-island, Guangzhou, China.
- The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.
- Shanghai Institute for Advanced Immunochemical Studies, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, Shenzhen, China.
| | - Yang Mao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Drug Non-Clinical Evaluation and Research, Guangzhou, China.
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2
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Ming A, Zhao J, Liu Y, Wang Y, Wang X, Li J, Zhang L. O-glycosylation in viruses: A sweet tango. MLIFE 2024; 3:57-73. [PMID: 38827513 PMCID: PMC11139210 DOI: 10.1002/mlf2.12105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/26/2023] [Accepted: 11/07/2023] [Indexed: 06/04/2024]
Abstract
O-glycosylation is an ancient yet underappreciated protein posttranslational modification, on which many bacteria and viruses heavily rely to perform critical biological functions involved in numerous infectious diseases or even cancer. But due to the innate complexity of O-glycosylation, research techniques have been limited to study its exact role in viral attachment and entry, assembly and exit, spreading in the host cells, and the innate and adaptive immunity of the host. Recently, the advent of many newly developed methodologies (e.g., mass spectrometry, chemical biology tools, and molecular dynamics simulations) has renewed and rekindled the interest in viral-related O-glycosylation in both viral proteins and host cells, which is further fueled by the COVID-19 pandemic. In this review, we summarize recent advances in viral-related O-glycosylation, with a particular emphasis on the mucin-type O-linked α-N-acetylgalactosamine (O-GalNAc) on viral proteins and the intracellular O-linked β-N-acetylglucosamine (O-GlcNAc) modifications on host proteins. We hope to provide valuable insights into the development of antiviral reagents or vaccines for better prevention or treatment of infectious diseases.
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Affiliation(s)
- Annan Ming
- Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Jianxin Zhao
- Beijing Key Laboratory of DNA Damage Response and College of Life SciencesCapital Normal UniversityBeijingChina
| | - Yihan Liu
- Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
| | - Yibo Wang
- Laboratory of Chemical BiologyChangchun Institute of Applied Chemistry, Chinese Academy of SciencesChangchunChina
| | - Xiaohui Wang
- Laboratory of Chemical BiologyChangchun Institute of Applied Chemistry, Chinese Academy of SciencesChangchunChina
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiChina
- Beijing National Laboratory for Molecular SciencesBeijingChina
| | - Jing Li
- Beijing Key Laboratory of DNA Damage Response and College of Life SciencesCapital Normal UniversityBeijingChina
| | - Leiliang Zhang
- Shandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanChina
- Medical Science and Technology Innovation CenterShandong First Medical University & Shandong Academy of Medical SciencesJinanChina
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3
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Hanisch FG. Site-Specific O-glycosylation of SARS-CoV-2 Spike Protein and Its Impact on Immune and Autoimmune Responses. Cells 2024; 13:107. [PMID: 38247799 PMCID: PMC10814047 DOI: 10.3390/cells13020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
The world-wide COVID-19 pandemic has promoted a series of alternative vaccination strategies aiming to elicit neutralizing adaptive immunity in the human host. However, restricted efficacies of these vaccines targeting epitopes on the spike (S) protein that is involved in primary viral entry were observed and putatively assigned to viral glycosylation as an effective escape mechanism. Besides the well-recognized N-glycan shield covering SARS-CoV-2 spike (S) proteins, immunization strategies may be hampered by heavy O-glycosylation and variable O-glycosites fluctuating depending on the organ sites of primary infection and those involved in immunization. A further complication associated with viral glycosylation arises from the development of autoimmune antibodies to self-carbohydrates, including O-linked blood group antigens, as structural parts of viral proteins. This outline already emphasizes the importance of viral glycosylation in general and, in particular, highlights the impact of the site-specific O-glycosylation of virions, since this modification is independent of sequons and varies strongly in dependence on cell-specific repertoires of peptidyl-N-acetylgalactosaminyltransferases with their varying site preferences and of glycan core-specific glycosyltransferases. This review summarizes the current knowledge on the viral O-glycosylation of the SARS-CoV-2 spike protein and its impact on virulence and immune modulation in the host.
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Affiliation(s)
- Franz-Georg Hanisch
- Center of Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, 50931 Cologne, Germany
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4
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Zhou W, Sui Z, Liu J, He Y, Yuan H, Sun Y, Liang Z, Yang K, Zhang L, Zhang Y. High-Sensitivity Detection toward SARS-CoV-2 S1 Glycoprotein by Parallel Reaction Monitoring Mass Spectrometry. Anal Chem 2023; 95:8752-8757. [PMID: 37246519 DOI: 10.1021/acs.analchem.2c05770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) has overwhelmed the global economy and human well-being. On account of the sharp increase in test demand, there is a need for an accurate and alternative diagnosis method for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, with the aim to specifically identify the trace SARS-CoV-2 S1 glycoprotein, we developed a high-sensitivity and high-selectivity diagnostic method based on the targeted parallel reaction monitoring (PRM) assay of eight selected peptides. This study emphasizes the outstanding detection sensitivity of 0.01 pg of the SARS-CoV-2 S1 glycoprotein even in the interference of other structural proteins, which to our knowledge is the current minimum limit of detection for the SARS-CoV-2 S1 glycoprotein. This technology could further identify 0.01 pg of the SARS-CoV-2 S1 glycoprotein in a spike pseudovirus, revealing its practical effectiveness. All our preliminary results throw light on the capability of the mass spectrometry-based targeted PRM assay to identify SARS-CoV-2 as a practicable orthogonal diagnostic tool. Furthermore, this technology could be extended to other pathogens (e.g., MERS-CoV S1 protein or SARS-CoV S1 protein) by quickly adjusting the targeted peptides of MS data acquisition. In summary, this strategy is universal and flexible and could be quickly adjusted to detect and discriminate different mutants and pathogens.
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Affiliation(s)
- Wen Zhou
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhigang Sui
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jianhui Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yingyun He
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huiming Yuan
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yue Sun
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kaiguang Yang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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5
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Huang J, Hou S, An J, Zhou C. In-depth characterization of protein N-glycosylation for a COVID-19 variant-design vaccine spike protein. Anal Bioanal Chem 2023; 415:1455-1464. [PMID: 36698045 PMCID: PMC9878482 DOI: 10.1007/s00216-023-04533-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/25/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
COVID-19 is caused by SARS-CoV-2 infection and remains one of the biggest pandemics around the world since 2019. Vaccination has proved to be an effective way of preventing SARS-CoV-2 infection and alleviating the hospitalization burden. Among different forms of COVID-19 vaccine design, the spike protein of SARS-CoV-2 virus is widely used as a candidate vaccine antigen. As a surface protein on the virus envelop, the spike was reported to be heavily N-glycosylated and glycosylation had a great impact on its immunogenicity and efficacy. Besides, N-glycosylation might vary greatly on different expression systems and sequence variant designs. Therefore, comprehensive analysis of spike N-glycosylation is of great significance for better vaccine understanding and quality control. In this study, full characterization of N-glycosylation was performed for a Chinese Hamster Ovary (CHO) cell expressed variant-designed spike protein. The spike protein featured the latest six-proline substitution design together with the incorporation of a combination of mutation sites. Trypsin and Glu-C digestion coupled with PNGase F strategies were adopted, and effective LC-MS/MS methods were applied to analyze samples. As a result, a total of 19 N-glycosites were identified in the recombinant pike protein at intact N-glycopeptide level. Quantitative analysis of released glycan by LC-MS/MS was also performed, and 31 high-abundance N-glycans were identified. Sequencing analysis of glycan was further provided to assist glycan structure confirmation. Moreover, all of the analyses were performed on three consecutive manufactured batches and the glycosylation results on both glycosite and glycans showed good batch-to-batch consistency. Thus, the reported analytical strategy and N-glycosylation information may well facilitate studies on SARS-CoV-2 spike protein analysis and quality studies.
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Affiliation(s)
| | - Shouzeng Hou
- Shanghai Zerun Biotech Co., Ltd, Shanghai, China
| | - Jiao An
- Shanghai Zerun Biotech Co., Ltd, Shanghai, China
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6
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Derivatization of sialylated glycopeptides plus based sialoglycopeptides enrichment using cation exchange media. Anal Chim Acta 2022; 1233:340492. [DOI: 10.1016/j.aca.2022.340492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/28/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022]
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7
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Dong X, Li X, Chen C, Zhang X, Liang X. Systematic analysis and comparison of O-glycosylation of five recombinant spike proteins in β-coronaviruses. Anal Chim Acta 2022; 1230:340394. [PMID: 36192065 PMCID: PMC9478876 DOI: 10.1016/j.aca.2022.340394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/27/2022] [Accepted: 09/11/2022] [Indexed: 12/01/2022]
Abstract
β-coronaviruses (β-CoVs), representative with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), depend on their highly glycosylated spike proteins to mediate cell entry and membrane fusion. Compared with the extensively identified N-glycosylation, less is known about O-glycosylation of β-CoVs S proteins, let alone its biological functions. Herein we comprehensively characterized O-glycosylation of five recombinant β-CoVs S1 subunits and revealed the macro- and micro-heterogeneity nature of site-specific O-glycosylation. We also uncovered the O-glycosylation differences between SARS-CoV-2 and its natural D614G mutant on functional domains. This work describes the systematic O-glycosylation analysis of β-CoVs S1 proteins and will help to guide the related vaccines and antiviral drugs development.
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Affiliation(s)
- Xuefang Dong
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Xiuling Li
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China; Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, PR China.
| | - Cheng Chen
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Xiaofei Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Xinmiao Liang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China; Ganjiang Chinese Medicine Innovation Center, Nanchang, 330000, PR China.
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8
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Wang J, Wang X, Li J, Xia Y, Gao M, Zhang X, Huang LH. A novel hydrophilic MOFs-303-functionalized magnetic probe for the highly efficient analysis of N-linked glycopeptides. J Mater Chem B 2022; 10:2011-2018. [PMID: 35244662 DOI: 10.1039/d1tb02827h] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The effective analysis of glycoproteomics in clinical complex samples is of vital importance for the diagnosis and therapy of diseases. In this study, a hydrophilic MOFs-303-functionalized magnetic probe (GO@Fe3O4@MOF-303) is designed and fabricated to profile N-linked glycopeptides. Owing to its strong magnetic property, large surface area (845 m2 g-1), excellent hydrophilicity and suitable porous structure, the GO@Fe3O4@MOF-303 probe exhibits an ultralow detection limit (0.1 fmol μL-1), perfect size-exclusion effect (HRP digests/BSA protein/HRP protein, 1 : 1000 : 1000, w/w/w), a high binding capacity (200 mg g-1) and excellent reusability in the capture of standard N-linked glycopeptides. More excitingly, the GO@Fe3O4@MOF-303 probe also shows remarkable performance in practical applications, where 274 N-linked glycopeptides from 101 glycoproteins were identified in total for healthy controls, while a total of 265 N-linked glycopeptides from 102 glycoproteins were identified in serum (1 μL) with hepatocellular carcinoma (HCC). In addition, we discovered 4 up-regulated and 19 down-regulated serum glycoproteins in HCC patients by the hierarchical clustering heatmap. All results demonstrated that the reusable GO@Fe3O4@MOF-303 probe has great potential in profiling different N-linked glycopeptides in complex clinical samples. This study not only developed a novel probe for the highly effective capture of N-linked glycopeptides but also contributed to further understanding the mechanism of HCC and provides guidance for the development of novel clinical diagnostic methods.
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Affiliation(s)
- Jiaxi Wang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China. .,Shanghai Qi Zhi Institute, Shanghai 200030, China
| | - Xinmei Wang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China.
| | - Jie Li
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China.
| | - Yan Xia
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China.
| | - Mingxia Gao
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China.
| | - Xiangmin Zhang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China.
| | - Li-Hao Huang
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Department of Chemistry and Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200032, China.
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9
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Fang P, Ji Y, Oellerich T, Urlaub H, Pan KT. Strategies for Proteome-Wide Quantification of Glycosylation Macro- and Micro-Heterogeneity. Int J Mol Sci 2022; 23:ijms23031609. [PMID: 35163546 PMCID: PMC8835892 DOI: 10.3390/ijms23031609] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/03/2022] Open
Abstract
Protein glycosylation governs key physiological and pathological processes in human cells. Aberrant glycosylation is thus closely associated with disease progression. Mass spectrometry (MS)-based glycoproteomics has emerged as an indispensable tool for investigating glycosylation changes in biological samples with high sensitivity. Following rapid improvements in methodologies for reliable intact glycopeptide identification, site-specific quantification of glycopeptide macro- and micro-heterogeneity at the proteome scale has become an urgent need for exploring glycosylation regulations. Here, we summarize recent advances in N- and O-linked glycoproteomic quantification strategies and discuss their limitations. We further describe a strategy to propagate MS data for multilayered glycopeptide quantification, enabling a more comprehensive examination of global and site-specific glycosylation changes. Altogether, we show how quantitative glycoproteomics methods explore glycosylation regulation in human diseases and promote the discovery of biomarkers and therapeutic targets.
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Affiliation(s)
- Pan Fang
- Department of Biochemistry and Molecular Biology, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China;
| | - Yanlong Ji
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany;
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
| | - Thomas Oellerich
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany;
- Institute of Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
- Correspondence: (H.U.); (K.-T.P.)
| | - Kuan-Ting Pan
- Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590 Frankfurt am Main, Germany;
- Frankfurt Cancer Institute, Johann Wolfgang Goethe University, 60596 Frankfurt am Main, Germany
- Correspondence: (H.U.); (K.-T.P.)
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10
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Zhao B, Wang Y, Ma J, Jia Q. Design of a hydrophilic mercaptosuccinic acid-functionalized β-cyclodextrin polymer via host–guest interaction: toward highly efficient glycopeptide enrichment. Analyst 2022; 147:4553-4561. [DOI: 10.1039/d2an01358d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel hydrophilic material (denoted as magCDP@Ada-MSA) was constructed through host–guest interaction between crosslinked β-cyclodextrin polymers and mercaptosuccinic acid derived adamantane, and was applied to specific glycopeptide enrichment.
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Affiliation(s)
- Binfen Zhao
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Yuxuan Wang
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Jiutong Ma
- College of Chemistry, Jilin University, Changchun 130012, China
| | - Qiong Jia
- College of Chemistry, Jilin University, Changchun 130012, China
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
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11
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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12
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Eldrid CS, Allen JD, Newby ML, Crispin M. Suppression of O-Linked Glycosylation of the SARS-CoV-2 Spike by Quaternary Structural Restraints. Anal Chem 2021; 93:14392-14400. [PMID: 34670086 PMCID: PMC8547167 DOI: 10.1021/acs.analchem.1c01772] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 01/08/2023]
Abstract
Understanding the glycosylation of the envelope spike (S) protein of SARS-CoV-2 is important in defining the antigenic surface of this key viral target. However, the underlying protein architecture may significantly influence glycan occupancy and processing. There is, therefore, potential for different recombinant fragments of S protein to display divergent glycosylation. Here, we show that the receptor binding domain (RBD), when expressed as a monomer, exhibits O-linked glycosylation, which is not recapitulated in the native-like soluble trimeric protein. We unambiguously assign O-linked glycosylation by homogenizing N-linked glycosylation using the enzymatic inhibitor, kifunensine, and then analyzing the resulting structures by electron-transfer higher-energy collision dissociation (EThcD) in an Orbitrap Eclipse Tribrid instrument. In the native-like trimer, we observe a single unambiguous O-linked glycan at T323, which displays very low occupancy. In contrast, several sites of O-linked glycosylation can be identified when RBD is expressed as a monomer, with T323 being almost completely occupied. We ascribe this effect to the relaxation of steric restraints arising from quaternary protein architecture. Our analytical approach has also highlighted that fragmentation ions arising from trace levels of truncated N-linked glycans can be misassigned as proximal putative O-linked glycan structures, particularly where a paucity of diagnostic fragments were obtained. Overall, we show that in matched expression systems the quaternary protein architecture limits O-linked glycosylation of the spike protein.
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Affiliation(s)
| | | | - Maddy L. Newby
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, U.K.
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Zhang Y, Zhao W, Mao Y, Chen Y, Zheng S, Cao W, Zhu J, Hu L, Gong M, Cheng J, Yang H. O-Glycosylation Landscapes of SARS-CoV-2 Spike Proteins. Front Chem 2021; 9:689521. [PMID: 34552909 PMCID: PMC8450404 DOI: 10.3389/fchem.2021.689521] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/24/2021] [Indexed: 02/05/2023] Open
Abstract
The densely glycosylated spike (S) proteins that are highly exposed on the surface of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) facilitate viral attachment, entry, and membrane fusion. We have previously reported all the 22 N-glycosites and site-specific N-glycans in the S protein protomer. Herein, we report the O-glycosylation landscapes of SARS-CoV-2 S proteins, which were characterized through high-resolution mass spectrometry. Following digestion with trypsin and trypsin/Glu-C, and de-N-glycosylation using PNGase F, we determined the GalNAc-type O-glycosylation pattern of S proteins, including O-glycosites and the six most common O-glycans occupying them, via Byonic identification and manual validation. Finally, 255 intact O-glycopeptides composed of 50 peptides sequences and 43 O-glycosites were discovered by higher energy collision-induced dissociation (HCD), and three O-glycosites were confidently identified by electron transfer/higher energy collision-induced dissociation (EThcD) in the insect cell-expressed S protein. Most glycosites were modified by non-sialylated O-glycans such as HexNAc(1) and HexNAc(1)Hex (1). In contrast, in the human cell-expressed S protein S1 subunit, 407 intact O-glycopeptides composed of 34 peptides sequences and 30 O-glycosites were discovered by HCD, and 11 O-glycosites were unambiguously assigned by EThcD. However, the measurement of O-glycosylation occupancy hasn’t been made. Most glycosites were modified by sialylated O-glycans such as HexNAc(1)Hex (1)NeuAc (1) and HexNAc(1)Hex (1)NeuAc (2). Our results reveal that the SARS-CoV-2 S protein is an O-glycoprotein; the O-glycosites and O-glycan compositions vary with the host cell type. These comprehensive O-glycosylation landscapes of the S protein are expected to provide novel insights into the viral binding mechanism and present a strategy for the development of vaccines and targeted drugs.
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Affiliation(s)
- Yong Zhang
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Wanjun Zhao
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yonghong Mao
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Yaohui Chen
- Institute of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
| | - Shanshan Zheng
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Cao
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiang Zhu
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Liqiang Hu
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Meng Gong
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Yang
- Key Laboratory of Transplant Engineering and Immunology, MOH, Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
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14
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Núñez-Muñoz L, Marcelino-Pérez G, Calderón-Pérez B, Pérez-Saldívar M, Acosta-Virgen K, González-Conchillos H, Vargas-Hernández B, Olivares-Martínez A, Ruiz-Medrano R, Roa-Velázquez D, Morales-Ríos E, Ramos-Flores J, Torres-Franco G, Peláez-González D, Fernández-Hernández J, Espinosa-Cantellano M, Tapia-Sidas D, Ramírez-Pool JA, Padilla-Viveros A, Xoconostle-Cázares B. Recombinant Antigens Based on Non-Glycosylated Regions from RBD SARS-CoV-2 as Potential Vaccine Candidates against COVID-19. Vaccines (Basel) 2021; 9:928. [PMID: 34452053 PMCID: PMC8402574 DOI: 10.3390/vaccines9080928] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 01/22/2023] Open
Abstract
The Receptor-Binding Domain (RBD) of the Spike (S) protein from Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has glycosylation sites which can limit the production of reliable antigens expressed in prokaryotic platforms, due to glycan-mediated evasion of the host immune response. However, protein regions without glycosylated residues capable of inducing neutralizing antibodies could be useful for antigen production in systems that do not carry the glycosylation machinery. To test this hypothesis, the potential antigens NG06 and NG19, located within the non-glycosylated S-RBD region, were selected and expressed in Escherichia coli, purified by FPLC and employed to determine their immunogenic potential through detection of antibodies in serum from immunized rabbits, mice, and COVID-19 patients. IgG antibodies from sera of COVID-19-recovered patients detected the recombinant antigens NG06 and NG19 (A450 nm = 0.80 ± 0.33; 1.13 ± 0.33; and 0.11 ± 0.08 for and negatives controls, respectively). Also, the purified antigens were able to raise polyclonal antibodies in animal models evoking a strong immune response with neutralizing activity in mice model. This research highlights the usefulness of antigens based on the non-N-glycosylated region of RBD from SARS-CoV-2 for candidate vaccine development.
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Affiliation(s)
- Leandro Núñez-Muñoz
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (L.N.-M.); (G.M.-P.); (B.C.-P.); (B.V.-H.); (A.O.-M.); (R.R.-M.); (D.T.-S.); (J.A.R.-P.)
| | - Gabriel Marcelino-Pérez
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (L.N.-M.); (G.M.-P.); (B.C.-P.); (B.V.-H.); (A.O.-M.); (R.R.-M.); (D.T.-S.); (J.A.R.-P.)
- Doctoral Program in Nanosciences and Nanotechnology, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico;
| | - Berenice Calderón-Pérez
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (L.N.-M.); (G.M.-P.); (B.C.-P.); (B.V.-H.); (A.O.-M.); (R.R.-M.); (D.T.-S.); (J.A.R.-P.)
| | - Miriam Pérez-Saldívar
- Department of Infectomics and Molecular Pathogenesis, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (M.P.-S.); (K.A.-V.); (H.G.-C.); (M.E.-C.)
| | - Karla Acosta-Virgen
- Department of Infectomics and Molecular Pathogenesis, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (M.P.-S.); (K.A.-V.); (H.G.-C.); (M.E.-C.)
| | - Hugo González-Conchillos
- Department of Infectomics and Molecular Pathogenesis, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (M.P.-S.); (K.A.-V.); (H.G.-C.); (M.E.-C.)
| | - Brenda Vargas-Hernández
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (L.N.-M.); (G.M.-P.); (B.C.-P.); (B.V.-H.); (A.O.-M.); (R.R.-M.); (D.T.-S.); (J.A.R.-P.)
| | - Ana Olivares-Martínez
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (L.N.-M.); (G.M.-P.); (B.C.-P.); (B.V.-H.); (A.O.-M.); (R.R.-M.); (D.T.-S.); (J.A.R.-P.)
| | - Roberto Ruiz-Medrano
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (L.N.-M.); (G.M.-P.); (B.C.-P.); (B.V.-H.); (A.O.-M.); (R.R.-M.); (D.T.-S.); (J.A.R.-P.)
| | - Daniela Roa-Velázquez
- Doctoral Program in Nanosciences and Nanotechnology, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico;
- Department of Biochemistry, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico;
| | - Edgar Morales-Ríos
- Department of Biochemistry, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico;
| | - Jorge Ramos-Flores
- Laboratory Animal Production and Experimentation Unit, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (J.R.-F.); (G.T.-F.); (D.P.-G.); (J.F.-H.)
| | - Gustavo Torres-Franco
- Laboratory Animal Production and Experimentation Unit, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (J.R.-F.); (G.T.-F.); (D.P.-G.); (J.F.-H.)
| | - Diana Peláez-González
- Laboratory Animal Production and Experimentation Unit, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (J.R.-F.); (G.T.-F.); (D.P.-G.); (J.F.-H.)
| | - Jorge Fernández-Hernández
- Laboratory Animal Production and Experimentation Unit, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (J.R.-F.); (G.T.-F.); (D.P.-G.); (J.F.-H.)
| | - Martha Espinosa-Cantellano
- Department of Infectomics and Molecular Pathogenesis, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (M.P.-S.); (K.A.-V.); (H.G.-C.); (M.E.-C.)
| | - Diana Tapia-Sidas
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (L.N.-M.); (G.M.-P.); (B.C.-P.); (B.V.-H.); (A.O.-M.); (R.R.-M.); (D.T.-S.); (J.A.R.-P.)
| | - José Abrahan Ramírez-Pool
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (L.N.-M.); (G.M.-P.); (B.C.-P.); (B.V.-H.); (A.O.-M.); (R.R.-M.); (D.T.-S.); (J.A.R.-P.)
| | - América Padilla-Viveros
- Transdisciplinary Doctoral Program in Scientific and Technological Development for Society, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico;
| | - Beatriz Xoconostle-Cázares
- Department of Biotechnology and Bioengineering, Centro de Investigación y de Estudios Avanzados (CINVESTAV), Av. Instituto Politécnico Nacional 2508, México City 07360, Mexico; (L.N.-M.); (G.M.-P.); (B.C.-P.); (B.V.-H.); (A.O.-M.); (R.R.-M.); (D.T.-S.); (J.A.R.-P.)
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